From 97d643c273d2e423be966b79469b24481a680f89 Mon Sep 17 00:00:00 2001
From: "Michael D. M. Dryden" <mk.dryden@utoronto.ca>
Date: Sun, 5 Dec 2021 17:43:45 -0500
Subject: [PATCH] New trio/CLI only version
---
MANIFEST.in | 14 -
conda-env.yml | 137 ---
dstat_interface/__init__.py | 4 +
dstat_interface/core/analysis.py | 194 ----
dstat_interface/core/daemon.py | 154 ++++
dstat_interface/core/dstat-cli.py | 135 +++
dstat_interface/core/dstat-interface.bat | 1 -
dstat_interface/core/dstat.spec | 25 -
dstat_interface/core/dstat/__init__.py | 3 -
dstat_interface/core/dstat/boards.py | 45 +-
dstat_interface/core/dstat/comm.py | 562 +++---------
dstat_interface/core/dstat/dfu.py | 375 --------
.../core/dstat/experiment_handler.py | 115 +++
.../core/dstat/experiment_process.py | 246 +++++
dstat_interface/core/dstat/simulator.py | 403 +++++++++
dstat_interface/core/dstat/state.py | 39 +-
dstat_interface/core/dstat/test/test_comm.py | 41 +
dstat_interface/core/dstat/utility.py | 123 +++
dstat_interface/core/errors.py | 47 -
dstat_interface/core/experiments/__init__.py | 17 -
dstat_interface/core/experiments/cal.py | 139 ---
dstat_interface/core/experiments/chronoamp.py | 226 ++---
dstat_interface/core/experiments/cv.py | 68 --
.../core/experiments/experiment_container.py | 153 ++++
.../core/experiments/experiment_loops.py | 201 -----
.../core/experiments/experiment_template.py | 571 ------------
dstat_interface/core/experiments/idle.py | 40 -
dstat_interface/core/experiments/lsv.py | 182 ++--
dstat_interface/core/experiments/pot.py | 80 --
dstat_interface/core/experiments/swv.py | 367 +++-----
dstat_interface/core/interface/__init__.py | 0
dstat_interface/core/interface/acv.glade | 445 ---------
dstat_interface/core/interface/adc_pot.glade | 412 ---------
dstat_interface/core/interface/adc_pot.py | 139 ---
.../core/interface/analysis_options.glade | 159 ----
dstat_interface/core/interface/calib.glade | 363 --------
.../core/interface/chronoamp.glade | 186 ----
dstat_interface/core/interface/cv.glade | 362 --------
dstat_interface/core/interface/data_view.py | 81 --
dstat_interface/core/interface/db.glade | 204 -----
dstat_interface/core/interface/db.py | 143 ---
dstat_interface/core/interface/dpv.glade | 404 ---------
.../core/interface/dstatinterface.glade | 737 ---------------
dstat_interface/core/interface/exp_int.py | 540 -----------
dstat_interface/core/interface/exp_window.py | 129 ---
dstat_interface/core/interface/hw_info.py | 110 ---
dstat_interface/core/interface/lsv.glade | 307 -------
dstat_interface/core/interface/pd.glade | 348 -------
dstat_interface/core/interface/plot.py | 94 --
dstat_interface/core/interface/plot_ui.py | 33 -
dstat_interface/core/interface/potexp.glade | 97 --
dstat_interface/core/interface/save.py | 226 -----
dstat_interface/core/interface/swv.glade | 433 ---------
dstat_interface/core/microdrop.py | 90 --
dstat_interface/core/params.py | 82 --
dstat_interface/core/plugin.py | 161 ----
dstat_interface/core/state.py | 10 +
dstat_interface/core/tasks.py | 35 +
dstat_interface/core/utils/__init__.py | 0
dstat_interface/core/utils/version.py | 137 ---
dstat_interface/main.py | 854 ------------------
dstat_interface/utils.py | 25 +
pavement.py | 31 -
poetry.lock | 199 ++++
pyproject.toml | 27 +
version.py | 137 ---
66 files changed, 2211 insertions(+), 10236 deletions(-)
delete mode 100644 MANIFEST.in
delete mode 100644 conda-env.yml
delete mode 100755 dstat_interface/core/analysis.py
create mode 100644 dstat_interface/core/daemon.py
create mode 100644 dstat_interface/core/dstat-cli.py
delete mode 100644 dstat_interface/core/dstat-interface.bat
delete mode 100644 dstat_interface/core/dstat.spec
delete mode 100755 dstat_interface/core/dstat/dfu.py
create mode 100644 dstat_interface/core/dstat/experiment_handler.py
create mode 100644 dstat_interface/core/dstat/experiment_process.py
create mode 100644 dstat_interface/core/dstat/simulator.py
create mode 100644 dstat_interface/core/dstat/test/test_comm.py
create mode 100644 dstat_interface/core/dstat/utility.py
delete mode 100755 dstat_interface/core/errors.py
delete mode 100644 dstat_interface/core/experiments/__init__.py
delete mode 100755 dstat_interface/core/experiments/cal.py
delete mode 100644 dstat_interface/core/experiments/cv.py
create mode 100644 dstat_interface/core/experiments/experiment_container.py
delete mode 100644 dstat_interface/core/experiments/experiment_loops.py
delete mode 100755 dstat_interface/core/experiments/experiment_template.py
delete mode 100644 dstat_interface/core/experiments/idle.py
delete mode 100644 dstat_interface/core/experiments/pot.py
delete mode 100644 dstat_interface/core/interface/__init__.py
delete mode 100644 dstat_interface/core/interface/acv.glade
delete mode 100644 dstat_interface/core/interface/adc_pot.glade
delete mode 100755 dstat_interface/core/interface/adc_pot.py
delete mode 100644 dstat_interface/core/interface/analysis_options.glade
delete mode 100644 dstat_interface/core/interface/calib.glade
delete mode 100644 dstat_interface/core/interface/chronoamp.glade
delete mode 100644 dstat_interface/core/interface/cv.glade
delete mode 100644 dstat_interface/core/interface/data_view.py
delete mode 100644 dstat_interface/core/interface/db.glade
delete mode 100755 dstat_interface/core/interface/db.py
delete mode 100644 dstat_interface/core/interface/dpv.glade
delete mode 100644 dstat_interface/core/interface/dstatinterface.glade
delete mode 100755 dstat_interface/core/interface/exp_int.py
delete mode 100755 dstat_interface/core/interface/exp_window.py
delete mode 100755 dstat_interface/core/interface/hw_info.py
delete mode 100644 dstat_interface/core/interface/lsv.glade
delete mode 100644 dstat_interface/core/interface/pd.glade
delete mode 100755 dstat_interface/core/interface/plot.py
delete mode 100644 dstat_interface/core/interface/plot_ui.py
delete mode 100644 dstat_interface/core/interface/potexp.glade
delete mode 100755 dstat_interface/core/interface/save.py
delete mode 100644 dstat_interface/core/interface/swv.glade
delete mode 100644 dstat_interface/core/microdrop.py
delete mode 100755 dstat_interface/core/params.py
delete mode 100644 dstat_interface/core/plugin.py
create mode 100644 dstat_interface/core/state.py
create mode 100644 dstat_interface/core/tasks.py
delete mode 100644 dstat_interface/core/utils/__init__.py
delete mode 100644 dstat_interface/core/utils/version.py
delete mode 100755 dstat_interface/main.py
create mode 100644 dstat_interface/utils.py
delete mode 100644 pavement.py
create mode 100644 poetry.lock
create mode 100644 pyproject.toml
delete mode 100644 version.py
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 711422b..0000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,14 +0,0 @@
-include RELEASE-VERSION
-include version.py
-include setup.py
-include main.py
-include paver-minilib.zip
-include LICENSE
-include CHANGELOG
-include README.markdown
-include core/utils/RELEASE-VERSION
-recursive-include dstat_interface *
-recursive-exclude dstat_interface *.pyc
-recursive-exclude dstat_interface *~
-recursive_exclude core last_params.yml
-recursive-exclude . .DS_Store
\ No newline at end of file
diff --git a/conda-env.yml b/conda-env.yml
deleted file mode 100644
index 8bce2bc..0000000
--- a/conda-env.yml
+++ /dev/null
@@ -1,137 +0,0 @@
-name: dstat
-channels:
- - conda-forge
- - mdryden
- - defaults
-dependencies:
- - ca-certificates=2018.4.16=0
- - certifi=2018.4.16=py27_0
- - nb_conda_kernels=2.1.0=py27_0
- - openssl=1.0.2o=0
- - appnope=0.1.0=py27_0
- - backports=1.0=py27_0
- - backports_abc=0.5=py27_0
- - bleach=1.5.0=py27_0
- - configparser=3.5.0=py27_0
- - curl=7.54.1=0
- - cycler=0.10.0=py27_0
- - decorator=4.1.2=py27_0
- - entrypoints=0.2.3=py27_0
- - enum34=1.1.6=py27_0
- - expat=2.1.0=0
- - freetype=2.5.5=2
- - funcsigs=1.0.2=py27hb9f6266_0
- - functools32=3.2.3.2=py27_0
- - get_terminal_size=1.0.0=py27_0
- - gettext=0.19.8=1
- - git=2.11.1=0
- - html5lib=0.9999999=py27_0
- - icu=54.1=0
- - intel-openmp=2018.0.0=h8158457_8
- - ipykernel=4.6.1=py27_0
- - ipython=5.3.0=py27_0
- - ipython-notebook=4.0.4=py27_0
- - ipython_genutils=0.2.0=py27_0
- - jbig=2.1=0
- - jinja2=2.9.6=py27_0
- - jpeg=9b=0
- - jsonschema=2.6.0=py27_0
- - jupyter_client=5.1.0=py27_0
- - jupyter_core=4.3.0=py27_0
- - krb5=1.13.2=0
- - libcxx=4.0.1=h579ed51_0
- - libcxxabi=4.0.1=hebd6815_0
- - libffi=3.2.1=1
- - libgfortran=3.0.1=h93005f0_2
- - libiconv=1.14=0
- - libpng=1.6.30=1
- - libssh2=1.8.0=0
- - libtiff=4.0.6=3
- - llvmlite=0.21.0=py27hac8ee23_0
- - markupsafe=1.0=py27_0
- - matplotlib=2.0.2=np113py27_0
- - mistune=0.7.4=py27_0
- - mkl=2018.0.1=hfbd8650_4
- - nbconvert=5.2.1=py27_0
- - nbformat=4.4.0=py27_0
- - notebook=5.0.0=py27_0
- - numba=0.36.2=np113py27h7c931aa_0
- - numpy=1.13.3=py27h62f9060_0
- - pandas=0.20.3=py27_0
- - pandocfilters=1.4.2=py27_0
- - path.py=10.3.1=py27_0
- - pathlib2=2.3.0=py27_0
- - patsy=0.4.1=py27_0
- - pcre=8.39=1
- - pexpect=4.2.1=py27_0
- - pickleshare=0.7.4=py27_0
- - pip=9.0.1=py27_1
- - prompt_toolkit=1.0.15=py27_0
- - ptyprocess=0.5.2=py27_0
- - pygments=2.2.0=py27_0
- - pyparsing=2.2.0=py27_0
- - pyqt=5.6.0=py27_2
- - python=2.7.13=0
- - python-dateutil=2.6.1=py27_0
- - pytz=2017.2=py27_0
- - pyyaml=3.12=py27_0
- - pyzmq=16.0.2=py27_0
- - qt=5.6.2=2
- - readline=6.2=2
- - scandir=1.5=py27_0
- - scipy=1.0.0=py27h793f721_0
- - seaborn=0.8=py27_0
- - setuptools=36.4.0=py27_0
- - simplegeneric=0.8.1=py27_1
- - singledispatch=3.4.0.3=py27_0
- - sip=4.18=py27_0
- - six=1.10.0=py27_0
- - sqlite=3.13.0=0
- - ssl_match_hostname=3.5.0.1=py27_0
- - statsmodels=0.8.0=np113py27_0
- - subprocess32=3.2.7=py27_0
- - terminado=0.6=py27_0
- - testpath=0.3.1=py27_0
- - tk=8.5.18=0
- - tornado=4.5.2=py27_0
- - traitlets=4.3.2=py27_0
- - wcwidth=0.1.7=py27_0
- - wheel=0.29.0=py27_0
- - xz=5.2.3=0
- - yaml=0.1.6=0
- - zlib=1.2.11=0
- - adwaita-icon-theme=3.24.0=1
- - arrow=0.10.0=py27_0
- - at-spi2-atk=2.24.1=2
- - at-spi2-core=2.24.1=2
- - atk=2.24.0=3
- - cairo-gobject=1.14.8=8
- - dbus-client=1.10.18=0
- - dfu-programmer=0.7.2=2
- - dstat-interface=1.4.6=py27_0
- - dstat-interface-deps=1.0=0
- - gdk-pixbuf=2.36.6=2
- - glib=2.52.2=5
- - gobject-introspection=1.52.1=2
- - gtk3=3.22.15=4
- - harfbuzz=1.4.6=3
- - libepoxy=1.4.2=5
- - libusb=1.0.21=0
- - pango=1.40.6=2
- - pixman=0.34.0=1
- - py2cairo=1.10.0=py27_0
- - pygobject3=3.24.2=py27_3
- - pyserial=3.3=py27_0
- - zmq-plugin=0.2.post14=py27_0
- - pip:
- - backports.shutil-get-terminal-size==1.0.0
- - backports.shutil-which==3.5.1
- - backports.ssl-match-hostname==3.5.0.1
- - chardet==3.0.4
- - colorama==0.3.9
- - idna==2.6
- - paver==1.2.4
- - pygobject==3.24.1
- - requests==2.18.4
- - urllib3==1.22
- - vmprof==0.4.10
diff --git a/dstat_interface/__init__.py b/dstat_interface/__init__.py
index e69de29..6206dbf 100644
--- a/dstat_interface/__init__.py
+++ b/dstat_interface/__init__.py
@@ -0,0 +1,4 @@
+from pathlib import Path
+from single_source import get_version
+
+__version__ = get_version(__name__, Path(__file__).parent.parent)
diff --git a/dstat_interface/core/analysis.py b/dstat_interface/core/analysis.py
deleted file mode 100755
index 747df18..0000000
--- a/dstat_interface/core/analysis.py
+++ /dev/null
@@ -1,194 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-"""
-Functions for analyzing data.
-"""
-import logging
-import os
-
-from numpy import mean, trapz
-
-logger = logging.getLogger(__name__)
-mod_dir = os.path.dirname(os.path.abspath(__file__))
-
-class AnalysisOptions(object):
- """Analysis options window."""
- def __init__(self, builder):
- self.builder = builder
- self.builder.add_from_file(
- os.path.join(mod_dir, 'interface/analysis_options.glade'))
- self.builder.connect_signals(self)
-
- self.window = self.builder.get_object('analysis_dialog')
- self.stats_button = self.builder.get_object('stats_button')
- self.stats_start = self.builder.get_object('stats_start_spin')
- self.stats_start_button = self.builder.get_object('stats_start_button')
- self.stats_stop = self.builder.get_object('stats_stop_spin')
- self.stats_stop_button = self.builder.get_object('stats_stop_button')
-
- self.stats_button.connect('toggled',
- self.on_button_toggled_hide,
- [self.stats_stop,
- self.stats_stop_button,
- self.stats_start,
- self.stats_start_button
- ]
- )
-
- self._params = {'stats_true':False,
- 'stats_start_true':False,
- 'stats_stop':0,
- 'stats_stop_true':False,
- 'stats_start':0
- }
-
- def show(self):
- """Show options window."""
- self.window.run()
- self.window.hide()
-
- def on_button_toggled_hide(self, control, widgets):
- """Hide unchecked fields"""
- active = control.get_active()
-
- for widget in widgets:
- widget.set_sensitive(active)
-
- @property
- def params(self):
- """Getter for analysis params"""
- self._params['stats_true'] = self.stats_button.get_active()
-
- self._params['stats_start_true'] = self.stats_start_button.get_active()
- self._params['stats_start'] = self.stats_start.get_value()
-
- self._params['stats_stop_true'] = self.stats_stop_button.get_active()
- self._params['stats_stop'] = self.stats_stop.get_value()
-
- return self._params
-
- @params.setter
- def params(self, params):
- for key in self._params:
- if key in params:
- self._params[key] = params[key]
-
- self.stats_button.set_active(self._params['stats_true'])
- self.stats_start_button.set_active(self._params['stats_start_true'])
- self.stats_start.set_value(self._params['stats_start'])
- self.stats_stop_button.set_active(self._params['stats_stop_true'])
- self.stats_stop.set_value(self._params['stats_stop'])
-
-def do_analysis(experiment):
- """Takes an experiment class instance and runs selected analysis."""
-
- experiment.analysis = {}
-
- if experiment.parameters['stats_true']:
- if (experiment.parameters['stats_start_true'] or
- experiment.parameters['stats_stop_true']):
-
- if experiment.parameters['stats_start_true']:
- start = experiment.parameters['stats_start']
- else:
- start = min(experiment.data['data'][0][0])
-
- if experiment.parameters['stats_stop_true']:
- stop = experiment.parameters['stats_stop']
- else:
- stop = min(experiment.data['data'][0][0])
-
- data = _data_slice(experiment.data['data'],
- start,
- stop
- )
- else:
- data = experiment.data['data']
-
- experiment.analysis.update(_summary_stats(data))
-
- try:
- x, y = experiment.data['ft'][0]
- experiment.analysis['FT Integral'] = _integrateSpectrum(
- x,
- y,
- float(experiment.parameters['sync_freq']),
- float(experiment.parameters['fft_int'])
- )
-
- except KeyError:
- pass
-
-def _data_slice(data, start, stop):
- """Accepts data (as list of tuples of lists) and returns copy of data
- between start and stop (in whatever x-axis units for the experiment type).
- """
- output = []
-
- for scan in range(len(data)):
- t = []
- for i in range(len(data[scan])):
- t.append([])
- output.append(tuple(t))
-
- for i in range(len(data[scan][0])): # x-axis column
- if data[scan][0][i] >= start or data[scan][0][i] <= stop:
- for d in range(len(output[scan])):
- output[scan][d].append(data[scan][d][i])
-
- return output
-
-def _summary_stats(data):
- """Takes data and returns summary statistics of first y variable as dict of
- name, (scan, values).
- """
-
- stats = {'min':[],'max':[], 'mean':[]}
-
- for scan in range(len(data)):
- stats['min'].append(
- (scan, min(data[scan][1]))
- )
- stats['max'].append(
- (scan, max(data[scan][1]))
- )
- stats['mean'].append(
- (scan, mean(data[scan][1]))
- )
- return stats
-
-def _integrateSpectrum(x, y, target, bandwidth):
- """
- Returns integral of range of bandwidth centered on target.
- """
- j = 0
- k = len(x)
-
- for i in range(len(x)):
- if x[i] >= target-bandwidth/2:
- j = i
- break
-
- for i in range(j,len(x)):
- if x[i] >= target+bandwidth/2:
- k = i
- break
-
- return [(0, trapz(y=y[j:k], x=x[j:k]))]
\ No newline at end of file
diff --git a/dstat_interface/core/daemon.py b/dstat_interface/core/daemon.py
new file mode 100644
index 0000000..9703c88
--- /dev/null
+++ b/dstat_interface/core/daemon.py
@@ -0,0 +1,154 @@
+import logging
+import pickle
+from math import ceil
+
+import pynng
+import trio
+
+from dstat_interface.core.dstat.comm import SerialDevices, dstat_connect
+from dstat_interface.core.dstat.comm import state as dstat_state
+from dstat_interface.core.experiments.experiment_container import ExperimentContainer
+from dstat_interface.core.experiments.lsv import LSVExperimentContainer, CVExperimentContainer
+from dstat_interface.core.experiments.swv import SWVExperimentContainer, DPVExperimentContainer
+from dstat_interface.core.experiments.chronoamp import CAExperimentContainer
+from dstat_interface.core.tasks import ExperimentBaseTasks
+from utils import runtime_dir
+
+logger = logging.getLogger(__name__)
+
+e = [LSVExperimentContainer, CVExperimentContainer, SWVExperimentContainer, DPVExperimentContainer, CAExperimentContainer]
+experiments: dict[str, type[ExperimentContainer]] = {exp.experiment_id: exp for exp in e}
+
+
+class DaemonExperimentTasks(ExperimentBaseTasks):
+ def __init__(self, exp_con: ExperimentContainer, socket: pynng.Pub0, socket_int: pynng.Bus0):
+ super().__init__(exp_con)
+ self.socket = socket
+ self.socket_int = socket_int
+ self.data_index = 0
+ self.tasks += [self.send_data, self.check_interrupts]
+
+ async def update_progress(self, cancel_scope: trio.CancelScope):
+ while True:
+ scan = self.exp_con.progress_scan
+ last_progress = 0
+
+ while True:
+ await trio.sleep(0.2)
+ try:
+ progress = ceil(self.exp_con.get_progress())
+
+ # End of Scan
+ except StopIteration:
+ await self.socket.asend(f'progress: {scan}, 100'.encode('utf-8'))
+ break
+
+ if progress > last_progress:
+ await self.socket.asend(f'progress: {scan}, {progress}'.encode('utf-8'))
+ last_progress = progress
+ if progress >= 100:
+ break
+
+ async def send_data(self, cancel_scope: trio.CancelScope):
+ while True:
+ await trio.sleep(0.2)
+ new_index = len(self.exp_con.handler_instance.data['timestamp'])
+ if new_index == 0:
+ continue
+ data = {key: value[self.data_index:new_index] for key, value in self.exp_con.handler_instance.data.items()}
+
+ await self.socket.asend(b'data:' + pickle.dumps(data))
+ self.data_index = new_index
+ if self.exp_con.handler_instance.done:
+ cancel_scope.cancel()
+ return
+
+ async def check_interrupts(self, cancel_scope: trio.CancelScope):
+ while True:
+ msg = await self.socket_int.arecv()
+ if msg == b'ABORT':
+ dstat_state.ser.stop_exp()
+
+
+class DStatDaemon(object):
+ def __init__(self, listen_addr_pub=None, listen_addr_ctrl=None, listen_addr_interrupt=None):
+ if listen_addr_pub is None:
+ self.address_pub = 'ipc://' + runtime_dir() + '/dstat-interfaced-pub'
+ if listen_addr_ctrl is None:
+ self.address_ctrl = 'ipc://' + runtime_dir() + '/dstat-interfaced-ctrl'
+ if listen_addr_interrupt is None:
+ self.address_int = 'ipc://' + runtime_dir() + '/dstat-interfaced-int'
+
+ self.socket_pub = pynng.Pub0(listen=self.address_pub)
+ self.socket_ctrl = pynng.Rep0(listen=self.address_ctrl)
+ self.socket_interrupt = pynng.Bus0(listen=self.address_int)
+
+ self.device_list = SerialDevices()
+ self.connected = False
+
+ self.command_map = {'fetch_devices': self.fetch_devices,
+ 'connect_dstat': self.connect_dstat,
+ 'disconnect_dstat': self.disconnect_dstat,
+ 'fetch_experiments': self.fetch_experiments,
+ 'run_experiment': self.run_experiment}
+
+ async def fetch_devices(self, payload: dict = None) -> dict:
+ self.device_list.refresh()
+ return {'ports': self.device_list.ports}
+
+ async def connect_dstat(self, payload: dict = None) -> dict:
+ if not self.connected:
+ self.connected = dstat_connect(payload['port'])
+ msg = f'DStat connected: {self.connected}'
+ else:
+ msg = "DStat already connected"
+ return {'connected': self.connected,
+ 'dstat_version': dstat_state.dstat_version,
+ 'firmware_version': dstat_state.firmware_version,
+ 'board': dstat_state.board_instance,
+ 'msg': msg}
+
+ async def disconnect_dstat(self, payload: dict = None):
+ if self.connected:
+ dstat_state.ser.close()
+ self.connected = False
+ return {'connected': False, 'msg': 'DStat disconnected'}
+ else:
+ return {'connected': False, 'msg': 'DStat already disconnected'}
+
+ async def fetch_experiments(self, payload: dict = None):
+ return {'experiments': list(experiments.values())}
+
+ async def run_experiment(self, exp_dict: dict):
+ exp = exp_dict['experiment_id']
+ del exp_dict['experiment_id']
+
+ experiment_container = experiments[exp](exp_dict, mux=dstat_state.board_instance.channels)
+ dstat_state.ser.start_exp(experiment_container.get_proc())
+ experiment_container.start_handler(dstat_state.ser)
+ tasks = DaemonExperimentTasks(experiment_container, self.socket_pub, self.socket_interrupt)
+ await tasks.loop()
+ return {'status': 'done'}
+
+ async def run(self):
+ while True:
+ command: str
+ payload: dict
+ command, payload = pickle.loads(await self.socket_ctrl.arecv())
+ await self.socket_ctrl.asend(pickle.dumps(await (self.command_map[command](payload))))
+
+ def close(self):
+ self.socket_pub.close()
+ self.socket_ctrl.close()
+
+ def __del__(self):
+ self.close()
+
+
+async def main():
+ daemon = DStatDaemon()
+ async with trio.open_nursery() as nursery:
+ nursery.start_soon(daemon.run)
+
+if __name__ == '__main__':
+ trio.run(main)
diff --git a/dstat_interface/core/dstat-cli.py b/dstat_interface/core/dstat-cli.py
new file mode 100644
index 0000000..28e361a
--- /dev/null
+++ b/dstat_interface/core/dstat-cli.py
@@ -0,0 +1,135 @@
+import argparse
+import logging
+import pathlib
+import sys
+from math import ceil
+
+from tqdm import tqdm
+import pandas as pd
+import trio
+
+from dstat_interface.core.tasks import ExperimentBaseTasks
+from . import state
+from .dstat.comm import SerialDevices, dstat_connect, read_settings
+from .experiments.experiment_container import ExperimentContainer
+from .experiments.lsv import LSVExperimentContainer, CVExperimentContainer
+from .experiments.swv import SWVExperimentContainer, DPVExperimentContainer
+from .dstat.state import DStatState
+
+# Setup Logging
+logger = logging.getLogger(__name__)
+
+logging_choices = {'DEBUG': logging.DEBUG,
+ 'INFO': logging.INFO,
+ 'WARNING': logging.WARNING,
+ 'ERROR': logging.ERROR}
+
+experiments = [LSVExperimentContainer, CVExperimentContainer, SWVExperimentContainer, DPVExperimentContainer]
+
+dstat_state = DStatState()
+
+
+class CLIExperimentTasks(ExperimentBaseTasks):
+ async def update_progress(self, cancel_scope):
+ scan = 0
+ while True:
+ if scan == self.exp_con.progress_iters-1: # Inner loop broken when already at last scan (iters 0-indexed)
+ break
+ scan = self.exp_con.progress_scan
+ last_progress = 0
+ with tqdm(total=100, unit='%', dynamic_ncols=True, desc=f'Scan {scan+1}',
+ bar_format='{l_bar}{bar}[{elapsed}]') as pbar:
+ while True:
+ try:
+ progress = ceil(self.exp_con.get_progress())
+ except StopIteration:
+ pbar.update(100 - last_progress)
+ break
+ pbar.update(progress-last_progress)
+ last_progress = progress
+ if progress >= 100:
+ break
+ await trio.sleep(0.2)
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--log-level', choices=logging_choices, default="INFO")
+ parser.add_argument('--experiment-path', type=str, default=None)
+ parser.add_argument('-s', '--simulator', action='store_true')
+ experiment_subparsers = parser.add_subparsers(title="Experiments:", required=True)
+
+ for exp in experiments:
+ experiment = exp({})
+ exp_parser = experiment_subparsers.add_parser(name=experiment.experiment_id)
+ exp_parser.set_defaults(experiment=exp)
+ arguments = experiment.param_input
+ for i in arguments:
+ kind = arguments[i]
+ try:
+ default = experiment.defaults[i]
+ except KeyError:
+ default = None
+ try:
+ doc = experiment.param_docs[i]
+ except KeyError:
+ doc = ''
+
+ if kind is bool:
+ exp_parser.add_argument(f'--{i}', action=f'store_{not experiment.defaults[i]}'.lower(), help=doc)
+ elif isinstance(kind, list):
+ if default is not None:
+ exp_parser.add_argument(f'--{i}', choices=kind, default=default, help=doc)
+ else:
+ exp_parser.add_argument(i, metavar=i, choices=kind, help=doc)
+ else:
+ if default is not None:
+ exp_parser.add_argument(f'--{i}', type=kind, default=default, help=doc)
+ else:
+ exp_parser.add_argument(i, type=kind, help=doc)
+
+ args = parser.parse_args()
+
+ if args.experiment_path is not None:
+ state.experiment_folder_location = pathlib.Path(args.experiment_path).expanduser() / state.experiment_name
+
+ # Make sure paths exist
+ pathlib.Path(state.experiment_folder_location).mkdir(parents=True, exist_ok=True)
+ pathlib.Path(state.app_dirs.user_config_dir).mkdir(parents=True, exist_ok=True)
+
+ # Logging
+ logfile = state.experiment_folder_location / f'{state.experiment_name}.log'
+ root_logger = logging.getLogger()
+ for handler in logging.root.handlers[:]:
+ logging.root.removeHandler(handler)
+ log_handlers = [logging.StreamHandler(), logging.FileHandler(logfile)]
+ log_formatter = logging.Formatter(
+ fmt='%(asctime)s %(levelname)s: [%(name)s] %(message)s',
+ datefmt='%H:%M:%S',
+ )
+
+ for handler in log_handlers:
+ handler.setFormatter(log_formatter)
+ root_logger.addHandler(handler)
+ root_logger.setLevel(logging_choices[args.log_level])
+
+ if args.simulator:
+ dstat_connect('simulator')
+ else:
+ ports = SerialDevices()
+ dstat_connect(ports.ports[0])
+
+ logger.info('DStat ver: %s Firmware ver: %s', dstat_state.dstat_version, dstat_state.firmware_version)
+ read_settings()
+ exp: ExperimentContainer = args.experiment(vars(args)) # Convert namespace to dict
+
+ dstat_state.ser.start_exp(exp.get_proc())
+
+ exp.start_handler(dstat_state.ser)
+ tasks = CLIExperimentTasks(exp)
+
+ trio.run(tasks.loop)
+ data = pd.DataFrame(exp.handler_instance.data)
+ data.iloc[1:].to_csv(state.experiment_folder_location / 'data.csv')
+ dstat_state.ser.close()
+ sys.exit()
diff --git a/dstat_interface/core/dstat-interface.bat b/dstat_interface/core/dstat-interface.bat
deleted file mode 100644
index da83e27..0000000
--- a/dstat_interface/core/dstat-interface.bat
+++ /dev/null
@@ -1 +0,0 @@
-python .\main.py
diff --git a/dstat_interface/core/dstat.spec b/dstat_interface/core/dstat.spec
deleted file mode 100644
index c0f001d..0000000
--- a/dstat_interface/core/dstat.spec
+++ /dev/null
@@ -1,25 +0,0 @@
-# -*- mode: python -*-
-a = Analysis(['./main.py'],
- pathex=['/Users/mdryden/src/dstat-interface2/dstatInterface'],
- hiddenimports=[],
- hookspath=None,
- runtime_hooks=None)
-pyz = PYZ(a.pure)
-exe = EXE(pyz,
- a.scripts,
- exclude_binaries=True,
- name='DStat',
- debug=False,
- strip=None,
- upx=True,
- console=False )
-coll = COLLECT(exe,
- a.binaries,
- a.zipfiles,
- a.datas,
- strip=None,
- upx=True,
- name='DStat')
-app = BUNDLE(coll,
- name='DStat.app',
- icon=None)
diff --git a/dstat_interface/core/dstat/__init__.py b/dstat_interface/core/dstat/__init__.py
index 1fb1ae9..e69de29 100644
--- a/dstat_interface/core/dstat/__init__.py
+++ b/dstat_interface/core/dstat/__init__.py
@@ -1,3 +0,0 @@
-from . import comm
-from . import dfu
-from . import state
\ No newline at end of file
diff --git a/dstat_interface/core/dstat/boards.py b/dstat_interface/core/dstat/boards.py
index da4927f..31c0581 100755
--- a/dstat_interface/core/dstat/boards.py
+++ b/dstat_interface/core/dstat/boards.py
@@ -22,20 +22,51 @@ from __future__ import division, absolute_import, print_function, unicode_litera
import sys
import inspect
import logging
+from abc import ABCMeta, abstractmethod
+from typing import Union, Type
from pkg_resources import parse_version, parse_requirements
logger = logging.getLogger(__name__)
-class BaseBoard(object):
+class BaseBoard(object, metaclass=ABCMeta):
pcb_version = 'x.x.x'
booster = False
+ mux = False
+ channels = 1
def __init__(self):
self.max_freq = 5000
self.max_scans = 255
self.max_time = 65535
+ self.mv_max = 1500
+ self.mv_min = -1500
+
+ self.gain = [1, 1e2, 3e3, 3e4, 3e5, 3e6, 3e7, 1e8]
+ self.gain_labels = ["Bypass", "100 Ω (15 mA FS)", "3 kΩ (500 µA FS)",
+ "30 kΩ (50 µA FS)", "300 kΩ (5 µA FS)",
+ "3 MΩ (500 nA FS)", "30 MΩ (50 nA FS)",
+ "100 MΩ (15 nA FS)"
+ ]
+
+ self.adc_rate_labels = ['2.5', '5', '10', '15', '25', '30', '50', '60', '100', '500', '1000', '2000', '3750',
+ '7500', '15000', '30000']
+
+ self.adc_rate_codes = [3, 19, 35, 51, 67, 83, 99, 114, 130, 146, 161, 176, 192, 208, 224, 240]
+ self.adc_rate_default_index = 7
+
+ self.adc_pga = [1, 2, 4, 8, 16, 32, 64]
+ self.adc_pga_labels = [f'{pga}X' for pga in self.adc_pga]
+ self.adc_pga_codes = list(range(7))
+ self.adc_pga_default_index = 1
+
+ self.gain_trim = [None, 'r100_trim', 'r3k_trim',
+ 'r30k_trim', 'r300k_trim', 'r3M_trim',
+ 'r30M_trim', 'r100M_trim']
+ self.gain_settings = len(self.gain)
+ self.gain_default_index = 2
+ self.re_voltage_scale = 1
self.setup()
assert len(self.gain) == self.gain_settings
@@ -43,6 +74,7 @@ class BaseBoard(object):
if self.gain_trim is not None:
assert len(self.gain_trim) == self.gain_settings
+ @abstractmethod
def setup(self):
"""Override in subclasses to provide correct numbers"""
self.gain = [1, 1e2, 3e3, 3e4, 3e5, 3e6, 3e7, 1e8]
@@ -114,6 +146,11 @@ class V1_2Board(BaseBoard):
self.re_voltage_scale = 1
+class V1_2BoardMUX(V1_2Board):
+ mux = True
+ channels = 16
+
+
def __get_all_subclasses(cls):
all_subclasses = []
@@ -124,13 +161,13 @@ def __get_all_subclasses(cls):
return all_subclasses
-def find_board(version, booster=False):
+def find_board(version, booster=False, mux=False) -> Union[None, Type[BaseBoard]]:
"""Returns highest compatible board class or None if none available."""
boards = __get_all_subclasses(BaseBoard)
candidates = []
for board in boards:
- req = parse_requirements('dstat~={}'.format(board.pcb_version)).next()
- if board.booster == booster and version in req:
+ req = next(parse_requirements('dstat~={}'.format(board.pcb_version)))
+ if board.booster == booster and board.mux == mux and version in req:
candidates.append(board)
try:
picked = sorted(candidates,
diff --git a/dstat_interface/core/dstat/comm.py b/dstat_interface/core/dstat/comm.py
index d78ea58..916a8fd 100755
--- a/dstat_interface/core/dstat/comm.py
+++ b/dstat_interface/core/dstat/comm.py
@@ -17,119 +17,108 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
-import time
-import struct
-import multiprocessing as mp
-from collections import OrderedDict
import logging
+import multiprocessing as mp
+import time
+from datetime import datetime
+from typing import Union, Tuple
-from pkg_resources import parse_version
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print "ERR: GTK not available"
- sys.exit(1)
import serial
+from pkg_resources import parse_version
from serial.tools import list_ports
-from ..errors import InputError, VarError
+from dstat_interface.core.dstat import boards
+from dstat_interface.core.dstat.state import DStatState
+from .utility import SettingsProcess, VersionCheckProcess
+from .experiment_process import BaseExperimentProcess
+from .simulator import SerialSim
logger = logging.getLogger(__name__)
-dstat_logger = logging.getLogger("{}.DSTAT".format(__name__))
-exp_logger = logging.getLogger("{}.Experiment".format(__name__))
+dstat_logger = logging.getLogger(f'{__name__}.DSTAT')
+exp_logger = logging.getLogger(f'{__name__}.Experiment')
+
+state = DStatState()
-from . import state
class AlreadyConnectedError(Exception):
def __init__(self):
- super(AlreadyConnectedError, self).__init__(self,
- "Serial instance already connected.")
+ super().__init__('Serial instance already connected.')
+
class NotConnectedError(Exception):
def __init__(self):
- super(NotConnectedError, self).__init__(self,
- "Serial instance not connected.")
-
-class ConnectionError(Exception):
- def __init__(self):
- super(ConnectionError, self).__init__(self,
- "Could not connect.")
+ super().__init__('Serial instance not connected.')
+
class TransmitError(Exception):
def __init__(self):
- super(TransmitError, self).__init__(self,
- "No reply received.")
+ super().__init__('No reply received.')
-def _serial_process(ser_port, proc_pipe, ctrl_pipe, data_pipe):
+def _serial_process(ser_port: str, proc_pipe: mp.connection.Connection, ctrl_pipe: mp.connection.Connection,
+ data_pipe: mp.connection.Connection, poll_s: float = .1):
ser_logger = logging.getLogger("{}._serial_process".format(__name__))
- connected = False
+ exc = None
for i in range(5):
- time.sleep(1) # Give OS time to enumerate
-
+ time.sleep(1) # Give OS time to enumerate
+
try:
- ser = serial.Serial(ser_port, timeout=1)
- # ser = serial.Serial(ser_port, timeout=1)
- ser_logger.info("Connecting")
- time.sleep(.5)
- connected = True
- except serial.SerialException:
- pass
-
- if connected is True:
+ if ser_port == 'simulator':
+ ser = SerialSim(ser_port, timeout=1)
+ else:
+ ser = serial.Serial(ser_port, timeout=1)
+ ser_logger.info('Connecting')
break
-
- try:
- if ser.isOpen() is False:
- ser_logger.info("Connection Error")
- proc_pipe.send("SERIAL_ERROR")
- return 1
- except UnboundLocalError: # ser doesn't exist
- ser_logger.info("Connection Error")
- proc_pipe.send("SERIAL_ERROR")
- return 1
-
- ser.write('!0 ')
-
+ except serial.SerialException as e:
+ exc = e
+ else:
+ if exc:
+ raise exc
+ else:
+ raise serial.SerialException(f'Could not connect on {ser_port}')
+
+ ser.write(b'!0 ')
+
for i in range(10):
- if ser.readline().rstrip()=="@ACK 0":
- if ser.readline().rstrip()=="@RCV 0":
+ if ser.readline().rstrip() == b'@ACK 0':
+ if ser.readline().rstrip() == b'@RCV 0':
break
else:
time.sleep(.5)
ser.reset_input_buffer()
- ser.write('!0 ')
- time.sleep(.1)
+ ser.write(b'!0 ')
+ time.sleep(poll_s)
+ else:
+ raise TransmitError()
while True:
- # These can only be called when no experiment is running
- if ctrl_pipe.poll():
- ctrl_buffer = ctrl_pipe.recv()
+ # These can only be called when no experiment is running, otherwise ctrl_pipe passes to proc
+ if ctrl_pipe.poll():
+ ctrl_buffer: str = ctrl_pipe.recv()
if ctrl_buffer in ('a', "DISCONNECT"):
proc_pipe.send("ABORT")
try:
- ser.write('a')
+ ser.write(b'a')
except serial.SerialException:
return 0
ser_logger.info("ABORT")
-
+
if ctrl_buffer == "DISCONNECT":
ser_logger.info("DISCONNECT")
ser.rts = False
ser._update_dtr_state() # Need DTR update on Windows
-
ser.close()
proc_pipe.send("DISCONNECT")
return 0
else:
- ser.write(ctrl_buffer)
-
+ ser.write(ctrl_buffer.encode('ascii'))
+
elif proc_pipe.poll():
+ # Flush ctrl_pipe
while ctrl_pipe.poll():
ctrl_pipe.recv()
+
try:
return_code = proc_pipe.recv().run(ser, ctrl_pipe, data_pipe)
except serial.SerialException:
@@ -141,59 +130,49 @@ def _serial_process(ser_port, proc_pipe, ctrl_pipe, data_pipe):
ser_logger.info('Return code: %s', str(return_code))
proc_pipe.send(return_code)
-
+
else:
- time.sleep(.1)
-
+ time.sleep(poll_s)
-class SerialConnection(GObject.Object):
- __gsignals__ = {
- 'connected': (GObject.SIGNAL_RUN_FIRST, None, ()),
- 'disconnected': (GObject.SIGNAL_RUN_FIRST, None, ())
- }
-
+class SerialConnection(object):
def __init__(self):
- super(SerialConnection, self).__init__()
self.connected = False
-
- def connect(self, ser_port):
+ self.proc_pipe_p, self.proc_pipe_c = mp.Pipe(duplex=True)
+ self.ctrl_pipe_p, self.ctrl_pipe_c = mp.Pipe(duplex=True)
+ self.data_pipe_p, self.data_pipe_c = mp.Pipe(duplex=True)
+ self.proc: Union[None, mp.Process] = None
+
+ def open(self, ser_port: str):
if self.connected is False:
self.proc_pipe_p, self.proc_pipe_c = mp.Pipe(duplex=True)
self.ctrl_pipe_p, self.ctrl_pipe_c = mp.Pipe(duplex=True)
self.data_pipe_p, self.data_pipe_c = mp.Pipe(duplex=True)
-
+
self.proc = mp.Process(target=_serial_process, args=(ser_port,
- self.proc_pipe_c, self.ctrl_pipe_c,
- self.data_pipe_c))
+ self.proc_pipe_c, self.ctrl_pipe_c, self.data_pipe_c))
self.proc.start()
- time.sleep(2)
if self.proc.is_alive() is False:
raise ConnectionError()
- return False
self.connected = True
- self.emit('connected')
return True
else:
raise AlreadyConnectedError()
- return False
-
+
def assert_connected(self):
if self.connected is False:
raise NotConnectedError()
-
- def start_exp(self, exp):
+
+ def start_exp(self, exp: BaseExperimentProcess):
self.assert_connected()
-
self.proc_pipe_p.send(exp)
-
+
def stop_exp(self):
self.send_ctrl('a')
-
+
def get_proc(self, block=False):
self.assert_connected()
-
- if block is True:
+ if block:
return self.proc_pipe_p.recv()
else:
if self.proc_pipe_p.poll() is True:
@@ -203,8 +182,7 @@ class SerialConnection(GObject.Object):
def get_ctrl(self, block=False):
self.assert_connected()
-
- if block is True:
+ if block:
return self.ctrl_pipe_p.recv()
else:
if self.ctrl_pipe_p.poll() is True:
@@ -212,379 +190,139 @@ class SerialConnection(GObject.Object):
else:
return None
- def get_data(self, block=False):
+ def get_data(self, block=False) -> Union[None, Tuple[datetime, int, bytes]]:
self.assert_connected()
-
- if block is True:
+ if block:
return self.data_pipe_p.recv()
else:
- if self.data_pipe_p.poll() is True:
+ if self.data_pipe_p.poll():
return self.data_pipe_p.recv()
else:
return None
-
+
def flush_data(self):
self.assert_connected()
-
while self.data_pipe_p.poll() is True:
self.data_pipe_p.recv()
-
- def send_ctrl(self, ctrl):
+
+ def send_ctrl(self, ctrl: str):
self.assert_connected()
-
self.ctrl_pipe_p.send(ctrl)
-
- def disconnect(self):
- logger.info("Disconnecting")
+
+ def close(self):
+ logger.info('Disconnecting')
self.send_ctrl('DISCONNECT')
self.proc.join()
- self.emit('disconnected')
self.connected = False
-class VersionCheck(object):
- def __init__(self):
- pass
-
- def run(self, ser, ctrl_pipe, data_pipe):
- """Tries to contact DStat and get version. Returns a tuple of
- (major, minor). If no response, returns empty tuple.
-
- Arguments:
- ser_port -- address of serial port to use
- """
- try:
- ser.reset_input_buffer()
- ser.write('!1\n')
-
- for i in range(10):
- if ser.readline().rstrip()=="@ACK 1":
- ser.write('V\n')
- if ser.readline().rstrip()=="@RCV 1":
- break
- else:
- time.sleep(.5)
- ser.reset_input_buffer()
- ser.write('!1\n')
- time.sleep(.1)
-
- for line in ser:
- dstat_logger.info(line.decode('utf-8'))
- if line.startswith('V'):
- input = line.lstrip('V')
- elif line.startswith("#"):
- dstat_logger.info(line.lstrip().rstrip())
- elif line.lstrip().startswith("@DONE"):
- dstat_logger.debug(line.lstrip().rstrip())
- ser.reset_input_buffer()
- break
-
- pcb, sep, firmware = input.strip().rpartition('-')
-
- if pcb == "":
- pcb = firmware
- firmware = False
- logger.info("Your firmware does not support version detection.")
-
- data_pipe.send((pcb, False))
-
- else:
- logger.info(
- "Firmware Version: {}".format(
- hex(int(firmware)).lstrip('0x')
- )
- )
- data_pipe.send((
- pcb,
- hex(int(firmware)).lstrip('0x')
- ))
-
- logger.info(
- "PCB Version: {}".format(pcb)
- )
-
- status = "DONE"
-
- except UnboundLocalError as e:
- status = "SERIAL_ERROR"
- except SerialException as e:
- logger.error('SerialException: %s', e)
- status = "SERIAL_ERROR"
- finally:
- return status
-
-def version_check(ser_port):
+
+def dstat_connect(ser_port) -> bool:
"""Tries to contact DStat and get version. Stores version in state.
If no response, returns False, otherwise True.
-
+
Arguments:
ser_port -- address of serial port to use
- """
+ """
state.ser = SerialConnection()
-
- state.ser.connect(ser_port)
- state.ser.start_exp(VersionCheck())
+
+ state.ser.open(ser_port)
+ state.ser.start_exp(VersionCheckProcess())
result = state.ser.get_proc(block=True)
- if result == "SERIAL_ERROR":
+ if result == 'SERIAL_ERROR':
state.dstat_version = None
state.firmware_version = None
return False
- else:
- buffer = state.ser.get_data(block=True)
+
+ cmd, buffer = state.ser.get_data(block=True)
+ if cmd != 'V':
+ logger.error('DStat did not respond correctly')
+ return False
version, state.firmware_version = buffer
state.dstat_version = parse_version(version)
- logger.debug("version_check done")
+
+ cmd, buffer = state.ser.get_data(block=True)
+ if cmd != 'X':
+ logger.error('DStat did not reply to mux channel request')
+ return False
+
+ if buffer > 1:
+ mux = True
+ else:
+ mux = False
+
+ board = boards.find_board(state.dstat_version, mux=mux)
+ if board:
+ state.board_instance = board()
+ logger.debug('version_check done')
time.sleep(.1)
-
+
return True
-class Settings(object):
- def __init__(self, task, settings=None):
- self.task = task
- self.settings = settings
-
- def run(self, ser, ctrl_pipe, data_pipe):
- """Tries to contact DStat and get settings. Returns dict of
- settings.
- """
-
- self.ser = ser
-
- if 'w' in self.task:
- self.write()
-
- if 'r' in self.task:
- data_pipe.send(self.read())
-
- status = "DONE"
-
- return status
-
- def read(self):
- settings = OrderedDict()
- self.ser.reset_input_buffer()
- self.ser.write('!2\n')
-
- for i in range(10):
- if self.ser.readline().rstrip()=="@ACK 2":
- self.ser.write('SR\n')
- if self.ser.readline().rstrip()=="@RCV 2":
- break
- else:
- time.sleep(.5)
- self.ser.reset_input_buffer()
- self.ser.write('!2\n')
- time.sleep(.1)
-
- for line in self.ser:
- if line.lstrip().startswith('S'):
- input = line.lstrip().lstrip('S')
- elif line.lstrip().startswith("#"):
- dstat_logger.info(line.lstrip().rstrip())
- elif line.lstrip().startswith("@DONE"):
- dstat_logger.debug(line.lstrip().rstrip())
- self.ser.reset_input_buffer()
- break
-
- parted = input.rstrip().split(':')
-
- for i in range(len(parted)):
- settings[parted[i].split('.')[0]] = [i, parted[i].split('.')[1]]
-
- return settings
-
- def write_command(self, cmd, params=None, retry=5):
- """Write command to serial with optional number of retries."""
- def get_reply(retries = 3):
- while True:
- reply = self.ser.readline().rstrip()
- if reply.startswith('#'):
- dstat_logger.info(reply)
- elif reply == "":
- retries -= 1
- if retries <= 0:
- raise TransmitError
- else:
- return reply
-
- n = len(cmd)
- if params is not None:
- n_params = len(params)
-
- for _ in range(retry):
- tries = 5
- while True:
- time.sleep(0.2)
- self.ser.reset_input_buffer()
- self.ser.write('!{}\n'.format(n))
- time.sleep(.1)
-
- try:
- reply = get_reply()
- except TransmitError:
- if tries <= 0:
- continue
- tries -= 1
- pass
- else:
- break
-
- if reply != "@ACK {}".format(n):
- logger.warning("Expected ACK got: {}".format(reply))
- continue
-
- tries = 5
-
- while True:
- self.ser.write('{}\n'.format(cmd))
- try:
- reply = get_reply()
- except TransmitError:
- if tries <= 0:
- continue
- tries -= 1
- pass
- else:
- break
-
- if reply != "@RCV {}".format(n):
- logger.warning("Expected RCV got: {}".format(reply))
- continue
-
- if params is None:
- return True
-
- tries = 5
-
- while True:
- try:
- reply = get_reply()
- except TransmitError:
- if tries <= 0:
- continue
- tries -= 1
- pass
- else:
- break
-
- if reply != "@RQP {}".format(n_params):
- logger.warning("Expected RQP got: {}".format(reply))
- continue
-
- tries = 5
-
- for i in params:
- while True:
- self.ser.write(i + " ")
- try:
- reply = get_reply()
- if reply == "@RCVC {}".format(i):
- break
- except TransmitError:
- if tries <= 0:
- continue
- tries -= 1
- pass
- else:
- break
- return True
- return False
-
- def write(self):
- write_buffer = range(len(self.settings))
-
- for i in self.settings: # make sure settings are in right order
- write_buffer[self.settings[i][0]] = self.settings[i][1]
-
- to_write = " ".join(write_buffer) + " "
- n = len(to_write)
- logger.debug("to_write = %s", to_write)
-
- if not self.write_command('SW' + to_write):
- logger.error("Could not write command.")
-
+
def read_settings():
"""Tries to contact DStat and get settings. Returns dict of
settings.
"""
-
state.ser.flush_data()
- state.ser.start_exp(Settings(task='r'))
+ state.ser.start_exp(SettingsProcess(task='r'))
state.settings = state.ser.get_data(block=True)
logger.info("Read settings from DStat")
logger.debug("read_settings: %s", state.ser.get_proc(block=True))
-
- return
-
+
+
def write_settings():
"""Tries to write settings to DStat from global settings var.
"""
-
logger.debug("Settings to write: %s", state.settings)
-
+
state.ser.flush_data()
- state.ser.start_exp(Settings(task='w', settings=state.settings))
+ state.ser.start_exp(SettingsProcess(task='w', settings=state.settings))
logger.info("Wrote settings to DStat")
logger.debug("write_settings: %s", state.ser.get_proc(block=True))
-
- return
-
-class LightSensor:
- def __init__(self):
- pass
-
- def run(self, ser, ctrl_pipe, data_pipe):
- """Tries to contact DStat and get light sensor reading. Returns uint of
- light sensor clear channel.
- """
-
- ser.reset_input_buffer()
- ser.write('!')
-
- while not ser.read()=="@":
- self.ser.reset_input_buffer()
- ser.write('!')
-
- ser.write('T')
- for line in ser:
- if line.lstrip().startswith('T'):
- input = line.lstrip().lstrip('T')
- elif line.lstrip().startswith("#"):
- dstat_logger.info(line.lstrip().rstrip())
- elif line.lstrip().startswith("@DONE"):
- dstat_logger.debug(line.lstrip().rstrip())
- ser.reset_input_buffer()
- break
-
- parted = input.rstrip().split('.')
-
- data_pipe.send(parted[0])
- status = "DONE"
-
- return status
-
-def read_light_sensor():
- """Tries to contact DStat and get light sensor reading. Returns uint of
- light sensor clear channel.
- """
-
- state.ser.flush_data()
- state.ser.start_exp(LightSensor())
-
- logger.debug("read_light_sensor: %s", state.ser.get_proc(block=True))
-
- return state.ser.get_data(block=True)
+
class SerialDevices(object):
"""Retrieves and stores list of serial devices in self.ports"""
def __init__(self):
self.ports = []
self.refresh()
-
+
def refresh(self):
"""Refreshes list of ports."""
try:
self.ports, _, _ = zip(*list_ports.grep("DSTAT"))
except ValueError:
self.ports = []
- logger.error("No serial ports found")
\ No newline at end of file
+ logger.error("No serial ports found")
+
+
+if __name__ == '__main__':
+ root_logger = logging.getLogger()
+ for handler in logging.root.handlers[:]:
+ logging.root.removeHandler(handler)
+ log_handlers = [logging.StreamHandler()]
+ log_formatter = logging.Formatter(
+ fmt='%(asctime)u %(levelname)u: [%(name)u] %(message)u',
+ datefmt='%H:%M:%S',
+ )
+ for handler in log_handlers:
+ handler.setFormatter(log_formatter)
+ root_logger.addHandler(handler)
+ root_logger.setLevel(logging.DEBUG)
+
+ ports = SerialDevices()
+
+ while True:
+ try:
+ dstat_connect(ports.ports[0])
+ # dstat_connect('simulator')
+ logger.info('DStat ver: %s Firmware ver: %s', state.dstat_version, state.firmware_version)
+ read_settings()
+ logger.info('Settings:\n\t%s', '\n\t'.join([f'{key}: {value}' for key, value in state.settings.items()]))
+ break
+ except IndexError:
+ logger.info('No DStat Found')
+ time.sleep(5)
+ ports.refresh()
+ state.ser.close()
diff --git a/dstat_interface/core/dstat/dfu.py b/dstat_interface/core/dstat/dfu.py
deleted file mode 100755
index 3b56288..0000000
--- a/dstat_interface/core/dstat/dfu.py
+++ /dev/null
@@ -1,375 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-from __future__ import (absolute_import, division,
- print_function, unicode_literals)
-
-import subprocess
-import sys
-import os
-import time
-import logging
-from tempfile import mkdtemp
-from zipfile import ZipFile
-
-if sys.version_info >= (3,):
- import urllib.request as urllib2
- import urllib.parse as urlparse
-else:
- import urllib2
- import urlparse
-
-logger = logging.getLogger(__name__)
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk
-except ImportError:
- print("ERR: GTK not available")
- sys.exit(1)
-
-import serial
-
-from . import state
-from .comm import dstat_logger, exp_logger
-
-fwurl = "http://microfluidics.utoronto.ca/gitlab/api/v4/projects/4/jobs/artifacts/master/download?job=1.2.3&private_token=zkgSx1FaaTP7yLyFKkX6"
-
-class FWDialog(object):
- def __init__(self, parent, connect, stop_callback, disconnect_callback, signal='activate'):
- self.parent = parent
- self.stop = stop_callback
- self.disconnect = disconnect_callback
- connect.connect(signal, self.activate)
-
- def activate(self, widget=None, data=None):
- for name, result in assert_deps().items():
- if result is not True:
- logger.error("Can't use firmware update module.")
- self.missing_deps()
- return
-
- self.stop() # Stop OCP
- version_result, master = test_firmware_version()
-
- if version_result is False:
- self.git_error()
- return
-
- if version_result == 'latest':
- message = "Your firmware is already up to date."
- secondary = "Click yes to reflash firmware anyways."
- elif version_result == 'devel':
- message = "Your firmware is not on the master branch."
- secondary = "You may have a development version. " +\
- "Click yes to reflash firmware anyways."
- elif version_result == 'old':
- message = "Your firmware is out of date."
- secondary = "Click yes to flash the latest firmware."
-
- dialog = Gtk.MessageDialog(self.parent, 0, Gtk.MessageType.INFO,
- Gtk.ButtonsType.YES_NO, message)
- dialog.format_secondary_text(secondary)
- dialog.get_content_area().add(
- Gtk.Label(
- label="Installed version: {}".format(state.firmware_version)))
-
- dialog.get_content_area().add(
- Gtk.Label(label="Latest version: {}".format(master)))
-
- dialog.show_all()
- response = dialog.run()
-
- if response == Gtk.ResponseType.YES:
- try:
- download_fw()
- except:
- self.dl_error()
- return
-
- dstat_enter_dfu()
-
- self.dfu_notice()
- self.disconnect()
- try:
- dfu_program()
- except:
- self.dfu_error()
-
- dialog.destroy()
-
- else:
- dialog.destroy()
-
- def missing_deps(self):
- dialog = Gtk.MessageDialog(
- self.parent, 0, Gtk.MessageType.ERROR,
- Gtk.ButtonsType.OK, "Missing Dependencies")
-
- dialog.format_secondary_text('Check console for more info.')
-
- dialog.connect('response', self.destroy)
- dialog.show()
-
- def git_error(self):
- dialog = Gtk.MessageDialog(
- self.parent, 0, Gtk.MessageType.ERROR,
- Gtk.ButtonsType.OK, "Git Error")
-
- dialog.format_secondary_text('Check console for more info.')
-
- dialog.connect('response', self.destroy)
- dialog.show()
-
- def dl_error(self):
- dialog = Gtk.MessageDialog(
- self.parent, 0, Gtk.MessageType.ERROR,
- Gtk.ButtonsType.OK, "Download Error")
-
- dialog.format_secondary_text('Check console for more info.')
-
- dialog.connect('response', self.destroy)
- dialog.show()
-
- def dfu_notice(self):
- dialog = Gtk.MessageDialog(
- self.parent, 0, Gtk.MessageType.INFO,
- Gtk.ButtonsType.OK, "Note about DFU")
-
- dialog.format_secondary_text("Click OK once the DStat has connected in "
- + "DFU mode. Windows doesn't seem to like the automatic reboot. "
- + "Try holding down the reset button while plugging the "
- + 'USB port in (No LEDs should be lit), then click OK. Make sure '
- + 'the DFU driver from the dfu-programmer directory is installed.')
-
- dialog.run()
- dialog.destroy()
-
- def dfu_error(self):
- dialog = Gtk.MessageDialog(
- self.parent, 0, Gtk.MessageType.ERROR,
- Gtk.ButtonsType.OK, "Could not update over DFU")
-
- dialog.format_secondary_text('Check console for more info.')
-
- dialog.connect('response', self.destroy)
- dialog.show()
-
- def destroy(self, widget=None, data=None):
- widget.destroy()
-
-
-def assert_deps():
- deps = {'git' : 'git --version',
- 'dfu-programmer' : 'dfu-programmer --version'}
-
- result = {}
-
- for key, command in deps.items():
- try:
- output = subprocess.check_output(command.split(),
- stderr=subprocess.STDOUT)
- logger.info("%s\n%s", command, output)
- result[key] = True
- except subprocess.CalledProcessError:
- logger.warning("{} is not available.".format(key))
- result[key] = False
-
- return result
-
-def download_fw(): # from https://stackoverflow.com/a/16518224
- temp_dir = mkdtemp()
- logger.info("Temporary directory: {}".format(temp_dir))
- os.chdir(temp_dir) # Go to temporary directory
-
- u = urllib2.urlopen(fwurl)
-
- scheme, netloc, path, query, fragment = urlparse.urlsplit(fwurl)
- filename = os.path.basename(path)
- if not filename:
- filename = 'downloaded.file'
-
- with open(filename, 'wb') as f:
- meta = u.info()
- meta_func = meta.getheaders if hasattr(meta, 'getheaders') else meta.get_all
- meta_length = meta_func("Content-Length")
- file_size = None
- if meta_length:
- file_size = int(meta_length[0])
- logger.info("Downloading: {0} Bytes: {1}".format(fwurl, file_size))
-
- file_size_dl = 0
- block_sz = 8192
- while True:
- buffer = u.read(block_sz)
- if not buffer:
- break
-
- file_size_dl += len(buffer)
- f.write(buffer)
-
- status = "{0:16}".format(file_size_dl)
- if file_size:
- status += " [{0:6.2f}%]".format(file_size_dl * 100 / file_size)
- status += chr(13)
- logger.info(status)
-
- with ZipFile(filename, mode='r') as z:
- fw_path = z.extract('dstat-firmware.hex')
-
- return fw_path
-
-def test_firmware_version(current=None):
- if current is None:
- current = state.firmware_version
-
- temp_dir = mkdtemp()
- logger.info("Temporary directory: {}".format(temp_dir))
- os.chdir(temp_dir) # Go to temporary directory
-
- command = "git clone http://microfluidics.utoronto.ca/gitlab/dstat/dstat-firmware.git"
- logger.info('Cloning master.')
- try:
- output = subprocess.check_output(command.split(),
- stderr=subprocess.STDOUT)
- except subprocess.CalledProcessError as e:
- logger.error("git failed with error code {}".format(e.returncode))
- logger.error("Output: {}".format(e.output))
- return False, None
- logger.info(output)
-
- os.chdir("./dstat-firmware")
-
- command = "git rev-parse --short master"
- master = subprocess.check_output(command.split(), stderr=subprocess.STDOUT)
- logger.info("Current master commit: {}".format(master))
-
- command = "git merge-base --is-ancestor master {}".format(current)
- test = subprocess.call(command.split())
-
- if test == 0: # already newest
- logger.info('Firmware is latest available.')
- return 'latest', master
- elif test == 1: # old version
- logger.info('Firmware is out of date.')
- return 'old', master
- elif test == 128: # newer or different branch
- logger.info('Firmware is not on the master branch.')
- return 'devel', master
- else:
- logger.error('Unexpected git error. Git exited {}'.format(test))
- return False, None
-
-def dfu_program(path='./dstat-firmware.hex'):
- """Tries to program DStat over USB with DFU with hex file at path."""
- try:
- command = "dfu-programmer atxmega256a3u erase"
- output = subprocess.check_output(command.split(),
- stderr=subprocess.STDOUT)
- logger.info("%s\n%s", command, output)
- command = "dfu-programmer atxmega256a3u flash {}".format(path)
- output = subprocess.check_output(command.split(),
- stderr=subprocess.STDOUT)
- logger.info("%s\n%s", command, output)
- command = "dfu-programmer atxmega256a3u launch"
- output = subprocess.check_output(command.split(),
- stderr=subprocess.STDOUT)
- logger.info("%s\n%s", command, output)
- except subprocess.CalledProcessError as e:
- logger.error("{} failed with output:".format(" ".join(e.cmd)))
- logger.error(e.output)
- raise
-
-
-def dstat_enter_dfu():
- """Tries to contact DStat and get version. Stores version in state.
- If no response, returns False, otherwise True.
-
- Arguments:
- ser_port -- address of serial port to use
- """
- exp = DFUMode()
- state.ser.start_exp(exp)
- while True:
- result = state.ser.get_proc(block=True)
- if result in ('SERIAL_ERROR', 'DONE'):
- break
- logger.info(result)
- # state.ser.disconnect()
-
- time.sleep(.1)
-
- return True
-
-
-class DFUMode(object):
- def __init__(self):
- pass
-
- def run(self, ser, ctrl_pipe, data_pipe):
- """Tries to contact DStat and get version. Returns a tuple of
- (major, minor). If no response, returns empty tuple.
-
- Arguments:
- ser_port -- address of serial port to use
- """
- status = None
- try:
- ser.write(b'!2\n')
- exp_logger.info('!2')
-
- for i in range(10):
- if ser.readline().rstrip() == b"@ACK 2":
- dstat_logger.info('@ACK 2')
- ser.write(b'SF\n')
- exp_logger.info('SF')
- status = "DONE"
- time.sleep(5)
- break
- else:
- time.sleep(.5)
- ser.reset_input_buffer()
- ser.write(b'!2\n')
- exp_logger.info('!2')
- time.sleep(.1)
-
- except UnboundLocalError as e:
- status = "SERIAL_ERROR"
- except serial.SerialException as e:
- logger.error('SerialException: %s', e)
- status = "SERIAL_ERROR"
- finally:
- return status
-
-
-if __name__ == "__main__":
- log_handler = logging.StreamHandler()
- log_formatter = logging.Formatter(
- fmt='%(asctime)s %(levelname)s: [%(name)s] %(message)s',
- datefmt='%H:%M:%S'
- )
- log_handler.setFormatter(log_formatter)
- logger.setLevel(level=logging.INFO)
- logger.addHandler(log_handler)
-
- dstat_enter_dfu()
- time.sleep(2)
- dfu_program(sys.argv[1])
\ No newline at end of file
diff --git a/dstat_interface/core/dstat/experiment_handler.py b/dstat_interface/core/dstat/experiment_handler.py
new file mode 100644
index 0000000..5daa436
--- /dev/null
+++ b/dstat_interface/core/dstat/experiment_handler.py
@@ -0,0 +1,115 @@
+from datetime import datetime
+import logging
+import struct
+from typing import Callable, Union, Sequence, Tuple
+
+from .comm import SerialConnection
+
+
+logger = logging.getLogger(__name__)
+dstat_logger = logging.getLogger("{}.DSTAT".format(__name__))
+exp_logger = logging.getLogger("{}.Experiment".format(__name__))
+
+
+class ExperimentHandler(object):
+ def __init__(self, ser: SerialConnection, data_cols: Sequence[str] = ('voltage', 'current'),
+ data_format: str = 'vA'):
+
+ self.ser = ser
+ self.data = {'timestamp': [], 'scan': []}
+ self.data |= {i: [] for i in data_cols}
+ self.data_cols = data_cols
+ self.data_convert = [self.get_data_converter(i) for i in data_format]
+ struct_formats = ['H' if i.islower() else 'l' for i in data_format]
+ self.struct = struct.Struct(f'<{"".join(struct_formats)}')
+ self.done = False
+
+ self.adc_trim = 0
+ self.adc_gain = 3000
+ self.adc_pga = 2
+
+ self.first_skipped = False
+
+ def get_data_converter(self, fmt: str) -> Union[Callable, None]:
+ converters = {'v': self.dac_to_volts, 'A': self.adc_to_amps, 'm': self.ms_to_s}
+ try:
+ return converters[fmt]
+ except KeyError:
+ return None
+
+ @staticmethod
+ def dac_to_volts(dac: int) -> float:
+ return (dac - 32768) * 3000. / 65536
+
+ def adc_to_amps(self, adc: int) -> float:
+ return (adc + self.adc_trim) * (1.5 / self.adc_gain / 8388607) / (self.adc_pga / 2)
+
+ @staticmethod
+ def ms_to_s(ms: int) -> float:
+ return ms/1000.
+
+ def experiment_running_data(self):
+ """Receive data from experiment process and add to
+ current_exp.data['data].
+ """
+ try:
+ incoming = self.ser.get_data()
+ if incoming is not None:
+ if not self.first_skipped:
+ self.first_skipped = True
+ return True
+ self.data_handler(incoming)
+ return True
+
+ except EOFError as err:
+ logger.error(err)
+ return False
+ except IOError as err:
+ logger.error(err)
+ return False
+
+ def get_all_data(self):
+ """
+ Processes remaining data in queue
+ """
+ while True:
+ incoming = self.ser.get_data()
+ if incoming is not None:
+ self.data_handler(incoming)
+ else:
+ self.done = True
+ return
+
+ def data_handler(self, data_input: Tuple[datetime, int, bytes]):
+ date, scan, data = data_input
+ unpacked = self.struct.unpack(data)
+ self.data['scan'].append(scan)
+ self.data['timestamp'].append(date)
+
+ for n, i in enumerate(unpacked):
+ try:
+ self.data[self.data_cols[n]].append(self.data_convert[n](i))
+ except TypeError: # If no converter
+ self.data[self.data_cols[n]].append(i)
+
+ def experiment_running_proc(self):
+ """Receive proc signals from experiment process."""
+ try:
+ proc_buffer = self.ser.get_proc()
+ if proc_buffer is not None:
+ if proc_buffer in ["DONE", "SERIAL_ERROR", "ABORT"]:
+ if proc_buffer == "SERIAL_ERROR":
+ self.ser.close()
+
+ else:
+ logger.warning("Unrecognized experiment return code: %s",
+ proc_buffer)
+ return False
+ return True
+
+ except EOFError as err:
+ logger.warning("EOFError: %s", err)
+ return False
+ except IOError as err:
+ logger.warning("IOError: %s", err)
+ return False
diff --git a/dstat_interface/core/dstat/experiment_process.py b/dstat_interface/core/dstat/experiment_process.py
new file mode 100644
index 0000000..b82ea0b
--- /dev/null
+++ b/dstat_interface/core/dstat/experiment_process.py
@@ -0,0 +1,246 @@
+import logging
+import time
+from abc import ABC, abstractmethod
+from multiprocessing.connection import Connection
+from typing import Union
+from functools import singledispatchmethod
+
+import serial
+
+logger = logging.getLogger(__name__)
+dstat_logger = logging.getLogger("{}.DSTAT".format(__name__))
+exp_logger = logging.getLogger("{}.Experiment".format(__name__))
+
+
+class BaseExperimentProcess(ABC):
+ def __init__(self, *args, **kwargs):
+ self.data_bytes = 0
+ self.serial: Union[None, serial.Serial] = None
+ self.ctrl_pipe: Union[None, Connection] = None
+ self.data_pipe: Union[None, Connection] = None
+
+ self.commands = []
+
+ @singledispatchmethod
+ def parse_command_string(self, cmd_str, params: dict):
+ raise NotImplementedError("cmd_str has unrecognized type %s", type(cmd_str))
+
+ @parse_command_string.register
+ def _(self, cmd_str: str, params: dict):
+ self.commands += [cmd_str.format(**params)]
+
+ @parse_command_string.register
+ def _(self, cmd_str: tuple, params: dict):
+ cmd: str
+ data: tuple
+ cmd, data = cmd_str
+
+ cmd = cmd.format(**params)
+ data_parsed = []
+ for i in data:
+ data_parsed += [str(i) for i in params[i]]
+
+ self.commands += [(cmd, data_parsed)]
+
+ def write_command(self, cmd, params=None, retry=5):
+ """Write command to serial with optional number of retries."""
+
+ def get_reply(retries=3):
+ while True:
+ reply = self.serial.readline().rstrip().decode('ascii')
+ print(reply)
+ if reply.startswith('#'):
+ dstat_logger.info(reply)
+ elif reply == "":
+ retries -= 1
+ if retries <= 0:
+ raise serial.SerialException()
+ else:
+ return reply
+
+ n = len(cmd)
+ if params is not None:
+ n_params = len(params)
+
+ for _ in range(retry):
+ tries = 5
+ while True:
+ time.sleep(0.2)
+ self.serial.reset_input_buffer()
+ self.serial.write(f'!{n}\n'.encode('ascii'))
+ time.sleep(.1)
+
+ try:
+ reply = get_reply()
+ except serial.SerialException:
+ if tries <= 0:
+ continue
+ tries -= 1
+ pass
+ else:
+ break
+
+ if reply != f"@ACK {n}":
+ logger.warning("Expected ACK got: {}".format(reply))
+ continue
+
+ tries = 5
+
+ while True:
+ self.serial.write(f'{cmd}\n'.encode('ascii'))
+ print(cmd)
+ try:
+ reply = get_reply()
+ except serial.SerialException:
+ if tries <= 0:
+ continue
+ tries -= 1
+ pass
+ else:
+ break
+
+ if reply != f"@RCV {n}":
+ logger.warning("Expected RCV got: {}".format(reply))
+ continue
+
+ if params is None:
+ return True
+
+ tries = 5
+
+ while True:
+ try:
+ reply = get_reply()
+ except serial.SerialException:
+ if tries <= 0:
+ continue
+ tries -= 1
+ pass
+ else:
+ break
+
+ if reply != f"@RQP {n_params}":
+ logger.warning("Expected RQP %s got: %s", n_params, reply)
+ continue
+
+ tries = 5
+
+ for i in params:
+ while True:
+ self.serial.write(f"{i} ".encode('ascii'))
+ try:
+ reply = get_reply()
+ if reply == f"@RCVC {i}":
+ break
+ except serial.SerialException:
+ if tries <= 0:
+ continue
+ tries -= 1
+ pass
+ else:
+ break
+ return True
+ return False
+
+ def run(self, ser: serial.Serial, ctrl_pipe: Connection, data_pipe: Connection):
+ """Execute experiment. Connects and sends handshake signal to DStat
+ then sends self.commands. Don't call directly as a process in Windows,
+ use run_wrapper instead.
+ """
+ self.serial = ser
+ self.ctrl_pipe = ctrl_pipe
+ self.data_pipe = data_pipe
+
+ exp_logger.info('Experiment running')
+ status = 'DONE'
+
+ try:
+ for i in self.commands:
+ status = 'DONE'
+ if isinstance(i, str):
+ logger.info('Command: %s', i)
+ print(f'command: {i}')
+
+ if not self.write_command(i):
+ status = 'ABORT'
+ break
+
+ else:
+ cmd, data = i
+ print(f'command: {i}')
+ logger.info("Command: %s", cmd)
+
+ if not self.write_command(cmd, params=data):
+ status = 'ABORT'
+ break
+
+ if not self.serial_handler():
+ status = 'ABORT'
+ break
+
+ time.sleep(0.25)
+
+ except serial.SerialException:
+ status = 'SERIAL_ERROR'
+ finally:
+ while self.ctrl_pipe.poll():
+ self.ctrl_pipe.recv()
+ return status
+
+ @abstractmethod
+ def serial_handler(self):
+ pass
+
+
+class ExperimentProcess(BaseExperimentProcess):
+ def __init__(self):
+ """Adds commands for gain and ADC."""
+ super(ExperimentProcess, self).__init__()
+ self.datapoint = 0
+ self.scan = 0
+ self.time = 0
+
+ def serial_handler(self):
+ """Handles incoming serial transmissions from DStat. Returns False
+ if stop button pressed and sends abort signal to instrument. Sends
+ data to self.data_pipe as result of self.data_handler).
+ """
+ scan = 0
+ start = None
+ try:
+ while True:
+ if self.ctrl_pipe.poll():
+ ctrl = self.ctrl_pipe.recv()
+ logger.debug("serial_handler: %s", ctrl)
+ if ctrl == "DISCONNECT":
+ self.serial.write(b'a')
+ self.serial.reset_input_buffer()
+ logger.info("serial_handler: ABORT pressed!")
+ time.sleep(.3)
+ return False
+ elif ctrl == 'a':
+ self.serial.write(b'a')
+
+ for line in self.serial:
+ if self.ctrl_pipe.poll():
+ if self.ctrl_pipe.recv() == 'a':
+ self.serial.write(b'a')
+
+ if line.startswith(b'B'):
+ if not start:
+ start = time.perf_counter()
+ data = (time.perf_counter()-start, scan, self.serial.read(size=self.data_bytes))
+ self.data_pipe.send(data)
+
+ elif line.lstrip().startswith(b'S'):
+ scan += 1
+
+ elif line.lstrip().startswith(b"#"):
+ dstat_logger.info(line.strip().decode('ascii'))
+
+ elif line.lstrip().startswith(b"@DONE"):
+ dstat_logger.debug(line.strip().decode('ascii'))
+ return True
+
+ except serial.SerialException:
+ return False
diff --git a/dstat_interface/core/dstat/simulator.py b/dstat_interface/core/dstat/simulator.py
new file mode 100644
index 0000000..575f781
--- /dev/null
+++ b/dstat_interface/core/dstat/simulator.py
@@ -0,0 +1,403 @@
+from copy import copy
+from io import IOBase
+from math import ceil, floor
+import logging
+import struct
+from time import sleep
+import re
+from typing import Callable, Union
+
+import numpy as np
+
+logger = logging.getLogger("dstat.simulator")
+digit_pattern = re.compile(rb'(\d+)')
+
+
+class Simulator(object):
+ default_settings = {'max5443_offset': 0,
+ 'tcs_enabled': 1,
+ 'tcs_clear_threshold': 10000,
+ 'r100_trim': 0,
+ 'r3k_trim': 0,
+ 'r30k_trim': 0,
+ 'r300k_trim': 0,
+ 'r3M_trim': 0,
+ 'r30M_trim': 0,
+ 'r100M_trim': 0,
+ 'eis_cal1': 0,
+ 'eis_cal2': 0,
+ 'dac_units_true': 1}
+
+ def __init__(self):
+ self.current_state = self.main
+ self.next_state: Union[None, Callable] = None
+ self.output: bytes = b''
+ self.input_str: bytes = b''
+ self.cmd_length: int = 0
+ self.command_str: bytes = b''
+
+ self.waiting_for_params: int = 0
+ self.extra_params = []
+ self.current_cmd: bytes = b''
+ self.current_params: list = []
+
+ self.settings_dict = copy(Simulator.default_settings)
+
+ def _get_input(self, size=1) -> bytes:
+ if size > len(self.input_str):
+ logger.error("Not enough characters in input buffer")
+ raise IndexError("Not enough characters in input buffer")
+
+ string = self.input_str[:size]
+ self.input_str = self.input_str[size:]
+ return string
+
+ def _get_command(self):
+ string = self.command_str[:1]
+ self.command_str = self.command_str[1:]
+ return string
+
+ def _get_params(self, n):
+ params = self.command_str.split(None, n)
+ if len(params) > n:
+ self.input_str = params.pop()
+ elif len(params) < n:
+ raise IndexError("Not enough characters in command buffer")
+ return params
+
+ def input(self, string):
+ logger.debug("input: {}".format(string))
+ self.input_str = string
+ while len(self.input_str) > 0:
+ self.current_state()
+
+ def main(self):
+ char = self._get_input()
+
+ if char == b'!':
+ try:
+ match = re.match(digit_pattern, self.input_str)
+ cmd_length = match.group(1)
+ except AttributeError:
+ logger.error("No character count received")
+ self.input_str = b''
+ return
+ self.cmd_length = int(cmd_length)
+ self.input_str = self.input_str[len(cmd_length) + 1:]
+ self.output += f'@ACK {self.cmd_length}\n'.encode('ascii')
+ if self.cmd_length == 0:
+ self.output += b'@RCV 0\n'
+ return
+ self.current_state = self.command
+
+ if self.input_str:
+ self.current_state()
+
+ def command(self):
+ def restart():
+ logger.info("USB restart received")
+ return
+
+ def version():
+ logger.info("Version Check")
+ self.output += f'V1.2.3-{0xfffffff:d}\n'.encode('ascii')
+ return
+
+ command_map = {b'E': self.experiment,
+ b'S': self.settings,
+ b'R': restart,
+ b'V': version}
+
+ self.command_str = self._get_input(self.cmd_length + 1)
+ self.output += f'@RCV {self.cmd_length}\n'.encode('ascii')
+
+ char = self.command_str[:1]
+ self.command_str = self.command_str[1:-1] # Remove delimiter
+
+ try:
+ if command_map[char]():
+ self.current_state = self.input_params
+ return
+ except KeyError:
+ logger.warning("Unrecognized command {}".format(char))
+ self.output += f"#ERR: Command {char} not recognized\n".encode('ascii')
+
+ if self.current_state.__name__ != self.abort_wait.__name__:
+ self.output += b"@DONE\n"
+ self.current_state = self.main
+ else:
+ logger.info("abort_wait state")
+ logger.info("Command {} Finished".format(char))
+
+ def abort_wait(self):
+ logger.info("abort_wait() called")
+ self.current_state = self.abort_wait
+ if self._get_input() == b'a':
+ logger.info("Abort signal received")
+ self.output += b"@DONE\n"
+ self.current_state = self.main
+
+ def input_params(self):
+ param = self._get_params(1)
+ self.extra_params.append(param)
+ self.output += f'@RCVC {param}\n'.encode('ascii')
+ self.waiting_for_params -= 1
+
+ if self.waiting_for_params == 0:
+ self.next_state()
+
+ def settings(self):
+ def reset():
+ logger.info("Settings reset")
+ self.settings_dict = self.default_settings.copy()
+
+ def firmware():
+ logger.info("Firmware update mode")
+
+ def read():
+ self.output += b"S"
+ for key, value in self.settings_dict.items():
+ self.output += f"{key}.{value}:".encode('ascii')
+ self.output = self.output.rstrip(b':')
+ self.output += b"\n"
+
+ def write():
+ params = self._get_params(10)
+ for n, i in enumerate(self.settings_dict):
+ self.settings_dict[i] = int(params[n])
+
+ settings_map = {b'D': reset,
+ b'F': firmware,
+ b'R': read,
+ b'W': write
+ }
+
+ char = self.command_str[:1]
+ self.command_str = self.command_str[1:]
+
+ try:
+ settings_map[char]()
+ except KeyError:
+ logger.warning("Settings control %s not found", char)
+
+ def experiment(self):
+ def ads1255():
+ params = self._get_params(3)
+ logger.info("ADS1255 params: %s", params)
+ self.output += f'#A: {params[0]} {params[1]} {params[2]}\n'.encode('ascii')
+
+ def gain():
+ params = self._get_params(2)
+ logger.info("IV gain: %s", params)
+ self.output += f'#G: {params[0]} {params[1]}\n'.encode('ascii')
+
+ def lsv():
+ params = self._get_params(7)
+ start = int(params[-3])
+ stop = int(params[-2])
+ slope = int(params[-1])
+
+ logger.info("LSV params: %s", params)
+
+ for i in np.arange(start, stop, slope//10):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hl', i, 500 * (i-32698))
+ self.output += b"\n"
+
+ def cv():
+ params = self._get_params(9)
+ start = int(params[-3])
+ v1 = int(params[-5])
+ v2 = int(params[-4])
+ scans = int(params[-2])
+ slope = int(params[-1])
+
+ logger.info("CV params: %s", params)
+
+ for scan in range(scans):
+ for i in np.arange(start, v1, slope//100):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hl', i, 500 * (i-32698) + 100 * scan)
+ self.output += b"\n"
+ for i in np.arange(v1, v2, slope//100):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hl', i, 500 * (i - 32698) + 100 * scan)
+ self.output += b"\n"
+ for i in np.arange(v2, start, slope//100):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hl', i, 500 * (i - 32698) + 100 * scan)
+ self.output += b"\n"
+ self.output += b"S\n"
+ self.output += b"D\n"
+
+ def swv():
+ params = self._get_params(10)
+ start = int(params[-6])
+ stop = int(params[-5])
+ step = int(int(params[-4])*3000/65536.)
+ scans = int(params[-1])
+
+ logger.info("SWV params: %s", params)
+
+ if scans < 1:
+ scans = 1
+
+ for scan in range(scans):
+ for i in np.arange(start, stop, step):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hll', i, 500 * (i - 32698) + 100 * scan, 0)
+ self.output += b"\n"
+ for i in np.arange(stop, start, step):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hll', i, 500 * (i - 32698) + 100 * scan, 0)
+ self.output += b"\n"
+ self.output += b"S\n"
+ self.output += b"D\n"
+
+ def dpv():
+ params = self._get_params(10)
+ start = int(params[-6])
+ stop = int(params[-5])
+
+ logger.info("DPV params: %s", params)
+
+ for i in np.arange(start, stop, 1):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hll', i, 500 * (i - 32698), 0)
+ self.output += b"\n"
+
+ self.output += b"D\n"
+
+ def pmt():
+ logger.info("PMT Idle mode entered")
+ self.abort_wait()
+
+ def pot():
+ params = self._get_params(2)
+ seconds = int(params[0])
+ logger.info("POT params: %s", params)
+
+ if seconds == 0:
+ self.abort_wait()
+ else:
+ for i in range(seconds):
+ self.output += b"B\n"
+ self.output += struct.pack('<Hll', i, 0, 100)
+
+ def ca():
+ params = self._get_params(2)
+ steps = int(params[0])
+ tcs = int(params[1])
+
+ self.current_params = [steps, tcs]
+ self.waiting_for_params = steps * 2
+ self.output += f"@RQP {steps * 2}\n".encode("ascii")
+ self.next_state = self.experiment
+ return True
+
+ def ca_params(steps, tcs):
+ times = [int(i) for i in self.extra_params[steps:]]
+ seconds = sum(times)
+
+ for i in range(seconds):
+ logger.info(i)
+ self.output += b"B\n"
+ self.output += struct.pack('<HHl', i, 0, 100 * i)
+ self.output += b"\n"
+ sleep(1)
+ self.extra_params = []
+
+ def sync():
+ params = self._get_params(1)
+ logger.info('Shutter Sync %s Hz', params[0])
+
+ def shut_off():
+ logger.info('Shutter Sync Off')
+
+ def shut_close():
+ logger.info('Shutter closed')
+
+ def shut_open():
+ logger.info('Shutter open')
+
+ experiment_map = {b'A': ads1255,
+ b'G': gain,
+ b'L': lsv,
+ b'C': cv,
+ b'S': swv,
+ b'D': dpv,
+ b'M': pmt,
+ b'P': pot,
+ b'R': ca,
+ b'Z': sync,
+ b'z': shut_off,
+ b'1': shut_close,
+ b'2': shut_open
+ }
+
+ experiment_post_params_map = {b'R': ca_params}
+
+ if self.next_state:
+ experiment_post_params_map[self.current_cmd](*self.current_params)
+ self.current_params = []
+ self.next_state = None
+ else:
+ char = self._get_command()
+
+ try:
+ return experiment_map[char]()
+ except KeyError:
+ logger.warning('Unrecognized exp command %s', char)
+ self.output += f'#ERR: Command {char} not recognized\n'.encode('ascii')
+
+
+class SerialSim(IOBase):
+ def __init__(self, *args, **kwargs):
+ self.sim = Simulator()
+ self.is_open = True
+
+ def open(self):
+ self.is_open = True
+
+ def close(self):
+ self.is_open = False
+ self.reset_input_buffer()
+
+ def write(self, string: bytes):
+ self.sim.input(string)
+
+ def read(self, size=1) -> bytes:
+ output = self.sim.output[0:size]
+ self.sim.output = self.sim.output[size:]
+ return output
+
+ def reset_input_buffer(self):
+ self.sim.output = b""
+
+ def next(self) -> bytes:
+ if self.sim.output == b"":
+ raise StopIteration
+
+ return self.readline()
+
+ def readline(self, size=-1) -> bytes:
+ if len(self.sim.output) == 0:
+ return b""
+
+ if size > 0:
+ output, sep, remain = self.sim.output[:size].partition(b'\n')
+ else:
+ output, sep, remain = self.sim.output.partition(b'\n')
+
+ if sep != b'\n':
+ return b""
+
+ self.sim.output = self.sim.output[len(output) + 1:]
+
+ return output + b'\n'
+
+ def __iter__(self):
+ return self
+
+ def _update_dtr_state(self):
+ pass
diff --git a/dstat_interface/core/dstat/state.py b/dstat_interface/core/dstat/state.py
index 12262c4..538c4a4 100644
--- a/dstat_interface/core/dstat/state.py
+++ b/dstat_interface/core/dstat/state.py
@@ -1,14 +1,25 @@
-from collections import OrderedDict
-
-def reset():
- settings = OrderedDict()
- ser = None
- dstat_version = None
- firmware_version = None
- board_instance = None
-
-settings = OrderedDict()
-ser = None
-dstat_version = None
-firmware_version = None
-board_instance = None
\ No newline at end of file
+from __future__ import annotations
+from typing import Union, TYPE_CHECKING
+
+from dstat_interface.utils import Singleton
+
+if TYPE_CHECKING:
+ from pkg_resources._vendor.packaging import version
+ from dstat_interface.dstat.comm import SerialConnection
+ from dstat_interface.dstat.boards import BaseBoard
+
+
+class DStatState(object, metaclass=Singleton):
+ def __init__(self):
+ self.settings = {}
+ self.ser: Union[None, SerialConnection] = None
+ self.dstat_version: Union[None, version.Version] = None
+ self.firmware_version: Union[None, str] = None
+ self.board_instance: Union[None, BaseBoard] = None
+
+ def reset(self):
+ self.settings = {}
+ self.ser = None
+ self.dstat_version = None
+ self.firmware_version = None
+ self.board_instance = None
diff --git a/dstat_interface/core/dstat/test/test_comm.py b/dstat_interface/core/dstat/test/test_comm.py
new file mode 100644
index 0000000..9e776a2
--- /dev/null
+++ b/dstat_interface/core/dstat/test/test_comm.py
@@ -0,0 +1,41 @@
+import pytest
+from pkg_resources import parse_version
+
+from dstat_interface.dstat.comm import dstat_connect, read_settings, write_settings
+from dstat_interface.dstat import simulator, state
+
+
+class TestDStat:
+ @pytest.yield_fixture(autouse=True)
+ def dstat_connect_simulator(self):
+ dstat_connect('simulator')
+ yield
+ state.ser.close()
+
+ def test_dstat_connect(self):
+ assert state.dstat_version == parse_version('1.2.3') and state.firmware_version == 'fffffff'
+
+ def test_read_settings(self):
+ read_settings()
+ assert state.settings == simulator.Simulator.default_settings
+
+ def test_write_settings(self):
+ new_settings = dict([('max5443_offset', 200),
+ ('tcs_enabled', 0),
+ ('tcs_clear_threshold', 19000),
+ ('r100_trim', 23),
+ ('r3k_trim', 14),
+ ('r30k_trim', 56),
+ ('r300k_trim', 3),
+ ('r3M_trim', 2),
+ ('r30M_trim', -34),
+ ('r100M_trim', -60)
+ ('eis_cal1', 0),
+ ('eis_cal2', 0),
+ ('dac_units_true', 1)
+ ])
+ state.settings = new_settings
+ write_settings()
+ state.settings = {}
+ read_settings()
+ assert state.settings == new_settings
diff --git a/dstat_interface/core/dstat/utility.py b/dstat_interface/core/dstat/utility.py
new file mode 100644
index 0000000..00860fb
--- /dev/null
+++ b/dstat_interface/core/dstat/utility.py
@@ -0,0 +1,123 @@
+import logging
+from multiprocessing.connection import Connection
+from typing import Union
+
+from serial import Serial, SerialException
+
+from .experiment_process import BaseExperimentProcess
+from dstat_interface.core.dstat.state import DStatState
+
+logger = logging.getLogger(__name__)
+dstat_logger = logging.getLogger("{}.DSTAT".format(__name__))
+exp_logger = logging.getLogger("{}.Experiment".format(__name__))
+
+state = DStatState()
+
+
+def abs_mv_to_dac(mv: float) -> int:
+ dac = int(mv / state.board_instance.re_voltage_scale * (65536. / 3000) + 32768)
+ assert 0 <= dac <= 65535
+ return dac
+
+
+def rel_mv_to_dac(mv: float) -> int:
+ dac = int(mv / state.board_instance.re_voltage_scale * (65536. / 3000))
+ assert 0 < dac <= 65535 # DStat params that take relative mv don't accept 0
+ return dac
+
+
+def param_test_uint16(u: int) -> int:
+ assert 0 <= u <= 65535
+ return u
+
+
+def param_test_non_zero_uint16(u: int) -> int:
+ assert 0 < u <= 65535
+ return u
+
+
+def param_test_uint8(u: int) -> int:
+ assert 0 < u <= 255
+ return u
+
+
+def param_test_non_zero_uint8(u: int) -> int:
+ assert 0 < u <= 255
+ return u
+
+
+class VersionCheckProcess(BaseExperimentProcess):
+ def __init__(self, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.commands += ['V', 'X']
+
+ def serial_handler(self):
+ try:
+ while True:
+ for line in self.serial:
+ if line.lstrip().startswith(b"#"):
+ dstat_logger.info(line.strip().decode('ascii'))
+ elif line.lstrip().startswith(b"@DONE"):
+ dstat_logger.debug(line.strip().decode('ascii'))
+ return True
+ elif line.startswith(b'V'):
+ ver_str = line.lstrip(b'V').decode('ascii')
+ pcb, sep, firmware = ver_str.strip().rpartition('-')
+
+ if pcb == "":
+ pcb = firmware
+ logger.info('Your firmware does not support PCB version detection.')
+ self.data_pipe.send(('V', (pcb, False)))
+ else:
+ logger.info(f"Firmware Version: {hex(int(firmware)).lstrip('0x')}")
+ self.data_pipe.send(('V', (pcb, hex(int(firmware)).lstrip('0x'))))
+
+ logger.info(f'PCB Version: {pcb}')
+ elif line.startswith(b'X'):
+ mux_str = line.lstrip(b'X').decode('ascii')
+ self.data_pipe.send(('X', int(mux_str)))
+
+ except SerialException:
+ return False
+
+
+class SettingsProcess(BaseExperimentProcess):
+ def __init__(self, task, settings: Union[None, dict[str, str]] = None, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.task = task
+ self.settings = settings
+
+ self.serial: Union[None, Serial] = None
+ self.ctrl_pipe: Union[None, Connection] = None
+ self.data_pipe: Union[None, Connection] = None
+
+ if self.task == 'w':
+ write_buffer = [str(i) for i in self.settings.values()]
+ to_write = ' '.join(write_buffer) + ' '
+ logger.debug('to_write = %s', to_write)
+
+ self.commands += ['SW' + to_write]
+
+ elif self.task == 'r':
+ self.commands += ['SR']
+
+ def serial_handler(self):
+ ser_logger = logging.getLogger(f'{__name__}._serial_process')
+ try:
+ while True:
+ for line in self.serial:
+ if line.lstrip().startswith(b"#"):
+ ser_logger.info(line.strip().decode('ascii'))
+
+ elif line.lstrip().startswith(b"@DONE"):
+ ser_logger.debug(line.strip().decode('ascii'))
+ return True
+
+ if line.lstrip().startswith(b'S'):
+ input_line = line.lstrip()[1:].decode('ascii')
+ parted = input_line.rstrip().split(':')
+ settings = {key: int(value) for key, value in [i.split('.') for i in parted]}
+
+ self.data_pipe.send(settings)
+ except SerialException:
+ return False
diff --git a/dstat_interface/core/errors.py b/dstat_interface/core/errors.py
deleted file mode 100755
index 9661262..0000000
--- a/dstat_interface/core/errors.py
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-class Error(Exception):
- """Copies Exception class"""
- pass
-
-class InputError(Error):
- """Exception raised for errors in the input. Extends Error class.
-
- Attributes:
- expr -- input expression in which the error occurred
- msg -- error message
- """
-
- def __init__(self, expr, msg):
- self.expr = expr
- self.msg = msg
-
-class VarError(Error):
- """Exception raised for internal variable errors. Extends Error class.
-
- Attributes:
- var -- var in which the error occurred
- msg -- error message
- """
-
- def __init__(self, var, msg):
- self.var = var
- self.msg = msg
\ No newline at end of file
diff --git a/dstat_interface/core/experiments/__init__.py b/dstat_interface/core/experiments/__init__.py
deleted file mode 100644
index 6991a97..0000000
--- a/dstat_interface/core/experiments/__init__.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# __all__ = []
-#
-# import pkgutil
-# import inspect
-# from . import cal, chronoamp, cv
-#
-#
-# for loader, name, is_pkg in pkgutil.walk_packages(__path__):
-# print loader, name, is_pkg
-# module = loader.find_module(name).load_module(name)
-#
-# for name, value in inspect.getmembers(module):
-# if name.startswith('__'):
-# continue
-#
-# globals()[name] = value
-# __all__.append(name)
\ No newline at end of file
diff --git a/dstat_interface/core/experiments/cal.py b/dstat_interface/core/experiments/cal.py
deleted file mode 100755
index 3da9280..0000000
--- a/dstat_interface/core/experiments/cal.py
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2017 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import time
-import struct
-import logging
-logger = logging.getLogger(__name__)
-
-import serial
-
-from ..errors import InputError, VarError
-from ..dstat import state
-from ..experiments.experiment_template import Experiment, dstat_logger
-
-
-def measure_offset(time):
- gain_trim_table = [None, 'r100_trim', 'r3k_trim', 'r30k_trim', 'r300k_trim',
- 'r3M_trim', 'r30M_trim', 'r100M_trim']
-
- parameters = {}
- parameters['time'] = time
-
- gain_offset = {}
-
- for i in range(1,8):
- parameters['gain'] = i
- state.ser.start_exp(CALExp(parameters))
- logger.info("measure_offset: %s", state.ser.get_proc(block=True))
- gain_offset[gain_trim_table[i]] = state.ser.get_data(block=True)
-
- return gain_offset
-
-
-class CALExp(Experiment):
- id = 'cal'
- """Offset calibration experiment"""
- def __init__(self, parameters):
- self.parameters = parameters
- self.databytes = 8
- self.scan = 0
- self.data = []
-
- self.commands = ["EA2 3 1 ", "EG"]
-
- self.commands[1] += str(self.parameters['gain'])
- self.commands[1] += " "
- self.commands[1] += "0 "
-
- self.commands.append(
- ("ER1 0", ["32768", str(self.parameters['time'])])
- )
-
-
- def serial_handler(self):
- """Handles incoming serial transmissions from DStat. Returns False
- if stop button pressed and sends abort signal to instrument. Sends
- data to self.data_pipe as result of self.data_handler).
- """
-
- try:
- while True:
- if self.ctrl_pipe.poll():
- input = self.ctrl_pipe.recv()
- logger.debug("serial_handler: %s", input)
- if input == ('a' or "DISCONNECT"):
- self.serial.write('a')
- logger.info("serial_handler: ABORT pressed!")
- return False
-
- for line in self.serial:
- if self.ctrl_pipe.poll():
- if self.ctrl_pipe.recv() == 'a':
- self.serial.write('a')
- logger.info("serial_handler: ABORT pressed!")
- return False
-
- if line.startswith('B'):
- self.data.append(self.data_handler(
- self.serial.read(size=self.databytes)))
-
- elif line.lstrip().startswith("#"):
- dstat_logger.info(line.lstrip().rstrip())
-
- elif line.lstrip().startswith("@DONE"):
- dstat_logger.debug(line.lstrip().rstrip())
- self.serial.flushInput()
- self.experiment_done()
- return True
-
- except serial.SerialException:
- return False
-
- def data_handler(self, data):
- """Takes data_input as tuple -- (scan, data).
- Returns:
- current
- """
-
- seconds, milliseconds, current = struct.unpack('<HHl', data)
- return current
-
- def experiment_done(self):
- """Averages data points
- """
- try:
- sum = 0
- self.data[0] = 0 # Skip first point
-
- except IndexError:
- return
-
- for i in self.data:
- sum += i
-
- sum /= len(self.data)
-
- if (sum > 32767):
- sum = 32767
- elif (sum < -32768):
- sum = -32768
-
- self.data_pipe.send(sum)
\ No newline at end of file
diff --git a/dstat_interface/core/experiments/chronoamp.py b/dstat_interface/core/experiments/chronoamp.py
index 94c7484..665ba64 100644
--- a/dstat_interface/core/experiments/chronoamp.py
+++ b/dstat_interface/core/experiments/chronoamp.py
@@ -1,170 +1,70 @@
-import time
-import struct
-import numpy as np
-import serial
-from ..interface.plot import mean, plotSpectrum, findBounds
-
-from .experiment_template import PlotBox, Experiment, exp_logger
-
-
-class ChronoampBox(PlotBox):
- def setup(self):
- self.plot_format = {
- 'current_time': {'xlabel': "Time (s)",
- 'ylabel': "Current (A)"
- }
- }
-
- def format_plots(self):
- """
- Creates and formats subplots needed. Overrides superclass.
- """
- self.subplots = {'current_time': self.figure.add_subplot(111)}
-
- for key, subplot in self.subplots.items():
- subplot.ticklabel_format(style='sci', scilimits=(0, 3),
- useOffset=False, axis='y')
- subplot.plot([],[])
- subplot.set_xlabel(self.plot_format[key]['xlabel'])
- subplot.set_ylabel(self.plot_format[key]['ylabel'])
-
-
-class Chronoamp(Experiment):
- id = 'cae'
- """Chronoamperometry experiment"""
- def setup(self):
- self.datatype = "linearData"
- self.datalength = 2
- self.databytes = 8
- self.data = {'current_time' : [([],[])]}
- self.columns = ['Time (s)', 'Current (A)']
- self.total_time = sum(self.parameters['time'])
- self.plotlims = {'current_time': {'xlims': (0, self.total_time)}
- }
-
- self.commands.append(
- ("ER" + str(len(self.parameters['potential'])) + " 0 ", [])
- )
-
- for i in self.parameters['potential']:
- self.commands[-1][1].append(str(int(i*(65536./3000)+32768)))
- for i in self.parameters['time']:
- self.commands[-1][1].append(str(i))
-
- plot = ChronoampBox(['current_time'])
- plot.setlims('current_time', **self.plotlims['current_time'])
-
- self.plots.append(plot)
-
- def data_handler(self, data_input):
- """Overrides Experiment method to not convert x axis to mV."""
- scan, data = data_input
- # 2*uint16 + int32
- seconds, milliseconds, current = struct.unpack('<HHl', data)
- return (scan, (
- seconds+milliseconds/1000.,
- (current+self.gain_trim)*(1.5/self.gain/8388607)
- )
- )
-
- def store_data(self, incoming, newline):
- """Stores data in data attribute. Should not be called from subprocess.
- Can be overriden for custom experiments."""
- line, data = incoming
-
- if newline is True:
- self.data['current_time'].append(deepcopy(self.line_data))
-
- for i, item in enumerate(self.data['current_time'][line]):
- item.append(data[i])
+from datetime import datetime
+from typing import Any
+
+from ..dstat.experiment_handler import ExperimentHandler
+from ..dstat.experiment_process import ExperimentProcess
+from ..dstat.utility import abs_mv_to_dac, rel_mv_to_dac, param_test_uint16, param_test_non_zero_uint8
+from ..experiments.experiment_container import ExperimentContainer
+
+
+class CAExperimentHandler(ExperimentHandler):
+ def __init__(self, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.data['time'] = []
+
+ def data_handler(self, data_input: tuple[datetime, int, bytes]):
+ unpacked: tuple[int, int, int]
+ date, scan, data = data_input
+ unpacked = self.struct.unpack(data)
+ self.data['scan'].append(scan)
+ self.data['timestamp'].append(date)
+
+ for n, i in enumerate(unpacked):
+ try:
+ self.data[self.data_cols[n]].append(self.data_convert[n](i))
+ except TypeError: # If no converter
+ self.data[self.data_cols[n]].append(i)
+ self.data['time'].append(self.data['time_s'][-1] + self.data['time_ms'][-1])
+
+
+class CAExperimentContainer(ExperimentContainer):
+ experiment_id = 'ca'
+ display_name = 'Chronoamperometry'
+ process = ExperimentProcess
+ handler = CAExperimentHandler
+ data_bytes = 0
+
+ def __init__(self, params: dict[str, Any], mux: int = 1):
+ super().__init__(params, mux=mux)
+
+ self.data_cols = ['time_s', 'time_ms', 'current']
+ self.data_format = 'smA'
+
+ self.cmd_str += [('ER{n_steps} 0 ', ('voltages', 'times'))]
+ self.param_input |= {'times': list, 'voltages': list}
+ self.param_input_display_names |= {'times': 'Time (s)', 'voltages': 'Voltage (mV)'}
+ self.param_tables = {'Steps:': ['times', 'voltages']}
+ self.param_input_limits |= {'times': (0, 'time_max'), 'voltages': ('mv_min', 'mv_max'), }
+ self.param_converters |= {'times': lambda x: [param_test_uint16(i) for i in x],
+ 'voltages': lambda x: [abs_mv_to_dac(i) for i in x], }
+ self.defaults |= {'times': 0, 'voltages': 0}
+
+ if params:
+ self.progress_end = sum(self.params['times'])
+ self.params['n_steps'] = len(self.params['times'])
+ else:
+ self.progress_max = 0
+ self.progress_iters = 1
+ self.data_bytes = self.calculate_data_bytes()
- def get_progress(self):
+ def get_progress(self) -> float:
+ if self.handler_instance.done:
+ return 100
try:
- return self.data['current_time'][-1][0][-1]/self.total_time
+ return (1 - abs(
+ self.progress_end - self.handler_instance.data['time_s'][-1]) / self.progress_end) * 100
except IndexError:
return 0
-class PDExp(Chronoamp):
- """Photodiode/PMT experiment"""
- id = 'pde'
- def setup(self):
- self.plots.append(ChronoampBox('current_time'))
-
- self.datatype = "linearData"
- self.datalength = 2
- self.databytes = 8
- self.data = {'current_time' : [([],[])]}
- self.columns = ['Time (s)', 'Current (A)']
- self.plot_format = {
- 'current_time' : {
- 'labels' : self.columns,
- 'xlims' : (0, int(self.parameters['time']))
- }
- }
- self.total_time = int(self.parameters['time'])
-
- if self.parameters['shutter_true']:
- if self.parameters['sync_true']:
- self.commands.append("EZ")
- self.commands[-1] += str(self.parameters['sync_freq'])
- self.commands[-1] += " "
- else:
- self.commands.append(("E2", []))
-
- command = "ER1 "
- params = []
-
- if self.parameters['interlock_true']:
- command += "1 "
- else:
- command += "0 "
-
- if self.parameters['voltage'] == 0: # Special case where V=0
- params.append("65535")
- else:
- params.append(str(int(
- 65535-(self.parameters['voltage']*(65536./3000))))
- )
- params.append(str(self.parameters['time']))
-
- self.commands.append((command, params))
- if self.parameters['shutter_true']:
- if self.parameters['sync_true']:
- self.commands.append("Ez")
- else:
- self.commands.append("E1")
-
-class FT_Box(PlotBox):
- def updateline(self, Experiment, line_number):
- def search_value(data, target):
- for i in range(len(data)):
- if data[i] > target:
- return i
-
- y = Experiment.data['data'][line_number][1]
- x = Experiment.data['data'][line_number][0]
- freq = Experiment.parameters['adc_rate_hz']
- i = search_value(x, float(Experiment.parameters['fft_start']))
- y1 = y[i:]
- x1 = x[i:]
- avg = mean(y1)
- min_index, max_index = findBounds(y1)
- y1[min_index] = avg
- y1[max_index] = avg
- f, Y = plotSpectrum(y1[min_index:max_index],freq)
- self.axe1.lines[line_number].set_ydata(Y)
- self.axe1.lines[line_number].set_xdata(f)
- Experiment.data['ft'] = [(f, Y)]
-
- def changetype(self, Experiment):
- """Change plot type. Set axis labels and x bounds to those stored
- in the Experiment instance. Stores class instance in Experiment.
- """
- self.axe1.set_xlabel("Freq (Hz)")
- self.axe1.set_ylabel("|Y| (A/Hz)")
- self.axe1.set_xlim(0, Experiment.parameters['adc_rate_hz']/2)
-
- Experiment.plots['ft'] = self
- self.figure.canvas.draw()
\ No newline at end of file
diff --git a/dstat_interface/core/experiments/cv.py b/dstat_interface/core/experiments/cv.py
deleted file mode 100644
index c08e610..0000000
--- a/dstat_interface/core/experiments/cv.py
+++ /dev/null
@@ -1,68 +0,0 @@
-import time
-import struct
-
-from .experiment_template import PlotBox, Experiment
-
-
-class CVExp(Experiment):
- id = 'cve'
- """Cyclic Voltammetry experiment"""
- def setup(self):
- self.plotlims['current_voltage']['xlims'] = tuple(
- sorted((int(self.parameters['v1']), int(self.parameters['v2'])))
- )
- super(CVExp, self).setup()
-
- self.datatype = "CVData"
- self.xlabel = "Voltage (mV)"
- self.ylabel = "Current (A)"
- self.datalength = 2 * self.parameters['scans'] # x and y for each scan
- self.databytes = 6 # uint16 + int32
-
- self.commands += "E"
- self.commands[2] += "C"
- self.commands[2] += str(self.parameters['clean_s'])
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['dep_s'])
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['clean_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['dep_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['v1'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['v2'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['start'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['scans'])
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['slope'])/
- self.re_voltage_scale*
- (65536./3000)
- ))
- self.commands[2] += " "
-
- def get_progress(self):
- return (len(self.data['current_voltage'])-1) / float(self.parameters['scans'])
diff --git a/dstat_interface/core/experiments/experiment_container.py b/dstat_interface/core/experiments/experiment_container.py
new file mode 100644
index 0000000..2e192bc
--- /dev/null
+++ b/dstat_interface/core/experiments/experiment_container.py
@@ -0,0 +1,153 @@
+import logging
+import struct
+from abc import ABC, abstractmethod, ABCMeta
+from typing import Type, Callable, Union, Any, List
+
+from ..dstat.comm import SerialConnection
+from ..dstat.experiment_handler import ExperimentHandler
+from ..dstat.experiment_process import BaseExperimentProcess
+from ..dstat.state import DStatState
+from ..dstat.boards import V1_2Board
+
+logger = logging.getLogger(__name__)
+
+state = DStatState()
+board = V1_2Board()
+
+
+class ExperimentContainer(ABC, metaclass=ABCMeta):
+ dstat_params = {'buffer_false': bool, 'adc_rate': str,
+ 'adc_pga': str, 'gain': int,
+ 'short_true': bool, 'mux_channel': int}
+
+ @abstractmethod
+ def __init__(self, params: dict[str, Any], mux: int = 1):
+ self.mux = mux
+
+ self.data_cols: Union[None, list[str]] = None
+ self.data_format: str = ''
+ self.cmd_str: list[str] = ["EA{buffer} {adc_rate:x} {adc_pga:x} ",
+ "EG{gain} {short_true:d} "]
+
+ self.adc_rates = {label: code for label, code
+ in zip(board.adc_rate_labels, board.adc_rate_codes)}
+ self.adc_pga = {label: code for label, code
+ in zip(board.adc_pga_labels, board.adc_pga_codes)}
+
+ self.param_input: dict[str, Union[Callable, List]] = {'buffer_false': bool,
+ 'adc_rate': list(self.adc_rates.keys()),
+ 'adc_pga': list(self.adc_pga.keys()),
+ 'gain': int,
+ 'short_true': bool,
+ }
+ self.param_input_limits: dict[str, tuple[Union[str, int], Union[str, int]]] = {}
+ self.param_input_display_names: dict[str, str] = {}
+ self.param_tables: dict[str, list[str]] = {}
+
+ self.param_docs: dict[str, str] = {'buffer_false': 'Disable ADC buffer',
+ 'adc_rate': 'ADC sample rate',
+ 'adc_pga': 'ADC PGA value',
+ 'gain': 'IV converter gain',
+ 'short_true': 'Short RE and CE internally'}
+ self.param_converters: dict[str, Callable] = {}
+ self.defaults: dict = {'buffer_false': False, 'short_true': False, 'adc_rate': '60', 'adc_pga': '2',
+ 'gain': 3000}
+ self.params = params
+ self.progress_max = 0
+ self.progress_iters = 0
+ self.progress_scan = 0
+
+ self.handler_instance: Union[None, ExperimentHandler] = None
+
+ self.commands: List[str] = []
+ self.calculate_data_bytes()
+
+ if mux > 1:
+ self.cmd_str += ['EX{mux_channel} ']
+ self.param_input['mux_channel'] = list(range(mux))
+ self.param_docs['mux_channel'] = 'Multiplexer Channel'
+ self.defaults['mux_channel'] = 0
+
+ @property
+ @abstractmethod
+ def experiment_id(self) -> Type[str]:
+ raise NotImplementedError
+
+ @property
+ @abstractmethod
+ def display_name(self) -> Type[str]:
+ raise NotImplementedError
+
+ @property
+ @abstractmethod
+ def data_bytes(self) -> Type[ExperimentHandler]:
+ raise NotImplementedError
+
+ @property
+ @abstractmethod
+ def handler(self) -> Type[ExperimentHandler]:
+ raise NotImplementedError
+
+ @property
+ @abstractmethod
+ def process(self) -> Type[BaseExperimentProcess]:
+ raise NotImplementedError
+
+ @property
+ def plots(self) -> dict[str, dict[str, str]]:
+ return {'current': {'x': 'voltage', 'y': 'current'}}
+
+ def calculate_data_bytes(self) -> int:
+ struct_formats = ['H' if i.islower() else 'l' for i in self.data_format]
+ return struct.Struct(f'<{"".join(struct_formats)}').size
+
+ def add_missing_from_defaults(self):
+ params = self.params
+ self.params = self.defaults.copy()
+ self.params |= params
+
+ self.commands = []
+ for i in self.cmd_str:
+ try:
+ cmd, params = i
+ param_list = []
+ for param in params:
+ param_list += self.params[param]
+
+ self.commands += [(cmd.format(**self.params), param_list)]
+ except ValueError:
+ self.commands += [i.format(**self.params)]
+
+ def parse_params(self):
+ self.params |= {key: self.param_converters[key](value) for key, value in self.params.items()
+ if key in self.param_converters}
+
+ self.params['adc_rate'] = self.adc_rates[self.params['adc_rate']]
+ self.params['adc_pga'] = self.adc_pga[self.params['adc_pga']]
+ self.params['gain'] = state.board_instance.gain.index(self.params['gain'])
+
+ if self.params['buffer_false']:
+ self.params['buffer'] = '0'
+ else:
+ self.params['buffer'] = '2'
+ logger.info(self.params)
+
+ def get_proc(self) -> BaseExperimentProcess:
+ proc = self.process()
+ self.parse_params()
+
+ for i in self.cmd_str:
+ proc.parse_command_string(i, self.params)
+
+ proc.data_bytes = self.data_bytes
+ return proc
+
+ def start_handler(self, ser: SerialConnection):
+ self.handler_instance = self.handler(ser=ser, data_cols=self.data_cols, data_format=self.data_format)
+ self.handler_instance.adc_gain = state.board_instance.gain[self.params['gain']]
+ self.handler_instance.adc_pga = state.board_instance.adc_pga[
+ state.board_instance.adc_pga_codes.index(self.params['adc_pga'])]
+
+ @abstractmethod
+ def get_progress(self) -> float:
+ pass
diff --git a/dstat_interface/core/experiments/experiment_loops.py b/dstat_interface/core/experiments/experiment_loops.py
deleted file mode 100644
index a350de8..0000000
--- a/dstat_interface/core/experiments/experiment_loops.py
+++ /dev/null
@@ -1,201 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-from __future__ import division, absolute_import, print_function, unicode_literals
-
-from ..dstat import state
-
-import logging
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print("ERR: GTK not available")
- sys.exit(1)
-
-logger = logging.getLogger(__name__)
-
-
-class BaseLoop(GObject.GObject):
- __gsignals__ = {
- b'experiment_done': (GObject.SIGNAL_RUN_FIRST, None, tuple()),
- b'progress_update': (GObject.SIGNAL_RUN_FIRST, None, (float,))
- }
-
- def __init__(self, experiment, callbacks=None):
- GObject.GObject.__init__(self)
- self.line = None
- self.lastdataline = 0
- self.current_exp = experiment
- self.experiment_proc = None
-
- for signal, cb in callbacks.items():
- try:
- self.connect(signal, cb)
- except TypeError:
- logger.warning("Invalid signal %s", signal)
-
- def run(self):
- self.experiment_proc = [
- GObject.idle_add(self.experiment_running_data),
- GObject.idle_add(self.experiment_running_proc),
- GObject.timeout_add(100, self.update_progress)
- ]
-
- def experiment_running_data(self):
- """Receive data from experiment process and add to
- current_exp.data['data].
- Run in GTK main loop.
-
- Returns:
- True -- when experiment is continuing to keep function in GTK's queue.
- False -- when experiment process signals EOFError or IOError to remove
- function from GTK's queue.
- """
- try:
- incoming = state.ser.get_data()
- while incoming is not None:
- try:
- self.line = incoming[0]
- if self.line > self.lastdataline:
- newline = True
- try:
- logger.info("running scan_process()")
- self.current_exp.scan_process(self.lastdataline)
- except AttributeError:
- pass
- self.lastdataline = self.line
- else:
- newline = False
- self.current_exp.store_data(incoming, newline)
- except TypeError:
- pass
-
- incoming = state.ser.get_data()
- return True
-
- except EOFError as err:
- logger.error(err)
- self.experiment_done()
- return False
- except IOError as err:
- logger.error(err)
- self.experiment_done()
- return False
-
- def experiment_running_proc(self):
- """Receive proc signals from experiment process.
- Run in GTK main loop.
-
- Returns:
- True -- when experiment is continuing to keep function in GTK's queue.
- False -- when experiment process signals EOFError or IOError to remove
- function from GTK's queue.
- """
- try:
- ctrl_buffer = state.ser.get_ctrl()
- try:
- if ctrl_buffer is not None:
- self.current_exp.ctrl_loop(ctrl_buffer)
- except AttributeError:
- pass
-
- proc_buffer = state.ser.get_proc()
- if proc_buffer is not None:
- if proc_buffer in ["DONE", "SERIAL_ERROR", "ABORT"]:
- self.experiment_done()
- if proc_buffer == "SERIAL_ERROR":
- self.on_serial_disconnect_clicked()
-
- else:
- logger.warning("Unrecognized experiment return code: %s",
- proc_buffer)
- return False
- return True
-
- except EOFError as err:
- logger.warning("EOFError: %s", err)
- self.experiment_done()
- return False
- except IOError as err:
- logger.warning("IOError: %s", err)
- self.experiment_done()
- return False
-
- def experiment_done(self):
- logger.info("Experiment done")
- for proc in self.experiment_proc:
- GObject.source_remove(proc)
- self.current_exp.scan_process(self.lastdataline)
- self.current_exp.experiment_done()
- self.emit("experiment_done")
-
- def update_progress(self):
- try:
- progress = self.current_exp.get_progress()
- except AttributeError:
- progress = -1
- self.emit("progress_update", progress)
- return True
-
-
-class PlotLoop(BaseLoop):
- def experiment_running_plot(self, force_refresh=False):
- """Plot all data in current_exp.data.
- Run in GTK main loop. Always returns True so must be manually
- removed from GTK's queue.
- """
- if self.line is None:
- return True
- for plot in self.current_exp.plots:
- if (plot.scan_refresh and self.line > self.lastdataline):
- while self.line > self.lastline:
- # make sure all of last line is added
- plot.updateline(self.current_exp, self.lastdataline)
- self.lastdataline += 1
- plot.updateline(self.current_exp, self.line)
- plot.redraw()
- else:
- while self.line > self.lastdataline:
- # make sure all of last line is added
- plot.updateline(self.current_exp, self.lastdataline)
- self.lastdataline += 1
- plot.updateline(self.current_exp, self.line)
-
- if plot.continuous_refresh is True or force_refresh is True:
- plot.redraw()
- return True
-
- def run(self):
- super(PlotLoop, self).run()
- self.experiment_proc.append(
- GObject.timeout_add(200, self.experiment_running_plot)
- )
-
- def experiment_done(self):
- logger.info("Experiment done")
- for proc in self.experiment_proc:
- GObject.source_remove(proc)
- self.current_exp.scan_process(self.lastdataline)
- self.current_exp.experiment_done()
- self.experiment_running_plot(force_refresh=True)
- self.emit("experiment_done")
\ No newline at end of file
diff --git a/dstat_interface/core/experiments/experiment_template.py b/dstat_interface/core/experiments/experiment_template.py
deleted file mode 100755
index 05a17a1..0000000
--- a/dstat_interface/core/experiments/experiment_template.py
+++ /dev/null
@@ -1,571 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2017 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-import logging
-import struct
-import time
-from collections import OrderedDict
-from copy import deepcopy
-from datetime import datetime
-from math import ceil
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print "ERR: GTK not available"
- sys.exit(1)
-
-
-from matplotlib.figure import Figure
-import matplotlib.gridspec as gridspec
-
-from matplotlib.backends.backend_gtk3agg \
- import FigureCanvasGTK3Agg as FigureCanvas
-
-from pandas import DataFrame
-import seaborn as sns
-sns.set(context='paper', style='darkgrid')
-
-import serial
-
-from ..dstat import state, comm
-from ..dstat.comm import TransmitError
-from . import experiment_loops
-
-logger = logging.getLogger(__name__)
-dstat_logger = logging.getLogger("{}.DSTAT".format(comm.__name__))
-exp_logger = logging.getLogger("{}.Experiment".format(__name__))
-
-
-class Experiment(GObject.Object):
- """Store and acquire a potentiostat experiment. Meant to be subclassed
- to by different experiment types and not used instanced directly. Subclass
- must instantiate self.plotbox as the PlotBox class to use and define id as
- a class attribute.
- """
- id = None
- Loops = experiment_loops.PlotLoop
- __gsignals__ = {
- b'exp_ready': (GObject.SIGNAL_RUN_FIRST, None, ()),
- b'exp_done': (GObject.SIGNAL_RUN_FIRST, None, ()),
- }
-
- def __init__(self, parameters):
- """Adds commands for gain and ADC."""
- super(Experiment, self).__init__()
- self.current_command = None
- self.parameters = parameters
- self.databytes = 8
- self.datapoint = 0
- self.scan = 0
- self.time = 0
- self.plots = []
-
- self.re_voltage_scale = state.board_instance.re_voltage_scale
-
- self.gain = state.board_instance.gain[int(self.parameters['gain'])]
-
- try:
- self.gain_trim = int(
- state.settings[
- state.board_instance.gain_trim[int(self.parameters['gain'])]
- ][1]
- )
- except AttributeError:
- logger.debug("No gain trim table.")
-
- self.commands = ["EA", "EG"]
-
- if self.parameters['buffer_true']:
- self.commands[0] += "2"
- else:
- self.commands[0] += "0"
- self.commands[0] += " {p[adc_rate]} {p[adc_pga]} ".format(
- p=self.parameters)
- self.commands[1] += "{p[gain]} {p[short_true]:d} ".format(
- p=self.parameters)
-
- self.plotlims = {'current_voltage' : {'xlims' : (0, 1)}
- }
-
- self.setup()
- self.time = [datetime.utcnow()]
-
- def setup_loops(self, callbacks):
- self.loops = self.__class__.Loops(self, callbacks)
- self.loops.run()
-
- def setup(self):
- self.data = OrderedDict(current_voltage=[([], [])])
- self.columns = ['Voltage (mV)', 'Current (A)']
-
- # list of scans, tuple of dimensions, list of data
- self.line_data = ([], [])
-
- plot = PlotBox(['current_voltage'])
- plot.setlims('current_voltage', **self.plotlims['current_voltage'])
-
- self.plots.append(plot)
-
- def write_command(self, cmd, params=None, retry=5):
- """Write command to serial with optional number of retries."""
- def get_reply(retries=3):
- while True:
- reply = self.serial.readline().rstrip()
- if reply.startswith('#'):
- dstat_logger.info(reply)
- elif reply == "":
- retries -= 1
- if retries <= 0:
- raise TransmitError
- else:
- return reply
-
- n = len(cmd)
- if params is not None:
- n_params = len(params)
-
- for _ in range(retry):
- tries = 5
- while True:
- time.sleep(0.2)
- self.serial.reset_input_buffer()
- self.serial.write('!{}\n'.format(n))
- time.sleep(.1)
-
- try:
- reply = get_reply()
- except TransmitError:
- if tries <= 0:
- continue
- tries -= 1
- pass
- else:
- break
-
- if reply != "@ACK {}".format(n):
- logger.warning("Expected ACK got: {}".format(reply))
- continue
-
- tries = 5
-
- while True:
- self.serial.write('{}\n'.format(cmd))
- try:
- reply = get_reply()
- except TransmitError:
- if tries <= 0:
- continue
- tries -= 1
- pass
- else:
- break
-
- if reply != "@RCV {}".format(n):
- logger.warning("Expected RCV got: {}".format(reply))
- continue
-
- if params is None:
- return True
-
- tries = 5
-
- while True:
- try:
- reply = get_reply()
- except TransmitError:
- if tries <= 0:
- break
- tries -= 1
- pass
- else:
- break
-
- if reply != "@RQP {}".format(n_params):
- logger.warning("Expected RQP got: {}".format(reply))
- continue
-
- tries = 5
-
- for i in params:
- while True:
- self.serial.write(i + " ")
- try:
- reply = get_reply()
- if reply == "@RCVC {}".format(i):
- break
- except TransmitError:
- if tries <= 0:
- continue
- tries -= 1
- pass
- else:
- break
- return True
- return False
-
- def run(self, ser, ctrl_pipe, data_pipe):
- """Execute experiment. Connects and sends handshake signal to DStat
- then sends self.commands.
- """
- self.serial = ser
- self.ctrl_pipe = ctrl_pipe
- self.data_pipe = data_pipe
-
- exp_logger.info("Experiment running")
-
- try:
- for i in self.commands:
- self.current_command = i
- status = "DONE"
- if isinstance(i, (str, unicode)):
- logger.info("Command: %s", i)
-
- if not self.write_command(i):
- status = "ABORT"
- break
-
- else:
- cmd = i[0]
- data = i[1]
-
- logger.info("Command: {}".format(cmd))
-
- if not self.write_command(cmd, params=data):
- status = "ABORT"
- break
-
- if not self.serial_handler():
- status = "ABORT"
- break
-
- time.sleep(0.5)
-
- except serial.SerialException:
- status = "SERIAL_ERROR"
- finally:
- while self.ctrl_pipe.poll():
- self.ctrl_pipe.recv()
- return status
-
- def serial_handler(self):
- """Handles incoming serial transmissions from DStat. Returns False
- if stop button pressed and sends abort signal to instrument. Sends
- data to self.data_pipe as result of self.data_handler).
- """
- scan = 0
-
- def check_ctrl():
- if self.ctrl_pipe.poll():
- input = self.ctrl_pipe.recv()
- logger.info("serial_handler: %s", input)
- if input == "DISCONNECT":
- self.serial.write('a')
- self.serial.reset_input_buffer()
- logger.info("serial_handler: ABORT pressed!")
- time.sleep(.3)
- return False
- elif input == 'a':
- self.serial.write('a')
- else:
- self.serial.write(input)
-
- try:
- while True:
- check_ctrl()
- for line in self.serial:
- check_ctrl()
-
- if line.startswith('B'):
- data = self.data_handler(
- (scan, self.serial.read(size=self.databytes)))
- data = self.data_postprocessing(data)
- if data is not None:
- self.data_pipe.send(data)
- try:
- self.datapoint += 1
- except AttributeError: #Datapoint counting is optional
- pass
-
- elif line.lstrip().startswith('S'):
- scan += 1
-
- elif line.lstrip().startswith("#"):
- dstat_logger.info(line.lstrip().rstrip())
-
- elif line.lstrip().startswith("@DONE"):
- dstat_logger.debug(line.lstrip().rstrip())
- time.sleep(.3)
- return True
-
- except serial.SerialException:
- return False
-
- def data_handler(self, data_input):
- """Takes data_input as tuple -- (scan, data).
- Returns:
- (scan number, (voltage, current)) -- voltage in mV, current in A
- """
- scan, data = data_input
- voltage, current = struct.unpack('<Hl', data) #uint16 + int32
- return (scan, (
- (voltage-32768)*(3000./65536)*self.re_voltage_scale,
- (current+self.gain_trim)*(1.5/8388607)/self.gain
- )
- )
-
- def store_data(self, incoming, newline):
- """Stores data in data attribute. Should not be called from subprocess.
- Can be overriden for custom experiments."""
- line, data = incoming
-
- if newline is True:
- self.data['current_voltage'].append(deepcopy(self.line_data))
-
- for i, item in enumerate(self.data['current_voltage'][line]):
- item.append(data[i])
-
- def data_postprocessing(self, data):
- """Discards first data point (usually gitched) by default, can be overridden
- in subclass.
- """
- try:
- if self.datapoint <= 1:
- return None
- except AttributeError: # Datapoint counting is optional
- pass
-
- return data
-
- def scan_process(self, line):
- pass
-
- def experiment_done(self):
- """Runs when experiment is finished (all data acquired)"""
- self.data_to_pandas()
- self.time += [datetime.utcnow()]
-
- def export(self):
- """Return a dict containing data for saving."""
- output = {
- "datatype" : self.datatype,
- "xlabel" : self.xlabel,
- "ylabel" : self.ylabel,
- "xmin" : self.xmin,
- "xmax" : self.xmax,
- "parameters" : self.parameters,
- "data" : self.data,
- "commands" : self.commands
- }
-
- return output
-
- def data_to_pandas(self):
- """Convert data to pandas DataFrame and set as member of .df
- attribute."""
- self.df = OrderedDict()
-
- for name, data in self.data.items():
- try:
- df = DataFrame(
- columns=['Scan'] + list(self.plot_format[name]['labels']))
-
- for n, line in enumerate(data): # Each scan
- df = df.append(
- DataFrame(
- OrderedDict(zip(
- ['Scan'] + list(self.plot_format[name]['labels']),
- [n] + list(line))
- )
- ), ignore_index = True
- )
- except (AttributeError, KeyError):
- try:
- df = DataFrame(
- columns=['Scan'] + list(self.columns))
-
- for n, line in enumerate(data): # Each scan
- df = df.append(
- DataFrame(
- OrderedDict(zip(
- ['Scan'] + list(self.columns),
- [n] + list(line))
- )
- ), ignore_index = True
- )
- except AttributeError as e: # Fallback if no self.columns
- df = DataFrame(
- columns=['Scan'] + ["{}{}".format(name, n)
- for n in range(len(data))]
- )
-
- for n, line in enumerate(data):
- df = df.append(
- DataFrame(
- OrderedDict(zip(
- ['Scan'] + ["{}{}".format(name, n)
- for n in range(len(data))],
- [n] + list(line))
- )
- ), ignore_index = True
- )
-
- self.df[name] = df
-
- def get_info_text(self):
- """Return string of text to disply on Info tab."""
- buf = "#Time: S{} E{}\n".format(self.time[0], self.time[1])
- buf += "#Commands:\n"
-
- for line in self.commands:
- buf += '#{}\n'.format(line)
-
- return buf
-
- def get_save_strings(self):
- """Return dict of strings with experiment parameters and data."""
- buf = {}
- buf['params'] = self.get_info_text()
- buf.update(
- {exp : df.to_csv(sep='\t', encoding='utf-8')
- for exp, df in self.df.items()}
- )
-
- return buf
-
-
-class PlotBox(object):
- """Contains data plot and associated methods."""
- def __init__(self, plots=None):
- """Initializes plots. self.box should be reparented."""
- self.name = "Main"
- self.continuous_refresh = True
- self.scan_refresh = False
-
- if plots is not None:
- self.plotnames = plots
- else:
- self.plotnames = []
- self.subplots = {}
-
- self.figure = Figure()
- # self.figure.subplots_adjust(left=0.07, bottom=0.07,
- # right=0.96, top=0.96)
-
- self.setup()
- self.format_plots() # Should be overriden by subclass
-
- self.figure.set_tight_layout(True)
-
- self.canvas = FigureCanvas(self.figure)
- self.canvas.set_vexpand(True)
-
- self.box = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
- self.box.pack_start(self.canvas, expand=True, fill=True, padding=0)
-
- def setup(self):
- self.plot_format = {
- 'current_voltage': {'xlabel': "Voltage (mV)",
- 'ylabel': "Current (A)"
- }
- }
-
- def format_plots(self):
- """
- Creates and formats subplots needed. Should be overriden by subclass
- """
- # Calculate size of grid needed
-
- if len(self.plotnames) > 1:
- gs = gridspec.GridSpec(int(ceil(len(self.plotnames)/2.)),2)
- else:
- gs = gridspec.GridSpec(1,1)
- for n, i in enumerate(self.plotnames):
- self.subplots[i] = self.figure.add_subplot(gs[n])
-
- for key, subplot in self.subplots.items():
- subplot.ticklabel_format(style='sci', scilimits=(0, 3),
- useOffset=False, axis='y')
- subplot.plot([], [])
- subplot.set_xlabel(self.plot_format[key]['xlabel'])
- subplot.set_ylabel(self.plot_format[key]['ylabel'])
-
- def clearall(self):
- """Remove all lines on plot. """
- for name, plot in self.subplots.items():
- for line in reversed(plot.lines):
- line.remove()
- self.addline()
-
- def clearline(self, subplot, line_number):
- """Remove a single line.
-
- Arguments:
- subplot -- key in self.subplots
- line_number -- line number in subplot
- """
- self.subplots[subplot].lines[line_number].remove()
-
- def addline(self):
- """Add a new line to plot. (initialized with dummy data)))"""
- for subplot in self.subplots.values():
- subplot.plot([], [])
-
- def updateline(self, Experiment, line_number):
- """Update a line specified with new data.
-
- Arguments:
- Experiment -- Experiment instance
- line_number -- line number to update
- """
- for subplot in Experiment.data:
- while True:
- try:
- self.subplots[subplot].lines[line_number].set_xdata(
- Experiment.data[subplot][line_number][0])
- self.subplots[subplot].lines[line_number].set_ydata(
- Experiment.data[subplot][line_number][1])
- except IndexError:
- self.addline()
- except KeyError:
- pass
- else:
- break
- # logger.warning("Tried to set line %s that doesn't exist.", line_number)
-
- def setlims(self, plot, xlims=None, ylims=None):
- """Sets x and y limits.
- """
- if xlims is not None:
- self.subplots[plot].set_xlim(xlims)
- if ylims is not None:
- self.subplots[plot].set_ylim(ylims)
-
- self.figure.canvas.draw()
-
- def redraw(self):
- """Autoscale and refresh the plot."""
- for name, plot in self.subplots.items():
- plot.relim()
- plot.autoscale(True, axis = 'y')
- self.figure.canvas.draw()
-
- return True
\ No newline at end of file
diff --git a/dstat_interface/core/experiments/idle.py b/dstat_interface/core/experiments/idle.py
deleted file mode 100644
index b8caf4d..0000000
--- a/dstat_interface/core/experiments/idle.py
+++ /dev/null
@@ -1,40 +0,0 @@
-import time
-import struct
-
-from .experiment_template import Experiment
-from ..dstat import state
-
-class OCPExp(Experiment):
- """Open circuit potential measumement in statusbar."""
- id = 'ocp'
-
- def __init__(self):
- self.re_voltage_scale = state.board_instance.re_voltage_scale
- self.databytes = 8
-
- self.commands = ["EA", "EP0 0 "]
-
- self.commands[0] += "2 " # input buffer
- self.commands[0] += "3 " # 2.5 Hz sample rate
- self.commands[0] += "1 " # 2x PGA
-
- def data_handler(self, data_input):
- """Overrides Experiment method to only send ADC values."""
- scan, data = data_input
- # 2*uint16 + int32
- seconds, milliseconds, voltage = struct.unpack('<HHl', data)
- return voltage/5.592405e6*self.re_voltage_scale
-
-
-class PMTIdle(Experiment):
- """PMT idle mode."""
- id = "pmt_idle"
-
- def __init__(self):
- self.databytes = 8
-
- self.commands = ["EA", "EM"]
-
- self.commands[0] += "2 " # input buffer
- self.commands[0] += "3 " # 2.5 Hz sample rate
- self.commands[0] += "1 " # 2x PGA
diff --git a/dstat_interface/core/experiments/lsv.py b/dstat_interface/core/experiments/lsv.py
index ce2a2e1..68b5091 100644
--- a/dstat_interface/core/experiments/lsv.py
+++ b/dstat_interface/core/experiments/lsv.py
@@ -1,67 +1,123 @@
-import time
-import struct
-
-from .experiment_template import PlotBox, Experiment
-
-class LSVExp(Experiment):
- """Linear Scan Voltammetry experiment"""
- id = 'lsv'
- def setup(self):
- self.plotlims['current_voltage']['xlims'] = tuple(
- sorted(
- (int(self.parameters['start']),
- int(self.parameters['stop']))
- )
- )
-
- super(LSVExp, self).setup()
-
- self.datatype = "linearData"
- self.datalength = 2
- self.databytes = 6 # uint16 + int32
-
- self.stop_mv = int(self.parameters['stop'])
- self.max_mv = abs(int(self.parameters['start'])-int(self.parameters['stop']))
-
- self.commands += "E"
- self.commands[2] += "L"
- self.commands[2] += str(self.parameters['clean_s'])
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['dep_s'])
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['clean_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['dep_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['start'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['stop'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['slope'])/
- self.re_voltage_scale*
- (65536./3000)
- ))
- self.commands[2] += " "
+from typing import Any
+
+from ..dstat.experiment_handler import ExperimentHandler
+from ..dstat.experiment_process import ExperimentProcess
+from ..dstat.utility import abs_mv_to_dac, rel_mv_to_dac, param_test_uint16, param_test_non_zero_uint8
+from ..experiments.experiment_container import ExperimentContainer
+
+
+class LSVExperimentContainer(ExperimentContainer):
+ experiment_id = 'lsv'
+ display_name = 'Linear Scan Voltammetry'
+ process = ExperimentProcess
+ handler = ExperimentHandler
+ data_bytes = 0
+
+ def __init__(self, params: dict[str, Any], mux: int = 1):
+ super().__init__(params, mux=mux)
+
+ self.data_cols = ['voltage', 'current']
+ self.data_format = 'vA'
+
+ self.cmd_str += ['EL{clean_s} {dep_s} {clean_mv} {dep_mv} {start} {stop} {slope} ']
+ self.param_input |= {'clean_s': int, 'dep_s': int, 'clean_mv': int, 'dep_mv': int,
+ 'start': int, 'stop': int, 'slope': int}
+ self.param_input_display_names |= {'clean_s': 't_clean (s)', 'dep_s': 't_dep (s)',
+ 'clean_mv': 'V_clean (mV)', 'dep_mv': 'V_dep (mV)',
+ 'start': 'V_start (mV)', 'stop': 'V_stop (mV)', 'slope': 'Slope (mV/s)', }
+ self.param_input_limits |= {'clean_s': (0, 'time_max'), 'dep_s': (0, 'time_max'),
+ 'clean_mv': ('mv_min', 'mv_max'), 'dep_mv': ('mv_min', 'mv_max'),
+ 'start': ('mv_min', 'mv_max'), 'stop': ('mv_min', 'mv_max'),
+ 'slope': (1, 5000)}
+ self.param_converters |= {'clean_s': param_test_uint16, 'dep_s': param_test_uint16,
+ 'clean_mv': abs_mv_to_dac, 'dep_mv': abs_mv_to_dac,
+ 'start': abs_mv_to_dac, 'stop': abs_mv_to_dac, 'slope': rel_mv_to_dac}
+ self.defaults |= {'clean_s': 0, 'dep_s': 0, 'clean_mv': 0, 'dep_mv': 0}
+ if params:
+ self.progress_max = abs(self.params['stop'] - self.params['start'])
+ self.progress_end = self.params['stop']
+ else:
+ self.progress_max = 0
+ self.progress_iters = 1
+ self.data_bytes = self.calculate_data_bytes()
+
+ def get_progress(self) -> float:
+ if self.handler_instance.done:
+ return 100
+ try:
+ return (1 - abs(self.progress_end - self.handler_instance.data['voltage'][-1]) / self.progress_max) * 100
+ except IndexError:
+ return 0
+
+
+class CVExperimentContainer(ExperimentContainer):
+ experiment_id = 'cv'
+ display_name = 'Cyclic Voltammetry'
+ process = ExperimentProcess
+ handler = ExperimentHandler
+ plots = {'current': {'x': 'voltage', 'y': 'current', 'hue': 'scan'}}
+ data_bytes = 0
+
+ def __init__(self, params: dict[str, Any], mux: int = 1):
+ super().__init__(params, mux=mux)
+
+ self.data_cols = ['voltage', 'current']
+ self.data_format = 'vA'
+
+ self.cmd_str += ['EC{clean_s} {dep_s} {clean_mv} {dep_mv} {v1} {v2} {start} {scans} {slope} ']
+ self.param_input |= {'clean_s': int, 'dep_s': int, 'clean_mv': int, 'dep_mv': int, 'v1': int, 'v2': int,
+ 'start': int, 'scans': int, 'slope': int}
+ self.param_input_display_names |= {'clean_s': 't_clean (s)', 'dep_s': 't_dep (s)',
+ 'clean_mv': 'V_clean (mV)', 'dep_mv': 'V_dep (mV)',
+ 'start': 'V_start (mV)', 'v1': 'V_1 (mV)', 'v2': 'V_2 (mV)',
+ 'scans': 'Scans', 'slope': 'Slope (mV/s)'}
+ self.param_input_limits |= {'clean_s': (0, 'time_max'), 'dep_s': (0, 'time_max'),
+ 'clean_mv': ('mv_min', 'mv_max'), 'dep_mv': ('mv_min', 'mv_max'),
+ 'start': ('mv_min', 'mv_max'), 'v1': ('mv_min', 'mv_max'),
+ 'v2': ('mv_min', 'mv_max'),
+ 'scans': (1, 'scans_max'), 'slope': (1, 5000)}
+ self.param_converters |= {'clean_s': param_test_uint16, 'dep_s': param_test_uint16,
+ 'clean_mv': abs_mv_to_dac, 'dep_mv': abs_mv_to_dac,
+ 'v1': abs_mv_to_dac, 'v2': abs_mv_to_dac, 'start': abs_mv_to_dac,
+ 'scans': param_test_non_zero_uint8,
+ 'slope': rel_mv_to_dac}
+ self.defaults |= {'clean_s': 0, 'dep_s': 0, 'clean_mv': 0, 'dep_mv': 0}
+ if params:
+ self.progress_max = 2 * abs(self.params['v1'] - self.params['v2'])
+ self.progress_start = self.params['start']
+ self.progress_v1 = self.params['v1']
+ self.progress_v2 = self.params['v2']
+ self.progress_iters = self.params['scans']
+ self.progress_scan = 0
+ self.progress_lastmv = self.params['start']
+ else:
+ self.progress_max = 0
+
+ self.data_bytes = self.calculate_data_bytes()
def get_progress(self):
try:
- return 1 - (abs(self.stop_mv - self.data['current_voltage'][-1][0][-1])/self.max_mv)
+ if self.handler_instance.done:
+ return 100
+
+ if self.handler_instance.data['scan'][-1] > self.progress_scan:
+ self.progress_scan = self.handler_instance.data['scan'][-1]
+ self.progress_lastmv = self.progress_start
+ raise StopIteration
+
+ current_mv = self.handler_instance.data['voltage'][-1]
+
+ # if moving towards v1
+ if abs(self.progress_v1 - self.progress_lastmv) > abs(self.progress_v1 - current_mv):
+ # Between v2 and start v1-mv and start-mv have same sign
+ if (self.progress_v1 - current_mv > 0) == (self.progress_start - current_mv > 0):
+ progress = 100 * (1 - abs(self.progress_start - current_mv) / self.progress_max)
+ else:
+ progress = 100 * (.25 - abs(self.progress_v1 - current_mv) / self.progress_max)
+ else:
+ progress = 100 * (.75 - abs(self.progress_v2 - current_mv) / self.progress_max)
+
+ self.progress_lastmv = current_mv
+ return progress
except IndexError:
- return 0
\ No newline at end of file
+ return 0
diff --git a/dstat_interface/core/experiments/pot.py b/dstat_interface/core/experiments/pot.py
deleted file mode 100644
index 0f5971c..0000000
--- a/dstat_interface/core/experiments/pot.py
+++ /dev/null
@@ -1,80 +0,0 @@
-import time
-import struct
-
-from .experiment_template import PlotBox, Experiment
-
-
-class PotBox(PlotBox):
- def setup(self):
- self.plot_format = {
- 'voltage_time': {'xlabel': "Time (s)",
- 'ylabel': "Voltage (V)"
- }
- }
-
- def format_plots(self):
- """
- Creates and formats subplots needed. Overrides superclass.
- """
- self.subplots = {'voltage_time': self.figure.add_subplot(111)}
-
- for key, subplot in self.subplots.items():
- subplot.ticklabel_format(style='sci', scilimits=(0, 3),
- useOffset=False, axis='y')
- subplot.plot([],[])
- subplot.set_xlabel(self.plot_format[key]['xlabel'])
- subplot.set_ylabel(self.plot_format[key]['ylabel'])
-
-
-class PotExp(Experiment):
- id = 'pot'
- """Potentiometry experiment"""
- def setup(self):
- self.plots.append(PotBox(['voltage_time']))
-
- self.datatype = "linearData"
- self.datalength = 2
- self.databytes = 8
- self.data = {'voltage_time' : [([],[])]}
- self.columns = ['Time (s)', 'Voltage (V)']
- self.plotlims = {
- 'voltage_time': {
- 'xlims': (0, int(self.parameters['time']))
- }
- }
- self.plots[-1].setlims('voltage_time', **self.plotlims['voltage_time'])
-
- self.total_time = int(self.parameters['time'])
-
- self.commands += "E"
- self.commands[2] += "P"
- self.commands[2] += str(self.parameters['time'])
- self.commands[2] += " 1 " # potentiometry mode
-
- def data_handler(self, data_input):
- """Overrides Experiment method to not convert x axis to mV."""
- scan, data = data_input
- # 2*uint16 + int32
- seconds, milliseconds, voltage = struct.unpack('<HHl', data)
- return (scan, (
- seconds+milliseconds/1000.,
- voltage*self.re_voltage_scale*(1.5/8388607.)
- )
- )
-
- def store_data(self, incoming, newline):
- """Stores data in data attribute. Should not be called from subprocess.
- Can be overriden for custom experiments."""
- line, data = incoming
-
- if newline is True:
- self.data['voltage_time'].append(deepcopy(self.line_data))
-
- for i, item in enumerate(self.data['voltage_time'][line]):
- item.append(data[i])
-
- def get_progress(self):
- try:
- return self.data['voltage_time'][-1][0][-1]/self.total_time
- except IndexError:
- return 0
\ No newline at end of file
diff --git a/dstat_interface/core/experiments/swv.py b/dstat_interface/core/experiments/swv.py
index d60c447..11c2d8c 100644
--- a/dstat_interface/core/experiments/swv.py
+++ b/dstat_interface/core/experiments/swv.py
@@ -1,236 +1,155 @@
-import time
-import struct
-from copy import deepcopy
-
-from .experiment_template import PlotBox, Experiment
-
-
-class SWVBox(PlotBox):
- def setup(self):
- self.plot_format = {
- 'swv': {'xlabel': "Voltage (mV)",
- 'ylabel': "Current (A)"
- }
- }
- def format_plots(self):
- """
- Creates and formats subplots needed. Overrides superclass.
- """
- self.subplots = {'swv': self.figure.add_subplot(111)}
-
- for key, subplot in self.subplots.items():
- subplot.ticklabel_format(style='sci', scilimits=(0, 3),
- useOffset=False, axis='y')
- subplot.plot([],[])
- subplot.set_xlabel(self.plot_format[key]['xlabel'])
- subplot.set_ylabel(self.plot_format[key]['ylabel'])
-
-
-class SWVExp(Experiment):
- """Square Wave Voltammetry experiment"""
- id = 'swv'
-
- def setup(self):
- self.datatype = "SWVData"
- self.xlabel = "Voltage (mV)"
- self.ylabel = "Current (A)"
- self.data = {
- 'swv' : [([], [], [], [])]
- } # voltage, current, forwards, reverse
- self.line_data = ([], [], [], [])
- self.datalength = 2 * self.parameters['scans']
- self.databytes = 10
- self.columns = ['Voltage (mV)', 'Net Current (A)',
- 'Forward Current (A)', 'Reverse Current (A)']
- self.plotlims = {
- 'swv': {
- 'xlims': tuple(sorted(
- (int(self.parameters['start']),
- int(self.parameters['stop']))
- )
- )
- }
- }
-
- plot = SWVBox()
- plot.setlims('swv', **self.plotlims['swv'])
- self.plots.append(plot)
-
- self.stop_mv = int(self.parameters['stop'])
- self.max_mv = abs(int(self.parameters['start']) - int(self.parameters['stop']))
- self.scan_points = self.max_mv * 2 / float(self.parameters['step'])
-
- self.commands += "E"
- self.commands[2] += "S"
- self.commands[2] += str(self.parameters['clean_s'])
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['dep_s'])
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['clean_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['dep_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['start'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['stop'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['step'])/
- self.re_voltage_scale*
- (65536./3000)
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['pulse'])/
- self.re_voltage_scale*
- (65536./3000)
- ))
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['freq'])
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['scans'])
- self.commands[2] += " "
-
- def data_handler(self, input_data):
- """Overrides Experiment method to calculate difference current"""
- scan, data = input_data
- # uint16 + int32
- voltage, forward, reverse = struct.unpack('<Hll', data)
- f_trim = forward+self.gain_trim
- r_trim = reverse+self.gain_trim
-
- return (scan, (
- (voltage-32768)*3000./65536*self.re_voltage_scale,
- (f_trim-r_trim)*(1.5/self.gain/8388607),
- f_trim*(1.5/self.gain/8388607),
- r_trim*(1.5/self.gain/8388607)
- )
- )
-
- def store_data(self, incoming, newline):
- """Stores data in data attribute. Should not be called from subprocess.
- Can be overriden for custom experiments."""
- line, data = incoming
-
- if newline is True:
- self.data['swv'].append(deepcopy(self.line_data))
-
- for i, item in enumerate(self.data['swv'][line]):
- item.append(data[i])
+from datetime import datetime
+from typing import Any, Tuple
+
+from ..dstat.experiment_handler import ExperimentHandler
+from ..dstat.experiment_process import ExperimentProcess
+from ..dstat.utility import abs_mv_to_dac, rel_mv_to_dac, param_test_non_zero_uint16, \
+ param_test_uint16, param_test_uint8
+from ..experiments.experiment_container import ExperimentContainer
+
+
+class SWVExperimentHandler(ExperimentHandler):
+ def __init__(self, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.data['current'] = []
+
+ def data_handler(self, data_input: Tuple[datetime, int, bytes]):
+ unpacked: Tuple[int, int, int]
+ date, scan, data = data_input
+ unpacked = self.struct.unpack(data)
+ self.data['scan'].append(scan)
+ self.data['timestamp'].append(date)
+
+ for n, i in enumerate(unpacked):
+ try:
+ self.data[self.data_cols[n]].append(self.data_convert[n](i))
+ except TypeError: # If no converter
+ self.data[self.data_cols[n]].append(i)
+ self.data['current'].append(self.adc_to_amps(unpacked[1] - unpacked[2])) # forward - reverse
+
+
+class SWVExperimentContainer(ExperimentContainer):
+ experiment_id = 'swv'
+ display_name = 'Square Wave Voltammetry'
+ process = ExperimentProcess
+ handler = SWVExperimentHandler
+ plots = {'current': {'x': 'voltage', 'y': 'current', 'hue': 'scan'}}
+ data_bytes = 0
+
+ def __init__(self, params: dict[str, Any], mux: int = 1):
+ super().__init__(params, mux=mux)
+
+ self.data_cols = ['voltage', 'forward', 'reverse']
+ self.data_format = 'vAA'
+
+ self.cmd_str += ['ES{clean_s} {dep_s} {clean_mv} {dep_mv} {start} {stop} {step} {pulse} {freq} {scans} ']
+ self.param_input |= {'clean_s': int, 'dep_s': int, 'clean_mv': int, 'dep_mv': int,
+ 'start': int, 'stop': int, 'step': int, 'pulse': int, 'freq': int,
+ 'scans': int}
+ self.param_input_display_names |= {'clean_s': 't_clean (s)', 'dep_s': 't_dep (s)',
+ 'clean_mv': 'V_clean (mV)', 'dep_mv': 'V_dep (mV)',
+ 'start': 'V_start (mV)', 'stop': 'V_stop (mV)', 'step': 'V_step (mV)',
+ 'pulse': 'V_pulse (mV)', 'freq': 'f (Hz)',
+ 'scans': 'Scans'}
+ self.param_input_limits |= {'clean_s': (0, 'time_max'), 'dep_s': (0, 'time_max'),
+ 'clean_mv': ('mv_min', 'mv_max'), 'dep_mv': ('mv_min', 'mv_max'),
+ 'start': ('mv_min', 'mv_max'), 'stop': ('mv_min', 'mv_max'),
+ 'step': (1, 1000), 'pulse': (1, 1000), 'freq': (1, 'freq_max'),
+ 'scans': (0, 'scans_max')}
+ self.param_converters |= {'clean_s': param_test_uint16, 'dep_s': param_test_uint16,
+ 'clean_mv': abs_mv_to_dac, 'dep_mv': abs_mv_to_dac,
+ 'start': abs_mv_to_dac, 'stop': abs_mv_to_dac, 'step': rel_mv_to_dac,
+ 'pulse': rel_mv_to_dac, 'freq': param_test_non_zero_uint16,
+ 'scans': param_test_uint8}
+ self.defaults |= {'clean_s': 0, 'dep_s': 0, 'clean_mv': 0, 'dep_mv': 0}
+ if params:
+ if self.params['scans'] > 0:
+ self.progress_max = 2 * abs(self.params['stop'] - self.params['start'])
+ else:
+ self.progress_max = abs(self.params['stop'] - self.params['start'])
+ self.progress_start = self.params['start']
+ self.progress_stop = self.params['stop']
+ self.progress_iters = self.params['scans']
+ self.progress_scan = 0
+ self.progress_lastmv = self.params['start']
+ else:
+ self.progress_max = 0
+ self.data_bytes = self.calculate_data_bytes()
def get_progress(self):
+ if self.handler_instance.done:
+ return 100
try:
- if int(self.parameters['scans']) != 0:
- scans_prog = (len(self.data['swv'])-1) / float(self.parameters['scans'])
- scan_prog = (len(self.data['swv'][-1][0])-1) / self.scan_points / float(self.parameters['scans'])
- prog = scans_prog + scan_prog
- if prog > 1:
- prog = 1
- return prog
+ if self.params['scans'] > 0:
+ if self.handler_instance.data['scan'][-1] > self.progress_scan:
+ self.progress_scan = self.handler_instance.data['scan'][-1]
+ self.progress_lastmv = self.progress_start
+ raise StopIteration
+
+ current_mv = self.handler_instance.data['voltage'][-1]
+
+ if abs(self.progress_stop - self.progress_lastmv) > abs(self.progress_stop - current_mv):
+ progress = 100 * (.5 - abs(self.progress_stop - current_mv) / self.progress_max)
+ else:
+ progress = 100 * (1 - abs(self.progress_start - current_mv) / self.progress_max)
+
+ self.progress_lastmv = current_mv
+ return progress
else:
- return 1 - (abs(self.stop_mv - self.data['swv'][-1][0][-1])/self.max_mv)
+ return (1 - abs(
+ self.progress_stop - self.handler_instance.data['voltage'][-1]) / self.progress_max) * 100
except IndexError:
return 0
-class DPVExp(SWVExp):
- """Diffential Pulse Voltammetry experiment."""
- id = 'dpv'
- def setup(self):
- self.datatype = "SWVData"
- self.xlabel = "Voltage (mV)"
- self.ylabel = "Current (A)"
- self.data = {
- 'swv' : [([], [], [], [])]
- } # voltage, current, forwards, reverse
- self.line_data = ([], [], [], [])
- self.datalength = 2
- self.databytes = 10
- self.columns = ['Voltage (mV)', 'Net Current (A)',
- 'Forward Current (A)', 'Reverse Current (A)']
-
- self.plotlims = {
- 'swv': {
- 'xlims': tuple(sorted(
- (int(self.parameters['start']),
- int(self.parameters['stop']))
- )
- )
- }
- }
-
- plot = SWVBox()
- plot.setlims('swv', **self.plotlims['swv'])
- self.plots.append(plot)
-
- self.stop_mv = int(self.parameters['stop'])
- self.max_mv = abs(int(self.parameters['start']) - int(self.parameters['stop']))
-
- self.commands += "E"
- self.commands[2] += "D"
- self.commands[2] += str(self.parameters['clean_s'])
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['dep_s'])
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['clean_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['dep_mV'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['start'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['stop'])/
- self.re_voltage_scale*
- (65536./3000)+32768
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['step'])/
- self.re_voltage_scale*
- (65536./3000)
- ))
- self.commands[2] += " "
- self.commands[2] += str(int(
- int(self.parameters['pulse'])/
- self.re_voltage_scale*
- (65536./3000)
- ))
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['period'])
- self.commands[2] += " "
- self.commands[2] += str(self.parameters['width'])
- self.commands[2] += " "
+class DPVExperimentContainer(ExperimentContainer):
+ experiment_id = 'dpv'
+ display_name = 'Differential Pulse Voltammetry'
+ process = ExperimentProcess
+ handler = SWVExperimentHandler
+ data_bytes = 0
+
+ def __init__(self, params: dict[str, Any], mux: int = 1):
+ super().__init__(params, mux=mux)
+
+ self.data_cols = ['voltage', 'forward', 'reverse']
+ self.data_format = 'vAA'
+
+ self.cmd_str += ['ED{clean_s} {dep_s} {clean_mv} {dep_mv} {start} {stop} {step} {pulse} {period} {width} ']
+ self.param_input |= {'clean_s': int, 'dep_s': int, 'clean_mv': int, 'dep_mv': int,
+ 'start': int, 'stop': int, 'step': int, 'pulse': int, 'period': int, 'width': int}
+ self.param_input_display_names |= {'clean_s': 't_clean (s)', 'dep_s': 't_dep (s)',
+ 'clean_mv': 'V_clean (mV)', 'dep_mv': 'V_dep (mV)',
+ 'start': 'V_start (mV)', 'stop': 'V_stop (mV)', 'step': 'V_step (mV)',
+ 'pulse': 'V_pulse (mV)', 'period': 'Pulse Period (ms)',
+ 'width': 'Pulse Width (ms)'}
+ self.param_input_limits |= {'clean_s': (0, 'time_max'), 'dep_s': (0, 'time_max'),
+ 'clean_mv': ('mv_min', 'mv_max'), 'dep_mv': ('mv_min', 'mv_max'),
+ 'start': ('mv_min', 'mv_max'), 'stop': ('mv_min', 'mv_max'),
+ 'step': (1, 1000), 'pulse': (1, 1000), 'period': (1, 1000),
+ 'width': (1, 1000)}
+ self.param_converters |= {'clean_s': param_test_uint16, 'dep_s': param_test_uint16,
+ 'clean_mv': abs_mv_to_dac, 'dep_mv': abs_mv_to_dac,
+ 'start': abs_mv_to_dac, 'stop': abs_mv_to_dac, 'step': rel_mv_to_dac,
+ 'pulse': rel_mv_to_dac, 'period': param_test_uint16,
+ 'width': param_test_non_zero_uint16}
+ self.defaults |= {'clean_s': 0, 'dep_s': 0, 'clean_mv': 0, 'dep_mv': 0}
+
+ if params:
+ self.progress_max = abs(self.params['stop'] - self.params['start'])
+ self.progress_start = self.params['start']
+ self.progress_stop = self.params['stop']
+ self.progress_scan = 0
+ self.progress_iters = 1
+ else:
+ self.progress_max = 0
+ self.data_bytes = self.calculate_data_bytes()
def get_progress(self):
+ if self.handler_instance.done:
+ return 100
try:
- return 1 - (abs(self.stop_mv - self.data['swv'][-1][0][-1])/self.max_mv)
+ return (1 - abs(
+ self.progress_stop - self.handler_instance.data['voltage'][-1]) / self.progress_max) * 100
except IndexError:
- return 0
\ No newline at end of file
+ return 0
diff --git a/dstat_interface/core/interface/__init__.py b/dstat_interface/core/interface/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/dstat_interface/core/interface/acv.glade b/dstat_interface/core/interface/acv.glade
deleted file mode 100644
index d664e83..0000000
--- a/dstat_interface/core/interface/acv.glade
+++ /dev/null
@@ -1,445 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkFrame" id="frame2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="label" translatable="yes">Start (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label9">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="label" translatable="yes">Stop (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label10">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="label" translatable="yes">Slope (mV/s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="start_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="stop_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="slope_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label11">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="label" translatable="yes">Amplitude (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label12">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="label" translatable="yes">Frequency (Hz)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="amplitude_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="freq_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkFrame" id="frame1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Potential (mV)</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="label" translatable="yes">Cleaning</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="label" translatable="yes">Deposition</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="left_attach">9</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Preconditioning</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label13">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment not yet implemented</property>
- <attributes>
- <attribute name="weight" value="bold"/>
- </attributes>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="padding">6</property>
- <property name="position">2</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/adc_pot.glade b/dstat_interface/core/interface/adc_pot.glade
deleted file mode 100644
index fcb0d6e..0000000
--- a/dstat_interface/core/interface/adc_pot.glade
+++ /dev/null
@@ -1,412 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkListStore" id="gain_liststore">
- <columns>
- <!-- column-name index -->
- <column type="guint"/>
- <!-- column-name label -->
- <column type="gchararray"/>
- <!-- column-name command -->
- <column type="gchararray"/>
- </columns>
- <data>
- <row>
- <col id="0">0</col>
- <col id="1" translatable="yes">100 Ω (15 mA FS)</col>
- <col id="2" translatable="yes">0</col>
- </row>
- <row>
- <col id="0">1</col>
- <col id="1" translatable="yes">300 Ω (5 mA FS)</col>
- <col id="2" translatable="yes">1</col>
- </row>
- <row>
- <col id="0">2</col>
- <col id="1" translatable="yes">3 kΩ (500 µA FS)</col>
- <col id="2" translatable="yes">2</col>
- </row>
- <row>
- <col id="0">3</col>
- <col id="1" translatable="yes">30 kΩ (50 µA FS)</col>
- <col id="2" translatable="yes">3</col>
- </row>
- <row>
- <col id="0">4</col>
- <col id="1" translatable="yes">300 kΩ (5 µA FS)</col>
- <col id="2" translatable="yes">4</col>
- </row>
- <row>
- <col id="0">5</col>
- <col id="1" translatable="yes">3 MΩ (500 nA FS)</col>
- <col id="2" translatable="yes">5</col>
- </row>
- <row>
- <col id="0">6</col>
- <col id="1" translatable="yes">30 MΩ (50 nA FS)</col>
- <col id="2" translatable="yes">6</col>
- </row>
- <row>
- <col id="0">7</col>
- <col id="1" translatable="yes">500 MΩ (3 nA FS)</col>
- <col id="2" translatable="yes">7</col>
- </row>
- </data>
- </object>
- <object class="GtkListStore" id="pga_liststore">
- <columns>
- <!-- column-name index -->
- <column type="guint"/>
- <!-- column-name label -->
- <column type="gchararray"/>
- <!-- column-name command -->
- <column type="gchararray"/>
- </columns>
- <data>
- <row>
- <col id="0">0</col>
- <col id="1" translatable="yes">1x</col>
- <col id="2" translatable="yes">0</col>
- </row>
- <row>
- <col id="0">1</col>
- <col id="1" translatable="yes">2x</col>
- <col id="2" translatable="yes">1</col>
- </row>
- <row>
- <col id="0">2</col>
- <col id="1" translatable="yes">4x</col>
- <col id="2" translatable="yes">2</col>
- </row>
- <row>
- <col id="0">3</col>
- <col id="1" translatable="yes">8x</col>
- <col id="2" translatable="yes">3</col>
- </row>
- <row>
- <col id="0">4</col>
- <col id="1" translatable="yes">16x</col>
- <col id="2" translatable="yes">4</col>
- </row>
- <row>
- <col id="0">5</col>
- <col id="1" translatable="yes">32x</col>
- <col id="2" translatable="yes">5</col>
- </row>
- <row>
- <col id="0">6</col>
- <col id="1" translatable="yes">64x</col>
- <col id="2" translatable="yes">6</col>
- </row>
- </data>
- </object>
- <object class="GtkListStore" id="srate_liststore">
- <columns>
- <!-- column-name index -->
- <column type="guint"/>
- <!-- column-name label -->
- <column type="gchararray"/>
- <!-- column-name command -->
- <column type="gchararray"/>
- </columns>
- <data>
- <row>
- <col id="0">0</col>
- <col id="1" translatable="yes">2.5 Hz</col>
- <col id="2" translatable="yes">03</col>
- </row>
- <row>
- <col id="0">1</col>
- <col id="1" translatable="yes">5 Hz</col>
- <col id="2" translatable="yes">13</col>
- </row>
- <row>
- <col id="0">2</col>
- <col id="1" translatable="yes">10 Hz</col>
- <col id="2" translatable="yes">23</col>
- </row>
- <row>
- <col id="0">3</col>
- <col id="1" translatable="yes">15 Hz</col>
- <col id="2" translatable="yes">33</col>
- </row>
- <row>
- <col id="0">4</col>
- <col id="1" translatable="yes">25 Hz</col>
- <col id="2" translatable="yes">43</col>
- </row>
- <row>
- <col id="0">5</col>
- <col id="1" translatable="yes">30 Hz</col>
- <col id="2" translatable="yes">53</col>
- </row>
- <row>
- <col id="0">6</col>
- <col id="1" translatable="yes">50 Hz</col>
- <col id="2" translatable="yes">63</col>
- </row>
- <row>
- <col id="0">7</col>
- <col id="1" translatable="yes">60 Hz</col>
- <col id="2" translatable="yes">72</col>
- </row>
- <row>
- <col id="0">8</col>
- <col id="1" translatable="yes">100 Hz</col>
- <col id="2" translatable="yes">82</col>
- </row>
- <row>
- <col id="0">9</col>
- <col id="1" translatable="yes">500 Hz</col>
- <col id="2" translatable="yes">92</col>
- </row>
- <row>
- <col id="0">10</col>
- <col id="1" translatable="yes">1 kHz</col>
- <col id="2" translatable="yes">A1</col>
- </row>
- <row>
- <col id="0">11</col>
- <col id="1" translatable="yes">2 kHz</col>
- <col id="2" translatable="yes">B0</col>
- </row>
- <row>
- <col id="0">12</col>
- <col id="1" translatable="yes">3.75 kHz</col>
- <col id="2" translatable="yes">C0</col>
- </row>
- <row>
- <col id="0">13</col>
- <col id="1" translatable="yes">7.5 kHz</col>
- <col id="2" translatable="yes">D0</col>
- </row>
- <row>
- <col id="0">14</col>
- <col id="1" translatable="yes">15 kHz</col>
- <col id="2" translatable="yes">E0</col>
- </row>
- <row>
- <col id="0">15</col>
- <col id="1" translatable="yes">30 kHz</col>
- <col id="2" translatable="yes">F0</col>
- </row>
- </data>
- </object>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkBox" id="vbox2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkFrame" id="adc_frame">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="tooltip_text" translatable="yes">Gain of the ADC's programmable gain amplifier. Default is 2 - gives full scale input.</property>
- <property name="label" translatable="yes">PGA Setting</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Sample Rate</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="buffer_checkbutton">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="active">True</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="tooltip_text" translatable="yes">The ADC's input buffer greatly increases input impedance. Should generally be enabled.</property>
- <property name="label" translatable="yes">Input Buffer</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkComboBox" id="pga_combobox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="model">pga_liststore</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkComboBox" id="srate_combobox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="model">srate_liststore</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="tooltip_text" translatable="yes">Short CE and RE terminals together.</property>
- <property name="label" translatable="yes">2 Electrode Mode</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="short_checkbutton">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">ADC Settings</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkFrame" id="pstat_frame">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="tooltip_text" translatable="yes">Gain of the I-V converter. Increasing this improves S/N, unlike the ADC's PGA.</property>
- <property name="label" translatable="yes">Gain</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkComboBox" id="gain_combobox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="model">gain_liststore</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Potentiostat Settings</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">0</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/adc_pot.py b/dstat_interface/core/interface/adc_pot.py
deleted file mode 100755
index 77efe5e..0000000
--- a/dstat_interface/core/interface/adc_pot.py
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-import os.path
-from pkg_resources import parse_version
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk
-except ImportError:
- print "ERR: GTK not available"
- sys.exit(1)
-
-from ..errors import InputError, VarError
-from ..dstat import state
-
-mod_dir = os.path.dirname(os.path.abspath(__file__))
-
-class adc_pot(object):
- def __init__(self):
- self.builder = Gtk.Builder()
- self.builder.add_from_file(os.path.join(mod_dir,'adc_pot.glade'))
- self.builder.connect_signals(self)
- self.cell = Gtk.CellRendererText()
-
- ui_keys = ['buffer_true',
- 'short_true',
- 'pga_index',
- 'srate_index',
- 'gain_index'
- ]
- ui_cont = map(self.builder.get_object, ['buffer_checkbutton',
- 'short_checkbutton',
- 'pga_combobox',
- 'srate_combobox',
- 'gain_combobox'
- ]
- )
- self.ui = dict(zip(ui_keys, ui_cont))
-
- #initialize comboboxes
- self.ui['pga_index'].pack_start(self.cell, True)
- self.ui['pga_index'].add_attribute(self.cell, 'text', 1)
- self.ui['pga_index'].set_active(1)
-
- self.ui['srate_index'].pack_start(self.cell, True)
- self.ui['srate_index'].add_attribute(self.cell, 'text', 1)
- self.ui['srate_index'].set_active(7)
-
- self.gain_liststore = self.builder.get_object('gain_liststore')
- self.ui['gain_index'].pack_start(self.cell, True)
- self.ui['gain_index'].add_attribute(self.cell, 'text', 1)
- # self.ui['gain_index'].set_active(2)
-
- self._params = {}
-
- @property
- def params(self):
- """Dict of parameters."""
- try:
- self._get_params()
- except InputError as e:
- raise e
- finally:
- return self._params
-
- def _get_params(self):
- """Updates self._params from UI."""
- for i in self.ui:
- self._params[i] = self.ui[i].get_active()
-
- srate_model = self.ui['srate_index'].get_model()
- self._params['adc_rate'] = srate_model[self._params['srate_index']][2]
- srate = srate_model[self._params['srate_index']][1]
-
- if srate.endswith("kHz"):
- sample_rate = float(srate.rstrip(" kHz"))*1000
- else:
- sample_rate = float(srate.rstrip(" Hz"))
-
- self._params['adc_rate_hz'] = sample_rate
-
- pga_model = self.ui['pga_index'].get_model()
- self._params['adc_pga'] = pga_model[self._params['pga_index']][2]
-
- gain_model = self.ui['gain_index'].get_model()
- self._params['gain'] = gain_model[self._params['gain_index']][2]
- if self._params['gain_index'] not in range(len(gain_model)):
- raise InputError(self._params['gain_index'],
- "Select a potentiostat gain.")
-
- @params.setter
- def params(self, params):
- if self._params is {}:
- self._params = dict.fromkeys(self.ui.keys())
-
- for i in self._params:
- if i in params:
- self._params[i] = params[i]
- self._set_params()
-
- def _set_params(self):
- """Updates UI with new parameters."""
- for i in self.ui:
- self.ui[i].set_active(self._params[i])
-
- def set_version(self, boost=None):
- """ Sets menus for DStat version. """
- try:
- if self.version == state.board_instance:
- return
- except AttributeError:
- pass
-
- self.version = state.board_instance
-
- self.gain_liststore.clear()
-
- for n, i in enumerate(self.version.gain_labels):
- self.gain_liststore.append((n, i, str(n)))
-
- self.ui['gain_index'].set_active(self.version.gain_default_index)
\ No newline at end of file
diff --git a/dstat_interface/core/interface/analysis_options.glade b/dstat_interface/core/interface/analysis_options.glade
deleted file mode 100644
index dda2e6c..0000000
--- a/dstat_interface/core/interface/analysis_options.glade
+++ /dev/null
@@ -1,159 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkDialog" id="analysis_dialog">
- <property name="can_focus">False</property>
- <property name="border_width">5</property>
- <property name="title" translatable="yes">Analysis Options…</property>
- <property name="type_hint">dialog</property>
- <child internal-child="vbox">
- <object class="GtkBox" id="dialog-vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <property name="spacing">2</property>
- <child internal-child="action_area">
- <object class="GtkButtonBox" id="dialog-action_area1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="layout_style">end</property>
- <child>
- <placeholder/>
- </child>
- <child>
- <object class="GtkButton" id="ok_button">
- <property name="label">gtk-ok</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkSpinButton" id="stats_start_spin">
- <property name="visible">True</property>
- <property name="sensitive">False</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="text" translatable="yes">0.00</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="adjustment">stats_start_adj</property>
- <property name="climb_rate">0.050000000000000003</property>
- <property name="digits">2</property>
- <property name="numeric">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkSpinButton" id="stats_stop_spin">
- <property name="visible">True</property>
- <property name="sensitive">False</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="text" translatable="yes">0.00</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="adjustment">stats_stop_adj</property>
- <property name="climb_rate">0.050000000000000003</property>
- <property name="digits">2</property>
- <property name="numeric">True</property>
- <property name="update_policy">if-valid</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="stats_button">
- <property name="label" translatable="yes">Generate Summary Stats</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="halign">center</property>
- <property name="image_position">bottom</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- <property name="width">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="stats_start_button">
- <property name="label" translatable="yes">Stat Start (mV or s)</property>
- <property name="visible">True</property>
- <property name="sensitive">False</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="hexpand">True</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="stats_stop_button">
- <property name="label" translatable="yes">Stat Stop (mV or s)</property>
- <property name="visible">True</property>
- <property name="sensitive">False</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="hexpand">True</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- <action-widgets>
- <action-widget response="0">ok_button</action-widget>
- </action-widgets>
- </object>
- <object class="GtkAdjustment" id="stats_start_adj">
- <property name="lower">-3000</property>
- <property name="upper">9999</property>
- <property name="step_increment">0.5</property>
- <property name="page_increment">10</property>
- </object>
- <object class="GtkAdjustment" id="stats_stop_adj">
- <property name="lower">-3000</property>
- <property name="upper">9999</property>
- <property name="step_increment">0.5</property>
- <property name="page_increment">10</property>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/calib.glade b/dstat_interface/core/interface/calib.glade
deleted file mode 100644
index ff4b40f..0000000
--- a/dstat_interface/core/interface/calib.glade
+++ /dev/null
@@ -1,363 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <child>
- <object class="GtkEntry" id="time_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">5</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Measurement Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Resistor</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Trim Value (ADC units)</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">100 Ω</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">3 kΩ</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">30 kΩ</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">300 kΩ</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">6</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">3 MΩ</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">7</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label9">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">30 MΩ</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">8</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label10">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">100 MΩ</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">9</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="30k_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="3k_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="100_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="300k_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">6</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="3M_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">7</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="30M_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">8</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="100M_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">9</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="read_button">
- <property name="label" translatable="yes">Read from EEPROM</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_read_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">11</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="write_button">
- <property name="label" translatable="yes">Write to EEPROM</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_write_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">12</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="measure_button">
- <property name="label" translatable="yes">Measure</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_measure_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">10</property>
- </packing>
- </child>
- <child>
- <object class="GtkSeparator">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- <property name="width">2</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label13">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <property name="label" translatable="yes">Measure with WE open.
-Offsets cannot exceed 16 bit unsigned int.</property>
- <attributes>
- <attribute name="weight" value="bold"/>
- </attributes>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/chronoamp.glade b/dstat_interface/core/interface/chronoamp.glade
deleted file mode 100644
index e0a22de..0000000
--- a/dstat_interface/core/interface/chronoamp.glade
+++ /dev/null
@@ -1,186 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkListStore" id="ca_list">
- <columns>
- <!-- column-name millivolts -->
- <column type="gint"/>
- <!-- column-name seconds -->
- <column type="guint"/>
- </columns>
- </object>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <property name="default_width">300</property>
- <property name="default_height">500</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Potential (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="potential_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">5</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="truncate_multiline">True</property>
- <property name="caps_lock_warning">False</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="time_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">5</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="truncate_multiline">True</property>
- <property name="caps_lock_warning">False</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="add_button">
- <property name="label">gtk-add</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- <signal name="clicked" handler="on_add_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="remove_button">
- <property name="label">gtk-remove</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- <signal name="clicked" handler="on_remove_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkTreeView" id="treeview">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="model">ca_list</property>
- <property name="reorderable">True</property>
- <property name="rules_hint">True</property>
- <property name="enable_search">False</property>
- <property name="search_column">0</property>
- <property name="fixed_height_mode">True</property>
- <property name="show_expanders">False</property>
- <property name="rubber_banding">True</property>
- <property name="enable_grid_lines">both</property>
- <child internal-child="selection">
- <object class="GtkTreeSelection"/>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkStatusbar" id="statusbar">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="spacing">2</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/cv.glade b/dstat_interface/core/interface/cv.glade
deleted file mode 100644
index 9cc5d7f..0000000
--- a/dstat_interface/core/interface/cv.glade
+++ /dev/null
@@ -1,362 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkFrame" id="frame1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="vexpand">False</property>
- <property name="label" translatable="yes">Potential (mV)</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Cleaning</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Deposition</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Preconditioning</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkFrame" id="frame2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Start (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label9">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Vertex 1 (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label10">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Vertex 2 (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="start_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="v1_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="v2_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label11">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Slope (mV/s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label12">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Scans</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="slope_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="scans_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">1</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/data_view.py b/dstat_interface/core/interface/data_view.py
deleted file mode 100644
index e7c4db6..0000000
--- a/dstat_interface/core/interface/data_view.py
+++ /dev/null
@@ -1,81 +0,0 @@
-from __future__ import division, absolute_import, print_function, unicode_literals
-
-import logging
-logger = logging.getLogger(__name__)
-
-from collections import OrderedDict
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk
-except ImportError:
- print("ERR: GTK not available")
- sys.exit(1)
-
-class DataPage(object):
- def __init__(self, notebook, name="Data"):
- """Make new notebook page and adds to notebook."""
- self.box = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
- self.combobox = Gtk.ComboBoxText()
- self.scroll = Gtk.ScrolledWindow(vexpand=True)
- self.textview = Gtk.TextView(cursor_visible=False, monospace=True,
- editable=False)
- self.scroll.add(self.textview)
- self.box.add(self.combobox)
- self.box.add(self.scroll)
- self.name = name
- self.buffers = {}
-
- self.combobox.connect('changed', self.combobox_changed)
-
- notebook.append_page(self.box, Gtk.Label(label=name))
-
- def add_exp(self, exp):
- """Add all data from exp to page."""
- for name, df in exp.df.items():
- self.combobox.append(id=name, text=name)
- self.buffers[name] = Gtk.TextBuffer()
- self.buffers[name].set_text(df.to_string())
- self.box.show_all()
-
- self.combobox.set_active(0)
-
- def clear_exps(self):
- self.combobox.remove_all()
- self.buffers = {}
-
- def combobox_changed(self, object):
- """Switch displayed data buffer."""
- try:
- self.textview.set_buffer(
- self.buffers[self.combobox.get_active_id()]
- )
- except KeyError:
- pass
-
-class InfoPage(object):
- def __init__(self, notebook, name="Info"):
- """Make new notebook page and adds to notebook."""
- self.box = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
- self.buffer = Gtk.TextBuffer()
- self.scroll = Gtk.ScrolledWindow(vexpand=True)
- self.textview = Gtk.TextView(cursor_visible=False, monospace=True,
- editable=False, buffer=self.buffer)
- self.scroll.add(self.textview)
- self.box.add(self.scroll)
-
- self.name = name
-
- notebook.append_page(self.box, Gtk.Label(label=name))
- self.box.show_all()
-
- def clear(self):
- """Clear buffer"""
- self.buffer.set_text('')
-
- def set_text(self, text):
- self.buffer.set_text(text)
-
- def add_line(self, line):
- self.buffer.insert_at_cursor('{}\n'.format(line))
\ No newline at end of file
diff --git a/dstat_interface/core/interface/db.glade b/dstat_interface/core/interface/db.glade
deleted file mode 100644
index e65d520..0000000
--- a/dstat_interface/core/interface/db.glade
+++ /dev/null
@@ -1,204 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkWindow" id="db_window">
- <property name="can_focus">False</property>
- <property name="title" translatable="yes">Database</property>
- <property name="window_position">center-on-parent</property>
- <property name="destroy_with_parent">True</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkCheckButton" id="db_enable_checkbutton">
- <property name="label" translatable="yes">Enable Database saving</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="active">True</property>
- <property name="draw_indicator">True</property>
- <signal name="toggled" handler="on_db_enable_checkbutton_toggled" swapped="no"/>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkGrid" id="db_control_table">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Measurement ID</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment ID</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="exp_id_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="measure_id_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="editable">False</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="patient_id_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="editable">False</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Patient ID</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="exp_id_autogen_button">
- <property name="label" translatable="yes">Generate New</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_exp_id_autogen_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">DB Path</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="db_path_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="db_apply_button">
- <property name="label" translatable="yes">Apply</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_db_apply_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Measurement Name</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="measure_name_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/db.py b/dstat_interface/core/interface/db.py
deleted file mode 100755
index e362292..0000000
--- a/dstat_interface/core/interface/db.py
+++ /dev/null
@@ -1,143 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import os
-import sys
-import logging
-from uuid import uuid4
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print "ERR: GTK not available"
- sys.exit(1)
-
-logger = logging.getLogger(__name__)
-
-class DB_Window(GObject.GObject):
- __gsignals__ = {
- 'db-reset' : (GObject.SIGNAL_RUN_LAST,
- GObject.TYPE_NONE,
- (GObject.TYPE_STRING,)
- )
- }
- def __init__(self):
- GObject.GObject.__init__(self)
-
- self.builder = Gtk.Builder()
- self.builder.add_from_file('interface/db.glade')
- self.builder.connect_signals(self)
-
- self.window = self.builder.get_object('db_window')
- # Make sure window isn't destroyed if checkbox hit.
- self.window.connect('delete-event', self.on_delete_event)
- self.db_control_table = self.builder.get_object('db_control_table')
-
- ui_keys = ['exp_id_entry',
- 'measure_id_entry',
- 'patient_id_entry',
- 'measure_name_entry',
- 'db_path_entry',
- 'db_apply_button',
- 'exp_id_autogen_button',
- 'db_enable_checkbutton'
- ]
- self.persistent_keys = ['db_path_entry','db_enable_checkbutton']
- self.ui = {}
- for i in ui_keys:
- self.ui[i] = self.builder.get_object(i)
-
- self.metadata_map = [('experiment_uuid', 'exp_id_entry'),
- ('patient_id', 'patient_id_entry'),
- ('name', 'measure_name_entry')]
-
- self._params = {}
-
- @property
- def persistent_params(self):
- """Dict of parameters that should be saved."""
- self._get_params()
- return {k:self._params[k] for k in self.persistent_keys}
-
- @property
- def params(self):
- """Dict of parameters."""
- self._get_params()
- return self._params
-
- def _get_params(self):
- """Updates self._params from UI."""
- for i in self.ui:
- if i.endswith('checkbutton'):
- self._params[i] = self.ui[i].get_active()
- elif i.endswith('entry'):
- text = self.ui[i].get_text()
- if text == "":
- text = None
- self._params[i] = text
-
- @params.setter
- def params(self, params):
- if self._params is {}:
- self._params = dict.fromkeys(self.ui.keys())
-
- for i in self._params:
- if i in params:
- self._params[i] = params[i]
- self._set_params()
-
- def _set_params(self):
- """Updates UI with new parameters."""
- for i in self.ui:
- if i.endswith('checkbutton'):
- self.ui[i].set_active(self._params[i])
- elif i.endswith('entry'):
- if self._params[i] is not None:
- self.ui[i].set_text(self._params[i])
- else:
- self.ui[i].set_text("")
-
- def update_from_metadata(self, metadata):
- params = {k : metadata[j] for j, k in self.metadata_map
- if j in metadata}
- self.params = params
-
- def show(self):
- self.window.show_all()
- self.on_db_enable_checkbutton_toggled()
-
- def on_db_enable_checkbutton_toggled(self, *args):
- if self.ui['db_enable_checkbutton'].get_active():
- self.db_control_table.show()
- else:
- self.db_control_table.hide()
-
- def on_exp_id_autogen_button_clicked(self, *args):
- self.ui['exp_id_entry'].set_text(uuid4().hex)
-
- def on_db_apply_button_clicked(self, widget=None, *data):
- self.emit('db-reset', self.params['db_path_entry'])
-
- def on_delete_event(self, widget=None, *data):
- widget.hide()
- return True
-
-GObject.type_register(DB_Window)
\ No newline at end of file
diff --git a/dstat_interface/core/interface/dpv.glade b/dstat_interface/core/interface/dpv.glade
deleted file mode 100644
index 9143f88..0000000
--- a/dstat_interface/core/interface/dpv.glade
+++ /dev/null
@@ -1,404 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkFrame" id="frame1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkEntry" id="clean_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Deposition</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Cleaning</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Potential (mV)</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Preconditioning</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkFrame" id="frame2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Start (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label9">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Stop (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label10">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Step Size (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="start_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="stop_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="step_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label11">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Pulse Height (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label12">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Pulse Width (ms)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="pulse_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="width_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label14">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="tooltip_text" translatable="yes">Scan both forwards and backwards.</property>
- <property name="label" translatable="yes">Pulse Period (ms)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="period_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label13">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Note: ADC samples 1/(ADC Frequency) before end of pulse. 1/(ADC frequency) should be significantly shorter than pulse period to reduce capacitive current.</property>
- <property name="wrap">True</property>
- <property name="wrap_mode">word-char</property>
- <property name="width_chars">43</property>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">2</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/dstatinterface.glade b/dstat_interface/core/interface/dstatinterface.glade
deleted file mode 100644
index 889e1d6..0000000
--- a/dstat_interface/core/interface/dstatinterface.glade
+++ /dev/null
@@ -1,737 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkAboutDialog" id="aboutdialog1">
- <property name="can_focus">False</property>
- <property name="border_width">5</property>
- <property name="destroy_with_parent">True</property>
- <property name="type_hint">dialog</property>
- <property name="program_name">DStat-interface</property>
- <property name="copyright" translatable="yes">© Michael Dryden 2014</property>
- <property name="comments" translatable="yes">This software is licensed under the GNU GPL v3</property>
- <property name="website">http://microfluidics.utoronto.ca/dstat</property>
- <property name="website_label" translatable="yes">Wheeler Microfuidics Lab</property>
- <property name="authors">Michael Dryden
-Thanks to Christian Fobel for help with Dropbot Plugin</property>
- <property name="documenters"/>
- <property name="logo_icon_name">image-missing</property>
- <property name="license_type">gpl-3-0</property>
- <child internal-child="vbox">
- <object class="GtkBox" id="dialog-vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <property name="spacing">2</property>
- <child internal-child="action_area">
- <object class="GtkButtonBox" id="dialog-action_area1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="layout_style">end</property>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- </object>
- </child>
- </object>
- <object class="GtkTextBuffer" id="databuffer1"/>
- <object class="GtkTextBuffer" id="databuffer2"/>
- <object class="GtkImage" id="image1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="halign">center</property>
- <property name="stock">gtk-missing-image</property>
- </object>
- <object class="GtkImage" id="image2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="icon_name">image7</property>
- </object>
- <object class="GtkImage" id="image3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="stock">gtk-save-as</property>
- </object>
- <object class="GtkImage" id="image4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="stock">gtk-save-as</property>
- </object>
- <object class="GtkImage" id="image5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="stock">gtk-open</property>
- </object>
- <object class="GtkImage" id="image6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="stock">gtk-preferences</property>
- </object>
- <object class="GtkImage" id="image7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="icon_name">image7</property>
- </object>
- <object class="GtkImage" id="image8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="stock">gtk-save-as</property>
- </object>
- <object class="GtkImage" id="image9">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="icon_name">image7</property>
- </object>
- <object class="GtkListStore" id="serial_liststore">
- <columns>
- <!-- column-name serial -->
- <column type="gchararray"/>
- </columns>
- </object>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <property name="border_width">6</property>
- <property name="title" translatable="yes">Main</property>
- <property name="default_width">1200</property>
- <property name="default_height">800</property>
- <signal name="destroy" handler="on_window1_destroy" swapped="no"/>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkMenuBar" id="menubar1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkMenuItem" id="menuitem1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">File</property>
- <child type="submenu">
- <object class="GtkMenu" id="menu1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkImageMenuItem" id="file_save_exp">
- <property name="label" translatable="yes">Save Experiment Data…</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image8</property>
- <property name="use_stock">False</property>
- <signal name="activate" handler="on_file_save_exp_activate" swapped="no"/>
- </object>
- </child>
- <child>
- <object class="GtkImageMenuItem" id="file_save_plot">
- <property name="label" translatable="yes">Save Plot…</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image3</property>
- <property name="use_stock">False</property>
- <signal name="activate" handler="on_file_save_plot_activate" swapped="no"/>
- </object>
- </child>
- <child>
- <object class="GtkImageMenuItem" id="file_save_params">
- <property name="label" translatable="yes">Save Parameters…</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image4</property>
- <property name="use_stock">False</property>
- <signal name="activate" handler="on_file_save_params_activate" swapped="no"/>
- </object>
- </child>
- <child>
- <object class="GtkImageMenuItem" id="file_load_params">
- <property name="label" translatable="yes">Load Parameters…</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image5</property>
- <property name="use_stock">False</property>
- <signal name="activate" handler="on_file_load_params_activate" swapped="no"/>
- </object>
- </child>
- <child>
- <object class="GtkImageMenuItem" id="gtk_quit">
- <property name="label">gtk-quit</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="use_underline">True</property>
- <property name="use_stock">True</property>
- <signal name="activate" handler="on_gtk_quit_activate" swapped="no"/>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child>
- <object class="GtkMenuItem" id="menu_dstat">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">DStat</property>
- <child type="submenu">
- <object class="GtkMenu" id="menu5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkImageMenuItem" id="menu_dstat_info">
- <property name="label">System Information</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image7</property>
- <property name="use_stock">False</property>
- </object>
- </child>
- <child>
- <object class="GtkImageMenuItem" id="menu_dstat_fw">
- <property name="label" translatable="yes">Firmware…</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image2</property>
- <property name="use_stock">False</property>
- </object>
- </child>
- <child>
- <object class="GtkImageMenuItem" id="menu_dstat_reset">
- <property name="label">Reset EEPROM</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image9</property>
- <property name="use_stock">False</property>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child>
- <object class="GtkMenuItem" id="menu_dropbot">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Dropbot</property>
- <child type="submenu">
- <object class="GtkMenu" id="menu2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkImageMenuItem" id="menu_dropbot_connect">
- <property name="label">gtk-connect</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="use_underline">True</property>
- <property name="use_stock">True</property>
- <signal name="activate" handler="on_menu_dropbot_connect_activate" swapped="no"/>
- </object>
- </child>
- <child>
- <object class="GtkImageMenuItem" id="menu_dropbot_disconnect">
- <property name="label">gtk-disconnect</property>
- <property name="visible">True</property>
- <property name="sensitive">False</property>
- <property name="can_focus">False</property>
- <property name="use_underline">True</property>
- <property name="use_stock">True</property>
- <signal name="activate" handler="on_menu_dropbot_disconnect_activate" swapped="no"/>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child>
- <object class="GtkMenuItem" id="menu_analysis">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Analysis</property>
- <child type="submenu">
- <object class="GtkMenu" id="menu4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkImageMenuItem" id="menu_analysis_options">
- <property name="label" translatable="yes">Analysis Options…</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="image">image6</property>
- <property name="use_stock">False</property>
- <signal name="activate" handler="on_menu_analysis_options_activate" swapped="no"/>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child>
- <object class="GtkMenuItem" id="menuitem4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">About</property>
- <child type="submenu">
- <object class="GtkMenu" id="menu3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkImageMenuItem" id="gtk_about">
- <property name="label">gtk-about</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="use_underline">True</property>
- <property name="use_stock">True</property>
- <signal name="activate" handler="on_gtk_about_activate" swapped="no"/>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkPaned">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="position">300</property>
- <property name="position_set">True</property>
- <property name="wide_handle">True</property>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkBox" id="gain_adc_box">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <placeholder/>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment:</property>
- <attributes>
- <attribute name="weight" value="semibold"/>
- </attributes>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">10</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- <child>
- <object class="GtkComboBoxText" id="expcombobox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">3</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkBox" id="exp_section_box">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <placeholder/>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkButton" id="pot_start">
- <property name="label">gtk-execute</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- <signal name="clicked" handler="on_pot_start_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="pot_stop">
- <property name="label">gtk-stop</property>
- <property name="visible">True</property>
- <property name="sensitive">False</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- <signal name="clicked" handler="on_pot_stop_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkSpinner" id="spinner">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">2</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkProgressBar" id="exp_progressbar">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="show_text">True</property>
- <property name="margin_top">10</property>
- <property name="margin_bottom">15</property>
- <property name="margin_right">5</property>
- <property name="margin_left">2</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">3</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="resize">False</property>
- <property name="shrink">True</property>
- </packing>
- </child>
- <child>
- <object class="GtkNotebook" id="main_notebook">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="scrollable">True</property>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkNotebook" id="plot_notebook">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="tab_pos">bottom</property>
- <child>
- <placeholder/>
- </child>
- <child type="tab">
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child type="tab">
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child type="tab">
- <placeholder/>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">-1</property>
- </packing>
- </child>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="valign">start</property>
- <child>
- <object class="GtkCheckButton" id="autosave_checkbutton">
- <property name="label" translatable="yes">Autosave</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkFileChooserButton" id="autosavedir_button">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="valign">start</property>
- <property name="action">select-folder</property>
- <property name="preview_widget_active">False</property>
- <property name="title" translatable="yes">Select a Save Folder</property>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="autosavename">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="has_tooltip">True</property>
- <property name="valign">start</property>
- <property name="max_length">32</property>
- <property name="invisible_char">â—</property>
- <property name="text" translatable="yes">filename</property>
- <property name="caps_lock_warning">False</property>
- <property name="primary_icon_stock">gtk-file</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="primary_icon_tooltip_text" translatable="yes">File name</property>
- <property name="primary_icon_tooltip_markup" translatable="yes">File name</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">2</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">0</property>
- </packing>
- </child>
- </object>
- </child>
- <child type="tab">
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Plot</property>
- </object>
- <packing>
- <property name="tab_fill">False</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- <child type="tab">
- <placeholder/>
- </child>
- <child>
- <placeholder/>
- </child>
- <child type="tab">
- <placeholder/>
- </child>
- </object>
- <packing>
- <property name="resize">True</property>
- <property name="shrink">True</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkBox">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <child>
- <object class="GtkStatusbar" id="statusbar">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="spacing">2</property>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="pack_type">end</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Serial Port:</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="padding">5</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkComboBox" id="serial_combobox">
- <property name="width_request">128</property>
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="halign">start</property>
- <property name="model">serial_liststore</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="serial_connect">
- <property name="label">gtk-connect</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- <signal name="clicked" handler="on_serial_connect_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="pmt_mode">
- <property name="label" translatable="yes">Connect (PMT mode)</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <signal name="clicked" handler="on_serial_connect_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="serial_disconnect">
- <property name="label">gtk-disconnect</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- <signal name="clicked" handler="on_serial_disconnect_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="serial_refresh">
- <property name="label">gtk-refresh</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="use_stock">True</property>
- <signal name="clicked" handler="on_serial_refresh_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">6</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="ocp_disp">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="halign">start</property>
- <property name="label" translatable="yes">OCP:</property>
- <property name="single_line_mode">True</property>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">3</property>
- <property name="position">7</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">True</property>
- <property name="position">2</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- <object class="GtkAdjustment" id="updatesamples_adj">
- <property name="upper">100</property>
- <property name="value">5</property>
- <property name="step_increment">1</property>
- <property name="page_increment">10</property>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/exp_int.py b/dstat_interface/core/interface/exp_int.py
deleted file mode 100755
index a4aba0e..0000000
--- a/dstat_interface/core/interface/exp_int.py
+++ /dev/null
@@ -1,540 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-from __future__ import division, absolute_import, print_function, unicode_literals
-
-import os
-import sys
-import logging
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print("ERR: GTK not available")
- sys.exit(1)
-
-from ..dstat import comm, state
-from ..experiments import (cal, chronoamp, cv, experiment_template,
- idle, lsv, pot, swv)
-import __main__
-from ..errors import InputError, VarError
-
-logger = logging.getLogger(__name__)
-
-mod_dir = os.path.dirname(os.path.abspath(__file__))
-
-
-class ExpInterface(GObject.Object):
- """Generic experiment interface class. Should be subclassed to implement
- experiment interfaces by populating self.entry. Override class attributes
- to set id and experiment class to run.
- """
- __gsignals__ = {
- b'run_utility': (GObject.SIGNAL_RUN_FIRST, None, ()),
- b'done_utility': (GObject.SIGNAL_RUN_FIRST, None, ())
- }
-
- id = None
- experiment = None
-
- def __init__(self, glade_path):
- super(ExpInterface, self).__init__()
- self.builder = Gtk.Builder()
- self.builder.add_from_file(glade_path)
- self.builder.connect_signals(self)
- self.entry = {} # to be used only for str parameters
- self._params = None
-
- def get_experiment(self, parameters):
- return self.__class__.experiment(parameters)
-
- def _fill_params(self):
- self._params = dict.fromkeys(self.entry.keys())
-
- @property
- def params(self):
- """Dict of parameters"""
- if self._params is None:
- self._fill_params()
- self._get_params()
- return self._params
-
- def _get_params(self):
- """Updates self._params from UI."""
- for i in self.entry:
- self._params[i] = self.entry[i].get_text()
-
- @params.setter
- def params(self, params):
- if self._params is None:
- self._fill_params()
- for i in self._params:
- try:
- self._params[i] = params[i]
- except KeyError as e:
- logger.warning("Invalid parameter key: %s" % e)
- self._set_params()
-
- def _set_params(self):
- """Updates UI with new parameters."""
- for i in self.entry:
- self.entry[i].set_text(self._params[i])
-
- def get_window(self):
- return self.builder.get_object('scrolledwindow1')
- def on_run_utility(self, data=None):
- self.emit('run_utility')
- def on_done_utility(self, data=None):
- self.emit('done_utility')
-
-
-class Chronoamp(ExpInterface):
- """Experiment class for chronoamperometry. Extends ExpInterface class to
- support treeview neeeded for CA.
-
- Public methods:
- on_add_button_clicked(self, widget)
- on_remove_button_clicked(self, widget)
- get_params(self)
- """
- id = 'cae'
- experiment = chronoamp.Chronoamp
- def __init__(self):
- """Extends superclass method to support treeview."""
- super(Chronoamp, self).__init__(os.path.join(mod_dir, 'chronoamp.glade'))
-
- self.name = "Chronoamperometry"
-
- self.statusbar = self.builder.get_object('statusbar')
- self.model = self.builder.get_object('ca_list')
- self.treeview = self.builder.get_object('treeview')
- self.treeview.set_fixed_height_mode(False)
-
- for i, column_title in enumerate(["Potential", "Time"]):
- renderer = Gtk.CellRendererText()
- column = Gtk.TreeViewColumn(column_title, renderer, text=i)
- column.set_expand(True)
- self.treeview.append_column(column)
-
- self.selection = self.treeview.get_selection()
- self.selection.set_mode(Gtk.SelectionMode.MULTIPLE)
-
- def _fill_params(self):
- super(Chronoamp, self)._fill_params()
- self._params['potential'] = []
- self._params['time'] = []
-
- def on_add_button_clicked(self, widget):
- """Add current values in potential_entry and time_entry to model."""
-
- self.statusbar.remove_all(0)
-
- try:
- potential = int(
- self.builder.get_object('potential_entry').get_text())
- time = int(self.builder.get_object('time_entry').get_text())
-
- if not state.board_instance.test_mv(potential):
- raise ValueError("Potential out of range")
- if not state.board_instance.test_s(time):
- raise ValueError("Time out of range")
-
- self.model.append([potential, time])
-
- except ValueError as err:
- self.statusbar.push(0, str(err))
- except TypeError as err:
- self.statusbar.push(0, str(err))
-
- def on_remove_button_clicked(self, widget):
- """Remove currently selected items from model."""
- # returns 2-tuple: treemodel, list of paths of selected rows
- selected_rows = list(self.selection.get_selected_rows()[1])
- referencelist = []
-
- for i in selected_rows:
- referencelist.append(Gtk.TreeRowReference(self.model, i))
-
- for i in referencelist:
- self.model.remove(self.model.get_iter(i.get_path()))
-
- def _get_params(self):
- """Updates self._params from UI. Overrides superclass method."""
-
- self._params['potential'] = [int(r[0]) for r in self.model]
- self._params['time'] = [int(r[1]) for r in self.model]
-
- def _set_params(self):
- """Updates UI from self._params. Overrides superclass method."""
-
- self.model.clear()
-
- table = zip(self._params['potential'], self._params['time'])
-
- for i in table:
- self.model.append(i)
-
-class LSV(ExpInterface):
- """Experiment class for LSV."""
- id = 'lsv'
- experiment = lsv.LSVExp
- def __init__(self):
- """Adds entry listings to superclass's self.entry dict"""
- super(LSV, self).__init__(os.path.join(mod_dir, 'lsv.glade'))
- self.name = "Linear Sweep Voltammetry"
-
- self.entry['clean_mV'] = self.builder.get_object('clean_mV')
- self.entry['clean_s'] = self.builder.get_object('clean_s')
- self.entry['dep_mV'] = self.builder.get_object('dep_mV')
- self.entry['dep_s'] = self.builder.get_object('dep_s')
- self.entry['start'] = self.builder.get_object('start_entry')
- self.entry['stop'] = self.builder.get_object('stop_entry')
- self.entry['slope'] = self.builder.get_object('slope_entry')
-
-class CV(ExpInterface):
- """Experiment class for CV."""
- id = 'cve'
- experiment = cv.CVExp
- def __init__(self):
- """Adds entry listings to superclass's self.entry dict"""
- super(CV, self).__init__(os.path.join(mod_dir, 'cv.glade'))
- self.name = "Cyclic Voltammetry"
-
- self.entry['clean_mV'] = self.builder.get_object('clean_mV')
- self.entry['clean_s'] = self.builder.get_object('clean_s')
- self.entry['dep_mV'] = self.builder.get_object('dep_mV')
- self.entry['dep_s'] = self.builder.get_object('dep_s')
- self.entry['start'] = self.builder.get_object('start_entry')
- self.entry['v1'] = self.builder.get_object('v1_entry')
- self.entry['v2'] = self.builder.get_object('v2_entry')
- self.entry['slope'] = self.builder.get_object('slope_entry')
- self.entry['scans'] = self.builder.get_object('scans_entry')
-
-class SWV(ExpInterface):
- """Experiment class for SWV."""
- id = 'swv'
- experiment = swv.SWVExp
- def __init__(self):
- """Adds entry listings to superclass's self.entry dict"""
- super(SWV, self).__init__(os.path.join(mod_dir, 'swv.glade'))
- self.name = "Square Wave Voltammetry"
-
- self.entry['clean_mV'] = self.builder.get_object('clean_mV')
- self.entry['clean_s'] = self.builder.get_object('clean_s')
- self.entry['dep_mV'] = self.builder.get_object('dep_mV')
- self.entry['dep_s'] = self.builder.get_object('dep_s')
- self.entry['start'] = self.builder.get_object('start_entry')
- self.entry['stop'] = self.builder.get_object('stop_entry')
- self.entry['step'] = self.builder.get_object('step_entry')
- self.entry['pulse'] = self.builder.get_object('pulse_entry')
- self.entry['freq'] = self.builder.get_object('freq_entry')
- self.entry['scans'] = self.builder.get_object('scans_entry')
-
- def _fill_params(self):
- super(SWV, self)._fill_params()
-
- self._params['cyclic_true'] = False
-
- def _get_params(self):
- """Updates self._params from UI."""
- super(SWV, self)._get_params()
-
- self._params['cyclic_true'] = self.builder.get_object(
- 'cyclic_checkbutton').get_active()
-
- def _set_params(self):
- """Updates UI with new parameters."""
- super(SWV, self)._set_params()
-
- self.builder.get_object('cyclic_checkbutton').set_active(
- self._params['cyclic_true'])
-
-class DPV(ExpInterface):
- """Experiment class for DPV."""
- id = 'dpv'
- experiment = swv.DPVExp
- def __init__(self):
- """Adds entry listings to superclass's self.entry dict"""
- super(DPV, self).__init__(os.path.join(mod_dir, 'dpv.glade'))
-
- self.name = "Differential Pulse Voltammetry"
-
- self.entry['clean_mV'] = self.builder.get_object('clean_mV')
- self.entry['clean_s'] = self.builder.get_object('clean_s')
- self.entry['dep_mV'] = self.builder.get_object('dep_mV')
- self.entry['dep_s'] = self.builder.get_object('dep_s')
- self.entry['start'] = self.builder.get_object('start_entry')
- self.entry['stop'] = self.builder.get_object('stop_entry')
- self.entry['step'] = self.builder.get_object('step_entry')
- self.entry['pulse'] = self.builder.get_object('pulse_entry')
- self.entry['period'] = self.builder.get_object('period_entry')
- self.entry['width'] = self.builder.get_object('width_entry')
-
-# class ACV(ExpInterface):
-# """Experiment class for ACV."""
-# id = 'acv'
-# def __init__(self):
-# """Adds entry listings to superclass's self.entry dict"""
-# super(ACV, self).__init__('interface/acv.glade')
-# self.name = "AC Voltammetry"
-#
-# self.entry['start'] = self.builder.get_object('start_entry')
-# self.entry['stop'] = self.builder.get_object('stop_entry')
-# self.entry['slope'] = self.builder.get_object('slope_entry')
-# self.entry['amplitude'] = self.builder.get_object('amplitude_entry')
-# self.entry['freq'] = self.builder.get_object('freq_entry')
-
-class PD(ExpInterface):
- """Experiment class for PD."""
- id = 'pde'
- experiment = chronoamp.PDExp
- def __init__(self):
- """Adds entry listings to superclass's self.entry dict"""
- super(PD, self).__init__(os.path.join(mod_dir, 'pd.glade'))
- self.name = "Photodiode/PMT"
-
-
- self.entry['time'] = self.builder.get_object('time_entry')
- self.entry['sync_freq'] = self.builder.get_object('sync_freq')
- self.entry['fft_start'] = self.builder.get_object('fft_entry')
- self.entry['fft_int'] = self.builder.get_object('fft_int_entry')
-
- self.buttons = map(self.builder.get_object,
- ['light_button', 'threshold_button'])
-
- self.shutter_buttons = map(
- self.builder.get_object,
- ['sync_button', 'sync_freq', 'fft_label', 'fft_entry', 'fft_label2',
- 'fft_int_entry']
- )
-
- bool_keys = ['interlock_true', 'shutter_true', 'sync_true']
- bool_cont = map(self.builder.get_object,
- ['interlock_button',
- 'shutter_button',
- 'sync_button']
- )
- self.bool = dict(zip(bool_keys, bool_cont))
-
- def _fill_params(self):
- super(PD, self)._fill_params()
-
- for i in self.bool:
- self._params[i] = self.bool[i].get_active()
- self._params['voltage'] = 0
-
- def _get_params(self):
- """Updates self._params from UI."""
- super(PD, self)._get_params()
-
- for i in self.bool:
- self._params[i] = self.bool[i].get_active()
-
- self._params['voltage'] = self.builder.get_object(
- 'voltage_adjustment').get_value()
-
- def _set_params(self):
- """Updates UI with new parameters."""
- super(PD, self)._set_params()
-
- for i in self.bool:
- self.bool[i].set_active(self._params[i])
-
- self.builder.get_object('voltage_adjustment').set_value(
- self._params['voltage'])
-
- def on_light_button_clicked(self, data=None):
- __main__.MAIN.on_pot_stop_clicked()
- __main__.MAIN.stop_ocp()
-
- for i in self.buttons:
- i.set_sensitive(False)
-
- try:
- self.builder.get_object('light_label').set_text(str(
- dstat_comm.read_light_sensor()))
- comm.read_settings()
- state.settings['tcs_enabled'][1] = '1' # Make sure TCS enabled
- comm.write_settings()
-
- self.builder.get_object('threshold_entry').set_text(str(
- state.settings['tcs_clear_threshold'][1]))
- __main__.MAIN.start_ocp()
-
- finally:
- GObject.timeout_add(700, restore_buttons, self.buttons)
-
- def on_threshold_button_clicked(self, data=None):
- __main__.MAIN.on_pot_stop_clicked()
- __main__.MAIN.stop_ocp()
-
- for i in self.buttons:
- i.set_sensitive(False)
-
- try:
- state.settings['tcs_clear_threshold'][1] = self.builder.get_object(
- 'threshold_entry').get_text()
- comm.write_settings()
- comm.read_settings()
- self.builder.get_object('threshold_entry').set_text(
- str(state.settings['tcs_clear_threshold'][1]))
- __main__.MAIN.start_ocp()
-
- finally:
- GObject.timeout_add(700, restore_buttons, self.buttons)
-
- def on_shutter_button_toggled(self, widget):
- if self.bool['shutter_true'].get_active():
- for i in self.shutter_buttons:
- i.set_sensitive(True)
- else:
- for i in self.shutter_buttons:
- i.set_sensitive(False)
-
-
-class POT(ExpInterface):
- """Experiment class for Potentiometry."""
- id = 'pot'
- experiment = pot.PotExp
- def __init__(self):
- """Adds entry listings to superclass's self.entry dict"""
- super(POT, self).__init__(os.path.join(mod_dir, 'potexp.glade'))
- self.name = "Potentiometry"
-
- self.entry['time'] = self.builder.get_object('time_entry')
-
-class CAL(ExpInterface):
- """Experiment class for Calibrating gain."""
- id = 'cal'
- experiment = cal.CALExp
- def __init__(self):
- """Adds entry listings to superclass's self.entry dict"""
- super(CAL, self).__init__(os.path.join(mod_dir, 'calib.glade'))
- self.name = "Calilbration"
-
- self.entry['time'] = self.builder.get_object('time_entry')
- self.entry['R100'] = self.builder.get_object('100_entry')
- self.entry['R3k'] = self.builder.get_object('3k_entry')
- self.entry['R30k'] = self.builder.get_object('30k_entry')
- self.entry['R300k'] = self.builder.get_object('300k_entry')
- self.entry['R3M'] = self.builder.get_object('3M_entry')
- self.entry['R30M'] = self.builder.get_object('30M_entry')
- self.entry['R100M'] = self.builder.get_object('100M_entry')
-
- self.buttons = [self.builder.get_object('read_button'),
- self.builder.get_object('write_button'),
- self.builder.get_object('measure_button')]
-
- def on_read_button_clicked(self, data=None):
- for i in self.buttons:
- i.set_sensitive(False)
-
- try:
- __main__.MAIN.on_pot_stop_clicked()
- __main__.MAIN.stop_ocp()
- comm.read_settings()
-
- self.entry['R100'].set_text(str(
- state.settings['r100_trim'][1]))
- self.entry['R3k'].set_text(str(
- state.settings['r3k_trim'][1]))
- self.entry['R30k'].set_text(str(
- state.settings['r30k_trim'][1]))
- self.entry['R300k'].set_text(str(
- state.settings['r300k_trim'][1]))
- self.entry['R3M'].set_text(str(
- state.settings['r3M_trim'][1]))
- self.entry['R30M'].set_text(str(
- state.settings['r30M_trim'][1]))
- self.entry['R100M'].set_text(str(
- state.settings['r100M_trim'][1]))
-
- __main__.MAIN.start_ocp()
-
- finally:
- GObject.timeout_add(700, restore_buttons, self.buttons)
-
- def on_write_button_clicked(self, data=None):
- for i in self.buttons:
- i.set_sensitive(False)
-
- try:
- __main__.MAIN.on_pot_stop_clicked()
- __main__.MAIN.stop_ocp()
-
- state.settings['r100_trim'][1] = self.entry['R100'].get_text()
- state.settings['r3k_trim'][1] = self.entry['R3k'].get_text()
- state.settings['r30k_trim'][1] = self.entry['R30k'].get_text()
- state.settings['r300k_trim'][1] = self.entry['R300k'].get_text()
- state.settings['r3M_trim'][1] = self.entry['R3M'].get_text()
- state.settings['r30M_trim'][1] = self.entry['R30M'].get_text()
- state.settings['r100M_trim'][1] = self.entry['R100M'].get_text()
- comm.write_settings()
-
- __main__.MAIN.start_ocp()
-
- finally:
- GObject.timeout_add(700, restore_buttons, self.buttons)
-
- def on_measure_button_clicked(self, data=None):
- if int(self.entry['time'].get_text()) <= 0 or int(self.entry['time'].get_text()) > 65535:
- logger.error("ERR: Time out of range")
- return
-
- for i in self.buttons:
- i.set_sensitive(False)
-
- try:
- __main__.MAIN.stop_ocp()
- __main__.MAIN.spinner.start()
-
- offset = cal.measure_offset(self.params['time'])
-
- for i in offset:
- logger.info("{} {}".format(i, str(-offset[i])))
- state.settings[i][1] = str(-offset[i])
-
- self.entry['R100'].set_text(str(
- state.settings['r100_trim'][1]))
- self.entry['R3k'].set_text(str(
- state.settings['r3k_trim'][1]))
- self.entry['R30k'].set_text(str(
- state.settings['r30k_trim'][1]))
- self.entry['R300k'].set_text(str(
- state.settings['r300k_trim'][1]))
- self.entry['R3M'].set_text(str(
- state.settings['r3M_trim'][1]))
- self.entry['R30M'].set_text(str(
- state.settings['r30M_trim'][1]))
- self.entry['R100M'].set_text(str(
- state.settings['r100M_trim'][1]))
- __main__.MAIN.start_ocp()
-
- finally:
- GObject.timeout_add(700, restore_buttons, self.buttons)
- __main__.MAIN.spinner.stop()
-
-
-def restore_buttons(buttons):
- """ Should be called with GObject callback """
- for i in buttons:
- i.set_sensitive(True)
-
- return False
\ No newline at end of file
diff --git a/dstat_interface/core/interface/exp_window.py b/dstat_interface/core/interface/exp_window.py
deleted file mode 100755
index 61906b5..0000000
--- a/dstat_interface/core/interface/exp_window.py
+++ /dev/null
@@ -1,129 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import inspect
-import logging
-from collections import OrderedDict
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print "ERR: GTK not available"
- sys.exit(1)
-
-from . import exp_int
-
-logger = logging.getLogger(__name__)
-
-
-class Experiments(GObject.Object):
- __gsignals__ = {
- 'run_utility': (GObject.SIGNAL_RUN_FIRST, None, ()),
- 'done_utility': (GObject.SIGNAL_RUN_FIRST, None, ())
- }
-
- def __init__(self, builder):
- super(Experiments,self).__init__()
- self.builder = builder
- self.builder.connect_signals(self)
-
- # (experiment index in UI, experiment)
-
- classes = {c.id : c() # Make class instances
- for _, c in inspect.getmembers(exp_int, inspect.isclass)
- if issubclass(c, exp_int.ExpInterface)
- and c is not exp_int.ExpInterface
- }
-
- self.classes = OrderedDict(sorted(classes.items()))
-
- # fill exp_section
- exp_section = self.builder.get_object('exp_section_box')
- self.containers = {}
-
- for key, c in self.classes.items():
- c.connect('run_utility', self.on_run_utility)
- c.connect('done_utility', self.on_done_utility)
- self.containers[key] = c.get_window()
-
- for key in self.containers:
- try:
- self.containers[key].get_parent().remove(self.containers[key])
- except AttributeError:
- pass
-
- exp_section.add(self.containers[key])
-
- self.expcombobox = self.builder.get_object('expcombobox')
- self.expcombobox.connect('changed', self.on_expcombobox_changed)
-
- for c in self.classes.values():
- self.expcombobox.append(id=c.id, text=c.name)
-
- def on_run_utility(self, data=None):
- self.emit('run_utility')
-
- def on_done_utility(self, data=None):
- self.emit('done_utility')
-
- def on_expcombobox_changed(self, data=None):
- """Change the experiment window when experiment box changed."""
- self.set_exp(self.expcombobox.get_active_id())
-
- def setup_exp(self, parameters):
- """Takes parameters.
- Returns experiment instance.
- """
- exp = self.classes[self.expcombobox.get_active_id()]
- try:
- exp.param_test(parameters)
- except AttributeError:
- logger.warning(
- "Experiment {} has no defined parameter test.".format(
- exp.name)
- )
- return exp.get_experiment(parameters)
-
- def hide_exps(self):
- for key in self.containers:
- self.containers[key].hide()
-
- def set_exp(self, selection):
- """Changes parameter tab to selected experiment. Returns True if
- successful, False if invalid selection received.
-
- Arguments:
- selection -- id string of experiment type
- """
- self.hide_exps()
- self.containers[selection].show()
- self.selected_exp = selection
-
- return True
-
- def get_params(self, experiment):
- return self.classes[experiment].params
-
- def set_params(self, experiment, parameters):
- try:
- self.classes[experiment].params = parameters
- except KeyError as e:
- logger.warning("Tried to load inavlid experiment with id %s", e.args)
\ No newline at end of file
diff --git a/dstat_interface/core/interface/hw_info.py b/dstat_interface/core/interface/hw_info.py
deleted file mode 100755
index 3a8228b..0000000
--- a/dstat_interface/core/interface/hw_info.py
+++ /dev/null
@@ -1,110 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from __future__ import (absolute_import, division,
- print_function, unicode_literals)
-
-from ..dstat import state, dfu
-from ..dstat.comm import dstat_logger, exp_logger
-
-import logging
-import time
-import serial
-
-logger = logging.getLogger(__name__)
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print("ERR: GTK not available")
- sys.exit(1)
-
-class InfoDialog(object):
- def __init__(self, parent, connect, signal='activate'):
- self.parent = parent
- connect.connect(signal, self.activate)
-
- def activate(self, object=None, data=None):
- self.dialog = Gtk.MessageDialog(self.parent, 0, Gtk.MessageType.INFO,
- Gtk.ButtonsType.OK, "DStat Info")
- self.dialog.format_secondary_text(
- "PCB Version: {}\n".format(state.dstat_version.base_version) +
- "Firmware Version: {}".format(state.firmware_version)
- )
-
- self.dialog.connect('response', self.destroy)
- self.dialog.show()
-
- def destroy(self, object=None, data=None):
- self.dialog.destroy()
-
-
-class ResetDialog(object):
- def __init__(self, parent, connect, stop_callback, disconnect_callback, signal='activate'):
- self.parent = parent
- self.stop = stop_callback
- self.disconnect = disconnect_callback
- connect.connect(signal, self.activate)
-
- def activate(self, object=None, data=None):
- dialog = Gtk.MessageDialog(self.parent, 0, Gtk.MessageType.WARNING,
- Gtk.ButtonsType.OK_CANCEL, "EEPROM Reset")
- dialog.format_secondary_text("This will reset the DStat's EEPROM settings, then disconneect."
- )
-
- response = dialog.run()
- if response == Gtk.ResponseType.OK:
- self.dstat_reset_eeprom()
- dialog.destroy()
-
- def dstat_reset_eeprom(self):
- """Tries to contact DStat and resets EEPROM.
- If no response, returns False, otherwise True.
- """
- self.stop()
- exp = EEPROMReset()
- state.ser.start_exp(exp)
- logger.info("Resetting DStat EEPROM…")
- while True:
- result = state.ser.get_proc(block=True)
- if result in ('SERIAL_ERROR', 'DONE', 'ABORT'):
- break
- logger.info(result)
-
- self.disconnect()
-
-
-class EEPROMReset(object):
- def __init__(self):
- pass
-
- def run(self, ser, ctrl_pipe, data_pipe):
- status = None
- try:
- ser.write(b'!2\n')
- exp_logger.info('!2')
-
- for i in range(10):
- if ser.readline().rstrip() == b"@ACK 2":
- dstat_logger.info('@ACK 2')
- ser.write(b'SD\n')
- exp_logger.info('SD')
- status = "DONE"
- time.sleep(5)
- break
- else:
- time.sleep(.5)
- ser.reset_input_buffer()
- ser.write(b'!2\n')
- exp_logger.info('!2')
- time.sleep(.1)
-
- except UnboundLocalError as e:
- status = "SERIAL_ERROR"
- except serial.SerialException as e:
- logger.error('SerialException: %s', e)
- status = "SERIAL_ERROR"
- finally:
- return status
\ No newline at end of file
diff --git a/dstat_interface/core/interface/lsv.glade b/dstat_interface/core/interface/lsv.glade
deleted file mode 100644
index 404e1e4..0000000
--- a/dstat_interface/core/interface/lsv.glade
+++ /dev/null
@@ -1,307 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkFrame" id="frame1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Potential (mV)</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Cleaning</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Deposition</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Preconditioning</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkFrame" id="frame2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Start (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label9">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Stop (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label10">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Slope (mV/s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="start_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="stop_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="slope_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/pd.glade b/dstat_interface/core/interface/pd.glade
deleted file mode 100644
index c39930e..0000000
--- a/dstat_interface/core/interface/pd.glade
+++ /dev/null
@@ -1,348 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkAdjustment" id="voltage_adjustment">
- <property name="upper">3000</property>
- <property name="step_increment">1</property>
- <property name="page_increment">10</property>
- </object>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkEntry" id="time_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Bias Voltage (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Measurement Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkSpinButton" id="spinbutton1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">4</property>
- <property name="invisible_char">â—</property>
- <property name="text" translatable="yes">0</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- <property name="adjustment">voltage_adjustment</property>
- <property name="climb_rate">1</property>
- <property name="snap_to_ticks">True</property>
- <property name="numeric">True</property>
- <property name="wrap">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Ambient Light Interlock</property>
- <attributes>
- <attribute name="weight" value="bold"/>
- </attributes>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="interlock_button">
- <property name="label" translatable="yes">Enable interlock</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="active">True</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="threshold_button">
- <property name="label" translatable="yes">Set threshold</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="halign">center</property>
- <signal name="clicked" handler="on_threshold_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="threshold_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkButton" id="light_button">
- <property name="label" translatable="yes">Refresh light measurement</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">True</property>
- <property name="halign">center</property>
- <signal name="clicked" handler="on_light_button_clicked" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="light_label">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">0</property>
- <property name="justify">center</property>
- <property name="track_visited_links">False</property>
- <attributes>
- <attribute name="weight" value="medium"/>
- </attributes>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Electromechanical Shutter</property>
- <attributes>
- <attribute name="weight" value="bold"/>
- </attributes>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">7</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="sync_button">
- <property name="label" translatable="yes">Synchronous Detection (Hz)</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="halign">center</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">8</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="sync_freq">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">8</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="shutter_button">
- <property name="label" translatable="yes">Enable Shutter</property>
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="active">True</property>
- <property name="draw_indicator">True</property>
- <signal name="toggled" handler="on_shutter_button_toggled" swapped="no"/>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">7</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="fft_label">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Start FFT after (s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">9</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="fft_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">2</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text">1</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">9</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="fft_label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">FFT Integral bandwidth (Hz)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">10</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="fft_int_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="max_length">6</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text">1</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">10</property>
- </packing>
- </child>
- <child>
- <object class="GtkSeparator">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="margin_top">5</property>
- <property name="margin_bottom">5</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- <property name="width">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkSeparator">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="margin_top">5</property>
- <property name="margin_bottom">5</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">6</property>
- <property name="width">2</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label13">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <attributes>
- <attribute name="weight" value="bold"/>
- </attributes>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/plot.py b/dstat_interface/core/interface/plot.py
deleted file mode 100755
index 7e87c41..0000000
--- a/dstat_interface/core/interface/plot.py
+++ /dev/null
@@ -1,94 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-"""
-Creates data plot.
-"""
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk
-except ImportError:
- print "ERR: GTK not available"
- sys.exit(1)
-
-from matplotlib.figure import Figure
-
-from matplotlib.backends.backend_gtk3agg \
- import FigureCanvasGTK3Agg as FigureCanvas
-from matplotlib.backends.backend_gtk3 \
- import NavigationToolbar2GTK3 as NavigationToolbar
-try:
- import seaborn as sns
-except ImportError:
- pass
-
-from numpy import sin, linspace, pi, mean, trapz
-from scipy import fft, arange
-
-def plotSpectrum(y,Fs):
- """
- Plots a Single-Sided Amplitude Spectrum of y(t)
- """
- y = y-mean(y)
- n = len(y) # length of the signal
- k = arange(n)
- T = n/Fs
- frq = k/T # two sides frequency range
- frq = frq[range(n/2)] # one side frequency range
- Y = fft(y)/n # fft computing and normalization
- Y = abs(Y[range(n/2)])
-
- return (frq, Y)
-
-def integrateSpectrum(x, y, target, bandwidth):
- """
- Returns integral of range of bandwidth centered on target (both in Hz).
- """
- j = 0
- k = len(x)
-
- for i in range(len(x)):
- if x[i] >= target-bandwidth/2:
- j = i
- break
-
- for i in range(j,len(x)):
- if x[i] >= target+bandwidth/2:
- k = i
- break
-
- return trapz(y=y[j:k], x=x[j:k])
-
-def findBounds(y):
- start_index = 0;
- stop_index = len(y)-1;
-
- for i in range(len(y)):
- if (y[i] <= mean(y) and y[i+1] > mean(y)):
- start_index = i
- break
-
- for i in range(len(y)):
- if (y[-(i+1)] <= mean(y) and y[-i] > mean(y)):
- stop_index = len(y)-1-i # len(y) is last index + 1
- break
-
- return (start_index, stop_index)
-
diff --git a/dstat_interface/core/interface/plot_ui.py b/dstat_interface/core/interface/plot_ui.py
deleted file mode 100644
index b0013e8..0000000
--- a/dstat_interface/core/interface/plot_ui.py
+++ /dev/null
@@ -1,33 +0,0 @@
-import logging
-logger = logging.getLogger(__name__)
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk
-except ImportError:
- print "ERR: GTK not available"
- sys.exit(1)
-
-from matplotlib.backends.backend_gtk3 \
- import NavigationToolbar2GTK3 as NavigationToolbar
-
-def clear_notebook(notebook):
- for pages in range(notebook.get_n_pages()):
- notebook.remove_page(0)
-
-def add_exp_to_notebook(notebook, exp):
- for plot in exp.plots:
- label = Gtk.Label.new(plot.name)
- notebook.append_page(plot.box, label)
- plot.box.show_all()
-
-def replace_notebook_exp(notebook, exp, window):
- clear_notebook(notebook)
- add_exp_to_notebook(notebook, exp)
- add_navigation_toolbars(exp, window)
-
-def add_navigation_toolbars(exp, window):
- for plot in exp.plots:
- toolbar = NavigationToolbar(plot.canvas, window)
- plot.box.pack_start(toolbar, expand=False, fill=False, padding=0)
\ No newline at end of file
diff --git a/dstat_interface/core/interface/potexp.glade b/dstat_interface/core/interface/potexp.glade
deleted file mode 100644
index d4ec1e6..0000000
--- a/dstat_interface/core/interface/potexp.glade
+++ /dev/null
@@ -1,97 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkListStore" id="ca_list">
- <columns>
- <!-- column-name millivolts -->
- <column type="gint"/>
- <!-- column-name seconds -->
- <column type="guint"/>
- </columns>
- </object>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <property name="default_width">300</property>
- <property name="default_height">500</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="time_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">5</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="truncate_multiline">True</property>
- <property name="caps_lock_warning">False</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Connect the electrodes to the RE input and the W_SHIELD connectors.
-The ADC's PGA can be used to amplify the input signal, but note that the plot's y-axis is only correct for PGA 2x.</property>
- <property name="wrap">True</property>
- <property name="width_chars">30</property>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">1</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/interface/save.py b/dstat_interface/core/interface/save.py
deleted file mode 100755
index 44a7884..0000000
--- a/dstat_interface/core/interface/save.py
+++ /dev/null
@@ -1,226 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-from __future__ import division, absolute_import, print_function, unicode_literals
-
-import io
-import os
-import logging
-logger = logging.getLogger(__name__)
-
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk
-except ImportError:
- print("ERR: GTK not available")
- sys.exit(1)
-import numpy as np
-
-from ..errors import InputError, VarError
-from ..params import save_params, load_params
-
-def manSave(current_exp):
- fcd = Gtk.FileChooserDialog("Save…", None, Gtk.FileChooserAction.SAVE,
- (Gtk.STOCK_CANCEL, Gtk.ResponseType.CANCEL,
- Gtk.STOCK_SAVE, Gtk.ResponseType.OK))
-
- filters = [Gtk.FileFilter()]
- filters[0].set_name("Tab-separated Text (.txt)")
- filters[0].add_pattern("*.txt")
-
- fcd.set_do_overwrite_confirmation(True)
- for i in filters:
- fcd.add_filter(i)
-
- response = fcd.run()
-
- if response == Gtk.ResponseType.OK:
- path = fcd.get_filename().decode("utf-8")
- logger.info("Selected filepath: %s", path)
- filter_selection = fcd.get_filter().get_name().decode("utf-8")
-
- if filter_selection.endswith("(.txt)"):
- save_text(current_exp, path)
-
- fcd.destroy()
-
- elif response == Gtk.ResponseType.CANCEL:
- fcd.destroy()
-
-def plot_save_dialog(plots):
- fcd = Gtk.FileChooserDialog("Save Plot…", None,
- Gtk.FileChooserAction.SAVE,
- (Gtk.STOCK_CANCEL, Gtk.ResponseType.CANCEL,
- Gtk.STOCK_SAVE, Gtk.ResponseType.OK))
-
- filters = [Gtk.FileFilter()]
- filters[0].set_name("Portable Document Format (.pdf)")
- filters[0].add_pattern("*.pdf")
- filters.append(Gtk.FileFilter())
- filters[1].set_name("Portable Network Graphics (.png)")
- filters[1].add_pattern("*.png")
-
- fcd.set_do_overwrite_confirmation(True)
- for i in filters:
- fcd.add_filter(i)
-
- response = fcd.run()
-
- if response == Gtk.ResponseType.OK:
- path = fcd.get_filename().decode("utf-8")
- logger.info("Selected filepath: %r", path)
- filter_selection = fcd.get_filter().get_name().decode("utf-8")
-
- if filter_selection.endswith("(.pdf)"):
- if not path.endswith(".pdf"):
- path += ".pdf"
-
- elif filter_selection.endswith("(.png)"):
- if not path.endswith(".png"):
- path += ".png"
-
- save_plot(plots, path)
-
- fcd.destroy()
-
- elif response == Gtk.ResponseType.CANCEL:
- fcd.destroy()
-
-
-def man_param_save(window):
- fcd = Gtk.FileChooserDialog("Save Parameters…",
- None,
- Gtk.FileChooserAction.SAVE,
- (Gtk.STOCK_CANCEL, Gtk.ResponseType.CANCEL,
- Gtk.STOCK_SAVE, Gtk.ResponseType.OK))
-
- filters = [Gtk.FileFilter()]
- filters[0].set_name("Parameter File (.yml)")
- filters[0].add_pattern("*.yml")
-
- fcd.set_do_overwrite_confirmation(True)
- for i in filters:
- fcd.add_filter(i)
-
- response = fcd.run()
-
- if response == Gtk.ResponseType.OK:
- path = fcd.get_filename().decode("utf-8")
- logger.info("Selected filepath: %s", path)
-
- if not path.endswith(".yml"):
- path += '.yml'
-
- save_params(window, path)
-
- fcd.destroy()
-
- elif response == Gtk.ResponseType.CANCEL:
- fcd.destroy()
-
-def man_param_load(window):
- fcd = Gtk.FileChooserDialog("Load Parameters…",
- None,
- Gtk.FileChooserAction.OPEN,
- (Gtk.STOCK_CANCEL, Gtk.ResponseType.CANCEL,
- Gtk.STOCK_OPEN, Gtk.ResponseType.OK))
-
- filters = [Gtk.FileFilter()]
- filters[0].set_name("Parameter File (.yml)")
- filters[0].add_pattern("*.yml")
-
- for i in filters:
- fcd.add_filter(i)
-
- response = fcd.run()
-
- if response == Gtk.ResponseType.OK:
- path = fcd.get_filename().decode("utf-8")
- logger.info("Selected filepath: %s", path)
-
- load_params(window, path)
-
- fcd.destroy()
-
- elif response == Gtk.ResponseType.CANCEL:
- fcd.destroy()
-
-def autoSave(exp, path, name):
- if name == "":
- name = "file"
-
- path += '/'
- path += name
-
- save_text(exp, path)
-
-def autoPlot(exp, path, name):
- if name == "":
- name = "file"
-
- path += '/'
- path += name
-
- if not (path.endswith(".pdf") or path.endswith(".png")):
- path += ".pdf"
-
- save_plot(exp, path)
-
-def save_text(exp, path):
- savestrings = exp.get_save_strings()
- path = path.rstrip('.txt')
-
- num = ''
- j = 0
-
- for key, text in savestrings.items(): # Test for existing files of any kind
- while os.path.exists("{}{}-{}.txt".format(path, num, key)):
- j += 1
- num = j
-
- save_path = "{}{}".format(path, num)
-
- for key, text in savestrings.items():
- with open('{}-{}.txt'.format(save_path, key), 'w') as f:
- f.write(text)
-
-def save_plot(exp, path):
- """Saves everything in exp.plots to path. Appends a number for duplicates.
- If no file extension or unknown, uses pdf.
- """
- name, _sep, ext = path.rpartition('.')
- if _sep == '':
- name = ext
- ext = 'pdf'
-
- num = ''
- j = 0
-
- for i in exp.plots: # Test for any existing files
- plot_type = '_'.join(i.name.lower().split())
- while os.path.exists("{}{}-{}.{}".format(name, num, plot_type, ext)):
- j += 1
- num = j
-
- for i in exp.plots: # save data
- plot_type = '_'.join(i.name.lower().split())
- i.figure.savefig("{}{}-{}.{}".format(name, num, plot_type, ext))
\ No newline at end of file
diff --git a/dstat_interface/core/interface/swv.glade b/dstat_interface/core/interface/swv.glade
deleted file mode 100644
index 0a1e326..0000000
--- a/dstat_interface/core/interface/swv.glade
+++ /dev/null
@@ -1,433 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Generated with glade 3.20.0 -->
-<interface>
- <requires lib="gtk+" version="3.10"/>
- <object class="GtkWindow" id="window1">
- <property name="can_focus">False</property>
- <child>
- <object class="GtkScrolledWindow" id="scrolledwindow1">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="hexpand">True</property>
- <property name="vexpand">True</property>
- <child>
- <object class="GtkViewport" id="viewport1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="shadow_type">none</property>
- <child>
- <object class="GtkBox" id="vbox1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="orientation">vertical</property>
- <child>
- <object class="GtkFrame" id="frame1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkLabel" id="label3">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Potential (mV)</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label4">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Time (s)</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label5">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label6">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Cleaning</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label7">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Deposition</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_mV">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="dep_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="clean_s">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">2</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <placeholder/>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label1">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Preconditioning</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkFrame" id="frame2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label_xalign">0</property>
- <property name="shadow_type">out</property>
- <child>
- <object class="GtkAlignment" id="alignment2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="bottom_padding">5</property>
- <property name="left_padding">5</property>
- <property name="right_padding">5</property>
- <child>
- <object class="GtkGrid">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="row_homogeneous">True</property>
- <property name="column_homogeneous">True</property>
- <child>
- <object class="GtkEntry" id="scans_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">6</property>
- </packing>
- </child>
- <child>
- <object class="GtkCheckButton" id="cyclic_checkbutton">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="receives_default">False</property>
- <property name="halign">center</property>
- <property name="valign">center</property>
- <property name="use_stock">True</property>
- <property name="draw_indicator">True</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label15">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Scans</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">6</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label14">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="tooltip_text" translatable="yes">Scan both forwards and backwards.</property>
- <property name="label" translatable="yes">Cyclic Mode</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">5</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="freq_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="pulse_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label12">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Frequency (Hz)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">4</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label11">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Pulse Height (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">3</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="step_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="stop_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkEntry" id="start_entry">
- <property name="visible">True</property>
- <property name="can_focus">True</property>
- <property name="invisible_char">â—</property>
- <property name="width_chars">8</property>
- <property name="text" translatable="yes">0</property>
- <property name="xalign">1</property>
- <property name="primary_icon_activatable">False</property>
- <property name="secondary_icon_activatable">False</property>
- </object>
- <packing>
- <property name="left_attach">1</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label10">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Step Size (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">2</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label9">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Stop (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label8">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Start (mV)</property>
- </object>
- <packing>
- <property name="left_attach">0</property>
- <property name="top_attach">0</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- <child type="label">
- <object class="GtkLabel" id="label2">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Experiment</property>
- <property name="use_markup">True</property>
- </object>
- </child>
- </object>
- <packing>
- <property name="expand">False</property>
- <property name="fill">False</property>
- <property name="padding">2</property>
- <property name="position">1</property>
- </packing>
- </child>
- <child>
- <object class="GtkLabel" id="label13">
- <property name="visible">True</property>
- <property name="can_focus">False</property>
- <property name="label" translatable="yes">Note: ADC samples 1/(ADC Frequency) before end of pulse. ADC frequency should be significantly larger than SWV frequency to reduce capacitive current.</property>
- <property name="wrap">True</property>
- <property name="wrap_mode">word-char</property>
- <property name="width_chars">43</property>
- </object>
- <packing>
- <property name="expand">True</property>
- <property name="fill">True</property>
- <property name="position">2</property>
- </packing>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
- </child>
- </object>
-</interface>
diff --git a/dstat_interface/core/microdrop.py b/dstat_interface/core/microdrop.py
deleted file mode 100644
index 3970bfa..0000000
--- a/dstat_interface/core/microdrop.py
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-import zmq
-
-#signals
-CONREQ = "0"
-CONREP = "1"
-STARTEXP = "start"
-START_REP = "started"
-EXP_FINISH_REQ = "notify_completion"
-EXPFINISHED = "completed"
-INVAL_CMD = "99"
-
-#States
-RECV = 0
-SEND = 1
-
-class microdropConnection(object):
- """Manages microdrop connection over TCP with zmq"""
- def __init__(self, port=6789):
- """Create zmq context and bind to port. Should be called manually
- to reinitialize if reset is called.
-
- Keyword arguments:
- port -- the TCP to bind to on localhost
- """
- self.port = port
- self.connected = False
- self.state = RECV
-
- self.ctx = zmq.Context()
- self.soc = zmq.Socket(self.ctx, zmq.REP)
- self.soc.bind("".join(['tcp://*:', str(self.port)]))
-
- def listen(self):
- """Perform non-blocking recv on zmq port. self.state must be RECV.
- Returns a tuple:
- [0] -- True if a message was received, False otherwise.
- [1] -- The recieved message or "" if no message received.
- """
- if self.state == SEND:
- print "WAR: [uDrop-listen] Connection state invalid, resetting..."
- # self.reset()
- # self.__init__(self.port)
- return (False, "")
-
- try:
- message = self.soc.recv(flags=zmq.NOBLOCK, copy=True)
- self.state = SEND
- return (True, message)
- except zmq.Again:
- return (False, "")
-
- def reply(self, data):
- """Sends a reply on zmq port. self.state must be SEND.
-
- Arguments:
- data -- a str to be sent
- """
- if self.state == RECV:
- print "WAR: [uDrop-reply] Connection state invalid, resetting..."
- self.reset()
- self.__init__(self.port)
- return False
- self.state = RECV
- self.soc.send(data)
- return True
-
- def reset(self):
- """Reset zmq interface. Must call __init__ again to reinitialize."""
- self.soc.unbind("".join(['tcp://*:', str(self.port)]))
- del self.soc
- del self.ctx
diff --git a/dstat_interface/core/params.py b/dstat_interface/core/params.py
deleted file mode 100755
index 63c1ae3..0000000
--- a/dstat_interface/core/params.py
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-import logging
-
-import yaml
-
-from errors import InputError
-
-logger = logging.getLogger(__name__)
-
-
-def get_params(window):
- """Fetches and returns dict of all parameters for saving."""
-
- selection = window.exp_window.expcombobox.get_active_id()
- parameters = {'experiment_index' : selection}
-
- try:
- parameters['version'] = window.version
- except AttributeError: # Will be thrown if not connected to DStat
- pass
-
- try:
- parameters.update(window.adc_pot.params)
- except InputError:
- logger.info("No gain selected.")
- parameters.update(window.exp_window.get_params(selection))
- parameters.update(window.analysis_opt_window.params)
-
- return parameters
-
-
-def save_params(window, path):
- """Fetches current params and saves to path."""
- logger.info("Save to: %s", path)
- params = get_params(window)
-
- with open(path, 'w') as f:
- yaml.dump(params, f)
-
-
-def load_params(window, path):
- """Loads params from a path into UI elements."""
-
- try:
- get_params(window)
- except InputError: # Will be thrown because no experiment will be selected
- pass
- except KeyError: # Will be thrown because no experiment will be selected
- pass
-
- with open(path, 'r') as f:
- params = yaml.load(f)
- set_params(window, params)
-
-
-def set_params(window, params):
- window.adc_pot.params = params
- if 'experiment_index' in params:
- window.exp_window.expcombobox.set_active_id(params['experiment_index'])
- window.exp_window.set_params(params['experiment_index'], params)
-
- window.analysis_opt_window.params = params
-
- window.params_loaded = True
diff --git a/dstat_interface/core/plugin.py b/dstat_interface/core/plugin.py
deleted file mode 100644
index 59ec93d..0000000
--- a/dstat_interface/core/plugin.py
+++ /dev/null
@@ -1,161 +0,0 @@
-# -*- coding: utf-8 -*-
-import logging
-
-from params import get_params, set_params, load_params, save_params
-from interface.save import save_text, save_plot
-from zmq_plugin.plugin import Plugin as ZmqPlugin
-from zmq_plugin.schema import decode_content_data
-import gtk
-import zmq
-
-logger = logging.getLogger(__name__)
-
-
-def get_hub_uri(default='tcp://localhost:31000', parent=None):
- message = 'Please enter 0MQ hub URI:'
- d = gtk.MessageDialog(parent=parent, flags=gtk.DIALOG_MODAL |
- gtk.DIALOG_DESTROY_WITH_PARENT,
- type=gtk.MESSAGE_INFO, buttons=gtk.BUTTONS_OK_CANCEL,
- message_format=message)
- entry = gtk.Entry()
- entry.set_text(default)
- d.vbox.pack_end(entry)
- d.vbox.show_all()
- entry.connect('activate', lambda _: d.response(gtk.RESPONSE_OK))
- d.set_default_response(gtk.RESPONSE_OK)
-
- r = d.run()
- text = entry.get_text().decode('utf8')
- d.destroy()
- if r == gtk.RESPONSE_OK:
- return text
- else:
- return None
-
-
-class DstatPlugin(ZmqPlugin):
- '''
- Public 0MQ plugin API.
- '''
- def __init__(self, parent, *args, **kwargs):
- self.parent = parent
- super(DstatPlugin, self).__init__(*args, **kwargs)
-
- def check_sockets(self):
- '''
- Check for messages on command and subscription sockets and process
- any messages accordingly.
- '''
- try:
- msg_frames = self.command_socket.recv_multipart(zmq.NOBLOCK)
- except zmq.Again:
- pass
- else:
- self.on_command_recv(msg_frames)
-
- try:
- msg_frames = self.subscribe_socket.recv_multipart(zmq.NOBLOCK)
- source, target, msg_type, msg_json = msg_frames
- self.most_recent = msg_json
- except zmq.Again:
- pass
- except:
- logger.error('Error processing message from subscription '
- 'socket.', exc_info=True)
- return True
-
- def on_execute__load_params(self, request):
- '''
- Args
- ----
-
- params_path (str) : Path to file for parameters yaml file.
- '''
- data = decode_content_data(request)
- load_params(self.parent, data['params_path'])
-
- def on_execute__save_params(self, request):
- '''
- Args
- ----
-
- params_path (str) : Path to file for parameters yaml file.
- '''
- data = decode_content_data(request)
- save_params(self.parent, data['params_path'])
-
- def on_execute__set_params(self, request):
- '''
- Args
- ----
-
- (dict) : Parameters dictionary in format returned by `get_params`.
- '''
- data = decode_content_data(request)
- set_params(self.parent, data['params'])
-
- def on_execute__get_params(self, request):
- return get_params(self.parent)
-
- def on_execute__run_active_experiment(self, request):
- data = decode_content_data(request)
- self.parent.statusbar.push(self.parent.message_context_id, "µDrop "
- "acquisition requested.")
- return self.parent.run_active_experiment(
- param_override=data.get('params'),
- metadata=data.get('metadata')
- )
-
- def on_execute__set_metadata(self, request=None):
- '''
- Args
- ----
-
- (dict) : Dictionary of metadata to be used in subsequent
- experiments. Should include `device_id`, `patient_id`, and
- `experiment_id`. Leave blank to reset all metadata fields or set
- individual keys to `None` to reset individual values.
- '''
- data = decode_content_data(request)
- self.parent.metadata = request
-
- def on_execute__save_text(self, request):
- '''
- Args
- ----
-
- save_data_path (str) : Path to file to save text data.
- '''
- data = decode_content_data(request)
- save_text(self.parent.current_exp, data['save_data_path'])
-
- def on_execute__save_plot(self, request):
- '''
- Args
- ----
-
- save_plot_path (str) : Path to file to save plot.
- '''
- data = decode_content_data(request)
- save_plot(self.parent.current_exp, data['save_plot_path'])
-
- def on_execute__acquisition_complete(self, request):
- '''
- Args
- ----
-
- Returns
- -------
-
- (datetime.datetime or None) : The completion time of the experiment
- corresponding to the specified UUID.
- '''
- data = decode_content_data(request)
- self.parent.statusbar.push(self.parent.message_context_id, "µDrop "
- "notified of completed acquisition.")
- if data['experiment_id'] in self.parent.completed_experiment_ids:
- return self.parent.completed_experiment_ids[data['experiment_id']]
- elif data['experiment_id'] == self.parent.active_experiment_id:
- return None
- else:
- raise KeyError('Unknown experiment ID: %s' % data['experiment_id'])
diff --git a/dstat_interface/core/state.py b/dstat_interface/core/state.py
new file mode 100644
index 0000000..87c770e
--- /dev/null
+++ b/dstat_interface/core/state.py
@@ -0,0 +1,10 @@
+from datetime import datetime
+import os
+from pathlib import Path
+
+from appdirs import AppDirs
+
+
+app_dirs = AppDirs("dstat-interface", "Wheeler Lab")
+experiment_name = 'experiment_{}'.format(datetime.now().strftime('%y-%m-%d_%H.%M.%S'))
+experiment_folder_location: Path = Path(app_dirs.user_data_dir) / 'Experiments' / experiment_name
diff --git a/dstat_interface/core/tasks.py b/dstat_interface/core/tasks.py
new file mode 100644
index 0000000..7ba8c97
--- /dev/null
+++ b/dstat_interface/core/tasks.py
@@ -0,0 +1,35 @@
+from abc import ABCMeta, abstractmethod
+
+import trio
+
+from dstat_interface.core.experiments.experiment_container import ExperimentContainer
+
+
+class BaseTasks(object, metaclass=ABCMeta):
+ def __init__(self):
+ self.tasks = []
+
+ async def loop(self):
+ async with trio.open_nursery() as nursery:
+ for task in self.tasks:
+ nursery.start_soon(task, nursery.cancel_scope)
+
+
+class ExperimentBaseTasks(BaseTasks):
+ def __init__(self, exp_con: ExperimentContainer):
+ super().__init__()
+ self.exp_con = exp_con
+ self.tasks += [self.update_progress, self.exp_runner]
+
+ @abstractmethod
+ async def update_progress(self, cancel_scope: trio.CancelScope):
+ pass
+
+ async def exp_runner(self, cancel_scope: trio.CancelScope):
+ while True:
+ if not self.exp_con.handler_instance.experiment_running_data():
+ return
+ if not self.exp_con.handler_instance.experiment_running_proc():
+ self.exp_con.handler_instance.get_all_data()
+ return
+ await trio.sleep(0)
diff --git a/dstat_interface/core/utils/__init__.py b/dstat_interface/core/utils/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/dstat_interface/core/utils/version.py b/dstat_interface/core/utils/version.py
deleted file mode 100644
index ae2f3d2..0000000
--- a/dstat_interface/core/utils/version.py
+++ /dev/null
@@ -1,137 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""Calculates the current version number.
-
-If possible, uses output of “git describe†modified to conform to the
-visioning scheme that setuptools uses (see PEP 386). Releases must be
-labelled with annotated tags (signed tags are annotated) of the following
-format:
-
- v<num>(.<num>)+ [ {a|b|c|rc} <num> (.<num>)* ]
-
-If “git describe†returns an error (likely because we're in an unpacked copy
-of a release tarball, rather than a git working copy), or returns a tag that
-does not match the above format, version is read from RELEASE-VERSION file.
-
-To use this script, simply import it your setup.py file, and use the results
-of getVersion() as your package version:
-
- import version
- setup(
- version=version.getVersion(),
- .
- .
- .
- )
-
-This will automatically update the RELEASE-VERSION file. The RELEASE-VERSION
-file should *not* be checked into git but it *should* be included in sdist
-tarballs (as should version.py file). To do this, run:
-
- echo include RELEASE-VERSION version.py >>MANIFEST.in
- echo RELEASE-VERSION >>.gitignore
-
-With that setup, a new release can be labelled by simply invoking:
-
- git tag -s v1.0
-"""
-
-__author__ = ('Douglas Creager <dcreager@dcreager.net>',
- 'Michal Nazarewicz <mina86@mina86.com>')
-__license__ = 'This file is placed into the public domain.'
-__maintainer__ = 'Michal Nazarewicz'
-__email__ = 'mina86@mina86.com'
-
-__all__ = ('getVersion')
-
-
-import re
-import subprocess
-import sys
-import os.path
-import inspect
-
-RELEASE_VERSION_FILE = '{}/RELEASE-VERSION'.format(
- os.path.dirname(os.path.abspath(inspect.stack()[0][1])))
-
-# http://www.python.org/dev/peps/pep-0386/
-_PEP386_SHORT_VERSION_RE = r'\d+(?:\.\d+)+(?:(?:[abc]|rc)\d+(?:\.\d+)*)?'
-_PEP386_VERSION_RE = r'^%s(?:\.post\d+)?(?:\.dev\d+)?$' % (
- _PEP386_SHORT_VERSION_RE)
-_GIT_DESCRIPTION_RE = r'^v(?P<ver>%s)-(?P<commits>\d+)-g(?P<sha>[\da-f]+)$' % (
- _PEP386_SHORT_VERSION_RE)
-
-
-def readGitVersion():
- try:
- proc = subprocess.Popen(('git', 'describe', '--long',
- '--match', 'v[0-9]*.*'),
- stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- data, _ = proc.communicate()
- if proc.returncode:
- return None
- ver = data.splitlines()[0].strip()
- proc = subprocess.Popen(('git', 'rev-parse', '--abbrev-ref', 'HEAD'),
- stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- branch, _ = proc.communicate()
- if proc.returncode:
- return None
- except:
- return None
-
- if not ver:
- return None
- m = re.search(_GIT_DESCRIPTION_RE, ver)
- if not m:
- sys.stderr.write('version: git description (%s) is invalid, '
- 'ignoring\n' % ver)
- return None
-
- commits = int(m.group('commits'))
-
- if not commits:
- version = m.group('ver')
- else:
- version = '%s.post%d' % (
- m.group('ver'), commits)
-
- if branch.strip() != 'master':
- version += '.dev%d' % int(m.group('sha'), 16)
-
- return version
-
-
-def readReleaseVersion():
- try:
- fd = open(RELEASE_VERSION_FILE)
- try:
- ver = fd.readline().strip()
- finally:
- fd.close()
- if not re.search(_PEP386_VERSION_RE, ver):
- sys.stderr.write('version: release version (%s) is invalid, '
- 'will use it anyway\n' % ver)
- return ver
- except:
- return None
-
-
-def writeReleaseVersion(version):
- fd = open(RELEASE_VERSION_FILE, 'w')
- fd.write('%s\n' % version)
- fd.close()
-
-
-def getVersion():
- release_version = readReleaseVersion()
- version = readGitVersion() or release_version
- if not version:
- raise ValueError('Cannot find the version number')
- if version != release_version:
- writeReleaseVersion(version)
- return version
-
-
-if __name__ == '__main__':
- print getVersion()
-
diff --git a/dstat_interface/main.py b/dstat_interface/main.py
deleted file mode 100755
index 32caa5d..0000000
--- a/dstat_interface/main.py
+++ /dev/null
@@ -1,854 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-""" GUI Interface for Wheeler Lab DStat """
-
-from __future__ import division, absolute_import, print_function, unicode_literals
-
-import sys
-import os
-import platform
-import multiprocessing
-import uuid
-from collections import OrderedDict
-from datetime import datetime
-import logging
-from pkg_resources import parse_version
-
-from serial import SerialException
-import zmq
-
-
-from dstat_interface.core.utils.version import getVersion
-from dstat_interface.core.experiments import idle, pot
-from dstat_interface.core import params, analysis, dstat
-from dstat_interface.core.dstat import boards
-from dstat_interface.core.interface import (exp_window, adc_pot, plot_ui, data_view,
- save, hw_info)
-from dstat_interface.core.errors import InputError
-from dstat_interface.core.plugin import DstatPlugin, get_hub_uri
-
-try:
- import gi
- gi.require_version('Gtk', '3.0')
- from gi.repository import Gtk, GObject
-except ImportError:
- print("ERR: GTK not available")
- sys.exit(1)
-
-mod_dir = os.path.dirname(os.path.abspath(__file__))
-conf_path = os.path.join(os.path.expanduser("~"), '.dstat-interface')
-
-# if __name__ == "__parents_main__": # Only runs for forking emulation on win
-# sys.path.append(mod_dir)
-
-# Setup Logging
-logger = logging.getLogger(__name__)
-core_logger = logging.getLogger("dstat_interface.core")
-loggers = [logger, core_logger]
-
-log_handler = logging.StreamHandler()
-log_formatter = logging.Formatter(
- fmt='%(asctime)s %(levelname)s: [%(name)s] %(message)s',
- datefmt='%H:%M:%S'
- )
-log_handler.setFormatter(log_formatter)
-
-for log in loggers:
- log.setLevel(level=logging.INFO)
- log.addHandler(log_handler)
-
-
-class Main(GObject.Object):
- """Main program """
- __gsignals__ = {
- b'exp_start': (GObject.SIGNAL_RUN_FIRST, None, ()),
- b'exp_stop': (GObject.SIGNAL_RUN_FIRST, None, ())
- }
-
- def __init__(self):
- super(Main, self).__init__()
- self.builder = Gtk.Builder()
- self.builder.add_from_file(
- os.path.join(mod_dir, 'core/interface/dstatinterface.glade'))
- self.builder.connect_signals(self)
- self.cell = Gtk.CellRendererText()
-
- # Create instance of interface components
- self.statusbar = self.builder.get_object('statusbar')
- self.ocp_disp = self.builder.get_object('ocp_disp')
- self.window = self.builder.get_object('window1')
- self.aboutdialog = self.builder.get_object('aboutdialog1')
- self.stopbutton = self.builder.get_object('pot_stop')
- self.startbutton = self.builder.get_object('pot_start')
- self.startbutton.set_sensitive(False)
- self.exp_progressbar = self.builder.get_object('exp_progressbar')
- self.adc_pot = adc_pot.adc_pot()
-
- self.error_context_id = self.statusbar.get_context_id("error")
- self.message_context_id = self.statusbar.get_context_id("message")
-
- self.exp_window = exp_window.Experiments(self.builder)
- self.exp_window.connect('run_utility', self.stop_ocp)
- self.exp_window.connect('done_utility', self.start_ocp)
-
- self.analysis_opt_window = analysis.AnalysisOptions(self.builder)
-
- # Setup Autosave
- self.autosave_checkbox = self.builder.get_object('autosave_checkbutton')
- self.autosavedir_button = self.builder.get_object('autosavedir_button')
- self.autosavename = self.builder.get_object('autosavename')
-
- # Setup Plots
- self.plot_notebook = self.builder.get_object('plot_notebook')
- self.main_notebook = self.builder.get_object('main_notebook')
- self.data_view = data_view.DataPage(self.main_notebook)
- self.info_page = data_view.InfoPage(self.main_notebook)
-
- # fill adc_pot_box
- self.adc_pot_box = self.builder.get_object('gain_adc_box')
- self.adc_pot_container = self.adc_pot.builder.get_object('vbox1')
- self.adc_pot_container.reparent(self.adc_pot_box)
-
- # fill serial
- self.serial_connect = self.builder.get_object('serial_connect')
- self.serial_pmt_connect = self.builder.get_object('pmt_mode')
- self.serial_disconnect = self.builder.get_object('serial_disconnect')
- self.serial_disconnect.set_sensitive(False)
- self.serial_combobox = self.builder.get_object('serial_combobox')
- self.serial_combobox.pack_start(self.cell, True)
- self.serial_combobox.add_attribute(self.cell, 'text', 0)
- self.serial_liststore = self.builder.get_object('serial_liststore')
- self.serial_devices = dstat.comm.SerialDevices()
-
- for i in self.serial_devices.ports:
- self.serial_liststore.append([i])
-
- self.serial_combobox.set_active(0)
-
- self.spinner = self.builder.get_object('spinner')
-
- self.mainwindow = self.builder.get_object('window1')
-
- self.menu_dstat_info = self.builder.get_object('menu_dstat_info')
- self.menu_dstat_info.set_sensitive(False)
- self.dstat_info_window = hw_info.InfoDialog(
- parent=self.mainwindow,
- connect=self.menu_dstat_info
- )
- self.menu_dstat_fw = self.builder.get_object('menu_dstat_fw')
- self.menu_dstat_fw.set_sensitive(False)
- self.dstat_fw_window = dstat.dfu.FWDialog(
- parent=self.mainwindow,
- connect=self.menu_dstat_fw,
- stop_callback=self.stop_ocp,
- disconnect_callback=self.on_serial_disconnect_clicked
- )
- self.menu_dstat_reset = self.builder.get_object('menu_dstat_reset')
- self.menu_dstat_reset.set_sensitive(False)
- self.menu_dstat_reset_window = hw_info.ResetDialog(
- parent=self.mainwindow,
- connect=self.menu_dstat_reset,
- stop_callback=self.stop_ocp,
- disconnect_callback=self.on_serial_disconnect_clicked
- )
-
- # Set Version Strings
- try:
- ver = getVersion()
- except ValueError:
- ver = "1.x"
- logger.warning("Could not fetch version number")
- self.mainwindow.set_title(" ".join(("DStat Interface", ver)))
- self.aboutdialog.set_version(ver)
-
- self.mainwindow.show_all()
- self.exp_window.hide_exps()
-
- self.expnumber = 0
-
- self.connected = False
- self.pmt_mode = False
-
- self.menu_dropbot_connect = self.builder.get_object(
- 'menu_dropbot_connect')
- self.menu_dropbot_disconnect = self.builder.get_object(
- 'menu_dropbot_disconnect')
- self.dropbot_enabled = False
- self.dropbot_triggered = False
-
- self.metadata = None # Should only be added to by plugin interface
-
- self.params_loaded = False
- # Disable 0MQ plugin API by default.
- self.plugin = None
- self.plugin_timeout_id = None
- # UUID for active experiment.
- self.active_experiment_id = None
- # UUIDs for completed experiments.
- self.completed_experiment_ids = OrderedDict()
-
- def on_window1_destroy(self, object, data=None):
- """ Quit when main window closed."""
- self.quit()
-
- def on_gtk_quit_activate(self, menuitem, data=None):
- """Quit when Quit selected from menu."""
- self.quit()
-
- def quit(self):
- """Disconnect and save parameters on quit."""
-
- try:
- params.save_params(self, os.path.join(conf_path, 'last_params.yml'))
- self.on_serial_disconnect_clicked()
- except KeyError:
- pass
-
- mainloop.quit()
-
- def on_gtk_about_activate(self, menuitem, data=None):
- """Display the about window."""
- self.aboutdialog.run() # waits for user to click close
- self.aboutdialog.hide()
-
- def on_menu_analysis_options_activate(self, menuitem, data=None):
- self.analysis_opt_window.show()
-
- def on_serial_refresh_clicked(self, data=None):
- """Refresh list of serial devices."""
- try:
- self.serial_devices.refresh()
- self.serial_liststore.clear()
- except ValueError:
- logger.warning("No DStats found")
-
- for i in self.serial_devices.ports:
- self.serial_liststore.append([i])
-
- def on_serial_connect_clicked(self, widget):
- """Connect and retrieve DStat version."""
- selection = self.serial_combobox.get_active_iter()
- if selection is None:
- return
-
- if widget is self.serial_pmt_connect:
- self.pmt_mode = True
- self.adc_pot.ui['short_true'].set_active(True)
- self.adc_pot.ui['short_true'].set_sensitive(False)
-
- try:
- self.serial_connect.set_sensitive(False)
- self.serial_pmt_connect.set_sensitive(False)
- dstat.comm.version_check(
- self.serial_liststore.get_value(selection, 0)
- )
-
- dstat.state.board_instance = boards.find_board(
- dstat.state.dstat_version)()
-
- self.statusbar.remove_all(self.error_context_id)
-
- self.adc_pot.set_version()
- self.statusbar.push(
- self.message_context_id,
- "DStat version: {}".format(
- dstat.state.dstat_version.base_version)
- )
-
- dstat.comm.read_settings()
-
- try:
- if dstat.state.settings['dac_units_true'][1] != b'1':
- dstat.state.settings['dac_units_true'][1] = b'1'
- dstat.comm.write_settings()
- except KeyError:
- logger.warning("Connected DStat does not support sending DAC units.")
- dialog = Gtk.MessageDialog(
- self.window, 0, Gtk.MessageType.WARNING,
- Gtk.ButtonsType.OK, "Connected DStat does not support sending DAC units." +
- "Update firmware or set potentials will be incorrect!")
-
- dialog.run()
- dialog.destroy()
-
- self.start_ocp()
- self.connected = True
- self.serial_disconnect.set_sensitive(True)
-
- except:
- self.serial_connect.set_sensitive(True)
- self.serial_pmt_connect.set_sensitive(True)
- self.adc_pot.ui['short_true'].set_sensitive(True)
- raise
-
- if self.params_loaded == False:
- try:
- try:
- os.makedirs(conf_path)
- except OSError:
- if not os.path.isdir(conf_path):
- raise
- params.load_params(self,
- os.path.join(conf_path, 'last_params.yml')
- )
- except IOError:
- logger.info("No previous parameters found.")
-
- def on_serial_disconnect_clicked(self, data=None):
- """Disconnect from DStat."""
- if self.connected == False:
- return
-
- try:
- if self.ocp_is_running:
- self.stop_ocp()
- else:
- self.on_pot_stop_clicked()
- dstat.state.ser.disconnect()
-
- except AttributeError as err:
- logger.warning("AttributeError: %s", err)
- pass
-
- if self.pmt_mode is True:
- self.adc_pot.ui['short_true'].set_sensitive(True)
-
- self.pmt_mode = False
- self.connected = False
- self.serial_connect.set_sensitive(True)
- self.serial_pmt_connect.set_sensitive(True)
- self.serial_disconnect.set_sensitive(False)
- self.startbutton.set_sensitive(False)
- self.stopbutton.set_sensitive(False)
- self.menu_dstat_info.set_sensitive(False)
- self.menu_dstat_fw.set_sensitive(False)
- self.menu_dstat_reset.set_sensitive(False)
- self.adc_pot.ui['short_true'].set_sensitive(True)
-
- dstat.state.reset()
-
- def start_ocp(self, data=None):
- """Start OCP measurements."""
- if dstat.state.dstat_version >= parse_version('1.2'):
- # Flush data pipe
- dstat.state.ser.flush_data()
-
- if self.pmt_mode is True:
- logger.info("Start PMT idle mode")
- dstat.state.ser.start_exp(idle.PMTIdle())
- self.ocp_is_running = True
- self.ocp_proc = (GObject.timeout_add(250, self.ocp_running_proc)
- ,
- )
-
- else:
- logger.info("Start OCP")
- dstat.state.ser.start_exp(idle.OCPExp())
-
- self.ocp_proc = (GObject.timeout_add(300, self.ocp_running_data),
- GObject.timeout_add(250, self.ocp_running_proc)
- )
- self.ocp_is_running = False
-
- GObject.timeout_add(100, self.ocp_assert) # Check if getting data
-
- else:
- logger.info("OCP measurements not supported on v1.1 boards.")
- return
-
- def stop_ocp(self, data=None):
- """Stop OCP measurements."""
-
- if dstat.state.dstat_version >= parse_version('1.2'):
- if self.pmt_mode == True:
- logger.info("Stop PMT idle mode")
- else:
- logger.info("Stop OCP")
- dstat.state.ser.send_ctrl('a')
-
- for i in self.ocp_proc:
- GObject.source_remove(i)
- while self.ocp_running_proc():
- pass
- self.ocp_disp.set_text("")
- self.ocp_is_running = False
- self.startbutton.set_sensitive(True)
- self.menu_dstat_info.set_sensitive(True)
- self.menu_dstat_fw.set_sensitive(True)
- self.menu_dstat_reset.set_sensitive(True)
- else:
- logger.error("OCP measurements not supported on v1.1 boards.")
- return
-
- def ocp_assert(self):
- if self.ocp_is_running:
- self.startbutton.set_sensitive(True)
- self.menu_dstat_info.set_sensitive(True)
- self.menu_dstat_fw.set_sensitive(True)
- self.menu_dstat_reset.set_sensitive(True)
- return False
- else:
- return True
-
- def ocp_running_data(self):
- """Receive OCP value from experiment process and update ocp_disp field
-
- Returns:
- True -- when experiment is continuing to keep function in GTK's queue.
- False -- when experiment process signals EOFError or IOError to remove
- function from GTK's queue.
- """
-
- try:
- incoming = dstat.state.ser.get_data()
- while incoming is not None:
- if isinstance(incoming, basestring): # test if incoming is str
- self.on_serial_disconnect_clicked()
- return False
-
- try:
- data = "".join(["OCP: ",
- "{0:.3f}".format(incoming),
- " V"])
- self.ocp_disp.set_text(data)
- self.ocp_is_running = True
- except ValueError:
- pass
-
- incoming = dstat.state.ser.get_data()
-
- return True
-
- except EOFError:
- return False
- except IOError:
- return False
-
- def ocp_running_proc(self):
- """Handles signals on proc_pipe_p for OCP.
-
- Returns:
- True -- when experiment is continuing to keep function in GTK's queue.
- False -- when experiment process signals EOFError or IOError to remove
- function from GTK's queue.
- """
-
- try:
- proc_buffer = dstat.state.ser.get_proc()
- while proc_buffer is not None:
- logger.debug("ocp_running_proc: %s", proc_buffer)
- if proc_buffer in ["DONE", "SERIAL_ERROR", "ABORT"]:
- if proc_buffer == "SERIAL_ERROR":
- self.on_serial_disconnect_clicked()
-
- dstat.state.ser.flush_data()
- return False
- proc_buffer = dstat.state.ser.get_proc()
- return True
-
- except EOFError:
- return False
- except IOError:
- return False
-
- def on_pot_start_clicked(self, data=None):
- try:
- self.run_active_experiment()
- except (ValueError, KeyError, InputError, SerialException,
- AssertionError):
- # Ignore expected exceptions when triggering experiment from UI.
- pass
-
- def run_active_experiment(self, param_override=None, metadata=None):
- """Run currently visible experiment."""
- # Assign current experiment a unique identifier.
- experiment_id = uuid.uuid4()
- self.active_experiment_id = experiment_id
- logger.info("Current measurement id: %s", experiment_id.hex)
-
- self.metadata = metadata
-
- if self.metadata is not None:
- logger.info("Loading external metadata")
-
- def exceptions():
- """ Cleans up after errors """
- self.spinner.stop()
- self.startbutton.set_sensitive(True)
- self.stopbutton.set_sensitive(False)
- self.start_ocp()
-
- self.stop_ocp()
- self.statusbar.remove_all(self.error_context_id)
-
- dstat.state.ser.flush_data()
-
- parameters = {}
- parameters['metadata'] = self.metadata
-
- # Make sure these are defined
- parameters['sync_true'] = False
- parameters['shutter_true'] = False
- try:
- if param_override is not None:
- params.set_params(self, param_override)
-
- parameters.update(params.get_params(self))
-
- self.line = 0
- self.lastline = 0
- self.lastdataline = 0
-
- self.spinner.start()
- self.startbutton.set_sensitive(False)
- self.stopbutton.set_sensitive(True)
- self.statusbar.remove_all(self.error_context_id)
-
- try:
- del self.current_exp
- except AttributeError:
- pass
-
- callbacks = {'experiment_done' : self.experiment_done,
- 'progress_update' : self.progress_update}
-
- self.current_exp = self.exp_window.setup_exp(parameters)
-
- plot_ui.replace_notebook_exp(
- self.plot_notebook, self.current_exp, self.window
- )
-
- self.data_view.clear_exps()
- self.info_page.clear()
-
- dstat.state.ser.start_exp(self.current_exp)
-
- # Flush data pipe
- dstat.state.ser.flush_data()
- self.current_exp.setup_loops(callbacks)
- return experiment_id
-
- except ValueError as i:
- logger.info("ValueError: %s",i)
- self.statusbar.push(self.error_context_id,
- "Experiment parameters must be integers.")
- exceptions()
- raise
-
- except KeyError as i:
- import traceback
- traceback.print_exc()
- logger.info("KeyError: %s", i)
- self.statusbar.push(self.error_context_id,
- "Experiment parameters must be integers.")
- exceptions()
- raise
-
- except InputError as err:
- logger.info("InputError: %s", err)
- self.statusbar.push(self.error_context_id, err.msg)
- exceptions()
- raise
-
- except SerialException as err:
- logger.info("SerialException: %s", err)
- self.statusbar.push(self.error_context_id,
- "Could not establish serial connection.")
- exceptions()
- raise
-
- except AssertionError as err:
- logger.info("AssertionError: %s", err)
- self.statusbar.push(self.error_context_id, str(err))
- exceptions()
- raise
-
- def progress_update(self, widget, progress):
- if 0 <= progress <= 1:
- self.exp_progressbar.set_fraction(progress)
- else:
- self.exp_progressbar.pulse()
-
- def experiment_running_data(self):
- """Receive data from experiment process and add to
- current_exp.data['data].
- Run in GTK main loop.
-
- Returns:
- True -- when experiment is continuing to keep function in GTK's queue.
- False -- when experiment process signals EOFError or IOError to remove
- function from GTK's queue.
- """
- try:
- incoming = dstat.state.ser.get_data()
- while incoming is not None:
- try:
- self.line, data = incoming
- if self.line > self.lastdataline:
- newline = True
- try:
- logger.info("running scan_process()")
- self.current_exp.scan_process(self.lastdataline)
- except AttributeError:
- pass
- self.lastdataline = self.line
- else:
- newline = False
- self.current_exp.store_data(incoming, newline)
-
- if newline:
- self.experiment_running_plot()
- except TypeError:
- pass
- incoming = dstat.state.ser.get_data()
- return True
-
- except EOFError as err:
- logger.error(err)
- self.experiment_done()
- return False
- except IOError as err:
- logger.error(err)
- self.experiment_done()
- return False
-
- def experiment_running_proc(self):
- """Receive proc signals from experiment process.
- Run in GTK main loop.
-
- Returns:
- True -- when experiment is continuing to keep function in GTK's queue.
- False -- when experiment process signals EOFError or IOError to remove
- function from GTK's queue.
- """
- try:
- ctrl_buffer = dstat.state.ser.get_ctrl()
- try:
- if ctrl_buffer is not None:
- self.current_exp.ctrl_loop(ctrl_buffer)
- except AttributeError:
- pass
-
- proc_buffer = dstat.state.ser.get_proc()
- if proc_buffer is not None:
- if proc_buffer in ["DONE", "SERIAL_ERROR", "ABORT"]:
- self.experiment_done()
- if proc_buffer == "SERIAL_ERROR":
- self.on_serial_disconnect_clicked()
-
- else:
- logger.warning("Unrecognized experiment return code: %s",
- proc_buffer)
- return False
- return True
-
- except EOFError as err:
- logger.warning("EOFError: %s", err)
- self.experiment_done()
- return False
- except IOError as err:
- logger.warning("IOError: %s", err)
- self.experiment_done()
- return False
-
- def experiment_running_plot(self, force_refresh=False):
- """Plot all data in current_exp.data.
- Run in GTK main loop. Always returns True so must be manually
- removed from GTK's queue.
- """
- for plot in self.current_exp.plots:
- if (plot.scan_refresh and self.line > self.lastline):
- while self.line > self.lastline:
- # make sure all of last line is added
- plot.updateline(self.current_exp, self.lastline)
- self.lastline += 1
- plot.updateline(self.current_exp, self.line)
- plot.redraw()
- else:
- while self.line > self.lastline:
- # make sure all of last line is added
- plot.updateline(self.current_exp, self.lastline)
- self.lastline += 1
- plot.updateline(self.current_exp, self.line)
-
- if plot.continuous_refresh is True or force_refresh is True:
- plot.redraw()
- return True
-
- def experiment_done(self, widget=None):
- """Clean up after data acquisition is complete. Update plot and
- copy data to raw data tab. Saves data if autosave enabled.
- """
- try:
- # Run Analysis
- analysis.do_analysis(self.current_exp)
-
- # Write DStat commands
- self.info_page.set_text(self.current_exp.get_info_text())
-
- try:
- self.statusbar.push(
- self.message_context_id,
- "Integral: %s A" % self.current_exp.analysis['FT Integral'][0][1]
- )
- except KeyError:
- pass
-
- # Data Output
- analysis_buffer = []
-
- if self.current_exp.analysis != {}:
- analysis_buffer.append("# ANALYSIS")
- for key, value in self.current_exp.analysis.iteritems():
- analysis_buffer.append("# %s:" % key)
- for scan in value:
- number, result = scan
- analysis_buffer.append(
- "# Scan %s -- %s" % (number, result)
- )
-
- for i in analysis_buffer:
- self.info_page.add_line(i)
-
- self.data_view.add_exp(self.current_exp)
-
- # Autosaving
- if self.autosave_checkbox.get_active():
- save.autoSave(self.current_exp,
- self.autosavedir_button.get_filename().decode('utf-8'),
- self.autosavename.get_text()
- )
-
- save.autoPlot(self.current_exp,
- self.autosavedir_button.get_filename().decode('utf-8'),
- self.autosavename.get_text()
- )
-
- # uDrop
- # UI stuff
- finally:
- self.metadata = None # Reset metadata
-
- self.spinner.stop()
- self.exp_progressbar.set_fraction(0)
- self.stopbutton.set_sensitive(False)
-
- self.start_ocp()
- self.completed_experiment_ids[self.active_experiment_id] =\
- datetime.utcnow()
-
- # Temporary fix for weird drawing bug on windows Gtk+3
- if platform.system() == 'Windows':
- position = self.window.get_position()
- self.window.hide()
- self.window.show()
- self.window.move(*position)
-
- def on_pot_stop_clicked(self, data=None):
- """Stop current experiment. Signals experiment process to stop."""
- try:
- dstat.state.ser.stop_exp()
-
- except AttributeError:
- pass
- except:
- logger.warning(sys.exc_info())
-
- def on_file_save_exp_activate(self, menuitem, data=None):
- """Activate dialogue to save current experiment data. """
- try:
- save.manSave(self.current_exp)
- except AttributeError:
- logger.warning("Tried to save with no experiment run")
-
- def on_file_save_plot_activate(self, menuitem, data=None):
- """Activate dialogue to save current plot."""
- try:
- save.plot_save_dialog(self.current_exp)
- except AttributeError:
- logger.warning("Tried to save with no experiment run")
-
- def on_file_save_params_activate(self, menuitem, data=None):
- """Activate dialogue to save current experiment parameters. """
- save.man_param_save(self)
-
- def on_file_load_params_activate(self, menuitem, data=None):
- """Activate dialogue to load experiment parameters from file. """
- save.man_param_load(self)
-
- def on_menu_dropbot_connect_activate(self, menuitem, data=None):
- """Listen for remote control connection from µDrop."""
-
- # Prompt user for 0MQ plugin hub URI.
- zmq_plugin_hub_uri = get_hub_uri(parent=self.window)
-
- self.dropbot_enabled = True
- self.menu_dropbot_connect.set_sensitive(False)
- self.menu_dropbot_disconnect.set_sensitive(True)
- self.statusbar.push(self.message_context_id,
- "Waiting for µDrop to connect…")
- self.enable_plugin(zmq_plugin_hub_uri)
-
- def on_menu_dropbot_disconnect_activate(self, menuitem=None, data=None):
- """Disconnect µDrop connection and stop listening."""
- self.cleanup_plugin()
- self.dropbot_enabled = False
- self.menu_dropbot_connect.set_sensitive(True)
- self.menu_dropbot_disconnect.set_sensitive(False)
- self.statusbar.push(self.message_context_id, "µDrop disconnected.")
-
- def enable_plugin(self, hub_uri):
- '''
- Connect to 0MQ plugin hub to expose public D-Stat API.
-
- Args
- ----
-
- hub_uri (str) : URI for 0MQ plugin hub.
- '''
- self.cleanup_plugin()
- # Initialize 0MQ hub plugin and subscribe to hub messages.
- self.plugin = DstatPlugin(self, 'dstat-interface', hub_uri,
- subscribe_options={zmq.SUBSCRIBE: ''})
- # Initialize sockets.
- self.plugin.reset()
-
- # Periodically process outstanding message received on plugin sockets.
- self.plugin_timeout_id = Gtk.timeout_add(500,
- self.plugin.check_sockets)
-
- def cleanup_plugin(self):
- if self.plugin_timeout_id is not None:
- GObject.source_remove(self.plugin_timeout_id)
- if self.plugin is not None:
- self.plugin = None
-
-
-if __name__ == "__main__":
- multiprocessing.freeze_support()
- GObject.threads_init()
- MAIN = Main()
- mainloop = GObject.MainLoop()
- try:
- mainloop.run()
- except KeyboardInterrupt:
- logger.info('Ctrl+C hit, quitting')
- MAIN.quit()
diff --git a/dstat_interface/utils.py b/dstat_interface/utils.py
new file mode 100644
index 0000000..cad25a9
--- /dev/null
+++ b/dstat_interface/utils.py
@@ -0,0 +1,25 @@
+import os
+import sys
+from pathlib import Path
+
+
+class Singleton(type):
+ _instances = {}
+
+ def __call__(cls, *args, **kwargs):
+ if cls not in cls._instances:
+ cls._instances[cls] = super(Singleton, cls).__call__(*args, **kwargs)
+ return cls._instances[cls]
+
+
+def runtime_dir():
+ """Get the runtime directory where we can create named pipes"""
+ if sys.platform.startswith('linux'):
+ return os.environ['XDG_RUNTIME_DIR']
+ elif sys.platform == 'darwin':
+ return '/private/var/tmp'
+ elif sys.platform == 'win32':
+ # Windows uses named pipes which aren't part of the normal filesystem
+ return ''
+ else:
+ raise NotImplementedError('Where do I create named pipes on this platform?')
diff --git a/pavement.py b/pavement.py
deleted file mode 100644
index fc19855..0000000
--- a/pavement.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import sys
-
-from paver.easy import task, needs, path, sh, cmdopts, options
-from paver.setuputils import setup, install_distutils_tasks, find_packages
-from distutils.extension import Extension
-from distutils.dep_util import newer
-
-sys.path.insert(0, path('.').abspath())
-import version
-
-setup(name='dstat_interface',
- version=version.getVersion(),
- description='Interface software for DStat potentiostat.',
- keywords='',
- author='Michael D. M Dryden',
- author_email='mdryden@chem.utoronto.ca',
- url='http://microfluidics.utoronto.ca/dstat',
- license='GPLv3',
- packages=find_packages(),
- install_requires=['matplotlib', 'numpy', 'pyserial', 'pyzmq',
- 'pyyaml','seaborn', 'setuptools',
- 'zmq-plugin>=0.2.post2'],
- # Install data listed in `MANIFEST.in`
- include_package_data=True)
-
-
-@task
-@needs('generate_setup', 'minilib', 'setuptools.command.sdist')
-def sdist():
- """Overrides sdist to make sure that our setup.py is generated."""
- pass
diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..88e5fef
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,199 @@
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "numpy"
+version = "1.19.4"
+description = "NumPy is the fundamental package for array computing with Python."
+category = "main"
+optional = false
+python-versions = ">=3.6"
+
+[[package]]
+name = "pyserial"
+version = "3.4"
+description = "Python Serial Port Extension"
+category = "main"
+optional = false
+python-versions = "*"
+
+[[package]]
+name = "pyside2"
+version = "5.15.1"
+description = "Python bindings for the Qt cross-platform application and UI framework"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <3.10"
+
+[package.dependencies]
+shiboken2 = "5.15.1"
+
+[[package]]
+name = "pyyaml"
+version = "5.3.1"
+description = "YAML parser and emitter for Python"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
+[[package]]
+name = "pyzmq"
+version = "19.0.2"
+description = "Python bindings for 0MQ"
+category = "main"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*"
+
+[[package]]
+name = "shiboken2"
+version = "5.15.1"
+description = "Python / C++ bindings helper module"
+category = "main"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <3.10"
+
+[[package]]
+name = "single-source"
+version = "0.2.0"
+description = "Access to the project version in Python code for PEP 621-style projects"
+category = "main"
+optional = false
+python-versions = ">=3.6,<4.0"
+
+[[package]]
+name = "tqdm"
+version = "4.51.0"
+description = "Fast, Extensible Progress Meter"
+category = "main"
+optional = false
+python-versions = ">=2.6, !=3.0.*, !=3.1.*"
+
+[package.extras]
+dev = ["py-make (>=0.1.0)", "twine", "argopt", "pydoc-markdown"]
+
+[metadata]
+lock-version = "1.1"
+python-versions = ">=3.8,<3.10"
+content-hash = "0f3e920ba999f9294c04581da00d38a389fbb7f0cf3e693c1138bb64d06ccf06"
+
+[metadata.files]
+appdirs = [
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diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..2163f8d
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,27 @@
+[tool.poetry]
+name = "dstat-interface"
+version = "2.0.0"
+description = "Interface for the DStat potentiostat (https://microfluidics.utoronto.ca/dstat)."
+authors = ["Michael DM Dryden <mk.dryden@utoronto.ca>"]
+license = "gpl-3.0-or-later"
+
+[tool.poetry.dependencies]
+python = ">=3.8,<3.10"
+PySide2 = "^5.15.1"
+pyserial = "^3.4"
+pyzmq = "^19.0.2"
+PyYAML = "^5.3.1"
+numpy = "^1.19.2"
+appdirs = "^1.4.4"
+tqdm = "^4.51.0"
+single-source = "^0.2.0"
+
+[tool.poetry.dev-dependencies]
+
+[tool.poetry-dynamic-versioning]
+enable = true
+vcs = "git"
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
+build-backend = "poetry.core.masonry.api"
diff --git a/version.py b/version.py
deleted file mode 100644
index ae2f3d2..0000000
--- a/version.py
+++ /dev/null
@@ -1,137 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""Calculates the current version number.
-
-If possible, uses output of “git describe†modified to conform to the
-visioning scheme that setuptools uses (see PEP 386). Releases must be
-labelled with annotated tags (signed tags are annotated) of the following
-format:
-
- v<num>(.<num>)+ [ {a|b|c|rc} <num> (.<num>)* ]
-
-If “git describe†returns an error (likely because we're in an unpacked copy
-of a release tarball, rather than a git working copy), or returns a tag that
-does not match the above format, version is read from RELEASE-VERSION file.
-
-To use this script, simply import it your setup.py file, and use the results
-of getVersion() as your package version:
-
- import version
- setup(
- version=version.getVersion(),
- .
- .
- .
- )
-
-This will automatically update the RELEASE-VERSION file. The RELEASE-VERSION
-file should *not* be checked into git but it *should* be included in sdist
-tarballs (as should version.py file). To do this, run:
-
- echo include RELEASE-VERSION version.py >>MANIFEST.in
- echo RELEASE-VERSION >>.gitignore
-
-With that setup, a new release can be labelled by simply invoking:
-
- git tag -s v1.0
-"""
-
-__author__ = ('Douglas Creager <dcreager@dcreager.net>',
- 'Michal Nazarewicz <mina86@mina86.com>')
-__license__ = 'This file is placed into the public domain.'
-__maintainer__ = 'Michal Nazarewicz'
-__email__ = 'mina86@mina86.com'
-
-__all__ = ('getVersion')
-
-
-import re
-import subprocess
-import sys
-import os.path
-import inspect
-
-RELEASE_VERSION_FILE = '{}/RELEASE-VERSION'.format(
- os.path.dirname(os.path.abspath(inspect.stack()[0][1])))
-
-# http://www.python.org/dev/peps/pep-0386/
-_PEP386_SHORT_VERSION_RE = r'\d+(?:\.\d+)+(?:(?:[abc]|rc)\d+(?:\.\d+)*)?'
-_PEP386_VERSION_RE = r'^%s(?:\.post\d+)?(?:\.dev\d+)?$' % (
- _PEP386_SHORT_VERSION_RE)
-_GIT_DESCRIPTION_RE = r'^v(?P<ver>%s)-(?P<commits>\d+)-g(?P<sha>[\da-f]+)$' % (
- _PEP386_SHORT_VERSION_RE)
-
-
-def readGitVersion():
- try:
- proc = subprocess.Popen(('git', 'describe', '--long',
- '--match', 'v[0-9]*.*'),
- stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- data, _ = proc.communicate()
- if proc.returncode:
- return None
- ver = data.splitlines()[0].strip()
- proc = subprocess.Popen(('git', 'rev-parse', '--abbrev-ref', 'HEAD'),
- stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- branch, _ = proc.communicate()
- if proc.returncode:
- return None
- except:
- return None
-
- if not ver:
- return None
- m = re.search(_GIT_DESCRIPTION_RE, ver)
- if not m:
- sys.stderr.write('version: git description (%s) is invalid, '
- 'ignoring\n' % ver)
- return None
-
- commits = int(m.group('commits'))
-
- if not commits:
- version = m.group('ver')
- else:
- version = '%s.post%d' % (
- m.group('ver'), commits)
-
- if branch.strip() != 'master':
- version += '.dev%d' % int(m.group('sha'), 16)
-
- return version
-
-
-def readReleaseVersion():
- try:
- fd = open(RELEASE_VERSION_FILE)
- try:
- ver = fd.readline().strip()
- finally:
- fd.close()
- if not re.search(_PEP386_VERSION_RE, ver):
- sys.stderr.write('version: release version (%s) is invalid, '
- 'will use it anyway\n' % ver)
- return ver
- except:
- return None
-
-
-def writeReleaseVersion(version):
- fd = open(RELEASE_VERSION_FILE, 'w')
- fd.write('%s\n' % version)
- fd.close()
-
-
-def getVersion():
- release_version = readReleaseVersion()
- version = readGitVersion() or release_version
- if not version:
- raise ValueError('Cannot find the version number')
- if version != release_version:
- writeReleaseVersion(version)
- return version
-
-
-if __name__ == '__main__':
- print getVersion()
-
--
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