diff --git a/.gitignore b/.gitignore index 868139ac84a3c9d54009d39932c400f70aa6b886..a9d44d884ce7f4318b0e306224c2fdfdb8562ee1 100644 --- a/.gitignore +++ b/.gitignore @@ -13,3 +13,7 @@ setup.py *.egg-info last_params last_params.yml + +\.idea/ + +dstat_interface/core/experiments/__pycache__/ diff --git a/CHANGELOG b/CHANGELOG index 8dd9358a63960720b0e749f002d1433ec44f87e0..49d3422436f22443c08a2983abe0f1f20db0c5d9 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,35 @@ +Version 1.4.6 + -Fixed data output for SWV/DPV forward/reverse current + -Working progress bars + -Refactored a lot of plotting code + -Calibration should work properly now + +Version 1.4.5 + -Made board definitions modular + -Fix several bugs with experiment parameters + -Uses DAC unit based parameters now (**REQUIRES dstat-firmware@9e4a9f or higher**) + -Change package import structure again (main must always be run as module now) + -Workaround for weird Gtk+3 redrawing bug on Windows + +Version 1.4.4 + -Make connection code more robust + -Execute button disabled until DStat is ready to start + -Supports new firmware version strings added in dstat-firmware@c5f9701 + -Experimental firmware upgrade tool (see DStat Menu) + -Fix many bugs + +Version 1.4.3 + -Fix another critical bug with Windows multiprocessing + -Allow normal exit even if DStat was never connected + -Store last parameters in user folder + +Version 1.4.2 + -Refactor to fix critical bug preventing running packaged versions. + +Version 1.4.1 + -Fixed voltage axis orientation for LSV, CV, SWV, and DPV (Thanks to Dan Bizzotto @ UBC) + -Tweaked paver files to make version detection work without git. + Version 1.4 -Switched to GTK+3 -Support new DStat communications protocol (requires dstat-firmware>fe50c38) diff --git a/MANIFEST.in b/MANIFEST.in index fefb590607d8a1af6e0f25aa8254d806bced5d50..711422bec61f13a1cdd36f8ff1f9c15f689fd444 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,7 +1,14 @@ 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/README.markdown b/README.markdown index e47af15c9e60b4222d8462ea70f6718e752a1e65..573ea72e58b8d3271257dd55d6771a725a724edb 100644 --- a/README.markdown +++ b/README.markdown @@ -1,6 +1,8 @@ ##### _DStat is described in detail in [Dryden MDM, Wheeler AR (2015) DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration. PLoS ONE 10(10): e0140349. doi: 10.1371/journal.pone.0140349](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140349) If you use this information in published work, please cite accordingly._ --- +## Python 2.7 is now discontinued and gtk has always been a pain for cross-platform use, so I am in the process of writing a new interface in Python 3 and Qt that I hope will be working before too long. + This is the documentation for the DStat interface software. The DStat interface is written primarily in Python and runs on Linux, Mac, and Windows. It is the main method for running experiments on the DStat, controlling experimental parameters and collecting and plotting data. @@ -14,6 +16,7 @@ It currently has no abilities for analyzing recorded data or opening previously 2. [Old Homebrew Instructions](#old-homebrew-instructions) 1. [Linux](#linux) 2. [Windows](#windows) + 3. [Upgrading](#upgrading) 2. [Getting Started](#Getting-Started) # Introduction @@ -30,8 +33,10 @@ dstat-interface has moved to gtk+3 and we now recommend Anaconda/Miniconda for i 1. [Install Miniconda](https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh) It doesn't matter if you pick Python 2.7 or 3.5—this just sets Miniconda's default Python. (Skip if Miniconda or Anaconda are already installed) - 2. Create a new environment for dstat. In a terminal type: -````conda create -n dstat -c mdryden python=2.7 dstat-interface dstat-interface-deps```` + 2. Download the [conda env file](conda-env.yml). + + 3. In the terminal, create the dstat environment (replacing with the actual path to the file on your computer): +````conda env create -f ```` 3. Then to run dstat-interface: ````source activate dstat @@ -40,10 +45,12 @@ dstat-interface has moved to gtk+3 and we now recommend Anaconda/Miniconda for i #### Old Homebrew Instructions The easiest way to get most of the necessary requirements to run dstat-interface is using [Homebrew](http://brew.sh): - brew tap homebrew/python - brew update - brew install python gobject-introspection gtk+3 pygobject3 py2cairo scipy zeromq - brew install matplotlib --with-pygtk +```shell +brew tap homebrew/python +brew update +brew install python gobject-introspection gtk+3 pygobject3 py2cairo scipy zeromq +brew install matplotlib --with-pygtk +``` Be patient on the last step—matplotlib needs to be compiled and may take 2 or 3 minutes. @@ -56,17 +63,26 @@ The final requirements, can be installed using python's pip system: ## Linux Linux prerequisite installation is similar to that of MacOS with Homebrew, only using your distribution's native package manager rather than Homebrew, and X11 will likely be installed already. Some distributions may not have packages available for installing matplotlib or numpy, in which case, they should be installed using pip. -The final requirements, can be installed using python's pip system: +These instructions were tested on Ubuntu 17.04: - pip install pandas pyserial pyzmq pyyaml seaborn zmq-plugin +````shell +sudo apt-get install gobject-introspection python-gobject python-pip +pip install dstat-interface +```` + +You will need to add your user to the `dialout` group to access virtual serial ports (replace with your username): + +```shell +sudo usermod -a -G dialout +``` ## Windows The following terminal commands will result in a full installation of dstat-interface and its requirements, assuming [64-bit Miniconda][1] is installed: -```` +```shell conda create -n dstat -c mdryden python=2 dstat-interface activate dstat -```` +``` To finish the installation, GTK+3 and its Python bindings must be installed: @@ -84,12 +100,35 @@ and `deactivate` will return to the root environment. Therefore, to run dstat-interface from our environment, we must first activate it (if not already done) before launching it: - activate dstat - python -m dstat_interface.main +```shell +activate dstat +python -m dstat_interface.main +``` [1]: https://repo.continuum.io/miniconda/Miniconda2-latest-Windows-x86_64.exe [2]: https://sourceforge.net/projects/pygobjectwin32/ +## Upgrading + +Anaconda builds can be upgraded to the latest version by issuing this command (from an activated conda environment): + +```shell +conda upgrade -c mdryden dstat-interface # For MacOS, be sure to upgrade dstat-interface-deps as well +``` + +pip installs can be upgraded similarly: + +```shell +pip install --upgrade dstat-interface +``` + +You can also run development builds directly from a cloned git repository (from an activated conda environment): + +```shell +cd ~/src/dstat-interface/dstat_interface # Replace with path to dstat_interface folder inside repository +python -m main +``` + # Getting started ## Interface overview diff --git a/conda-env.yml b/conda-env.yml new file mode 100644 index 0000000000000000000000000000000000000000..8bce2bc1d5361d1cc80348a6a2fc7797b0d6820e --- /dev/null +++ b/conda-env.yml @@ -0,0 +1,137 @@ +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/interface/__init__.py b/dstat_interface/core/__init__.py similarity index 100% rename from dstat_interface/interface/__init__.py rename to dstat_interface/core/__init__.py diff --git a/dstat_interface/analysis.py b/dstat_interface/core/analysis.py similarity index 96% rename from dstat_interface/analysis.py rename to dstat_interface/core/analysis.py index 3190989961710fef302ce07853761fe666b4d331..747df181ff7a3c1dacbe68a158c536b88704b6f2 100755 --- a/dstat_interface/analysis.py +++ b/dstat_interface/core/analysis.py @@ -21,16 +21,19 @@ Functions for analyzing data. """ import logging +import os from numpy import mean, trapz -logger = logging.getLogger('dstat.analysis') +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('interface/analysis_options.glade') + 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') diff --git a/dstat_interface/drivers/VirtualSerial.inf b/dstat_interface/core/drivers/VirtualSerial.inf similarity index 100% rename from dstat_interface/drivers/VirtualSerial.inf rename to dstat_interface/core/drivers/VirtualSerial.inf diff --git a/dstat_interface/dstat-interface.bat b/dstat_interface/core/dstat-interface.bat similarity index 100% rename from dstat_interface/dstat-interface.bat rename to dstat_interface/core/dstat-interface.bat diff --git a/dstat_interface/dstat.spec b/dstat_interface/core/dstat.spec similarity index 100% rename from dstat_interface/dstat.spec rename to dstat_interface/core/dstat.spec diff --git a/dstat_interface/core/dstat/__init__.py b/dstat_interface/core/dstat/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..1fb1ae912ef9bcc22c488a7df37de0af8ac3385f --- /dev/null +++ b/dstat_interface/core/dstat/__init__.py @@ -0,0 +1,3 @@ +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 new file mode 100755 index 0000000000000000000000000000000000000000..421e02c2ae406533241b1008d85ee97d650154d0 --- /dev/null +++ b/dstat_interface/core/dstat/boards.py @@ -0,0 +1,142 @@ +#!/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 +# +# +# 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 . + +from __future__ import division, absolute_import, print_function, unicode_literals +import sys +import inspect +import logging + +from pkg_resources import parse_version, parse_requirements + +logger = logging.getLogger(__name__) + + +class BaseBoard(object): + pcb_version = 'x.x.x' + booster = False + + def __init__(self): + self.max_freq = 5000 + self.max_scans = 255 + self.max_time = 65535 + + self.setup() + assert len(self.gain) == self.gain_settings + assert len(self.gain_labels) == self.gain_settings + if self.gain_trim is not None: + assert len(self.gain_trim) == self.gain_settings + + def setup(self): + """Override in subclasses to provide correct numbers""" + 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.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 + + def test_mv(self, mv): + """Return true if voltage in mV is in range.""" + dac = float(mv)*self.re_voltage_scale/(3000./65536) + 32768 + + if 0 <= dac <= 65535: + return True + else: + return False + + def test_freq(self, hz): + """Return true if frequency in Hz is in range.""" + return 0 < float(hz) < self.max_freq + + def test_scans(self, n): + """Return true if number of scans is valid.""" + return 0 < int(n) < self.max_scans + + def test_s(self, s): + """Return true if time in integer seconds is valid.""" + return 0 < int(s) < self.max_time + + +class V1_1Board(BaseBoard): + pcb_version = '1.1' + + def setup(self): + self.gain = [1e2, 3e2, 3e3, 3e4, 3e5, 3e6, 3e7, 5e8] + self.gain_labels = [None, "300 Ω (5 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)", "500 MΩ (3 nA FS)" + ] + self.gain_trim = None + self.gain_settings = len(self.gain) + self.gain_default_index = 2 + self.re_voltage_scale = 1 + + +class V1_2Board(BaseBoard): + pcb_version = '1.2' + + def setup(self): + 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.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 + + +def __get_all_subclasses(cls): + all_subclasses = [] + + for subclass in cls.__subclasses__(): + all_subclasses.append(subclass) + all_subclasses.extend(__get_all_subclasses(subclass)) + + return all_subclasses + + +def find_board(version, booster=False): + """Returns highest compatible board class or None if none available.""" + boards = __get_all_subclasses(BaseBoard) + candidates = [] + for board in boards: + req = next(parse_requirements('dstat~={}'.format(board.pcb_version))) + if board.booster == booster and version in req: + candidates.append(board) + try: + picked = sorted(candidates, + key=lambda board: parse_version(board.pcb_version))[-1] + logger.info("Picked %s", picked) + return picked + except IndexError: + logger.warning("No matching board definition for ver: %s.", version) + return None diff --git a/dstat_interface/core/dstat/comm.py b/dstat_interface/core/dstat/comm.py new file mode 100755 index 0000000000000000000000000000000000000000..605961d47f3bf18699537d75515432d483ae9081 --- /dev/null +++ b/dstat_interface/core/dstat/comm.py @@ -0,0 +1,622 @@ +#!/usr/bin/env python +# DStat Interface - An interface for the open hardware DStat potentiostat +# Copyright (C) 2014 Michael D. M. Dryden - +# Wheeler Microfluidics Laboratory +# +# +# 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 . +from __future__ import division, absolute_import, print_function, unicode_literals + +import time +import struct +import multiprocessing as mp +from collections import OrderedDict +import logging + +from pkg_resources import parse_version + +try: + import gi + + gi.require_version('Gtk', '3.0') + from gi.repository import Gtk, GObject +except ImportError: + import sys + + print("ERR: GTK not available") + sys.exit(1) +import serial +from serial.tools import list_ports + +from . import state +from ..errors import InputError, VarError + +logger = logging.getLogger(__name__) +dstat_logger = logging.getLogger("{}.DSTAT".format(__name__)) +exp_logger = logging.getLogger("{}.Experiment".format(__name__)) + + +class AlreadyConnectedError(Exception): + def __init__(self): + super(AlreadyConnectedError, self).__init__(self, + "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.") + + +class TransmitError(Exception): + def __init__(self): + super(TransmitError, self).__init__(self, + "No reply received.") + + +def _serial_process(ser_port, proc_pipe, ctrl_pipe, data_pipe): + ser_logger = logging.getLogger("{}._serial_process".format(__name__)) + connected = False + + for i in range(5): + time.sleep(1) # Give OS time to enumerate + + try: + ser = serial.Serial(ser_port, timeout=1) + ser_logger.info("Connecting") + time.sleep(.5) + connected = True + except serial.SerialException: + pass + + if connected is True: + 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(b'!0 ') + + for i in range(10): + 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(b'!0 ') + time.sleep(.1) + + while True: + # These can only be called when no experiment is running + if ctrl_pipe.poll(): + ctrl_buffer = ctrl_pipe.recv() + if ctrl_buffer in ('a', "DISCONNECT"): + proc_pipe.send("ABORT") + try: + 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.encode('ascii')) + + elif proc_pipe.poll(): + while ctrl_pipe.poll(): + ctrl_pipe.recv() + try: + proc, params, state = proc_pipe.recv() + if params is None: + return_code = proc(state=state).run(ser, ctrl_pipe, data_pipe) + else: + return_code = proc(params, state).run(ser, ctrl_pipe, data_pipe) + except serial.SerialException: + proc_pipe.send("DISCONNECT") + ser.rts = False + ser._update_dtr_state() # Need DTR update on Windows + ser.close() + return 0 + ser_logger.info('Return code: %s', str(return_code)) + + proc_pipe.send(return_code) + + else: + time.sleep(.1) + + +class SerialConnection(GObject.Object): + __gsignals__ = { + 'connected': (GObject.SIGNAL_RUN_FIRST, None, ()), + 'disconnected': (GObject.SIGNAL_RUN_FIRST, None, ()) + } + + def __init__(self): + super(SerialConnection, self).__init__() + self.connected = False + + def connect(self, ser_port): + 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.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): + self.assert_connected() + clean_state = exp.state + try: + clean_state['dstat_version'] = None # Remove unpickleable Version class instance + except (TypeError, KeyError): + pass + try: + self.proc_pipe_p.send((type(exp), exp.parameters, clean_state)) + except AttributeError: + self.proc_pipe_p.send((type(exp), None, clean_state)) + + def stop_exp(self): + self.send_ctrl('a') + + def get_proc(self, block=False): + self.assert_connected() + + if block is True: + return self.proc_pipe_p.recv() + else: + if self.proc_pipe_p.poll() is True: + return self.proc_pipe_p.recv() + else: + return None + + def get_ctrl(self, block=False): + self.assert_connected() + + if block is True: + return self.ctrl_pipe_p.recv() + else: + if self.ctrl_pipe_p.poll() is True: + return self.ctrl_pipe_p.recv() + else: + return None + + def get_data(self, block=False): + self.assert_connected() + + if block is True: + return self.data_pipe_p.recv() + else: + if self.data_pipe_p.poll() is True: + 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): + self.assert_connected() + + self.ctrl_pipe_p.send(ctrl) + + def disconnect(self): + logger.info("Disconnecting") + self.send_ctrl('DISCONNECT') + self.proc.join() + self.emit('disconnected') + self.connected = False + + +class VersionCheck(object): + def __init__(self, parameters=None, state=None): + self.parameters = parameters + self.state = state + + 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'.encode('ascii')) + + for i in range(10): + if ser.readline().rstrip() == b"@ACK 1": + ser.write(b'V\n') + if ser.readline().rstrip() == b"@RCV 1": + break + else: + time.sleep(.5) + ser.reset_input_buffer() + ser.write(b'!1\n') + time.sleep(.1) + + for line in ser: + line = line.decode('ascii') + dstat_logger.info(line) + if line.startswith('V'): + input = line.lstrip('V') + elif line.startswith("#"): + dstat_logger.info(line.strip()) + elif line.lstrip().startswith("@DONE"): + dstat_logger.debug(line.strip()) + 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 serial.SerialException as e: + logger.error('SerialException: %s', e) + status = "SERIAL_ERROR" + finally: + return status + + +def version_check(ser_port): + """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()) + result = state.ser.get_proc(block=True) + if result == "SERIAL_ERROR": + state.dstat_version = None + state.firmware_version = None + return False + else: + buffer = state.ser.get_data(block=True) + version, state.firmware_version = buffer + state.dstat_version = parse_version(version) + logger.debug("version_check done") + time.sleep(.1) + + return True + + +class Settings(object): + def __init__(self, parameters=None, state=None): + self.parameters = parameters + self.state = state + self.task = parameters['task'] + try: + self.settings = parameters['settings'] + except KeyError: + pass + + def run(self, ser, ctrl_pipe, data_pipe): + """Tries to contact DStat and get settings. Returns dict of + settings. + """ + + self.ser = ser + + if self.task == 'w': + self.write() + + if self.task == 'r': + data_pipe.send(self.read()) + + status = "DONE" + + return status + + def read(self): + self.ser.reset_input_buffer() + self.ser.write('!2\n'.encode('ascii')) + + for i in range(10): + if self.ser.readline().rstrip() == b"@ACK 2": + self.ser.write('SR\n'.encode('ascii')) + if self.ser.readline().rstrip() == b"@RCV 2": + break + else: + time.sleep(.5) + self.ser.reset_input_buffer() + self.ser.write('!2\n'.encode('ascii')) + time.sleep(.1) + + for line in self.ser: + line_in = line.decode('ascii') + if line_in.lstrip().startswith('S'): + input = line_in.lstrip().lstrip('S') + elif line_in.lstrip().startswith("#"): + dstat_logger.info(line_in.strip()) + elif line_in.lstrip().startswith("@DONE"): + dstat_logger.debug(line_in.strip()) + self.ser.reset_input_buffer() + break + + parted = input.rstrip().split(':') + settings = OrderedDict((setting.split('.')[0], setting.split('.')[1]) for setting in parted) + + 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(b'#'): + dstat_logger.info(reply) + elif reply == b"": + 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).encode('ascii')) + time.sleep(.1) + + try: + reply = get_reply() + except TransmitError: + if tries <= 0: + continue + tries -= 1 + pass + else: + break + + if reply != f"@ACK {n}".encode('ascii'): + logger.warning("Expected ACK got: {}".format(reply)) + continue + + tries = 5 + + while True: + self.ser.write('{}\n'.format(cmd).encode('ascii')) + try: + reply = get_reply() + except TransmitError: + if tries <= 0: + continue + tries -= 1 + pass + else: + break + + if reply != f"@RCV {n}".encode('ascii'): + 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 != f"@RQP {n_params}".encode('ascii'): + logger.warning("Expected RQP got: {}".format(reply)) + continue + + tries = 5 + + for i in params: + while True: + self.ser.write(i + " ".encode('ascii')) + try: + reply = get_reply() + if reply == f"@RCVC {i}".encode('ascii'): + 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(self.settings.values()) + " " + # 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(parameters={'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(parameters={'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(object): + 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('!'.encode('ascii')) + + while not ser.read() == b"@": + self.ser.reset_input_buffer() + ser.write('!'.encode('ascii')) + + ser.write('T'.encode('ascii')) + for line in ser: + if line.lstrip().startswith(b'T'): + input = line.lstrip().lstrip(b'T') + elif line.lstrip().startswith(b"#"): + dstat_logger.info(line.lstrip().rstrip()) + elif line.lstrip().startswith(b"@DONE"): + dstat_logger.debug(line.lstrip().rstrip()) + ser.reset_input_buffer() + break + + parted = input.rstrip().split(b'.') + + 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") diff --git a/dstat_interface/core/dstat/dfu.py b/dstat_interface/core/dstat/dfu.py new file mode 100755 index 0000000000000000000000000000000000000000..a903a7f40c8023caf0027f5ca150e4c54d79ecfb --- /dev/null +++ b/dstat_interface/core/dstat/dfu.py @@ -0,0 +1,380 @@ +#!/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 +# +# +# 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 . + +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. (or on a descendent branch)" + 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).decode(sys.stdout.encoding) + logger.info("Assert: %s", command) + logger.info("Result: %s", 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).decode(sys.stdout.encoding) + 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).decode(sys.stdout.encoding) + logger.info("Current master commit: {}".format(master)) + + command = "git merge-base --is-ancestor master {}".format(current) + test = subprocess.call(command.split()) + logger.info(test) + + if test == 0: # already newest + logger.info('Firmware is latest available (or on a newer descendent branch).') + 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).decode(sys.stdout.encoding) + logger.info("%s\n%s", command, output) + command = "dfu-programmer atxmega256a3u flash {}".format(path) + output = subprocess.check_output(command.split(), + stderr=subprocess.STDOUT).decode(sys.stdout.encoding) + logger.info("%s\n%s", command, output) + command = "dfu-programmer atxmega256a3u launch" + output = subprocess.check_output(command.split(), + stderr=subprocess.STDOUT).decode(sys.stdout.encoding) + 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) + + 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/state.py b/dstat_interface/core/dstat/state.py new file mode 100644 index 0000000000000000000000000000000000000000..49064813b2abe4c4074bf706f3ce48500e0d6380 --- /dev/null +++ b/dstat_interface/core/dstat/state.py @@ -0,0 +1,29 @@ +from collections import OrderedDict + + +def reset(): + """Resets state variables.""" + + settings = OrderedDict() + ser = None + dstat_version = None + firmware_version = None + board_instance = None + + +def get_state(): + """ + Get state variables + :return dict of pickleable state variables + """ + return {'settings': settings, + 'dstat_version': dstat_version, + 'firmware_version': firmware_version, + 'board_instance': board_instance} + + +settings = OrderedDict() +ser = None +dstat_version = None +firmware_version = None +board_instance = None diff --git a/dstat_interface/errors.py b/dstat_interface/core/errors.py similarity index 100% rename from dstat_interface/errors.py rename to dstat_interface/core/errors.py diff --git a/dstat_interface/core/experiments/__init__.py b/dstat_interface/core/experiments/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..6991a974fe8d810854f78bd2c311ce17ec56619e --- /dev/null +++ b/dstat_interface/core/experiments/__init__.py @@ -0,0 +1,17 @@ +# __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/experiments/cal.py b/dstat_interface/core/experiments/cal.py similarity index 87% rename from dstat_interface/experiments/cal.py rename to dstat_interface/core/experiments/cal.py index 98d82b6bbd0c15467ee4cc41d65455a5917bcd7d..3da92806959b3c4cb9d1dc2407190a9facfd1058 100755 --- a/dstat_interface/experiments/cal.py +++ b/dstat_interface/core/experiments/cal.py @@ -21,15 +21,14 @@ import time import struct import logging - -from errors import InputError, VarError +logger = logging.getLogger(__name__) import serial -logger = logging.getLogger("dstat.experiments.cal") +from ..errors import InputError, VarError +from ..dstat import state +from ..experiments.experiment_template import Experiment, dstat_logger -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', @@ -48,6 +47,7 @@ def measure_offset(time): return gain_offset + class CALExp(Experiment): id = 'cal' """Offset calibration experiment""" @@ -57,15 +57,16 @@ class CALExp(Experiment): self.scan = 0 self.data = [] - self.commands = ["EA2 3 1 ", "EG", "ER"] + self.commands = ["EA2 3 1 ", "EG"] self.commands[1] += str(self.parameters['gain']) self.commands[1] += " " self.commands[1] += "0 " - self.commands[2] += "1 32768 " - self.commands[2] += str(self.parameters['time']) - self.commands[2] += " " - self.commands[2] += "0 " # disable photodiode interlock + + self.commands.append( + ("ER1 0", ["32768", str(self.parameters['time'])]) + ) + def serial_handler(self): """Handles incoming serial transmissions from DStat. Returns False @@ -100,6 +101,7 @@ class CALExp(Experiment): elif line.lstrip().startswith("@DONE"): dstat_logger.debug(line.lstrip().rstrip()) self.serial.flushInput() + self.experiment_done() return True except serial.SerialException: @@ -114,13 +116,16 @@ class CALExp(Experiment): seconds, milliseconds, current = struct.unpack(' +# +# +# 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 . + +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: + import sys + print("ERR: GTK not available") + sys.exit(1) + +logger = logging.getLogger(__name__) + + +class BaseLoop(GObject.GObject): + __gsignals__ = { + 'experiment_done': (GObject.SIGNAL_RUN_FIRST, None, tuple()), + '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/experiments/experiment_template.py b/dstat_interface/core/experiments/experiment_template.py similarity index 52% rename from dstat_interface/experiments/experiment_template.py rename to dstat_interface/core/experiments/experiment_template.py index 29aa8393aa81d89eb7bb2dc7a6763881bb45f342..32b1d290594bd2895d574c6cbc6f7eb56a94be19 100755 --- a/dstat_interface/experiments/experiment_template.py +++ b/dstat_interface/core/experiments/experiment_template.py @@ -17,85 +17,92 @@ # # You should have received a copy of the GNU General Public License # along with this program. If not, see . +from __future__ import division, absolute_import, print_function, unicode_literals + import logging import struct -from datetime import datetime +import time from collections import OrderedDict from copy import deepcopy +from datetime import datetime from math import ceil -import time try: import gi gi.require_version('Gtk', '3.0') from gi.repository import Gtk, GObject except ImportError: - print "ERR: GTK not available" + import sys + print("ERR: GTK not available") sys.exit(1) - + + from matplotlib.figure import Figure import matplotlib.gridspec as gridspec -import matplotlib.pyplot as plt -from matplotlib.backends.backend_gtk3agg \ - import FigureCanvasGTK3Agg as FigureCanvas - +# from matplotlib.backends.backend_gtk3agg \ + # import FigureCanvasGTK3Agg as FigureCanvas + +from matplotlib.backends.backend_gtk3cairo \ + import FigureCanvasGTK3Cairo as FigureCanvas + + from pandas import DataFrame - -try: - import seaborn as sns - sns.set(context='paper', style='darkgrid') -except ImportError: - pass +import seaborn as sns +sns.set(context='paper', style='darkgrid') + import serial -logger = logging.getLogger("dstat.comm") -dstat_logger = logging.getLogger("dstat.comm.DSTAT") -exp_logger = logging.getLogger("dstat.comm.Experiment") +from ..dstat import 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__)) -from errors import InputError, VarError -import state -class Experiment(object): +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 - - def __init__(self, parameters): + Loops = experiment_loops.PlotLoop + __gsignals__ = { + 'exp_ready': (GObject.SIGNAL_RUN_FIRST, None, ()), + 'exp_done': (GObject.SIGNAL_RUN_FIRST, None, ()), + } + + def __init__(self, parameters=None, state=None): """Adds commands for gain and ADC.""" + super(Experiment, self).__init__() + self.current_command = None self.parameters = parameters + self.state = state self.databytes = 8 self.datapoint = 0 self.scan = 0 self.time = 0 self.plots = [] - - major, minor = state.dstat_version - if major >= 1: - if minor == 1: - self.__gaintable = [1e2, 3e2, 3e3, 3e4, 3e5, 3e6, 3e7, 5e8] - elif minor >= 2: - self.__gaintable = [1, 1e2, 3e3, 3e4, 3e5, 3e6, 3e7, 1e8] - self.__gain_trim_table = ['r100_trim', 'r100_trim', 'r3k_trim', - 'r30k_trim', 'r300k_trim', 'r3M_trim', - 'r30M_trim', 'r100M_trim'] - else: - raise VarError(parameters['version'], "Invalid version parameter.") - - self.gain = self.__gaintable[int(self.parameters['gain'])] - self.gain_trim = int( - state.settings[ - self.__gain_trim_table[int(self.parameters['gain'])] - ][1] - ) + self.re_voltage_scale = self.state['board_instance'].re_voltage_scale + + self.gain = self.state['board_instance'].gain[int(self.parameters['gain'])] + + try: + self.gain_trim = int( + self.state['settings'][ + self.state['board_instance'].gain_trim[int(self.parameters['gain'])] + ] + ) + except AttributeError: + logger.debug("No gain trim table.") self.commands = ["EA", "EG"] - if self.parameters['buffer_true']: + if self.parameters['buffer_true']: self.commands[0] += "2" else: self.commands[0] += "0" @@ -103,82 +110,129 @@ class Experiment(object): 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.data = OrderedDict(current_voltage=[([], [])]) self.columns = ['Voltage (mV)', 'Current (A)'] - self.plot_format = { - 'current_voltage' : {'labels' : self.columns, - 'xlims' : (0, 1) - } - } + # 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) - self.plots.append(PlotBox(['current_voltage'])) - - def write_command(self, cmd, params=None, retry=10): + def write_command(self, cmd, params=None, retry=5): """Write command to serial with optional number of retries.""" - def get_reply(): - reply = self.serial.readline().rstrip() - if reply.startswith('#'): - dstat_logger.info(reply) - return get_reply() - return reply + def get_reply(retries=3): + while True: + reply = self.serial.readline().decode('ascii').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): - time.sleep(0.2) - self.serial.reset_input_buffer() - self.serial.write('!{}\n'.format(n)) - time.sleep(.1) - - reply = get_reply() - + tries = 5 + while True: + time.sleep(0.2) + self.serial.reset_input_buffer() + self.serial.write('!{}\n'.format(n).encode('ascii')) + 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("Invalid response: {}".format(reply)) + logger.warning("Expected ACK got: {}".format(reply)) continue - - self.serial.write('{}\n'.format(cmd)) - reply = get_reply() + tries = 5 + while True: + self.serial.write('{}\n'.format(cmd).encode('ascii')) + try: + reply = get_reply() + except TransmitError: + if tries <= 0: + continue + tries -= 1 + pass + else: + break + if reply != "@RCV {}".format(n): - logger.warning("Invalid response: {}".format(reply)) + logger.warning("Expected RCV got: {}".format(reply)) continue if params is None: return True - reply = get_reply() + 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("Invalid response: {}".format(reply)) + logger.warning("Expected RQP got: {}".format(reply)) continue - - self.serial.write(" ".join(params) + " ") - - reply = get_reply() - if reply != "@RCP {}".format(n_params): - logger.warning("Invalid response: {}".format(reply)) - continue + tries = 5 + for i in params: + while True: + self.serial.write("{} ".format(i).encode('ascii')) + 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. Don't call directly as a process in Windows, - use run_wrapper instead. + then sends self.commands. """ self.serial = ser self.ctrl_pipe = ctrl_pipe @@ -188,8 +242,9 @@ class Experiment(object): try: for i in self.commands: + self.current_command = i status = "DONE" - if isinstance(i, (str, unicode)): + if isinstance(i, (str, bytes)): logger.info("Command: %s", i) if not self.write_command(i): @@ -225,26 +280,30 @@ class Experiment(object): 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 == b"DISCONNECT": + self.serial.write(b'a') + self.serial.reset_input_buffer() + logger.info("serial_handler: ABORT pressed!") + time.sleep(.3) + return False + elif input == 'a': + self.serial.write(b'a') + else: + self.serial.write(input) + try: while True: - if self.ctrl_pipe.poll(): - input = self.ctrl_pipe.recv() - logger.debug("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') - + check_ctrl() for line in self.serial: - if self.ctrl_pipe.poll(): - if self.ctrl_pipe.recv() == 'a': - self.serial.write('a') - - if line.startswith('B'): + check_ctrl() + line_in = line.decode("ascii") + + if line_in.startswith('B'): data = self.data_handler( (scan, self.serial.read(size=self.databytes))) data = self.data_postprocessing(data) @@ -252,24 +311,23 @@ class Experiment(object): self.data_pipe.send(data) try: self.datapoint += 1 - except AttributeError: #Datapoint counting is optional + except AttributeError: # Datapoint counting is optional pass - elif line.lstrip().startswith('S'): + elif line_in.lstrip().startswith('S'): scan += 1 - elif line.lstrip().startswith("#"): - dstat_logger.info(line.lstrip().rstrip()) + elif line_in.lstrip().startswith("#"): + dstat_logger.info(line_in.strip()) - elif line.lstrip().startswith("@DONE"): - dstat_logger.debug(line.lstrip().rstrip()) + elif line_in.lstrip().startswith("@DONE"): + dstat_logger.debug(line_in.strip()) time.sleep(.3) return True except serial.SerialException: return False - - + def data_handler(self, data_input): """Takes data_input as tuple -- (scan, data). Returns: @@ -278,8 +336,8 @@ class Experiment(object): scan, data = data_input voltage, current = struct.unpack(' 1: + prog = 1 + return prog + else: + return 1 - (abs(self.stop_mv - self.data['swv'][-1][0][-1])/self.max_mv) + 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] += " " + + def get_progress(self): + try: + return 1 - (abs(self.stop_mv - self.data['swv'][-1][0][-1])/self.max_mv) + except IndexError: + return 0 diff --git a/dstat_interface/core/interface/__init__.py b/dstat_interface/core/interface/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/dstat_interface/interface/acv.glade b/dstat_interface/core/interface/acv.glade similarity index 100% rename from dstat_interface/interface/acv.glade rename to dstat_interface/core/interface/acv.glade diff --git a/dstat_interface/interface/adc_pot.glade b/dstat_interface/core/interface/adc_pot.glade similarity index 100% rename from dstat_interface/interface/adc_pot.glade rename to dstat_interface/core/interface/adc_pot.glade diff --git a/dstat_interface/interface/adc_pot.py b/dstat_interface/core/interface/adc_pot.py similarity index 78% rename from dstat_interface/interface/adc_pot.py rename to dstat_interface/core/interface/adc_pot.py index 8e731629f4091076d045d58c7031346b24407ae7..a8c25c787d5183cd0494476ce36fe63d713cf805 100755 --- a/dstat_interface/interface/adc_pot.py +++ b/dstat_interface/core/interface/adc_pot.py @@ -17,40 +17,28 @@ # # You should have received a copy of the GNU General Public License # along with this program. If not, see . +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" + import sys + print("ERR: GTK not available") sys.exit(1) -from errors import InputError, VarError +from ..errors import InputError, VarError +from ..dstat import state -v1_1_gain = [(0, "100 Ω (15 mA FS)", "0"), - (1, "300 Ω (5 mA FS)", "1"), - (2, "3 kΩ (500 µA FS)", "2"), - (3, "30 kΩ (50 µA FS)", "3"), - (4, "300 kΩ (5 µA FS)", "4"), - (5, "3 MΩ (500 nA FS)", "5"), - (6, "30 MΩ (50 nA FS)", "6"), - (7, "500 MΩ (3 nA FS)", "7")] +mod_dir = os.path.dirname(os.path.abspath(__file__)) -v1_2_gain = [(0, "Bypass", "0"), - (1, "100 Ω (15 mA FS)", "1"), - (2, "3 kΩ (500 µA FS)", "2"), - (3, "30 kΩ (50 µA FS)", "3"), - (4, "300 kΩ (5 µA FS)", "4"), - (5, "3 MΩ (500 nA FS)", "5"), - (6, "30 MΩ (50 nA FS)", "6"), - (7, "100 MΩ (15 nA FS)", "7")] - class adc_pot(object): def __init__(self): self.builder = Gtk.Builder() - self.builder.add_from_file('interface/adc_pot.glade') + self.builder.add_from_file(os.path.join(mod_dir,'adc_pot.glade')) self.builder.connect_signals(self) self.cell = Gtk.CellRendererText() @@ -81,7 +69,7 @@ class adc_pot(object): 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.ui['gain_index'].set_active(2) self._params = {} @@ -135,15 +123,19 @@ class adc_pot(object): for i in self.ui: self.ui[i].set_active(self._params[i]) - def set_version(self, version): + 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() - if version[0] == 1: - if version[1] == 1: - for i in v1_1_gain: - self.gain_liststore.append(str(i)) - elif version[1] >= 2: - for i in v1_2_gain: - self.gain_liststore.append(i) + + for n, i in enumerate(self.version.gain_labels): + self.gain_liststore.append((n, i, str(n))) - \ No newline at end of file + self.ui['gain_index'].set_active(self.version.gain_default_index) \ No newline at end of file diff --git a/dstat_interface/interface/analysis_options.glade b/dstat_interface/core/interface/analysis_options.glade similarity index 100% rename from dstat_interface/interface/analysis_options.glade rename to dstat_interface/core/interface/analysis_options.glade diff --git a/dstat_interface/interface/calib.glade b/dstat_interface/core/interface/calib.glade similarity index 100% rename from dstat_interface/interface/calib.glade rename to dstat_interface/core/interface/calib.glade diff --git a/dstat_interface/interface/chronoamp.glade b/dstat_interface/core/interface/chronoamp.glade similarity index 100% rename from dstat_interface/interface/chronoamp.glade rename to dstat_interface/core/interface/chronoamp.glade diff --git a/dstat_interface/interface/cv.glade b/dstat_interface/core/interface/cv.glade similarity index 100% rename from dstat_interface/interface/cv.glade rename to dstat_interface/core/interface/cv.glade diff --git a/dstat_interface/interface/data_view.py b/dstat_interface/core/interface/data_view.py similarity index 95% rename from dstat_interface/interface/data_view.py rename to dstat_interface/core/interface/data_view.py index e4bd711f0d2af0f95f9bbda50a591419019644f2..e7c4db65ea4a99114c760dd14df70e3bc16104ed 100644 --- a/dstat_interface/interface/data_view.py +++ b/dstat_interface/core/interface/data_view.py @@ -1,7 +1,7 @@ from __future__ import division, absolute_import, print_function, unicode_literals import logging -logger = logging.getLogger("dstat.interface.data_view") +logger = logging.getLogger(__name__) from collections import OrderedDict diff --git a/dstat_interface/interface/db.glade b/dstat_interface/core/interface/db.glade similarity index 100% rename from dstat_interface/interface/db.glade rename to dstat_interface/core/interface/db.glade diff --git a/dstat_interface/interface/db.py b/dstat_interface/core/interface/db.py similarity index 98% rename from dstat_interface/interface/db.py rename to dstat_interface/core/interface/db.py index cc31db72e427d88d504ab7100992404621cdb5b6..e3622924e57590fc850be2dc95d7b2d5396bc881 100755 --- a/dstat_interface/interface/db.py +++ b/dstat_interface/core/interface/db.py @@ -30,7 +30,7 @@ except ImportError: print "ERR: GTK not available" sys.exit(1) -logger = logging.getLogger('dstat.interface.db') +logger = logging.getLogger(__name__) class DB_Window(GObject.GObject): __gsignals__ = { diff --git a/dstat_interface/interface/dpv.glade b/dstat_interface/core/interface/dpv.glade similarity index 100% rename from dstat_interface/interface/dpv.glade rename to dstat_interface/core/interface/dpv.glade diff --git a/dstat_interface/core/interface/dstatinterface.glade b/dstat_interface/core/interface/dstatinterface.glade new file mode 100644 index 0000000000000000000000000000000000000000..889e1d671a3b61dbabb1b9e230f73bfb00b4367c --- /dev/null +++ b/dstat_interface/core/interface/dstatinterface.glade @@ -0,0 +1,737 @@ + + + + + + False + 5 + True + dialog + DStat-interface + © Michael Dryden 2014 + This software is licensed under the GNU GPL v3 + http://microfluidics.utoronto.ca/dstat + Wheeler Microfuidics Lab + Michael Dryden +Thanks to Christian Fobel for help with Dropbot Plugin + + image-missing + gpl-3-0 + + + True + False + vertical + 2 + + + True + False + end + + + True + True + 0 + + + + + + + + + + + + True + False + center + gtk-missing-image + + + True + False + image7 + + + True + False + gtk-save-as + + + True + False + gtk-save-as + + + True + False + gtk-open + + + True + False + gtk-preferences + + + True + False + image7 + + + True + False + gtk-save-as + + + True + False + image7 + + + + + + + + + False + 6 + Main + 1200 + 800 + + + + True + False + vertical + + + True + False + + + True + False + File + + + True + False + + + Save Experiment Data… + True + False + image8 + False + + + + + + Save Plot… + True + False + image3 + False + + + + + + Save Parameters… + True + False + image4 + False + + + + + + Load Parameters… + True + False + image5 + False + + + + + + gtk-quit + True + False + True + True + + + + + + + + + + True + False + DStat + + + True + False + + + System Information + True + False + image7 + False + + + + + Firmware… + True + False + image2 + False + + + + + Reset EEPROM + True + False + image9 + False + + + + + + + + + True + False + Dropbot + + + True + False + + + gtk-connect + True + False + True + True + + + + + + gtk-disconnect + True + False + False + True + True + + + + + + + + + + True + False + Analysis + + + True + False + + + Analysis Options… + True + False + image6 + False + + + + + + + + + + True + False + About + + + True + False + + + gtk-about + True + False + True + True + + + + + + + + + + False + True + 0 + + + + + True + True + 300 + True + True + + + True + False + vertical + + + True + False + vertical + + + True + False + vertical + + + + + + False + False + 0 + + + + + True + False + Experiment: + + + + + + False + False + 10 + 1 + + + + + + + + True + False + + + False + True + 3 + + + + + False + False + 0 + + + + + True + False + vertical + + + + + + True + True + 1 + + + + + True + False + + + gtk-execute + True + True + True + True + + + + True + True + 0 + + + + + gtk-stop + True + False + True + True + True + + + + True + True + 1 + + + + + True + False + + + True + True + 2 + + + + + False + False + 2 + + + + + True + False + True + 10 + 15 + 5 + 2 + + + False + True + 3 + + + + + False + True + + + + + True + True + True + + + True + False + vertical + + + True + True + bottom + + + + + + + + + + + + + + + + + + + + + True + True + -1 + + + + + True + False + start + + + Autosave + True + True + False + True + + + False + True + 0 + + + + + True + False + start + select-folder + False + Select a Save Folder + + + True + True + 1 + + + + + True + True + True + start + 32 + ● + filename + False + gtk-file + False + False + File name + File name + + + False + True + 2 + + + + + False + False + 0 + + + + + + + True + False + Plot + + + False + + + + + + + + + + + + + + + + + True + True + + + + + True + True + 1 + + + + + True + False + + + True + False + 2 + + + True + True + end + 0 + + + + + True + False + Serial Port: + + + False + True + 5 + 1 + + + + + 128 + True + False + start + serial_liststore + + + False + False + 2 + + + + + gtk-connect + True + True + True + True + + + + False + False + 3 + + + + + Connect (PMT mode) + True + True + True + + + + False + False + 4 + + + + + gtk-disconnect + True + True + True + True + + + + False + False + 5 + + + + + gtk-refresh + True + True + True + True + + + + False + False + 6 + + + + + True + False + start + OCP: + True + + + False + False + 3 + 7 + + + + + False + True + 2 + + + + + + + 100 + 5 + 1 + 10 + + diff --git a/dstat_interface/interface/exp_int.py b/dstat_interface/core/interface/exp_int.py similarity index 84% rename from dstat_interface/interface/exp_int.py rename to dstat_interface/core/interface/exp_int.py index 397fe91bcc1c2dfb393d54cd3168604c2c31d79e..401c2cdb21f02d308f8721e32ea1958c15f80329 100755 --- a/dstat_interface/interface/exp_int.py +++ b/dstat_interface/core/interface/exp_int.py @@ -27,16 +27,20 @@ try: gi.require_version('Gtk', '3.0') from gi.repository import Gtk, GObject except ImportError: + import sys print("ERR: GTK not available") sys.exit(1) -import dstat_comm -import state -import experiments as exp -import experiments.cal as cal +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("dstat.interface.exp_int") +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 @@ -44,8 +48,8 @@ class ExpInterface(GObject.Object): 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, ()) + 'run_utility': (GObject.SIGNAL_RUN_FIRST, None, ()), + 'done_utility': (GObject.SIGNAL_RUN_FIRST, None, ()) } id = None @@ -58,14 +62,17 @@ class ExpInterface(GObject.Object): self.builder.connect_signals(self) self.entry = {} # to be used only for str parameters self._params = None - + + def get_experiment(self, parameters, state=None): + return self.__class__.experiment(parameters, state) + def _fill_params(self): self._params = dict.fromkeys(self.entry.keys()) @property def params(self): """Dict of parameters""" - if self._params == None: + if self._params is None: self._fill_params() self._get_params() return self._params @@ -77,7 +84,7 @@ class ExpInterface(GObject.Object): @params.setter def params(self, params): - if self._params == None: + if self._params is None: self._fill_params() for i in self._params: try: @@ -97,7 +104,8 @@ class ExpInterface(GObject.Object): 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. @@ -108,10 +116,10 @@ class Chronoamp(ExpInterface): get_params(self) """ id = 'cae' - experiment = exp.Chronoamp + experiment = chronoamp.Chronoamp def __init__(self): """Extends superclass method to support treeview.""" - super(Chronoamp, self).__init__('interface/chronoamp.glade') + super(Chronoamp, self).__init__(os.path.join(mod_dir, 'chronoamp.glade')) self.name = "Chronoamperometry" @@ -144,9 +152,9 @@ class Chronoamp(ExpInterface): self.builder.get_object('potential_entry').get_text()) time = int(self.builder.get_object('time_entry').get_text()) - if (potential > 1499 or potential < -1500): + if not state.board_instance.test_mv(potential): raise ValueError("Potential out of range") - if (time < 1 or time > 65535): + if not state.board_instance.test_s(time): raise ValueError("Time out of range") self.model.append([potential, time]) @@ -187,10 +195,10 @@ class Chronoamp(ExpInterface): class LSV(ExpInterface): """Experiment class for LSV.""" id = 'lsv' - experiment = exp.LSVExp + experiment = lsv.LSVExp def __init__(self): """Adds entry listings to superclass's self.entry dict""" - super(LSV, self).__init__('interface/lsv.glade') + 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') @@ -204,10 +212,10 @@ class LSV(ExpInterface): class CV(ExpInterface): """Experiment class for CV.""" id = 'cve' - experiment = exp.CVExp + experiment = cv.CVExp def __init__(self): """Adds entry listings to superclass's self.entry dict""" - super(CV, self).__init__('interface/cv.glade') + 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') @@ -223,10 +231,10 @@ class CV(ExpInterface): class SWV(ExpInterface): """Experiment class for SWV.""" id = 'swv' - experiment = exp.SWVExp + experiment = swv.SWVExp def __init__(self): """Adds entry listings to superclass's self.entry dict""" - super(SWV, self).__init__('interface/swv.glade') + 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') @@ -262,10 +270,10 @@ class SWV(ExpInterface): class DPV(ExpInterface): """Experiment class for DPV.""" id = 'dpv' - experiment = exp.DPVExp + experiment = swv.DPVExp def __init__(self): """Adds entry listings to superclass's self.entry dict""" - super(DPV, self).__init__('interface/dpv.glade') + super(DPV, self).__init__(os.path.join(mod_dir, 'dpv.glade')) self.name = "Differential Pulse Voltammetry" @@ -297,10 +305,10 @@ class DPV(ExpInterface): class PD(ExpInterface): """Experiment class for PD.""" id = 'pde' - experiment = exp.PDExp + experiment = chronoamp.PDExp def __init__(self): """Adds entry listings to superclass's self.entry dict""" - super(PD, self).__init__('interface/pd.glade') + super(PD, self).__init__(os.path.join(mod_dir, 'pd.glade')) self.name = "Photodiode/PMT" @@ -351,7 +359,7 @@ class PD(ExpInterface): self.bool[i].set_active(self._params[i]) self.builder.get_object('voltage_adjustment').set_value( - self._params['voltage'] ) + self._params['voltage']) def on_light_button_clicked(self, data=None): __main__.MAIN.on_pot_stop_clicked() @@ -363,12 +371,12 @@ class PD(ExpInterface): try: self.builder.get_object('light_label').set_text(str( dstat_comm.read_light_sensor())) - dstat_comm.read_settings() - state.settings['tcs_enabled'][1] = '1' # Make sure TCS enabled - dstat_comm.write_settings() + comm.read_settings() + state.settings['tcs_enabled'] = '1' # Make sure TCS enabled + comm.write_settings() self.builder.get_object('threshold_entry').set_text(str( - state.settings['tcs_clear_threshold'][1])) + state.settings['tcs_clear_threshold'])) __main__.MAIN.start_ocp() finally: @@ -382,12 +390,12 @@ class PD(ExpInterface): i.set_sensitive(False) try: - state.settings['tcs_clear_threshold'][1] = self.builder.get_object( + state.settings['tcs_clear_threshold'] = self.builder.get_object( 'threshold_entry').get_text() - dstat_comm.write_settings() - dstat_comm.read_settings() + comm.write_settings() + comm.read_settings() self.builder.get_object('threshold_entry').set_text( - str(state.settings['tcs_clear_threshold'][1])) + str(state.settings['tcs_clear_threshold'])) __main__.MAIN.start_ocp() finally: @@ -405,10 +413,10 @@ class PD(ExpInterface): class POT(ExpInterface): """Experiment class for Potentiometry.""" id = 'pot' - experiment = exp.PotExp + experiment = pot.PotExp def __init__(self): """Adds entry listings to superclass's self.entry dict""" - super(POT, self).__init__('interface/potexp.glade') + super(POT, self).__init__(os.path.join(mod_dir, 'potexp.glade')) self.name = "Potentiometry" self.entry['time'] = self.builder.get_object('time_entry') @@ -416,10 +424,10 @@ class POT(ExpInterface): class CAL(ExpInterface): """Experiment class for Calibrating gain.""" id = 'cal' - experiment = exp.CALExp + experiment = cal.CALExp def __init__(self): """Adds entry listings to superclass's self.entry dict""" - super(CAL, self).__init__('interface/calib.glade') + super(CAL, self).__init__(os.path.join(mod_dir, 'calib.glade')) self.name = "Calilbration" self.entry['time'] = self.builder.get_object('time_entry') @@ -442,22 +450,22 @@ class CAL(ExpInterface): try: __main__.MAIN.on_pot_stop_clicked() __main__.MAIN.stop_ocp() - dstat_comm.read_settings() + comm.read_settings() self.entry['R100'].set_text(str( - state.settings['r100_trim'][1])) + state.settings['r100_trim'])) self.entry['R3k'].set_text(str( - state.settings['r3k_trim'][1])) + state.settings['r3k_trim'])) self.entry['R30k'].set_text(str( - state.settings['r30k_trim'][1])) + state.settings['r30k_trim'])) self.entry['R300k'].set_text(str( - state.settings['r300k_trim'][1])) + state.settings['r300k_trim'])) self.entry['R3M'].set_text(str( - state.settings['r3M_trim'][1])) + state.settings['r3M_trim'])) self.entry['R30M'].set_text(str( - state.settings['r30M_trim'][1])) + state.settings['r30M_trim'])) self.entry['R100M'].set_text(str( - state.settings['r100M_trim'][1])) + state.settings['r100M_trim'])) __main__.MAIN.start_ocp() @@ -472,14 +480,14 @@ class CAL(ExpInterface): __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() - dstat_comm.write_settings() + state.settings['r100_trim'] = self.entry['R100'].get_text() + state.settings['r3k_trim'] = self.entry['R3k'].get_text() + state.settings['r30k_trim'] = self.entry['R30k'].get_text() + state.settings['r300k_trim'] = self.entry['R300k'].get_text() + state.settings['r3M_trim'] = self.entry['R3M'].get_text() + state.settings['r30M_trim'] = self.entry['R30M'].get_text() + state.settings['r100M_trim'] = self.entry['R100M'].get_text() + comm.write_settings() __main__.MAIN.start_ocp() @@ -487,7 +495,7 @@ class CAL(ExpInterface): 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): + if int(self.entry['time'].get_text()) <= 0 or int(self.entry['time'].get_text()) > 65535: logger.error("ERR: Time out of range") return @@ -502,28 +510,29 @@ class CAL(ExpInterface): for i in offset: logger.info("{} {}".format(i, str(-offset[i]))) - state.settings[i][1] = str(-offset[i]) + state.settings[i] = str(-offset[i]) self.entry['R100'].set_text(str( - state.settings['r100_trim'][1])) + state.settings['r100_trim'])) self.entry['R3k'].set_text(str( - state.settings['r3k_trim'][1])) + state.settings['r3k_trim'])) self.entry['R30k'].set_text(str( - state.settings['r30k_trim'][1])) + state.settings['r30k_trim'])) self.entry['R300k'].set_text(str( - state.settings['r300k_trim'][1])) + state.settings['r300k_trim'])) self.entry['R3M'].set_text(str( - state.settings['r3M_trim'][1])) + state.settings['r3M_trim'])) self.entry['R30M'].set_text(str( - state.settings['r30M_trim'][1])) + state.settings['r30M_trim'])) self.entry['R100M'].set_text(str( - state.settings['r100M_trim'][1])) + state.settings['r100M_trim'])) __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: diff --git a/dstat_interface/interface/exp_window.py b/dstat_interface/core/interface/exp_window.py similarity index 84% rename from dstat_interface/interface/exp_window.py rename to dstat_interface/core/interface/exp_window.py index 413d43a2e8d00a8004ffc7bf0ac432448c3dad68..cced5a5905e914f13428da170b8f1c7e9b3b4075 100755 --- a/dstat_interface/interface/exp_window.py +++ b/dstat_interface/core/interface/exp_window.py @@ -26,18 +26,21 @@ try: gi.require_version('Gtk', '3.0') from gi.repository import Gtk, GObject except ImportError: - print "ERR: GTK not available" + import sys + print("ERR: GTK not available") sys.exit(1) -import interface.exp_int as exp +from . import exp_int + +logger = logging.getLogger(__name__) -logger = logging.getLogger("dstat.interface.exp_window") 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 @@ -46,13 +49,14 @@ class Experiments(GObject.Object): # (experiment index in UI, experiment) classes = {c.id : c() # Make class instances - for _, c in inspect.getmembers(exp, inspect.isclass) - if issubclass(c, exp.ExpInterface) - and c is not exp.ExpInterface + 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 + + # fill exp_section exp_section = self.builder.get_object('exp_section_box') self.containers = {} @@ -85,7 +89,10 @@ class Experiments(GObject.Object): """Change the experiment window when experiment box changed.""" self.set_exp(self.expcombobox.get_active_id()) - def setup_exp(self, parameters): + def setup_exp(self, parameters, state=None): + """Takes parameters. + Returns experiment instance. + """ exp = self.classes[self.expcombobox.get_active_id()] try: exp.param_test(parameters) @@ -94,8 +101,8 @@ class Experiments(GObject.Object): "Experiment {} has no defined parameter test.".format( exp.name) ) - return exp.experiment(parameters) - + return exp.get_experiment(parameters, state) + def hide_exps(self): for key in self.containers: self.containers[key].hide() @@ -117,4 +124,7 @@ class Experiments(GObject.Object): return self.classes[experiment].params def set_params(self, experiment, parameters): - self.classes[experiment].params = parameters \ No newline at end of file + 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 new file mode 100755 index 0000000000000000000000000000000000000000..3a8228b91893a103debf76d5867e09dc129996c9 --- /dev/null +++ b/dstat_interface/core/interface/hw_info.py @@ -0,0 +1,110 @@ +#!/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/interface/lsv.glade b/dstat_interface/core/interface/lsv.glade similarity index 100% rename from dstat_interface/interface/lsv.glade rename to dstat_interface/core/interface/lsv.glade diff --git a/dstat_interface/interface/pd.glade b/dstat_interface/core/interface/pd.glade similarity index 100% rename from dstat_interface/interface/pd.glade rename to dstat_interface/core/interface/pd.glade diff --git a/dstat_interface/plot.py b/dstat_interface/core/interface/plot.py similarity index 98% rename from dstat_interface/plot.py rename to dstat_interface/core/interface/plot.py index 7e87c41b05021601d353953f9ddc9ce2bdbbefa8..cc0d89b70368c777b427919639caa2649edc074e 100755 --- a/dstat_interface/plot.py +++ b/dstat_interface/core/interface/plot.py @@ -25,7 +25,8 @@ try: gi.require_version('Gtk', '3.0') from gi.repository import Gtk except ImportError: - print "ERR: GTK not available" + import sys + print("ERR: GTK not available") sys.exit(1) from matplotlib.figure import Figure diff --git a/dstat_interface/interface/plot_ui.py b/dstat_interface/core/interface/plot_ui.py similarity index 90% rename from dstat_interface/interface/plot_ui.py rename to dstat_interface/core/interface/plot_ui.py index b0ff570fb85c4875576e73cdcb6a663c3d7a7c77..5976273fced0ff0c8d5cbb3de893ee35bd8ae258 100644 --- a/dstat_interface/interface/plot_ui.py +++ b/dstat_interface/core/interface/plot_ui.py @@ -1,12 +1,13 @@ import logging -logger = logging.getLogger("dstat.interface.plot_ui") +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" + import sys + print("ERR: GTK not available") sys.exit(1) from matplotlib.backends.backend_gtk3 \ diff --git a/dstat_interface/interface/potexp.glade b/dstat_interface/core/interface/potexp.glade similarity index 100% rename from dstat_interface/interface/potexp.glade rename to dstat_interface/core/interface/potexp.glade diff --git a/dstat_interface/interface/save.py b/dstat_interface/core/interface/save.py similarity index 97% rename from dstat_interface/interface/save.py rename to dstat_interface/core/interface/save.py index 76a714e49b41d0fb54347b224bf2aec2984aa573..cde0ca39043753ec7a57dd1e6076adb1fb38fb8f 100755 --- a/dstat_interface/interface/save.py +++ b/dstat_interface/core/interface/save.py @@ -22,21 +22,20 @@ from __future__ import division, absolute_import, print_function, unicode_litera 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: + import sys print("ERR: GTK not available") sys.exit(1) -import numpy as np -import logging -logger = logging.getLogger("dstat.interface.save") - -from errors import InputError, VarError -from params import save_params, load_params +from ..params import save_params, load_params def manSave(current_exp): fcd = Gtk.FileChooserDialog("Save…", None, Gtk.FileChooserAction.SAVE, @@ -164,6 +163,7 @@ def man_param_load(window): elif response == Gtk.ResponseType.CANCEL: fcd.destroy() + def autoSave(exp, path, name): if name == "": name = "file" @@ -173,6 +173,7 @@ def autoSave(exp, path, name): save_text(exp, path) + def autoPlot(exp, path, name): if name == "": name = "file" @@ -202,7 +203,8 @@ def save_text(exp, path): 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. diff --git a/dstat_interface/interface/swv.glade b/dstat_interface/core/interface/swv.glade similarity index 100% rename from dstat_interface/interface/swv.glade rename to dstat_interface/core/interface/swv.glade diff --git a/dstat_interface/microdrop.py b/dstat_interface/core/microdrop.py similarity index 100% rename from dstat_interface/microdrop.py rename to dstat_interface/core/microdrop.py diff --git a/dstat_interface/params.py b/dstat_interface/core/params.py similarity index 93% rename from dstat_interface/params.py rename to dstat_interface/core/params.py index 0aa85802c1dd47a248743b01beb1c8dc84b55f74..a42778c04d4bc25fca9a0d3a74cea4fedea2fef7 100755 --- a/dstat_interface/params.py +++ b/dstat_interface/core/params.py @@ -21,16 +21,16 @@ import logging import yaml -from errors import InputError +from .errors import InputError + +logger = logging.getLogger(__name__) -logger = logging.getLogger('dstat.params') def get_params(window): """Fetches and returns dict of all parameters for saving.""" selection = window.exp_window.expcombobox.get_active_id() - parameters = {} - parameters['experiment_index'] = selection + parameters = {'experiment_index' : selection} try: parameters['version'] = window.version @@ -46,6 +46,7 @@ def get_params(window): return parameters + def save_params(window, path): """Fetches current params and saves to path.""" logger.info("Save to: %s", path) @@ -54,6 +55,7 @@ def save_params(window, path): with open(path, 'w') as f: yaml.dump(params, f) + def load_params(window, path): """Loads params from a path into UI elements.""" @@ -65,9 +67,10 @@ def load_params(window, path): pass with open(path, 'r') as f: - params = yaml.load(f) + params = yaml.load(f, Loader=yaml.SafeLoader) set_params(window, params) + def set_params(window, params): window.adc_pot.params = params if 'experiment_index' in params: diff --git a/dstat_interface/plugin.py b/dstat_interface/core/plugin.py similarity index 95% rename from dstat_interface/plugin.py rename to dstat_interface/core/plugin.py index 59ec93d013d7c1a6e3410f6722fc4b6ed5f55edb..ad1058edfa072c17b7c6c253a4f3123a3d1d1d7c 100644 --- a/dstat_interface/plugin.py +++ b/dstat_interface/core/plugin.py @@ -1,10 +1,10 @@ # -*- 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 +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 diff --git a/dstat_interface/core/utils/__init__.py b/dstat_interface/core/utils/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/dstat_interface/version.py b/dstat_interface/core/utils/version.py similarity index 81% rename from dstat_interface/version.py rename to dstat_interface/core/utils/version.py index 343f158f74594923d656e5be8ad57b09b3c56a1c..0bc434bb77f6e19c3cf7febde5bfa45636fafec4 100644 --- a/dstat_interface/version.py +++ b/dstat_interface/core/utils/version.py @@ -35,6 +35,7 @@ With that setup, a new release can be labelled by simply invoking: git tag -s v1.0 """ +from __future__ import division, absolute_import, print_function, unicode_literals __author__ = ('Douglas Creager ', 'Michal Nazarewicz ') @@ -48,9 +49,14 @@ __all__ = ('getVersion') import re import subprocess import sys +import os.path +import inspect +import logging +logger = logging.getLogger(__name__) -RELEASE_VERSION_FILE = 'RELEASE-VERSION' +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+)*)?' @@ -60,7 +66,7 @@ _GIT_DESCRIPTION_RE = r'^v(?P%s)-(?P\d+)-g(?P[\da-f]+)$' % ( _PEP386_SHORT_VERSION_RE) -def readGitVersion(): +def read_git_version(): try: proc = subprocess.Popen(('git', 'describe', '--long', '--match', 'v[0-9]*.*'), @@ -68,7 +74,7 @@ def readGitVersion(): data, _ = proc.communicate() if proc.returncode: return None - ver = data.splitlines()[0].strip() + ver = data.splitlines()[0].strip().decode('utf-8') proc = subprocess.Popen(('git', 'rev-parse', '--abbrev-ref', 'HEAD'), stdout=subprocess.PIPE, stderr=subprocess.PIPE) branch, _ = proc.communicate() @@ -80,9 +86,9 @@ def readGitVersion(): 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) + logger.warning('Git description (%s) is invalid, ignoring', ver) return None commits = int(m.group('commits')) @@ -99,7 +105,7 @@ def readGitVersion(): return version -def readReleaseVersion(): +def read_release_version(): try: fd = open(RELEASE_VERSION_FILE) try: @@ -107,29 +113,28 @@ def readReleaseVersion(): 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) + logger.warning('release version (%s) is invalid, will use it anyways', ver) return ver except: return None -def writeReleaseVersion(version): +def write_release_version(version): fd = open(RELEASE_VERSION_FILE, 'w') fd.write('%s\n' % version) fd.close() -def getVersion(): - release_version = readReleaseVersion() - version = readGitVersion() or release_version +def get_version(): + release_version = read_release_version() + version = read_git_version() or release_version if not version: raise ValueError('Cannot find the version number') if version != release_version: - writeReleaseVersion(version) + write_release_version(version) return version if __name__ == '__main__': - print getVersion() + print(get_version()) diff --git a/dstat_interface/dstat_comm.py b/dstat_interface/dstat_comm.py deleted file mode 100755 index b50aa6434b3b3070d37bfacaebe3a89807c4b920..0000000000000000000000000000000000000000 --- a/dstat_interface/dstat_comm.py +++ /dev/null @@ -1,466 +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 -# -# -# 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 . - -import serial -from serial.tools import list_ports -import time -import struct -import multiprocessing as mp -from collections import OrderedDict -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 errors import InputError, VarError - -logger = logging.getLogger("dstat.comm") -dstat_logger = logging.getLogger("dstat.comm.DSTAT") -exp_logger = logging.getLogger("dstat.comm.Experiment") - -import state - -class AlreadyConnectedError(Exception): - def __init__(self): - super(AlreadyConnectedError, self).__init__(self, - "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.") - - -def _serial_process(ser_port, proc_pipe, ctrl_pipe, data_pipe): - ser_logger = logging.getLogger("dstat.comm._serial_process") - - connected = False - - try: - ser = serial.Serial(ser_port, timeout=1) - time.sleep(2) - ser.reset_input_buffer() - ser_logger.info("Reattaching DStat udc") - # ser.write("!R") # Send restart command - ser.close() - except serial.SerialException: - return 1 - - for i in range(5): - time.sleep(1) # Give OS time to enumerate - - try: - ser = serial.Serial(ser_port, timeout=1) - ser_logger.info("Connecting") - time.sleep(2) - connected = True - except serial.SerialException: - pass - - if connected is True: - break - - if ser.isOpen() is False: - ser_logger.info("Connection Error") - return 1 - - ser.write('!0 ') - - for i in range(10): - if ser.readline().rstrip()=="@ACK 0": - if ser.readline().rstrip()=="@RCV 0": - break - else: - time.sleep(.5) - ser.reset_input_buffer() - ser.write('!0 ') - time.sleep(.1) - - - while True: - # These can only be called when no experiment is running - if ctrl_pipe.poll(): - ctrl_buffer = ctrl_pipe.recv() - - if ctrl_buffer == ('a' or "DISCONNECT"): - proc_pipe.send("ABORT") - ser.write('a') - ser_logger.info("ABORT") - - if ctrl_buffer == "DISCONNECT": - ser_logger.info("DISCONNECT") - ser.close() - proc_pipe.send("DISCONNECT") - return 0 - - elif proc_pipe.poll(): - while ctrl_pipe.poll(): - ctrl_pipe.recv() - try: - return_code = proc_pipe.recv().run(ser, ctrl_pipe, data_pipe) - except serial.SerialException: - proc_pipe.send("DISCONNECT") - return 0 - ser_logger.info('Return code: %s', str(return_code)) - - proc_pipe.send(return_code) - - else: - time.sleep(.1) - - - -class SerialConnection(GObject.Object): - __gsignals__ = { - 'connected': (GObject.SIGNAL_RUN_FIRST, None, ()), - 'disconnected': (GObject.SIGNAL_RUN_FIRST, None, ()) - } - - def __init__(self): - super(SerialConnection, self).__init__() - self.connected = False - - def connect(self, ser_port): - 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.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): - self.assert_connected() - - self.proc_pipe_p.send(exp) - - def stop_exp(self): - self.assert_connected() - self.send_ctrl('a') - - def get_proc(self, block=False): - self.assert_connected() - - if block is True: - return self.proc_pipe_p.recv() - else: - if self.proc_pipe_p.poll() is True: - return self.proc_pipe_p.recv() - else: - return None - - def get_data(self, block=False): - self.assert_connected() - - if block is True: - return self.data_pipe_p.recv() - else: - if self.data_pipe_p.poll() is True: - 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): - self.assert_connected() - - self.ctrl_pipe_p.send(ctrl) - - def disconnect(self): - self.send_ctrl('a') - time.sleep(.2) - self.proc.terminate() - 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) - 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 - - parted = input.rstrip().split('.') - e = "PCB version: " - e += str(input.rstrip()) - dstat_logger.info(e) - - data_pipe.send((int(parted[0]), int(parted[1]))) - 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): - """Tries to contact DStat and get version. Returns a list of - [(major, minor), serial instance]. If no response, returns empty tuple. - - Arguments: - ser_port -- address of serial port to use - """ - state.ser = SerialConnection() - - state.ser.connect(ser_port) - state.ser.start_exp(VersionCheck()) - result = state.ser.get_proc(block=True) - if result == "SERIAL_ERROR": - buffer = 1 - else: - buffer = state.ser.get_data(block=True) - logger.debug("version_check done") - time.sleep(.1) - - return buffer - - -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(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) - - self.ser.reset_input_buffer() - self.ser.write('!{}\n'.format(n)) - - for i in range(10): - if self.ser.readline().rstrip()=="@ACK {}".format(n): - self.ser.write('SW\n') - if self.ser.readline().rstrip()=="@RCV {}".format(n): - break - else: - time.sleep(.5) - self.ser.reset_input_buffer() - self.ser.write('!{}\n'.format(n)) - time.sleep(.1) - - for line in self.ser: - if 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 - -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.settings = state.ser.get_data(block=True) - - 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. - """ - - state.ser.flush_data() - state.ser.start_exp(Settings(task='w', settings=state.settings)) - - 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): - try: - self.ports, _, _ = zip(*list_ports.comports()) - except ValueError: - self.ports = [] - logger.error("No serial ports found") - - def refresh(self): - """Refreshes list of ports.""" - self.ports, _, _ = zip(*list_ports.comports()) \ No newline at end of file diff --git a/dstat_interface/experiments/__init__.py b/dstat_interface/experiments/__init__.py deleted file mode 100644 index b1fb5aef786aa35925adcf27bdf6b5f62d4be960..0000000000000000000000000000000000000000 --- a/dstat_interface/experiments/__init__.py +++ /dev/null @@ -1,14 +0,0 @@ -__all__ = [] - -import pkgutil -import inspect - -for loader, name, is_pkg in pkgutil.walk_packages(__path__): - 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/experiments/cv.py b/dstat_interface/experiments/cv.py deleted file mode 100644 index fbeda5653354d01592b20cf5ca4bba310a81d527..0000000000000000000000000000000000000000 --- a/dstat_interface/experiments/cv.py +++ /dev/null @@ -1,42 +0,0 @@ -import time -import struct - -from experiments.experiment_template import PlotBox, Experiment - -class CVExp(Experiment): - id = 'cve' - """Cyclic Voltammetry experiment""" - def setup(self): - 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.plot_format['current_voltage']['xlims'] = ( - int(self.parameters['v1']), - int(self.parameters['v2']) - ) - - 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'])* - (65536./3000)+32768)) - self.commands[2] += " " - self.commands[2] += str(int(int(self.parameters['dep_mV'])* - (65536./3000)+32768)) - self.commands[2] += " " - self.commands[2] += str(self.parameters['v1']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['v2']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['start']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['scans']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['slope']) - self.commands[2] += " " \ No newline at end of file diff --git a/dstat_interface/experiments/lsv.py b/dstat_interface/experiments/lsv.py deleted file mode 100644 index 9042a5e4c01fea7eaed4d595ede6f31fe89594fd..0000000000000000000000000000000000000000 --- a/dstat_interface/experiments/lsv.py +++ /dev/null @@ -1,37 +0,0 @@ -import time -import struct - -from experiments.experiment_template import PlotBox, Experiment - -class LSVExp(Experiment): - """Linear Scan Voltammetry experiment""" - id = 'lsv' - def setup(self): - super(LSVExp, self).setup() - - self.datatype = "linearData" - self.datalength = 2 - self.databytes = 6 # uint16 + int32 - self.plot_format['current_voltage']['xlims'] = ( - 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'])* - (65536./3000)+32768)) - self.commands[2] += " " - self.commands[2] += str(int(int(self.parameters['dep_mV'])* - (65536./3000)+32768)) - self.commands[2] += " " - self.commands[2] += str(self.parameters['start']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['stop']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['slope']) - self.commands[2] += " " \ No newline at end of file diff --git a/dstat_interface/experiments/swv.py b/dstat_interface/experiments/swv.py deleted file mode 100644 index 2f3ba803da10e61f15078946485867b641081547..0000000000000000000000000000000000000000 --- a/dstat_interface/experiments/swv.py +++ /dev/null @@ -1,147 +0,0 @@ -import time -import struct -from copy import deepcopy - -from experiments.experiment_template import PlotBox, Experiment - -class SWVBox(PlotBox): - 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([],[]) - -class SWVExp(Experiment): - """Square Wave Voltammetry experiment""" - id = 'swv' - def setup(self): - self.plots.append(SWVBox(['swv'])) - - 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.plot_format = { - 'swv' : {'labels' : ('Voltage (mV)', - 'Current (A)' - ), - 'xlims' : (int(self.parameters['start']), - int(self.parameters['stop'])) - } - } - - 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'])* - (65536./3000)+32768)) - self.commands[2] += " " - self.commands[2] += str(int(int(self.parameters['dep_mV'])* - (65536./3000)+32768)) - self.commands[2] += " " - self.commands[2] += str(self.parameters['start']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['stop']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['step']) - self.commands[2] += " " - self.commands[2] += str(self.parameters['pulse']) - 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(' - - - - - False - 5 - True - dialog - DStat-interface - 1.0.3 - © Michael Dryden 2014 - This software is licensed under the GNU GPL v3 - http://microfluidics.utoronto.ca/dstat - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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- - - - False - False - 0 - - - - - True - False - vertical - - - - - - True - True - 1 - - - - - True - False - - - gtk-execute - True - True - True - True - - - - True - True - 0 - - - - - gtk-stop - True - False - True - True - True - - - - True - True - 1 - - - - - True - False - - - True - True - 2 - - - - - False - False - 2 - - - - - False - True - - - - - True - True - True - - - True - False - vertical - - - True - True - bottom - - - - - - - - - - - - - - - - - - - - - True - True - -1 - - - - - True - False - start - - - Autosave - True - True - False - True - - - False - True - 0 - - - - - True - False - start - select-folder - False - Select a Save Folder - - - True - True - 1 - - - - - True - True - True - start - 32 - ● - filename - False - gtk-file - False - False - File name - File name - - - False - True - 2 - - - - - False - False - 0 - - - - - - - True - False - Plot - - - False - - - - - - - - - - - - - - - - - True - True - - - - - True - True - 1 - - - - - True - False - - - True - False - 2 - - - True - True - end - 0 - - - - - True - False - Serial Port: - - - False - True - 5 - 1 - - - - - 128 - True - False - start - serial_liststore - - - False - False - 2 - - - - - gtk-connect - True - True - True - True - - - - False - False - 3 - - - - - Connect (PMT mode) - True - True - True - - - - False - False - 4 - - - - - gtk-disconnect - True - True - True - True - - - - False - False - 5 - - - - - gtk-refresh - True - True - True - True - - - - False - False - 6 - - - - - True - False - start - OCP: - True - - - False - False - 3 - 7 - - - - - False - True - 2 - - - - - - - 100 - 5 - 1 - 10 - - diff --git a/dstat_interface/interface_test.spec.bak b/dstat_interface/interface_test.spec.bak deleted file mode 100644 index 2a51ef2895825490862096abd32fa88549014575..0000000000000000000000000000000000000000 --- a/dstat_interface/interface_test.spec.bak +++ /dev/null @@ -1,25 +0,0 @@ -# -*- mode: python -*- -a = Analysis(['interface_test.py'], - hiddenimports=[], - hookspath=None, - runtime_hooks=None) -glade_tree = Tree('./interface', prefix = 'interface', excludes=['*.py','*.pyc']) -drivers_tree = Tree('./drivers', prefix = 'drivers') -pyz = PYZ(a.pure) -exe = EXE(pyz, - a.scripts, - exclude_binaries=True, - name='interface_test.exe', - debug=False, - strip=None, - upx=True, - console=True ) -coll = COLLECT(exe, - drivers_tree, - glade_tree, - a.binaries, - a.zipfiles, - a.datas, - strip=None, - upx=True, - name='interface_test') diff --git a/dstat_interface/main.py b/dstat_interface/main.py index 32c58f027b2662765dcebdd8e843e047f95eaac5..4fd1164b91dfa18957ba90ef71d6b8a9a4b2f234 100755 --- a/dstat_interface/main.py +++ b/dstat_interface/main.py @@ -20,68 +20,71 @@ """ 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 copy import deepcopy 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 get_version +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 pygtk -# pygtk.require('2.0') -# except ImportError: -# print "ERR: PyGTK 2.0 not available" -# sys.exit(1) try: import gi gi.require_version('Gtk', '3.0') - from gi.repository import Gtk, GObject + from gi.repository import Gtk, GObject, GLib except ImportError: - print "ERR: GTK not available" + print("ERR: GTK not available") sys.exit(1) -from serial import SerialException -import logging -os.chdir(os.path.dirname(os.path.abspath(sys.argv[0]))) - -from version import getVersion -import interface.save as save -import dstat_comm as comm -import experiments as exp -import interface.exp_window as exp_window -import interface.adc_pot as adc_pot -import interface.plot_ui -import interface.data_view -import plot -import params -import parameter_test -import analysis -import zmq -import state -from errors import InputError - -from plugin import DstatPlugin, get_hub_uri +mod_dir = os.path.dirname(os.path.abspath(__file__)) +conf_path = os.path.join(os.path.expanduser("~"), '.dstat-interface') # Setup Logging -root_logger = logging.getLogger("dstat") -root_logger.setLevel(level=logging.INFO) +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) -root_logger.addHandler(log_handler) -logger = logging.getLogger("dstat.main") +for log in loggers: + log.setLevel(level=logging.INFO) + log.addHandler(log_handler) -class Main(object): + +class Main(GObject.Object): """Main program """ + __gsignals__ = { + 'exp_start': (GObject.SignalFlags.RUN_FIRST, None, ()), + 'exp_stop': (GObject.SignalFlags.RUN_FIRST, None, ()) + } + def __init__(self): + super(Main, self).__init__() self.builder = Gtk.Builder() - self.builder.add_from_file('interface/dstatinterface.glade') + self.builder.add_from_file( + os.path.join(mod_dir, 'core/interface/dstatinterface.glade')) self.builder.connect_signals(self) self.cell = Gtk.CellRendererText() @@ -92,6 +95,8 @@ class Main(object): 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") @@ -111,15 +116,15 @@ class Main(object): # Setup Plots self.plot_notebook = self.builder.get_object('plot_notebook') self.main_notebook = self.builder.get_object('main_notebook') - self.data_view = interface.data_view.DataPage(self.main_notebook) - self.info_page = interface.data_view.InfoPage(self.main_notebook) + self.data_view = data_view.DataPage(self.main_notebook) + self.info_page = data_view.InfoPage(self.main_notebook) - #fill adc_pot_box + # 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 + # 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') @@ -127,9 +132,8 @@ class Main(object): 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 = comm.SerialDevices() + self.serial_devices = dstat.comm.SerialDevices() for i in self.serial_devices.ports: self.serial_liststore.append([i]) @@ -139,10 +143,33 @@ class Main(object): 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() + ver = get_version() except ValueError: ver = "1.x" logger.warning("Could not fetch version number") @@ -152,12 +179,11 @@ class Main(object): 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( @@ -186,72 +212,105 @@ class Main(object): def quit(self): """Disconnect and save parameters on quit.""" - params.save_params(self, 'last_params.yml') - - self.on_serial_disconnect_clicked() + + 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.response = self.aboutdialog.run() # waits for user to click close + 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.""" - self.serial_devices.refresh() - self.serial_liststore.clear() + 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, data=None): + 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) - state.dstat_version = comm.version_check(self.serial_liststore.get_value( - self.serial_combobox.get_active_iter(), 0)) + 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) - if not len(state.dstat_version) == 2: - self.statusbar.push(self.error_context_id, - "Communication Error") - return + self.adc_pot.set_version() + self.statusbar.push( + self.message_context_id, + "DStat version: {}".format( + dstat.state.dstat_version.base_version) + ) - else: - self.adc_pot.set_version(state.dstat_version) - self.statusbar.push(self.error_context_id, - "".join(["DStat version: ", - str(state.dstat_version[0]), - ".", str(state.dstat_version[1])]) - ) + dstat.comm.read_settings() - comm.read_settings() + try: + if dstat.state.settings['dac_units_true'] != '1': + dstat.state.settings['dac_units_true'] = '1' + dstat.comm.write_settings() + except KeyError: + logger.warning("Connected DStat does not support sending DAC units.") + dialog = Gtk.MessageDialog( + parent=self.window, + flags=0, message_type=Gtk.MessageType.WARNING, + buttons=Gtk.ButtonsType.OK, + text="Connected DStat does not support sending DAC units." + + "Update firmware or set potentials will be incorrect!") - self.start_ocp() - self.connected = True - self.serial_connect.set_sensitive(False) - self.serial_pmt_connect.set_sensitive(False) - self.serial_disconnect.set_sensitive(True) + dialog.run() + dialog.destroy() - except AttributeError as err: - logger.warning("AttributeError: %s", err) - self.serial_connect.set_sensitive(True) - except TypeError as err: - logger.warning("TypeError: %s", err) + 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: - params.load_params(self, 'last_params.yml') + 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: @@ -262,46 +321,53 @@ class Main(object): self.stop_ocp() else: self.on_pot_stop_clicked() - state.ser.send_ctrl("DISCONNECT") - state.ser.disconnect() + 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) - - def on_pmt_mode_clicked(self, data=None): - """Connect in PMT mode""" - self.pmt_mode = True - self.adc_pot.ui['short_true'].set_active(True) - self.adc_pot.ui['short_true'].set_sensitive(False) - self.on_serial_connect_clicked() + + dstat.state.reset() def start_ocp(self, data=None): """Start OCP measurements.""" - - if state.dstat_version[0] >= 1 and state.dstat_version[1] >= 2: + if dstat.state.dstat_version >= parse_version('1.2'): # Flush data pipe - state.ser.flush_data() + dstat.state.ser.flush_data() - if self.pmt_mode == True: + if self.pmt_mode is True: logger.info("Start PMT idle mode") - state.ser.start_exp(exp.PMTIdle()) + dstat.state.ser.start_exp(idle.PMTIdle(state=dstat.state.get_state())) + self.ocp_is_running = True + self.ocp_proc = (GLib.timeout_add(250, self.ocp_running_proc) + , + ) else: logger.info("Start OCP") - state.ser.start_exp(exp.OCPExp()) + dstat.state.ser.start_exp(idle.OCPExp(state=dstat.state.get_state())) - self.ocp_proc = (GObject.timeout_add(300, self.ocp_running_data), - GObject.timeout_add(250, self.ocp_running_proc) - ) - self.ocp_is_running = True + self.ocp_proc = (GLib.timeout_add(300, self.ocp_running_data), + GLib.timeout_add(250, self.ocp_running_proc) + ) + self.ocp_is_running = False + + GLib.timeout_add(100, self.ocp_assert) # Check if getting data else: logger.info("OCP measurements not supported on v1.1 boards.") @@ -310,23 +376,37 @@ class Main(object): def stop_ocp(self, data=None): """Stop OCP measurements.""" - if state.dstat_version[0] >= 1 and state.dstat_version[1] >= 2: + 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") - state.ser.send_ctrl('a') - + dstat.state.ser.send_ctrl('a') + for i in self.ocp_proc: - GObject.source_remove(i) + GLib.source_remove(i) while self.ocp_running_proc(): pass - self.ocp_is_running = False 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 @@ -337,9 +417,9 @@ class Main(object): """ try: - incoming = state.ser.get_data() + incoming = dstat.state.ser.get_data() while incoming is not None: - if isinstance(incoming, basestring): # test if incoming is str + if isinstance(incoming, bytes): # test if incoming is str self.on_serial_disconnect_clicked() return False @@ -348,10 +428,11 @@ class Main(object): "{0:.3f}".format(incoming), " V"]) self.ocp_disp.set_text(data) + self.ocp_is_running = True except ValueError: pass - incoming = state.ser.get_data() + incoming = dstat.state.ser.get_data() return True @@ -370,16 +451,16 @@ class Main(object): """ try: - proc_buffer = state.ser.get_proc() + 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() - state.ser.flush_data() + dstat.state.ser.flush_data() return False - proc_buffer = state.ser.get_proc() + proc_buffer = dstat.state.ser.get_proc() return True except EOFError: @@ -417,7 +498,7 @@ class Main(object): self.stop_ocp() self.statusbar.remove_all(self.error_context_id) - state.ser.flush_data() + dstat.state.ser.flush_data() parameters = {} parameters['metadata'] = self.metadata @@ -439,35 +520,33 @@ class Main(object): 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, state=dstat.state.get_state()) - self.current_exp = self.exp_window.setup_exp(parameters) - - interface.plot_ui.replace_notebook_exp( + plot_ui.replace_notebook_exp( self.plot_notebook, self.current_exp, self.window ) - - for plot in self.current_exp.plots: - plot.changetype(self.current_exp) self.data_view.clear_exps() self.info_page.clear() - state.ser.start_exp(self.current_exp) + dstat.state.ser.start_exp(self.current_exp) # Flush data pipe - state.ser.flush_data() - - self.plot_proc = GObject.timeout_add(200, - self.experiment_running_plot) - self.experiment_proc = ( - GObject.idle_add(self.experiment_running_data), - GObject.idle_add(self.experiment_running_proc) - ) - + dstat.state.ser.flush_data() + self.current_exp.setup_loops(callbacks) return experiment_id except ValueError as i: - logger.info("ValueError: %s",i) + logger.info("ValueError: %s", i) self.statusbar.push(self.error_context_id, "Experiment parameters must be integers.") exceptions() @@ -501,6 +580,12 @@ class Main(object): 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]. @@ -512,27 +597,35 @@ class Main(object): function from GTK's queue. """ try: - incoming = state.ser.get_data() + 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 = state.ser.get_data() + incoming = dstat.state.ser.get_data() return True except EOFError as err: - print err + logger.error(err) self.experiment_done() return False except IOError as err: - print err + logger.error(err) self.experiment_done() return False @@ -546,7 +639,14 @@ class Main(object): function from GTK's queue. """ try: - proc_buffer = state.ser.get_proc() + 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() @@ -574,53 +674,32 @@ class Main(object): removed from GTK's queue. """ for plot in self.current_exp.plots: - if self.line > self.lastline: - plot.addline() - # make sure all of last line is added - plot.updateline(self.current_exp, self.lastline) - self.lastline = self.line - plot.updateline(self.current_exp, self.line) + 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): + 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: - self.current_exp.experiment_done() - GObject.source_remove(self.experiment_proc[0]) - GObject.source_remove(self.plot_proc) # stop automatic plot update - self.experiment_running_plot(force_refresh=True) - - - # # Shutter stuff - # if (self.current_exp.parameters['shutter_true'] and - # self.current_exp.parameters['sync_true']): - # self.ft_plot.updateline(self.current_exp, 0) - # self.ft_plot.redraw() - # - # line_buffer = [] - # - # for scan in self.current_exp.data['ft']: - # for dimension in scan: - # for i in range(len(dimension)): - # try: - # line_buffer[i] += "%s " % dimension[i] - # except IndexError: - # line_buffer.append("") - # line_buffer[i] += "%s " % dimension[i] - # - # for i in line_buffer: - # self.databuffer.insert_at_cursor("%s\n" % i) - # Run Analysis analysis.do_analysis(self.current_exp) - self.current_exp.experiment_done() - # Write DStat commands self.info_page.set_text(self.current_exp.get_info_text()) @@ -668,17 +747,24 @@ class Main(object): self.metadata = None # Reset metadata self.spinner.stop() - self.startbutton.set_sensitive(True) + 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: - state.ser.stop_exp() + dstat.state.ser.stop_exp() except AttributeError: pass @@ -711,14 +797,14 @@ class Main(object): """Listen for remote control connection from µDrop.""" # Prompt user for 0MQ plugin hub URI. - zmq_plugin_hub_uri = get_hub_uri(parent=self.window) + # 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) + # self.enable_plugin(zmq_plugin_hub_uri) def on_menu_dropbot_disconnect_activate(self, menuitem=None, data=None): """Disconnect µDrop connection and stop listening.""" @@ -739,14 +825,14 @@ class Main(object): ''' 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) + # 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: @@ -757,9 +843,8 @@ class Main(object): if __name__ == "__main__": multiprocessing.freeze_support() - GObject.threads_init() MAIN = Main() - mainloop = GObject.MainLoop() + mainloop = GLib.MainLoop() try: mainloop.run() except KeyboardInterrupt: diff --git a/dstat_interface/mr_db b/dstat_interface/mr_db deleted file mode 160000 index 72481e585d92d0adab6537718a4d18164df1b445..0000000000000000000000000000000000000000 --- a/dstat_interface/mr_db +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 72481e585d92d0adab6537718a4d18164df1b445 diff --git a/dstat_interface/parameter_test.py b/dstat_interface/parameter_test.py deleted file mode 100755 index ec629439eac8b2f53edaa63ea6590fa0c9ef0319..0000000000000000000000000000000000000000 --- a/dstat_interface/parameter_test.py +++ /dev/null @@ -1,242 +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 -# -# -# 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 . - -import logging - -from errors import InputError - -logger = logging.getLogger("dstat.parameter_test") - -def lsv_test(params): - """Test LSV parameters for sanity""" - test_parameters = ['clean_mV', 'dep_mV', 'clean_s', 'dep_s', 'start', - 'stop', 'slope'] - parameters = {} - for i in params: - if i in test_parameters: - parameters[i] = int(params[i]) - - if (parameters['clean_mV'] > 1499 or - parameters['clean_mV'] < -1500): - raise InputError(parameters['clean_mV'], - "Clean potential exceeds hardware limits.") - if (parameters['dep_mV'] > 1499 or - parameters['dep_mV'] < -1500): - raise InputError(parameters['dep_mV'], - "Deposition potential exceeds hardware limits.") - if (parameters['clean_s'] < 0): - raise InputError(parameters['clean_s'], - "Clean time cannot be negative.") - if (parameters['dep_s'] < 0): - raise InputError(parameters['dep_s'], - "Deposition time cannot be negative.") - if (parameters['start'] > 1499 or parameters['start'] < -1500): - raise InputError(parameters['start'], - "Start parameter exceeds hardware limits.") - if (parameters['stop'] > 1499 or parameters['stop'] < -1500): - raise InputError(parameters['stop'], - "Stop parameter exceeds hardware limits.") - if (parameters['slope'] > 2000 or parameters['slope'] < 1): - raise InputError(parameters['slope'], - "Slope parameter exceeds hardware limits.") - if parameters['start'] == parameters['stop']: - raise InputError(parameters['start'], - "Start cannot equal Stop.") - -def cv_test(params): - """Test CV parameters for sanity""" - test_parameters = ['clean_mV', 'dep_mV', 'clean_s', 'dep_s', 'start', - 'stop', 'slope', 'v1', 'v2', 'scans'] - parameters = {} - for i in params: - if i in test_parameters: - parameters[i] = int(params[i]) - - if (parameters['clean_mV'] > 1499 or - parameters['clean_mV'] < -1500): - raise InputError(parameters['clean_mV'], - "Clean potential exceeds hardware limits.") - if (parameters['dep_mV'] > 1499 or - parameters['dep_mV'] < -1500): - raise InputError(parameters['dep_mV'], - "Deposition potential exceeds hardware limits.") - if (parameters['clean_s'] < 0): - raise InputError(parameters['clean_s'], - "Clean time cannot be negative.") - if (parameters['dep_s'] < 0): - raise InputError(parameters['dep_s'], - "Deposition time cannot be negative.") - if (parameters['start'] > 1499 or parameters['start'] < -1500): - raise InputError(parameters['start'], - "Start parameter exceeds hardware limits.") - if (parameters['slope'] > 2000 or parameters['slope'] < 1): - raise InputError(parameters['slope'], - "Slope parameter exceeds hardware limits.") - if (parameters['v1'] > 1499 or parameters['v1'] < -1500): - raise InputError(parameters['v1'], - "Vertex 1 parameter exceeds hardware limits.") - if (parameters['v2'] > 1499 or parameters['v2'] < -1500): - raise InputError(parameters['v2'], - "Vertex 2 parameter exceeds hardware limits.") - if (parameters['scans'] < 1 or parameters['scans'] > 255): - raise InputError(parameters['scans'], - "Scans parameter outside limits.") - if parameters['v1'] == parameters['v2']: - raise InputError(parameters['v1'], - "Vertex 1 cannot equal Vertex 2.") - -def swv_test(params): - """Test SWV parameters for sanity""" - test_parameters = ['clean_mV', 'dep_mV', 'clean_s', 'dep_s', 'start', - 'stop', 'step', 'pulse', 'freq'] - parameters = {} - for i in params: - if i in test_parameters: - parameters[i] = int(params[i]) - - if params['cyclic_true'] : - if int(params['scans']) < 1: - raise InputError(params['scans'], - "Must have at least one scan.") - else: - params['scans'] = 0 - - # check parameters are within hardware limits (doesn't - # check if pulse will go out of bounds, but instrument - # checks this (I think)) - if (parameters['clean_mV'] > 1499 or - parameters['clean_mV'] < -1500): - raise InputError(parameters['clean_mV'], - "Clean potential exceeds hardware limits.") - if (parameters['dep_mV'] > 1499 or - parameters['dep_mV'] < -1500): - raise InputError(parameters['dep_mV'], - "Deposition potential exceeds hardware limits.") - if (parameters['clean_s'] < 0): - raise InputError(parameters['clean_s'], - "Clean time cannot be negative.") - if (parameters['dep_s'] < 0): - raise InputError(parameters['dep_s'], - "Deposition time cannot be negative.") - if (parameters['start'] > 1499 or parameters['start'] < -1500): - raise InputError(parameters['start'], - "Start parameter exceeds hardware limits.") - if (parameters['step'] > 200 or parameters['step'] < 1): - raise InputError(parameters['step'], - "Step height parameter exceeds hardware limits.") - if (parameters['stop'] > 1499 or parameters['stop'] < -1500): - raise InputError(parameters['stop'], - "Stop parameter exceeds hardware limits.") - if (parameters['pulse'] > 150 or parameters['pulse'] < 1): - raise InputError(parameters['pulse'], - "Pulse height parameter exceeds hardware limits.") - if (parameters['freq'] < 1 or parameters['freq'] > 1000): - raise InputError(parameters['freq'], - "Frequency parameter outside limits.") - if parameters['start'] == parameters['stop']: - raise InputError(parameters['start'], - "Start cannot equal Stop.") - -def dpv_test(params): - """Test DPV parameters for sanity""" - test_parameters = ['clean_mV', 'dep_mV', 'clean_s', 'dep_s', 'start', - 'stop', 'step', 'pulse', 'period', 'width'] - parameters = {} - for i in params: - if i in test_parameters: - parameters[i] = int(params[i]) - - if (parameters['clean_mV'] > 1499 or - parameters['clean_mV'] < -1500): - raise InputError(parameters['clean_mV'], - "Clean potential exceeds hardware limits.") - if (parameters['dep_mV'] > 1499 or - parameters['dep_mV'] < -1500): - raise InputError(parameters['dep_mV'], - "Deposition potential exceeds hardware limits.") - if (parameters['clean_s'] < 0): - raise InputError(parameters['clean_s'], - "Clean time cannot be negative.") - if (parameters['dep_s'] < 0): - raise InputError(parameters['dep_s'], - "Deposition time cannot be negative.") - if (parameters['start'] > 1499 or parameters['start'] < -1500): - raise InputError(parameters['start'], - "Start parameter exceeds hardware limits.") - if (parameters['step'] > 200 or parameters['step'] < 1): - raise InputError(parameters['step'], - "Step height parameter exceeds hardware limits.") - if (parameters['stop'] > 1499 or parameters['stop'] < -1500): - raise InputError(parameters['stop'], - "Stop parameter exceeds hardware limits.") - if (parameters['pulse'] > 150 or parameters['pulse'] < 1): - raise InputError(parameters['pulse'], - "Pulse height parameter exceeds hardware limits.") - if (parameters['period'] < 1 or parameters['period'] > 1000): - raise InputError(parameters['period'], - "Period parameter outside limits.") - if (parameters['width'] < 1 or parameters['width'] > 1000): - raise InputError(parameters['width'], - "Width parameter outside limits.") - if parameters['period'] <= parameters['width']: - raise InputError(parameters['width'], - "Width must be less than period.") - if parameters['start'] == parameters['stop']: - raise InputError(parameters['start'], - "Start cannot equal Stop.") - -def pd_test(parameters): - """Test PD parameters for sanity""" - - if (int(parameters['time']) <= 0): - raise InputError(parameters['time'], - "Time must be greater than zero.") - if (int(parameters['time']) > 65535): - raise InputError(parameters['time'], - "Time must fit in 16-bit counter.") - if (parameters['sync_true'] and parameters['shutter_true']): - if (float(parameters['sync_freq']) > 30 or - float(parameters['sync_freq']) <= 0): - raise InputError(parameters['sync_freq'], - "Frequency must be between 0 and 30 Hz.") - if (float(parameters['fft_start']) < 0 or - float(parameters['fft_start']) > float(parameters['time'])-1): - raise InputError(parameters['fft_start'], - "FFT must start between 0 and time-1.") - if float(parameters['fft_int']) < 0: - raise InputError( - parameters['fft_int'], - "Integral bandwidth must be greater than 0" - ) - -def pot_test(params): - """Test POT parameters for sanity""" - test_parameters = ['time'] - parameters = {} - for i in params: - if i in test_parameters: - parameters[i] = int(params[i]) - - if (int(parameters['time']) <= 0): - raise InputError(parameters['time'], - "Time must be greater than zero.") - if (int(parameters['time']) > 65535): - raise InputError(parameters['time'], - "Time must fit in 16-bit counter.") \ No newline at end of file diff --git a/dstat_interface/state.py b/dstat_interface/state.py deleted file mode 100644 index 7e3f1958894aab4a5482c65cca03cb5f3cdd1d93..0000000000000000000000000000000000000000 --- a/dstat_interface/state.py +++ /dev/null @@ -1,5 +0,0 @@ -from collections import OrderedDict - -settings = OrderedDict() -ser = None -dstat_version = None \ No newline at end of file diff --git a/images/k.pdf b/images/k.pdf deleted file mode 100644 index c831664d9292c8f42f4c5a20dc52a31e1d64fe25..0000000000000000000000000000000000000000 Binary files a/images/k.pdf and /dev/null differ diff --git a/pavement.py b/pavement.py index 0aea7f58afe84674e34958f65404241569de2066..fc1985513bd26b0dcc6e930acc67ab36cf3bfdda 100644 --- a/pavement.py +++ b/pavement.py @@ -1,7 +1,7 @@ import sys from paver.easy import task, needs, path, sh, cmdopts, options -from paver.setuputils import setup, install_distutils_tasks +from paver.setuputils import setup, install_distutils_tasks, find_packages from distutils.extension import Extension from distutils.dep_util import newer @@ -13,12 +13,13 @@ setup(name='dstat_interface', description='Interface software for DStat potentiostat.', keywords='', author='Michael D. M Dryden', - author_email='mdryden@chemutoronto.ca', + author_email='mdryden@chem.utoronto.ca', url='http://microfluidics.utoronto.ca/dstat', license='GPLv3', - packages=['dstat_interface', ], + packages=find_packages(), install_requires=['matplotlib', 'numpy', 'pyserial', 'pyzmq', - 'pyyaml','seaborn', 'zmq-plugin>=0.2.post2'], + 'pyyaml','seaborn', 'setuptools', + 'zmq-plugin>=0.2.post2'], # Install data listed in `MANIFEST.in` include_package_data=True) diff --git a/version.py b/version.py index 343f158f74594923d656e5be8ad57b09b3c56a1c..ae2f3d2232f717f9989c82b4efeb1344111aadd9 100644 --- a/version.py +++ b/version.py @@ -48,9 +48,11 @@ __all__ = ('getVersion') import re import subprocess import sys +import os.path +import inspect - -RELEASE_VERSION_FILE = 'RELEASE-VERSION' +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+)*)?'