diff --git a/dstat_interface/analysis.py b/dstat_interface/analysis.py
index fe73ea4d1e29d6350826d5c7ec2ba115daee4fbe..33144c068e58bb9184991549bc0b0d5865e96e22 100755
--- a/dstat_interface/analysis.py
+++ b/dstat_interface/analysis.py
@@ -26,7 +26,7 @@ import pygtk
import gtk
from numpy import mean, trapz
-logger = logging.getLogger(__name__)
+logger = logging.getLogger('dstat.analysis')
class AnalysisOptions(object):
"""Analysis options window."""
@@ -109,24 +109,24 @@ def do_analysis(experiment):
if experiment.parameters['stats_start_true']:
start = experiment.parameters['stats_start']
else:
- start = min(experiment.data[0][0])
+ start = min(experiment.data['data'][0][0])
if experiment.parameters['stats_stop_true']:
stop = experiment.parameters['stats_stop']
else:
- stop = min(experiment.data[0][0])
+ stop = min(experiment.data['data'][0][0])
- data = _data_slice(experiment.data,
+ data = _data_slice(experiment.data['data'],
start,
stop
)
else:
- data = experiment.data
+ data = experiment.data['data']
experiment.analysis.update(_summary_stats(data))
try:
- x, y = experiment.ftdata[0]
+ x, y = experiment.data['ft'][0]
experiment.analysis['FT Integral'] = _integrateSpectrum(
x,
y,
@@ -134,7 +134,7 @@ def do_analysis(experiment):
float(experiment.parameters['fft_int'])
)
- except AttributeError:
+ except KeyError:
pass
def _data_slice(data, start, stop):
diff --git a/dstat_interface/build_windows.py b/dstat_interface/build_windows.py
deleted file mode 100644
index d8e31ca546e5f34ff57e5c5b3f89ac0f5ac7e998..0000000000000000000000000000000000000000
--- a/dstat_interface/build_windows.py
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-__requires__ = 'PyInstaller==2.1'
-
-
-import os, sys
-os.chdir(os.path.dirname(sys.argv[0]))
-
-args = ['dstat.spec']
-args.extend(sys.argv[1:])
-
-import PyInstaller.main as pyi #For some reason, it gets the path here, so working dir must be set first
-pyi.run(args)
diff --git a/dstat_interface/dstat_comm.py b/dstat_interface/dstat_comm.py
index d002e006781b0364d7cad44f8ab381595fbdcea9..ffa43f2217b119b21acd8e2bce98f4edb03cb13d 100755
--- a/dstat_interface/dstat_comm.py
+++ b/dstat_interface/dstat_comm.py
@@ -22,13 +22,20 @@ from serial.tools import list_ports
import time
import struct
import multiprocessing as mp
-from errors import InputError, VarError, ErrorLogger
-_logger = ErrorLogger(sender="dstat_comm")
+import logging
+
+from errors import InputError, VarError
+
+logger = logging.getLogger("dstat.comm")
+dstat_logger = logging.getLogger("dstat.comm.DSTAT")
+exp_logger = logging.getLogger("dstat.comm.Experiment")
def _serial_process(ser_port, proc_pipe, ctrl_pipe, data_pipe):
+ ser_logger = logging.getLogger("dstat.comm._serial_process")
+
ser = delayedSerial(ser_port, baudrate=1000000, timeout=1)
- _logger.error("_serial_process() Connecting", 'INFO')
+ ser_logger.info("Connecting")
ser.write("ck")
@@ -50,23 +57,20 @@ def _serial_process(ser_port, proc_pipe, ctrl_pipe, data_pipe):
if ctrl_buffer == ('a' or "DISCONNECT"):
proc_pipe.send("ABORT")
ser.write('a')
- _logger.error("_serial_process(): ABORT", 'INFO')
+ ser_logger.info("ABORT")
if ctrl_buffer == "DISCONNECT":
- _logger.error("_serial_process(): DISCONNECT", 'INFO')
+ ser_logger.info("DISCONNECT")
ser.close()
proc_pipe.send("DISCONNECT")
return False
-
elif proc_pipe.poll():
while ctrl_pipe.poll():
ctrl_pipe.recv()
return_code = proc_pipe.recv().run(ser, ctrl_pipe, data_pipe)
- e = "_serial_process: "
- e += str(return_code)
- _logger.error(e,'INFO')
+ ser_logger.info('Return code: %s', str(return_code))
proc_pipe.send(return_code)
@@ -104,27 +108,24 @@ class VersionCheck:
if line.startswith('V'):
input = line.lstrip('V')
elif line.startswith("#"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "INFO")
+ dstat_logger.info(line.lstrip().rstrip())
elif line.lstrip().startswith("no"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "DBG")
+ dstat_logger.debug(line.lstrip().rstrip())
ser.flushInput()
break
parted = input.rstrip().split('.')
- e = "DStat PCB version: "
+ e = "PCB version: "
e += str(input.rstrip())
- _logger.error(e, "INFO")
+ dstat_logger.info(e)
data_pipe.send((int(parted[0]), int(parted[1])))
status = "DONE"
except UnboundLocalError as e:
- _logger.error(e, "ERR")
status = "SERIAL_ERROR"
except SerialException as e:
- _logger.error(e, "ERR")
+ logger.error('SerialException: %s', e)
status = "SERIAL_ERROR"
finally:
@@ -147,7 +148,7 @@ def version_check(ser_port):
buffer = 1
else:
buffer = serial_instance.data_pipe_p.recv()
- _logger.error("version_check done", "DBG")
+ logger.debug("version_check done")
return buffer
@@ -191,11 +192,9 @@ class Settings:
if line.lstrip().startswith('S'):
input = line.lstrip().lstrip('S')
elif line.lstrip().startswith("#"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "INFO")
+ dstat_logger.info(line.lstrip().rstrip())
elif line.lstrip().startswith("no"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "DBG")
+ dstat_logger.debug(line.lstrip().rstrip())
self.ser.flushInput()
break
@@ -240,8 +239,7 @@ def read_settings():
serial_instance.proc_pipe_p.send(Settings(task='r'))
settings = serial_instance.data_pipe_p.recv()
- _logger.error("".join(("read_settings: ",
- serial_instance.proc_pipe_p.recv())),'DBG')
+ logger.debug("read_settings: %s", serial_instance.proc_pipe_p.recv())
return
@@ -254,8 +252,7 @@ def write_settings():
serial_instance.proc_pipe_p.send(Settings(task='w', settings=settings))
- _logger.error("".join(("write_settings: ",
- serial_instance.proc_pipe_p.recv())),'DBG')
+ logger.debug("write_settings: %s", serial_instance.proc_pipe_p.recv())
return
@@ -281,11 +278,9 @@ class LightSensor:
if line.lstrip().startswith('T'):
input = line.lstrip().lstrip('T')
elif line.lstrip().startswith("#"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "INFO")
+ dstat_logger.info(line.lstrip().rstrip())
elif line.lstrip().startswith("no"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "DBG")
+ dstat_logger.debug(line.lstrip().rstrip())
ser.flushInput()
break
@@ -306,8 +301,7 @@ def read_light_sensor():
serial_instance.proc_pipe_p.send(LightSensor())
- _logger.error("".join(("read_light_sensor: ",
- serial_instance.proc_pipe_p.recv())),'DBG')
+ logger.info("read_light_sensor: %s", serial_instance.proc_pipe_p.recv())
return serial_instance.data_pipe_p.recv()
@@ -328,7 +322,7 @@ class SerialDevices(object):
self.ports, _, _ = zip(*list_ports.comports())
except ValueError:
self.ports = []
- _logger.error("No serial ports found", "ERR")
+ logger.error("No serial ports found")
def refresh(self):
"""Refreshes list of ports."""
@@ -345,9 +339,11 @@ class Experiment(object):
self.databytes = 8
self.scan = 0
self.time = 0
+ self.plots = {}
+ self.data = {}
# list of scans, tuple of dimensions, list of data
- self.data = [([], [])]
+ self.data['data'] = [([], [])]
self.line_data = ([], [])
major, minor = self.parameters['version']
@@ -392,14 +388,14 @@ class Experiment(object):
self.ctrl_pipe = ctrl_pipe
self.data_pipe = data_pipe
- _logger.error("Experiment running", "INFO")
+ exp_logger.info("Experiment running")
try:
self.serial.flushInput()
status = "DONE"
for i in self.commands:
- _logger.error("".join(("Command: ",i)), "INFO")
+ logger.info("Command: %s", i)
self.serial.write('!')
while not self.serial.read().startswith("C"):
@@ -427,17 +423,17 @@ class Experiment(object):
while True:
if self.ctrl_pipe.poll():
input = self.ctrl_pipe.recv()
- _logger.error("".join(("serial_handler: ", input)),"DBG")
+ logger.debug("serial_handler: %s", input)
if input == ('a' or "DISCONNECT"):
self.serial.write('a')
- _logger.error("serial_handler: ABORT pressed!","INFO")
+ logger.info("serial_handler: ABORT pressed!")
return False
for line in self.serial:
if self.ctrl_pipe.poll():
if self.ctrl_pipe.recv() == 'a':
self.serial.write('a')
- _logger.error("serial_handler: ABORT pressed!","INFO")
+ logger.info("serial_handler: ABORT pressed!")
return False
if line.startswith('B'):
@@ -449,12 +445,10 @@ class Experiment(object):
scan += 1
elif line.lstrip().startswith("#"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "INFO")
+ dstat_logger.info(line.lstrip().rstrip())
elif line.lstrip().startswith("no"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "DBG")
+ dstat_logger.debug(line.lstrip().rstrip())
self.serial.flushInput()
return True
@@ -509,17 +503,17 @@ class CALExp(Experiment):
while True:
if self.ctrl_pipe.poll():
input = self.ctrl_pipe.recv()
- _logger.error("".join(("serial_handler: ", input)))
+ logger.debug("serial_handler: %s", input)
if input == ('a' or "DISCONNECT"):
self.serial.write('a')
- _logger.error("serial_handler: ABORT pressed!","INFO")
+ logger.info("serial_handler: ABORT pressed!")
return False
for line in self.serial:
if self.ctrl_pipe.poll():
if self.ctrl_pipe.recv() == 'a':
self.serial.write('a')
- _logger.error("serial_handler: ABORT pressed!","INFO")
+ logger.info("serial_handler: ABORT pressed!")
return False
if line.startswith('B'):
@@ -527,12 +521,10 @@ class CALExp(Experiment):
self.serial.read(size=self.databytes)))
elif line.lstrip().startswith("#"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "INFO")
+ dstat_logger.info(line.lstrip().rstrip())
elif line.lstrip().startswith("no"):
- _logger.error("".join(
- ("DSTAT: ",line.lstrip().rstrip())), "DBG")
+ dstat_logger.debug(line.lstrip().rstrip())
self.serial.flushInput()
return True
@@ -753,7 +745,7 @@ class SWVExp(Experiment):
self.datatype = "SWVData"
self.xlabel = "Voltage (mV)"
self.ylabel = "Current (A)"
- self.data = [([], [], [], [])] # voltage, current, forwards, reverse
+ self.data['data'] = [([], [], [], [])] # voltage, current, forwards, reverse
self.line_data = ([], [], [], [])
self.datalength = 2 * self.parameters['scans']
self.databytes = 10
@@ -812,7 +804,7 @@ class DPVExp(SWVExp):
self.datatype = "SWVData"
self.xlabel = "Voltage (mV)"
self.ylabel = "Current (A)"
- self.data = [([], [], [], [])] # voltage, current, forwards, reverse
+ self.data['data'] = [([], [], [], [])] # voltage, current, forwards, reverse
self.line_data = ([], [], [], [])
self.datalength = 2
self.databytes = 10
@@ -889,9 +881,7 @@ def measure_offset(time):
for i in range(1,8):
parameters['gain'] = i
serial_instance.proc_pipe_p.send(CALExp(parameters))
- _logger.error("".join(
- ("measure_offset: ", serial_instance.proc_pipe_p.recv())),
- "INFO")
+ logger.info("measure_offset: %s", serial_instance.proc_pipe_p.recv())
gain_offset[gain_trim_table[i]] = serial_instance.data_pipe_p.recv()
return gain_offset
\ No newline at end of file
diff --git a/dstat_interface/interface/save.py b/dstat_interface/interface/save.py
index 578b1777da841f78b278b3f3d25fe677c7a0438a..675bcd1c2f29ba738c63a20dc8f0a43eb0748858 100755
--- a/dstat_interface/interface/save.py
+++ b/dstat_interface/interface/save.py
@@ -1,20 +1,20 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
+# Copyright (C) 2014 Michael D. M. Dryden -
# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
+#
+#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
-#
+#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
@@ -23,49 +23,42 @@ import os
import gtk
import numpy as np
+import logging
-from errors import InputError, VarError, ErrorLogger
-_logger = ErrorLogger(sender="dstat-interface-save")
+logger = logging.getLogger("dstat.interface.save")
+
+from errors import InputError, VarError
from params import save_params, load_params
def manSave(current_exp):
fcd = gtk.FileChooserDialog("Save...", None, gtk.FILE_CHOOSER_ACTION_SAVE,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
gtk.STOCK_SAVE, gtk.RESPONSE_OK))
-
+
filters = [gtk.FileFilter()]
filters[0].set_name("Space separated text (.txt)")
filters[0].add_pattern("*.txt")
-
+
fcd.set_do_overwrite_confirmation(True)
for i in filters:
fcd.add_filter(i)
-
+
response = fcd.run()
-
+
if response == gtk.RESPONSE_OK:
path = fcd.get_filename()
- _logger.error(" ".join(("Selected filepath:", path)),'INFO')
+ logger.info("Selected filepath: %s", path)
filter_selection = fcd.get_filter().get_name()
-
- if filter_selection.endswith("(.npy)"):
- if (current_exp.parameters['shutter_true'] and current_exp.parameters['sync_true']):
- npy(current_exp, current_exp.data, "-".join((path,'data')))
- npy(current_exp, current_exp.ftdata, "-".join((path,'ft')))
- else:
- npy(current_exp, current_exp.data, path, auto=True)
- elif filter_selection.endswith("(.txt)"):
- if (current_exp.parameters['shutter_true'] and current_exp.parameters['sync_true']):
- text(current_exp, current_exp.data, "-".join((path,'data')))
- text(current_exp, current_exp.ftdata, "-".join((path,'ft')))
- else:
- text(current_exp, current_exp.data, path, auto=True)
+
+ if filter_selection.endswith("(.txt)"):
+ save_text(current_exp, path)
+
fcd.destroy()
-
+
elif response == gtk.RESPONSE_CANCEL:
fcd.destroy()
-def plotSave(plots):
+def plot_save_dialog(plots):
fcd = gtk.FileChooserDialog("Save Plot…", None,
gtk.FILE_CHOOSER_ACTION_SAVE,
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
@@ -77,37 +70,34 @@ def plotSave(plots):
filters.append(gtk.FileFilter())
filters[1].set_name("Portable Network Graphics (.png)")
filters[1].add_pattern("*.png")
-
+
fcd.set_do_overwrite_confirmation(True)
for i in filters:
fcd.add_filter(i)
-
+
response = fcd.run()
-
+
if response == gtk.RESPONSE_OK:
path = fcd.get_filename()
- _logger.error(" ".join(("Selected filepath:", path)),'INFO')
+ logger.info("Selected filepath: %s", path)
filter_selection = fcd.get_filter().get_name()
- for i in plots:
- save_path = path
- save_path += '-'
- save_path += i
+ if filter_selection.endswith("(.pdf)"):
+ if not path.endswith(".pdf"):
+ path += ".pdf"
+
+ elif filter_selection.endswith("(.png)"):
+ if not path.endswith(".png"):
+ path += ".png"
- if filter_selection.endswith("(.pdf)"):
- if not save_path.endswith(".pdf"):
- save_path += ".pdf"
-
- elif filter_selection.endswith("(.png)"):
- if not save_path.endswith(".png"):
- save_path += ".png"
-
- plots[i].figure.savefig(save_path) # determines format from file extension
+ save_plot(plots, path)
+
fcd.destroy()
-
+
elif response == gtk.RESPONSE_CANCEL:
fcd.destroy()
+
def man_param_save(window):
fcd = gtk.FileChooserDialog("Save Parameters…",
None,
@@ -115,28 +105,28 @@ def man_param_save(window):
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
gtk.STOCK_SAVE, gtk.RESPONSE_OK)
)
-
+
filters = [gtk.FileFilter()]
filters[0].set_name("Parameter File (.yml)")
filters[0].add_pattern("*.yml")
-
+
fcd.set_do_overwrite_confirmation(True)
for i in filters:
fcd.add_filter(i)
-
+
response = fcd.run()
-
+
if response == gtk.RESPONSE_OK:
path = fcd.get_filename()
- _logger.error(" ".join(("Selected filepath:", path)),'INFO')
-
+ logger.info("Selected filepath: %s", path)
+
if not path.endswith(".yml"):
path += '.yml'
-
+
save_params(window, path)
fcd.destroy()
-
+
elif response == gtk.RESPONSE_CANCEL:
fcd.destroy()
@@ -147,136 +137,122 @@ def man_param_load(window):
(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
gtk.STOCK_OPEN, gtk.RESPONSE_OK)
)
-
+
filters = [gtk.FileFilter()]
filters[0].set_name("Parameter File (.yml)")
filters[0].add_pattern("*.yml")
for i in filters:
fcd.add_filter(i)
-
+
response = fcd.run()
-
+
if response == gtk.RESPONSE_OK:
path = fcd.get_filename()
- _logger.error(" ".join(("Selected filepath:", path)),'INFO')
-
+ logger.info("Selected filepath: %s", path)
+
load_params(window, path)
fcd.destroy()
-
+
elif response == gtk.RESPONSE_CANCEL:
fcd.destroy()
-def autoSave(current_exp, dir_button, name, expnumber):
+def autoSave(exp, path, name):
if name == "":
name = "file"
- path = dir_button.get_filename()
+
path += '/'
path += name
- path += '-'
- path += str(expnumber)
-
- if (current_exp.parameters['shutter_true'] and current_exp.parameters['sync_true']):
- text(current_exp, current_exp.data, "-".join((path,'data')), auto=True)
- text(current_exp, current_exp.ftdata, "-".join((path,'ft')), auto=True)
- else:
- text(current_exp, current_exp.data, path, auto=True)
-
-def autoPlot(plots, dir_button, name, expnumber):
- for i in plots:
- if name == "":
- name = "file"
-
- path = dir_button.get_filename()
- path += '/'
- path += name
- path += '-'
- path += str(expnumber)
- path += '-'
- path += i
+
+ save_text(exp, path)
+
+def autoPlot(exp, path, name):
+ if name == "":
+ name = "file"
- if path.endswith(".pdf"):
- path = path.rstrip(".pdf")
-
- j = 1
- while os.path.exists("".join([path, ".pdf"])):
- if j > 1:
- path = path[:-len(str(j))]
- path += str(j)
- j += 1
-
+ path += '/'
+ path += name
+
+ if not (path.endswith(".pdf") or path.endswith(".png")):
path += ".pdf"
- plots[i].figure.savefig(path)
-
-def npy(exp, data, path, auto=False):
- if path.endswith(".npy"):
- path = path.rstrip(".npy")
-
- if auto == True:
- j = 1
- while os.path.exists("".join([path, ".npy"])):
- if j > 1:
- path = path[:-len(str(j))]
- path += str(j)
- j += 1
- np.save(path, data)
+ save_plot(exp, path)
-def text(exp, data, path, auto=False):
- if path.endswith(".txt"):
- path = path.rstrip(".txt")
+def save_text(exp, path):
+ name, _sep, ext = path.rpartition('.') # ('','',string) if no match
+ if _sep == '':
+ name = ext
+ ext = 'txt'
- if auto == True:
- j = 1
-
- while os.path.exists("".join([path, ".txt"])):
- if j > 1:
- path = path[:-len(str(j))]
- path += str(j)
- j += 1
+ num = ''
+ j = 0
- path += ".txt"
- file = open(path, 'w')
+ for dname in exp.data: # Test for any existing files
+ while os.path.exists("%s%s-%s.%s" % (name, num, dname, ext)):
+ j += 1
+ num = j
- time = exp.time
+ for dname in exp.data: # save data
+ file = open("%s%s-%s.%s" % (name, num, dname, ext), 'w')
- header = "".join(['# TIME ', time.isoformat(), "\n"])
+ time = exp.time
+ header = "".join(['# TIME ', time.isoformat(), "\n"])
- header += "# DSTAT COMMANDS\n# "
- for i in exp.commands:
- header += i
+ header += "# DSTAT COMMANDS\n# "
+ for i in exp.commands:
+ header += i
- file.write("".join([header, '\n']))
+ file.write("".join([header, '\n']))
- analysis_buffer = []
+ analysis_buffer = []
- if exp.analysis != {}:
- analysis_buffer.append("# ANALYSIS")
- for key, value in exp.analysis.iteritems():
- analysis_buffer.append("# %s:" % key)
- for scan in value:
- number, result = scan
- analysis_buffer.append(
- "# Scan %s -- %s" % (number, result)
- )
+ if exp.analysis != {}:
+ analysis_buffer.append("# ANALYSIS")
+ for key, value in exp.analysis.iteritems():
+ analysis_buffer.append("# %s:" % key)
+ for scan in value:
+ number, result = scan
+ analysis_buffer.append(
+ "# Scan %s -- %s" % (number, result)
+ )
- for i in analysis_buffer:
- file.write("%s\n" % i)
+ for i in analysis_buffer:
+ file.write("%s\n" % i)
- # Write out actual data
- line_buffer = []
+ # Write out actual data
+ line_buffer = []
- for scan in zip(*data):
- 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 scan in zip(*exp.data[dname]):
+ 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:
- file.write("%s\n" % i)
+ for i in line_buffer:
+ file.write("%s\n" % i)
+
+ file.close()
+
+def save_plot(exp, path):
+ """Saves everything in exp.plots to path. Appends a number for duplicates.
+ If no file extension or unknown, uses pdf.
+ """
+ name, _sep, ext = path.rpartition('.')
+ if _sep == '':
+ name = ext
+ ext = 'pdf'
+
+ num = ''
+ j = 0
+
+ for i in exp.plots: # Test for any existing files
+ while os.path.exists("%s%s-%s.%s" % (name, num, i, ext)):
+ j += 1
+ num = j
- file.close()
+ for i in exp.plots: # save data
+ exp.plots[i].figure.savefig("%s%s-%s.%s" % (name, num, i, ext))
\ No newline at end of file
diff --git a/dstat_interface/main.py b/dstat_interface/main.py
index 4fd214cb2d3b63e3a15c6d5952bc273ee70c19ad..146c83b41c9eabf884a9c133d6f8a2f544630a5e 100755
--- a/dstat_interface/main.py
+++ b/dstat_interface/main.py
@@ -1,20 +1,20 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
+# Copyright (C) 2014 Michael D. M. Dryden -
# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
+#
+#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
-#
+#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
@@ -23,8 +23,9 @@
import sys
import os
import multiprocessing
-import time
+import uuid
from copy import deepcopy
+from collections import OrderedDict
from datetime import datetime
try:
@@ -44,8 +45,7 @@ except ImportError:
print "ERR: gobject not available"
sys.exit(1)
from serial import SerialException
-from datetime import datetime
-
+import logging
os.chdir(os.path.dirname(os.path.abspath(sys.argv[0])))
from version import getVersion
@@ -54,12 +54,26 @@ import dstat_comm as comm
import interface.exp_window as exp_window
import interface.adc_pot as adc_pot
import plot
-import microdrop
import params
import parameter_test
import analysis
-from errors import InputError, VarError, ErrorLogger
-_logger = ErrorLogger(sender="dstat-interface-main")
+import zmq
+from errors import InputError
+
+from plugin import DstatPlugin, get_hub_uri
+
+# Setup Logging
+root_logger = logging.getLogger("dstat")
+root_logger.setLevel(level=logging.INFO)
+log_handler = logging.StreamHandler()
+log_formatter = logging.Formatter(
+ fmt='%(asctime)s [%(name)s](%(levelname)s) %(message)s',
+ datefmt='%H:%M:%S'
+ )
+log_handler.setFormatter(log_formatter)
+root_logger.addHandler(log_handler)
+
+logger = logging.getLogger("dstat.main")
class Main(object):
"""Main program """
@@ -79,33 +93,33 @@ class Main(object):
self.stopbutton = self.builder.get_object('pot_stop')
self.startbutton = self.builder.get_object('pot_start')
self.adc_pot = adc_pot.adc_pot()
-
+
self.error_context_id = self.statusbar.get_context_id("error")
self.message_context_id = self.statusbar.get_context_id("message")
-
+
self.plotwindow = self.builder.get_object('plotbox')
self.ft_window = self.builder.get_object('ft_box')
self.period_window = self.builder.get_object('period_box')
-
+
self.exp_window = exp_window.Experiments(self.builder)
self.analysis_opt_window = analysis.AnalysisOptions(self.builder)
-
+
# Setup Autosave
self.autosave_checkbox = self.builder.get_object('autosave_checkbutton')
self.autosavedir_button = self.builder.get_object('autosavedir_button')
self.autosavename = self.builder.get_object('autosavename')
-
+
# Setup Plots
self.plot_notebook = self.builder.get_object('plot_notebook')
-
- self.plot = plot.plotbox(self.plotwindow)
- self.ft_plot = plot.ft_box(self.ft_window)
-
+
+ self.plot = plot.PlotBox(self.plotwindow)
+ self.ft_plot = plot.FT_Box(self.ft_window)
+
#fill adc_pot_box
self.adc_pot_box = self.builder.get_object('gain_adc_box')
self.adc_pot_container = self.adc_pot.builder.get_object('vbox1')
self.adc_pot_container.reparent(self.adc_pot_box)
-
+
#fill serial
self.serial_connect = self.builder.get_object('serial_connect')
self.serial_pmt_connect = self.builder.get_object('pmt_mode')
@@ -114,57 +128,63 @@ 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()
-
+
for i in self.serial_devices.ports:
self.serial_liststore.append([i])
-
+
self.serial_combobox.set_active(0)
-
+
#initialize experiment selection combobox
self.expcombobox = self.builder.get_object('expcombobox')
self.expcombobox.pack_start(self.cell, True)
self.expcombobox.add_attribute(self.cell, 'text', 2)
self.expcombobox.set_active(0)
-
+
self.spinner = self.builder.get_object('spinner')
self.mainwindow = self.builder.get_object('window1')
-
+
# Set Version Strings
try:
ver = getVersion()
except ValueError:
ver = "1.x"
- _logger.error("Could not fetch version number", "WAR")
+ logger.warning("Could not fetch version number")
self.mainwindow.set_title(" ".join(("DStat Interface", ver)))
self.aboutdialog.set_version(ver)
-
+
self.mainwindow.show_all()
-
+
self.on_expcombobox_changed()
self.expnumber = 0
-
+
self.connected = False
self.pmt_mode = False
-
+
self.menu_dropbot_connect = self.builder.get_object(
'menu_dropbot_connect')
self.menu_dropbot_disconnect = self.builder.get_object(
'menu_dropbot_disconnect')
self.dropbot_enabled = False
self.dropbot_triggered = False
-
+
self.plot_notebook.get_nth_page(
self.plot_notebook.page_num(self.ft_window)).hide()
self.plot_notebook.get_nth_page(
self.plot_notebook.page_num(self.period_window)).hide()
-
+
self.params_loaded = False
-
+ # Disable 0MQ plugin API by default.
+ self.plugin = None
+ self.plugin_timeout_id = None
+ # UUID for active experiment.
+ self.active_experiment_id = None
+ # UUIDs for completed experiments.
+ self.completed_experiment_ids = OrderedDict()
def on_window1_destroy(self, object, data=None):
""" Quit when main window closed."""
@@ -173,11 +193,11 @@ class Main(object):
def on_gtk_quit_activate(self, menuitem, data=None):
"""Quit when Quit selected from menu."""
self.quit()
-
+
def quit(self):
"""Disconnect and save parameters on quit."""
params.save_params(self, 'last_params.yml')
-
+
self.on_serial_disconnect_clicked()
gtk.main_quit()
@@ -185,7 +205,7 @@ class Main(object):
"""Display the about window."""
self.response = 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()
@@ -202,25 +222,25 @@ class Main(object):
"""Refresh list of serial devices."""
self.serial_devices.refresh()
self.serial_liststore.clear()
-
+
for i in self.serial_devices.ports:
self.serial_liststore.append([i])
-
+
def on_serial_connect_clicked(self, data=None):
"""Connect and retrieve DStat version."""
-
+
try:
self.serial_connect.set_sensitive(False)
self.version = comm.version_check(self.serial_liststore.get_value(
self.serial_combobox.get_active_iter(), 0))
-
+
self.statusbar.remove_all(self.error_context_id)
-
+
if not len(self.version) == 2:
self.statusbar.push(self.error_context_id,
"Communication Error")
return
-
+
else:
self.adc_pot.set_version(self.version)
self.statusbar.push(self.error_context_id,
@@ -228,33 +248,33 @@ class Main(object):
str(self.version[0]),
".", str(self.version[1])])
)
-
+
comm.read_settings()
-
+
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)
-
+
except AttributeError as err:
- _logger.error(err, 'WAR')
+ logger.warning("AttributeError: %s", err)
self.serial_connect.set_sensitive(True)
except TypeError as err:
- _logger.error(err, 'WAR')
+ logger.warning("TypeError: %s", err)
self.serial_connect.set_sensitive(True)
-
+
if self.params_loaded == False:
try:
params.load_params(self, 'last_params.yml')
except IOError:
- _logger.error("No previous parameters found.", 'INFO')
-
+ logger.info("No previous parameters found.")
+
def on_serial_disconnect_clicked(self, data=None):
"""Disconnect from DStat."""
if self.connected == False:
return
-
+
try:
if self.ocp_is_running:
self.stop_ocp()
@@ -262,18 +282,18 @@ class Main(object):
self.on_pot_stop_clicked()
comm.serial_instance.ctrl_pipe_p.send("DISCONNECT")
comm.serial_instance.proc.terminate()
-
+
except AttributeError as err:
- _logger.error(err, 'WAR')
+ logger.warning("AttributeError: %s", err)
pass
-
+
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.adc_pot.ui['short_true'].set_sensitive(True)
-
+
def on_pmt_mode_clicked(self, data=None):
"""Connect in PMT mode"""
self.pmt_mode = True
@@ -283,37 +303,37 @@ class Main(object):
def start_ocp(self):
"""Start OCP measurements."""
-
+
if self.version[0] >= 1 and self.version[1] >= 2:
# Flush data pipe
while comm.serial_instance.data_pipe_p.poll():
comm.serial_instance.data_pipe_p.recv()
-
+
if self.pmt_mode == True:
- _logger.error("Start PMT idle mode", "INFO")
+ logger.info("Start PMT idle mode")
comm.serial_instance.proc_pipe_p.send(comm.PMTIdle())
-
+
else:
- _logger.error("Start OCP", "INFO")
+ logger.info("Start OCP")
comm.serial_instance.proc_pipe_p.send(comm.OCPExp())
-
+
self.ocp_proc = (gobject.timeout_add(300, self.ocp_running_data),
gobject.timeout_add(250, self.ocp_running_proc)
)
self.ocp_is_running = True
-
+
else:
- _logger.error("OCP measurements not supported on v1.1 boards.",'INFO')
+ logger.info("OCP measurements not supported on v1.1 boards.")
return
-
+
def stop_ocp(self):
"""Stop OCP measurements."""
if self.version[0] >= 1 and self.version[1] >= 2:
if self.pmt_mode == True:
- _logger.error("Stop PMT idle mode",'INFO')
+ logger.info("Stop PMT idle mode")
else:
- _logger.error("Stop OCP",'INFO')
+ logger.info("Stop OCP")
comm.serial_instance.ctrl_pipe_p.send('a')
for i in self.ocp_proc:
@@ -323,37 +343,37 @@ class Main(object):
self.ocp_is_running = False
self.ocp_disp.set_text("")
else:
- logger.error("OCP measurements not supported on v1.1 boards.",'INFO')
+ logger.error("OCP measurements not supported on v1.1 boards.")
return
-
+
def ocp_running_data(self):
"""Receive OCP value from experiment process and update ocp_disp field
-
+
Returns:
True -- when experiment is continuing to keep function in GTK's queue.
False -- when experiment process signals EOFError or IOError to remove
function from GTK's queue.
"""
-
+
try:
- if comm.serial_instance.data_pipe_p.poll():
+ if comm.serial_instance.data_pipe_p.poll():
incoming = comm.serial_instance.data_pipe_p.recv()
-
+
if isinstance(incoming, basestring): # test if incoming is str
self.on_serial_disconnect_clicked()
return False
-
+
data = "".join(["OCP: ",
"{0:.3f}".format(incoming),
" V"])
self.ocp_disp.set_text(data)
-
+
if comm.serial_instance.data_pipe_p.poll():
self.ocp_running_data()
return True
-
+
return True
-
+
except EOFError:
return False
except IOError:
@@ -361,58 +381,62 @@ class Main(object):
def ocp_running_proc(self):
"""Handles signals on proc_pipe_p for OCP.
-
+
Returns:
True -- when experiment is continuing to keep function in GTK's queue.
False -- when experiment process signals EOFError or IOError to remove
function from GTK's queue.
"""
-
+
try:
- if comm.serial_instance.proc_pipe_p.poll():
+ if comm.serial_instance.proc_pipe_p.poll():
proc_buffer = comm.serial_instance.proc_pipe_p.recv()
- _logger.error("".join(("ocp_running_proc: ", proc_buffer)), 'DBG')
- if proc_buffer in ["DONE", "SERIAL_ERROR", "ABORT"]:
+ 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()
-
+
while comm.serial_instance.data_pipe_p.poll():
comm.serial_instance.data_pipe_p.recv()
-
- gobject.source_remove(self.ocp_proc[0])
return False
-
+
return True
-
+
return True
-
+
except EOFError:
return False
except IOError:
return False
-
+
def on_pot_start_clicked(self, data=None):
+ try:
+ self.run_active_experiment()
+ except (ValueError, KeyError, InputError, SerialException,
+ AssertionError):
+ # Ignore expected exceptions when triggering experiment from UI.
+ pass
+
+ def run_active_experiment(self):
"""Run currently visible experiment."""
+ # Assign current experiment a unique identifier.
+ experiment_id = uuid.uuid4()
+ self.active_experiment_id = experiment_id
+
def exceptions():
""" Cleans up after errors """
- if self.dropbot_enabled == True:
- if self.dropbot_triggered == True:
- self.dropbot_triggered = False
- self.microdrop.reply(microdrop.EXPFINISHED)
- self.microdrop_proc = gobject.timeout_add(500,
- self.microdrop_listen)
self.spinner.stop()
self.startbutton.set_sensitive(True)
self.stopbutton.set_sensitive(False)
self.start_ocp()
-
+
def run_experiment():
""" Starts experiment """
self.plot.clearall()
self.plot.changetype(self.current_exp)
-
+
nb = self.plot_notebook
-
+
if (parameters['sync_true'] and parameters['shutter_true']):
nb.get_nth_page(
nb.page_num(self.ft_window)).show()
@@ -425,7 +449,7 @@ class Main(object):
# nb.get_nth_page(nb.page_num(self.period_window)).hide()
comm.serial_instance.proc_pipe_p.send(self.current_exp)
-
+
# Flush data pipe
while comm.serial_instance.data_pipe_p.poll():
comm.serial_instance.data_pipe_p.recv()
@@ -436,18 +460,17 @@ class Main(object):
gobject.idle_add(self.experiment_running_data),
gobject.idle_add(self.experiment_running_proc)
)
-
-
+
self.stop_ocp()
self.statusbar.remove_all(self.error_context_id)
-
+
while comm.serial_instance.data_pipe_p.poll(): # Clear data pipe
comm.serial_instance.data_pipe_p.recv()
-
+
selection = self.expcombobox.get_active()
parameters = {}
parameters['version'] = self.version
-
+
# Make sure these are defined
parameters['sync_true'] = False
parameters['shutter_true'] = False
@@ -458,7 +481,7 @@ class Main(object):
self.line = 0
self.lastline = 0
self.lastdataline = 0
-
+
self.spinner.start()
self.startbutton.set_sensitive(False)
self.stopbutton.set_sensitive(True)
@@ -470,140 +493,144 @@ class Main(object):
if not parameters['potential']:
raise InputError(parameters['potential'],
"Step table is empty")
-
-
+
self.current_exp = comm.Chronoamp(parameters)
-
+
self.rawbuffer.set_text("")
self.rawbuffer.place_cursor(self.rawbuffer.get_start_iter())
-
+
for i in self.current_exp.commands:
self.rawbuffer.insert_at_cursor(i)
-
+
run_experiment()
-
- return
-
+
+ return experiment_id
+
elif selection == 1: # LSV
parameters.update(self.exp_window.get_params('lsv'))
parameter_test.lsv_test(parameters)
-
+
self.current_exp = comm.LSVExp(parameters)
run_experiment()
- return
-
+ return experiment_id
+
elif selection == 2: # CV
parameters.update(self.exp_window.get_params('cve'))
- parameter_test.cv_test(parameters)
-
+ parameter_test.cv_test(parameters)
+
self.current_exp = comm.CVExp(parameters)
run_experiment()
-
- return
-
+
+ return experiment_id
+
elif selection == 3: # SWV
parameters.update(self.exp_window.get_params('swv'))
parameter_test.swv_test(parameters)
-
+
self.current_exp = comm.SWVExp(parameters)
run_experiment()
-
- return
-
+
+ return experiment_id
+
elif selection == 4: # DPV
parameters.update(self.exp_window.get_params('dpv'))
parameter_test.dpv_test(parameters)
-
+
self.current_exp = comm.DPVExp(parameters)
run_experiment()
-
- return
-
- elif selection == 6: # PD
+
+ return experiment_id
+
+ elif selection == 6: # PD
parameters.update(self.exp_window.get_params('pde'))
parameter_test.pd_test(parameters)
-
+
self.current_exp = comm.PDExp(parameters)
run_experiment()
-
- return
-
+
+ return experiment_id
+
elif selection == 7: # POT
if not (self.version[0] >= 1 and self.version[1] >= 2):
- self.statusbar.push(self.error_context_id,
+ self.statusbar.push(self.error_context_id,
"v1.1 board does not support potentiometry.")
exceptions()
return
-
+
parameters.update(self.exp_window.get_params('pot'))
parameter_test.pot_test(parameters)
-
+
self.current_exp = comm.PotExp(parameters)
run_experiment()
-
- return
-
+
+ return experiment_id
+
else:
- self.statusbar.push(self.error_context_id,
+ self.statusbar.push(self.error_context_id,
"Experiment not yet implemented.")
exceptions()
-
+
except ValueError as i:
- _logger.error(i, "INFO")
- self.statusbar.push(self.error_context_id,
+ logger.info("ValueError: %s",i)
+ self.statusbar.push(self.error_context_id,
"Experiment parameters must be integers.")
exceptions()
-
+ raise
+
except KeyError as i:
- _logger.error("KeyError: %s" % i, "INFO")
+ logger.info("KeyError: %s", i)
self.statusbar.push(self.error_context_id,
"Experiment parameters must be integers.")
exceptions()
-
+ raise
+
except InputError as err:
- _logger.error(err, "INFO")
+ logger.info("InputError: %s", err)
self.statusbar.push(self.error_context_id, err.msg)
exceptions()
-
+ raise
+
except SerialException as err:
- _logger.error(err, "INFO")
- self.statusbar.push(self.error_context_id,
+ logger.info("SerialException: %s", err)
+ self.statusbar.push(self.error_context_id,
"Could not establish serial connection.")
exceptions()
+ raise
except AssertionError as err:
- _logger.error(err, "INFO")
+ logger.info("AssertionError: %s", err)
self.statusbar.push(self.error_context_id, str(err))
exceptions()
-
+ raise
def experiment_running_data(self):
- """Receive data from experiment process and add to current_exp.data.
+ """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:
- if comm.serial_instance.data_pipe_p.poll():
+ if comm.serial_instance.data_pipe_p.poll():
incoming = comm.serial_instance.data_pipe_p.recv()
-
+
self.line, data = incoming
if self.line > self.lastdataline:
- self.current_exp.data.append(
+ self.current_exp.data['data'].append(
deepcopy(self.current_exp.line_data))
self.lastdataline = self.line
- for i in range(len(self.current_exp.data[self.line])):
- self.current_exp.data[self.line][i].append(data[i])
-
+ for i in range(len(self.current_exp.data['data'][self.line])):
+ self.current_exp.data['data'][self.line][i].append(data[i])
+
if comm.serial_instance.data_pipe_p.poll():
self.experiment_running_data()
return True
-
+
return True
except EOFError as err:
@@ -614,43 +641,42 @@ class Main(object):
print 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:
- if comm.serial_instance.proc_pipe_p.poll():
+ if comm.serial_instance.proc_pipe_p.poll():
proc_buffer = comm.serial_instance.proc_pipe_p.recv()
-
+
if proc_buffer in ["DONE", "SERIAL_ERROR", "ABORT"]:
self.experiment_done()
if proc_buffer == "SERIAL_ERROR":
self.on_serial_disconnect_clicked()
-
+
else:
- e = "Unrecognized experiment return code "
- e += proc_buffer
- _logger.error(e, 'WAR')
-
+ logger.warning("Unrecognized experiment return code: %s",
+ proc_buffer)
+
return False
-
+
return True
except EOFError as err:
- _logger.error(err, 'WAR')
+ logger.warning("EOFError: %s", err)
self.experiment_done()
return False
except IOError as err:
- _logger.error(err, 'WAR')
+ logger.warning("IOError: %s", err)
self.experiment_done()
return False
-
+
def experiment_running_plot(self):
"""Plot all data in current_exp.data.
Run in GTK main loop. Always returns True so must be manually
@@ -659,7 +685,7 @@ class Main(object):
if self.line > self.lastline:
self.plot.addline()
# make sure all of last line is added
- self.plot.updateline(self.current_exp, self.lastline)
+ self.plot.updateline(self.current_exp, self.lastline)
self.lastline = self.line
self.plot.updateline(self.current_exp, self.line)
self.plot.redraw()
@@ -673,45 +699,53 @@ class Main(object):
gobject.source_remove(self.experiment_proc[0])
gobject.source_remove(self.plot_proc) # stop automatic plot update
self.experiment_running_plot() # make sure all data updated on plot
-
-
self.databuffer.set_text("")
self.databuffer.place_cursor(self.databuffer.get_start_iter())
self.rawbuffer.insert_at_cursor("\n")
self.rawbuffer.set_text("")
self.rawbuffer.place_cursor(self.rawbuffer.get_start_iter())
-
+
# 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.updateline(self.current_exp, 0)
self.ft_plot.redraw()
- for col in zip(*self.current_exp.ftdata):
- for row in col:
- self.databuffer.insert_at_cursor(str(row)+ " ")
- self.databuffer.insert_at_cursor("\n")
-
+
+ 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)
-
+
# Write DStat commands
for i in self.current_exp.commands:
self.rawbuffer.insert_at_cursor(i)
self.rawbuffer.insert_at_cursor("\n")
-
+
try:
self.statusbar.push(
- self.message_context_id,
+ self.message_context_id,
"Integral: %s A" % self.current_exp.analysis['FT Integral'][0][1]
)
except KeyError:
pass
-
+
# Data Output
analysis_buffer = []
-
+
if self.current_exp.analysis != {}:
analysis_buffer.append("# ANALYSIS")
for key, value in self.current_exp.analysis.iteritems():
@@ -721,13 +755,13 @@ class Main(object):
analysis_buffer.append(
"# Scan %s -- %s" % (number, result)
)
-
+
for i in analysis_buffer:
self.rawbuffer.insert_at_cursor("%s\n" % i)
-
+
line_buffer = []
-
- for scan in self.current_exp.data:
+
+ for scan in self.current_exp.data['data']:
for dimension in scan:
for i in range(len(dimension)):
try:
@@ -735,38 +769,31 @@ class Main(object):
except IndexError:
line_buffer.append("")
line_buffer[i] += "%s " % dimension[i]
-
+
for i in line_buffer:
self.rawbuffer.insert_at_cursor("%s\n" % i)
-
+
# Autosaving
if self.autosave_checkbox.get_active():
- save.autoSave(self.current_exp, self.autosavedir_button,
- self.autosavename.get_text(), self.expnumber)
- plots = {'data':self.plot}
-
- if (self.current_exp.parameters['shutter_true'] and
- self.current_exp.parameters['sync_true']):
- plots['ft'] = self.ft_plot
-
- save.autoPlot(plots, self.autosavedir_button,
- self.autosavename.get_text(), self.expnumber)
- self.expnumber += 1
-
+ save.autoSave(self.current_exp,
+ self.autosavedir_button.get_filename(),
+ self.autosavename.get_text()
+ )
+
+ save.autoPlot(self.current_exp,
+ self.autosavedir_button.get_filename(),
+ self.autosavename.get_text()
+ )
+
# uDrop
- if self.dropbot_enabled == True:
- if self.dropbot_triggered == True:
- self.dropbot_triggered = False
- self.microdrop.reply(microdrop.EXPFINISHED)
- self.microdrop_proc = gobject.timeout_add(500,
- self.microdrop_listen)
-
# UI stuff
self.spinner.stop()
self.startbutton.set_sensitive(True)
self.stopbutton.set_sensitive(False)
-
+
self.start_ocp()
+ self.completed_experiment_ids[self.active_experiment_id] =\
+ datetime.utcnow()
def on_pot_stop_clicked(self, data=None):
"""Stop current experiment. Signals experiment process to stop."""
@@ -776,89 +803,80 @@ class Main(object):
except AttributeError:
pass
except:
- _logger.error(sys.exc_info(),'WAR')
-
+ logger.warning(sys.exc_info())
+
def on_file_save_exp_activate(self, menuitem, data=None):
"""Activate dialogue to save current experiment data. """
- if self.current_exp:
+ try:
save.manSave(self.current_exp)
-
+ except AttributeError:
+ logger.warning("Tried to save with no experiment run")
+
def on_file_save_plot_activate(self, menuitem, data=None):
"""Activate dialogue to save current plot."""
- plots = {'data':self.plot}
-
- if (self.current_exp.parameters['shutter_true'] and
- self.current_exp.parameters['sync_true']):
- plots['ft'] = self.ft_plot
-
- save.plotSave(plots)
-
+ try:
+ save.plot_save_dialog(self.current_exp)
+ except AttributeError:
+ logger.warning("Tried to save with no experiment run")
+
def on_file_save_params_activate(self, menuitem, data=None):
"""Activate dialogue to save current experiment parameters. """
save.man_param_save(self)
-
+
def on_file_load_params_activate(self, menuitem, data=None):
"""Activate dialogue to load experiment parameters from file. """
save.man_param_load(self)
-
+
def on_menu_dropbot_connect_activate(self, menuitem, data=None):
"""Listen for remote control connection from µDrop."""
- self.microdrop = microdrop.microdropConnection()
+
+ # Prompt user for 0MQ plugin hub URI.
+ zmq_plugin_hub_uri = get_hub_uri(parent=self.window)
+
self.dropbot_enabled = True
self.menu_dropbot_connect.set_sensitive(False)
self.menu_dropbot_disconnect.set_sensitive(True)
self.statusbar.push(self.message_context_id,
"Waiting for µDrop to connect…")
- self.microdrop_proc = gobject.timeout_add(500, self.microdrop_listen)
-
+ self.enable_plugin(zmq_plugin_hub_uri)
+
def on_menu_dropbot_disconnect_activate(self, menuitem=None, data=None):
"""Disconnect µDrop connection and stop listening."""
- gobject.source_remove(self.microdrop_proc)
- self.microdrop.reset()
- del self.microdrop
+ self.cleanup_plugin()
self.dropbot_enabled = False
self.menu_dropbot_connect.set_sensitive(True)
self.menu_dropbot_disconnect.set_sensitive(False)
self.statusbar.push(self.message_context_id, "µDrop disconnected.")
- def microdrop_listen(self):
- """Manage signals from µDrop. Must be added to GTK's main loop to
- run periodically.
- """
- drdy, data = self.microdrop.listen()
- if drdy == False:
- return True
+ def enable_plugin(self, hub_uri):
+ '''
+ Connect to 0MQ plugin hub to expose public D-Stat API.
- if data == microdrop.EXP_FINISH_REQ:
- if self.dropbot_triggered:
- if self.connected:
- self.on_pot_start_clicked()
- else:
- _logger.error("µDrop requested experiment but DStat disconnected",
- 'WAR')
- self.statusbar.push(self.message_context_id,
- "Listen stopped—DStat disconnected.")
- self.microdrop.reply(microdrop.EXPFINISHED)
- self.on_menu_dropbot_disconnect_activate()
- return False # Removes function from GTK's main loop
- else:
- _logger.error("µDrop requested experiment finish confirmation without starting experiment.",
- 'WAR')
- self.microdrop.reply(microdrop.EXPFINISHED)
-
- elif data == microdrop.STARTEXP:
- self.microdrop.connected = True
- self.statusbar.push(self.message_context_id, "µDrop connected.")
- self.dropbot_triggered = True
- self.microdrop.reply(microdrop.START_REP)
- else:
- _logger.error("Received invalid command from µDrop",'WAR')
- self.microdrop.reply(microdrop.INVAL_CMD)
- return True
+ Args
+ ----
+
+ hub_uri (str) : URI for 0MQ plugin hub.
+ '''
+ self.cleanup_plugin()
+ # Initialize 0MQ hub plugin and subscribe to hub messages.
+ self.plugin = DstatPlugin(self, 'dstat-interface', hub_uri,
+ subscribe_options={zmq.SUBSCRIBE: ''})
+ # Initialize sockets.
+ self.plugin.reset()
+
+ # Periodically process outstanding message received on plugin sockets.
+ self.plugin_timeout_id = gtk.timeout_add(500,
+ self.plugin.check_sockets)
+
+ def cleanup_plugin(self):
+ if self.plugin_timeout_id is not None:
+ gobject.source_remove(self.plugin_timeout_id)
+ if self.plugin is not None:
+ self.plugin = None
if __name__ == "__main__":
multiprocessing.freeze_support()
gobject.threads_init()
MAIN = Main()
- gtk.main()
\ No newline at end of file
+ gtk.main()
diff --git a/dstat_interface/parameter_test.py b/dstat_interface/parameter_test.py
index 4330815a3b6a2f627390649f4319b496db570372..5600a8dd1a0d619c65baf72e83e28f6de9c1656f 100755
--- a/dstat_interface/parameter_test.py
+++ b/dstat_interface/parameter_test.py
@@ -18,8 +18,11 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
-from errors import ErrorLogger, InputError
-_logger = ErrorLogger(sender="dstat-interface-parameters")
+import logging
+
+from errors import InputError
+
+logger = logging.getLogger("dstat.parameter_test")
def lsv_test(params):
"""Test LSV parameters for sanity"""
diff --git a/dstat_interface/params.py b/dstat_interface/params.py
index 91be3801feae32056d23ffdb9a785946c6d1dd02..3ad6181c450daadf97263b06ce2439ee33eb465b 100755
--- a/dstat_interface/params.py
+++ b/dstat_interface/params.py
@@ -1,20 +1,20 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
+# Copyright (C) 2014 Michael D. M. Dryden -
# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
+#
+#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
-#
+#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
-#
+#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
@@ -25,53 +25,55 @@ _logger = ErrorLogger(sender="dstat-interface-params")
def get_params(window):
"""Fetches and returns dict of all parameters for saving."""
-
+
parameters = {}
-
+
selection = window.exp_window.select_to_key[window.expcombobox.get_active()]
parameters['experiment_index'] = selection
-
+
try:
parameters['version'] = window.version
except AttributeError: # Will be thrown if not connected to DStat
pass
-
+
try:
parameters.update(window.adc_pot.params)
except InputError:
- _logger.error("No gain selected.", 'INFO')
+ logger.info("No gain selected.")
parameters.update(window.exp_window.get_params(selection))
parameters.update(window.analysis_opt_window.params)
-
+
return parameters
def save_params(window, path):
"""Fetches current params and saves to path."""
-
+
params = get_params(window)
-
+
with open(path, 'w') as f:
yaml.dump(params, f)
-
+
def load_params(window, path):
"""Loads params from a path into UI elements."""
-
+
try:
get_params(window)
except InputError: # Will be thrown because no experiment will be selected
pass
-
+
with open(path, 'r') as f:
params = yaml.load(f)
-
+ set_params(window, params)
+
+def set_params(window, params):
window.adc_pot.params = params
-
+
if not 'experiment_index' in params:
- _logger.error("Missing experiment parameters.", 'WAR')
+ logger.warning("Missing experiment parameters.")
return
window.expcombobox.set_active(
window.exp_window.classes[params['experiment_index']][0])
window.exp_window.set_params(params['experiment_index'], params)
window.analysis_opt_window.params = params
-
- window.params_loaded = True
\ No newline at end of file
+
+ window.params_loaded = True
diff --git a/dstat_interface/plot.py b/dstat_interface/plot.py
index 4509428dd6b8fd34f6e105b18a339ffc5d61693c..7c5c017f371e2ea7a00a1a02b2a347bb02d6c9fd 100755
--- a/dstat_interface/plot.py
+++ b/dstat_interface/plot.py
@@ -90,7 +90,7 @@ def findBounds(y):
return (start_index, stop_index)
-class plotbox(object):
+class PlotBox(object):
"""Contains main data plot and associated methods."""
def __init__(self, plotwindow_instance):
"""Creates plot and moves it to a gtk container.
@@ -138,20 +138,22 @@ class plotbox(object):
the Experiment instance.
"""
# limits display to 2000 data points per line
- divisor = len(Experiment.data[line_number][0]) // 2000 + 1
+ divisor = len(Experiment.data['data'][line_number][0]) // 2000 + 1
self.axe1.lines[line_number].set_ydata(
- Experiment.data[line_number][1][1::divisor])
+ Experiment.data['data'][line_number][1][1::divisor])
self.axe1.lines[line_number].set_xdata(
- Experiment.data[line_number][0][1::divisor])
+ Experiment.data['data'][line_number][0][1::divisor])
def changetype(self, Experiment):
"""Change plot type. Set axis labels and x bounds to those stored
- in the Experiment instance.
+ in the Experiment instance. Stores class instance in Experiment.
"""
self.axe1.set_xlabel(Experiment.xlabel)
self.axe1.set_ylabel(Experiment.ylabel)
self.axe1.set_xlim(Experiment.xmin, Experiment.xmax)
+
+ Experiment.plots['data'] = self
self.figure.canvas.draw()
@@ -163,15 +165,15 @@ class plotbox(object):
return True
-class ft_box(plotbox):
+class FT_Box(PlotBox):
def updateline(self, Experiment, line_number):
def search_value(data, target):
for i in range(len(data)):
if data[i] > target:
return i
- y = Experiment.data[line_number][1]
- x = Experiment.data[line_number][0]
+ y = Experiment.data['data'][line_number][1]
+ x = Experiment.data['data'][line_number][0]
freq = Experiment.parameters['adc_rate_hz']
i = search_value(x, float(Experiment.parameters['fft_start']))
y1 = y[i:]
@@ -183,15 +185,17 @@ class ft_box(plotbox):
f, Y = plotSpectrum(y1[min_index:max_index],freq)
self.axe1.lines[line_number].set_ydata(Y)
self.axe1.lines[line_number].set_xdata(f)
- Experiment.ftdata = [(f, Y)]
+ Experiment.data['ft'] = [(f, Y)]
def changetype(self, Experiment):
"""Change plot type. Set axis labels and x bounds to those stored
- in the Experiment instance.
+ in the Experiment instance. Stores class instance in Experiment.
"""
self.axe1.set_xlabel("Freq (Hz)")
self.axe1.set_ylabel("|Y| (A/Hz)")
self.axe1.set_xlim(0, Experiment.parameters['adc_rate_hz']/2)
+
+ Experiment.plots['ft'] = self
self.figure.canvas.draw()
diff --git a/dstat_interface/plugin.py b/dstat_interface/plugin.py
new file mode 100644
index 0000000000000000000000000000000000000000..ebe2493324f4a2dc449128aace59ef83c6f0d506
--- /dev/null
+++ b/dstat_interface/plugin.py
@@ -0,0 +1,144 @@
+# -*- coding: utf-8 -*-
+import logging
+
+from params import get_params, set_params, load_params, save_params
+from interface.save import save_text, save_plot
+from zmq_plugin.plugin import Plugin as ZmqPlugin
+from zmq_plugin.schema import decode_content_data
+import gtk
+import zmq
+
+logger = logging.getLogger(__name__)
+
+
+def get_hub_uri(default='tcp://localhost:31000', parent=None):
+ message = 'Please enter 0MQ hub URI:'
+ d = gtk.MessageDialog(parent=parent, flags=gtk.DIALOG_MODAL |
+ gtk.DIALOG_DESTROY_WITH_PARENT,
+ type=gtk.MESSAGE_INFO, buttons=gtk.BUTTONS_OK_CANCEL,
+ message_format=message)
+ entry = gtk.Entry()
+ entry.set_text(default)
+ d.vbox.pack_end(entry)
+ d.vbox.show_all()
+ entry.connect('activate', lambda _: d.response(gtk.RESPONSE_OK))
+ d.set_default_response(gtk.RESPONSE_OK)
+
+ r = d.run()
+ text = entry.get_text().decode('utf8')
+ d.destroy()
+ if r == gtk.RESPONSE_OK:
+ return text
+ else:
+ return None
+
+
+class DstatPlugin(ZmqPlugin):
+ '''
+ Public 0MQ plugin API.
+ '''
+ def __init__(self, parent, *args, **kwargs):
+ self.parent = parent
+ super(DstatPlugin, self).__init__(*args, **kwargs)
+
+ def check_sockets(self):
+ '''
+ Check for messages on command and subscription sockets and process
+ any messages accordingly.
+ '''
+ try:
+ msg_frames = self.command_socket.recv_multipart(zmq.NOBLOCK)
+ except zmq.Again:
+ pass
+ else:
+ self.on_command_recv(msg_frames)
+
+ try:
+ msg_frames = self.subscribe_socket.recv_multipart(zmq.NOBLOCK)
+ source, target, msg_type, msg_json = msg_frames
+ self.most_recent = msg_json
+ except zmq.Again:
+ pass
+ except:
+ logger.error('Error processing message from subscription '
+ 'socket.', exc_info=True)
+ return True
+
+ def on_execute__load_params(self, request):
+ '''
+ Args
+ ----
+
+ params_path (str) : Path to file for parameters yaml file.
+ '''
+ data = decode_content_data(request)
+ load_params(self.parent, data['params_path'])
+
+ def on_execute__save_params(self, request):
+ '''
+ Args
+ ----
+
+ params_path (str) : Path to file for parameters yaml file.
+ '''
+ data = decode_content_data(request)
+ save_params(self.parent, data['params_path'])
+
+ def on_execute__set_params(self, request):
+ '''
+ Args
+ ----
+
+ (dict) : Parameters dictionary in format returned by `get_params`.
+ '''
+ data = decode_content_data(request)
+ set_params(self.parent, data['params'])
+
+ def on_execute__get_params(self, request):
+ return get_params(self.parent)
+
+ def on_execute__run_active_experiment(self, request):
+ self.parent.statusbar.push(self.parent.message_context_id, "µDrop "
+ "acquisition requested.")
+ return self.parent.run_active_experiment()
+
+ def on_execute__save_text(self, request):
+ '''
+ Args
+ ----
+
+ save_data_path (str) : Path to file to save text data.
+ '''
+ data = decode_content_data(request)
+ save_text(self.parent.current_exp, data['save_data_path'])
+
+ def on_execute__save_plot(self, request):
+ '''
+ Args
+ ----
+
+ save_plot_path (str) : Path to file to save plot.
+ '''
+ data = decode_content_data(request)
+ save_plot(self.parent.current_exp, data['save_plot_path'])
+
+ def on_execute__acquisition_complete(self, request):
+ '''
+ Args
+ ----
+
+ Returns
+ -------
+
+ (datetime.datetime or None) : The completion time of the experiment
+ corresponding to the specified UUID.
+ '''
+ data = decode_content_data(request)
+ self.parent.statusbar.push(self.parent.message_context_id, "µDrop "
+ "notified of completed acquisition.")
+ if data['experiment_id'] in self.parent.completed_experiment_ids:
+ return self.parent.completed_experiment_ids[data['experiment_id']]
+ elif data['experiment_id'] == self.parent.active_experiment_id:
+ return None
+ else:
+ raise KeyError('Unknown experiment ID: %s' % data['experiment_id'])
diff --git a/dstat_interface/setup.py b/dstat_interface/setup.py
deleted file mode 100644
index bbecb41acec29bb97c71ccd93dafc4d7b46db15e..0000000000000000000000000000000000000000
--- a/dstat_interface/setup.py
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/usr/bin/env python
-# DStat Interface - An interface for the open hardware DStat potentiostat
-# Copyright (C) 2014 Michael D. M. Dryden -
-# Wheeler Microfluidics Laboratory <http://microfluidics.utoronto.ca>
-#
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-from distutils.core import setup
-from Cython.Build import cythonize
-
-setup(
- ext_modules = cythonize("*.pyx")
- )
\ No newline at end of file
diff --git a/pavement.py b/pavement.py
index 86235fd40cfea4b4ff4af324feb7bd0439e5de95..0aea7f58afe84674e34958f65404241569de2066 100644
--- a/pavement.py
+++ b/pavement.py
@@ -17,14 +17,14 @@ setup(name='dstat_interface',
url='http://microfluidics.utoronto.ca/dstat',
license='GPLv3',
packages=['dstat_interface', ],
- install_requires=['matplotlib', 'numpy', 'pyserial',
- 'pyzmq', 'pyyaml','seaborn'],
+ install_requires=['matplotlib', 'numpy', 'pyserial', 'pyzmq',
+ 'pyyaml','seaborn', 'zmq-plugin>=0.2.post2'],
# Install data listed in `MANIFEST.in`
include_package_data=True)
@task
-@needs('generate_setup', 'minilib', 'setuptools.command.sdist')
+@needs('generate_setup', 'minilib', 'setuptools.command.sdist')
def sdist():
"""Overrides sdist to make sure that our setup.py is generated."""
pass