From 7a73a69f1519a9ddf25f907958c7b4db96d9f880 Mon Sep 17 00:00:00 2001
From: "Michael D. M. Dryden" <mdryden@chem.utoronto.ca>
Date: Mon, 25 Aug 2014 18:27:20 -0400
Subject: [PATCH] Added docstrings, fixed code conventions
---
dstat-interface/dstat-interface/dstat_comm.py | 164 ++++++++++++------
.../dstat-interface/interface/chronoamp.py | 9 +-
.../dstat-interface/interface/save.py | 11 +-
dstat-interface/dstat-interface/microdrop.py | 23 ++-
dstat-interface/dstat-interface/mpltest.py | 57 ++++--
5 files changed, 187 insertions(+), 77 deletions(-)
diff --git a/dstat-interface/dstat-interface/dstat_comm.py b/dstat-interface/dstat-interface/dstat_comm.py
index 69ceb4c..d701287 100644
--- a/dstat-interface/dstat-interface/dstat_comm.py
+++ b/dstat-interface/dstat-interface/dstat_comm.py
@@ -1,26 +1,36 @@
#!/usr/bin/env python
-import serial, io, time, struct, sys, os
-from types import *
+import serial
from serial.tools import list_ports
-import numpy as np
+import time
+import struct
import multiprocessing as mp
-from Queue import Empty
def call_it(instance, name, args=(), kwargs=None):
- "indirect caller for instance methods and multiprocessing"
+ """Indirect caller for instance methods and multiprocessing.
+
+ Arguments:
+ instance -- instance to which the method belongs
+ name -- method to call
+ args -- passed to method
+ kwargs -- passed to method
+ """
if kwargs is None:
kwargs = {}
return getattr(instance, name)(*args, **kwargs)
-class delayedSerial(serial.Serial): #overrides normal serial write so that characters are output individually with a slight delay
+class delayedSerial(serial.Serial):
+ """Extends Serial.write so that characters are output individually
+ with a slight delay
+ """
def write(self, data):
for i in data:
serial.Serial.write(self, i)
time.sleep(.001)
class SerialDevices:
+ """Retrieves and stores list of serial devices in self.ports"""
def __init__(self):
try:
self.ports, _, _ = zip(*list_ports.comports())
@@ -29,22 +39,33 @@ class SerialDevices:
print "No serial ports found"
def refresh(self):
+ """Refreshes list of ports."""
self.ports, _, _ = zip(*list_ports.comports())
class Experiment:
+ """Store and acquire a potentiostat experiment. Meant to be subclassed
+ to by different experiment types and not used instanced directly.
+ """
def run_wrapper(self, *argv):
- self.p = mp.Process(target=call_it, args=(self, 'run', argv))
- self.p.start()
+ """Execute experiment indirectly using call_it to bypass lack of fork()
+ on Windows for multiprocessing.
+ """
+ self.proc = mp.Process(target=call_it, args=(self, 'run', argv))
+ self.proc.start()
- def __init__(self): #will always be overriden, but self.parameters, self.viewparameters, and self.databytes should be defined
- pass
+ def __init__(self, parameters, main_pipe):
+ """Must be overridden to define self.parameters, and self.databytes."""
+ self.parameters = parameters
+ self.main_pipe = main_pipe
+ self.databytes = 8
def init(self):
- self.data_extra = [] #must be defined even when not needed
+ """Adds commands for gain and ADC."""
+ self.data_extra = [] # must be defined even when not needed
self.__gaintable = [1e2, 3e2, 3e3, 3e4, 3e5, 3e6, 3e7, 5e8]
self.gain = self.__gaintable[int(self.parameters['gain'])]
- self.commands = ["A","G"]
+ self.commands = ["A", "G"]
self.commands[0] += (self.parameters['adc_buffer'])
self.commands[0] += " "
@@ -55,8 +76,15 @@ class Experiment:
self.commands[1] += (self.parameters['gain'])
self.commands[1] += " "
- def run(self, strPort):
- self.serial = delayedSerial(strPort, 1024000, timeout=1)
+ def run(self, ser_port):
+ """Execute experiment. Connects and sends handshake signal to DStat
+ then sendsself.commands. Don't call directly as a process in Windows,
+ use run_wrapper instead.
+
+ Arguments:
+ ser_port -- address of serial port to use
+ """
+ self.serial = delayedSerial(ser_port, 1024000, timeout=1)
self.serial.write("ck")
self.serial.flushInput()
@@ -77,6 +105,10 @@ class Experiment:
self.main_pipe.close()
def serial_handler(self):
+ """Handles incoming serial transmissions from DStat. Returns False
+ if stop button pressed and sends abort signal to instrument. Sends
+ data to self.main_pipe as result of self.data_handler).
+ """
scan = 0
while True:
if self.main_pipe.poll():
@@ -87,7 +119,8 @@ class Experiment:
for line in self.serial:
if line.startswith('B'):
- self.main_pipe.send(self.data_handler((scan, self.serial.read(size=self.databytes))))
+ self.main_pipe.send(self.data_handler(
+ (scan, self.serial.read(size=self.databytes))))
elif line.startswith('S'):
scan += 1
elif line.startswith("#"):
@@ -98,22 +131,31 @@ class Experiment:
return True
- def data_handler(self, input):
- scan, data = input
+ def data_handler(self, data_input):
+ """Takes data_input as tuple -- (scan, data).
+ Returns:
+ (scan number, [voltage, current]) -- voltage in mV, current in A
+ """
+ scan, data = data_input
voltage, current = struct.unpack('<Hl', data) #uint16 + int32
- return (scan, [(voltage-32768)*3000./65536, current*(1.5/self.gain/8388607)])
+ return (scan,
+ [(voltage-32768)*3000./65536, current*(1.5/self.gain/8388607)])
def data_postprocessing(self):
+ """No data postprocessing done by default, can be overridden
+ in subclass.
+ """
pass
class chronoamp(Experiment):
+ """Chronoamperometry experiment"""
def __init__(self, parameters, main_pipe):
self.main_pipe = main_pipe
self.parameters = parameters
self.datatype = "linearData"
self.xlabel = "Time (s)"
self.ylabel = "Current (A)"
- self.data = [[],[]]
+ self.data = [[], []]
self.datalength = 2
self.databytes = 8
self.xmin = 0
@@ -122,7 +164,7 @@ class chronoamp(Experiment):
for i in self.parameters['time']:
self.xmax += int(i)
- self.init() #need to call after xmin and xmax are set
+ self.init() # need to call after xmin and xmax are set
self.commands += "R"
self.commands[2] += str(len(self.parameters['potential']))
@@ -134,12 +176,16 @@ class chronoamp(Experiment):
self.commands[2] += str(i)
self.commands[2] += " "
- def data_handler(self, input): #overrides inherited method to not convert x axis
- scan, data = input
- seconds, milliseconds, current = struct.unpack('<HHl', data) #2*uint16 + int32
- return (scan, [seconds+milliseconds/1000., current*(1.5/self.gain/8388607)])
+ def data_handler(self, data_input):
+ """Overrides Experiment method to not convert x axis to mV."""
+ scan, data = data_input
+ # 2*uint16 + int32
+ seconds, milliseconds, current = struct.unpack('<HHl', data)
+ return (scan,
+ [seconds+milliseconds/1000., current*(1.5/self.gain/8388607)])
class lsv_exp(Experiment):
+ """Linear Scan Voltammetry experiment"""
def __init__(self, parameters, send_pipe):
self.main_pipe = send_pipe
self.parameters = parameters
@@ -147,22 +193,24 @@ class lsv_exp(Experiment):
self.datatype = "linearData"
self.xlabel = "Voltage (mV)"
self.ylabel = "Current (A)"
- self.data = [[],[]]
+ self.data = [[], []]
self.datalength = 2
- self.databytes = 6 #uint16 + int32
+ self.databytes = 6 # uint16 + int32
self.xmin = self.parameters['start']
self.xmax = self.parameters['stop']
- self.init() #need to call after xmin and xmax are set
+ self.init() # need to call after xmin and xmax are set
self.commands += "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(self.parameters['clean_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['clean_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
- self.commands[2] += str(int(self.parameters['dep_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['dep_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
self.commands[2] += str(self.parameters['start'])
self.commands[2] += " "
@@ -172,6 +220,7 @@ class lsv_exp(Experiment):
self.commands[2] += " "
class cv_exp(Experiment):
+ """Cyclic Voltammetry experiment"""
def __init__(self, parameters, main_pipe):
self.main_pipe = main_pipe
self.parameters = parameters
@@ -179,9 +228,9 @@ class cv_exp(Experiment):
self.datatype = "CVData"
self.xlabel = "Voltage (mV)"
self.ylabel = "Current (A)"
- self.data = [[],[]] #Will have to alter data_handler to add new lists as needed
- self.datalength = 2 * self.parameters['scans'] #x and y for each scan
- self.databytes = 6 #uint16 + int32
+ self.data = [[], []]
+ self.datalength = 2 * self.parameters['scans'] # x and y for each scan
+ self.databytes = 6 # uint16 + int32
self.xmin = self.parameters['v1']
self.xmax = self.parameters['v2']
@@ -192,9 +241,11 @@ class cv_exp(Experiment):
self.commands[2] += " "
self.commands[2] += str(self.parameters['dep_s'])
self.commands[2] += " "
- self.commands[2] += str(int(self.parameters['clean_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['clean_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
- self.commands[2] += str(int(self.parameters['dep_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['dep_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
self.commands[2] += str(self.parameters['v1'])
self.commands[2] += " "
@@ -206,13 +257,9 @@ class cv_exp(Experiment):
self.commands[2] += " "
self.commands[2] += str(self.parameters['slope'])
self.commands[2] += " "
-
- def data_handler(self, input):
- scan, data = input
- voltage, current = struct.unpack('<Hl', data) #uint16 + int32
- return (scan, [(voltage-32768)*3000./65536, current*(1.5/self.gain/8388607)])
class swv_exp(Experiment):
+ """Square Wave Voltammetry experiment"""
def __init__(self, parameters, main_pipe):
self.main_pipe = main_pipe
self.parameters = parameters
@@ -220,7 +267,7 @@ class swv_exp(Experiment):
self.datatype = "SWVData"
self.xlabel = "Voltage (mV)"
self.ylabel = "Current (A)"
- self.data = [[],[]] #only difference stored here
+ self.data = [[], []] # only difference stored here
self.datalength = 2 * self.parameters['scans']
self.databytes = 10
@@ -228,16 +275,20 @@ class swv_exp(Experiment):
self.xmax = self.parameters['stop']
self.init()
- self.data_extra = [[],[]] #forward/reverse stored here - needs to be after self.init to keep from being redefined
+ # forward/reverse stored here - needs to be after
+ # self.init to keep from being redefined
+ self.data_extra = [[], []]
self.commands += "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(self.parameters['clean_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['clean_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
- self.commands[2] += str(int(self.parameters['dep_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['dep_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
self.commands[2] += str(self.parameters['start'])
self.commands[2] += " "
@@ -252,21 +303,28 @@ class swv_exp(Experiment):
self.commands[2] += str(self.parameters['scans'])
self.commands[2] += " "
- def data_handler(self, input):
- scan, data = input
- voltage, forward, reverse = struct.unpack('<Hll', data) #uint16 + int32
- return (scan, [(voltage-32768)*3000./65536, (forward-reverse)*(1.5/self.gain/8388607), forward*(1.5/self.gain/8388607), reverse*(1.5/self.gain/8388607)])
+ def data_handler(self, input_data):
+ """Overrides Experiment method to calculate difference current"""
+ scan, data = input_data
+ # uint16 + int32
+ voltage, forward, reverse = struct.unpack('<Hll', data)
+ return (scan, [(voltage-32768)*3000./65536,
+ (forward-reverse)*(1.5/self.gain/8388607),
+ forward*(1.5/self.gain/8388607),
+ reverse*(1.5/self.gain/8388607)])
class dpv_exp(swv_exp):
+ """Diffential Pulse Voltammetry experiment."""
def __init__(self, parameters, main_pipe):
+ """Overrides swv_exp method"""
self.main_pipe = main_pipe
self.parameters = parameters
self.datatype = "SWVData"
self.xlabel = "Voltage (mV)"
self.ylabel = "Current (A)"
- self.data = [[],[]] #only difference stored here
+ self.data = [[], []] # only difference stored here
self.datalength = 2
self.databytes = 10
@@ -274,16 +332,20 @@ class dpv_exp(swv_exp):
self.xmax = self.parameters['stop']
self.init()
- self.data_extra = [[],[]] #forward/reverse stored here - needs to be after self.init to keep from being redefined
+ # forward/reverse stored here - needs to be after self.init to
+ # keep from being redefined
+ self.data_extra = [[], []]
self.commands += "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(self.parameters['clean_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['clean_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
- self.commands[2] += str(int(self.parameters['dep_mV']*(65536./3000)+32768))
+ self.commands[2] += str(int(self.parameters['dep_mV']*
+ (65536./3000)+32768))
self.commands[2] += " "
self.commands[2] += str(self.parameters['start'])
self.commands[2] += " "
diff --git a/dstat-interface/dstat-interface/interface/chronoamp.py b/dstat-interface/dstat-interface/interface/chronoamp.py
index 0eb3b09..2ba1a2a 100644
--- a/dstat-interface/dstat-interface/interface/chronoamp.py
+++ b/dstat-interface/dstat-interface/interface/chronoamp.py
@@ -20,8 +20,10 @@ class chronoamp:
self.cell_renderer = gtk.CellRendererText()
- self.treeview.insert_column_with_attributes(-1, "Time", self.cell_renderer, text=1).set_expand(True)
- self.treeview.insert_column_with_attributes(-1, "Potential", self.cell_renderer, text=0).set_expand(True)
+ self.treeview.insert_column_with_attributes(-1, "Time",
+ self.cell_renderer, text=1).set_expand(True)
+ self.treeview.insert_column_with_attributes(-1, "Potential",
+ self.cell_renderer, text=0).set_expand(True)
self.treeviewselection = self.treeview.get_selection()
self.treeviewselection.set_mode(gtk.SELECTION_MULTIPLE)
@@ -46,7 +48,8 @@ class chronoamp:
self.statusbar.push(0, str(e))
def on_remove_button_clicked(self, widget):
- self.selected_rows = list(self.treeviewselection.get_selected_rows()[1]) #returns 2-tuple: treemodel, list of paths selected rows
+ # returns 2-tuple: treemodel, list of paths of selected rows
+ self.selected_rows = list(self.treeviewselection.get_selected_rows()[1])
self.referencelist = []
diff --git a/dstat-interface/dstat-interface/interface/save.py b/dstat-interface/dstat-interface/interface/save.py
index 4456d08..8cc67f2 100644
--- a/dstat-interface/dstat-interface/interface/save.py
+++ b/dstat-interface/dstat-interface/interface/save.py
@@ -7,7 +7,9 @@ from datetime import datetime
def manSave(current_exp):
exp = current_exp
- fcd = gtk.FileChooserDialog("Save...", None, gtk.FILE_CHOOSER_ACTION_SAVE, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK))
+ 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("NumPy binary (.npy)")
@@ -37,7 +39,10 @@ def manSave(current_exp):
fcd.destroy()
def plotSave(plot):
- fcd = gtk.FileChooserDialog("Save Plot…", None, gtk.FILE_CHOOSER_ACTION_SAVE, (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE, gtk.RESPONSE_OK))
+ fcd = gtk.FileChooserDialog("Save Plot…", 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("Portable Document Format (.pdf)")
@@ -65,7 +70,7 @@ def plotSave(plot):
if not path.endswith(".png"):
path += ".png"
- plot.figure.savefig(path) #savefig determines format from file extension
+ plot.figure.savefig(path) # determines format from file extension
fcd.destroy()
elif response == gtk.RESPONSE_CANCEL:
diff --git a/dstat-interface/dstat-interface/microdrop.py b/dstat-interface/dstat-interface/microdrop.py
index 217b571..917ef2c 100644
--- a/dstat-interface/dstat-interface/microdrop.py
+++ b/dstat-interface/dstat-interface/microdrop.py
@@ -15,17 +15,28 @@ RECV = 0
SEND = 1
class microdropConnection:
-
+ """Manages microdrop connection over TCP with zmq"""
def __init__(self, port=6789):
+ """Create zmq context and bind to port. Should be called manually
+ to reinitialize if reset is called.
+
+ Keyword arguments:
+ port -- the TCP to bind to on localhost
+ """
self.port = port
self.connected = False
self.state = RECV
self.ctx = zmq.Context()
self.soc = zmq.Socket(self.ctx, zmq.REP)
- self.soc.bind("".join(['tcp://*:',str(self.port)]))
+ self.soc.bind("".join(['tcp://*:', str(self.port)]))
def listen(self):
+ """Perform non-blocking recv on zmq port. self.state must be RECV.
+ Returns a tuple:
+ [0] -- True if a message was received, False otherwise.
+ [1] -- The recieved message or "" if no message received.
+ """
if self.state == SEND:
print "WAR: Microdrop Connection state invalid, resetting..."
self.reset()
@@ -38,6 +49,11 @@ class microdropConnection:
return (False, "")
def reply(self, data):
+ """Sends a reply on zmq port. self.state must be SEND.
+
+ Arguments:
+ data -- a str to be sent
+ """
if self.state == RECV:
print "WAR: Microdrop Connection state invalid, resetting..."
self.reset()
@@ -48,6 +64,7 @@ class microdropConnection:
return True
def reset(self):
- self.soc.unbind("".join(['tcp://*:',str(self.port)]))
+ """Reset zmq interface. Must call __init__ again to reinitialize."""
+ self.soc.unbind("".join(['tcp://*:', str(self.port)]))
del self.soc
del self.ctx
diff --git a/dstat-interface/dstat-interface/mpltest.py b/dstat-interface/dstat-interface/mpltest.py
index ea8bc75..7624499 100644
--- a/dstat-interface/dstat-interface/mpltest.py
+++ b/dstat-interface/dstat-interface/mpltest.py
@@ -1,27 +1,37 @@
#!/usr/bin/env python
"""
- show how to add a matplotlib FigureCanvasGTK or FigureCanvasGTKAgg widget to a
- gtk.Window
- """
+Creates data plot.
+"""
import gtk
from matplotlib.figure import Figure
-from matplotlib import pyplot as plt
-import numpy as np
-#from matplotlib.backends.backend_gtkcairo import FigureCanvasGTKCairo as FigureCanvas
-#from matplotlib.backends.backend_gtkcairo import NavigationToolbar2Cairo as NavigationToolbar
-from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas
-from matplotlib.backends.backend_gtkagg import NavigationToolbar2GTKAgg as NavigationToolbar
+#from matplotlib.backends.backend_gtkcairo\
+# import FigureCanvasGTKCairo as FigureCanvas
+#from matplotlib.backends.backend_gtkcairo\
+# import NavigationToolbar2Cairo as NavigationToolbar
+from matplotlib.backends.backend_gtkagg \
+ import FigureCanvasGTKAgg as FigureCanvas
+from matplotlib.backends.backend_gtkagg \
+ import NavigationToolbar2GTKAgg as NavigationToolbar
class plotbox:
+ """Contains main data plot and associated methods."""
def __init__(self, plotwindow_instance):
+ """Creates plot and moves it to a gtk container.
+
+ Arguments:
+ plotwindow_instance -- gtk container to hold plot.
+ """
+
self.figure = Figure()
- self.figure.subplots_adjust(left=0.07, bottom=0.07, right=0.96, top=0.96)
+ self.figure.subplots_adjust(left=0.07, bottom=0.07,
+ right=0.96, top=0.96)
self.axe1 = self.figure.add_subplot(111)
- self.lines = self.axe1.plot([0,1], [0,1])
+ self.lines = self.axe1.plot([0, 1], [0, 1])
- self.axe1.ticklabel_format(style='sci', scilimits=(0,3), useOffset=False, axis='y')
+ self.axe1.ticklabel_format(style='sci', scilimits=(0, 3),
+ useOffset=False, axis='y')
self.canvas = FigureCanvas(self.figure)
self.win = gtk.Window()
@@ -33,24 +43,36 @@ class plotbox:
self.vbox.reparent(plotwindow_instance)
def clearall(self):
+ """Remove all lines on plot. """
for i in self.lines:
i.remove()
- self.lines = self.axe1.plot([0,1], [0,1])
+ self.lines = self.axe1.plot([0, 1], [0, 1])
def clearline(self, line_number):
+ """Remove a line specified by line_number."""
self.lines[line_number].remove()
self.lines.pop(line_number)
def addline(self):
- self.lines.append(self.axe1.plot([0,1], [0,1])[0])
+ """Add a new line to plot. (initialized with dummy data)))"""
+ self.lines.append(self.axe1.plot([0, 1], [0, 1])[0])
def updateline(self, Experiment, line_number):
- divisor = len(Experiment.data[1+line_number*2]) // 2000 + 1 #limits display to 2000 data points per line
+ """Update a line specified by line_number with data stored in
+ the Experiment instance.
+ """
+ # limits display to 2000 data points per line
+ divisor = len(Experiment.data[1+line_number*2]) // 2000 + 1
- self.lines[line_number].set_ydata(Experiment.data[1+line_number*2][1::divisor])
- self.lines[line_number].set_xdata(Experiment.data[line_number*2][1::divisor])
+ self.lines[line_number].set_ydata(
+ Experiment.data[1+line_number*2][1::divisor])
+ self.lines[line_number].set_xdata(
+ Experiment.data[line_number*2][1::divisor])
def changetype(self, Experiment):
+ """Change plot type. Set axis labels and x bounds to those stored
+ in the Experiment instance.
+ """
self.axe1.set_xlabel(Experiment.xlabel)
self.axe1.set_ylabel(Experiment.ylabel)
self.axe1.set_xlim(Experiment.xmin, Experiment.xmax)
@@ -58,6 +80,7 @@ class plotbox:
self.figure.canvas.draw()
def redraw(self):
+ """Autoscale and refresh the plot."""
self.axe1.relim()
self.axe1.autoscale(True, axis = 'y')
self.figure.canvas.draw()
--
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