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Unverified Commit 7a73a69f authored by Michael DM Dryden's avatar Michael DM Dryden
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Added docstrings, fixed code conventions

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dstat-interface/dstat-interface/dstat_comm.py
+ 113
− 51
View file @ 7a73a69f
#!/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] += " "
......
dstat-interface/dstat-interface/interface/chronoamp.py
+ 6
− 3
View file @ 7a73a69f
......@@ -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 = []
......
dstat-interface/dstat-interface/interface/save.py
+ 8
− 3
View file @ 7a73a69f
......@@ -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:
......
dstat-interface/dstat-interface/microdrop.py
+ 20
− 3
View file @ 7a73a69f
......@@ -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
dstat-interface/dstat-interface/mpltest.py
+ 40
− 17
View file @ 7a73a69f
#!/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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