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PSDataPlot.py
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PSDataPlot.py
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# -*- coding: utf-8 -*-
"""
Created on Thu Mar 11 19:43:23 2021
@author: Stephan
"""
import matplotlib.pyplot as plt
class axis:
__slots__ = ['xvalues','yvalues']
def __init__(self):
self.xvalues = []
self.yvalues = []
class PSPlot:
@property
def titles(self):
return self._titles
@titles.setter
def titles(self, val):
self._titlesOn = True
self._titles = val
@property
def methodFilter(self):
return self._methodFilter
@methodFilter.setter
def methodFilter(self, val):
self._filterOnMethod = True
self._methodFilter = val
@property
def groups(self):
return self._groups
@groups.setter
def groups(self, val):
self._grouping = True
self._groups = val
def __init__(self, PSData):
self._filterOnMethod = False
self._PlotNotebookTags = []
self._PlotNotebookTagsIndex = 1
self._methodFilter = ''
self.methodType = MethodType()
self.baseline = Baseline()
self.legend_on = True
self.units_on = True
self._experimentList = []
self.eisTypes = EISMeasurement()
self.PSData = PSData
self.files = []
self._plots = {}
self._titles = []
self._titlesOn = False
self._titleIndex = 0
self.splitGraphs = False
self._grouping = False
self._groups = {}
self.peaks = {}
def show(self, experimentLabels = ''):
# Experimental, use at own risk
if self._PlotNotebookTagsIndex in self._PlotNotebookTags:
self._PlotNotebookTagsIndex = 1 + self._PlotNotebookTagsIndex
self._PlotNotebookTags.append(self._PlotNotebookTagsIndex)
if self._titlesOn:
graphCount = self._getGraphCount()
if len(self._titles) != graphCount:
print('Title count incorrect. Set ' + str(len(self._titles)) + '/' + str(graphCount))
return
experimentIndex = 0
canPlotAll = False
for currentMethod in self.PSData.experimentList:
canplot = True
if self._filterOnMethod and not self._methodFilter in currentMethod:
# filtermethod set and check the method
canplot = False
if not experimentLabels == '' and canplot:
# check if this is the experiment we want to plot, if experimentLabels is set
canplot = self.PSData.experimentList[experimentIndex] in experimentLabels
if canplot:
canPlotAll = True
if 'SWV' in currentMethod:
self._SWVAnalysis(self.PSData.data[self.PSData.experimentList[experimentIndex]],experimentIndex)
if 'CV' in currentMethod:
self._CVAnalysis(self.PSData.data[self.PSData.experimentList[experimentIndex]],experimentIndex)
#print('CV')
if 'EIS' in currentMethod:
self._EISAnalysis(self.PSData.data[self.PSData.experimentList[experimentIndex]],experimentIndex)
experimentIndex = experimentIndex + 1
if canPlotAll:
plt.show()
if len(self.groups) > 0:
self.getPeakRatios()
else:
if not self._methodFilter in experimentLabels:
print('All plot() arguments are filtered out by the method filter')
else:
print('No data found for: ' + self.methodFilter)
def getPeakRatios(self, printF = True):
# Beta
ratios = {}
for group in self.groups:
if len(self.groups[group]) == 2:
peak1 = 0
tag1 = ''
for exp in self.groups[group]:
if 'SWV' in exp:
if peak1 == 0:
peak1 = self.peaks[exp]
tag1 = exp
nr1 = int(tag1.split()[1])
else:
peak2 = self.peaks[exp]
nr2 = int(exp.split()[1])
returnTag = ''
returnValue = 0.0
if nr1 < nr2:
returnTag = tag1 + '/' + exp
returnValue = peak1/peak2
else:
returnTag = exp + '/' + tag1
returnValue = peak2/peak1
if printF:
print('Ratio: ' + returnTag + ' = ' + "{:.2f}".format(round((returnValue)*100, 2)) + r'%')
ratios[returnTag] = returnValue
return ratios
def _getGraphCount(self):
''' NB, change the amount of EIS graphs as they get developed '''
eisCount = len([i for i, s in enumerate(self.PSData.experimentList) if 'EIS' in s])*3
swvCount = len([ i for i, s in enumerate(self.PSData.experimentList) if 'SWV' in s])
cvCount = len([i for i, s in enumerate(self.PSData.experimentList) if 'CV' in s])
# set to zero those we do not want to plot
if not self.methodFilter in 'EIS':
eisCount = 0
if not self.methodFilter in 'SWV':
swvCount = 0
if not self.methodFilter in 'CV':
cvCount = 0
graphCount = 0
if self.splitGraphs:
# individual graphs, so count all
graphCount = eisCount + swvCount + cvCount
else:
# all of each sort on a graph
if eisCount > 0:
graphCount += 3
if swvCount > 0:
graphCount += 1
if cvCount > 0:
graphCount += 1
return graphCount
def _SWVAnalysis(self, measurement, experimentIndex):
# get units from the dictionary
units = {}
if (self.PSData.experimentList[experimentIndex] + ' Details') in self.PSData.data:
units = self.PSData.data[self.PSData.experimentList[experimentIndex] + ' Details']
else:
units['x'] = {}
units['y'] = {}
units['x']['unit'] = ''
units['y']['unit'] = ''
units['x']['scale'] = 1
units['y']['scale'] = 1
units['title'] = ''
PlotTag = str(self._PlotNotebookTagsIndex)
if self.splitGraphs:
# just create a new graph every time
figx, axx = plt.subplots()
axx.grid(True)
titleIndex = self._titleIndex
self._titleIndex += 1
else:
# check the dictionary for the graphs and add if exists
tag = self._getGraphTag('swv' + PlotTag,experimentIndex)
if self._grouping and tag == ('swv' + PlotTag):
# if we are grouping and tag is not in group, exit.
# not implemented for other methods
return
if not tag in self._plots:
figx, axx = plt.subplots()
axx.grid(True)
titleIndex = self._titleIndex
self._titleIndex += 1
self._plots[tag] = [figx, axx, titleIndex]
else:
plotdata = self._plots[tag]
figx = plotdata[0]
axx = plotdata[1]
titleIndex = plotdata[2]
# generate the baseline
self.baseline._generateBaseline(measurement.xvalues, measurement.yvalues)
# subtract the baseline
pos = 0
ax_baseline = axis()
for y in measurement.yvalues:
ax_baseline.xvalues.append(measurement.xvalues[pos]/units['x']['scale'])
ax_baseline.yvalues.append(self.baseline._subtract(measurement.xvalues[pos],y)/units['y']['scale'])
pos = pos + 1
# kind of backwards, translated to Ampere, and then we determine what would be the better scale
XUnits = self._setScale(max(ax_baseline.xvalues))
YUnits = self._setScale(max(ax_baseline.yvalues))
yMod = []
xMod = []
for x in ax_baseline.xvalues:
xMod.append(x/XUnits['scale'])
for y in ax_baseline.yvalues:
yMod.append(y/YUnits['scale'])
axx.plot(xMod, yMod, label=(self.PSData.experimentList[experimentIndex] + ' : ' + units['title']))
# get and save the minimum values
minv = min(yMod)
minv_index = yMod.index(minv)
print(self.PSData.experimentList[experimentIndex] + ' min: (' + str(xMod[minv_index]) + ',' + str(minv) + ')' )
if len(self.groups) > 0:
for group in self.groups:
for exp in self.groups[group]:
if self.PSData.experimentList[experimentIndex] == exp:
self.peaks[self.PSData.experimentList[experimentIndex]] = minv
if self.units_on:
axx.set_xlabel(XUnits['unit'] + 'V')
axx.set_ylabel(YUnits['unit'] + 'A')
if self.splitGraphs:
if self._titlesOn:
axx.set_title(self.titles[titleIndex])
else:
axx.set_title(self.PSData.experimentList[experimentIndex])
else:
axx.legend(bbox_to_anchor=(1.05,1.05))
if self._titlesOn:
axx.set_title(self.titles[titleIndex])
def _CVAnalysis(self, measurement, experimentIndex):
# get units from the dictionary
units = {}
if self.PSData.experimentList[experimentIndex] + ' Details' in self.PSData.data:
units = self.PSData.data[self.PSData.experimentList[experimentIndex] + ' Details']
else:
units['x'] = {}
units['y'] = {}
units['x']['unit'] = ''
units['y']['unit'] = ''
units['x']['scale'] = 1
units['y']['scale'] = 1
PlotTag = str(self._PlotNotebookTagsIndex)
if self.splitGraphs:
# just create a new graph every time
figx, axx = plt.subplots()
titleIndex = self._titleIndex
self._titleIndex += 1
axx.grid(True)
else:
# check the dictionary for the graphs and add if exists
tag = self._getGraphTag('cv' + PlotTag,experimentIndex)
if not tag in self._plots:
figx, axx = plt.subplots()
axx.grid(True)
titleIndex = self._titleIndex
self._titleIndex += 1
self._plots[tag] = [figx, axx, titleIndex]
else:
plotdata = self._plots[tag]
figx = plotdata[0]
axx = plotdata[1]
titleIndex = plotdata[2]
# convert to ampere
pos = 0
ax = axis()
for y in measurement.yvalues:
ax.xvalues.append(measurement.xvalues[pos]/units['x']['scale'])
ax.yvalues.append(y/units['y']['scale'])
pos = pos + 1
# and then go determine a better scale
XUnits = self._setScale(max(ax.xvalues))
YUnits = self._setScale(max(ax.yvalues))
yMod = []
xMod = []
for x in ax.xvalues:
xMod.append(x/XUnits['scale'])
for y in ax.yvalues:
yMod.append(y/YUnits['scale'])
axx.plot(xMod,yMod, label=self.PSData.experimentList[experimentIndex]+ ' : ' + units['title'])
if self.units_on:
axx.set_xlabel(XUnits['unit'] + 'V')
axx.set_ylabel(YUnits['unit'] + 'A')
if self.splitGraphs:
if self._titlesOn:
axx.set_title(self.titles[titleIndex])
else:
axx.set_title(self.PSData.experimentList[experimentIndex])
else:
axx.legend(bbox_to_anchor=(1.05,1.05))
if self._titlesOn:
axx.set_title(self.titles[titleIndex])
def _EISAnalysis(self, measurement, experimentIndex):
self._plotEISNyq(measurement, experimentIndex)
self._plotEISZdashes(measurement, experimentIndex)
self._plotEISYdash(measurement, experimentIndex)
self._plotEISCap(measurement, experimentIndex)
def _plotEISNyq(self, measurement, experimentIndex):
PlotTag = str(self._PlotNotebookTagsIndex)
if self.splitGraphs:
fig, ax1 = plt.subplots()
ax2 = ax1.twinx()
titleIndex = self._titleIndex
self._titleIndex += 1
else:
tag = self._getGraphTag('bode' + PlotTag,experimentIndex)
if not tag in self._plots:
fig, ax1 = plt.subplots()
ax2 = ax1.twinx()
titleIndex = self._titleIndex
self._titleIndex += 1
self._plots[tag] = [fig, ax1, ax2, titleIndex]
else:
plotdata = self._plots[tag]
fig = plotdata[0]
ax1 = plotdata[1]
ax2 = plotdata[2]
titleIndex = plotdata[3]
s = 4
ax1.loglog(measurement.freq, measurement.Z,'s-', label=self.PSData.experimentList[experimentIndex], markersize=s)
ax1.grid(True)
ax2.plot(measurement.freq, measurement.phase,'*-', label=self.PSData.experimentList[experimentIndex], markersize=s)
ax2.grid(True)
b, t = ax1.get_ylim()
b2, t2 = ax2.get_ylim()
ax1.set_ylim([b/10, t*3])
ax2.set_ylim([b2 - 10,t2 + 10])
ax1.set_xlabel(self.eisTypes.freq)
ax1.set_ylabel(self.eisTypes.Z + "/$\Omega$")
ax2.set_ylabel(self.eisTypes.phase + "/$^\circ$")
if self._titlesOn:
ax1.set_title(self.titles[titleIndex])
if self.splitGraphs:
ax2.set_title(self.PSData.experimentList[experimentIndex])
else:
ax2.legend(bbox_to_anchor=(1.3,1.05))
def _plotEISYdash(self, measurement, experimentIndex):
PlotTag = str(self._PlotNotebookTagsIndex)
if self.splitGraphs:
fig, ax1 = plt.subplots()
ax2 = ax1.twinx()
titleIndex = self._titleIndex
self._titleIndex += 1
else:
tag = self._getGraphTag('ydash' + PlotTag,experimentIndex)
if not tag in self._plots:
fig, ax1 = plt.subplots()
ax2 = ax1.twinx()
titleIndex = self._titleIndex
self._titleIndex += 1
self._plots[tag] = [fig, ax1, ax2, titleIndex]
else:
plotdata = self._plots[tag]
fig = plotdata[0]
ax1 = plotdata[1]
ax2 = plotdata[2]
titleIndex = plotdata[3]
s = 4
ax1.grid(True)
XUnits = self._setScale(max(measurement.YRe))
YUnits = self._setScale(max(measurement.YIm))
yMod = []
xMod = []
for x in measurement.YRe:
xMod.append(x/XUnits['scale'])
for y in measurement.YIm:
yMod.append(y/YUnits['scale'])
ax1.plot(xMod, yMod,'*-', label=self.PSData.experimentList[experimentIndex], markersize=s)
if self._titlesOn:
ax1.set_title(self.titles[titleIndex])
ax1.set_xlabel(self.eisTypes.YRe + "/" + XUnits['unit'] + "S")
ax1.set_ylabel(self.eisTypes.YIm + "/" + YUnits['unit'] + "S")
if self.splitGraphs:
ax1.set_title(self.PSData.experimentList[experimentIndex])
else:
ax1.legend(bbox_to_anchor=(1.3,1.05))
def _plotEISCap(self, measurement, experimentIndex):
PlotTag = str(self._PlotNotebookTagsIndex)
if self.splitGraphs:
fig2, ax3 = plt.subplots()
titleIndex = self._titleIndex
self._titleIndex += 1
else:
tag = self._getGraphTag('cap' + PlotTag,experimentIndex)
if not tag in self._plots:
fig2, ax3 = plt.subplots()
titleIndex = self._titleIndex
self._titleIndex += 1
self._plots[tag] = [fig2, ax3, titleIndex]
else:
plotdata = self._plots[tag]
fig2 = plotdata[0]
ax3 = plotdata[1]
titleIndex = plotdata[2]
s = 4
ax3.grid(True)
XUnits = self._setScale(max(measurement.Cdash))
YUnits = self._setScale(max(measurement.Cdashdash))
cdMod = []
cddMod = []
for cdash in measurement.Cdash:
cdMod.append(cdash/XUnits['scale'])
for cdashdash in measurement.Cdashdash:
cddMod.append(cdashdash/YUnits['scale'])
ax3.plot(cddMod,cdMod,'o-', label=self.PSData.experimentList[experimentIndex], markersize=s)
ax3.set_xlabel("C'/" + XUnits['unit'] + 'F')
ax3.set_ylabel("C''/" + YUnits['unit'] + 'F')
if self.splitGraphs:
if self._titlesOn:
ax3.set_title(self.titles[titleIndex])
self._titleIndex += 1
else:
ax3.set_title(self.PSData.experimentList[experimentIndex])
else:
ax3.legend(bbox_to_anchor=(1.25,1.05))
if self._titlesOn:
ax3.set_title(self.titles[titleIndex])
def _plotEISZdashes(self, measurement, experimentIndex):
PlotTag = str(self._PlotNotebookTagsIndex)
if self.splitGraphs:
fig2, ax3 = plt.subplots()
titleIndex = self._titleIndex
self._titleIndex += 1
else:
tag = self._getGraphTag('Nyq' + PlotTag,experimentIndex)
if not tag in self._plots:
fig2, ax3 = plt.subplots()
titleIndex = self._titleIndex
self._titleIndex += 1
self._plots[tag] = [fig2, ax3, titleIndex]
else:
plotdata = self._plots[tag]
fig2 = plotdata[0]
ax3 = plotdata[1]
titleIndex = plotdata[2]
XUnits = self._setScale(max(measurement.zdash))
YUnits = self._setScale(max(measurement.zdashneg))
xMod = []
yMod = []
for x in measurement.zdashneg:
xMod.append(x/XUnits['scale'])
for y in measurement.zdash:
yMod.append(y/YUnits['scale'])
s = 4
ax3.grid(True)
ax3.plot(xMod, yMod,'o-', label=self.PSData.experimentList[experimentIndex], markersize=s)
ax3.set_xlabel(self.eisTypes.zdashneg + "/" + XUnits['unit'] + "$\Omega$")
ax3.set_ylabel(self.eisTypes.zdash + "/" + YUnits['unit'] + "$\Omega$")
if self.splitGraphs:
if self._titlesOn:
ax3.set_title(self.titles[titleIndex])
self._titleIndex += 1
else:
ax3.set_title(self.PSData.experimentList[experimentIndex])
else:
ax3.legend(bbox_to_anchor=(1.05,1.05))
if self._titlesOn:
ax3.set_title(self.titles[titleIndex])
def _setScale(self, value):
value = abs(value)
ret = {}
ret['unit'] = ''
ret['scale'] = 1
if value < 0.009:
ret['unit'] = 'm'
ret['scale'] = 0.001
if value < 0.000009:
ret['unit'] = '\u03BC'
ret['scale'] = 0.000001
if value < 0.00000009:
ret['unit'] = 'n'
ret['scale'] = 0.00000001
if value < 0.0000000009:
ret['unit'] = 'p'
ret['scale'] = 0.0000000001
if value < 0.000000000009:
ret['unit'] = 'f'
ret['scale'] = 0.000000000001
if value < 0.00000000000009:
ret['unit'] = 'a'
ret['scale'] = 0.00000000000001
if value > pow(10,3):
ret['unit'] = 'k'
ret['scale'] = pow(10,3)
if value > pow(10,6):
ret['unit'] = 'M'
ret['scale'] = pow(10,6)
if value > pow(10,9):
ret['unit'] = 'G'
ret['scale'] = pow(10,9)
if value > pow(10,12):
ret['unit'] = 'T'
ret['scale'] = pow(10,12)
return ret
def _getScale(self):
if self.eisTypes.scale == pow(10,3):
return 'k'
if self.eisTypes.scale == pow(10,6):
return 'M'
if self.eisTypes.scale == pow(10,9):
return 'G'
if self.eisTypes.scale == pow(10,12):
return 'T'
return ''
def _getUnits(self, curveTitle):
details = curveTitle.split(" ")
return [details[3], details[1]]
def _getGraphTag(self, tag, experimentIndex):
if self._grouping:
for group in self._groups:
for item in self._groups[group]:
if self.PSData.experimentList[experimentIndex] == item:
tag = group + tag
return tag
class MethodType:
__slots__ = ['CV','SWV','EIS']
def __init__(self):
self.CV = 'CV'
self.SWV = 'SWV'
self.EIS = 'EIS'
class Baseline:
def __init__(self):
self._startPosition = -1
self._endPosition = -1
self._subtractBaseline = False
self._generatedBaseline = False
self.resetBaseline = False
self._gradient = 0
self._constant = 0
@property
def startPosition(self):
return self._startPosition
@startPosition.setter
def startPosition(self, val):
self._subtractBaseline = True
self.resetBaseline = False
self._startPosition = val
@property
def endPosition(self):
return self._endPosition
@endPosition.setter
def endPosition(self, val):
self._subtractBaseline = True
self.resetBaseline = False
self._endPosition = val
def _generateBaseline(self, x, y):
if self._subtractBaseline:
try:
if self.endPosition == -1:
self.endPosition = len(y) - self.startPosition
self._gradient = (y[self.startPosition] - y[self.endPosition])/(x[self.startPosition] - x[self.endPosition])
self._constant = y[self.startPosition] - (x[self.startPosition]*self._gradient)
self._generatedBaseline = True
except:
print('Exception: Could not generate baseline. Check validity of startPosition and endPosition.')
def _subtract(self, x, y):
if self._subtractBaseline and self._generatedBaseline and not self.resetBaseline:
return (y - (self._gradient*x + self._constant))
return y
class EISMeasurement:
__slots__ = ['freq','zdash','potential','zdashneg','Z','phase','current','npoints','tint','ymean','debugtext','Y','YRe','YIm','scale']
def __init__(self):
self.freq = "Frequency"
self.zdash = "Z'"
self.potential = "Potential"
self.zdashneg = "-Z''"
self.Z = "Z"
self.phase = "-Phase"
self.current = "Current"
self.npoints = "npoints"
self.tint = "tint"
self.ymean = "ymean"
self.debugtext = "debugtext"
self.Y = "Y"
self.YRe = "Y'"
self.YIm = "Y''"
self.scale = 100000 # standard set to mega ohms