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Merge pull request #13 from hrani/stable
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convert pylab to pyplot for mpld3
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@upibhalla
upibhalla authored Dec 25, 2018
2 parents 527d9bf + 66df833 commit c1dad5c
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Showing 2 changed files with 55 additions and 34 deletions.
86 changes: 53 additions & 33 deletions findSim.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
# -*- coding: utf-8 -*-

#
# 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, or
Expand Down Expand Up @@ -34,9 +33,9 @@
**********************************************************************/
'''
from __future__ import print_function, division
from __future__ import print_function
import heapq
import matplotlib.pyplot as plt
#import pylab
import numpy as np
import sys
import argparse
Expand All @@ -46,6 +45,22 @@
import ntpath
import time
import imp # This is apparently deprecated in Python 3.4 and up

import matplotlib.pyplot as pyplot,mpld3

#mpld3 hack
# suggested: https://github.com/mpld3/mpld3/issues/434
import json
class NumpyEncoder(json.JSONEncoder):
def default(self, obj):
import numpy as np
if isinstance(obj, np.ndarray):
return obj.tolist()
return json.JSONEncoder.default(self, obj)
from mpld3 import _display
_display.NumpyEncoder = NumpyEncoder


convertTimeUnits = {('sec','s') : 1.0,
('ms','millisec', 'msec') : 1e-3,('us','microsec') : 1e-6,
('ns','nanosec') : 1e-9, ('min','m') : 60.0,
Expand Down Expand Up @@ -281,11 +296,12 @@ def displayPlots( self, fname, modelLookup, stim, hideSubplots, exptType ):
elms = modelLookup[i]
for j in elms:
pp = PlotPanel( self, exptType, xlabel = j.name +'('+stim.quantityUnits+')' )
#pp.plotme( fname, pp.ylabel, joinSimPoints = True )
try:
pp.plotme( fname, pp.ylabel, joinSimPoints = True )
except Exception as e:
print('Warning: displayPlot: Failed to plot '
'%s due to "%s"' % (fname,e))
'%s due to "%s"' % (fname,e))
elif "barchart" in exptType:
for i in self.entities:
elms = modelLookup[i]
Expand Down Expand Up @@ -325,17 +341,17 @@ def displayPlots( self, fname, modelLookup, stim, hideSubplots, exptType ):
sumvec += ypts
if (not hideSubplots) and (len( elms ) > 1):
# Plot summed components
plt.plot( xpts, ypts, 'r:', label = j.name )
pyplot.plot( xpts, ypts, 'r:', label = j.name )

plt.plot( xpts, sumvec, 'r--' )
pyplot.plot( xpts, sumvec, 'r--' )
ylabel = pp.ylabel
if self.field in ( epspFields + epscFields ):
if self.field in ( epspFields ):
plt.ylabel( '{} Vm ({})'.format( self.entities[0], tsUnits ) )
pyplot.ylabel( '{} Vm ({})'.format( self.entities[0], tsUnits ) )
else:
plt.ylabel( '{} holding current ({})'.format( self.entities[0], tsUnits ) )
pyplot.ylabel( '{} holding current ({})'.format( self.entities[0], tsUnits ) )

plt.figure(2)
pyplot.figure(2)
if self.useNormalization:
ylabel = '{} Fold change'.format( self.field )
pp.plotme( fname, ylabel )
Expand Down Expand Up @@ -596,7 +612,8 @@ def deleteItems( self, kinpath ):
def subsetItems( self, kinpath ):
nonContainers, directContainers, indirectContainers = [],[],[]
for i in ['moregraphs', 'info', 'graphs']:
directContainers.append( moose.element( kinpath + '/' + i ) )
if moose.exists( kinpath + '/' + i ):
directContainers.append( moose.element( kinpath + '/' + i ) )
subsets = re.sub(r'\s', '', self.modelSubset).split(',')

for i in subsets:
Expand Down Expand Up @@ -1254,39 +1271,39 @@ def convertBarChartLabels( self, readout, stim ):
def plotbar( self, readout, stim, scriptName ):
barpos = np.arange( len( self.sim ) )
width = 0.35 # A reasonable looking bar width
exptBar = plt.bar(barpos - width/2, self.expt, width, yerr=self.yerror, color='SkyBlue', label='Experiment')
simBar = plt.bar(barpos + width/2, self.sim, width, color='IndianRed', label='Simulation')
plt.xlabel( "Stimulus combinations" )
plt.ylabel( self.ylabel )
plt.title(scriptName)
plt.legend(fontsize="small",loc="upper left")
exptBar = pyplot.bar(barpos - width/2, self.expt, width, yerr=self.yerror, color='SkyBlue', label='Experiment')
simBar = pyplot.bar(barpos + width/2, self.sim, width, color='IndianRed', label='Simulation')
pyplot.xlabel( "Stimulus combinations" )
pyplot.ylabel( self.ylabel )
pyplot.title(scriptName)
pyplot.legend(fontsize="small",loc="upper left")
ticklabels = [ i[0] + '\n' for i in readout.data ]
assert len( ticklabels ) == len( barpos )
ticklabels = self.convertBarChartLabels( readout, stim )
plt.xticks(barpos, ticklabels )
pyplot.xticks(barpos, ticklabels )

def plotme( self, scriptName, ylabel, joinSimPoints = False ):
sp = 'ro-' if joinSimPoints else 'ro'
if self.useXlog:
if self.useYlog:
plt.loglog( self.xpts, self.expt, 'bo-', label = 'expt', linewidth='2' )
plt.loglog( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )
pyplot.loglog( self.xpts, self.expt, 'bo-', label = 'expt', linewidth='2' )
pyplot.loglog( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )
else:
plt.semilogx( self.xpts, self.expt, 'bo-', label = 'expt', linewidth='2' )
plt.semilogx( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )
pyplot.semilogx( self.xpts, self.expt, 'bo-', label = 'expt', linewidth='2' )
pyplot.semilogx( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )
else:
if self.useYlog:
plt.semilogy( self.xpts, self.expt, 'bo-', label = 'expt', linewidth='2' )
plt.semilogy( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )
pyplot.semilogy( self.xpts, self.expt, 'bo-', label = 'expt', linewidth='2' )
pyplot.semilogy( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )
else:
plt.plot( self.xpts, self.expt,'bo-', label = 'experiment', linewidth='2' )
plt.errorbar( self.xpts, self.expt, yerr=self.yerror )
plt.plot( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )
pyplot.plot( self.xpts, self.expt,'bo-', label = 'experiment', linewidth='2' )
pyplot.errorbar( self.xpts, self.expt, yerr=self.yerror )
pyplot.plot( self.xpts, self.sim, sp, label = 'sim', linewidth='2' )

plt.xlabel( self.xlabel )
plt.ylabel( ylabel )
plt.title(scriptName)
plt.legend(fontsize="small",loc="lower right")
pyplot.xlabel( self.xlabel )
pyplot.ylabel( ylabel )
pyplot.title(scriptName)
pyplot.legend(fontsize="small",loc="lower right")

########################################################################
def loadTsv( fname ):
Expand Down Expand Up @@ -1595,10 +1612,13 @@ def innerMain( script, modelFile = "model/synSynth7.g", dumpFname = "", paramFna
if not hidePlot:
print( "Score = {:.3f} for\t{}\tElapsed Time = {:.1f} s".format( score, os.path.basename(script), elapsedTime ) )
for i in readouts:
plt.figure(1)
pyplot.figure(1)
i.displayPlots( script, model.modelLookup, stims[0], hideSubplots, expt.exptType )

plt.show()
pyplot.show()
#pyplot_fig = mpld3.fig_to_html(pyplot.figure(1))
#mpld3.show()

moose.delete( modelId )
if moose.exists( '/library' ):
moose.delete( '/library' )
Expand Down
3 changes: 2 additions & 1 deletion test.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@ else
$PYTHON -m pip install matplotlib --upgrade
$PYTHON -m pip install --upgrade
fi

$PYTHON -m pip install Jinja2
$PYTHON -m pip install mpld3
$PYTHON -m pip install pymoose --pre --upgrade
$PYTHON -m pip install pylint numpy --upgrade

Expand Down

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