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TrackClassGlobals.py
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/
TrackClassGlobals.py
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from TrackMeasurements import *
import os
#Degree of output from CMP to console
VERBOSE = True #very talkative
DEBUG = True #most talkative
SAVE_DIRECTORY = None #'/home/ahan/Desktop/analysis/' #'C:\\Users\\Andrew Han\\Desktop/analysis/'
#setting paths for reading and writing files
CMP_PATH = os.getcwd()
DATA_SAVE_PATH = CMP_PATH + '/data/'
TRACK_FILES_IMPORT_PATH = CMP_PATH + r"/TrackMate XMLs/"
ANALYSIS_SAVE_PATH = CMP_PATH + '/analysis/'
ANALYSIS_SAVE_NAME = ''
#Default experiment params used when loading
#experiment data folder to CMP
DefaultExpParams = {
'id' : None,
'gradientStrength' : 0,
'gradientVector' : [-1, 0],
'reverse' : False,
'maxX' : 10000, #must be defined. defines the width (um, chemical gradient dimension) of the experiment
'maxY' : 665, #must be defined. defines the height (um) of the experiment
'spatialConversionFactor' : 0.64, #microns per pixel
'frameInterval' : 10, #time between frames (in minutes)
'speedConversionFactor' : 3.84, #computed.
'DefaultAxisLimits' : DefaultAxesLimits #key: TrackMeasurement name, value: min max tuple
}
#Default track measurements available for analyis
#Must exist in TrackMeasurementClass
DefaultTrackMeasurements = {
"xPos" : xPos,
"yPos" : yPos,
"frames" : frames,
"avgMov" : avgMov ,
"velocity" : velocity ,
"concentration" : concentration ,
"directionality" : directionality ,
"mp" : getMP ,
"xStartPos" : getXStartPos ,
"xEndPos" : getXEndPos ,
"yStartPos" : getYStartPos ,
"yEndPos" : getYEndPos ,
"firstFrame" : firstFrame ,
"lastFrame" : lastFrame ,
"xMigrationSpeed" : xMigrationSpeed,
"yMigrationSpeed" : yMigrationSpeed,
"numFrames" : numFrames ,
"age" : age
}
#plot defualts
PlotDefaults = {
#general plot settings
'show' : False,
'save' : True,
'bins' : 20,
'norm' : False,
'percent' : False,
'title' : '',
'weights' : 'age',
'legend' : True,
'legendLoc' : 1,
'fontsize' : 9,
'newFig' : True,
'stdErrorBars' : True,
"average" : "weighted",
#cellVisualization settings
'colorMin' : -1,
'colorMax' : 1,
#percents
'percents' : [0, 25, 50, 75, 100]
}