#folder path to experiment-set track data
FILE_IMPORT_PATH = 'C:\Users/Andrew/CMP/Trackdata XMLs/test

#name of a saved copy of the imported trackfile data. 
#Once the data is saved to data/, trackmate file import 
#is not necessary and the data #can be reloaded with its name.
DATA_SAVE_NAME = 'test-files'

#folder path for analysis output
ANALYSIS_SAVE_PATH = 'C:\Users/ahan/Desktop/analysis/

	#import the experiment set from the xml files 
	data = import("C:\ahan\Desktop\test-experiment-dataset/, "testset") #path and savename.
	
	#imported data is saved to CMP/data/ and can be loaded
	data = load("testset")
	
	#create a copy 
	dataCopy = deepcopy(data)

	#filter any measurement defined in TrackMeasurements.py
	filters = {}
	
	#slices of experiment dimensions
	filters['frames'] = [[5, 147]]
	filters['xpos'] = [[100, 1390]]
	filters['ypos'] = [[100, 1390]]
	
	#track measurements calculated within those slices
	filters['age'] = [[15, float('inf')]]
	filters['directionality'] = [[-1, -0.8], [0.8, 1]]
	
	#keep only tracks that pass the filters and dimensions
	#select frames 5 to 147, and delete any track paths 
	#outside of xpos and ypox coordinates witih the experimentin microns.
	#then calculate age and directionality of tracks, and keep only tracks
	#the pass measurement filters
	dataCopy.selectData(filters)
	
	#save data whenever
	save(dataCopy, 'filteredData')
	
	

#select only one experiment to analyze
experimentA = data.experiments['experimentA']

#render the experiment
render(experimentA)

#plotScatter can be given 2 or 3 measurements to visualize
experimentA.plotScatter("xStartPos", "yStartPos", "avgMov")

#make a histogram of any measurement
experimentA.histogram("velocity")

#bin tracks by one measurement, and calculate number and age-weighted
#averages of another measurement
experiment.plotBinData("xpos", "velocity")

#bin tracks by measurement percentiles
experiment.plotPercentHistogram("avgMov", "directionality", percents = [0, 25, 75, 90, 100])

#Scan through frames 0 to 150 with 10 steps, and perform the same analysis as above.
experiment.scan("frames", 0, 10000, 10, TrackFile.plotBinData, "xPos", "velocity")

#Run your analysis functions on an entire set of experiments
data.iterate(TrackFile.plotBinData, "xPos", "velocity")
data.iterate(TrackFile.scan, "frames", 0, 10000, 10, TrackFile.plotBinData, "xPos", "velocity")
data.iterate(TrackFile.render)

#Compare results of your analyses
data.compare(TrackFile.plotBinData, "xPos", "velocity")
data.compare(TrackFile.plotScatter, "avgMov", "directionality")

#Write your project data to an excel file
data.writeData()

#Write analysis data to a specific excel file
xpos_velocity_book = createWorkbook()
experiment.plotBinData("xpos", "velocity", workbook = [xpos_velocity_book, "plotBinData"])
experiment.plotPercentHistogram("avgMov", "directionality", workbook = [xpos_velocity_book, "percHist"])

DefaultTrackMeasurements = {

#track-dimensions measurements. defined for slicing tracks and scanning

	"xPos"            : xPos,            # x-coordinate of the track
	"yPos"            : yPos,            # y-coordinate of the track
	"frames"          : frames,          # frame-coordinate of the track


#track measurements calculated with track-dimensions and experiment parameters

	"age"             : age,             # range of frames over which track exists
	"avgMov"          : avgMov         , # average movement of the track per frame
	"velocity"        : velocity       , # average migration distance of the track per frame
	"concentration"   : concentration  , # local chemical concentration of xStartPos
	"directionality"  : directionality , # uphill gradient track movement / total track movement
	"mp"              : getMP          , # degree that track moves in one direction
	"xMigrationSpeed" : xMigrationSpeed, # total x-direction migration distance
	"yMigrationSpeed" : yMigrationSpeed, # total y-direciton migration distance
	"numFrames"       : numFrames      , # number of frames in the track
	"xStartPos"       : getXStartPos   , 
	"xEndPos"         : getXEndPos     ,
	"yStartPos"       : getYStartPos   ,
	"yEndPos"         : getYEndPos     ,
	"firstFrame"      : firstFrame     ,
	"lastFrame"       : lastFrame  
}