CaTransDecodingCode/PLS_BootstrapDebugScript.py at master · rweaton/CaTransDecodingCode · GitHub

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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Jul 6 14:21:44 2019

@author: thugwithyoyo
"""
importnumpyasnp
fromPeriEventTraceFuncLibimport*

# Paths to data in .csv files
#PathToBehavFile = '/home/thugwithyoyo/Desktop/MAE298_Project/CalciumImagingData/20181210_both_001_1-01Dat.csv'
#PathToFluorFile = '/home/thugwithyoyo/Desktop/MAE298_Project/CalciumImagingData/20181210_001_Left_CellTraces.csv'

# Paths to data in JSON formatted files
#PathToBehavFile = '/home/thugwithyoyo/Desktop/MAE298_Project/CalciumImagingData/2018-12-10-11-37-56_B.json'
#PathToFluorFile = '/home/thugwithyoyo/Desktop/MAE298_Project/CalciumImagingData/2018-12-10-11-37-56_C.json'
PathToBehavFile='/home/thugwithyoyo/Desktop/MAE298_Project/CalciumImagingData/2018-12-05-11-29-45_B.json'
PathToFluorFile='/home/thugwithyoyo/Desktop/MAE298_Project/CalciumImagingData/2018-12-05-11-29-45_C.json'

#RefEventsList = ['M6T0_Entry_ts', 'M6T1_Entry_ts', 'M6CT_Exit_ts']
#RefEventsList = ['M6T0_Entry_ts', 'M6T1_Entry_ts']
RefEventsList= ['M6T0_Entry_ts', 'M7T1_Entry_ts']
AssignedEventVals= [-1, 1]
RefEventsDict= {'RefEventsList' : RefEventsList,
'AssignedEventVals' : AssignedEventVals}

# Set parameters for peri-event extraction
BoundaryWindow= [-1.0, 1.0]

# Set parameters for PLS
nLatents=5

# Set parameters for Monte Carlo estimation of confidence intervals
nRepetitions=10
ConfLevel=0.95

BehavDict=BehavDictGen(PathToBehavFile)

CellFluorTraces_Frame=CellFluorTraces_FrameGen(PathToFluorFile)

PeriEventExtractorDict=PeriEventExtractor_Trace(BehavDict, CellFluorTraces_Frame,
RefEventsDict, BoundaryWindow)

# Generate a set of indices to test the inclusion portion of the performance code.
PEA_Array=PeriEventExtractorDict['PEA_Array']
(nTotalTrials, nTotalFeatures) =PEA_Array.shape
InclusionSet=np.random.randint(0, high=nTotalTrials, size=(nTotalTrials,))

#PerformanceDict = PLS_DecoderPerformance(PeriEventExtractorDict, nLatents,
# trials_to_include=InclusionSet)
# Run performance statistics on sample set.
PerformanceDict=PLS_DecoderPerformance(PeriEventExtractorDict, nLatents)

# Bootstrap to obtain medians and confidence intervals of performance measures
MonteCarlo_ConfIntsDict=PLS_MonteCarlo(PeriEventExtractorDict,
nLatents, nRepetitions,
ConfLevel)

# Shuffle lables to evaluate chance band of decoder.
Shuffled_ConfIntsDict=PLS_Shuffle(PeriEventExtractorDict,
nLatents, nRepetitions,
ConfLevel)