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Copy pathHAWKPostHTSwapAnalysis.m
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HAWKPostHTSwapAnalysis.m
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%%%% Script: Perform the conversion of yaml data to mat data files in bulk
% Prompts user for a selection of folders containing data from HAWK. It
% then serially evaluates each folder, converting the yaml files into
% useable mat files for Matlab.
%
% Copyright 2015 Eileen Mazzochette, et al <[email protected]>
% This file is part of HAWK_AnalysisMethods.
%
%%%%%
clear all;
close all;
% Get Folder where all the files are:
clear all
if (ispc) %if on PC workstation in MERL 223
DestinationFolder = 'C:\Users\HAWK\Documents\HAWKData';
addpath(genpath('C:\Users\HAWK\Documents\HAWKDataAnalysisCode\YAMLMatlab_0.4.3'));
excelFile = 'C:\Users\HAWK\Dropbox\HAWK\HAWKExperimentLog.xls';
addpath('C:\Users\HAWK\Documents\HAWKDataAnalysisCode\20130227_xlwrite');
slash = '\';
% For excel writing, need these files linked:
% Initialisation of POI Libs
% Add Java POI Libs to matlab javapath
javaaddpath('20130227_xlwrite\20130227_xlwrite\poi_library\poi-3.8-20120326.jar');
javaaddpath('20130227_xlwrite\20130227_xlwrite\poi_library\poi-ooxml-3.8-20120326.jar');
javaaddpath('20130227_xlwrite\20130227_xlwrite\poi_library\poi-ooxml-schemas-3.8-20120326.jar');
javaaddpath('20130227_xlwrite\20130227_xlwrite\poi_library\xmlbeans-2.3.0.jar');
javaaddpath('20130227_xlwrite\20130227_xlwrite\poi_library\dom4j-1.6.1.jar');
javaaddpath('20130227_xlwrite\20130227_xlwrite\poi_library\stax-api-1.0.1.jar');
elseif (ismac) % if on Eileen's personal computer
DestinationFolder = '/Volumes/Backup Disc Celegans/HAWKData/';
addpath(genpath('/Users/emazzochette/Documents/MicrosystemsResearch/HAWK/HAWKDataAnalysisCode/HAWKDataAnalysisCode/YAMLMatlab_0.4.3'));
excelFile = '/Users/emazzochette/Box Sync/HAWK/HAWKExperimentLog.xls';
addpath('/Users/emazzochette/Documents/MicrosystemsResearch/HAWK/HAWKDataAnalysisCode/HAWKDataAnalysisCode/20130227_xlwrite');
slash = '/';
% For excel writing, need these files linked:
% Initialisation of POI Libs
% Add Java POI Libs to matlab javapath
javaaddpath('20130227_xlwrite/20130227_xlwrite/poi_library/poi-3.8-20120326.jar');
javaaddpath('20130227_xlwrite/20130227_xlwrite/poi_library/poi-ooxml-3.8-20120326.jar');
javaaddpath('20130227_xlwrite/20130227_xlwrite/poi_library/poi-ooxml-schemas-3.8-20120326.jar');
javaaddpath('20130227_xlwrite/20130227_xlwrite/poi_library/xmlbeans-2.3.0.jar');
javaaddpath('20130227_xlwrite/20130227_xlwrite/poi_library/dom4j-1.6.1.jar');
javaaddpath('20130227_xlwrite/20130227_xlwrite/poi_library/stax-api-1.0.1.jar');
end
%asks user for the directory where all the files are:
%directory = uigetdir(DestinationFolder,'Choose the folder where the data if located');
directories = uipickfiles( 'FilterSpec',DestinationFolder);
fileID = fopen('/Users/emazzochette/Documents/MicrosystemsResearch/HAWK/Experiments/ErrorList.txt','a');
dealWithOldData = true;
for dir = 1:length(directories)
%Select next directory:
directoryCell = directories(:,dir);
directory = directoryCell{1};
%determine experiment title based on file name:
experimentTitle = getExperimentTitle(directory);
%Save Stimulus file:
mat_file = fullfile(directory,strcat(experimentTitle,'_DataByStimulus.mat'));
if (exist(mat_file, 'file')==2)
try
TrackingData = getTrackingDataFromYAML(directory,experimentTitle);
FPGAData = getFPGADataFromYAML(directory, experimentTitle);
StimulusData = getStimulusDataFromYAML(directory,experimentTitle);
if TrackingData.NumberOfStimulus > 0
load(mat_file);
disp(strcat('Starting file: ',directory));
%Deal with old analysis:
% if dealWithOldData == 1
% % moveOldData(directory,TrackingData.NumberOfStimulus);
% % try Stimulus = rmfield(Stimulus, 'StimulusTiming'); end
% % try Stimulus = rmfield(Stimulus, 'BodyMorphology'); end
% % try Stimulus = rmfield(Stimulus, 'FramesByStimulus'); end
% % try Stimulus = rmfield(Stimulus, 'computerScoredBadFrames'); end
% % try Stimulus = rmfield(Stimulus, 'Trajectory'); end
% % try Stimulus = rmfield(Stimulus, 'SpatialResolution'); end
% % try Stimulus = rmfield(Stimulus, 'TrialScoring'); end
% % try Stimulus = rmfield(Stimulus, 'CurvatureAnalysis'); end
% % try Stimulus = rmfield(Stimulus, 'FrameScoring'); end
% % try Stimulus = rmfield(Stimulus, 'AppliedStimulus'); end
% try Stimulus = rmfield(Stimulus, 'Response'); end
% end
%
Stimulus = determineStimulusTiming(TrackingData, StimulusData, Stimulus, TrackingData.NumberOfStimulus);
Stimulus = calculateBodyMorphology(Stimulus,TrackingData.NumberOfStimulus);
Stimulus = filterFramesByBodyLength(Stimulus,TrackingData.NumberOfStimulus);
Stimulus = calculateWormCentroidMean(Stimulus,TrackingData.NumberOfStimulus);
Stimulus = calculateSmoothFitSkeleton(Stimulus, TrackingData.NumberOfStimulus);
Stimulus = sortFramesBasedOnStimulus(Stimulus, TrackingData.NumberOfStimulus);
Stimulus = findCurvature(Stimulus, TrackingData.NumberOfStimulus);
Stimulus = scoreFrames(Stimulus, TrackingData.NumberOfStimulus);
Stimulus = getWormIndentation(Stimulus, TrackingData, StimulusData, TrackingData.NumberOfStimulus);
Stimulus = determineWormTrajectory(Stimulus, TrackingData.NumberOfStimulus);
Stimulus = getTrackStatistics(Stimulus, TrackingData.NumberOfStimulus);
% createSkeletonRotationGIF(Stimulus, TrackingData.NumberOfStimulus, directory)
videoPresent = true;
Stimulus = spatialResolutionForceClamp(directory, Stimulus, TrackingData, TrackingData.NumberOfStimulus, videoPresent);
Stimulus = scoreTrials(TrackingData,Stimulus,TrackingData.NumberOfStimulus);
Stimulus = getVelocityFromCurvature(Stimulus, TrackingData.NumberOfStimulus);
Stimulus = calculateCurvatureParameters(Stimulus,TrackingData.NumberOfStimulus);
Stimulus = scoreBehaviorResponse(Stimulus, TrackingData.NumberOfStimulus);
plotData(Stimulus, TrackingData, TrackingData.NumberOfStimulus, directory)
% [NUM,TXT,RAW]=xlsread(excelFile,'ForceTouchAssay DataSet 3');
% [rowCount, columnCount] = size(RAW);
% experimentRow = rowCount+1;
% [experimentData, stimulusData ]= getDataForExcel(TrackingData, StimulusData, Stimulus,TrackingData.NumberOfStimulus, experimentTitle);
% for stim = 1:TrackingData.NumberOfStimulus
% xlwrite(excelFile, experimentData, 'ForceTouchAssay DataSet 3', strcat('A',num2str(experimentRow+stim-1)));
% end
% xlwrite(excelFile, stimulusData, 'ForceTouchAssay DataSet 3', strcat('AA',num2str(experimentRow)));
save(mat_file, 'Stimulus');
close all;
end
catch
disp(strcat('Error with: ',experimentTitle));
fprintf(fileID,'%s\n',experimentTitle);
end
end
end
fclose(fileID);