Merge pull request #140 from bahanonu/bahanonu/functionUpdates

New motion correction methods, CIAtah QoL updates, etc.

+ciapkg/+behavior/importDeepLabCutData.m

@@ -1,4 +1,4 @@
-function [mainTbl] = importDeepLabCutData(inputPath,varargin)
+function [mainTbl, mainTensor, mainCell] = importDeepLabCutData(inputPath,varargin)
 	% [outputTable] = importDeepLabCutData(inputPath,varargin)
 	% 
 	% Loads DeepLabCut processed CSV files and loads into a table or structure for use by other functions.
@@ -10,14 +10,17 @@
 	% 	inputPath - Str: path to DLC file.
 	% 
 	% Outputs
-	% 	mainTbl - Struct with fields named after body parts. Each field is [likelihood x y] matrix with rows equal to frames of the movie. 	
+	% 	mainTbl - Struct: with fields named after body parts. Each field is [likelihood x y] matrix with rows equal to frames of the movie. 	
+	% 	mainTensor - Tensor: format [nFeatures nDlcOutputs nFrames]. 
+	%	mainCell - Cell: format {1 nFeatures} with each cell containing a [likelihood x y] matrix with rows equal to frames of the movie. 
 	% 
 	% Options (input as Name-Value with Name = options.(Name))
 	% 	% DESCRIPTION
 	% 	options.exampleOption = '';
 
 	% Changelog
 		% 2022.03.14 [01:47:04] - Added nested and local functions to the example function.
+		% 2024.02.19 [09:25:58] - Added conversion to tensor and cell to the import function from other functions.
 	% TODO
 		%
 
@@ -47,26 +50,37 @@
 		% dlcTablePath = fullfile(rootAnalysisPath,dlcFileCSV{vidNo});
 		t1 = readtable(inputPath);
 		t2 = readlines(inputPath);
-		bodyPartListMain = strsplit(t2{2},',');
-		bodyPartList = unique(bodyPartListMain);
-		nBodyParts = length(bodyPartList)-1;
+		featuresListMain = strsplit(t2{2},',');
+		featuresList = unique(featuresListMain);
+		nfeaturess = length(featuresList)-1;
 
 		if options.dispPlots==1
 			figure;
 			set(gcf,'Color','k')
 		end
 
-		for partX = 1:nBodyParts
-			partName = bodyPartListMain{(partX-1)*3+4};
-			if partX==nBodyParts
+		mainCell = {};
+		nFrames = length(t1{:,(1-1)*3+2});
+		mainTensor = NaN([nfeaturess 3 nFrames]);
+
+		for partX = 1:nfeaturess
+			partName = featuresListMain{(partX-1)*3+4};
+			if partX==nfeaturess
 				fprintf('%s.\n',partName)				
 			else
 				fprintf('%s | ',partName)
 			end
 			conf1 = t1{:,(partX-1)*3+4};
 			dlcX = t1{:,(partX-1)*3+2};
 			dlcY = t1{:,(partX-1)*3+3};
-			mainTbl.(partName) = [conf1(:) dlcX(:) dlcY(:)];
+
+			mainMatrix = [conf1(:) dlcX(:) dlcY(:)];
+
+			mainTbl.(partName) = mainMatrix;
+
+			mainCell{partX} = mainMatrix;
+
+			mainTensor(partX,:,:) = mainMatrix';
 
 			if options.dispPlots==1
 				subplot(3,3,partX)
@@ -92,7 +106,25 @@
 		% outputs = ;
 	end	
 end
-function [outputs] = localfxn_exampleFxn(arg)
-	% Always start local functions with "localfxn_" prefix.
-	% outputs = ;
-end	
+% function [outputs] = localfxn_exampleFxn(arg)
+% 	opts.nFrames = size(inputMovie,3);
+% 	featurePts = cell([1 opts.nFrames]);
+% 	opts.nFields = fieldnames(dlcData);
+% 	featurePtsTensor = NaN([length(opts.nFields) 3 opts.nFrames]);
+
+% 	for i = 1:opts.nFrames
+% 		conf1 = [];
+% 		dlcX = [];
+% 		dlcY = [];
+% 		for partX = 1:length(opts.nFields)
+% 			thisField = opts.nFields{partX};
+% 			dlcDataNew.(thisField) = vertcat(dlcData.(thisField));
+% 			conf1(partX) = dlcDataNew.(thisField)(i,1);
+% 			dlcX(partX) = dlcDataNew.(thisField)(i,2);
+% 			dlcY(partX) = dlcDataNew.(thisField)(i,3);
+% 		end
+% 		featurePts{i} = [conf1(:) dlcX(:) dlcY(:)];
+% 		featurePtsTensor(:,:,i) = featurePts{i};
+% 	end
+% 	disp('Done!')
+% end	

+ciapkg/+classification/matchObjBtwnTrials.m

@@ -26,6 +26,7 @@
 		% 2019.10.29 [13:07:18] - Added support for sparse (ndSparse) array inputs.
 		% 2019.12.05 [10:37:17] - Fix for cases in which cells are lost when cropping all movies to the same size before starting cross-session alignment.
 		% 2021.08.08 [19:30:20] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
+		% 2023.05.09 [12:33:23] - Made ability to switch between different motion correction and image alignment methods user visible.
 	% notes
 		% the cell array of traces allows us to have arbitrary numbers of trials to align automatically,
 	% TODO
@@ -70,6 +71,14 @@
 	options.turboregZeroThres = 1e-6;
 	% Binary: 1 = check correlation matches visually
 	options.checkImageCorr = 0;
+	% Str: Register images using 'imtransform' or 'imwarp' (Matlab) or 'transfturboreg' (C)
+	options.registrationFxn = 'transfturboreg';
+	% Str: motion correction algorithm.
+		% 'turboreg' - TurboReg as developed by Philippe Thevenaz.
+		% 'normcorre' - NoRMCorre as developed by several authors at Flatiron Institute.
+		% 'imregdemons' - Displacement field alignment based on imregdemons.
+	options.mcMethod = 'turboreg';
+
 	options = getOptions(options,varargin);
 	%========================
 	% obtain trial stats
@@ -124,6 +133,10 @@
 		% =======
 		RegisTypeFinal = options.RegisTypeFinal;
 		% turboreg options.
+		ioptions.mcMethod = options.mcMethod;
+		% ioptions.registrationFxn = 'imtransform';
+		ioptions.registrationFxn = options.registrationFxn;
+
 		ioptions.meanSubtract = 0;
 		ioptions.complementMatrix = 0;
 		ioptions.normalizeType = [];
@@ -141,8 +154,6 @@
 		ioptions.cropCoords = [];
 		ioptions.closeMatlabPool = 0;
 		ioptions.removeEdges = 0;
-		% ioptions.registrationFxn = 'imtransform';
-		ioptions.registrationFxn = 'transfturboreg';
 		% =======
 		% turboreg all object maps to particular trial's map
 		if issparse(objectMap{options.trialToAlign})
@@ -211,10 +222,13 @@
 					ioptions.closeMatlabPool = 0;
 					ioptions.meanSubtract =  0;
 					ioptions.normalizeType = 'divideByLowpass';
-					ioptions.registrationFxn = 'transfturboreg';
+					% ioptions.registrationFxn = 'transfturboreg';
 					ioptions.removeEdges = 0;
 					ioptions.cropCoords = [];
 
+					ioptions.mcMethod = options.mcMethod;
+					ioptions.registrationFxn = options.registrationFxn;
+
 					for switchNo = 1:length(switchStrArray)
 						switch switchStrArray{switchNo}
 							case 'optional'
@@ -352,6 +366,7 @@
 		OutStruct.registrationCoords = registrationCoords;
 		OutStruct.coords = coords;
 		OutStruct.inputImages = inputImages;
+		% OutStruct.inputOptions = options;
 		if ~isempty(options.inputSignals)
 			OutStruct.inputSignals = options.inputSignals;
 		end