Merge pull request #108 from bahanonu/bahanonu/functionUpdates

Code and GUI improvements, NoRMCorre and additional file formats support, etc.

+ciapkg/+api/getMovieFileType.m

@@ -1,4 +1,4 @@
-function [movieType, supported, movieType2] = getMovieFileType(thisMoviePath)
+function [movieType, supported, movieType2] = getMovieFileType(thisMoviePath,varargin)
 	% Determine how to load movie, don't assume every movie in list is of the same type
 	% Biafra Ahanonu
 	% started: 2020.09.01 [‏‎14:16:57]

+ciapkg/+api/getSeriesNoFromName.m

@@ -0,0 +1,32 @@
+function [bfSeriesNo] = getSeriesNoFromName(inputMoviePath,bfSeriesName,varargin)
+	% [bfSeriesNo] = getSeriesNoFromName(inputFilePath,bfSeriesName,varargin)
+	% 
+	% Returns series number for Bio-Formats series with name given by user.
+	% 
+	% Biafra Ahanonu
+	% started: 2022.07.15 [08:10:16]
+	% 
+	% Inputs
+	% 	inputFilePath - Str: path to Bio-Formats compatible file.
+	% 	bfSeriesName - Str: name of series within the file. Can be a regular expression.
+	% 
+	% Outputs
+	% 	bfSeriesNo - Int: series number (1-based indexing) matching the input series name. NaN is output if no series is found.
+	% 
+	% Options (input as Name-Value with Name = options.(Name))
+	% 	% File ID connection from calling bfGetReader(inputFilePath), this is to save time on larger files by avoiding opening the connection again.
+	% 	options.fileIdOpen = '';
+
+	% Changelog
+		%
+	% TODO
+		%
+
+	try
+		bfSeriesNo = ciapkg.bf.getSeriesNoFromName(inputMoviePath,bfSeriesName,'passArgs',varargin);
+	catch err
+		disp(repmat('@',1,7))
+		disp(getReport(err,'extended','hyperlinks','on'));
+		disp(repmat('@',1,7))
+	end
+end

+ciapkg/+api/loadSignalExtractionSorting.m

@@ -0,0 +1,27 @@
+function [valid, algorithmStr, infoStruct] = loadSignalExtractionSorting(inputFilePath,varargin)
+	% [valid,algorithmStr,infoStruct] = loadSignalExtractionSorting(inputFilePath,varargin)
+	% 
+	% Loads manual or automated (e.g. CLEAN) sorting..
+	% 
+	% Biafra Ahanonu
+	% started: 2022.05.31 [20:14:54] (branched from modelVarsFromFiles)
+	% 
+	% Inputs
+	% 	inputFilePath - Str: path to signal extraction output.
+	% 
+	% Outputs
+	% 	valid - logical vector: indicating which signals are valid and should be kept.
+	% 	algorithmStr - Str: algorithm name.
+	% 	infoStruct - Struct: contains information about the file, e.g. the 'description' property that can contain information about the algorithm.
+	% 
+	% Options (input as Name-Value with Name = options.(Name))
+	% 	% DESCRIPTION
+	% 	options.exampleOption = '';
+
+	% Changelog
+		%
+	% TODO
+		%
+
+	[valid, algorithmStr, infoStruct] = ciapkg.io.loadSignalExtractionSorting(inputFilePath,'passArgs', varargin);
+end

+ciapkg/+api/manageParallelWorkers.m

@@ -3,5 +3,12 @@
 	% Biafra Ahanonu
 	% started: 2015.12.01
 
-	[success] = ciapkg.io.manageParallelWorkers('passArgs', varargin);
+	% changelog
+		% 2022.02.28 [18:36:15] - Added ability to input just the number of workers to open as 1st single input argument that aliases for the "setNumCores" Name-Value input, still support other input arguments as well.
+
+	if length(varargin)==1
+		[success] = ciapkg.io.manageParallelWorkers(varargin{1});
+	else
+		[success] = ciapkg.io.manageParallelWorkers('passArgs', varargin);
+	end
 end

+ciapkg/+api/mergeStructs.m

@@ -0,0 +1,17 @@
+function [pullStruct] = mergeStructs(toStruct,fromStruct,varargin)
+    % [toStruct] = mergeStructs(fromStruct,toStruct,overwritePullFields)
+    %
+    % Copies fields in fromStruct into toStruct, if there is an overlap in field names, fromStruct overwrites toStruct unless specified otherwise.
+    %
+    % Biafra Ahanonu
+    % started: 2014.02.12
+    %
+    % inputs
+    %   toStruct - Structure that is to be updated with values from fromStruct.
+    %   fromStruct - structure to use to overwrite toStruct.
+    %   overwritePullFields - 1 = overwrite toStruct fields with fromStruct, 0 = don't overwrite.
+    % outputs
+    %   toStruct - structure with fromStructs values added.
+
+    [pullStruct] = ciapkg.io.mergeStructs(toStruct,fromStruct,'passArgs', varargin);
+end

+ciapkg/+api/normalizeSignalExtractionActivityTraces.m

@@ -1,5 +1,8 @@
 function inputSignals = normalizeSignalExtractionActivityTraces(inputSignals,inputImages, varargin)
+	% [inputSignals] = ciapkg.signal_extraction.normalizeSignalExtractionActivityTraces(inputSignals,inputImages,'passArgs', varargin);
+	% 
 	% Normalizes cell activity traces by the max value in the associated image, normally to produce dF/F equivalent activity traces
+	%
 	% started: 2019.08.25 [18:19:34]
 	% Biafra Ahanonu
 	% Branched from normalizeCELLMaxTraces (Lacey Kitch and Biafra Ahanonu)

+ciapkg/+bf/dispFileSeries.m

@@ -0,0 +1,76 @@
+function [seriesNameArray] = dispFileSeries(inputFilePath,varargin)
+	% [bfSeriesNo] = getSeriesNoFromName(inputFilePath,bfSeriesName,varargin)
+	% 
+	% Returns series number for Bio-Formats series with name given by user.
+	% 
+	% Biafra Ahanonu
+	% started: 2022.07.15 [08:10:16]
+	% 
+	% Inputs
+	% 	inputFilePath - Str: path to Bio-Formats compatible file.
+	% 
+	% Outputs
+	% 	bfSeriesNo - Int: series number (1-based indexing) matching the input series name. NaN is output if no series is found.
+	% 
+	% Options (input as Name-Value with Name = options.(Name))
+	% 	% File ID connection from calling bfGetReader(inputFilePath), this is to save time on larger files by avoiding opening the connection again.
+	% 	options.fileIdOpen = '';
+
+	% Changelog
+		%
+	% TODO
+		%
+
+	% ========================
+	% File ID connection from calling bfGetReader(inputFilePath), this is to save time on larger files by avoiding opening the connection again.
+	options.fileIdOpen = [];
+	% get options
+	options = ciapkg.io.getOptions(options,varargin);
+	% disp(options)
+	% unpack options into current workspace
+	% fn=fieldnames(options);
+	% for i=1:length(fn)
+	% 	eval([fn{i} '=options.' fn{i} ';']);
+	% end
+	% ========================
+
+	try
+		% By default output NaN if no series found.
+		seriesNameArray = {};
+
+		if isempty(options.fileIdOpen)
+			disp(['Opening connection to Bio-Formats file:' inputFilePath])
+			startReadTime = tic;
+			fileIdOpen = bfGetReader(inputFilePath);
+			toc(startReadTime)
+		else
+			fileIdOpen = options.fileIdOpen;
+		end
+		omeMeta = fileIdOpen.getMetadataStore();
+
+		nSeries = fileIdOpen.getSeriesCount();
+		seriesNameArray = cell([1 nSeries]);
+		disp('===')
+		disp(['Series in file: ' inputFilePath])
+		for seriesNo = 1:nSeries
+			% Convert 1-based to 0-based indexing.
+			thisStr = char(omeMeta.getImageName(seriesNo-1));
+			seriesNameArray{seriesNo} = thisStr;
+			disp([num2str(seriesNo) ': "' thisStr '"'])
+		end
+		disp('===')
+	catch err
+		disp(repmat('@',1,7))
+		disp(getReport(err,'extended','hyperlinks','on'));
+		disp(repmat('@',1,7))
+	end
+
+	function [outputs] = nestedfxn_exampleFxn(arg)
+		% Always start nested functions with "nestedfxn_" prefix.
+		% outputs = ;
+	end	
+end
+function [outputs] = localfxn_exampleFxn(arg)
+	% Always start local functions with "localfxn_" prefix.
+	% outputs = ;
+end	

+ciapkg/+bf/getSeriesNoFromName.m

@@ -0,0 +1,88 @@
+function [bfSeriesNo] = getSeriesNoFromName(inputFilePath,bfSeriesName,varargin)
+	% [bfSeriesNo] = getSeriesNoFromName(inputFilePath,bfSeriesName,varargin)
+	% 
+	% Returns series number for Bio-Formats series with name given by user.
+	% 
+	% Biafra Ahanonu
+	% started: 2022.07.15 [08:10:16]
+	% 
+	% Inputs
+	% 	inputFilePath - Str: path to Bio-Formats compatible file.
+	% 	bfSeriesName - Str: name of series within the file. Can be a regular expression.
+	% 
+	% Outputs
+	% 	bfSeriesNo - Int: series number (1-based indexing) matching the input series name. NaN is output if no series is found.
+	% 
+	% Options (input as Name-Value with Name = options.(Name))
+	% 	% File ID connection from calling bfGetReader(inputFilePath), this is to save time on larger files by avoiding opening the connection again.
+	% 	options.fileIdOpen = '';
+
+	% Changelog
+		%
+	% TODO
+		%
+
+	% ========================
+	% File ID connection from calling bfGetReader(inputFilePath), this is to save time on larger files by avoiding opening the connection again.
+	options.fileIdOpen = [];
+	% get options
+	options = ciapkg.io.getOptions(options,varargin);
+	% disp(options)
+	% unpack options into current workspace
+	% fn=fieldnames(options);
+	% for i=1:length(fn)
+	% 	eval([fn{i} '=options.' fn{i} ';']);
+	% end
+	% ========================
+
+	try
+		% By default output NaN if no series found.
+		bfSeriesNo = NaN;
+
+		if isempty(options.fileIdOpen)
+			disp(['Opening connection to Bio-Formats file:' inputFilePath])
+			startReadTime = tic;
+			fileIdOpen = bfGetReader(inputFilePath);
+			toc(startReadTime)
+		else
+			fileIdOpen = options.fileIdOpen;
+		end
+		omeMeta = fileIdOpen.getMetadataStore();
+
+		if isempty(bfSeriesName)
+			disp('Please provide a series name for Bio-Formats')
+		else
+			disp(['Searching for series: "' bfSeriesName '"'])
+			nSeries = fileIdOpen.getSeriesCount();
+			seriesNameArray = cell([1 nSeries]);
+			disp('===')
+			disp(['Series in file: ' inputFilePath])
+			for seriesNo = 1:nSeries
+				% Convert 1-based to 0-based indexing.
+				thisStr = char(omeMeta.getImageName(seriesNo-1));
+				seriesNameArray{seriesNo} = thisStr;
+				disp([num2str(seriesNo) ': "' thisStr '"'])
+			end
+			disp('===')
+			matchIdx = ~cellfun(@isempty,regexp(seriesNameArray,bfSeriesName));
+			if any(matchIdx)
+				bfSeriesNo = find(matchIdx);
+				bfSeriesNo = bfSeriesNo(1);
+				disp(['Series found: ' num2str(bfSeriesNo) ' - "' seriesNameArray{bfSeriesNo} '"'])
+			end
+		end
+	catch err
+		disp(repmat('@',1,7))
+		disp(getReport(err,'extended','hyperlinks','on'));
+		disp(repmat('@',1,7))
+	end
+
+	function [outputs] = nestedfxn_exampleFxn(arg)
+		% Always start nested functions with "nestedfxn_" prefix.
+		% outputs = ;
+	end	
+end
+function [outputs] = localfxn_exampleFxn(arg)
+	% Always start local functions with "localfxn_" prefix.
+	% outputs = ;
+end	

+ciapkg/+classification/signalSorter.m

@@ -1,20 +1,31 @@
 function [inputImages, inputSignals, choices] = signalSorter(inputImages,inputSignals,varargin)
+	% [inputImages, inputSignals, choices] = signalSorter(inputImages,inputSignals,varargin)
+	% 
 	% Displays a GUI for sorting images (e.g. cells) and their associated signals (e.g. fluorescence activity traces). Also does preliminary sorting based on image/signal properties if requested by user.
-	% See following URL for details of GUI and tips on manual sorting: https://github.com/bahanonu/calciumImagingAnalysis/wiki/Manual-cell-sorting-of-cell-extraction-outputs.
+	% 
+	% See following URL for details of GUI and tips on manual sorting: https://bahanonu.github.io/ciatah/help_manual_cell_sorting/.
+	% 
 	% Biafra Ahanonu
 	% started: 2013.10.08
+	% 
 	% Dependent code
-		% getOptions.m, createObjMap.m, removeSmallICs.m, identifySpikes.m, etc., see repository
-	% inputs
-		% inputImages - [x y N] matrix where N = number of images, x/y are dimensions. Use permute(inputImages,[2 3 1]) if you use [N x y] for matrix indexing.
-			% Alternatively, make inputImages = give path to NWB file and inputSignals = [] for signalSorter to automatically load NWB files.
-		% inputSignals - [N time] matrix where N = number of signals (traces) and time = frames.
-		% inputID - obsolete, kept for compatibility, just input empty []
-		% nSignals - obsolete, kept for compatibility
-	% outputs
-		% inputImages - [N x y] matrix where N = number of images, x/y are dimensions with only manual choices kept.
-		% inputSignals
-		% choices
+	% 	getOptions.m, createObjMap.m, removeSmallICs.m, identifySpikes.m, etc., see CIAtah repository.
+	% 
+	% Inputs
+	% 	<strong>inputImages</strong>
+	% 	  1) [x y N] matrix where N = number of images, x/y are dimensions. Use permute(inputImages,[2 3 1]) if you use [N x y] for matrix indexing.
+	% 	  2) Path to NWB file and inputSignals = [] for signalSorter to automatically load NWB files.
+	% 	<strong>inputSignals</strong> - [N time] matrix where N = number of signals (traces) and time = frames.
+	% 	inputID - obsolete, kept for compatibility, just input empty []
+	% 	nSignals - obsolete, kept for compatibility
+	% 
+	% Outputs
+	% 	<strong>inputImages</strong> - Matrix: filtered with only good outputs. [N x y] matrix where N = number of images, x/y are dimensions with only manual choices kept.
+	% 	<strong>inputSignals</strong> - Matrix: filtered with only good outputs. [N time] matrix where N = number of signals (traces) and time = frames.
+	% 	<strong>choices</strong> - [1 N] vector using the below key:
+	% 		1 = yes
+	% 		0 = no
+	% 		2 = not designated by user
 
 	% changelog
 		% 2013.10.xx changed to ginput and altered UI to show more relevant information, now shows a objMap overlayed with the current filter, etc.
@@ -78,6 +89,7 @@
 		% 2021.12.22 [08:19:19] - Updated suptitle to ciapkg.overloaded.suptitle. Also limit number of GUI re-runs to prevent infinite looping.
         % 2022.01.19 [12:35:42] - Fixed issue with `gca.XRuler.Axle.LineStyle` being an empty object when axes created, leading to failure to assign and error loops.
         % 2022.02.06 [20:06:19] - Make all openFigure to ciapkg.api.openFigure.
+        % 2022.03.14 [01:10:52] - Comments update.
 	% TODO
 		% DONE: New GUI interface to allow users to scroll through video and see cell activity at that point
 		% DONE: allow option to mark rest as bad signals
@@ -171,8 +183,9 @@
 	options.randomizeOrder = 0;
 	% show ROI traces in addition to input traces
 	options.showROITrace = 0;
-	% pre-compute signal peaks
+	% Matrix: save time if already computed peaks. [nSignals frame] matrix. Binary matrix with 1 = peaks, 0 = non-peaks.
 	options.signalPeaks = [];
+	% Cell array: save time if already computed peaks. {1 nSignals} cell array. Each cell contains [1 nPeaks] vector that stores the frame locations of each peak.
 	options.signalPeaksArray = [];
 	% ROI for peak signal plotting
 	options.peakROI = -20:20;
@@ -1550,17 +1563,18 @@ function plotSignalStatistics(inputSignals,inputImageSizes,inputStr,pointColor,
 					set(zoomHandle,'ActionPostCallback',@sliderZoomCallback);
 				end
 
+				% Create progress bar
+				[axValid, axValidAll] = subfxn_progressBarCreate(axValid, axValidAll);
+
 				set(objMapPlotLocHandle,'tag','objMapPlotLocHandle')
 				set(objMapZoomPlotLocHandle,'tag','objMapZoomPlotLocHandle')
 				% if strcmp(get(zoom(1),'Enable'),'off')
 				% 	pan on;
 				% end
 				set(objMapPlotLocHandle,'ButtonDownFcn',@subfxnSelectCellOnCellmap)
 				set(objMapZoomPlotLocHandle,'ButtonDownFcn',@subfxnSelectCellOnCellmap)
-				set(mainFig, 'KeyPressFcn', @(source,eventdata) figure(mainFig));
 
-				% Create progress bar
-				[axValid, axValidAll] = subfxn_progressBarCreate(axValid, axValidAll);
+				set(mainFig, 'KeyPressFcn', @(source,eventdata) figure(mainFig));
 
 				while strcmp(keyIn,'3')
 					frameNoTotal = frameNoTotal+1;
@@ -1583,6 +1597,8 @@ function plotSignalStatistics(inputSignals,inputImageSizes,inputStr,pointColor,
 				end
 				set(objMapPlotLocHandle,'tag','objMapPlotLocHandle')
 				set(objMapZoomPlotLocHandle,'tag','objMapZoomPlotLocHandle')
+				set(objMapPlotLocHandle,'ButtonDownFcn',@subfxnSelectCellOnCellmap)
+				set(objMapZoomPlotLocHandle,'ButtonDownFcn',@subfxnSelectCellOnCellmap)
 
 				reply = double(keyIn);
 				set(gcf,'currentch','3');
@@ -2109,6 +2125,7 @@ function mouseWheelChange(hObject, callbackdata, handles)
 		set(gcf,'uicontextmenu',conMenu);
 	end
 	function subfxnSelectCellOnCellmap(source,eventdata)
+		disp('Click screen')
 		if showCrossHairs==1
 			[xUser,yUser,~] = ciapkg.overloaded.ginputCustom(1);
 		else
@@ -2118,6 +2135,7 @@ function subfxnSelectCellOnCellmap(source,eventdata)
 		end
 		mapTags = {'objMapPlotLocHandle','objMapZoomPlotLocHandle'};
 		thisPlotTag = find(ismember(mapTags, get(gca,'tag')));
+		thisPlotTag
 		if isempty(thisPlotTag)
 			% zoom;
 		elseif thisPlotTag<0|thisPlotTag>length(mapTags)
@@ -2551,7 +2569,7 @@ function subfxnLostFocusMainFig(jAxis, jEventData, hFig)
 	croppedPeakImages = cat(3,meanTransientImage,croppedPeakImages);
 
 	croppedPeakImages222 = compareSignalToMovie(inputMovie, inputImage, thisTrace,'getOnlyPeakImages',1,'waitbarOn',0,'extendedCrosshairs',2,'crossHairVal',maxValMovie*options.crossHairPercent,'outlines',0,'signalPeakArray',signalPeakArray,'cropSize',cropSizeLength,'crosshairs',0,'addPadding',1,'xCoords',xCoords,'yCoords',yCoords,'outlineVal',NaN,'inputDatasetName',options.inputDatasetName,'inputMovieDims',options.inputMovieDims,'hdf5Fid',options.hdf5Fid,'keepFileOpen',options.keepFileOpen);
-	[thresholdedImages, boundaryIndices] = thresholdImages(croppedPeakImages222(:,:,1),'binary',1,'getBoundaryIndex',1,'threshold',options.thresholdOutline,'removeUnconnectedBinary',0);
+	[thresholdedImages, boundaryIndices] = thresholdImages(croppedPeakImages222(:,:,1),'binary',1,'getBoundaryIndex',1,'threshold',options.thresholdOutline,'removeUnconnectedBinary',0,'waitbarOn',0);
 	for imageNo = 1:size(croppedPeakImages,3)
 		tmpImg = croppedPeakImages(:,:,imageNo);
 		tmpImg(boundaryIndices{1}) = NaN;