Function updates and URLs for all major external programs.

- `loadBatchFxns` -  Update `_external_programs` to call ciapkg.getDirExternalPrograms() to standardize call across all functions. Do not add docs and data folders or sub-folders to the path. Update to fullfile call using filesep to make platform neutral.
- `@ciatah\viewMatchObjBtwnSessions` - Convert all suptitle to ciapkg.overloaded.suptitle.
- Updated `README` in external programs to contain URLs for major programs.

+ciapkg/loadBatchFxns.m

@@ -20,13 +20,15 @@ function loadBatchFxns(varargin)
 		% 2020.05.09 [16:40:13] - Updates to remove additional specific repositories that should not be loaded by default. Add support for overriding this feature.
 		% 2020.06.05 [23:35:43] - If user doesn't have Parallel Toolbox, still works
 		% 2020.07.21 [14:11:42] - Fix to make sure all sub-folders (not just the root) are also removed in the case of certain external_programs.
-		% 2021.02.01 [‏‎15:19:40] - Update `_external_programs` to call ciapkg.getDirExternalPrograms() to standardize call across all functions.
+		% 2021.02.01 [??‎15:19:40] - Update `_external_programs` to call ciapkg.getDirExternalPrograms() to standardize call across all functions.
 		% 2021.06.20 [00:22:38] - Added manageMiji('startStop','closeAllWindows'); support.
 		% 2021.07.16 [13:38:55] - Remove redundant loading and unloading of external programs via additional checks.
 		% 2021.07.22 [19:51:50] - Moved loadBatchFxns into ciapkg package. Use ciapkg.getDir to get directory as standard IO.
+		% 2021.08.09 [12:06:32] - Do not add docs and data folders or sub-folders to the path.
+		% 2021.08.24 [13:46:13] - Update to fullfile call using filesep to make platform neutral.
 	% TODO
 		%
-
+	
 	% Disable the handle graphics warning "The DrawMode property will be removed in a future release. Use the SortMethod property instead." from being displayed. Comment out this line for debugging purposes as needed.
 	warning('off','MATLAB:hg:WillBeRemovedReplaceWith')
 
@@ -78,6 +80,13 @@ function loadBatchFxns(varargin)
 		[pathListArray] = subfxnRemoveDirs(0,pathListArray);
 	end
 
+	% Remove 'docs' and 'data', don't need to be in the path.
+	matchIdxD = contains(pathListArray,[functionDir filesep 'docs']);
+	pathListArray = pathListArray(~matchIdxD);
+
+	matchIdxD = contains(pathListArray,[functionDir filesep 'data']);
+	pathListArray = pathListArray(~matchIdxD);
+
 	skipRemovePath = 0;
 	if isempty(pathListArray)
 		fprintf('MATALB path already has all needed non-private folders under: %s\n',functionDir);
@@ -112,7 +121,7 @@ function loadBatchFxns(varargin)
 	elseif ispc
 		baseInscopixPath = 'C:\Program Files\Inscopix\Data Processing';
 	else
-		disp('Platform not supported')
+		disp('Platform not supported for Inscopix Data Processing Software.')
 	end
 
 	pathFilter = ismember(baseInscopixPath,strsplit(path,pathsep));
@@ -234,7 +243,7 @@ function loadBatchFxns(varargin)
 						return;
 					end
 					extDir = extDir(3:end);
-					foundFiles = dir(fullfile([externalProgramsDir], ['**\' thisFxn '']));
+					foundFiles = dir(fullfile([externalProgramsDir], ['**' filesep thisFxn '']));
 					if isempty(foundFiles)
 						pathToRm = [];
 					else

@ciatah/viewMatchObjBtwnSessions.m

@@ -12,6 +12,7 @@
 		% 2019.04.23 [19:53:21] - a couple Windows specific path separators, switch to filesep
 		% 2019.07.03 [16:35:10] - Updated to allow GUI-less option so computeMatchObjBtwnTrials can run after cross-session alignment.
 		% 2020.12.08 [00:53:20] - Take out parfor in one loop that calls obj functions to eliminate serialization issues. Also change color mapping of cross session maps so that it covers the full range using the actual global IDs matched across sessions rather than diluting the range by including global IDs that don't meet the criteria. Makes the maps more colorful.
+		% 2021.08.24 [14:10:02] - Convert all suptitle to ciapkg.overloaded.suptitle.
 	% TODO
 		%
 
@@ -35,6 +36,7 @@
 	options.runGui = 1;
 	options.cellmapZoomPx = 10;
 	options.maxDistAccept = 10;
+	options.showFigures = 1;
 	% get options
 	options = getOptions(options,varargin);
 	% display(options)
@@ -82,6 +84,14 @@
 		pctSessionMatchChoices = [1 2 3];
 	end
 
+	if options.showFigures==1
+		for figNoFake = [342 343 344 9019 59857 65 66 42 1110+[0:6] 1 2 3]
+			[~, ~] = openFigure(figNoFake, '');
+			% clf
+		end
+		drawnow
+	end
+
 
 	nFiles = length(obj.rawSignals);
 	[fileIdxArray idNumIdxArray nFilesToAnalyze nFiles] = obj.getAnalysisSubsetsToAnalyze();
@@ -268,6 +278,7 @@
 						end
 						% disp([globalNo sessionIdx nMatchGlobalIDs(globalNo)>=2 NaN size(globalIDsImageList) NaN size(tmpSessionImgs)])
 						if sessionIdx~=0&nMatchGlobalIDs(globalNo)>=2
+                            % [sessionIdx size(tmpSessionImgs)]
 							tmpImg = tmpSessionImgs(:,:,sessionIdx);
 							globalIDsImageList{globalNo} = cat(3,globalIDsImageList{globalNo},tmpImg);
 							% globalToSessionIDs{sessionNo}(sessionIdx) = globalNo;
@@ -454,7 +465,7 @@
 			end
 			drawnow
 			openFigure(1112);
-				suptitle('Errors in cell alignment to "global" match cell centroid')
+				ciapkg.overloaded.suptitle('Errors in cell alignment to "global" match cell centroid')
 				subplot(1,2,1)
 					xlabel('X (px)')
 					ylabel('Y (px)')
@@ -466,24 +477,16 @@
 					title('Heat plot')
 					axis equal tight
 			openFigure(1110);
-				suptitle('Overlap of matched cells detected across at least (nSessions-1) sessions')
+				ciapkg.overloaded.suptitle('Overlap of matched cells detected across at least (nSessions-1) sessions')
 			openFigure(1114);
-				suptitle('Example cells matched across sessions')
+				ciapkg.overloaded.suptitle('Example cells matched across sessions')
 
 			newSubjStr = sprintf('%s_%d',thisSubjectStr,options.alignmentSetNum);
 			obj.globalIDs.matchCoords.(newSubjStr) = allCentroids;
 			obj.globalIDs.distances.(newSubjStr) = allDistances;
 			% return;
 			% pause
 
-			try
-				figure;
-					imagesc(nanmean(cat(3,obj_p435_p700.detailStats.outputCutMovie{:}),3));
-					colorbar;
-					axis equal tight;
-					title('m597 aligned sessions match cells');
-			catch
-			end
 			try
 				obj.detailStats.matchedGlobalCellsOverlap{subjectNo} = outputCutMovie;
 			catch

_external_programs/README.md

@@ -1,19 +1,22 @@
 # External software packages
 
-The folder `_external_programs` is for external software packages used by `calciumImagingAnalysis`.
+The folder `_external_programs` is for external software packages or algorithms used by `CIAtah`. These are automatically downloaded when running `obj.setup;` after creating a `CIAtah` object by calling `obj = CIAtah;` or directly by running `ciapkg.io.loadDependencies();`.
 
-The following are likely to be found here:
+The following programs will be found in this folder after downloading (e.g. after running  `ciapkg.io.loadDependencies`):
 - GUI and display
-	- `Fiji`
+	- `ImageJ/Fiji` - Miji to allow calling of ImageJ/Fiji, only download `mij.jar` and `ij.jar`. https://imagej.net/plugins/miji.
 - Cell extraction
-	- `CELLMax`
-	- `CNMF`
-	- `CNMF-E`
-	- `CVX`
-	- `EXTRACT`
+	- `CELLMax` - Will be made public upon publication.
+	- `CNMF` - https://github.com/flatironinstitute/CaImAn-MATLAB.
+	- `CNMF-E` - https://github.com/zhoupc/CNMF_E.
+	- `CVX` - http://cvxr.com/cvx/download/ (e.g. http://web.cvxr.com/cvx/cvx-rd.zip).
+	- `EXTRACT` - https://github.com/schnitzer-lab/EXTRACT-public.
 - NWB
-    - `nwb_schnitzer_lab`
-    - `yamlmatlab`
-    - `matnwb`
+    - `nwb_schnitzer_lab` - https://github.com/schnitzer-lab/nwb_schnitzer_lab.
+    - `yamlmatlab` - https://github.com/ewiger/yamlmatlab.
+    - `matnwb` - https://github.com/NeurodataWithoutBorders/matnwb.
+- File I/O
+	- `Bio-Formats` - MATLAB version at https://www.openmicroscopy.org/bio-formats/downloads/.
 - Motion correction
-	- `NoRMCorre`
+	- `Turboreg` - C and MEX function implementation of http://bigwww.epfl.ch/thevenaz/turboreg/.
+	- `NoRMCorre` - https://github.com/flatironinstitute/NoRMCorre.