Merge pull request #64 from bahanonu/bahanonu/functionUpdates

Adding ciapkg API sub-package, improved directory management, etc.

+ciapkg/+api/README.md

@@ -0,0 +1,7 @@
+# CIAtah API
+
+Biafra Ahanonu
+
+All functions in the `ciapkg.api` package are just pass-through functions to the actual underlying functions. This allows users to import all CIAtah functions into their function or script with `import ciapkg.api.*` as opposed to having to do that for each `ciapkg` sub-package.
+
+Else, users can call nearly all CIAtah functions using `ciapkg.api.[Function Name]`, which allows easier namespacing.

+ciapkg/+api/loadMovieList.m

@@ -0,0 +1,10 @@
+function [outputMovie, movieDims, nPixels, nFrames] = loadMovieList(movieList, varargin)
+	% Load movies, automatically detects type (avi, tif, or hdf5) and concatenates if multiple movies in a list.
+		% NOTE:
+			% The function assumes input is 2D time series movies with [x y frames] as dimensions
+			% If movies are different sizes, use largest dimensions and align all movies to top-left corner.
+	% Biafra Ahanonu
+	% started: 2013.11.01
+
+	[outputMovie, movieDims, nPixels, nFrames] = loadMovieList(movieList, 'passArgs', varargin);
+end

+ciapkg/+api/manageParallelWorkers.m

@@ -0,0 +1,7 @@
+function [success] = manageParallelWorkers(varargin)
+	% Manages loading and stopping parallel processing workers.
+	% Biafra Ahanonu
+	% started: 2015.12.01
+
+	[success] = manageParallelWorkers('passArgs', varargin);
+end

+ciapkg/+api/playMovie.m

@@ -0,0 +1,3 @@
+function [exitSignal, ostruct] = playMovie(inputMovie, varargin)
+	[exitSignal, ostruct] = playMovie(inputMovie,'passArgs', varargin);
+end

+ciapkg/+io/loadDependencies.m

@@ -0,0 +1,119 @@
+function loadDependencies(varargin)
+	% Download and load CIAtah dependencies.
+	% Biafra Ahanonu
+	% started: 2014.07.31
+		% 2021.02.01 [15:09:46] branched from CIAtah
+		% branch from calciumImagingAnalysis 2020.05.07 [15:47:29]
+	% inputs
+		%
+	% outputs
+		%
+
+	% changelog
+		% 2020.05.12 [17:40:37] - Updated to enable GUI-less loading of dependencies. In particular for easier unit testing.
+		% 2020.06.28 [14:25:04] - Added ability for users to force update.
+		% 2021.01.22 [13:42:36] - NWB from specific release to reduce compatibility errors.
+		% 2021.02.01 [15:10:41] - Separated into non-class function for use in more functions without needing to load CIAtah class.
+		% 2021.02.01 [‏‎15:19:40] - Update `_external_programs` to call ciapkg.getDirExternalPrograms() to standardize call across all functions.
+	% TODO
+		% Verify all dependencies download and if not ask user to download again.
+
+	%========================
+	% DESCRIPTION
+	options.externalProgramsDir = ciapkg.getDirExternalPrograms();
+	options.guiEnabled = 1;
+	options.dependencyStr = {'downloadMiji','downloadCnmfGithubRepositories','example_downloadTestData','loadMiji','downloadNeuroDataWithoutBorders'};
+
+	options.dispStr = {'Download Fiji (to run Miji)','Download CNMF, CNMF-E, and CVX code.','Download test one- and two photon datasets.','Load Fiji/Miji into MATLAB path.','Download NWB (NeuroDataWithoutBorders)'};
+	% Int vector: index of options.dependencyStr to run by default with no GUI
+	options.depIdxArray = [1 2 3 5];
+	% Binary: 1 = force update even if already downloaded. 0 = skip if already downloaded
+	options.forceUpdate = 0;
+	% get options
+	options = getOptions(options,varargin);
+	% display(options)
+	% unpack options into current workspace
+	% fn=fieldnames(options);
+	% for i=1:length(fn)
+	% 	eval([fn{i} '=options.' fn{i} ';']);
+	% end
+	%========================
+
+	scnsize = get(0,'ScreenSize');
+	if ischar(options.dispStr)
+		options.dispStr = {options.dispStr};
+	end
+	if ischar(options.dependencyStr)
+		options.dependencyStr = {options.dependencyStr};
+	end
+	dependencyStr = options.dependencyStr;
+
+	dispStr = options.dispStr;
+	if options.guiEnabled==1
+		[depIdxArray, ~] = listdlg('ListString',dispStr,'ListSize',[scnsize(3)*0.3 scnsize(4)*0.3],'Name','Which dependencies to load? (Can select multiple)','InitialValue',options.depIdxArray);
+
+		forceDownloadVec = [0 1];
+		[forceUpdate, ~] = listdlg('ListString',{'No - skip installing dependency if already available.','Yes - force update to most recent version of dependency.'},'ListSize',[scnsize(3)*0.3 scnsize(4)*0.3],'Name','Force download/update? (e.g. "Yes" to update dependencies)','InitialValue',[1]);
+		forceUpdate = forceDownloadVec(forceUpdate);
+	else
+		depIdxArray = options.depIdxArray;
+		forceUpdate = 0;
+	end
+	analysisTypeD = dependencyStr(depIdxArray);
+	dispStr = dispStr(depIdxArray);
+	for depNo = 1:length(depIdxArray)
+		disp([10 repmat('>',1,42)])
+		disp(dispStr{depNo})
+		switch analysisTypeD{depNo}
+			case 'downloadCnmfGithubRepositories'
+				[success] = downloadCnmfGithubRepositories('forceUpdate',forceUpdate);
+			case 'downloadMiji'
+				depStr = {'Save Fiji to default directory','Save Fiji to custom directory'};
+				if options.guiEnabled==1
+					[depIdxArray, ~] = listdlg('ListString',depStr,'ListSize',[scnsize(3)*0.2 scnsize(4)*0.25],'Name','Where to save Fiji?');
+				else
+					depIdxArray = 1;
+				end
+				depStr = depStr{depIdxArray};
+				if depIdxArray==1
+					downloadMiji();
+				else
+					downloadMiji('defaultDir','');
+				end
+				% if exist('pathtoMiji','var')
+				% end
+			case 'loadMiji'
+				modelAddOutsideDependencies('miji');
+			case 'example_downloadTestData'
+				example_downloadTestData();
+			case 'downloadCellExtraction'
+				optionsH.forceUpdate = forceUpdate;
+				optionsH.signalExtractionDir = options.externalProgramsDir;
+				optionsH.gitNameDisp = {'cellmax_clean','extract'};
+				optionsH.gitRepos = {'https://github.com/schnitzer-lab/CELLMax_CLEAN','https://github.com/schnitzer-lab/EXTRACT'};
+				optionsH.gitRepos = cellfun(@(x) [x '/archive/master.zip'],optionsH.gitRepos,'UniformOutput',false);
+				optionsH.outputDir = optionsH.gitNameDisp;
+				optionsH.gitName = cellfun(@(x) [x '-master'],optionsH.gitNameDisp,'UniformOutput',false);
+				[success] = downloadGithubRepositories('options',optionsH);
+			case 'downloadNeuroDataWithoutBorders'
+				optionsH.forceUpdate = forceUpdate;
+				optionsH.signalExtractionDir = options.externalProgramsDir;
+				optionsH.gitNameDisp = {'nwb_schnitzer_lab','yamlmatlab','matnwb'};
+				optionsH.gitRepos = {'https://github.com/schnitzer-lab/nwb_schnitzer_lab','https://github.com/ewiger/yamlmatlab'};
+
+				% 'https://github.com/NeurodataWithoutBorders/matnwb'
+				optionsH.gitRepos = cellfun(@(x) [x '/archive/master.zip'],optionsH.gitRepos,'UniformOutput',false);
+				optionsH.gitRepos = [optionsH.gitRepos 'https://github.com/NeurodataWithoutBorders/matnwb/archive/v2.2.5.3.zip'];
+				optionsH.outputDir = optionsH.gitNameDisp;
+				optionsH.gitName = cellfun(@(x) [x '-master'],optionsH.gitNameDisp,'UniformOutput',false);
+				optionsH.gitName{end} = 'matnwb-2.2.5.3';
+				[success] = downloadGithubRepositories('options',optionsH);
+
+				% Add NWB folders to path.
+				ciapkg.nwb.setupNwb;
+				% obj.loadBatchFunctionFolders;
+			otherwise
+				% nothing
+		end
+	end
+end

+ciapkg/+io/updatePkg.m

@@ -20,7 +20,7 @@
 		'ciapkg',...
 		'docs',...
 		'file_exchange'};
-	% Char: GitHub API URL to VERSION file on CIAPKG repository.
+	% [IGNORE] Char: GitHub API URL to VERSION file on CIAPKG repository.
 	options.versionURL = 'https://api.github.com/repos/bahanonu/calciumImagingAnalysis/contents/ciapkg/VERSION';
 	% Binary: 1 = pop-up GUI enabled
 	options.showGui = 1;
@@ -50,9 +50,9 @@
 		if verCompare==1
 			verInfoStr = 'Running most up-to-date version!';
 		elseif verCompare<1
-			verInfoStr = 'Running behind! Initiating update.';
+			verInfoStr = 'Running behind! Initiating update [IGNORE for now].';
 		elseif verCompare>1
-			verInfoStr = 'I do not know how, but you are running ahead! [Dev build]';
+			verInfoStr = 'I do not know how, but you are running a version ahead! [Dev build]';
 		end
 
 		disp(verInfoStr)

+ciapkg/+nwb/setupNwb.m

@@ -8,15 +8,15 @@
 		%
 
 	% changelog
-		%
+		% 2021.02.01 [‏‎15:19:40] - Update `_external_programs` to call ciapkg.getDirExternalPrograms() to standardize call across all functions.
 	% TODO
 		%
 
 	% ========================
 	% Str: default path for CIAtah
 	options.defaultObjDir = ciapkg.getDir;
 	% Str: default root path where all external programs are stored
-	options.externalProgramsDir = '_external_programs';
+	options.externalProgramsDir = ciapkg.getDirExternalPrograms();
 	% Str: default path for MatNWB Matlab code
 	options.matnwbDir = 'matnwb';
 	% get options

+ciapkg/getDirExternalPrograms.m

@@ -0,0 +1,35 @@
+function [externalProgramsDir] = getDirExternalPrograms(varargin)
+	% Returns the directory where external programs are stored. All functions should call this to find external program directory.
+	% Biafra Ahanonu
+	% started: 2021.02.02 [10:55:23]
+	% inputs
+		%
+	% outputs
+		%
+
+	% changelog
+		%
+	% TODO
+		%
+
+	%========================
+	% DESCRIPTION
+	% options.exampleOption = '';
+	% get options
+	% options = getOptions(options,varargin);
+	% display(options)
+	% unpack options into current workspace
+	% fn=fieldnames(options);
+	% for i=1:length(fn)
+	% 	eval([fn{i} '=options.' fn{i} ';']);
+	% end
+	%========================
+
+	try
+		externalProgramsDir = [ciapkg.getDir() filesep '_external_programs'];
+	catch err
+		disp(repmat('@',1,7))
+		disp(getReport(err,'extended','hyperlinks','on'));
+		disp(repmat('@',1,7))
+	end
+end

+ciapkg/getDirPkg.m

@@ -0,0 +1,41 @@
+function [ciapkgDir] = getDirPkg(dirType,varargin)
+	% Standardized location to obtain relevant CIAtah directories, e.g. location of default data folder.
+	% Biafra Ahanonu
+	% started: 2020.08.31 [12:46:57]
+	% inputs
+		%
+	% outputs
+		%
+
+	% changelog
+		%
+	% TODO
+		%
+
+	%========================
+	% DESCRIPTION
+	% options.exampleOption = '';
+	% get options
+	% options = getOptions(options,varargin);
+	% display(options)
+	% unpack options into current workspace
+	% fn=fieldnames(options);
+	% for i=1:length(fn)
+	% 	eval([fn{i} '=options.' fn{i} ';']);
+	% end
+	%========================
+
+	try
+		switch dirType
+			case 'data'
+				ciapkgDir = [ciapkg.getDir() filesep 'data'];
+			otherwise
+				ciapkgDir = '';
+				disp('Incorrect input, returning null.')
+		end
+	catch err
+		disp(repmat('@',1,7))
+		disp(getReport(err,'extended','hyperlinks','on'));
+		disp(repmat('@',1,7))
+	end
+end

+ciapkg/version.m

@@ -34,7 +34,7 @@
 		% versionStr = verStr{1};
 		% dateTimeStr = num2str(verStr{2});
 
-		verStr = readtable([ciapkg.getDir filesep 'ciapkg' filesep 'VERSION'],'ReadVariableNames',0,'FileType','text','Format','auto','TextType','string')
+		verStr = readtable([ciapkg.getDir filesep 'ciapkg' filesep 'VERSION'],'ReadVariableNames',0,'FileType','text','Format','auto','TextType','string');
 		versionStr = verStr{1,1}{1};
 		dateTimeStr = num2str(verStr{2,1}{1});
 	catch

+ciapkg/versionOnline.m

@@ -1,4 +1,4 @@
-function [onlineVersion] = versionOnline(varargin)
+function [onlineVersion, dateTimeStr] = versionOnline(varargin)
 	% Obtains the online repository version.
 	% Biafra Ahanonu
 	% started: 2020.08.18 [‏‎11:16:56]
@@ -8,7 +8,7 @@
 		%
 
 	% changelog
-		%
+		% 2021.02.02 [13:42:19] - Updated to handle new VERSION file that includes datestamp on 2nd line.
 	% TODO
 		%
 
@@ -29,6 +29,8 @@
 
 	try
 		success = 0;
+		onlineVersion = '';
+		dateTimeStr = '';
 
 		% Get version information online
 		% Get information about specific version file online using GitHub API
@@ -40,10 +42,17 @@
 				disp('Could not dowload CIAPKG version information.')
 				return;
 			end
+			if ~isempty(regexp(onlineVersion,'\n'))
+				onlineVersionTmp = strsplit(onlineVersion,'\n');
+				onlineVersion = onlineVersionTmp{1};
+				dateTimeStr = onlineVersionTmp{2};
+			end
 		end
 		success = 1;
 	catch err
 		onlineVersion = '';
+		dateTimeStr = '';
+		success = 0;
 		disp(repmat('@',1,7))
 		disp(getReport(err,'extended','hyperlinks','on'));
 		disp(repmat('@',1,7))

.gitignore

@@ -10,6 +10,10 @@ _external_programs/*/
 _external_programs/cnmf_current
 _external_programs/cnmfe
 _external_programs/cvx_rd
+_external_programs/matnwb
+_external_programs/nwb_schnitzer_lab
+_external_programs/yamlmatlab
+_external_programs/normcorre
 
 # Signal extraction dependency zips
 _external_programs/*.zip