Merge pull request #82 from bahanonu/bahanonu/functionUpdates

Updated to MIT license, move functions into ciapkg package, gramm graphics, detrend support, speed improvements, and more

+ciapkg/+demo/cmdLinePipeline.m

@@ -27,7 +27,7 @@
 nwbFileFolderPath = [analysisFolderPath filesep 'nwbFiles'];
 
 % Load CIAtah functions
-loadBatchFxns();
+ciapkg.loadBatchFxns();
 
 % =================================================
 %% Download test data, only a single session
@@ -166,7 +166,7 @@
 % =================================================
 %% Run EXTRACT cell extraction. Check each function with "edit" for options.
 % Load default configuration
-loadBatchFxns('loadEverything');
+ciapkg.loadBatchFxns('loadEverything');
 extractConfig = get_defaults([]);
 
 % See https://github.com/schnitzer-lab/EXTRACT-public#configurations.
@@ -196,7 +196,7 @@
 end
 
 % Remove EXTRACT from the path.
-loadBatchFxns();
+ciapkg.loadBatchFxns();
 
 % =================================================
 %% USER INTERFACE Run cell sorting using matrix outputs from cell extraction.

+ciapkg/+download/updatePathCleanup.m

@@ -36,7 +36,7 @@
 
 		% Remove references to MEX files
 		clear mex
-		loadBatchFxns('excludeExternalPrograms');
+		ciapkg.loadBatchFxns('excludeExternalPrograms');
 
 		pathCell = regexp(path, pathsep, 'split');
 		if verLessThan('matlab','9.1')

+ciapkg/+io/loadDependencies.m

@@ -19,18 +19,19 @@ function loadDependencies(varargin)
 		% 2021.06.19 [23:46:58] - Switched to support for original MIJ calling of ImageJ using just jar files, easier compatibility across MATLAB versions and OSes.
 		% 2021.06.21 [16:45:59] - Update order.
 		% 2021.07.13 [08:34:18] - Added backup URL for downloading mij.jar.
+		% 2021.07.23 [00:22:22] - Added gramm (https://github.com/piermorel/gramm) support/downloading for graphics plotting.
 	% TODO
 		% Verify all dependencies download and if not ask user to download again.
 
 	%========================
 	% DESCRIPTION
 	options.externalProgramsDir = ciapkg.getDirExternalPrograms();
 	options.guiEnabled = 1;
-	options.dependencyStr = {'downloadImageJ','downloadCnmfGithubRepositories','example_downloadTestData','downloadNeuroDataWithoutBorders','downloadEXTRACT','downloadBioFormats','downloadNoRMCorre','downloadMiji','loadMiji'};
+	options.dependencyStr = {'downloadImageJ','downloadCnmfGithubRepositories','example_downloadTestData','downloadNeuroDataWithoutBorders','downloadEXTRACT','downloadBioFormats','downloadGramm','downloadNoRMCorre','downloadMiji','loadMiji'};
 
-	options.dispStr = {'Download ImageJ','Download CNMF, CNMF-E, and CVX code.','Download test one- and two photon datasets.','Download NWB (NeuroDataWithoutBorders)','Download EXTRACT','Download Bio-Formats','Download NoRMCorre (motion correction)','Download Fiji (to run Miji)','Load Fiji/Miji into MATLAB path.'};
+	options.dispStr = {'Download ImageJ','Download CNMF, CNMF-E, and CVX code.','Download test one- and two photon datasets.','Download NWB (NeuroDataWithoutBorders)','Download EXTRACT','Download Bio-Formats','Download gramm (GRAMmar of graphics for Matlab, e.g. ggplot2-like)','Download NoRMCorre (motion correction)','Download Fiji (to run Miji)','Load Fiji/Miji into MATLAB path.'};
 	% Int vector: index of options.dependencyStr to run by default with no GUI
-	options.depIdxArray = [1 2 3 4 5 6];
+	options.depIdxArray = [1 2 3 4 5 6 7];
 	% Binary: 1 = force update even if already downloaded. 0 = skip if already downloaded
 	options.forceUpdate = 0;
 	% get options
@@ -109,6 +110,16 @@ function loadDependencies(varargin)
 				% optionsH.gitName = cellfun(@(x) [x '-master'],optionsH.gitNameDisp,'UniformOutput',false);
 				optionsH.gitName = {'NoRMCorre-public-master'};
 				[success] = downloadGithubRepositories('options',optionsH);
+			case 'downloadGramm'
+				optionsH.forceUpdate = forceUpdate;
+				optionsH.signalExtractionDir = options.externalProgramsDir;
+				optionsH.gitNameDisp = {'gramm'};
+				optionsH.gitRepos = {'https://github.com/piermorel/gramm'};
+				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);
+				optionsH.gitName = {'gramm-master'};
+				[success] = downloadGithubRepositories('options',optionsH);
 			case 'downloadEXTRACT'
 				optionsH.forceUpdate = forceUpdate;
 				optionsH.signalExtractionDir = options.externalProgramsDir;

+ciapkg/+io/updatePkg.m

@@ -79,15 +79,15 @@
 			verInfoStr = sprintf('%s\n Local version: %s (%s).\n Online version %s (%s).\n',verInfoStr2,currentVersion,currentDateTimeStr,onlineVersionTmp,onlineDateTimeStr);
 			warning(verInfoStr)
 			if verCompare<1
-				msgbox(verInfoStr,'Note on CIAtah version.')
+				ciapkg.overloaded.msgbox(verInfoStr,'Note on CIAtah version.')
 			end
 			success = 1;
 			return
 		end
 
 		disp(verInfoStr)
 		if options.showGui==1
-			uiwait(msgbox(verInfoStr));
+			uiwait(ciapkg.overloaded.msgbox(verInfoStr));
 		end
 
 		% If the user is behind, ask if they want to update then initiate download and update from online repository

+ciapkg/VERSION

@@ -1,2 +1,2 @@
-v3.33.0
-2021.07.13 [13:22:16]
+v3.35.1
+2021.07.25 [14:22:59]

+ciapkg/loadAllDirs.m

@@ -26,7 +26,7 @@ function loadAllDirs()
 	%========================
 
 	try
-		loadBatchFxns('loadEverything');
+		ciapkg.loadBatchFxns('loadEverything');
 	catch err
 		disp(repmat('@',1,7))
 		disp(getReport(err,'extended','hyperlinks','on'));

loadBatchFxns.m → +ciapkg/loadBatchFxns.m

@@ -22,6 +22,8 @@ function loadBatchFxns(varargin)
 		% 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.
 		% 2021.06.20 [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.
 	% TODO
 		%
 
@@ -30,10 +32,14 @@ function loadBatchFxns(varargin)
 
 	externalProgramsDir = ciapkg.getDirExternalPrograms();
 
+	removeDirFxnToFind = {'runCELLMax.m','extractor.m','normcorre.m'};
+	% 'cellmax.runCELLMax', 'CELLMax_Wrapper.m'
+
 	% Add calciumImagingAnalysis directory and subdirectories to path, use dbstack to ensure only add in the root directory regardless of where user has current MATLAB folder.
-	functionLocation = dbstack('-completenames');
-	functionLocation = functionLocation(1).file;
-	[functionDir,~,~] = fileparts(functionLocation);
+	% functionLocation = dbstack('-completenames');
+	% functionLocation = functionLocation(1).file;
+	% [functionDir,~,~] = fileparts(functionLocation);
+	functionDir = ciapkg.getDir;
 	pathList = genpath(functionDir);
 	% pathList = genpath(pwd);
 	pathListArray = strsplit(pathList,pathsep);
@@ -66,8 +72,16 @@ function loadBatchFxns(varargin)
 	pathListArray = pathListArray(~pathFilter);
 	pathFilter = ismember(pathListArray,strsplit(path,pathsep));
 	pathListArray = pathListArray(~pathFilter);
+
+	% If going to remove directories in removeDirFxnToFind then do so now to prevent redundant calls to addpath, etc.
+	if isempty(varargin)
+		[pathListArray] = subfxnRemoveDirs(0,pathListArray);
+	end
+
+	skipRemovePath = 0;
 	if isempty(pathListArray)
 		fprintf('MATALB path already has all needed non-private folders under: %s\n',functionDir);
+		skipRemovePath = 1;
 	else
 		fprintf('Adding all non-private folders under: %s\n',functionDir);
 		pathList = strjoin(pathListArray,pathsep);
@@ -84,7 +98,9 @@ function loadBatchFxns(varargin)
 		matchIdx2 = contains(pathListArray,externalProgramsDir);
 		pathListArray = pathListArray(~matchIdx2);
 	else
-		pathListArray = subfxnRemoveDirs(1,pathListArrayOriginal);
+		if skipRemovePath==0
+			pathListArray = subfxnRemoveDirs(1,pathListArrayOriginal);
+		end
 	end
 
 	% =================================================
@@ -203,23 +219,27 @@ function loadBatchFxns(varargin)
 		% =================================================
 		% List of functions in root of external program directories that should not be included by default.
 		try
-			fxnRootFolder = {'CELLMax_Wrapper.m','cellmax.runCELLMax','extractor.m','normcorre.m'};
+			fxnRootFolder = removeDirFxnToFind;
 			pathToRmCell = {};
 			for iNo = 1:length(fxnRootFolder)
 				thisFxn = fxnRootFolder{iNo};
 				if rmPathFlag==1
 					[pathToRm,~,~] = fileparts(which(thisFxn));
 				else
-					extDir = dir([functionDir filesep externalProgramsDir]);
+					% extDir = dir([functionDir filesep externalProgramsDir]);
+					extDir = dir([externalProgramsDir]);
 					extDir = extDir([extDir.isdir]);
 					if length(extDir)<3
 						disp('No external programs!')
 						return;
 					end
 					extDir = extDir(3:end);
-
-					foundFiles = dir(fullfile([functionDir filesep externalProgramsDir], ['**\' thisFxn '']));
-					pathToRm = foundFiles.folder;
+					foundFiles = dir(fullfile([externalProgramsDir], ['**\' thisFxn '']));
+					if isempty(foundFiles)
+						pathToRm = [];
+					else
+						pathToRm = foundFiles.folder;
+					end
 				end
 				if ~isempty(pathToRm)
 					if strcmp(thisFxn,'CELLMax_Wrapper.m')|strcmp(thisFxn,'cellmax.runCELLMax')
@@ -246,8 +266,10 @@ function loadBatchFxns(varargin)
 				end
 			end
 
-			%
-			rmpath(strjoin(pathToRmCell,pathsep));
+			% Only remove path if user requests
+			if rmPathFlag==1
+				rmpath(strjoin(pathToRmCell,pathsep));
+			end
 		catch err
 			disp(repmat('@',1,7))
 			disp(getReport(err,'extended','hyperlinks','on'));

+ciapkg/loadDirs.m

@@ -26,7 +26,7 @@ function loadDirs()
 	%========================
 
 	try
-		loadBatchFxns;
+		ciapkg.loadBatchFxns;
 	catch err
 		disp(repmat('@',1,7))
 		disp(getReport(err,'extended','hyperlinks','on'));

startup.m → +ciapkg/startup.m

@@ -1,12 +1,14 @@
 % Startup commands and graphics defaults
 % Biafra Ahanonu
 % started: 2013.12.07 [17:28:44]
+% changelog
+	% 2021.07.22 [19:55:49] - loadBatchFxns to ciapkg.loadBatchFxns.
 
-% If using startup, then restore default path before running
+% If using startup, then restore default path before running startup operations.
 restoredefaultpath
 
 % Load all needed ciapkg directories
-loadBatchFxns('skipLoadMiji');
+ciapkg.loadBatchFxns('skipLoadMiji');
 
 % set default figure properties
 setFigureDefaults();