Merge pull request #78 from bahanonu/bahanonu/functionUpdates

GUI updates, fast thresholding, and misc updates.

+ciapkg/+io/readFrame.m

@@ -1,7 +1,7 @@
 function [thisFrame,movieFileID,inputMovieDims] = readFrame(inputMoviePath,frameNo,varargin)
 	% Fast reading of frame from files on disk. This is an alternative to loadMovieList that is much faster when only a single frame needs to be read.
 	% Biafra Ahanonu
-	% started: 2020.10.19 [�‎11:45:24]
+	% started: 2020.10.19 [11:45:24]
 	% inputs
 		% inputMoviePath | Str: path to a movie. Supports TIFF, AVI, HDF5, NWB, or Inscopix ISXD.
 		% frameNo | Int: frame number.
@@ -15,6 +15,7 @@
 
 	% changelog
 		% 2021.06.30 [01:26:29] - Updated handling of no file path character input.
+		% 2021.07.03 [09:02:14] - Updated to have backup read method for different tiff styles.
 	% TODO
 		%
 
@@ -101,6 +102,14 @@
 					tiffID.setDirectory(frameNo);
 					thisFrame = read(tiffID);
 				catch
+					try
+						% thisFrame = imread(inputMoviePathHere, 'tif', 'Index', frameNo, 'Info', imgInfo);
+						thisFrame = imread(inputMoviePathHere, 'tif', 'Index', frameNo);
+					catch err
+						disp(repmat('@',1,7))
+						disp(getReport(err,'extended','hyperlinks','on'));
+						disp(repmat('@',1,7))
+					end
 					% err
 					% display(repmat('@',1,7))
 					% disp(getReport(err,'extended','hyperlinks','on'));

+ciapkg/+io/updatePkg.m

@@ -1,15 +1,18 @@
 function [success] = updatePkg(varargin)
 	% Checks ciapkg version against GitHub repo and updates `ciapkg` and `+ciapkg` folders.
 	% Biafra Ahanonu
-	% started: 2020.08.18 [‎11:16:56]
+	% started: 2020.08.18 [11:16:56]
 	% inputs
 		%
 	% outputs
 		%
+	% Notes
+		% Follows https://semver.org convention.
 
 	% changelog
 		% 2021.03.09 [21:34:52] - Option on whether to update package (only 0 for now). Also alert user if behind a version.
 		% 2021.06.21 [16:18:07] - Updated to ciatah from calciumImagingAnalysis URLs.
+		% 2021.07.06 [11:33:22] - Updated comparison to ensure ignoring of lower level versions after higher level versions are found to differ.
 	% TODO
 		% Only check once every couple of days to warn user instead of every time.
 
@@ -41,10 +44,11 @@
 	try
 		success = 0;
 
+		% Versions follow MAJOR.MINOR.PATCH convention.
 		% Get online CIAPKG version
-		[onlineVersion onlineDateTimeStr] = ciapkg.versionOnline;
+		[onlineVersion, onlineDateTimeStr] = ciapkg.versionOnline;
 		% Get local CIAPKG version
-		[currentVersion currentDateTimeStr] = ciapkg.version;
+		[currentVersion, currentDateTimeStr] = ciapkg.version;
 		% currentVersion = 'v3.19.20201021135616'
 		% currentVersion = 'v3.20.20201019131033';
 
@@ -71,7 +75,8 @@
 			else
 				onlineVersionTmp = onlineVersion;
 			end
-			verInfoStr = sprintf('%s\n Local version: %s.\n Online version %s.\n',verInfoStr2,currentVersion,onlineVersionTmp);
+			% verInfoStr = sprintf('%s\n Local version: %s.\n Online version %s.\n',verInfoStr2,currentVersion,onlineVersionTmp);
+			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.')
@@ -129,13 +134,20 @@
 		compareVector = zeros([1 max(length(verId1),length(verId2))]);
 		nLevels = length(compareVector);
 
+		% Following MAJOR.MINOR.PATCH convention
 		% Start at the highest level and only continue comparing while version 2 is greater than or equal to version 1.
 		lockOut = 0; % 1 = higher level is an old version, so only calculate version difference
 		for verLvl = 1:nLevels
 			compareVector(verLvl) = verId1(verLvl) - verId2(verLvl);
-			if compareVector(verLvl)<0 & lockOut==0 % This level indicates an old version
+			% If higher version is older or newer, lower version is irrelevant so skip.
+			if lockOut==1
+				compareVector(verLvl) = 0;
+			end
+			if compareVector(verLvl)<0 && lockOut==0 % This level indicates an old version
 				verCompare = 0;
 				lockOut = 1;
+			elseif compareVector(verLvl)>0 && lockOut==0 % This level indicates this level is a newer version
+				lockOut = 1;
 			end
 		end
 

+ciapkg/VERSION

@@ -1,2 +1,2 @@
-v3.31.3
-2021.06.30 [11:14:59]
+v3.32.1
+2021.07.06 [11:59:08]

+ciapkg/version.m

@@ -12,6 +12,7 @@
 		% 2021.01.21 [10:36:30] - Changed to use readtable instead of readcell to increase compatability across MATLAB versions.
 		% 2021.01.21 [17:03:54] - Added fscanf backup to readtable in case of Matlab compatibility issues, also specified more readtable defaults to avoid errors (Matlab 202a+ changed default behavior). Added last step backup of zero version.
 		% 2021.03.21 [17:41:54] - Update VERSION path.
+		% 2021.07.06 [11:33:22] - Updated to trim version string to make sure new line is removed.
 	% TODO
 		%
 
@@ -46,7 +47,9 @@
 			fclose(fileID);
 			verStr = strsplit(verStr,'\n');
 			versionStr = strrep(verStr{1},'\n','');
+			versionStr = strtrim(versionStr);
 			dateTimeStr = verStr{2};
+			dateTimeStr = strrep(dateTimeStr,'\n','');
 		catch err
 			versionStr = 'v0.00.0';
 			dateTimeStr = '00000000000000';

@ciatah/ciatah.m

@@ -34,7 +34,7 @@
 		% FPS of movie(s) being analyzed
 		FRAMES_PER_SECOND =  5;
 		% FPS of movie playback
-		FRAMES_PER_SECOND_PLAYBACK =  5;
+		FRAMES_PER_SECOND_PLAYBACK =  20;
 		% Int: what factor temporally are analyzed movie from raw data
 		DOWNSAMPLE_FACTOR =  4;
 		% Float: estimated um per pixel
@@ -74,7 +74,7 @@
 		concurrentAnalysisFilename = '_currentlyAnalyzingFolderCheck.mat';
 
 		% Cell array strings: List of methods to fast track folder to analyze dialog or skip altogether
-		methodExcludeList = {'showVars','showFolders','setMainSettings','modelAddNewFolders','loadDependencies','saveObj','setStimulusSettings','modelDownsampleRawMovies','setMovieInfo','setup','update'};
+		methodExcludeList = {'showVars','showFolders','setMainSettings','loadDependencies','saveObj','setStimulusSettings','modelDownsampleRawMovies','setMovieInfo','setup','update'};
 		methodExcludeListVer2 = {'modelEditStimTable','behaviorProtocolLoad','modelPreprocessMovie','modelModifyMovies','removeConcurrentAnalysisFiles'};
 		methodExcludeListStimuli = {'modelVarsFromFiles'};