Merge pull request #106 from bahanonu/bahanonu/functionUpdates

Update README and misc CIAtah methods

+ciapkg/+download/downloadCnmfGithubRepositories.m

@@ -6,9 +6,10 @@
 		% 2020.04.03 [14:02:33] - Save downloaded compressed files (e.g. zips) to a sub-folder.
 		% 2020.06.28 [13:08:16] - Final implementation of force update, to bring to most current version of all git directories.
 		% 2020.06.28 [14:01:17] - Switch to calling downloadGithubRepositories for downloads to prevent bugs introduced by similar code between two functions.
-		% 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.
 		% 2021.08.08 [19:30:20] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
 		% 2021.12.01 [20:09:10] - Update display of information if CVX is not automatically found.
+		% 2022.04.08 [15:37:36] - Download CVX from a custom URL since the main URL sometimes has a long response time, leading to timeouts.
 
 	import ciapkg.api.* % import CIAtah functions in ciapkg package API.
 
@@ -31,7 +32,12 @@
 		signalExtractionDir = options.defaultExternalProgramDir;
 
 		gitNameDisp = {'CNMF-E','CNMF | CaImAn','cvx-rd'};
-		gitRepos = {'https://github.com/bahanonu/CNMF_E/archive/master.zip','https://github.com/flatironinstitute/CaImAn-MATLAB/archive/master.zip','http://web.cvxr.com/cvx/cvx-rd.zip'};
+		gitRepos = {...
+			'https://github.com/bahanonu/CNMF_E/archive/master.zip';
+			'https://github.com/flatironinstitute/CaImAn-MATLAB/archive/master.zip';
+			'http://tiny.ucsf.edu/YR4gfF';
+			};
+			% 'http://web.cvxr.com/cvx/cvx-rd.zip';
 		outputDir = {'cnmfe','cnmf_current','cvx_rd'};
 		gitName = {'CNMF_E-master','CaImAn-MATLAB-master','cvx'};
 		nRepos = length(outputDir);

+ciapkg/VERSION

@@ -1,2 +1,2 @@
-v4.2.0
-2022.03.01 [04:18:22]
+v4.4.2
+2022.06.27 [13:51:31]

@ciatah/initializeObj.m

@@ -11,6 +11,7 @@
 		% 2020.06.05 [11:29:24] - Improved toolbox check.
 		% 2021.08.10 [09:57:36] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
 		% 2021.11.16 [11:13:07] - Wrap calls to diverging_map to avoid potential ciatah initialization errors on macOS.
+		% 2022.06.27 [12:48:22] - Ensure all save paths (pics, data, log, settings, video, etc.) use absolute CIAtah private directory to match CIAtah default properties initialization and to avoid instances where users have non-CIAtah root path working directory.
 	% TODO
 		%
 
@@ -47,11 +48,11 @@
 	disp(repmat('*',1,42))
 
 	% Ensure date paths are up to date
-	obj.picsSavePath = ['private' filesep 'pics' filesep datestr(now,'yyyymmdd','local') filesep];
-	obj.dataSavePath = ['private' filesep 'data' filesep datestr(now,'yyyymmdd','local') filesep];
-	obj.logSavePath = ['private' filesep 'logs' filesep datestr(now,'yyyymmdd','local') filesep];
-	obj.settingsSavePath = ['private' filesep 'settings'];
-	obj.videoSaveDir = ['private' filesep 'vids' filesep datestr(now,'yyyymmdd','local') filesep];
+	obj.picsSavePath = [ciapkg.getDir() filesep 'private' filesep 'pics' filesep datestr(now,'yyyymmdd','local') filesep];
+	obj.dataSavePath = [ciapkg.getDir() filesep 'private' filesep 'data' filesep datestr(now,'yyyymmdd','local') filesep];
+	obj.logSavePath = [ciapkg.getDir() filesep 'private' filesep 'logs' filesep datestr(now,'yyyymmdd','local') filesep];
+	obj.settingsSavePath = [ciapkg.getDir() filesep 'private' filesep 'settings'];
+	obj.videoSaveDir = [ciapkg.getDir() filesep 'private' filesep 'vids' filesep datestr(now,'yyyymmdd','local') filesep];
 
 	% ensure private folders are set
 	if ~exist(obj.picsSavePath,'dir');mkdir(obj.picsSavePath);fprintf('Creating directory: %s\n',obj.picsSavePath);end

@ciatah/modelExtractSignalsFromMovie.m

@@ -20,7 +20,7 @@
 		% 2019.10.29 [17:21:23] - Added a check to make sure that filenames produced are valid MATLAB ones for settings, e.g. for CNMF-e.
 		% 2019.11.10 [20:34:42] - Add a warning with some common tips for users if error during cell extraction. Skip modelVarsFromFiles and viewObjmaps loading to reduce user confusion for any folders that had issues during cell extraction.
 		% 2020.05.08 [20:01:52] - Make creation of settings an explicit option that the user can change.
-		% 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.
 		% 2021.02.25 [16:44:41] - Update `saveRunTimes` to handle case in which user selects multiple movies for cell extraction.
 		% 2021.03.20 [19:23:25] - Convert ndSparse outputs to single from cell-extraction algorithms (e.g. for CELLMax/EXTRACT) when saving as NWB. Updated EXTRACT support to include additional options.
 		% 2021.04.08 [16:23:20] - Use filesep in getAlgorithmRootPath to avoid issues in Unix-based systems.
@@ -29,6 +29,7 @@
 		% 2021.08.10 [09:57:36] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
 		% 2021.11.08 [12:42:12] - Add nwbpkg support.
 		% 2021.11.09 [15:29:01] - Updated EXTRACT support.
+		% 2022.06.27 [15:33:57] - matlab.desktop.editor.openDocument no longer uses pwd since options.settingsPrivateSaveFolder is based on an absolute path.
 	% TODO
 		%
 
@@ -1041,7 +1042,7 @@ function getAlgorithmOptions()
 						end
 						fclose(fileID);
 
-						h1 = matlab.desktop.editor.openDocument([pwd filesep newSettings]);
+						h1 = matlab.desktop.editor.openDocument([newSettings]);
 						disp(['Close "' newFile '.m" file in Editor to continue!'])
 						% pause while user edits
 						while h1.Opened==1;end

@ciatah/modelSaveMatchObjBtwnTrials.m

@@ -10,6 +10,7 @@
 	% changelog
 		% 2020.06.29 [19:28:33] - Updated implementation.
 		% 2021.08.10 [09:57:36] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
+		% 2022.06.27 [19:25:42] - Remove user selecting folder to save structure to and add additional instructions.
 	% TODO
 		%
 
@@ -29,22 +30,28 @@
 	%========================
 
 	try
-		disp('Method not implemented!')
+		% disp('Method not implemented!')
 
-		[filePath,folderPath,~] = uiputfile('*.*','select folder to save object mat file to','calciumImagingAnalysis_properties.mat');
+		% [filePath,folderPath,~] = uiputfile('*.*','select folder to save object mat file to','calciumImagingAnalysis_properties.mat');
 		% exit if user picks nothing
 		% if folderListInfo==0; return; end
-		savePath = [folderPath filesep filePath];
+		% savePath = [folderPath filesep filePath];
 
+		disp('Saving MAT-file for each subject (animal) containing structure. Global ID matrix [globalID sessionID] is found in <strong>alignmentStruct</strong> variable and fieldname <strong>alignmentStruct.globalIDs</strong>.')
+		disp('See additional details at <a href="https://bahanonu.github.io/ciatah/pipeline_detailed_cross_session/#output-of-computematchobjbtwntrials">https://bahanonu.github.io/ciatah/pipeline_detailed_cross_session/#output-of-computematchobjbtwntrials</a>.')
 		subjList = fieldnames(obj.globalIDStruct);
 		for subjNo = 1:length(subjList)
+			display(repmat('=',1,7))
 			thisSubjectStr = subjList{subjNo};
 			alignmentStruct = obj.globalIDStruct.(thisSubjectStr);
 
-			structSavePath = [obj.dataSavePath filesep 'ciapkg_crossSessionAlignment_' thisSubjectStr '_' datestr(now,'yyyymmdd_HHMMSS','local') '.mat'];
+			fprintf('Saving cross-session alignment for subject/animal: <strong>%s</strong>.\n',thisSubjectStr);
+			saveFileName = ['ciapkg_crossSessionAlignment_' thisSubjectStr '_' datestr(now,'yyyymmdd_HHMMSS','local') '.mat'];
+			structSavePath = fullfile(obj.dataSavePath,saveFileName);
 			fprintf('Saving to: %s\n',structSavePath)
 			save(structSavePath,'alignmentStruct','-v7.3');
 		end
+
 	catch err
 		display(repmat('@',1,7))
 		disp(getReport(err,'extended','hyperlinks','on'));

README.md

@@ -25,6 +25,9 @@
 
 Below are recordings and additional documents for users who want to learn more about calcium imaging analysis/experiments and the CIAtah pipeline.
 
+<ins> __Book chapter__ </ins> — We have a book chapter that goes over all steps of miniscope imaging: viral injections, GRIN lens probe implant, pain experimental design, data processing and neural/behavioral analysis, and more.
+- See [Ahanonu, B., Corder, G. (2022). _Recording Pain-Related Brain Activity in Behaving Animals Using Calcium Imaging and Miniature Microscopes_](https://doi.org/10.1007/978-1-0716-2039-7_13) (https://doi.org/10.1007/978-1-0716-2039-7_13).
+
 <ins>__Webinar__</ins> — This webinar gives an overview of calcium imaging analysis (with a focus on CIAtah) along with tips for improving experiments and analysis: https://info.inscopix.com/inscopix-inspire-view-webinarbiafra-ahanonu-signal-in-the-noise-distinguishing-relevant-neural-activity-in-calcium-imaging.
 
 <ins>__Workshop tutorial__</ins> — This recording gives an overview of setting up and using CIAtah: https://www.youtube.com/watch?v=I6abW3uuJJw.
@@ -66,6 +69,7 @@ Made in USA.<br>
 - Includes all major calcium imaging analysis steps:
   - Movie visualization (including reading from disk, for fast viewing of large movies);
   - pre-processing (motion correction, spatiotemporal downsampling, spatial filtering, relative fluorescence calculation, etc.);
+   <!-- - Pre-processing supports read-from-disk based analysis for movies that are too large to fit into RAM. -->
   - support for multiple cell-extraction methods (CELLMax, PCA-ICA, <a href='https://github.com/flatironinstitute/CaImAn-MATLAB' target='_blank'>CNMF</a>, CNMF-E, <a href='https://github.com/schnitzer-lab/EXTRACT-public' target='_blank'>EXTRACT</a>, etc.);
   - manual classification of cells via GUIs;
   - automated cell classification (i.e. CLEAN algorithm, coming soon!);
@@ -161,6 +165,12 @@ ciapkg.io.matlabToolboxCheck();
 
 ### Setup `CIAtah`
 
+- Download and install `CIAtah` dependencies. These will all be located in the `_external_programs` sub-folder within the CIAtah main code directory.
+
+```MATLAB
+ciapkg.io.loadDependencies;
+```
+
 - Run `CIAtah` using the below MATLAB commands. Call `obj;` in the MATLAB command window each time you want to go back to the main GUI. __Note: `calciumImagingAnalysis` class is now called `ciatah`, all functionality is the same.__
 
 ```MATLAB
@@ -245,6 +255,19 @@ Please cite [Corder*, Ahanonu*, et al. 2019](http://science.sciencemag.org/conte
 }
 ```
 
+Please cite the [Ahanonu and Corder, 2022](https://doi.org/10.1007/978-1-0716-2039-7_13) book chapter if you used procedures detailed therein.
+
+```bibtex
+@incollection{ahanonu2022recording,
+  title={Recording Pain-Related Brain Activity in Behaving Animals Using Calcium Imaging and Miniature Microscopes},
+  author={Ahanonu, Biafra and Corder, Gregory},
+  booktitle={Contemporary Approaches to the Study of Pain},
+  pages={217--276},
+  year={2022},
+  publisher={Springer}
+}
+```
+
 Please see https://bahanonu.github.io/ciatah/references/ for additional references depending on processing steps undertaken.
 
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@@ -274,4 +297,6 @@ This project is licensed under the terms of the MIT license. See LICENSE file fo
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