Merge pull request #90 from bahanonu/bahanonu/functionUpdates

CIAtah 4.0 and NWB compatibility updates, remove unused File Exchange, etc.

+ciapkg/+api/loadNeurodataWithoutBorders.m

@@ -10,5 +10,5 @@
 		% infoStruct - contains information about the file, e.g. the 'description' property that can contain information about the algorithm.
 		% algorithmStr - String of the algorithm name.
 
-	[inputImages,inputTraces,infoStruct, algorithmStr] = ciapkg.io.loadNeurodataWithoutBorders(inputFilePath,'passArgs', varargin);
+	[inputImages,inputTraces,infoStruct, algorithmStr] = ciapkg.nwb.loadNeurodataWithoutBorders(inputFilePath,'passArgs', varargin);
 end

+ciapkg/+api/saveNeurodataWithoutBorders.m

@@ -21,5 +21,5 @@
 	% TODO
 		%
 
-	[success] = ciapkg.io.saveNeurodataWithoutBorders(image_masks,roi_response_data,algorithm,outputFilePath,'passArgs', varargin);
+	[success] = ciapkg.nwb.saveNeurodataWithoutBorders(image_masks,roi_response_data,algorithm,outputFilePath,'passArgs', varargin);
 end

+ciapkg/+api/saveNwbMovie.m

@@ -0,0 +1,16 @@
+function [success] = saveNwbMovie(inputData,fileSavePath,varargin)
+	% Saves input matrix into NWB format output file.
+	% Biafra Ahanonu
+	% started: 2020.05.28 [09:51:52]
+	% inputs
+		%
+	% outputs
+		%
+
+	% changelog
+		%
+	% TODO
+		% Add structure that allows users to modify defaults for all the NWB settings
+
+	[success] = ciapkg.nwb.saveNwbMovie(inputData,fileSavePath,'passArgs', varargin);
+end

+ciapkg/+api/setupNwb.m

@@ -0,0 +1,17 @@
+function [success] = setupNwb(varargin)
+	% Checks that NWB code is present and setup correctly.
+	% Biafra Ahanonu
+	% started: 2021.01.24 [14:31:24]
+	% inputs
+		%
+	% outputs
+		%
+
+	% changelog
+		% 2021.02.01 [‏‎15:19:40] - Update `_external_programs` to call ciapkg.getDirExternalPrograms() to standardize call across all functions.
+		% 2021.03.26 [06:27:48] - Fix for options.defaultObjDir leading to incorrect NWB folder and cores not being generated.
+	% TODO
+		%
+
+	[success] = ciapkg.nwb.setupNwb('passArgs', varargin);
+end

+ciapkg/+io/loadDependencies.m

@@ -35,7 +35,7 @@ function loadDependencies(varargin)
 
 	options.dispStr = {'Download Turboreg (motion correction)','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 7];
+	options.depIdxArray = [1 2 3 4 5 6 7 8];
 	% Binary: 1 = force update even if already downloaded. 0 = skip if already downloaded
 	options.forceUpdate = 0;
 	% get options
@@ -146,19 +146,21 @@ function loadDependencies(varargin)
 			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'};
-
+				optionsH.gitNameDisp = {'nwbpkg','yamlmatlab','matnwb'};
+				optionsH.gitRepos = {'https://github.com/schnitzer-lab/nwbpkg','https://github.com/ewiger/yamlmatlab'};
 				% 'https://github.com/NeurodataWithoutBorders/matnwb'
 				optionsH.gitRepos = cellfun(@(x) [x '/archive/master.zip'],optionsH.gitRepos,'UniformOutput',false);
+
+                % Add matnwb
 				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;
+				ciapkg.nwb.setupNwb('checkDependencies',0);
 				% obj.loadBatchFunctionFolders;
 			case 'downloadBioFormats'
 				optionsH.forceUpdate = forceUpdate;

+ciapkg/+io/loadNeurodataWithoutBorders.m → +ciapkg/+nwb/loadNeurodataWithoutBorders.m

@@ -1,5 +1,5 @@
 function [inputImages,inputTraces,infoStruct, algorithmStr] = loadNeurodataWithoutBorders(inputFilePath,varargin)
-	% DESCRIPTION.
+	% Load NWB file containing cell-extraction data.
 	% Biafra Ahanonu
 	% started: 2020.04.04 [15:02:22]
 	% inputs
@@ -47,6 +47,9 @@
 	%========================
 
 	try
+		% Check that NWB code is downloaded and setup.
+		ciapkg.api.setupNwb('checkDependencies',1);
+
 		inputImages = [];
 		inputTraces = [];
 		infoStruct = struct;

+ciapkg/+io/saveNeurodataWithoutBorders.m → +ciapkg/+nwb/saveNeurodataWithoutBorders.m

@@ -19,14 +19,15 @@
 		% 2021.02.03 [12:34:06] - Added a check for inputs with a single signal and function returns as it is not supported.
 		% 2021.03.20 [19:35:28] - Update to checking if only a single signal input.
 		% 2021.08.08 [19:30:20] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
+		% 2021.11.08 [11:52:13] - Added nwbpkg support.
 	% TODO
 		%
 
 	import ciapkg.api.* % import CIAtah functions in ciapkg package API.
 
 	%========================
 	% DESCRIPTION
-	options.fpathYML = [ciapkg.getDirExternalPrograms() filesep 'nwb_schnitzer_lab' filesep 'ExampleMetadata.yml'];
+	options.fpathYML = [ciapkg.getDirExternalPrograms() filesep 'nwbpkg' filesep '+nwbpkg' filesep 'ExampleMetadata.yml'];
 	% get options
 	options = getOptions(options,varargin);
 	% display(options)
@@ -39,37 +40,11 @@
 
 	success = 0;
 
-	try
-		% Check that all necessary files are loaded
-		loadDependenciesFlag = 0;
-		if length(which('yaml.ReadYaml'))==0
-			disp('yaml not loaded, loading now...')
-			loadDependenciesFlag = 1;
-		end
-		if length(which('get_input_args'))==0
-			disp('matnwb not loaded, loading now...')
-			loadDependenciesFlag = 1;
-		end
-		if length(which('add_processed_ophys'))==0
-			disp('nwb_schnitzer_lab not loaded, loading now...')
-			loadDependenciesFlag = 1;
-		end
-		if loadDependenciesFlag==1
-			ciapkg.io.loadDependencies(...
-				'guiEnabled',0,...
-				'depIdxArray',5,...
-				'forceUpdate',0);
-				% 'dependencyStr','downloadNeuroDataWithoutBorders',...
-				% 'dispStr','Download NWB (NeuroDataWithoutBorders)',...
-			ciapkg.loadDirs;
-		end
-	catch err
-		disp(repmat('@',1,7))
-		disp(getReport(err,'extended','hyperlinks','on'));
-		disp(repmat('@',1,7))
-	end
 
 	try
+		% Check that NWB code is downloaded and setup.
+		ciapkg.api.setupNwb('checkDependencies',1);
+
 		metadata = yaml.ReadYaml(options.fpathYML);
 		data_path = outputFilePath;
 
@@ -119,15 +94,15 @@
 		    roi_response_data.(['ROI_' num2str(i)]) = tmpData{i};
 		end
 
-		nwbfile_input_args = get_input_args(metadata, 'NWBFile');
+		nwbfile_input_args = nwbpkg.get_input_args(metadata, 'NWBFile');
 		% Convert to ISO 8601 format
 		nwbfile_input_args{4} = datestr(nwbfile_input_args{4}, 'yyyy-mm-dd HH:MM:SS');
 		nwb = NwbFile(nwbfile_input_args{:});
 
-		subject_input_args = get_input_args(metadata, 'Subject');
+		subject_input_args = nwbpkg.get_input_args(metadata, 'Subject');
 		nwb.general_subject = types.core.Subject(subject_input_args{:});
 
-		nwb = add_processed_ophys(nwb, metadata, image_masks, roi_response_data,data_type);
+		nwb = nwbpkg.add_processed_ophys(nwb, metadata, image_masks, roi_response_data,data_type);
 
 		% Remove previous file if it already exists
 		if exist(outputFilePath,'file')==2

+ciapkg/+nwb/saveNwbMovie.m

@@ -1,5 +1,5 @@
-function [output1,output2] = saveNwbMovie(inputData,fileSavePath,varargin)
-	% Saves input matrix into NWB format
+function [success] = saveNwbMovie(inputData,fileSavePath,varargin)
+	% Saves input matrix into NWB format output file.
 	% Biafra Ahanonu
 	% started: 2020.05.28 [09:51:52]
 	% inputs
@@ -8,10 +8,12 @@
 		%
 
 	% changelog
-		%
+		% 2021.08.10 [09:57:36] - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
 	% TODO
 		% Add structure that allows users to modify defaults for all the NWB settings
 
+	import ciapkg.api.* % import CIAtah functions in ciapkg package API.
+
 	%========================
 	% old way of saving, only temporary until full switch
 	options.datasetname = '/1';
@@ -42,6 +44,11 @@
 	%========================
 
 	try
+		success = 0;
+
+		% Check that NWB code is downloaded and setup.
+		ciapkg.api.setupNwb('checkDependencies',1);
+
 		if strcmp(options.writeMode,'new')
 			if exist(fileSavePath,'file')==2
 				fprintf('Deleting: %s.\n',fileSavePath)
@@ -151,6 +158,8 @@
 			end
 		end
 
+		success = 1;
+
 	catch err
 		disp(repmat('@',1,7))
 		disp(getReport(err,'extended','hyperlinks','on'));

+ciapkg/+nwb/setupNwb.m

@@ -1,7 +1,7 @@
 function [success] = setupNwb(varargin)
-	% DESCRIPTION.
+	% Checks that NWB code is present and setup correctly.
 	% Biafra Ahanonu
-	% started: INSERT_DATE
+	% started: 2021.01.24 [14:31:24]
 	% inputs
 		%
 	% outputs
@@ -10,6 +10,8 @@
 	% changelog
 		% 2021.02.01 [‏‎15:19:40] - Update `_external_programs` to call ciapkg.getDirExternalPrograms() to standardize call across all functions.
 		% 2021.03.26 [06:27:48] - Fix for options.defaultObjDir leading to incorrect NWB folder and cores not being generated.
+		% 2021.11.07 [16:13:44] - Update to include check for each of the NWB dependencies taken from saveNeurodataWithoutBorders.
+		% 2021.11.08 [11:52:13] - Added nwbpkg support.
 	% TODO
 		%
 
@@ -20,8 +22,10 @@
 	options.externalProgramsDir = ciapkg.getDirExternalPrograms();
 	% Str: default path for MatNWB Matlab code
 	options.matnwbDir = 'matnwb';
+	% Binary: 0 = skip the first check to prevent infinite loop during initial package setup
+	options.checkDependencies = 0;
 	% get options
-	options = getOptions(options,varargin);
+	options = ciapkg.api.getOptions(options,varargin);
 	% display(options)
 	% unpack options into current workspace
 	% fn=fieldnames(options);
@@ -32,6 +36,40 @@
 
 	try
 		success = 0;
+		try
+			if options.checkDependencies==1
+				% Check that all necessary files are loaded
+				loadDependenciesFlag = 0;
+				if length(which('yaml.ReadYaml'))==0
+					disp('yaml not loaded, loading now...')
+					loadDependenciesFlag = 1;
+				end
+				if length(which('NwbFile'))==0
+					disp('matnwb not loaded, loading now...')
+					loadDependenciesFlag = 1;
+				end
+				if length(which('nwbpkg.add_processed_ophys'))==0
+					disp('nwb_schnitzer_lab not loaded, loading now...')
+					loadDependenciesFlag = 1;
+				end
+				if loadDependenciesFlag==1&options.checkDependencies==1
+					ciapkg.io.loadDependencies(...
+						'guiEnabled',0,...
+						'depIdxArray',5,...
+						'forceUpdate',0);
+						% 'dependencyStr','downloadNeuroDataWithoutBorders',...
+						% 'dispStr','Download NWB (NeuroDataWithoutBorders)',...
+					ciapkg.loadDirs;
+				else
+					disp('NWB dependencies loaded.')
+				end
+			end
+		catch err
+			disp(repmat('@',1,7))
+			disp(getReport(err,'extended','hyperlinks','on'));
+			disp(repmat('@',1,7))
+		end
+
 		% Load NWB Schema as needed
 		if exist('types.core.Image')==0
 			try

+ciapkg/VERSION

@@ -1,2 +1,2 @@
-v4.0.0
-2021.08.10 [12:54:03]
+v4.0.2
+2021.11.09 [19:55:19]