Cleaned up inputs and improved functionality

Derivatives folder now follows BIDS pipeline folders.

data_functions/bidsFilename.m

@@ -1,65 +1,145 @@
-function [filename, folder] = bidsFilename(bids,description,type,derivative,detailedFile,bidsCategory)
+function [filename, folder] = bidsFilename(bids,cfg)
 % Function to create a BIDS style filename. It is useful for saving and
 % loading data. Use as:
-% Usual bids info as structure containing strings
+% Usual bids info as structure containing strings:
 % bids.sub		= 'pilot01';
 % bids.ses		= '002';
 % bids.run		= '003';
 % bids.task		= 'oddball';
 % bids.directory	= 'D:\data\MyBidsStudy'; % Folder must exist already
-% description		= 'test'; % Describe the file. e.g. 'freqData'
-% type			= '.mat'; % Usually a .mat
-% derivative		= true; % Place in derivative folder or main folder?
-% detailedFilename	= true; % Include ses,run,task info in filename?
-% bidsCategory		= true; % Can be empty, or 'meg'/'mot'/'beh' etc. It will
-%						reference the appropriate sub-folder, including ses.
 %
+% Config for variations on BIDS format:
+% cfg.category		= 'meg'; % BIDS category. If derivative, this is the current pipeline.
+% cfg.description	= 'test'; % Describe the file. e.g. 'freqData' or 'meg'.
+% cfg.type			= '.mat'; % File type or '.bin'. Default '.mat'.
+% cfg.derivative	= true; % or false. Reference derivative folder?
+% cfg.detailed		= true; % or false. Include ses/task/run info?
+% If cfg is empty, or not enough info is provided only a folder will be output
+% 
 % Author: Nicholas Alexander, [email protected]
 
+%% Check input
+% cfg
+folderOnly = false;
+if ~isstruct(cfg)
+	disp('cfg is empty. Only providing folder output.');
+	folderOnly = true;
+end
+if folderOnly
+	cfg.category = 'folderOnly';
+elseif	(~isfield(cfg,'category') || isempty(cfg.category))
+	disp('cfg.category not provided. Only returning folder output');
+	cfg.category = 'folderOnly';
+	folderOnly = true;
+end
+if folderOnly
+	cfg.description = 'folderOnly';
+elseif (~isfield(cfg,'description') || isempty(cfg.description))
+	disp('cfg.description is empty. Only returning folder output.')
+	cfg.description = 'folderOnly';
+	folderOnly = true;
+end
+if (~folderOnly && (~isfield(cfg,'type') || isempty(cfg.type)))
+	disp('Defaulting cfg.type to .mat')
+	cfg.type = '.mat';
+end
+if (~isfield(cfg,'derivative') || isempty(cfg.derivative))
+	disp('Defaulting cfg.derivative to true');
+	cfg.derivative = true;
+end
+if (~folderOnly && (~isfield(cfg,'detailed') || isempty(cfg.detailed)))
+	disp('Defaulting cfg.detailed to false');
+	cfg.detailed = false;
+end
+
+% bids
+if ~isstruct(bids)
+	error('bids is empty. Please provide at least bids.directory and bids.sub');
+elseif ((~isfield(bids,'directory') || isempty(bids.directory)) || (~isfield(bids,'sub') || isempty(bids.sub)))
+	error('Please provide both bids.directory and bids.sub');
+end
+
+if (~isfield(bids,'ses') || isempty(bids.ses))
+	cfg.detailed = false;
+	if ~cfg.derivative
+		error("Must provide bids.ses if cfg.derivative = false.")
+	end
+end
+if (~isfield(bids,'task') || isempty(bids.task))
+	cfg.detailed = false;
+end
+if (~isfield(bids,'run') || isempty(bids.run))
+	cfg.detailed = false;
+end
+
+%% Produce output filename
 % Check if the initial directory exists. 
 if isfolder(bids.directory)
 	% Check the backslash at the end
 	if bids.directory(end) ~= '\'
 		bids.directory = strcat(bids.directory,'\');
 	end
 	% If using the derivative folder, add that on, including sub
-	if derivative
-		if ~isempty(bidsCategory)
-			bids.directory = sprintf('%1$sderivatives\\sub-%2$s\\ses-%3$s\\%4$s\\',bids.directory,bids.sub,bids.ses,bidsCategory);
+	if cfg.derivative
+		if ~folderOnly
+			bids.directory = sprintf('%1$sderivatives\\%2$s\\sub-%3$s\\',bids.directory,cfg.category,bids.sub);
 		else
-			bids.directory = sprintf('%1$sderivatives\\sub-%2$s\\',bids.directory,bids.sub);
+			bids.directory = sprintf('%1$sderivatives\\sub-%3$s\\',bids.directory,bids.sub);
 		end
 
-
-
 		% Check that directory exists with the derivative folder
 		if ~isfolder(bids.directory)
 			warning("Creating new derivatives directory")
 			mkdir(bids.directory);
 		end
+
 	% Otherwise just add the subject folder
 	else
-		if ~isempty(bidsCategory)
-			bids.directory = sprintf('%1$ssub-%2$s\\ses-%3$s\\%4$s\\',bids.directory,bids.sub,bids.ses,bidsCategory);
+		if ~folderOnly
+			bids.directory = sprintf('%1$ssub-%2$s\\ses-%3$s\\%4$s\\',bids.directory,bids.sub,bids.ses,cfg.category);
 		else
-			bids.directory = sprintf('%1$ssub-%2$s\\',bids.directory,bids.sub);
+			bids.directory = sprintf('%1$ssub-%2$s\\ses-%3$s\\',bids.directory,bids.sub,bids.ses);
 		end
-
+
+		% This function should not interfere with the original data folder.
 		if ~isfolder(bids.directory)
-			error("Specified BIDS participant folder does not exist");
+			error("Specified BIDS folder does not exist.");
 		end
-
 	end
 else
 	error("Specified BIDS directory does not exist");
 end
 
 % Now create the filename with required detail
-if detailedFile
-	filename = sprintf('%1$ssub-%2$s_ses-%3$s_task-%4$s_run-%5$s_%6$s%7$s',bids.directory,bids.sub,bids.ses,bids.task,bids.run,description,type);
+if cfg.detailed
+	filename = sprintf('%1$ssub-%2$s_ses-%3$s_task-%4$s_run-%5$s_%6$s%7$s',bids.directory,bids.sub,bids.ses,bids.task,bids.run,cfg.description,cfg.type);
 else
-	filename = sprintf('%1$ssub-%2$s_%3$s%4$s',bids.directory,bids.sub,description,type);
+	filename = sprintf('%1$ssub-%2$s_%3$s%4$s',bids.directory,bids.sub,cfg.description,cfg.type);
 end
 
 % Get the folder separately
-[folder,~,~] = fileparts(filename);
+[folder,~,~] = fileparts(filename);
+
+% If not enough information was provided in the cfg, set filename to folder.
+if folderOnly
+	filename = folder;
+end
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