Initial MVP implementing a datastore for a common use case.

+openneuro/+datastore/Participantwise.m

@@ -0,0 +1,201 @@
+classdef Participantwise < matlab.io.Datastore
+    %PARTICIPANTWISE Summary of this class goes here
+    %   Detailed explanation goes here
+
+    properties (Constant, Hidden)
+        % Dictionary mapping type names to read settings
+        Type = containers.Map( ...
+            {'Anatomical NIfTI', 'EEG EDF', 'Functional NIfTI', 'DWI', 'Fieldmap', 'JSON Files', 'TSV Files'}, ...
+            {struct('ReadFcn', @niftiread, 'FileExtensions', {{'.nii.gz', '.nii'}}, 'FolderPath', 'anat'), ...
+            struct('ReadFcn', @edfread, 'FileExtensions', {{'.edf'}}, 'FolderPath', 'eeg'), ...
+            struct('ReadFcn', @niftiread, 'FileExtensions', {{'.nii.gz', '.nii'}}, 'FolderPath', 'func'), ...
+            struct('ReadFcn', @niftiread, 'FileExtensions', {{'.nii.gz', '.nii'}}, 'FolderPath', 'dwi'), ...
+            struct('ReadFcn', @niftiread, 'FileExtensions', {{'.nii.gz', '.nii'}}, 'FolderPath', 'fmap'), ...
+            struct('ReadFcn', @(f) jsondecode(fileread(f)), 'FileExtensions', {{'.json'}}, 'FolderPath', 'anat'), ...
+            struct('ReadFcn', @readtable, 'FileExtensions', {{'.tsv', '.txt'}}, 'FolderPath', 'anat') ...
+            } ...
+        )
+    end
+
+    properties (Dependent)
+        AvailableTypes  % List of supported type keys
+    end
+
+    properties
+        fileDatastoreObj  % Public fileDatastore object for MVP mode
+    end
+
+    properties (Access = private)
+        CurrentFileIndex    double;
+        FileSet matlab.io.datastore.DsFileSet;
+        isMVPMode           logical = false;  % Track which mode we're in
+    end
+
+    methods
+        function keys = get.AvailableTypes(obj)
+            % List available types from the Type dictionary
+            keys = obj.Type.keys;
+        end
+
+        function obj = Participantwise(dataset,spec)
+            % Constructor supporting both MVP mode and original mode
+            %
+            % MVP Mode (dictionary-based spec):
+            %   obj = Participantwise("Anatomical NIfTI")
+            %
+            % Original Mode (structure-based spec):
+            %   obj = Participantwise(dataset, filesetSpec)
+
+            if isStringScalar(spec) || (ischar(spec) && isvector(spec))
+                % MVP MODE: dictionary-based spec
+                %typeName = varargin{1};
+
+                % Validate type name against the Type dictionary using keys() method
+                if ~isKey(obj.Type, spec)
+                    error('Invalid type specified. Available types are: %s', strjoin(obj.AvailableTypes, ', '));
+                end
+
+                obj.isMVPMode = true;
+                obj = createMVPDatastore(obj, dataset, spec);
+
+            else %if nargin == 2
+                % ORIGINAL MODE: structure-based spec
+                %dataset = varargin{1};
+                filesetSpec = spec; %varargin{2};
+
+                % Validate arguments (original validation)
+                if ~isa(dataset, 'openneuro.Dataset')
+                    error('First argument must be an openneuro.Dataset object');
+                end
+                if ~isstruct(filesetSpec)
+                    error('Second argument must be a struct');
+                end
+
+                obj.isMVPMode = false;
+                obj = createOriginalDatastore(obj, dataset, filesetSpec);
+
+            % else
+            %     error('Constructor requires either 1 argument (MVP mode) or 2 arguments (original mode). Got %d arguments.', nargin);
+            end
+        end
+
+        function reset(obj)
+            % Reset to the start of the data.
+            if obj.isMVPMode && ~isempty(obj.fileDatastoreObj)
+                reset(obj.fileDatastoreObj);
+            else
+                reset(obj.FileSet);
+            end
+            obj.CurrentFileIndex = 1;
+        end
+
+        function tf = hasdata(obj)
+            % Return true if more data is available.
+            if obj.isMVPMode && ~isempty(obj.fileDatastoreObj)
+                tf = hasdata(obj.fileDatastoreObj);
+            else
+                tf = hasfile(obj.FileSet);
+            end
+        end
+
+        function [data, info] = read(obj)
+            % MVP read method - no arguments, dispatches appropriately
+            if obj.isMVPMode && ~isempty(obj.fileDatastoreObj)
+                % MVP mode: dispatch to fileDatastore.read()
+                [data, info] = read(obj.fileDatastoreObj);
+            else
+                % Original mode: use FileSet reading
+                if ~hasdata(obj)
+                    error(sprintf(['No more data to read.\nUse the reset ',...
+                        'method to reset the datastore to the start of ' ,...
+                        'the data. \nBefore calling the read method, ',...
+                        'check if data is available to read ',...
+                        'by using the hasdata method.']))
+                end
+
+                fileInfoTbl = nextfile(obj.FileSet);
+                data = MyFileReader(fileInfoTbl);
+                info.Size = size(data);
+                info.FileName = fileInfoTbl.FileName;
+                info.Offset = fileInfoTbl.Offset;
+
+                % Update CurrentFileIndex for tracking progress
+                if fileInfoTbl.Offset + fileInfoTbl.SplitSize >= ...
+                        fileInfoTbl.FileSize
+                    obj.CurrentFileIndex = obj.CurrentFileIndex + 1;
+                end
+            end
+        end
+    end
+
+    methods (Access = private)
+        function obj = createMVPDatastore(obj, dataset, typeName)
+            % Create MVP mode datastore using Type dictionary
+
+            % Get the specification for this type
+            spec = obj.Type(typeName);
+
+            % Construct fileDatastore object using the Type specification
+            %defaultPath = fullfile(pwd, "ds001415/");
+            %searchPath = fullfile(defaultPath, 'sub-01', spec.FolderPath);
+            searchPath = fullfile(dataset.URI,dataset.ParticipantIDs(1), spec.FolderPath);
+
+            try
+                obj.fileDatastoreObj = fileDatastore( ...
+                    searchPath, ...
+                    'ReadFcn', spec.ReadFcn, ...
+                    'IncludeSubfolders', true, ...
+                    'FileExtensions', spec.FileExtensions ...
+                );
+            catch e
+                warning('Failed to create MVP datastore:\n%s', getReport(e));
+                % Create empty datastore as fallback
+                obj.fileDatastoreObj = fileDatastore(pwd, 'ReadFcn', @readtable);
+                obj.fileDatastoreObj.Files = {};
+            end
+        end
+
+        function obj = createOriginalDatastore(obj, dataset, filesetSpec)
+            % Create original mode datastore (unchanged logic)
+
+            obj.FileSet = matlab.io.datastore.DsFileSet(computeLocations(dataset,filesetSpec),'FileExtensions',filesetSpec.extensionList);
+            obj.CurrentFileIndex = 1;
+            reset(obj);
+        end
+    end
+
+    methods (Access=protected)
+
+    end
+end
+
+%% LOCAL FUNCTIONS
+function data = MyFileReader(fileInfoTbl)
+% create a reader object using the FileName
+reader = matlab.io.datastore.DsFileReader(fileInfoTbl.FileName);
+
+% seek to the offset
+seek(reader,fileInfoTbl.Offset,'Origin','start-of-file');
+
+% read fileInfoTbl.SplitSize amount of data
+data = read(reader,fileInfoTbl.SplitSize);
+end
+
+
+function locations = computeLocations(dataset,filesetSpec)
+
+fs = filesetSpec;
+if all(cellfun(@isempty,{fs.sessions,fs.tasks,fs.runs},'UniformOutput',true))  % Maybe sessions is enough? Trigger an error if tasks/runs w/o sessions?
+    % "Core modality" special case
+    assert(isscalar(fs.extendedModality));
+    assert(isa(dataset,'openneuro.Dataset'));
+    locations = dataset.RootURI + "/" + string(dataset.ID) + "/" + dataset.ParticipantIDs + "/" + fs.extendedModality;
+
+else % General case (TODO; may encompass core modality special case, i.e., removing need for IF/ELSE)
+    %TODO
+end
+
+%
+% dir(b.encoding.dir + "/" + subjects{1} + "/" + sessions{1} + "/" +folders{1} + "/*" );
+
+end