Create bids_validate_file.m

matlab_wrapper/bids_validate_file.m

@@ -0,0 +1,66 @@
+function results = bids_validate_file(filepaths)
+
+% this is a Matlab wrapper that calls the BIDS validator python version to validate a file
+% make sure this is installed in your python environment: python -m pip install bids_validator
+% 
+% INPUT:
+% filepaths can be a string array: ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.json"]
+% filepaths can be a cell array:   {"/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.json"}
+% filepaths can be a single file:  "/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz"
+%
+% OUTPUT:
+% returns a logical array indicating whether each file is BIDS-compliant
+%
+% Cyril Pernet 08-10-2025
+
+    % Check if Python is available
+    try
+        pyenv;
+    catch
+        error('Python environment not available. Please configure Python for MATLAB using pyenv.');
+    end
+
+    % Ensure filepaths is a cell array
+    if ischar(filepaths)
+        % Single character string
+        filepaths = {filepaths};
+    elseif isstring(filepaths)
+        % String array - convert to cell array
+        filepaths = cellstr(filepaths);
+    elseif iscell(filepaths)
+        % Already a cell array - ensure all elements are char
+        filepaths = cellfun(@char, filepaths, 'UniformOutput', false);
+    else
+        error('filepaths must be a char, string array, or cell array of filenames');
+    end
+
+    % Initialize results array
+    results = false(length(filepaths), 1);
+
+    try
+        % Import and initialize the BIDS validator
+        pyrun("from bids_validator import BIDSValidator");
+        pyrun("validator = BIDSValidator()");
+
+        % Validate each file
+        for i = 1:length(filepaths)
+            filepath = filepaths{i};
+
+            % Use pyrun to call the validator
+            result = pyrun("result = validator.is_bids(filepath)", "result", filepath=filepath);
+            results(i) = logical(result);
+
+            % Display result
+            fprintf('File: %s -> BIDS valid: %s\n', filepath, string(results(i)));
+        end
+
+    catch ME
+        if contains(ME.message, 'bids_validator')
+            error(['BIDS validator not found. Please install it using:\n' ...
+                   'python -m pip install bids_validator\n' ...
+                   'Original error: %s'], ME.message);
+        else
+            rethrow(ME);
+        end
+    end
+