[ENH] use bids matlab transformer to filter TSV

.pre-commit-config.yaml

@@ -36,7 +36,7 @@ repos:
       additional_dependencies: [miss_hit]
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
+  rev: v4.3.0
   hooks:
     - id: trailing-whitespace
     - id: end-of-file-fixer

src/readAndFilterLogfile.m

@@ -10,17 +10,25 @@
     %   outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, cfg)
     %
     % :param columnName: the header of the column where the content of interest is stored
-    %                    (for example for ``trigger`` will be ``trial type``)
-    % :type columnName: string
-    % :param filterBy: the content of the column you want to filter out. It can take just
-    %                  part of the content name (for example, if you want to display the triggers
-    %                  and you have ``trigger_motion`` and ``trigger_static``,
-    %                  ``trigger`` as input will do)
-    % :type filterBy: string
+    %                    (for example for ``trigger`` will be ``trial_type``)
+    % :type columnName: char
+    %
+    % :param filterBy: The content of the column you want to filter out.
+    %                  Relies on the ``filter`` transformer of bids.matlab
+    %                  Supports:
+    %
+    %                    - ``>``, ``<``, ``>=``, ``<=``, ``==`` for numeric values
+    %                    - ``==`` for string operation (case sensitive)
+    %
+    %                  For example, ``trial_type==trigger`` or `onset > 1`.
+    % :type filterBy: char
+    %
     % :param saveOutputTsv: flag to save the filtered output in a tsv file
     % :type saveOutputTsv: boolean
+    %
     % :param tsvFile: TSV file to filter
     % :type tsvFile: string
+    %
     % :param cfg: Configuration. See ``checkCFG()``. If ``cfg`` is given as input the name
     %             of the TSV file to read will be infered from there.
     % :type cfg: structure
@@ -30,12 +38,13 @@
     %           :outputFiltered: dataset with only the specified content, to see it
     %                            in the command window use ``display(outputFiltered)``.
     %
+    %
+    % See also: bids.transformers.filter
+    %
+    %
     % (C) Copyright 2020 CPP_BIDS developers
 
-    % Create tag to add to output file in case you want to save it
-    outputFilterTag = ['_filteredBy-' columnName '_' filterBy '.tsv'];
-
-    % Checke if input is cfg or the file path and assign the output filename for later saving
+    % Check if input is cfg or the file path and assign the output filename for later saving
     if ischar(varargin{1})
 
         tsvFile = varargin{1};
@@ -48,9 +57,6 @@
 
     end
 
-    % Create output file name
-    outputFileName = strrep(tsvFile, '.tsv', outputFilterTag);
-
     % Check if the file exists
     if ~exist(tsvFile, 'file')
         error([newline 'Input file does not exist: %s'], tsvFile);
@@ -66,19 +72,40 @@
         output = bids.util.tsvread(tsvFile);
     end
 
-    % Get the index of the target contentent to filter and display
-    filterIdx = strncmp(output.(columnName), filterBy, length(filterBy));
+    transformers{1} = struct('Name', 'Filter', ...
+                             'Input', columnName, ...
+                             'Query', filterBy);
+
+    output = bids.transformers(transformers, output);
 
-    % apply the filter
+    % remove nans
+    if isnumeric(output.(columnName))
+        rowsToRemove = isnan(output.(columnName));
+    elseif iscell(output.(columnName))
+        rowsToRemove = cellfun(@(x) numel(x) == 1 && isnan(x), ...
+                               output.(columnName));
+    end
     listFields = fieldnames(output);
     for iField = 1:numel(listFields)
-        output.(listFields{iField})(~filterIdx) = [];
+        output.(listFields{iField})(rowsToRemove) = [];
     end
 
-    outputFiltered = output;
+    % Convert the structure to dataset
+    try
+        outputFiltered = struct2dataset(output);
+    catch
+        % dataset not yet supported by octave
+        outputFiltered = output;
+    end
 
     if saveOutputTsv
 
+        % Create tag to add to output file in case you want to save it
+        outputFilterTag = ['_filteredOn-' columnName '.tsv'];
+
+        % Create output file name
+        outputFileName = strrep(tsvFile, '.tsv', outputFilterTag);
+
         bids.util.tsvwrite(outputFileName, output);
 
     end

tests/test_readAndFilterLogfile.m

@@ -8,7 +8,7 @@
     initTestSuite;
 end
 
-function test_readAndFilterLogfileBasic()
+function test_readAndFilterLogfile_basic()
 
     %% set up
     [cfg, logFile] = setUp();
@@ -52,11 +52,11 @@ function test_readAndFilterLogfileBasic()
     saveEventsFile('close', cfg, logFile);
 
     % filter file
-    outputFiltered = readAndFilterLogfile('trial_type', 'motion_down', true, cfg);
+    readAndFilterLogfile('trial_type', 'trial_type==motion_down', true, cfg);
 
     %% test
     expectedFilename = strrep(cfg.fileName.events, '.tsv', ...
-                              ['_filteredBy-' 'trial_type' '_' 'motion_down' '.tsv']);
+                              '_filteredOn-trial_type.tsv');
     expectedFile = fullfile(cfg.dir.outputSubject, ...
                             cfg.fileName.modality, ...
                             expectedFilename);
@@ -70,26 +70,30 @@ function test_readAndFilterLogfileBasic()
     assertEqual(content.trial_type{1}, 'motion_down');
     assertEqual(content.trial_type{2}, 'motion_down');
 
+    delete(expectedFile);
+
 end
 
-function test_readAndFilterLogfileFromFile()
+function test_readAndFilterLogfile_from_file()
 
     %% set up
 
     inputFile = fullfile(fileparts(mfilename('fullpath')), 'testData', ...
                          'sub-blind01_ses-01_task-vislocalizer_events.tsv');
 
     % filter file
-    outputFiltered = readAndFilterLogfile('trial_type', 'VisStat', true, inputFile);
+    readAndFilterLogfile('trial_type', 'trial_type==VisStat', true, inputFile);
 
     %% test
     expectedFile = strrep(inputFile, '.tsv', ...
-                          ['_filteredBy-' 'trial_type' '_' 'VisStat' '.tsv']);
+                          '_filteredOn-trial_type.tsv');
 
     assertEqual(exist(expectedFile, 'file'), 2);
 
     content = bids.util.tsvread(expectedFile);
 
     assertEqual(content.trial_type{1}, 'VisStat');
 
+    delete(expectedFile);
+
 end

tests/utils/isOctave.m

@@ -0,0 +1,20 @@
+function retval = isOctave()
+    %
+    % Returns true if the environment is Octave.
+    %
+    % USAGE::
+    %
+    %   retval = isOctave()
+    %
+    % :returns: :retval: (boolean)
+    %
+    % (C) Copyright 2022 CPP_BIDS developers
+
+    persistent cacheval   % speeds up repeated calls
+
+    if isempty (cacheval)
+        cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
+    end
+
+    retval = cacheval;
+end