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Remi-GauRemi-Gau
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Merge pull request #104 from marcobarilari/marco_add-update-filter-func
add option to save a tsv filtered event file
2 parents faf45ad + b0db59c commit 26cd875

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+187
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lines changed

‎.gitignore‎

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@@ -7,13 +7,14 @@
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# exclude content of logfiles folders
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*output*
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*.tsv
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*.mat
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# exclude temp files from tests and coverage
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*test_code_report.txt
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*coverage*
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*filteredBy*
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tests/*.nii*
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tests/*.json*
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tests/*.tsv*

‎lib/bids-matlab‎

‎src/readAndFilterLogfile.m‎

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% (C) Copyright 2020 CPP_BIDS developers
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function outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, varargin)
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% outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, varargin)
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%
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% It will display in the command window the content of the `output.tsv' filtered by one element
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% of a target column.
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%
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% INPUT:
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%
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% - columnName: string, the header of the column where the content of insterest is stored
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% (e.g., for 'trigger' will be 'trial type')
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% - filterBy: string, the content of the column you want to filter out. It can take just
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% part of the content name (e.g., you want to display the triggers and you have
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% 'trigger_motion' and 'trigger_static', 'trigger' as input will do)
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% - saveOutputTsv: boolean to save the filtered ouput
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% - varargin: either cfg (to display the last run output) or the file path as string
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%
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% OUTPUT:
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%
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% - outputFiltered: dataset with only the specified content, to see it in the command window
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% use display(outputFiltered)
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% Create tag to add to output file in case you want to save it
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outputFilterTag = ['_filteredBy-' columnName '_' filterBy '.tsv'];
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% Checke if input is cfg or the file path and assign the output filename for later saving
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if ischar(varargin{1})
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tsvFile = varargin{1};
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elseif isstruct(varargin{1})
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tsvFile = fullfile(varargin{1}.dir.outputSubject, ...
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varargin{1}.fileName.modality, ...
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varargin{1}.fileName.events);
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end
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% Create output file name
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outputFileName = strrep(tsvFile, '.tsv', outputFilterTag);
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% Check if the file exists
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if ~exist(tsvFile, 'file')
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error([newline 'Input file does not exist: %s'], tsvFile);
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end
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try
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% Read the the tsv file and store each column in a field of `output` structure
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output = bids.util.tsvread(tsvFile);
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catch
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% Add the 'bids-matlab' in case is not in the path
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addpath(genpath(fullfile(pwd, '..', 'lib')));
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% Read the the tsv file and store each column in a field of `output` structure
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output = bids.util.tsvread(tsvFile);
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end
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% Get the index of the target contentent to filter and display
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filterIdx = strncmp(output.(columnName), filterBy, length(filterBy));
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% apply the filter
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listFields = fieldnames(output);
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for iField = 1:numel(listFields)
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output.(listFields{iField})(~filterIdx) = [];
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end
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% Convert the structure to dataset
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try
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outputFiltered = struct2dataset(output);
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catch
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% dataset not yet supported by octave
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outputFiltered = output;
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end
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if saveOutputTsv
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bids.util.tsvwrite(outputFileName, output);
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end
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end

‎src/subfun/utilsForTests/setUp.m‎

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% (C) Copyright 2020 CPP_BIDS developers
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function [cfg, logFile] = setUp()
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outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
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cfg.verbose = true;
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cfg.subject.subjectNb = 1;
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cfg.subject.runNb = 1;
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cfg.task.name = 'testtask';
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cfg.dir.output = outputDir;
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cfg.testingDevice = 'mri';
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cfg = createFilename(cfg);
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logFile.extraColumns.Speed.length = 1;
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logFile.extraColumns.LHL24.length = 12;
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logFile.extraColumns.is_Fixation.length = 1;
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end

‎tests/dummyData/sub-blind01_ses-01_task-vislocalizer_events.tsv‎

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onset duration trial_type
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2 15 VisMot
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25 15 VisStat

‎tests/test_readAndFilterLogfile.m‎

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function test_suite = test_readAndFilterLogfile %#ok<*STOUT>
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try % assignment of 'localfunctions' is necessary in Matlab >= 2016
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test_functions = localfunctions(); %#ok<*NASGU>
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catch % no problem; early Matlab versions can use initTestSuite fine
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end
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initTestSuite;
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end
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function test_readAndFilterLogfileBasic()
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%% set up
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[cfg, logFile] = setUp();
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% create the events file and header
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logFile = saveEventsFile('open', cfg, logFile);
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% ROW 2: normal events : all info is there
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logFile(1, 1).onset = 2;
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logFile(end, 1).trial_type = 'motion_up';
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logFile(end, 1).duration = 3;
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logFile(end, 1).Speed = 2;
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logFile(end, 1).is_Fixation = true;
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logFile(end, 1).LHL24 = 1:12;
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logFile(2, 1).onset = 2;
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logFile(end, 1).trial_type = 'motion_down';
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logFile(end, 1).duration = 3;
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logFile(end, 1).Speed = 2;
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logFile(end, 1).is_Fixation = true;
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logFile(end, 1).LHL24 = 2:13;
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logFile = saveEventsFile('save', cfg, logFile);
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% close the file
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saveEventsFile('close', cfg, logFile);
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% filter file
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outputFiltered = readAndFilterLogfile('trial_type', 'motion_down', true, cfg);
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%% test
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expectedFilename = strrep(cfg.fileName.events, '.tsv', ...
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['_filteredBy-' 'trial_type' '_' 'motion_down' '.tsv']);
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expectedFile = fullfile(cfg.dir.outputSubject, ...
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cfg.fileName.modality, ...
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expectedFilename);
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assertEqual(exist(expectedFile, 'file'), 2);
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content = bids.util.tsvread(expectedFile);
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assertEqual(content.trial_type{1}, 'motion_down');
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end
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function test_readAndFilterLogfileFromFile()
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%% set up
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inputFile = fullfile(fileparts(mfilename('fullpath')), 'dummyData', ...
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'sub-blind01_ses-01_task-vislocalizer_events.tsv');
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% filter file
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outputFiltered = readAndFilterLogfile('trial_type', 'VisStat', true, inputFile);
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%% test
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expectedFile = strrep(inputFile, '.tsv', ...
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['_filteredBy-' 'trial_type' '_' 'VisStat' '.tsv']);
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assertEqual(exist(expectedFile, 'file'), 2);
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content = bids.util.tsvread(expectedFile);
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assertEqual(content.trial_type{1}, 'VisStat');
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end

‎tests/test_saveEventsFileSave.m‎

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@@ -207,29 +207,6 @@ function test_saveEventsFileSaveErrors()
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end
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function [cfg, logFile] = setUp()
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outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
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cfg.verbose = true;
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cfg.subject.subjectNb = 1;
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cfg.subject.runNb = 1;
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cfg.task.name = 'testtask';
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cfg.dir.output = outputDir;
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cfg.testingDevice = 'mri';
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cfg = createFilename(cfg);
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logFile.extraColumns.Speed.length = 1;
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logFile.extraColumns.LHL24.length = 12;
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logFile.extraColumns.is_Fixation.length = 1;
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end
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function content = getFileContent(cfg, logFile)
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% check the extra columns of the header and some of the content

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