create test for read and filter log

Author: Remi-Gau

.gitignore

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

lib/bids-matlab

@@ -1,12 +1,9 @@
 function outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, varargin)
-    % outputFiltered = readOutputFilter(filterHeader, filterContent, varargin)
+    % outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, varargin)
     %
     % It will display in the command window the content of the `output.tsv' filtered by one element
     % of a target column.
     %
-    % DEPENDENCIES:
-    %  - bids_matlab (from CPP_BIDS)
-    %
     % INPUT:
     %
     %  - columnName: string, the header of the column where the content of insterest is stored
@@ -21,66 +18,59 @@
     %
     %  - outputFiltered: dataset with only the specified content, to see it in the command window
     %    use display(outputFiltered)
-
+    
     % 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
     if ischar(varargin{1})
-
+        
         tsvFile = varargin{1};
-
-        % Divide path and file name
-        fileSepPos = find(tsvFile == filesep, 1, 'last');
-        path1 = tsvFile(1:fileSepPos - 1);
-        path2 = tsvFile(fileSepPos + 1:end - 4);
-
-        % Create output file name
-        outputFileName = fullfile(path1, ...
-                                  [path2 ...
-                                   outputFilterTag]);
-
+        
     elseif isstruct(varargin{1})
-
+        
         tsvFile = fullfile(varargin{1}.dir.outputSubject, ...
-                           varargin{1}.fileName.modality, ...
-                           varargin{1}.fileName.events);
-
-        % Create output file name
-        outputFileName = fullfile(varargin{1}.dir.outputSubject, ...
-                                  varargin{1}.fileName.modality, ...
-                                  [varargin{1}.fileName.events(1:end - 4) ...
-                                   outputFilterTag]);
+            varargin{1}.fileName.modality, ...
+            varargin{1}.fileName.events);
+        
     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']);
+        error([newline 'Input file does not exist: %s'], tsvFile);
     end
-
+    
     try
         % Read the the tsv file and store each column in a field of `output` structure
         output = bids.util.tsvread(tsvFile);
     catch
         % Add the 'bids-matlab' in case is not in the path
-        addpath(genpath(fullfile(pwd, '../lib')));
+        addpath(genpath(fullfile(pwd, '..', 'lib')));
         % Read the the tsv file and store each column in a field of `output` structure
         output = bids.util.tsvread(tsvFile);
     end
-
+    
     % Get the index of the target contentent to filter and display
-    filterIdx = find(strncmp(output.(columnName), filterBy, length(filterBy)));
-
+    filterIdx = strncmp(output.(columnName), filterBy, length(filterBy));
+    
+    % apply the filter
+    listFields = fieldnames(output);      
+    for iField = 1:numel(listFields)
+        output.(listFields{iField})(~filterIdx) = [];
+    end
+    
     % Convert the structure to dataset
-    outputDataset = struct2dataset(output);
-
-    % Get the dataset with the content of intereset
-    outputFiltered = outputDataset(filterIdx, :);
-
+    outputFiltered = struct2dataset(output);
+    
     if saveOutputTsv
 
         bids.util.tsvwrite(outputFileName, output);
-
+        
     end
-
+    
 end
+
+

src/readAndFilterLogfile.m

@@ -0,0 +1,3 @@
+onset	duration	trial_type
+2	15	VisMot
+25	15	VisStat

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

@@ -0,0 +1,22 @@
+function [cfg, logFile] = setUp()
+
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
+
+    cfg.verbose = true;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'mri';
+
+    cfg = createFilename(cfg);
+
+    logFile.extraColumns.Speed.length = 1;
+    logFile.extraColumns.LHL24.length = 12;
+    logFile.extraColumns.is_Fixation.length = 1;
+
+end

tests/setUp.m

@@ -0,0 +1,77 @@
+function test_suite = test_readAndFilterLogfile %#ok<*STOUT>
+    try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+        test_functions = localfunctions(); %#ok<*NASGU>
+    catch % no problem; early Matlab versions can use initTestSuite fine
+    end
+    initTestSuite;
+end
+
+function test_readAndFilterLogfileBasic()
+
+    %% set up
+
+    [cfg, logFile] = setUp();
+
+    % create the events file and header
+    logFile = saveEventsFile('open', cfg, logFile);
+
+    % ROW 2: normal events : all info is there
+    logFile(1, 1).onset = 2;
+    logFile(end, 1).trial_type = 'motion_up';
+    logFile(end, 1).duration = 3;
+    logFile(end, 1).Speed = 2;
+    logFile(end, 1).is_Fixation = true;
+    logFile(end, 1).LHL24 = 1:12;
+    
+    logFile(2, 1).onset = 2;
+    logFile(end, 1).trial_type = 'motion_down';
+    logFile(end, 1).duration = 3;
+    logFile(end, 1).Speed = 2;
+    logFile(end, 1).is_Fixation = true;
+    logFile(end, 1).LHL24 = 2:13;
+
+    logFile = saveEventsFile('save', cfg, logFile);
+
+    % close the file
+    saveEventsFile('close', cfg, logFile);
+    
+    % filter file
+    outputFiltered = readAndFilterLogfile('trial_type', 'motion_down', true, cfg);
+
+    %% test
+    expectedFilename = strrep(cfg.fileName.events, '.tsv', ...
+                           ['_filteredBy-' 'trial_type' '_' 'motion_down' '.tsv']);
+    expectedFile = fullfile(cfg.dir.outputSubject, ...
+                           cfg.fileName.modality, ...
+                           expectedFilename);
+
+    assertEqual(exist(expectedFile, 'file'), 2)
+    
+    content = bids.util.tsvread(expectedFile);
+    
+    assertEqual(content.trial_type{1}, 'motion_down')
+    
+end
+
+
+function test_readAndFilterLogfileFromFile()
+
+    %% set up
+    
+    inputFile = fullfile(fileparts(mfilename('fullpath')), 'dummyData', ...
+        'sub-blind01_ses-01_task-vislocalizer_events.tsv');
+    
+    % filter file
+    outputFiltered = readAndFilterLogfile('trial_type', 'VisStat', true, inputFile);
+
+    %% test
+    expectedFile = strrep(inputFile, '.tsv', ...
+                           ['_filteredBy-' 'trial_type' '_' 'VisStat' '.tsv']);
+
+    assertEqual(exist(expectedFile, 'file'), 2)
+    
+    content = bids.util.tsvread(expectedFile);
+    
+    assertEqual(content.trial_type{1}, 'VisStat')
+    
+end

tests/test_readAndFilterLogfile.m

@@ -207,28 +207,6 @@ function test_saveEventsFileSaveErrors()
 
 end
 
-function [cfg, logFile] = setUp()
-
-    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
-
-    cfg.verbose = true;
-
-    cfg.subject.subjectNb = 1;
-    cfg.subject.runNb = 1;
-
-    cfg.task.name = 'testtask';
-
-    cfg.dir.output = outputDir;
-
-    cfg.testingDevice = 'mri';
-
-    cfg = createFilename(cfg);
-
-    logFile.extraColumns.Speed.length = 1;
-    logFile.extraColumns.LHL24.length = 12;
-    logFile.extraColumns.is_Fixation.length = 1;
-
-end
 
 function content = getFileContent(cfg, logFile)