Merge pull request #69 from Remi-Gau/remi-print_output_to_screen

saveEvents prints to screen / Badges / MRI suffixes

Author: Remi-Gau

README.md

@@ -1,5 +1,18 @@
-[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-) [![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS)
+**BIDS validator and linter**
 
+[![Build Status](https://travis-ci.com/cpp-lln-lab/CPP_BIDS.svg?branch=master)](https://travis-ci.com/cpp-lln-lab/CPP_BIDS)
+
+**Unit tests**
+
+[![](https://img.shields.io/badge/Octave-CI-blue?logo=Octave&logoColor=white)](https://github.com/cpp-lln-lab/CPP_BIDS/actions)
+![](https://github.com/cpp-lln-lab/CPP_BIDS/workflows/CI/badge.svg) 
+
+**Contributors**
+
+[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-) 
+
+---
+ 
 # CPP_BIDS
 
 <!-- TOC -->
@@ -18,6 +31,7 @@
   - [How to install](#how-to-install)
     - [Download with git](#download-with-git)
     - [Add as a submodule](#add-as-a-submodule)
+      - [Example for submodule usage](#example-for-submodule-usage)
     - [Direct download](#direct-download)
   - [Contributing](#contributing)
     - [Guidestyle](#guidestyle)

manualTests/test_makeRawDataset.m

@@ -7,38 +7,35 @@ function test_makeRawDataset()
     end
 
     %% set up
-
-    %%% set up
-
-    cfg.subject.subjectNb = 1;
-    cfg.subject.runNb = 1;
-
-    cfg.task.name = 'testtask';
-
     cfg.dir.output = outputDir;
 
     cfg.bids.datasetDescription.Name = 'dummy';
     cfg.bids.datasetDescription.BIDSVersion = '1.0.0';
     cfg.bids.datasetDescription.Authors = {'Jane Doe', 'John Doe'};
 
-    cfg.bids.mri.RepetitionTime = 1.56;
-
     cfg.testingDevice = 'mri';
 
+    %% MRI task data
+    cfg.mri.repetitionTime = 1.56;
+
+    cfg.subject.subjectNb = 1;
+    cfg.subject.runNb = 1;
+
+    cfg.task.name = 'testtask';
+
     logFile.extraColumns.Speed.length = 1;
     logFile.extraColumns.LHL24.length = 3;
     logFile.extraColumns.is_Fixation.length = 1;
 
-    %%% do stuff
-
     cfg = createFilename(cfg);
 
-    % create the events file and header
-    logFile = saveEventsFile('open', cfg, logFile);
-
     createBoldJson(cfg);
+
     createDatasetDescription(cfg);
 
+    % 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 = 'MotionUp';
@@ -74,11 +71,48 @@ function test_makeRawDataset()
     % add dummy functional data
     funcDir = fullfile(cfg.dir.output, 'source', 'sub-001', 'ses-001', 'func');
     boldFilename = 'sub-001_ses-001_task-testtask_run-001_bold.nii.gz';
+
     copyfile( ...
         fullfile('..', 'dummyData', 'dummyData.nii.gz'), ...
         fullfile(funcDir, boldFilename));
 
-    %%
+    %% MRI bold rest data and fancy suffixes
+    clear cfg;
+
+    cfg.dir.output = outputDir;
+
+    cfg.testingDevice = 'mri';
+
+    cfg.subject.subjectNb = 2;
+    cfg.subject.sessionNb = 3;
+    cfg.subject.runNb = 4;
+
+    cfg.mri.reconstruction = 'fast recon';
+    cfg.mri.contrastEnhancement = 'test';
+    cfg.mri.phaseEncodingDirection = 'y pos';
+    cfg.mri.echo = '1';
+    cfg.mri.acquisition = ' new tYpe';
+    cfg.mri.repetitionTime = 1.56;
+
+    cfg.task.name = 'rest';
+
+    cfg = createFilename(cfg);
 
+    createBoldJson(cfg);
+
+    % add dummy functional data
+    funcDir = fullfile(cfg.dir.output, 'source', 'sub-002', 'ses-003', 'func');
+    boldFilename = ['sub-002_ses-003_task-rest',  ...
+        '_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
+        '_run-004_echo-1_bold.nii.gz'];
+
+    copyfile( ...
+        fullfile('..', 'dummyData', 'dummyData.nii.gz'), ...
+        fullfile(funcDir, boldFilename));
+
+    %%
+    clear;
+    outputDir = fullfile(fileparts(mfilename('fullpath')), 'output');
+    cfg.dir.output = outputDir;
     convertSourceToRaw(cfg);
 end

src/convertSourceToRaw.m

@@ -11,7 +11,7 @@ function convertSourceToRaw(cfg)
     sourceDir = fullfile(cfg.dir.output, 'source');
     rawDir = fullfile(cfg.dir.output, 'rawdata');
 
-    % add dummy readme and change file
+    % add dummy README and CHANGE file
     copyfile(fullfile( ...
         fileparts(mfilename('fullpath')), '..', 'dummyData', 'README'), ...
         sourceDir);
@@ -28,6 +28,7 @@ function convertSourceToRaw(cfg)
         error('No subjects found in BIDS directory.');
     end
 
+    % go through the subject files and parses them to remove the date suffix
     for su = 1:numel(subjects)
 
         sess = cellstr(file_utils('List', fullfile(rawDir, subjects{su}), 'dir', '^ses-.*$'));

src/createFilename.m

@@ -1,4 +1,6 @@
 function cfg = createFilename(cfg)
+    % cfg = createFilename(cfg)
+    %
     % create the BIDS compliant directories and fileNames for the behavioral output
     % for this subject / session / run using the information from cfg and expParameters.
     % Will also create the right fileName for the eyetracking data file.
@@ -99,21 +101,39 @@
 
     cfg.fileName.suffix.run = ['_run-' sprintf(cfg.fileName.pattern, cfg.subject.runNb)];
 
+    %% MRI
     % set values for the suffixes for the different fields in the BIDS name
     fields2Check = { ...
+        'acquisition', ...
         'contrastEnhancement', ...
+        'echo', ...
         'phaseEncodingDirection', ...
         'reconstruction', ...
+        };
+
+    targetFields = { ...
+        'acq', ...
+        'ce', ...
         'echo', ...
-        'acquisition'
+        'dir', ...
+        'rec', ...
         };
 
     for iField = 1:numel(fields2Check)
+
         if isempty (cfg.mri.(fields2Check{iField})) %#ok<*GFLD>
+
             cfg.fileName.suffix.mri.(fields2Check{iField}) = ''; %#ok<*SFLD>
+
         else
+
+            % upper camelCase and remove invalid characters
+            thisField = getfield(cfg.mri, fields2Check{iField});
+            [~, validFieldName] = createValidName(thisField);
+
             cfg.fileName.suffix.mri.(fields2Check{iField}) = ...
-                ['_' fields2Check{iField} '-' getfield(cfg.mri, fields2Check{iField})];
+                ['_' targetFields{iField} '-' validFieldName];
+
         end
     end
 

src/saveEventsFile.m

@@ -152,6 +152,7 @@
 
     % print the basic BIDS columns
     fprintf(logFile.fileID, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
+    fprintf(1, '%s\t%s\t%s', 'onset', 'duration', 'trial_type');
 
     printHeaderExtraColumns(logFile);
 
@@ -174,6 +175,7 @@ function printHeaderExtraColumns(logFile)
             headerName = returnHeaderName(namesExtraColumns{iExtraColumn}, nbCol, iCol);
 
             fprintf(logFile.fileID, '\t%s', headerName);
+            fprintf(1, '\t%s', headerName);
 
         end
 
@@ -281,6 +283,7 @@ function printHeaderExtraColumns(logFile)
             printExtraColumns(logFile, iEvent);
 
             fprintf(logFile(1).fileID, '\n');
+            fprintf(1, '\n');
 
         end
     end
@@ -307,12 +310,15 @@ function printData(output, data)
     % for numeric data we replace any nan by n/a
     if ischar(data)
         fprintf(output, '%s\t', data);
+        fprintf(1, '%s\t', data);
     else
         for i = 1:numel(data)
             if isnan(data(i))
                 fprintf(output, '%s\t', 'n/a');
+                fprintf(1, '%s\t', 'n/a');
             else
                 fprintf(output, '%f\t', data(i));
+                fprintf(1, '%f\t', data(i));
             end
         end
     end

src/subfun/createTaskName.m renamed to src/subfun/createValidName.m

@@ -1,17 +1,17 @@
-function [taskName, taskNameValid] = createTaskName(taskName)
+function [name, nameValid] = createValidName(name)
     % [taskName, taskNameValid] = createTaskName(taskName)
     %
     % Name of the task (for resting state use the "rest" prefix). No two tasks
     % should have the same name. Task label is derived from this field by
     % removing all non alphanumeric ([a-zA-Z0-9]) characters.
 
     % camel case: upper case for first letter for all words but the first one
-    spaceIdx = regexp(taskName, '[a-zA-Z0-9]*', 'start');
-    taskName(spaceIdx(2:end)) = upper(taskName(spaceIdx(2:end)));
+    spaceIdx = regexp(name, '[a-zA-Z0-9]*', 'start');
+    name(spaceIdx(2:end)) = upper(name(spaceIdx(2:end)));
 
     % remove invalid characters
-    [unvalidCharacters] = regexp(taskName, '[^a-zA-Z0-9]');
-    taskNameValid = taskName;
-    taskNameValid(unvalidCharacters) = [];
+    [unvalidCharacters] = regexp(name, '[^a-zA-Z0-9]');
+    nameValid = name;
+    nameValid(unvalidCharacters) = [];
 
 end

src/subfun/transferInfoToBids.m

@@ -5,7 +5,7 @@
     % relevant field for its reuse for BIDS filenames or JSON later
 
     if isfield(cfg, 'task') && isfield(cfg.task, 'name')
-        [taskName, taskNameValid] = createTaskName(cfg.task.name);
+        [taskName, taskNameValid] = createValidName(cfg.task.name);
         fieldsToSet.fileName.task = taskNameValid;
         fieldsToSet.bids.meg.TaskName = taskName;
         fieldsToSet.bids.mri.TaskName = taskName;

tests/test_checkCFG.m

@@ -124,4 +124,4 @@ function test_checkCfgBasic()
 
     expectedCfgStructure = orderfields(expectedCfgStructure);
 
-end
+end

tests/test_createFilename.m

@@ -94,6 +94,52 @@ function test_createFilenameMriEyetracker()
 
 end
 
+function test_createFilenameMriSuffix()
+
+    outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');
+
+    %% set up
+
+    cfg.verbose = false;
+    cfg.subject.subjectGrp = 'ssri';
+    cfg.subject.subjectNb = 3;
+    cfg.subject.sessionNb = 4;
+    cfg.subject.runNb = 5;
+    cfg.task.name = 'rest';
+    cfg.dir.output = outputDir;
+
+    cfg.eyeTracker.do = false;
+    cfg.testingDevice = 'mri';
+
+    cfg.mri.reconstruction = 'fast recon';
+    cfg.mri.contrastEnhancement = 'test';
+    cfg.mri.phaseEncodingDirection = 'y pos';
+    cfg.mri.echo = '1';
+    cfg.mri.acquisition = ' new tYpe';
+
+    cfg = createFilename(cfg);
+
+    %% data to test against
+
+    funcDir = fullfile(outputDir, 'source', 'sub-ssri003', 'ses-004', 'func');
+
+    baseFilename = 'sub-ssri003_ses-004_task-rest';
+
+    eventFilename = ['sub-ssri003_ses-004_task-rest',  ...
+        '_acq-newTYpe_ce-test_dir-yPos_rec-fastRecon', ...
+        '_run-005_echo-1_events_date-' ...
+        cfg.fileName.date '.tsv'];
+
+    %% tests
+    % make sure the func dir is created
+    assertTrue(exist(funcDir, 'dir') == 7);
+
+    % make sure the right filenames are created
+    assertEqual(cfg.fileName.base, baseFilename);
+    assertEqual(cfg.fileName.events, eventFilename);
+
+end
+
 function test_createFilenameEeg()
 
     outputDir = fullfile(fileparts(mfilename('fullpath')), '..', 'output');

tests/test_createTaskName.m renamed to tests/test_createValidName.m

@@ -1,4 +1,4 @@
-function test_suite = test_createTaskName %#ok<*STOUT>
+function test_suite = test_createValidName %#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
@@ -12,7 +12,7 @@ function test_createTaskNameRemoveInvalidCharacters()
 
     taskName = '&|@#-_(§!{})[]ù%£+/=:;.?,\<> visual task';
 
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [~, taskNameValid] = createValidName(taskName);
 
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
 
@@ -22,15 +22,15 @@ function test_createTaskNameRemoveInvalidCharacters()
     %% set up
     taskName = ' 09 visual task';
 
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [~, taskNameValid] = createValidName(taskName);
 
     [unvalidCharacters] = regexp(taskNameValid, '[^a-zA-Z0-9]');
 
     %% test
     assertTrue(isempty(unvalidCharacters));
 
     taskName = 'foo bar';
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [taskName, taskNameValid] = createValidName(taskName);
     assert(isequal(taskName, 'foo Bar'));
     assert(isequal(taskNameValid, 'fooBar'));
 
@@ -40,7 +40,7 @@ function test_createTaskNameCamelCase()
 
     %% set up
     taskName = 'foo bar';
-    [taskName, taskNameValid] = createTaskName(taskName);
+    [taskName, taskNameValid] = createValidName(taskName);
 
     %% test
     assertEqual(taskName, 'foo Bar');