diff --git a/.gitignore b/.gitignore index cf03139e..6146b2ba 100644 --- a/.gitignore +++ b/.gitignore @@ -30,4 +30,11 @@ check_my_code_report.txt node_modules/* package-lock.json +# visual studio code stuff +.vscode +# virtual env +cpp_bids/* + +# documentation +docs/build/* diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 00000000..6f095f08 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,26 @@ +# .readthedocs.yml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: docs/source/conf.py + builder: html + fail_on_warning: true + +# Build documentation with MkDocs +#mkdocs: +# configuration: mkdocs.yml + +# Optionally build your docs in additional formats such as PDF +formats: + - pdf + +# Optionally set the version of Python and requirements required to build your docs +python: + version: 3.7 + install: + - requirements: docs/requirements.txt \ No newline at end of file diff --git a/.travis.yml b/.travis.yml index 009419e7..920f26b6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,17 +3,12 @@ # have set it up to run continuous integration on this this repo # Linux distribution (bionic beaver) -dist: bionic +dist: focal # Language and version language: node_js node_js: - - "10" - -cache: - apt: true # only works with Pro version - directories: - - node_modules # NPM packages for the remark markdown linter + - "11" branches: only: # only run the CI for those branches @@ -33,7 +28,7 @@ before_install: - travis_retry sudo apt-get -y install nodejs - travis_retry sudo apt-get -y install npm # Install BIDS-Validator - - sudo npm install -g bids-validator@1.5.6 + - sudo npm install -g bids-validator@1.5.7 install: # make octave file the JSONio submodule diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..d0c3cbf1 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 00000000..d34286ac --- /dev/null +++ b/docs/README.md @@ -0,0 +1,108 @@ +# Setting up sphinx to create a matlab doc + +## Set up virtual environment + +```bash +virtualenv -p python3 cpp_bids +source cpp_spm/bin/activate + +pip install -r requirements.txt +``` + +## Quick start on the doc + +See the [sphinx doc](https://www.sphinx-doc.org/en/master/usage/quickstart.html) +for more. + +This +[blog post](https://medium.com/@richdayandnight/a-simple-tutorial-on-how-to-document-your-python-project-using-sphinx-and-rinohtype-177c22a15b5b) +is also useful. + +```bash +cd docs +sphinx-quickstart # launch a basic interactive set up of sphinx +``` + +Answer the questions on prompt. + +## Setting up conf.py for matlab doc + +Following the documentation from +[matlabdomain for sphinx](https://github.com/sphinx-contrib/matlabdomain). + +Specify the extensions you are using: + +```python +extensions = [ + 'sphinxcontrib.matlab', + 'sphinx.ext.autodoc'] +``` + +`matlab_src_dir` in `docs/source/conf.py` should have the path (relative to +`conf.py`) to the folder containing your matlab code: + +```python +matlab_src_dir = os.path.dirname(os.path.abspath('../../src')) +``` + +## reStructured text markup + +reStructured text mark up primers: + +- on the [sphinx site](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html) + +- more + [python oriented](https://pythonhosted.org/an_example_pypi_project/sphinx.html) + +- typical doc strings templates + - [google way](https://www.sphinx-doc.org/en/master/usage/extensions/example_google.html) + - [numpy](https://www.sphinx-doc.org/en/master/usage/extensions/example_numpy.html#example-numpy) + +## "Templates" + +The templates to use for the doc are in the `src/templates` folder. + +You then just need to insert this in your `.rst` file for the documentation to +be done automatically. + +```rst + +.. automodule:: src.folder_name .. <-- This is necessary for auto-documenting the rest + +.. autofunction:: function to document + +``` + +To get the filenames of all the functions in a folder: + +``` bash +ls -l src/*.m | cut -c42- | rev | cut -c 3- | rev +``` + +Increase the `42` to crop more characters at the beginning. + +Change the `3` to crop more characters at the end. + +## Build the documentation locally + +From the `docs` directory: + +```bash +sphinx-build -b html source build +``` + +This will build an html version of the doc in the `build` folder. + +## Build the documentation with Read the Docs + +Add a [`.readthedocs.yml`](../.readthedocs.yml) file in the root of your repo. + +See [HERE](https://docs.readthedocs.io/en/stable/config-file/v2.html) for +details. + +You can then trigger the build of the doc by going to the +[read the docs website](https://readthedocs.org). + +You might need to be added as a maintainer of the doc. + +The doc can be built from any branch of a repo. diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..9534b018 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 00000000..42ea70da --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,5 @@ +Sphinx +sphinxcontrib-matlabdomain +sphinxcontrib-napoleon +sphinx_rtd_theme +miss_hit \ No newline at end of file diff --git a/docs/source/_static/cpp_lab_logo.png b/docs/source/_static/cpp_lab_logo.png new file mode 100644 index 00000000..89277c01 Binary files /dev/null and b/docs/source/_static/cpp_lab_logo.png differ diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 00000000..5a423f71 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,91 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import os +import sys +sys.path.insert(0, os.path.abspath('../..')) + + +# -- Project information ----------------------------------------------------- + +project = 'CPP BIDS' +copyright = '2020, the CPP BIDS dev team' +author = 'the CPP BIDS dev team' + +# The full version, including alpha/beta/rc tags +release = 'v1.0.0' + + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + 'sphinxcontrib.matlab', + 'sphinx.ext.autodoc'] +matlab_src_dir = os.path.dirname(os.path.abspath('../../src')) +primary_domain = 'mat' + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# The master toctree document. +master_doc = 'index' + +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = 'sphinx_rtd_theme' + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +html_logo = '_static/cpp_lab_logo.png' + +# html_theme_options = { +# 'github_user': 'cpp-lln-lab', +# 'github_repo': 'CPP_BIDS_SPM_pipeline', +# 'github_button': True, +# 'github_banner': True +# } +# html_theme_options = { +# 'collapse_navigation': False, +# 'display_version': False, +# 'navigation_depth': 4, +# } + +html_sidebars = { + '**': [ + 'about.html', + 'navigation.html', + 'relations.html', # needs 'show_related': True theme option to display + 'searchbox.html', + 'donate.html', + ] +} \ No newline at end of file diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst new file mode 100644 index 00000000..fb47029d --- /dev/null +++ b/docs/source/contributing.rst @@ -0,0 +1,104 @@ +Contributing +************ + +How to contribute to this project. + + +Function templates +================== + +.. automodule:: src.templates + +Template proposal +----------------- + +:: + + % (C) Copyright 2020 CPP BIDS developers + + function [argout1, argout2] = templateFunction(argin1, argin2, argin3) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + % .. todo: + % + % - item 1 + % - item 2 + + % The code goes below + + end + + + end + +.. autofunction:: templateFunction + + +Example code in the help section +-------------------------------- + +:: + + % (C) Copyright 2020 CPP BIDS developers + + function templateFunctionExample() + % This function illustrates a documentation test defined for MOdox. + % Other than that it does absolutely nothinghort description of what + % the function does goes here. + % + % Examples: + % a=2; + % disp(a) + % % Expected output is prefixed by '%||' as in the following line: + % %|| 2 + % % + % % The test continues because no interruption through whitespace, + % % as the previous line used a '%' comment character; + % % thus the 'a' variable is still in the namespace and can be + % % accessed. + % b=3+a; + % disp(a+[3 4]) + % %|| [5 6] + % + % % A new test starts here because the previous line was white-space + % % only. Thus the 'a' and 'b' variables are not present here anymore. + % % The following expression raises an error because the 'b' variable + % % is not defined (and does not carry over from the previous test). + % % Because the expected output indicates an error as well, + % % the test passes + % disp(b) + % %|| error('Some error') + % + % % A set of expressions is ignored if there is no expected output + % % (that is, no lines starting with '%||'). + % % Thus, the following expression is not part of any test, + % % and therefore does not raise an error. + % error('this is never executed) + % + % + % % tests end here because test indentation has ended + + % The code goes below + + end + +.. autofunction:: templateFunctionExample + + + diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst new file mode 100644 index 00000000..5a721c9c --- /dev/null +++ b/docs/source/function_description.rst @@ -0,0 +1,20 @@ +Function description +******************** + +List of functions in the ``src`` folder. + +---- + +.. automodule:: src + +.. autofunction:: checkCFG +.. autofunction:: convertSourceToRaw +.. autofunction:: createDataDictionary +.. autofunction:: createDatasetDescription +.. autofunction:: createFilename +.. autofunction:: createJson +.. autofunction:: readAndFilterLogfile +.. autofunction:: saveEventsFile +.. autofunction:: userInputs + + diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 00000000..c1b29398 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,31 @@ +.. cpp_bids_spm documentation master file, created by + sphinx-quickstart on Tue Oct 13 11:38:30 2020. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to CPP BIDS documentation! +********************************** + +.. toctree:: + :maxdepth: 2 + :caption: Content + + function_description + utilities + contributing + +This pipeline contains a set of functions to run fMRI analysis on a +[BIDS data set](https://bids.neuroimaging.io/) using SPM12. + + + + + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/source/utilities.rst b/docs/source/utilities.rst new file mode 100644 index 00000000..9197bd4a --- /dev/null +++ b/docs/source/utilities.rst @@ -0,0 +1,22 @@ +Utility functions +***************** + +List of functions in the ``utils`` folder. + +---- + +.. automodule:: src.utils + +.. autofunction:: checkCppBidsDependencies +.. autofunction:: createValidName +.. autofunction:: getFullFilename +.. autofunction:: initializeExtraColumns +.. autofunction:: isPositiveInteger +.. autofunction:: printCreditsCppBids +.. autofunction:: removeAllDateSuffix +.. autofunction:: removeDateSuffix +.. autofunction:: returnHeaderName +.. autofunction:: returnNamesExtraColumns +.. autofunction:: returnNbColumns +.. autofunction:: setDefaultFields +.. autofunction:: transferInfoToBids diff --git a/package-lock.json b/package-lock.json deleted file mode 100644 index 8698652d..00000000 --- a/package-lock.json +++ /dev/null @@ -1,3542 +0,0 @@ -{ - 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Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % cfg = checkCFG(cfg) % % check that we have all the fields that we need in the experiment parameters diff --git a/src/convertSourceToRaw.m b/src/convertSourceToRaw.m index f4b4ea4f..3684733f 100644 --- a/src/convertSourceToRaw.m +++ b/src/convertSourceToRaw.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function convertSourceToRaw(cfg) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % convertSourceToRaw(cfg) % % attempts to convert a source dataset created with CPP_BIDS into a valid diff --git a/src/createDataDictionary.m b/src/createDataDictionary.m index 061c0ef5..cf1fdf63 100644 --- a/src/createDataDictionary.m +++ b/src/createDataDictionary.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function createDataDictionary(cfg, logFile) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % createDataDictionary(cfg, logFile) % % creates the data dictionary to be associated with a _events.tsv file diff --git a/src/createDatasetDescription.m b/src/createDatasetDescription.m index 38e44fa2..84007bea 100644 --- a/src/createDatasetDescription.m +++ b/src/createDatasetDescription.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function createDatasetDescription(cfg) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % createDatasetDescription(cfg) % % creates the datasetDescription.json file that goes in the root of a BIDS diff --git a/src/createJson.m b/src/createJson.m index 3242d133..277d243a 100644 --- a/src/createJson.m +++ b/src/createJson.m @@ -1,29 +1,34 @@ % (C) Copyright 2020 CPP_BIDS developers function createJson(varargin) - % createBoldJson(cfg, varargin) % % Creates the side car JSON file for a run. - % This will only contain the minimum BIDS requirement and will likey be less - % complete than the info you could from a proper conversion. % - % USAGE + % For JSON sidecars for bold files, this will only contain the minimum BIDS + % requirement and will likey be less complete than the info you could from + % a proper BIDS conversion. % - % createJson(cfg, modality) + % USAGE:: % - % modality is string ('beh', 'func', 'eeg', 'ieeg', 'meg') to specify which - % JSON to save + % createJson(cfg [, modality] [, extraInfo]) + % createJson(cfg [, extraInfo]) % + % :param cfg: Configuration. See ``checkCFG()``. + % :type cfg: structure + % :param modality: can be any of the following ``'beh'``, ``'func'``, ``'eeg'``, + % ``'ieeg'``, ``'meg'``) to specify which JSON to save. If it is not + % provided it will read from ``cfg.fileName.modality``. + % :type modality: string + % :param extraInfo: contains information in the JSON file. Beware + % that the BIDS validator is pretty strict on what information can + % go in a JSON so this can be useful to store additional information + % in your source dataset but it might have to be cleaned up to create + % a valid BIDS dataset. + % :type extraInfo: structure % - % createJson(cfg, extraInfo) - % - % extraInfo is a strcuture to add axtra content can be added to the JSON file - % - % - % createJson(cfg, modality, extraInfo) - % - % both are possible + % .. TODO: % + % - use input parser for this one % [cfg, modality, extraInfo] = checkInput(varargin); diff --git a/src/gui/askForGroupAndOrSession.m b/src/gui/askForGroupAndOrSession.m new file mode 100644 index 00000000..271644c3 --- /dev/null +++ b/src/gui/askForGroupAndOrSession.m @@ -0,0 +1,40 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function cfg = askForGroupAndOrSession(cfg) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + + askGrpSess = [true true]; + + if isfield(cfg, 'subject') && ... + isfield(cfg.subject, 'askGrpSess') && ... + ~isempty(cfg.subject.askGrpSess) + + askGrpSess = cfg.subject.askGrpSess; + + end + + if numel(askGrpSess) < 2 + askGrpSess(2) = 1; + end + + cfg.subject.askGrpSess = askGrpSess; + +end diff --git a/src/subfun/askUserCli.m b/src/gui/askUserCli.m similarity index 56% rename from src/subfun/askUserCli.m rename to src/gui/askUserCli.m index 46491136..097465ba 100644 --- a/src/subfun/askUserCli.m +++ b/src/gui/askUserCli.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function responses = askUserCli(questions, responses) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % response = askUserCli(questions) % % command line interface to ask questions to user diff --git a/src/subfun/askUserGui.m b/src/gui/askUserGui.m similarity index 66% rename from src/subfun/askUserGui.m rename to src/gui/askUserGui.m index a141c637..1c72bfcc 100644 --- a/src/subfun/askUserGui.m +++ b/src/gui/askUserGui.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function responses = askUserGui(questions, responses) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % boolean for which question should be asked isQuestionToAsk = ~cellfun('isempty', questions.questionsToAsk(:, 1)); diff --git a/src/subfun/createQuestionList.m b/src/gui/createQuestionList.m similarity index 62% rename from src/subfun/createQuestionList.m rename to src/gui/createQuestionList.m index fc2c43b0..22d709b6 100644 --- a/src/subfun/createQuestionList.m +++ b/src/gui/createQuestionList.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function questions = createQuestionList(cfg) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % cfg = askForGroupAndOrSession(cfg); diff --git a/src/gui/getIsQuestionToAsk.m b/src/gui/getIsQuestionToAsk.m new file mode 100644 index 00000000..94d5fec1 --- /dev/null +++ b/src/gui/getIsQuestionToAsk.m @@ -0,0 +1,31 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function isQuestionToAsk = getIsQuestionToAsk(questions, responses) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + + isQuestionToAsk = cell2mat(questions.questionsToAsk(:, 2)); + for j = 1:size(isQuestionToAsk, 1) + input2check = str2double(responses{j}); + isQuestionToAsk(j, 2) = ~isPositiveInteger(input2check); + end + isQuestionToAsk = all(isQuestionToAsk, 2); + +end diff --git a/src/gui/setDefaultResponses.m b/src/gui/setDefaultResponses.m new file mode 100644 index 00000000..cb0d0597 --- /dev/null +++ b/src/gui/setDefaultResponses.m @@ -0,0 +1,46 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function [cfg, responses] = setDefaultResponses(cfg) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + + if nargin < 1 + cfg = struct('debug', []); + end + + if ~isfield(cfg, 'debug') || isempty(cfg.debug) + cfg.debug.do = false; + end + + responses{1, 1} = ''; % subjectGrp + responses{2, 1} = ''; % subjectNb + responses{3, 1} = 1; % session + responses{4, 1} = ''; % run + + if cfg.debug.do + + responses{1, 1} = 'ctrl'; + responses{2, 1} = 666; + responses{3, 1} = 666; + responses{4, 1} = 666; + + end + +end diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m index 1f791bab..b446f05c 100644 --- a/src/readAndFilterLogfile.m +++ b/src/readAndFilterLogfile.m @@ -1,25 +1,37 @@ % (C) Copyright 2020 CPP_BIDS developers function outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, 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. + % It will display in the command window the content of the ``output.tsv`` + % filtered by one element of a target column. % - % INPUT: + % USAGE:: % - % - columnName: string, the header of the column where the content of insterest is stored - % (e.g., for 'trigger' will be 'trial type') - % - filterBy: string, the content of the column you want to filter out. It can take just - % part of the content name (e.g., you want to display the triggers and you have - % 'trigger_motion' and 'trigger_static', 'trigger' as input will do) - % - saveOutputTsv: boolean to save the filtered ouput - % - varargin: either cfg (to display the last run output) or the file path as string + % outputFiltered = readAndFilterLogfile(columnName, filterBy, saveOutputTsv, tsvFile) % - % OUTPUT: + % 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 + % :param saveOutputTsv: flag to save output on 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 + % + % :returns: + % + % :outputFiltered: dataset with only the specified content, to see it + % in the command window use ``display(outputFiltered)``. % - % - 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']; diff --git a/src/saveEventsFile.m b/src/saveEventsFile.m index 1cec0cd1..6ccf2ee1 100644 --- a/src/saveEventsFile.m +++ b/src/saveEventsFile.m @@ -1,58 +1,68 @@ % (C) Copyright 2020 CPP_BIDS developers function [logFile] = saveEventsFile(action, cfg, logFile) - % [logFile] = saveEventsFile(action, cfg, logFile) % % Function to save output files for events that will be BIDS compliant. % - % USAGE + % USAGE:: % - % [logFile] = saveEventsFile('init', [cfg], logFile) - % [logFile] = saveEventsFile('open', [cfg], logFile) - % [logFile] = saveEventsFile('open_stim', [cfg], logFile) - % [logFile] = saveEventsFile('save', [cfg], logFile) - % [logFile] = saveEventsFile('close', cfg, logFile) + % [logFile] = saveEventsFile(action, cfg, logFile) + % + % logFile] = saveEventsFile('init', [cfg], logFile) + % logFile] = saveEventsFile('open', [cfg], logFile) + % logFile] = saveEventsFile('open_stim', [cfg], logFile) + % logFile] = saveEventsFile('save', [cfg], logFile) + % logFile] = saveEventsFile('close', cfg, logFile) % % INPUTS % % logFile: - % When you want to save your data logFile contains the data you want to save. - % The logFile variable that contains the n events you want to % save must be a nx1 structure. + % + % When you want to save your data ``logFile`` contains the data you want to save. + % The ``logFile`` variable that contains the n events you want to save must be a nx1 structure. % Each field will be saved in a separate column. % - % example: - % logFile(1,1).onset = 2; - % logFile(1,1).trial_type = 'motion_up'; - % logFile(1,1).duration = 1; - % logFile(1,1).speed = 2; - % logFile(1,1).is_fixation = true; + % example:: + % + % logFile(1,1).onset = 2; + % logFile(1,1).trial_type = 'motion_up'; + % logFile(1,1).duration = 1; + % logFile(1,1).speed = 2; + % logFile(1,1).is_fixation = true; % - % logFile(2,1).onset = 3; - % logFile(2,1).trial_type = 'static'; - % logFile(2,1).duration = 4; - % logFile(2,1).is_fixation = 3; + % logFile(2,1).onset = 3; + % logFile(2,1).trial_type = 'static'; + % logFile(2,1).duration = 4; + % logFile(2,1).is_fixation = 3; % % % action: - % - 'open': will create the file ID and return it in logFile.fileID using the information in - % the expParameters structure. This file ID is then reused when calling that function - % to save data into this file. - % This creates the header with the obligatory 'onset', 'trial_type', 'duration' required - % by BIDS and other columns can be specified in varargin. % - % example : logFile = saveEventsFile('open', cfg, [], 'direction', 'speed', 'target'); + % - ``'open'`` will create the file ID and return it in ``logFile.fileID`` using + % the information in the ``cfg`` structure. + % This file ID is then reused when calling that function to save data into this file. + % This creates the header with the obligatory ``'onset'``, ``'duration'`` required + % by BIDS and other columns can be specified in varargin. + % + % example:: + % + % logFile = saveEventsFile('open', cfg, [], 'direction', 'speed', 'target'); + % + % + % - ``'save'`` will save the data contained in logfile by using the file ID ``logFile.fileID``; + % logfile must then contain: + % + % - logFile.onset + % - logFile.trial_type + % - logFile.duration % - % - 'save': will save the data contained in logfile by using the file ID logFile.fileID; - % logfile must then contain: - % - logFile.onset - % - logFile.trial_type - % - logFile.duration % The name of any extra column whose content must be saved should be listed in varargin. % - % - 'close': closes the file with file ID logFile.fileID. If expParameters.verbose is set - % to true then this will tell you where the file is located. + % - ``'close'`` closes the file with file ID ``logFile.fileID``. If ``cfg.verbose`` is set + % to true then this will tell you where the file is located. + % + % See ``tests/test_saveEventsFile()`` for more details on how to use it. % - % See test_saveEventsFile in the test folder for more details on how to use it. if nargin < 1 error('Missing action input'); diff --git a/src/subfun/askForGroupAndOrSession.m b/src/subfun/askForGroupAndOrSession.m deleted file mode 100644 index bac91022..00000000 --- a/src/subfun/askForGroupAndOrSession.m +++ /dev/null @@ -1,21 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -function cfg = askForGroupAndOrSession(cfg) - - askGrpSess = [true true]; - - if isfield(cfg, 'subject') && ... - isfield(cfg.subject, 'askGrpSess') && ... - ~isempty(cfg.subject.askGrpSess) - - askGrpSess = cfg.subject.askGrpSess; - - end - - if numel(askGrpSess) < 2 - askGrpSess(2) = 1; - end - - cfg.subject.askGrpSess = askGrpSess; - -end diff --git a/src/subfun/createValidName.m b/src/subfun/createValidName.m deleted file mode 100644 index 57b905d4..00000000 --- a/src/subfun/createValidName.m +++ /dev/null @@ -1,19 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -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(name, '[a-zA-Z0-9]*', 'start'); - name(spaceIdx(2:end)) = upper(name(spaceIdx(2:end))); - - % remove invalid characters - [unvalidCharacters] = regexp(name, '[^a-zA-Z0-9]'); - nameValid = name; - nameValid(unvalidCharacters) = []; - -end diff --git a/src/subfun/getFullFilename.m b/src/subfun/getFullFilename.m deleted file mode 100644 index 5b389d6a..00000000 --- a/src/subfun/getFullFilename.m +++ /dev/null @@ -1,10 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -function fullFilename = getFullFilename(fileName, cfg) - - fullFilename = fullfile( ... - cfg.dir.outputSubject, ... - cfg.fileName.modality, ... - fileName); - -end diff --git a/src/subfun/getIsQuestionToAsk.m b/src/subfun/getIsQuestionToAsk.m deleted file mode 100644 index a8446235..00000000 --- a/src/subfun/getIsQuestionToAsk.m +++ /dev/null @@ -1,12 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -function isQuestionToAsk = getIsQuestionToAsk(questions, responses) - - isQuestionToAsk = cell2mat(questions.questionsToAsk(:, 2)); - for j = 1:size(isQuestionToAsk, 1) - input2check = str2double(responses{j}); - isQuestionToAsk(j, 2) = ~isPositiveInteger(input2check); - end - isQuestionToAsk = all(isQuestionToAsk, 2); - -end diff --git a/src/subfun/returnHeaderName.m b/src/subfun/returnHeaderName.m deleted file mode 100644 index fe59cbc3..00000000 --- a/src/subfun/returnHeaderName.m +++ /dev/null @@ -1,13 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -function headerName = returnHeaderName(columnName, nbCol, iCol) - % headerName = returnHeaderName(columnName, nbCol, iCol) - % - - if nbCol == 1 - headerName = sprintf('%s', columnName); - else - headerName = sprintf('%s_%02.0f', columnName, iCol); - end - -end diff --git a/src/subfun/returnNamesExtraColumns.m b/src/subfun/returnNamesExtraColumns.m deleted file mode 100644 index 39b17629..00000000 --- a/src/subfun/returnNamesExtraColumns.m +++ /dev/null @@ -1,13 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -function [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile) - % [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile) - % - - namesExtraColumns = []; - - if isfield(logFile, 'extraColumns') && ~isempty(logFile(1).extraColumns) - namesExtraColumns = fieldnames(logFile(1).extraColumns); - end - -end diff --git a/src/subfun/returnNbColumns.m b/src/subfun/returnNbColumns.m deleted file mode 100644 index 18234a7d..00000000 --- a/src/subfun/returnNbColumns.m +++ /dev/null @@ -1,14 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -function nbCol = returnNbColumns(logFile, nameExtraColumn) - % nbCol = returnNbColumns(logFile, nameExtraColumn) - % - - thisExtraColumn = logFile(1).extraColumns.(nameExtraColumn); - - nbCol = 1; - - if isfield(thisExtraColumn, 'length') - nbCol = thisExtraColumn.length; - end -end diff --git a/src/subfun/setDefaultResponses.m b/src/subfun/setDefaultResponses.m deleted file mode 100644 index d9814c45..00000000 --- a/src/subfun/setDefaultResponses.m +++ /dev/null @@ -1,27 +0,0 @@ -% (C) Copyright 2020 CPP_BIDS developers - -function [cfg, responses] = setDefaultResponses(cfg) - - if nargin < 1 - cfg = struct('debug', []); - end - - if ~isfield(cfg, 'debug') || isempty(cfg.debug) - cfg.debug.do = false; - end - - responses{1, 1} = ''; % subjectGrp - responses{2, 1} = ''; % subjectNb - responses{3, 1} = 1; % session - responses{4, 1} = ''; % run - - if cfg.debug.do - - responses{1, 1} = 'ctrl'; - responses{2, 1} = 666; - responses{3, 1} = 666; - responses{4, 1} = 666; - - end - -end diff --git a/src/templates/templateFunction.m b/src/templates/templateFunction.m new file mode 100644 index 00000000..b222ebc9 --- /dev/null +++ b/src/templates/templateFunction.m @@ -0,0 +1,30 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function [argout1, argout2] = templateFunction(argin1, argin2, argin3) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + % .. todo: + % + % - item 1 + % - item 2 + + % The code goes below + +end diff --git a/src/templates/templateFunctionExample.m b/src/templates/templateFunctionExample.m new file mode 100644 index 00000000..de35ef59 --- /dev/null +++ b/src/templates/templateFunctionExample.m @@ -0,0 +1,42 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function templateFunctionExample() + % This function illustrates a documentation test defined for MOdox. + % Other than that it does absolutely nothinghort description of what + % the function does goes here. + % + % Examples: + % a=2; + % disp(a) + % % Expected output is prefixed by '%||' as in the following line: + % %|| 2 + % % + % % The test continues because no interruption through whitespace, + % % as the previous line used a '%' comment character; + % % thus the 'a' variable is still in the namespace and can be + % % accessed. + % b=3+a; + % disp(a+[3 4]) + % %|| [5 6] + % + % % A new test starts here because the previous line was white-space + % % only. Thus the 'a' and 'b' variables are not present here anymore. + % % The following expression raises an error because the 'b' variable + % % is not defined (and does not carry over from the previous test). + % % Because the expected output indicates an error as well, + % % the test passes + % disp(b) + % %|| error('Some error') + % + % % A set of expressions is ignored if there is no expected output + % % (that is, no lines starting with '%||'). + % % Thus, the following expression is not part of any test, + % % and therefore does not raise an error. + % error('this is never executed) + % + % + % % tests end here because test indentation has ended + + % The code goes below + +end diff --git a/src/userInputs.m b/src/userInputs.m index 9264bf8b..4e9db1aa 100644 --- a/src/userInputs.m +++ b/src/userInputs.m @@ -1,17 +1,29 @@ % (C) Copyright 2020 CPP_BIDS developers function cfg = userInputs(cfg) - % cfg = userInputs(cfg) % % Get subject, run and session number and make sure they are % positive integer values. - % Will do ii with a graphic interface if possible. + % Can do a graphic user interface if ``cfg.useGUI`` is set to ``true`` + % + % USAGE:: + % + % cfg = userInputs([cfg]) + % + % :param cfg: Configuration. See ``checkCFG()``. + % :type cfg: structure + % + % :returns: + % + % :cfg: (structure) Configuration update with the name of info about the + % participants. + % + % Behavior of this functions depends on ``cfg.subject.askGrpSess`` + % a 1 X 2 array of booleans (default is ``[true true]``): + % + % - the first value set to ``false`` will skip asking for the participants group + % - the second value set to ``false`` will skip asking for the session % - % expParameters.subject.askGrpSess - % a 1 X 2 array of booleans (default is [true true] ): - % - the first value set to false will skip asking for the participants - % group - % - the second value set to false will skip asking for the session if nargin < 1 cfg = struct('debug', []); diff --git a/src/subfun/checkCppBidsDependencies.m b/src/utils/checkCppBidsDependencies.m similarity index 88% rename from src/subfun/checkCppBidsDependencies.m rename to src/utils/checkCppBidsDependencies.m index c0d794ff..e86503ab 100644 --- a/src/subfun/checkCppBidsDependencies.m +++ b/src/utils/checkCppBidsDependencies.m @@ -1,7 +1,12 @@ % (C) Copyright 2020 CPP_BIDS developers function checkCppBidsDependencies(cfg) - % checkCppBidsDependencies() + % + % Adds dependencies to the matlab path and make sure we got all of them/ + % + % USAGE:: + % + % checkCppBidsDependencies(cfg) % GITHUB_WORKSPACE = getenv('GITHUB_WORKSPACE'); diff --git a/src/utils/createValidName.m b/src/utils/createValidName.m new file mode 100644 index 00000000..8aa0c7e0 --- /dev/null +++ b/src/utils/createValidName.m @@ -0,0 +1,42 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function [name, nameValid] = createValidName(name) + % + % Creates a BIDS valid name: for the task in file names. + % + % USAGE:: + % + % [taskName, taskNameValid] = createTaskName(taskName) + % + % :param taskName: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: string + % + % :returns: + % :name: (string) returns the input with an upper case for first letter + % for all words but the first one (``camelCase``). + % :nameValid: (string) same as above but removes invalid characters (like spaces). + % + % 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. + % + % Example: + % % taskName = 'foo bar'; + % % [taskName, taskNameValid] = createValidName(taskName); + % % disp(taskName), + % % || 'foo Bar' + % % disp(taskNameValid) + % % || 'fooBar' + % + + % camel case: upper case for first letter for all words but the first one + spaceIdx = regexp(name, '[a-zA-Z0-9]*', 'start'); + name(spaceIdx(2:end)) = upper(name(spaceIdx(2:end))); + + % remove invalid characters + [unvalidCharacters] = regexp(name, '[^a-zA-Z0-9]'); + nameValid = name; + nameValid(unvalidCharacters) = []; + +end diff --git a/src/utils/getFullFilename.m b/src/utils/getFullFilename.m new file mode 100644 index 00000000..47ec96bd --- /dev/null +++ b/src/utils/getFullFilename.m @@ -0,0 +1,22 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function fullFilename = getFullFilename(fileName, cfg) + % + % Returns the full path of a file (fo a given subject and modality in a run). + % + % USAGE:: + % + % fullFilename = getFullFilename(fileName, cfg) + % + % :param fileName: + % :type fileName: string + % :param cfg: Configuration. See ``checkCFG()``. + % :type cfg: structure + % + + fullFilename = fullfile( ... + cfg.dir.outputSubject, ... + cfg.fileName.modality, ... + fileName); + +end diff --git a/src/subfun/initializeExtraColumns.m b/src/utils/initializeExtraColumns.m similarity index 75% rename from src/subfun/initializeExtraColumns.m rename to src/utils/initializeExtraColumns.m index 9b9cf8d9..0d974ec9 100644 --- a/src/subfun/initializeExtraColumns.m +++ b/src/utils/initializeExtraColumns.m @@ -1,11 +1,24 @@ % (C) Copyright 2020 CPP_BIDS developers function logFile = initializeExtraColumns(logFile) - % logFile = initializeExtraColumns(logFile) - % initialize the fields for the extra columns - % USAGE - % logfile.extraColumns{'Speed', 'Response key'} - % logFile = initializeExtraColumns(logFile) + % + % Initialize the fields for the extra columns + % + % USAGE:: + % + % logFile = initializeExtraColumns(logFile) + % + % :param logFile: + % :type logFile: structure + % + % :returns: :logFile: (structure) (dimension) + % + % Example:: + % + % logfile.extraColumns{'Speed', 'Response key'} + % logFile = initializeExtraColumns(logFile) + % + % fieldsToSet.length = 1; fieldsToSet.bids.LongName = ''; diff --git a/src/subfun/isPositiveInteger.m b/src/utils/isPositiveInteger.m similarity index 65% rename from src/subfun/isPositiveInteger.m rename to src/utils/isPositiveInteger.m index e3598544..1583ad11 100644 --- a/src/subfun/isPositiveInteger.m +++ b/src/utils/isPositiveInteger.m @@ -1,9 +1,17 @@ % (C) Copyright 2020 CPP_BIDS developers function trueOrFalse = isPositiveInteger(input2check) - % trueOrFalse = isPositiveInteger(input2check) % - % works on column vector of values + % + % + % USAGE:: + % + % trueOrFalse = isPositiveInteger(input2check) + % + % :param input2check: + % :type input2check: column vector + % + % :returns: :trueOrFalse: (boolean) % trueOrFalse = ~any([ ... diff --git a/src/subfun/printCreditsCppBids.m b/src/utils/printCreditsCppBids.m similarity index 72% rename from src/subfun/printCreditsCppBids.m rename to src/utils/printCreditsCppBids.m index 03947463..e6e652e8 100644 --- a/src/subfun/printCreditsCppBids.m +++ b/src/utils/printCreditsCppBids.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function printCreditsCppBids(cfg) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % try version = fileread(fullfile(fileparts(mfilename('fullpath')), ... diff --git a/src/subfun/removeAllDateSuffix.m b/src/utils/removeAllDateSuffix.m similarity index 71% rename from src/subfun/removeAllDateSuffix.m rename to src/utils/removeAllDateSuffix.m index d7ddba32..3abab5fd 100644 --- a/src/subfun/removeAllDateSuffix.m +++ b/src/utils/removeAllDateSuffix.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function removeAllDateSuffix(rawDir, subjName, sesName) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % removeAllDateSuffix(rawDir, subjName, sesName) % diff --git a/src/subfun/removeDateSuffix.m b/src/utils/removeDateSuffix.m similarity index 51% rename from src/subfun/removeDateSuffix.m rename to src/utils/removeDateSuffix.m index ab04cbb2..ae5e8a80 100644 --- a/src/subfun/removeDateSuffix.m +++ b/src/utils/removeDateSuffix.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function removeDateSuffix(filenames, subjectPath) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % removeDateSuffix(filenames, subjectPath) % % diff --git a/src/utils/returnHeaderName.m b/src/utils/returnHeaderName.m new file mode 100644 index 00000000..806f9d2c --- /dev/null +++ b/src/utils/returnHeaderName.m @@ -0,0 +1,32 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function headerName = returnHeaderName(columnName, nbCol, iCol) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + % headerName = returnHeaderName(columnName, nbCol, iCol) + % + + if nbCol == 1 + headerName = sprintf('%s', columnName); + else + headerName = sprintf('%s_%02.0f', columnName, iCol); + end + +end diff --git a/src/utils/returnNamesExtraColumns.m b/src/utils/returnNamesExtraColumns.m new file mode 100644 index 00000000..5b77ee37 --- /dev/null +++ b/src/utils/returnNamesExtraColumns.m @@ -0,0 +1,32 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + % [namesExtraColumns, logFile] = returnNamesExtraColumns(logFile) + % + + namesExtraColumns = []; + + if isfield(logFile, 'extraColumns') && ~isempty(logFile(1).extraColumns) + namesExtraColumns = fieldnames(logFile(1).extraColumns); + end + +end diff --git a/src/utils/returnNbColumns.m b/src/utils/returnNbColumns.m new file mode 100644 index 00000000..920890a6 --- /dev/null +++ b/src/utils/returnNbColumns.m @@ -0,0 +1,33 @@ +% (C) Copyright 2020 CPP_BIDS developers + +function nbCol = returnNbColumns(logFile, nameExtraColumn) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % + % nbCol = returnNbColumns(logFile, nameExtraColumn) + % + + thisExtraColumn = logFile(1).extraColumns.(nameExtraColumn); + + nbCol = 1; + + if isfield(thisExtraColumn, 'length') + nbCol = thisExtraColumn.length; + end +end diff --git a/src/subfun/setDefaultFields.m b/src/utils/setDefaultFields.m similarity index 68% rename from src/subfun/setDefaultFields.m rename to src/utils/setDefaultFields.m index 6cfad781..abcfdc16 100644 --- a/src/subfun/setDefaultFields.m +++ b/src/utils/setDefaultFields.m @@ -1,9 +1,20 @@ % (C) Copyright 2020 CPP_BIDS developers function structure = setDefaultFields(structure, fieldsToSet) - % structure = setDefaultFields(structure, fieldsToSet) % - % recursively loop through the fields of a structure and sets a value if they don't exist + % Recursively loop through the fields of a structure and sets a default value if + % they don't exist. + % + % USAGE:: + % + % structure = setDefaultFields(structure, fieldsToSet) + % + % :param structure: Structure to check. + % :type structure: structure + % :param fieldsToSet: Structure containing the defaults for the missing fields. + % :type fieldsToSet: structure + % + % :returns: :structure: (structure) % fieldsToSet = orderfields(fieldsToSet); diff --git a/src/subfun/transferInfoToBids.m b/src/utils/transferInfoToBids.m similarity index 63% rename from src/subfun/transferInfoToBids.m rename to src/utils/transferInfoToBids.m index f21950fd..a57a68f2 100644 --- a/src/subfun/transferInfoToBids.m +++ b/src/utils/transferInfoToBids.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function fieldsToSet = transferInfoToBids(fieldsToSet, cfg) + % + % Short description of what the function does goes here. + % + % USAGE:: + % + % [argout1, argout2] = templateFunction(argin1, [argin2 == default,] [argin3]) + % + % :param argin1: (dimension) obligatory argument. Lorem ipsum dolor sit amet, + % consectetur adipiscing elit. Ut congue nec est ac lacinia. + % :type argin1: type + % :param argin2: optional argument and its default value. And some of the + % options can be shown in litteral like ``this`` or ``that``. + % :type argin2: string + % :param argin3: (dimension) optional argument + % :type argin3: integer + % + % :returns: - :argout1: (type) (dimension) + % - :argout2: (type) (dimension) + % % fieldsToSet = transferInfoToBids(fieldsToSet, cfg) % % transfer any info that might have been provided by the user to the diff --git a/src/subfun/utilsForTests/setUp.m b/src/utils/utilsForTests/setUp.m similarity index 100% rename from src/subfun/utilsForTests/setUp.m rename to src/utils/utilsForTests/setUp.m