From f346cf13521e9e6e1e9357c339ac1eb7106cc9cc Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 08:03:02 +0100 Subject: [PATCH 01/14] move gui functions in subfolder --- src/{subfun => gui}/askForGroupAndOrSession.m | 0 src/{subfun => gui}/askUserCli.m | 0 src/{subfun => gui}/askUserGui.m | 0 src/{subfun => gui}/getIsQuestionToAsk.m | 0 src/{subfun => gui}/setDefaultResponses.m | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename src/{subfun => gui}/askForGroupAndOrSession.m (100%) rename src/{subfun => gui}/askUserCli.m (100%) rename src/{subfun => gui}/askUserGui.m (100%) rename src/{subfun => gui}/getIsQuestionToAsk.m (100%) rename src/{subfun => gui}/setDefaultResponses.m (100%) diff --git a/src/subfun/askForGroupAndOrSession.m b/src/gui/askForGroupAndOrSession.m similarity index 100% rename from src/subfun/askForGroupAndOrSession.m rename to src/gui/askForGroupAndOrSession.m diff --git a/src/subfun/askUserCli.m b/src/gui/askUserCli.m similarity index 100% rename from src/subfun/askUserCli.m rename to src/gui/askUserCli.m diff --git a/src/subfun/askUserGui.m b/src/gui/askUserGui.m similarity index 100% rename from src/subfun/askUserGui.m rename to src/gui/askUserGui.m diff --git a/src/subfun/getIsQuestionToAsk.m b/src/gui/getIsQuestionToAsk.m similarity index 100% rename from src/subfun/getIsQuestionToAsk.m rename to src/gui/getIsQuestionToAsk.m diff --git a/src/subfun/setDefaultResponses.m b/src/gui/setDefaultResponses.m similarity index 100% rename from src/subfun/setDefaultResponses.m rename to src/gui/setDefaultResponses.m From adbff0f0c4d591c692b9d0dcb51ae6e53ee9b5fa Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 08:04:21 +0100 Subject: [PATCH 02/14] rename subfun folder --- src/{subfun => gui}/createQuestionList.m | 0 src/{subfun => utils}/checkCppBidsDependencies.m | 0 src/{subfun => utils}/createValidName.m | 0 src/{subfun => utils}/getFullFilename.m | 0 src/{subfun => utils}/initializeExtraColumns.m | 0 src/{subfun => utils}/isPositiveInteger.m | 0 src/{subfun => utils}/printCreditsCppBids.m | 0 src/{subfun => utils}/removeAllDateSuffix.m | 0 src/{subfun => utils}/removeDateSuffix.m | 0 src/{subfun => utils}/returnHeaderName.m | 0 src/{subfun => utils}/returnNamesExtraColumns.m | 0 src/{subfun => utils}/returnNbColumns.m | 0 src/{subfun => utils}/setDefaultFields.m | 0 src/{subfun => utils}/transferInfoToBids.m | 0 src/{subfun => utils}/utilsForTests/setUp.m | 0 15 files changed, 0 insertions(+), 0 deletions(-) rename src/{subfun => gui}/createQuestionList.m (100%) rename src/{subfun => utils}/checkCppBidsDependencies.m (100%) rename src/{subfun => utils}/createValidName.m (100%) rename src/{subfun => utils}/getFullFilename.m (100%) rename src/{subfun => utils}/initializeExtraColumns.m (100%) rename src/{subfun => utils}/isPositiveInteger.m (100%) rename src/{subfun => utils}/printCreditsCppBids.m (100%) rename src/{subfun => utils}/removeAllDateSuffix.m (100%) rename src/{subfun => utils}/removeDateSuffix.m (100%) rename src/{subfun => utils}/returnHeaderName.m (100%) rename src/{subfun => utils}/returnNamesExtraColumns.m (100%) rename src/{subfun => utils}/returnNbColumns.m (100%) rename src/{subfun => utils}/setDefaultFields.m (100%) rename src/{subfun => utils}/transferInfoToBids.m (100%) rename src/{subfun => utils}/utilsForTests/setUp.m (100%) diff --git a/src/subfun/createQuestionList.m b/src/gui/createQuestionList.m similarity index 100% rename from src/subfun/createQuestionList.m rename to src/gui/createQuestionList.m diff --git a/src/subfun/checkCppBidsDependencies.m b/src/utils/checkCppBidsDependencies.m similarity index 100% rename from src/subfun/checkCppBidsDependencies.m rename to src/utils/checkCppBidsDependencies.m diff --git a/src/subfun/createValidName.m b/src/utils/createValidName.m similarity index 100% rename from src/subfun/createValidName.m rename to src/utils/createValidName.m diff --git a/src/subfun/getFullFilename.m b/src/utils/getFullFilename.m similarity index 100% rename from src/subfun/getFullFilename.m rename to src/utils/getFullFilename.m diff --git a/src/subfun/initializeExtraColumns.m b/src/utils/initializeExtraColumns.m similarity index 100% rename from src/subfun/initializeExtraColumns.m rename to src/utils/initializeExtraColumns.m diff --git a/src/subfun/isPositiveInteger.m b/src/utils/isPositiveInteger.m similarity index 100% rename from src/subfun/isPositiveInteger.m rename to src/utils/isPositiveInteger.m diff --git a/src/subfun/printCreditsCppBids.m b/src/utils/printCreditsCppBids.m similarity index 100% rename from src/subfun/printCreditsCppBids.m rename to src/utils/printCreditsCppBids.m diff --git a/src/subfun/removeAllDateSuffix.m b/src/utils/removeAllDateSuffix.m similarity index 100% rename from src/subfun/removeAllDateSuffix.m rename to src/utils/removeAllDateSuffix.m diff --git a/src/subfun/removeDateSuffix.m b/src/utils/removeDateSuffix.m similarity index 100% rename from src/subfun/removeDateSuffix.m rename to src/utils/removeDateSuffix.m diff --git a/src/subfun/returnHeaderName.m b/src/utils/returnHeaderName.m similarity index 100% rename from src/subfun/returnHeaderName.m rename to src/utils/returnHeaderName.m diff --git a/src/subfun/returnNamesExtraColumns.m b/src/utils/returnNamesExtraColumns.m similarity index 100% rename from src/subfun/returnNamesExtraColumns.m rename to src/utils/returnNamesExtraColumns.m diff --git a/src/subfun/returnNbColumns.m b/src/utils/returnNbColumns.m similarity index 100% rename from src/subfun/returnNbColumns.m rename to src/utils/returnNbColumns.m diff --git a/src/subfun/setDefaultFields.m b/src/utils/setDefaultFields.m similarity index 100% rename from src/subfun/setDefaultFields.m rename to src/utils/setDefaultFields.m diff --git a/src/subfun/transferInfoToBids.m b/src/utils/transferInfoToBids.m similarity index 100% rename from src/subfun/transferInfoToBids.m rename to src/utils/transferInfoToBids.m 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 From 05d7127856b11c84bfb5c783112b10346c41c839 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 08:21:02 +0100 Subject: [PATCH 03/14] add template functions --- src/templates/templateFunction.m | 29 +++++++++++++++++ src/templates/templateFunctionExample.m | 42 +++++++++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 src/templates/templateFunction.m create mode 100644 src/templates/templateFunctionExample.m diff --git a/src/templates/templateFunction.m b/src/templates/templateFunction.m new file mode 100644 index 00000000..46c52152 --- /dev/null +++ b/src/templates/templateFunction.m @@ -0,0 +1,29 @@ +% (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 diff --git a/src/templates/templateFunctionExample.m b/src/templates/templateFunctionExample.m new file mode 100644 index 00000000..f871f785 --- /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 From 5d8c48adabeb6452238f73facc3363d8041438a9 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 08:48:18 +0100 Subject: [PATCH 04/14] setup doc --- .gitignore | 7 ++ .readthedocs.yml | 26 +++++++ docs/Makefile | 20 +++++ docs/README.md | 108 +++++++++++++++++++++++++++ docs/make.bat | 35 +++++++++ docs/source/_static/cpp_lab_logo.png | Bin 0 -> 14519 bytes docs/source/conf.py | 91 ++++++++++++++++++++++ requirements.txt | 5 ++ 8 files changed, 292 insertions(+) create mode 100644 .readthedocs.yml create mode 100644 docs/Makefile create mode 100644 docs/README.md create mode 100644 docs/make.bat create mode 100644 docs/source/_static/cpp_lab_logo.png create mode 100644 docs/source/conf.py create mode 100644 requirements.txt 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..ec0951f4 --- /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: requirements.txt \ No newline at end of file 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/source/_static/cpp_lab_logo.png b/docs/source/_static/cpp_lab_logo.png new file mode 100644 index 0000000000000000000000000000000000000000..89277c01be2e8aa168a97b0ef45df516b1d91c26 GIT binary patch literal 14519 zcmaJ|Wmr|wwne(TJ4Cvrq#NmwknWW3mhO_01}UYH?ha{??gr`Zc#C`gzW4aP6P&YS zoxSIpbBr;^3RhB)LO~=%gn)oR`6w-}0$%T4AMmi?d0R0d4!l4+iGKV95B|L2O~Szc z2=>ySogg5Xsa_v%+zW(U!G{FS5}MAcc4p3QhK{BXZfBszp z5D?@LAH_vJxn~?@nj2tGuk>XvkC>@)wYp7;NsFGKd&2#qmsS;i2#rj6242# z(*pxX!g8{}?VFOA=tl~K{F{~P?Wed%_SAV3SGRZCj=tFg^BlW=($}fHPNVJci82M4 z(2$)L82g@((2)N6VFL)zRH0!R!mN(}`&&6@fj0qXDoQ#rTT{d)JGi;Ug{YA529^~5 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zXp^RqmZ3sYURR*BVCU4?Mc5*)Xk~O!=~WAjBL00%0iJ=}*EvA(pAY`mw;3;RWKUOY V41;c;z#>D4j}i*v<)Q`w{{su{0H6Q> literal 0 HcmV?d00001 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/requirements.txt b/requirements.txt new file mode 100644 index 00000000..42ea70da --- /dev/null +++ b/requirements.txt @@ -0,0 +1,5 @@ +Sphinx +sphinxcontrib-matlabdomain +sphinxcontrib-napoleon +sphinx_rtd_theme +miss_hit \ No newline at end of file From 1ad6439f81d2420e43a4778b162ac81feee952e9 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 09:56:50 +0100 Subject: [PATCH 05/14] first go at rewriting some help sections --- docs/source/contributing.rst | 104 +++++++++++++++++++++++++++ docs/source/function_description.rst | 20 ++++++ docs/source/index.rst | 31 ++++++++ docs/source/utilities.rst | 22 ++++++ src/createJson.m | 35 +++++---- src/readAndFilterLogfile.m | 38 ++++++---- src/saveEventsFile.m | 78 +++++++++++--------- src/templates/templateFunction.m | 1 + src/userInputs.m | 26 +++++-- src/utils/checkCppBidsDependencies.m | 9 ++- src/utils/createValidName.m | 25 ++++++- src/utils/getFullFilename.m | 12 ++++ src/utils/initializeExtraColumns.m | 23 ++++-- src/utils/isPositiveInteger.m | 16 +++-- src/utils/setDefaultFields.m | 18 +++-- 15 files changed, 373 insertions(+), 85 deletions(-) create mode 100644 docs/source/contributing.rst create mode 100644 docs/source/function_description.rst create mode 100644 docs/source/index.rst create mode 100644 docs/source/utilities.rst 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/src/createJson.m b/src/createJson.m index 3242d133..63a96514 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/readAndFilterLogfile.m b/src/readAndFilterLogfile.m index 1f791bab..47cd847b 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 + % 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) % - % - outputFiltered: dataset with only the specified content, to see it in the command window - % use display(outputFiltered) + % :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)``. + % % 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..4518dd7d 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(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) + % 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(2,1).onset = 3; - % logFile(2,1).trial_type = 'static'; - % logFile(2,1).duration = 4; - % logFile(2,1).is_fixation = 3; + % 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; % % % 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/templates/templateFunction.m b/src/templates/templateFunction.m index 46c52152..35b92f6f 100644 --- a/src/templates/templateFunction.m +++ b/src/templates/templateFunction.m @@ -15,6 +15,7 @@ % 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) diff --git a/src/userInputs.m b/src/userInputs.m index 9264bf8b..54142eb0 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/utils/checkCppBidsDependencies.m b/src/utils/checkCppBidsDependencies.m index c0d794ff..35bdc921 100644 --- a/src/utils/checkCppBidsDependencies.m +++ b/src/utils/checkCppBidsDependencies.m @@ -1,8 +1,13 @@ % (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 index 57b905d4..716250a6 100644 --- a/src/utils/createValidName.m +++ b/src/utils/createValidName.m @@ -1,11 +1,34 @@ % (C) Copyright 2020 CPP_BIDS developers function [name, nameValid] = createValidName(name) - % [taskName, taskNameValid] = createTaskName(taskName) + % + % 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'); diff --git a/src/utils/getFullFilename.m b/src/utils/getFullFilename.m index 5b389d6a..f4be56ef 100644 --- a/src/utils/getFullFilename.m +++ b/src/utils/getFullFilename.m @@ -1,6 +1,18 @@ % (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, ... diff --git a/src/utils/initializeExtraColumns.m b/src/utils/initializeExtraColumns.m index 9b9cf8d9..0d974ec9 100644 --- a/src/utils/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/utils/isPositiveInteger.m b/src/utils/isPositiveInteger.m index e3598544..44f31fa5 100644 --- a/src/utils/isPositiveInteger.m +++ b/src/utils/isPositiveInteger.m @@ -1,10 +1,18 @@ % (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([ ... ~isnumeric(input2check), ... diff --git a/src/utils/setDefaultFields.m b/src/utils/setDefaultFields.m index 6cfad781..9e327e5c 100644 --- a/src/utils/setDefaultFields.m +++ b/src/utils/setDefaultFields.m @@ -1,10 +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); From 1ebaee6030327dd8dd57560ef299cba86c8a5d8d Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 09:59:01 +0100 Subject: [PATCH 06/14] add template to help section to all other functions --- src/checkCFG.m | 19 +++++++++++++++++++ src/convertSourceToRaw.m | 19 +++++++++++++++++++ src/createDataDictionary.m | 19 +++++++++++++++++++ src/createDatasetDescription.m | 19 +++++++++++++++++++ src/gui/askForGroupAndOrSession.m | 19 +++++++++++++++++++ src/gui/askUserCli.m | 19 +++++++++++++++++++ src/gui/askUserGui.m | 19 +++++++++++++++++++ src/gui/createQuestionList.m | 19 +++++++++++++++++++ src/gui/getIsQuestionToAsk.m | 19 +++++++++++++++++++ src/gui/setDefaultResponses.m | 19 +++++++++++++++++++ src/utils/printCreditsCppBids.m | 19 +++++++++++++++++++ src/utils/removeAllDateSuffix.m | 19 +++++++++++++++++++ src/utils/removeDateSuffix.m | 19 +++++++++++++++++++ src/utils/returnHeaderName.m | 19 +++++++++++++++++++ src/utils/returnNamesExtraColumns.m | 19 +++++++++++++++++++ src/utils/returnNbColumns.m | 19 +++++++++++++++++++ src/utils/transferInfoToBids.m | 19 +++++++++++++++++++ 17 files changed, 323 insertions(+) diff --git a/src/checkCFG.m b/src/checkCFG.m index df2a69a8..4e731d63 100644 --- a/src/checkCFG.m +++ b/src/checkCFG.m @@ -1,6 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function cfg = checkCFG(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 = 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..e4441e67 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..f6ca01d0 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..b3a0cff0 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/gui/askForGroupAndOrSession.m b/src/gui/askForGroupAndOrSession.m index bac91022..e9060c41 100644 --- a/src/gui/askForGroupAndOrSession.m +++ b/src/gui/askForGroupAndOrSession.m @@ -1,6 +1,25 @@ % (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]; diff --git a/src/gui/askUserCli.m b/src/gui/askUserCli.m index 46491136..1c25545c 100644 --- a/src/gui/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/gui/askUserGui.m b/src/gui/askUserGui.m index a141c637..032b4568 100644 --- a/src/gui/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/gui/createQuestionList.m b/src/gui/createQuestionList.m index fc2c43b0..e05ea603 100644 --- a/src/gui/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 index a8446235..02a6c5c7 100644 --- a/src/gui/getIsQuestionToAsk.m +++ b/src/gui/getIsQuestionToAsk.m @@ -1,6 +1,25 @@ % (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) diff --git a/src/gui/setDefaultResponses.m b/src/gui/setDefaultResponses.m index d9814c45..ace3e6f0 100644 --- a/src/gui/setDefaultResponses.m +++ b/src/gui/setDefaultResponses.m @@ -1,6 +1,25 @@ % (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', []); diff --git a/src/utils/printCreditsCppBids.m b/src/utils/printCreditsCppBids.m index 03947463..f662e928 100644 --- a/src/utils/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/utils/removeAllDateSuffix.m b/src/utils/removeAllDateSuffix.m index d7ddba32..a27b5889 100644 --- a/src/utils/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/utils/removeDateSuffix.m b/src/utils/removeDateSuffix.m index ab04cbb2..06db002f 100644 --- a/src/utils/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 index fe59cbc3..d92ff78a 100644 --- a/src/utils/returnHeaderName.m +++ b/src/utils/returnHeaderName.m @@ -1,6 +1,25 @@ % (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) % diff --git a/src/utils/returnNamesExtraColumns.m b/src/utils/returnNamesExtraColumns.m index 39b17629..78536ba3 100644 --- a/src/utils/returnNamesExtraColumns.m +++ b/src/utils/returnNamesExtraColumns.m @@ -1,6 +1,25 @@ % (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) % diff --git a/src/utils/returnNbColumns.m b/src/utils/returnNbColumns.m index 18234a7d..f6063089 100644 --- a/src/utils/returnNbColumns.m +++ b/src/utils/returnNbColumns.m @@ -1,6 +1,25 @@ % (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) % diff --git a/src/utils/transferInfoToBids.m b/src/utils/transferInfoToBids.m index f21950fd..2b2140eb 100644 --- a/src/utils/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 From 866d9e2f8fddeb39b00c4187d9e34993f5ca6a24 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 10:01:30 +0100 Subject: [PATCH 07/14] mh_fix --- src/checkCFG.m | 38 ++++++------- src/convertSourceToRaw.m | 38 ++++++------- src/createDataDictionary.m | 38 ++++++------- src/createDatasetDescription.m | 38 ++++++------- src/createJson.m | 8 +-- src/gui/askForGroupAndOrSession.m | 38 ++++++------- src/gui/askUserCli.m | 38 ++++++------- src/gui/askUserGui.m | 38 ++++++------- src/gui/createQuestionList.m | 38 ++++++------- src/gui/getIsQuestionToAsk.m | 38 ++++++------- src/gui/setDefaultResponses.m | 38 ++++++------- src/readAndFilterLogfile.m | 14 ++--- src/saveEventsFile.m | 14 ++--- src/templates/templateFunction.m | 50 ++++++++--------- src/templates/templateFunctionExample.m | 74 ++++++++++++------------- src/userInputs.m | 8 +-- src/utils/checkCppBidsDependencies.m | 14 ++--- src/utils/createValidName.m | 6 +- src/utils/getFullFilename.m | 2 +- src/utils/isPositiveInteger.m | 24 ++++---- src/utils/printCreditsCppBids.m | 38 ++++++------- src/utils/removeAllDateSuffix.m | 38 ++++++------- src/utils/removeDateSuffix.m | 38 ++++++------- src/utils/returnHeaderName.m | 38 ++++++------- src/utils/returnNamesExtraColumns.m | 38 ++++++------- src/utils/returnNbColumns.m | 38 ++++++------- src/utils/setDefaultFields.m | 29 +++++----- src/utils/transferInfoToBids.m | 38 ++++++------- 28 files changed, 445 insertions(+), 444 deletions(-) diff --git a/src/checkCFG.m b/src/checkCFG.m index 4e731d63..4c3a3318 100644 --- a/src/checkCFG.m +++ b/src/checkCFG.m @@ -1,25 +1,25 @@ % (C) Copyright 2020 CPP_BIDS developers function cfg = checkCFG(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) - % + % + % 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 = 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 e4441e67..3684733f 100644 --- a/src/convertSourceToRaw.m +++ b/src/convertSourceToRaw.m @@ -1,25 +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) - % + % + % 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 f6ca01d0..cf1fdf63 100644 --- a/src/createDataDictionary.m +++ b/src/createDataDictionary.m @@ -1,25 +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) - % + % + % 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 b3a0cff0..84007bea 100644 --- a/src/createDatasetDescription.m +++ b/src/createDatasetDescription.m @@ -1,25 +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) - % + % + % 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 63a96514..277d243a 100644 --- a/src/createJson.m +++ b/src/createJson.m @@ -4,8 +4,8 @@ function createJson(varargin) % % Creates the side car JSON file for a run. % - % 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 + % 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. % % USAGE:: @@ -13,9 +13,9 @@ function createJson(varargin) % createJson(cfg [, modality] [, extraInfo]) % createJson(cfg [, extraInfo]) % - % :param cfg: Configuration. See ``checkCFG()``. + % :param cfg: Configuration. See ``checkCFG()``. % :type cfg: structure - % :param modality: can be any of the following ``'beh'``, ``'func'``, ``'eeg'``, + % :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 diff --git a/src/gui/askForGroupAndOrSession.m b/src/gui/askForGroupAndOrSession.m index e9060c41..271644c3 100644 --- a/src/gui/askForGroupAndOrSession.m +++ b/src/gui/askForGroupAndOrSession.m @@ -1,25 +1,25 @@ % (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) - % + % + % 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]; diff --git a/src/gui/askUserCli.m b/src/gui/askUserCli.m index 1c25545c..097465ba 100644 --- a/src/gui/askUserCli.m +++ b/src/gui/askUserCli.m @@ -1,25 +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) - % + % + % 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/gui/askUserGui.m b/src/gui/askUserGui.m index 032b4568..1c72bfcc 100644 --- a/src/gui/askUserGui.m +++ b/src/gui/askUserGui.m @@ -1,25 +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) - % + % + % 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/gui/createQuestionList.m b/src/gui/createQuestionList.m index e05ea603..22d709b6 100644 --- a/src/gui/createQuestionList.m +++ b/src/gui/createQuestionList.m @@ -1,25 +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) - % + % + % 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 index 02a6c5c7..94d5fec1 100644 --- a/src/gui/getIsQuestionToAsk.m +++ b/src/gui/getIsQuestionToAsk.m @@ -1,25 +1,25 @@ % (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) - % + % + % 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) diff --git a/src/gui/setDefaultResponses.m b/src/gui/setDefaultResponses.m index ace3e6f0..cb0d0597 100644 --- a/src/gui/setDefaultResponses.m +++ b/src/gui/setDefaultResponses.m @@ -1,25 +1,25 @@ % (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) - % + % + % 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', []); diff --git a/src/readAndFilterLogfile.m b/src/readAndFilterLogfile.m index 47cd847b..b446f05c 100644 --- a/src/readAndFilterLogfile.m +++ b/src/readAndFilterLogfile.m @@ -2,8 +2,8 @@ function 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. % % USAGE:: % @@ -15,8 +15,8 @@ % (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``, + % 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 @@ -27,11 +27,11 @@ % of the TSV file to read will be infered from there. % :type cfg: structure % - % :returns: + % :returns: % - % :outputFiltered: dataset with only the specified content, to see it + % :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 4518dd7d..6ccf2ee1 100644 --- a/src/saveEventsFile.m +++ b/src/saveEventsFile.m @@ -1,7 +1,7 @@ % (C) Copyright 2020 CPP_BIDS developers function [logFile] = saveEventsFile(action, cfg, logFile) - % + % % Function to save output files for events that will be BIDS compliant. % % USAGE:: @@ -17,7 +17,7 @@ % 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. % Each field will be saved in a separate column. @@ -38,14 +38,14 @@ % % action: % - % - ``'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. + % - ``'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:: - % + % example:: + % % logFile = saveEventsFile('open', cfg, [], 'direction', 'speed', 'target'); % % diff --git a/src/templates/templateFunction.m b/src/templates/templateFunction.m index 35b92f6f..b222ebc9 100644 --- a/src/templates/templateFunction.m +++ b/src/templates/templateFunction.m @@ -1,30 +1,30 @@ -% (C) Copyright 2020 CPP BIDS developers +% (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 + % + % 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 + % The code goes below end diff --git a/src/templates/templateFunctionExample.m b/src/templates/templateFunctionExample.m index f871f785..de35ef59 100644 --- a/src/templates/templateFunctionExample.m +++ b/src/templates/templateFunctionExample.m @@ -1,42 +1,42 @@ -% (C) Copyright 2020 CPP BIDS developers +% (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 + % 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 + % The code goes below end diff --git a/src/userInputs.m b/src/userInputs.m index 54142eb0..4e9db1aa 100644 --- a/src/userInputs.m +++ b/src/userInputs.m @@ -10,15 +10,15 @@ % % cfg = userInputs([cfg]) % - % :param cfg: Configuration. See ``checkCFG()``. + % :param cfg: Configuration. See ``checkCFG()``. % :type cfg: structure % - % :returns: + % :returns: % - % :cfg: (structure) Configuration update with the name of info about the + % :cfg: (structure) Configuration update with the name of info about the % participants. % - % Behavior of this functions depends on ``cfg.subject.askGrpSess`` + % 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 diff --git a/src/utils/checkCppBidsDependencies.m b/src/utils/checkCppBidsDependencies.m index 35bdc921..e86503ab 100644 --- a/src/utils/checkCppBidsDependencies.m +++ b/src/utils/checkCppBidsDependencies.m @@ -1,13 +1,13 @@ % (C) Copyright 2020 CPP_BIDS developers function checkCppBidsDependencies(cfg) - % - % Adds dependencies to the matlab path and make sure we got all of them/ - % - % USAGE:: - % - % checkCppBidsDependencies(cfg) - % + % + % 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 index 716250a6..8aa0c7e0 100644 --- a/src/utils/createValidName.m +++ b/src/utils/createValidName.m @@ -12,8 +12,8 @@ % 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 + % :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). % @@ -24,7 +24,7 @@ % Example: % % taskName = 'foo bar'; % % [taskName, taskNameValid] = createValidName(taskName); - % % disp(taskName), + % % disp(taskName), % % || 'foo Bar' % % disp(taskNameValid) % % || 'fooBar' diff --git a/src/utils/getFullFilename.m b/src/utils/getFullFilename.m index f4be56ef..47ec96bd 100644 --- a/src/utils/getFullFilename.m +++ b/src/utils/getFullFilename.m @@ -10,7 +10,7 @@ % % :param fileName: % :type fileName: string - % :param cfg: Configuration. See ``checkCFG()``. + % :param cfg: Configuration. See ``checkCFG()``. % :type cfg: structure % diff --git a/src/utils/isPositiveInteger.m b/src/utils/isPositiveInteger.m index 44f31fa5..1583ad11 100644 --- a/src/utils/isPositiveInteger.m +++ b/src/utils/isPositiveInteger.m @@ -1,18 +1,18 @@ % (C) Copyright 2020 CPP_BIDS developers function trueOrFalse = isPositiveInteger(input2check) - % - % - % - % USAGE:: - % - % trueOrFalse = isPositiveInteger(input2check) - % - % :param input2check: - % :type input2check: column vector - % - % :returns: :trueOrFalse: (boolean) - % + % + % + % + % USAGE:: + % + % trueOrFalse = isPositiveInteger(input2check) + % + % :param input2check: + % :type input2check: column vector + % + % :returns: :trueOrFalse: (boolean) + % trueOrFalse = ~any([ ... ~isnumeric(input2check), ... diff --git a/src/utils/printCreditsCppBids.m b/src/utils/printCreditsCppBids.m index f662e928..e6e652e8 100644 --- a/src/utils/printCreditsCppBids.m +++ b/src/utils/printCreditsCppBids.m @@ -1,25 +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) - % + % + % 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/utils/removeAllDateSuffix.m b/src/utils/removeAllDateSuffix.m index a27b5889..3abab5fd 100644 --- a/src/utils/removeAllDateSuffix.m +++ b/src/utils/removeAllDateSuffix.m @@ -1,25 +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) - % + % + % 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/utils/removeDateSuffix.m b/src/utils/removeDateSuffix.m index 06db002f..ae5e8a80 100644 --- a/src/utils/removeDateSuffix.m +++ b/src/utils/removeDateSuffix.m @@ -1,25 +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) - % + % + % 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 index d92ff78a..806f9d2c 100644 --- a/src/utils/returnHeaderName.m +++ b/src/utils/returnHeaderName.m @@ -1,25 +1,25 @@ % (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) - % + % + % 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) % diff --git a/src/utils/returnNamesExtraColumns.m b/src/utils/returnNamesExtraColumns.m index 78536ba3..5b77ee37 100644 --- a/src/utils/returnNamesExtraColumns.m +++ b/src/utils/returnNamesExtraColumns.m @@ -1,25 +1,25 @@ % (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) - % + % + % 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) % diff --git a/src/utils/returnNbColumns.m b/src/utils/returnNbColumns.m index f6063089..920890a6 100644 --- a/src/utils/returnNbColumns.m +++ b/src/utils/returnNbColumns.m @@ -1,25 +1,25 @@ % (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) - % + % + % 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) % diff --git a/src/utils/setDefaultFields.m b/src/utils/setDefaultFields.m index 9e327e5c..abcfdc16 100644 --- a/src/utils/setDefaultFields.m +++ b/src/utils/setDefaultFields.m @@ -1,20 +1,21 @@ % (C) Copyright 2020 CPP_BIDS developers function structure = setDefaultFields(structure, fieldsToSet) - % - % 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) - % + % + % 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/utils/transferInfoToBids.m b/src/utils/transferInfoToBids.m index 2b2140eb..a57a68f2 100644 --- a/src/utils/transferInfoToBids.m +++ b/src/utils/transferInfoToBids.m @@ -1,25 +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) - % + % + % 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 From 027fe9709d82da72c0eba12d92295b876e416da4 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 10:09:10 +0100 Subject: [PATCH 08/14] move requirements.txt --- requirements.txt => docs/requirements.txt | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename requirements.txt => docs/requirements.txt (100%) diff --git a/requirements.txt b/docs/requirements.txt similarity index 100% rename from requirements.txt rename to docs/requirements.txt From 9ac130e3297a72d83db73f02bb55379ff3fdbf52 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 10:12:38 +0100 Subject: [PATCH 09/14] update RTD yml file --- .readthedocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yml b/.readthedocs.yml index ec0951f4..6f095f08 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -23,4 +23,4 @@ formats: python: version: 3.7 install: - - requirements: requirements.txt \ No newline at end of file + - requirements: docs/requirements.txt \ No newline at end of file From 0db79052bd4dcdb2736c227e7f7bba36962053b6 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 10:19:08 +0100 Subject: [PATCH 10/14] update travis and remove package-lock --- .travis.yml | 2 +- package-lock.json | 3542 --------------------------------------------- 2 files changed, 1 insertion(+), 3543 deletions(-) delete mode 100644 package-lock.json diff --git a/.travis.yml b/.travis.yml index 009419e7..8d7c3503 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,7 +8,7 @@ dist: bionic # Language and version language: node_js node_js: - - "10" + - "11" cache: apt: true # only works with Pro version 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 @@ -{ - "requires": true, - "lockfileVersion": 1, - "dependencies": { - "@types/unist": { - "version": "2.0.3", - 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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 From 9453523507d63fdeec46d22126da8d07b2f735e3 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 11:11:07 +0100 Subject: [PATCH 12/14] remove node.js from cache in travis CI --- .travis.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index d5fa8977..feb0ac73 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,8 +12,6 @@ node_js: cache: apt: true # only works with Pro version - directories: - - node_modules # NPM packages for the remark markdown linter branches: only: # only run the CI for those branches From dbf56e8c7af22abe924162727735768ef88555d8 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 11:18:42 +0100 Subject: [PATCH 13/14] remove cache in travis CI --- .travis.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index feb0ac73..1a51e3b5 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,9 +10,6 @@ language: node_js node_js: - "11" -cache: - apt: true # only works with Pro version - branches: only: # only run the CI for those branches - master From 132647ee37c197deea64fc61315ee53fb80a946d Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sun, 8 Nov 2020 11:27:18 +0100 Subject: [PATCH 14/14] update linux verion to Focal in Travis CI --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 1a51e3b5..920f26b6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,7 +3,7 @@ # 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