Merge pull request #482 from Remi-Gau/remi-job_mat_to_mfile

[ENH] save jobs as m file
cpp-lln-lab · Jan 21, 2022 · be9ba3f · be9ba3f
2 parents 9d0275f + d5fcb7e
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diff --git a/CITATION.cff b/CITATION.cff
@@ -3,7 +3,7 @@ cff-version: 1.2.0
 title: "CPP SPM"
 
 version: 1.1.4dev
- 
+
 abstract: CPP_SPM is a set pipelines and tools for Octave/MATLAB to process and analyze BIDS data sets using SPM.
 
 message: "If you use this software, please cite it as below."

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,65 @@
+## Contributing guidelines
+
+Feel free to open issues to report a bug and ask for improvements.
+
+If you want to contribute, have a look at our
+[contributing guidelines](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md)
+that are meant to guide you and help you get started. If something is not clear
+or you get stuck: it is more likely we did not do good enough a job at
+explaining things. So do not hesitate to open an issue, just to ask for
+clarification.
+
+### Style guidelines
+
+We use `camelCase` to name functions and variables for the vast majority of the
+code in this repository.
+
+Scripts names in general and as well functions related to the demos use a
+`snake_case`.
+
+Constant are written in `UPPERCASE`.
+
+#### Input arguments ordering
+
+From more general to more specific
+
+`BIDS` > `opt` > `subject` > `session` > `run`
+
+-   `BIDS` (output from `getData` or `bids.layout`) restrict the set of possible
+    analysis one can run to this BIDS data set
+-   `opt` restricts this set even further
+-   `subject` / `session` / `run` even more
+
+```matlab
+% OK
+varargout = getInfo(BIDS, opt, subLabel, info, varargin)
+
+% not OK
+varargout = getInfo(subLabel, BIDS, opt, info, varargin)
+```
+
+#### Output arguments ordering
+
+Try to return them in order of importance first and in order of appearance
+otherwise.
+
+#### Exceptions
+
+If function creates or modifies a batch then `matlabbatch` is the first `argin`
+and first `argout`.
+
+If a function performs an "action" to be chosen from a one of several strings
+(with a switch statement), this string comes as first `argin` or second if
+`matlabbatch` is first.
+
+```matlab
+% OK
+varargout = getInfo('filename', BIDS, opt, subID, varargin)
+[matlabbatch, voxDim] = setBatchRealign(matlabbatch, [action = 'realign',] BIDS, opt, subID)
+
+% not OK
+% 'filename' is the name of the "action" or the info to get in this case
+% batch and action should go first
+varargout = getInfo(BIDS, opt, subID, 'filename', varargin)
+[matlabbatch, voxDim] = setBatchRealign(BIDS, opt, subID, matlabbatch, [action = 'realign'])
+```
diff --git a/Makefile b/Makefile
@@ -13,4 +13,3 @@ validate_cff: CITATION.cff
 
 manual:
 	cd docs && sh create_manual.sh
-
diff --git a/README.md b/README.md
@@ -71,76 +71,6 @@ Please see our
 [documentation](https://cpp_spm.readthedocs.io/en/latest/index.html) for more
 info.
 
-## Contributing
-
-Feel free to open issues to report a bug and ask for improvements.
-
-If you want to contribute, have a look at our
-[contributing guidelines](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md)
-that are meant to guide you and help you get started. If something is not clear
-or you get stuck: it is more likely we did not do good enough a job at
-explaining things. So do not hesitate to open an issue, just to ask for
-clarification.
-
-### Style guidelines
-
-These are some of the guidelines we try to follow. Several of them are described
-in our our
-[contributing guidelines](https://github.com/cpp-lln-lab/.github/blob/main/CONTRIBUTING.md).
-
-We use `camelCase` to name functions and variables for the vast majority of the
-code in this repository.
-
-Scripts names in general and as well functions related to the demos use a
-`snake_case`.
-
-Constant are written in `UPPERCASE`.
-
-#### Input arguments ordering
-
-From more general to more specific
-
-`BIDS` > `opt` > `subject` > `session` > `run`
-
--   `BIDS` (output from `getData` or `bids.layout`) restrict the set of possible
-    analysis one can run to this BIDS data set
--   `opt` restricts this set even further
--   `subject` / `session` / `run` even more
-
-```matlab
-% OK
-varargout = getInfo(BIDS, opt, subLabel, info, varargin)
-
-% not OK
-varargout = getInfo(subLabel, BIDS, opt, info, varargin)
-```
-
-#### Output arguments ordering
-
-Try to return them in order of importance first and in order of appearance
-otherwise.
-
-#### Exceptions
-
-If function creates or modifies a batch then `matlabbatch` is the first `argin`
-and first `argout`.
-
-If a function performs an "action" to be chosen from a one of several strings
-(with a switch statement), this string comes as first `argin` or second if
-`matlabbatch` is first.
-
-```matlab
-% OK
-varargout = getInfo('filename', BIDS, opt, subID, varargin)
-[matlabbatch, voxDim] = setBatchRealign(matlabbatch, [action = 'realign',] BIDS, opt, subID)
-
-% not OK
-% 'filename' is the name of the "action" or the info to get in this case
-% batch and action should go first
-varargout = getInfo(BIDS, opt, subID, 'filename', varargin)
-[matlabbatch, voxDim] = setBatchRealign(BIDS, opt, subID, matlabbatch, [action = 'realign'])
-```
-
 ## Citation
 
 ```bibtex

diff --git a/docs/source/architecture.rst b/docs/source/architecture.rst
@@ -74,40 +74,66 @@ Batches
 Low level functions description
 ===============================
 
-Utility functions
------------------
+BIDS related functions
+----------------------
 
-.. automodule:: src.utils
+.. automodule:: src.bids
 
-.. autofunction:: cleanCrash
+.. autofunction:: initBids
 
-.. autofunction:: saveOptions
-.. autofunction:: loadAndCheckOptions
+.. autofunction:: addStcToQuery
+.. autofunction:: removeEmptyQueryFields
+
+.. autofunction:: getROIs
 
-.. autofunction:: getInfo
 .. autofunction:: getData
 
-.. autofunction:: setDirectories
-.. autofunction:: createDataDictionary
-.. autofunction:: createDerivativeDir
-.. autofunction:: createGlmDirName
+.. autofunction:: getInfo
+.. autofunction:: getSubjectList
+.. autofunction:: getAndCheckRepetitionTime
+.. autofunction:: getAndCheckSliceOrder
 
-.. autofunction:: getAnatFilename
-.. autofunction:: getBoldFilename
-.. autofunction:: getMeanFuncFilename
 .. autofunction:: getTpmFilename
+.. autofunction:: getMeanFuncFilename
+.. autofunction:: getBoldFilename
+.. autofunction:: getAnatFilename
 
-.. autofunction:: getFuncVoxelDims
-.. autofunction:: getAndCheckSliceOrder
-.. autofunction:: getSubjectList
+Input / Output
+--------------
+
+.. automodule:: src.IO
+
+.. autofunction:: saveOptions
+.. autofunction:: loadAndCheckOptions
+
+.. autofunction:: overwriteDir
+.. autofunction:: createDerivativeDir
+
+.. autofunction:: saveSpmScript
+
+.. autofunction:: unzipAndReturnsFullpathName
+
+.. autofunction:: onsetsMatToTsv
+.. autofunction:: regressorsMatToTsv
 
-.. autofunction:: renameSegmentParameter
 .. autofunction:: renameUnwarpParameter
+.. autofunction:: renameSegmentParameter
+
+.. autofunction:: cleanCrash
+
+Utility functions
+-----------------
+
+.. automodule:: src.utils
+
+.. autofunction:: createDataDictionary
+.. autofunction:: createGlmDirName
+
+.. autofunction:: getFuncVoxelDims
 
 .. autofunction:: rmTrialTypeStr
 .. autofunction:: setFields
 
-.. autofunction:: unzipAndReturnsFullpathName
 .. autofunction:: validationInputFile
 
 

diff --git a/docs/source/defaults.rst b/docs/source/defaults.rst
@@ -11,6 +11,7 @@ checkOptions
 ============
 
 .. autofunction:: checkOptions
+.. autofunction:: setDirectories
 
 spm_my_defaults
 ===============

diff --git a/docs/source/function_description.rst b/docs/source/function_description.rst
diff --git a/docs/source/set_up.rst b/docs/source/set_up.rst
@@ -28,7 +28,7 @@ Selecting groups and subjects
 The way to select certain subjects is summarised in the documentation of the
 :func:`src/utils/getSubjectList` function.
 
-.. automodule:: src.utils
+.. automodule:: src.bids
 
 .. autofunction:: getSubjectList
     :noindex:

diff --git a/lib/miss_hit.cfg b/lib/miss_hit.cfg
@@ -1,2 +1 @@
 enable: false
-
diff --git a/requirements.txt b/requirements.txt
@@ -8,4 +8,3 @@ pre-commit
 jupyterlab
 octave_kernel
 rstcheck
-
diff --git a/src/utils/cleanCrash.m → src/IO/cleanCrash.m b/src/utils/cleanCrash.m → src/IO/cleanCrash.m
diff --git a/src/utils/createDerivativeDir.m → src/IO/createDerivativeDir.m b/src/utils/createDerivativeDir.m → src/IO/createDerivativeDir.m
diff --git a/src/utils/getData.m → src/IO/getData.m b/src/utils/getData.m → src/IO/getData.m
diff --git a/src/utils/loadAndCheckOptions.m → src/IO/loadAndCheckOptions.m b/src/utils/loadAndCheckOptions.m → src/IO/loadAndCheckOptions.m
diff --git a/src/utils/onsetsMatToTsv.m → src/IO/onsetsMatToTsv.m b/src/utils/onsetsMatToTsv.m → src/IO/onsetsMatToTsv.m
diff --git a/src/utils/overwriteDir.m → src/IO/overwriteDir.m b/src/utils/overwriteDir.m → src/IO/overwriteDir.m
diff --git a/src/utils/regressorsMatToTsv.m → src/IO/regressorsMatToTsv.m b/src/utils/regressorsMatToTsv.m → src/IO/regressorsMatToTsv.m
diff --git a/src/utils/renameSegmentParameter.m → src/IO/renameSegmentParameter.m b/src/utils/renameSegmentParameter.m → src/IO/renameSegmentParameter.m
diff --git a/src/utils/renameUnwarpParameter.m → src/IO/renameUnwarpParameter.m b/src/utils/renameUnwarpParameter.m → src/IO/renameUnwarpParameter.m
diff --git a/src/utils/saveOptions.m → src/IO/saveOptions.m b/src/utils/saveOptions.m → src/IO/saveOptions.m
@@ -19,9 +19,7 @@ function saveOptions(opt)
     taskString = ['_task-', strjoin(opt.taskName, '')];
   end
 
-  filename = fullfile(optionDir, [timeStamp(), '_options', ...
-                                  taskString, ...
-                                  '.json']);
+  filename = fullfile(optionDir, ['options', taskString, '_', timeStamp(), '.json']);
 
   jsonFormat.indent = '    ';
   spm_jsonwrite(filename, opt, jsonFormat);