add tests, pre commit and doc

Author: Remi-Gau

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+repos:
+
+-   repo: local
+
+    hooks:
+
+    - id: mh_style
+      name: mh_style
+      entry: mh_style
+      args: [--process-slx, --fix]
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    - id: mh_metric
+      name: mh_metric
+      entry: mh_metric
+      args: [--ci]
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit_core]
+
+    - id: mh_lint
+      name: mh_lint
+      entry: mh_lint
+      files: ^(.*\.(m|slx))$
+      language: python
+      additional_dependencies: [miss_hit]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.0.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files

README.md

@@ -85,6 +85,7 @@ TODO
 
 -   Can help generate ROI based on:
     -   the SPM Anatomy toolbox (INSERT URL)
+    -   the SPM neuromorphometric atlas
     -   neurosynth probabilty maps
     -   the probabilistic maps of visual topography in human cortex:
         -   https://scholar.princeton.edu/napl/resources
@@ -98,6 +99,8 @@ Also includes:
 -   Yeo's 7 networks "atlas"
     -   add REF and URL
 
+
+
 ## Contributing
 
 ## Contributors

atlas/space-IXI549Space_desc-neuromorphometrics_dseg.nii

@@ -18,3 +18,7 @@ help:
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+
+doc:
+	@$(SPHINXBUILD) -b html "$(SOURCEDIR)" "$(BUILDDIR)"

atlas/space-IXI549Space_desc-neuromorphometrics_mask.json

@@ -0,0 +1,23 @@
+Function description
+********************
+
+ROI
+===
+
+.. automodule:: src.roi
+
+.. autofunction:: createRoi
+
+Atlas
+=====
+
+.. automodule:: src.atlas
+
+.. autofunction:: returnAtlasDir
+
+Utilities
+=========
+
+.. automodule:: src.utils
+
+.. autofunction:: renameFile

docs/Makefile

@@ -1,63 +1,11 @@
-.. 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 SPM BIDS pipeline documentation!
-***********************************************
+Welcome to CPP_ROI documentation!
+*********************************
 
 .. toctree::
    :maxdepth: 2
    :caption: Content
 
-   set_up
-   workflows
-   QA
-   defaults
-   batches
    function_description
-   method_section_boilerplate
-   mancoreg
-   docker
-   contributing
-
-This pipeline contains a set of functions to run fMRI analysis on a
-[BIDS data set](https://bids.neuroimaging.io/) using SPM12.
-
-This can perform:
-
--   slice timing correction,
--   spatial preprocessing:
-
-    -   realignment, coregistration `func` to `anat`, `anat` segmention,
-        normalization to MNI space
-    -   realignm and unwarp, coregistration `func` to `anat`, `anat` segmention
-
--   smoothing,
--   Quality analysis:
-
-    -   for anatomical data
-    -   for functional data
--   GLM at the subject level
--   GLM at the group level à la SPM (meaning using a summary statistics approach).
-
-It can also prepare the data to run an MVPA analysis by running a GLM for each
-subject on non-normalized images and get one beta image for each condition to be
-used in the MVPA.
-
-
-Assumptions
-===========
-
-At the moment this pipeline makes some assumptions:
-
--   it assumes that the dummy scans have been removed from the BIDS data set and
-    it can jump straight into pre-processing,
--   it assumes the metadata for a given task are the same as those the first run
-    of the first subject this pipeline is being run on,
--   it assumes that group are defined in the subject field (eg `sub-ctrl01`,
-    `sub-blind01`, ...) and not in the `participants.tsv` file.
-
 
 
 Indices and tables

docs/source/function_description.rst

@@ -0,0 +1,3 @@
+# This is here to keep pre-commit-ci from going ape and running on the content
+# of this folder.
+enable: false

docs/source/index.rst

@@ -1,5 +1,7 @@
+project_root
+
 # styly guide (https://florianschanda.github.io/miss_hit/style_checker.html)
-line_length: 100
+line_length: 120
 
 regex_function_name: "[a-z]+(_*([a-zA-Z0-9]){1}[A-Za-z]+)*" # almost anything goes in the root folder
 regex_script_name: "[a-z0-9]+(_[a-z0-9]+)*"
@@ -13,5 +15,5 @@ tab_width: 2
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
 metric "file_length": limit 400
-metric "cyc": limit 12
-metric "parameters": limit 6
+metric "cyc": limit 16
+metric "parameters": limit 7

lib/miss_hit.cfg

@@ -11,13 +11,13 @@
     else
       sourceImage = maxProbaFiles(2, :);
     end
-    
+
   elseif   strcmp(atlas, 'neuromorphometrics')
-      
-      sourceImage = fullfile(returnAtlasDir(), 'space-IXI549Space_desc-neuromorphometrics_dseg.nii');
-      
-      roiLabels = getRoiLabelLookUpTable(atlas);
-    
+
+    sourceImage = fullfile(returnAtlasDir(), 'space-IXI549Space_desc-neuromorphometrics_dseg.nii');
+
+    roiLabels = getRoiLabelLookUpTable(atlas);
+
   end
 
   roiIdx = strcmp(roiName, roiLabels.ROI);