fix conflicts

Author: Remi-Gau

.github/workflows/miss_hit.yml renamed to .github/workflows/miss_hit_quality.yml

@@ -1,4 +1,4 @@
-name: miss_hit
+name: miss_hit_quality
 
 on:
   push:
@@ -28,10 +28,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
-
-    - name: MISS_HIT Code style
-      run: |
-        mh_style --process-slx
+        cd tests
+        make data
 
     - name: MISS_HIT Metrics
       run: |

.github/workflows/miss_hit_style.yml

@@ -0,0 +1,36 @@
+name: miss_hit_style
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches: '*'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+        fetch-depth: 1
+
+    - name: Set up Python 3.6
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.6
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip3 install -r requirements.txt
+        cd tests
+        make data
+
+    - name: MISS_HIT Code style
+      run: |
+        mh_style

.github/workflows/run_tests.yml

@@ -1,15 +1,15 @@
 name: tests and coverage
 
 # Uses the cron schedule for github actions
-# 
+#
 # https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
-# 
+#
 # ┌───────────── minute (0 - 59)
 # │ ┌───────────── hour (0 - 23)
 # │ │ ┌───────────── day of the month (1 - 31)
 # │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
 # │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
-# │ │ │ │ │                                   
+# │ │ │ │ │
 # │ │ │ │ │
 # │ │ │ │ │
 # * * * * *
@@ -41,7 +41,7 @@ jobs:
         sudo apt-get -y install octave liboctave-dev
         sudo apt-get -y install nodejs npm
 
-    - name: Clone cpp_spm         
+    - name: Clone cpp_spm
       uses: actions/checkout@v2
       with:
         submodules: true
@@ -60,16 +60,19 @@ jobs:
         git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
         make -C MOxUnit install
         git clone https://github.com/MOcov/MOcov.git --depth 1
-        make -C MOcov install    
-        
+        make -C MOcov install
+
+    - name: Add bids-matlab
+      run: |
+        git clone https://github.com/bids-standard/bids-matlab.git --depth 1
+
     - name: Update octave path
       run: |
         octave $OCTFLAGS --eval "initCppRoi; savepath();"
-        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"        
+        octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'bids-matlab')); savepath();"
 
     - name: Run tests
       run: |
-        octave $OCTFLAGS --eval "runTests"
+        octave $OCTFLAGS --eval "run_tests"
         cat test_report.log | grep 0
-        bash <(curl -s https://codecov.io/bash)         
-
+        bash <(curl -s https://codecov.io/bash)

.gitignore

@@ -1,32 +1,30 @@
 
 .DS_Store
+
+*.nii
+
 *.asv
 *.m~
 *.mat
-*.xml
-*.log
-*.html
-*.zip
-*.ps
-
-
 
+<<<<<<< HEAD
 # files in the demo folder related to running the demo analysis
 # demos/roi
+=======
+atlas/visual_topography_probability_atlas/
+>>>>>>> 4a2a3830905dfad9b61804bf99e2941a49e4e2fa
 
 # test folder and dummy data
 
 # ignore content of the build folder of the doc
 docs/build/*
 
 # ignore virtual env
-cpp_spm/*
 envs/*
 
 # visual studio code stuff
 .vscode
 
-
-
-
-
+demos/*/*.json
+demos/*/*/*.json
+demos/*/derivatives

.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: v4.0.1
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files

.readthedocs.yml

@@ -23,4 +23,4 @@ formats:
 python:
   version: 3.7
   install:
-    - requirements: requirements.txt
+    - requirements: requirements.txt

README.md

@@ -12,10 +12,96 @@
 
 # CPP ROI
 
+## :warning: :warning: :warning:
+
+**This code is fairly unstable (:boom:) and might still change a lot.**
+
+Also this code currently has 0% test coverage...
+
+---
+
+Set of Octave and Matlab functions, demos and scripts to help manage ROIs and to
+play nice with BIDS datasets.
+
+Mostly volume-based and SPM centric.
+
+For surface based and freesurfer ROIs see for example:
+
+-   https://github.com/noahbenson/neuropythy
+
 ## Installation
 
+Download this repository and unzip the content where you want to install it.
+
+Or clone the repo.
+
+```bash
+git clone https://github.com/cpp-lln-lab/CPP_ROI.git
+```
+
+Fire up Octave or Matlab and type
+
+```matlab
+
+cd CPP_ROI
+
+% Th following adds the relevant folders to your path.
+% This needs to be done once per session (your path will not be saved)
+
+initCppRoi
+
+```
+
+If you are using CPP_SPM, you got nothing to do as CPP_ROI is already installed
+as a submodule, and intitialized when running `initCppSpm`.
+
 ### Dependencies
 
+<<<<<<< HEAD
+=======
+TODO
+
+| Dependencies                                               | Used version |
+| ---------------------------------------------------------- | ------------ |
+| [Matlab](https://www.mathworks.com/products/matlab.html)   | 20???        |
+| or [octave](https://www.gnu.org/software/octave/)          | 4.?          |
+| [SPM12](https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) | v7487        |
+
+-   bids-matlab (INSERT URL)
+
+-   currently still needs some CPP_SPM function but ultimately should be
+    standalone: this will most likely happen when some functions are passed to
+    bids-matlab
+
+-   Other dependencies (MarsBar) are shipped with CPP_ROI in the `lib` folder.
+
+## Features
+
+-   create ROI from probability maps
+-   create ROI filenames that "BIDS-ish"
+-   extract ROI with a given numerical label
+-   extract ROI from one hemisphere
+-   breaks a cluster image into several ROIs with each their own label
+
+### Atlas
+
+-   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
+        -   Wang, L., Mruczek, R. E., Arcaro, M. J., & Kastner, S. (2015).
+            Probabilistic Maps of Visual Topography in Human Cortex. Cerebral
+            cortex (New York, N.Y. : 1991), 25(10), 3911–3931.
+            https://doi.org/10.1093/cercor/bhu277
+
+Also includes:
+
+-   Yeo's 7 networks "atlas"
+    -   add REF and URL
+
+>>>>>>> 4a2a3830905dfad9b61804bf99e2941a49e4e2fa
 
 
 ## Contributing