Merge 3261eec into 0fa7b4d

Author: Remi-Gau

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

@@ -1,41 +1,45 @@
-name: miss_hit_quality
+name: miss_hit
 
 on:
   push:
     branches:
       - main
-      - master
       - dev
+    paths:
+      - '**.m'
   pull_request:
     branches: ['*']
+    paths:
+      - '**.m'
 
 jobs:
-  build:
+
+  miss_hit:
 
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        command: ["mh_style", "mh_metric --ci && mh_lint"]
+      fail-fast: true  # cancel all jobs if one fails
+
     steps:
 
-    - name: Install CPP_ROI
-      uses: actions/checkout@v3
+    - uses: actions/checkout@v3
       with:
         submodules: true
         fetch-depth: 1
 
-    - name: Set up Python 3.6
+    - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.6
+        python-version: 3.9
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
         pip3 install -r requirements.txt
 
-    - name: MISS_HIT Metrics
-      run: |
-        mh_metric --ci
-
-    - name: MISS_HIT Bug finder
+    - name: ${{ matrix.command }}
       run: |
-        mh_lint
+        ${{ matrix.command }}

.github/workflows/miss_hit_style.yml

@@ -1,5 +1,4 @@
-[![miss_hit_style](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_style.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_style.yml)
-[![miss_hit_quality](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_quality.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit_quality.yml)
+[![miss_hit](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/miss_hit.yml)
 [![tests and coverage with matlab](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/run_tests_matlab.yml/badge.svg)](https://github.com/cpp-lln-lab/CPP_ROI/actions/workflows/run_tests_matlab.yml)
 [![codecov](https://codecov.io/gh/cpp-lln-lab/CPP_ROI/branch/main/graph/badge.svg?token=8IoRQtbFUV)](https://codecov.io/gh/cpp-lln-lab/CPP_ROI)
 

README.md

@@ -0,0 +1,17 @@
+% (C) Copyright 2020 CPP ROI developers
+
+% Shows how to get the peak coordinate within a ROI
+roiImage = extractRoiFromAtlas(pwd, 'wang', 'V1v', 'L');
+
+% Data to read the maximum from
+gunzip(fullfile(pwd, 'inputs', '*.gz'));
+dataImage = fullfile(pwd, 'inputs', 'TStatistic.nii');
+
+% If there is no value above a certain threshold the function will return NaN
+threshold = 1;
+
+% The image and the ROI must have the same dimension if we want to use the thresold option
+reslicedImages = resliceRoiImages(dataImage, roiImage);
+
+% Get to work.
+[worldCoord, voxelCoord, maxVal] = getPeakCoordinates(dataImage, reslicedImages, threshold);

demos/WIP/get_ROI_Coordinates.m

@@ -23,7 +23,8 @@
 author = "the CPP ROI dev team"
 
 # The full version, including alpha/beta/rc tags
-release = "v0.2.0dev"
+with open('../../version.txt', encoding='utf-8') as version_file:
+    release = version_file.read()
 
 
 # -- General configuration ---------------------------------------------------

demos/roi/get_peak_coordinates.m

@@ -4,7 +4,9 @@ Region of interest
 .. automodule:: src.roi
 
 .. autofunction:: createRoi
+.. autofunction:: getPeakCoordinates
 .. autofunction:: keepHemisphere
+.. autofunction:: plotDataInRoi
 .. autofunction:: thresholdToMask
 .. autofunction:: renameNeuroSynth
 .. autofunction:: resliceRoiImages

docs/source/conf.py

@@ -6,6 +6,7 @@
   %
   % :param referenceImage: better if fullfile path
   % :type referenceImage: string
+  %
   % :param imagesToCheck: better if fullfile path
   % :type imagesToCheck: string
   %