add tests, refactor and make sure output names are more bids compliant

.github/workflows/miss_hit.yml → .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

@@ -1,23 +1,23 @@
 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)
-# │ │ │ │ │                                   
+# │ │ │ │ │
 # │ │ │ │ │
 # │ │ │ │ │
 # * * * * *
 
 on:
   push:
     branches:
-      - dev
+      - '*'
   pull_request:
     branches: '*'
   schedule:
@@ -39,7 +39,7 @@ 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
@@ -58,20 +58,19 @@ 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      
-        
+      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, 'bids-matlab')); 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

@@ -20,7 +20,6 @@ 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: v2.0.0
+  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

@@ -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.csv

@@ -0,0 +1,137 @@
+label,ROI
+4,3rd Ventricle
+11,4th Ventricle
+23,Right Accumbens Area
+30,Left Accumbens Area
+31,Right Amygdala
+32,Left Amygdala
+35,Brain Stem
+36,Right Caudate
+37,Left Caudate
+38,Right Cerebellum Exterior
+39,Left Cerebellum Exterior
+40,Right Cerebellum White Matter
+41,Left Cerebellum White Matter
+44,Right Cerebral White Matter
+45,Left Cerebral White Matter
+46,CSF
+47,Right Hippocampus
+48,Left Hippocampus
+49,Right Inf Lat Vent
+50,Left Inf Lat Vent
+51,Right Lateral Ventricle
+52,Left Lateral Ventricle
+55,Right Pallidum
+56,Left Pallidum
+57,Right Putamen
+58,Left Putamen
+59,Right Thalamus Proper
+60,Left Thalamus Proper
+61,Right Ventral DC
+62,Left Ventral DC
+63,Right vessel
+64,Left vessel
+69,Optic Chiasm
+71,Cerebellar Vermal Lobules I-V
+72,Cerebellar Vermal Lobules VI-VII
+73,Cerebellar Vermal Lobules VIII-X
+75,Left Basal Forebrain
+76,Right Basal Forebrain
+100,Right ACgG anterior cingulate gyrus
+101,Left ACgG anterior cingulate gyrus
+102,Right AIns anterior insula
+103,Left AIns anterior insula
+104,Right AOrG anterior orbital gyrus
+105,Left AOrG anterior orbital gyrus
+106,Right AnG angular gyrus
+107,Left AnG angular gyrus
+108,Right Calc calcarine cortex
+109,Left Calc calcarine cortex
+112,Right CO central operculum
+113,Left CO central operculum
+114,Right Cun cuneus
+115,Left Cun cuneus
+116,Right Ent entorhinal area
+117,Left Ent entorhinal area
+118,Right FO frontal operculum
+119,Left FO frontal operculum
+120,Right FRP frontal pole
+121,Left FRP frontal pole
+122,Right FuG fusiform gyrus
+123,Left FuG fusiform gyrus
+124,Right GRe gyrus rectus
+125,Left GRe gyrus rectus
+128,Right IOG inferior occipital gyrus
+129,Left IOG inferior occipital gyrus
+132,Right ITG inferior temporal gyrus
+133,Left ITG inferior temporal gyrus
+134,Right LiG lingual gyrus
+135,Left LiG lingual gyrus
+136,Right LOrG lateral orbital gyrus
+137,Left LOrG lateral orbital gyrus
+138,Right MCgG middle cingulate gyrus
+139,Left MCgG middle cingulate gyrus
+140,Right MFC medial frontal cortex
+141,Left MFC medial frontal cortex
+142,Right MFG middle frontal gyrus
+143,Left MFG middle frontal gyrus
+144,Right MOG middle occipital gyrus
+145,Left MOG middle occipital gyrus
+146,Right MOrG medial orbital gyrus
+147,Left MOrG medial orbital gyrus
+148,Right MPoG postcentral gyrus medial segment
+149,Left MPoG postcentral gyrus medial segment
+150,Right MPrG precentral gyrus medial segment
+151,Left MPrG precentral gyrus medial segment
+152,Right MSFG superior frontal gyrus medial segment
+153,Left MSFG superior frontal gyrus medial segment
+154,Right MTG middle temporal gyrus
+155,Left MTG middle temporal gyrus
+156,Right OCP occipital pole
+157,Left OCP occipital pole
+160,Right OFuG occipital fusiform gyrus
+161,Left OFuG occipital fusiform gyrus
+162,Right OpIFG opercular part of the inferior frontal gyrus
+163,Left OpIFG opercular part of the inferior frontal gyrus
+164,Right OrIFG orbital part of the inferior frontal gyrus
+165,Left OrIFG orbital part of the inferior frontal gyrus
+166,Right PCgG posterior cingulate gyrus
+167,Left PCgG posterior cingulate gyrus
+168,Right PCu precuneus
+169,Left PCu precuneus
+170,Right PHG parahippocampal gyrus
+171,Left PHG parahippocampal gyrus
+172,Right PIns posterior insula
+173,Left PIns posterior insula
+174,Right PO parietal operculum
+175,Left PO parietal operculum
+176,Right PoG postcentral gyrus
+177,Left PoG postcentral gyrus
+178,Right POrG posterior orbital gyrus
+179,Left POrG posterior orbital gyrus
+180,Right PP planum polare
+181,Left PP planum polare
+182,Right PrG precentral gyrus
+183,Left PrG precentral gyrus
+184,Right PT planum temporale
+185,Left PT planum temporale
+186,Right SCA subcallosal area
+187,Left SCA subcallosal area
+190,Right SFG superior frontal gyrus
+191,Left SFG superior frontal gyrus
+192,Right SMC supplementary motor cortex
+193,Left SMC supplementary motor cortex
+194,Right SMG supramarginal gyrus
+195,Left SMG supramarginal gyrus
+196,Right SOG superior occipital gyrus
+197,Left SOG superior occipital gyrus
+198,Right SPL superior parietal lobule
+199,Left SPL superior parietal lobule
+200,Right STG superior temporal gyrus
+201,Left STG superior temporal gyrus
+202,Right TMP temporal pole
+203,Left TMP temporal pole
+204,Right TrIFG triangular part of the inferior frontal gyrus
+205,Left TrIFG triangular part of the inferior frontal gyrus
+206,Right TTG transverse temporal gyrus
+207,Left TTG transverse temporal gyrus

demos/atlas/create_roi_from_atlas.m

@@ -1,10 +1,12 @@
+% (C) Copyright 2021 CPP ROI developers
+
 opt.roi.atlas = 'wang';
 opt.roi.name = {'V1v', 'V1d'};
 opt.roi.dir = fullfile(pwd, 'derivatives', 'cpp_roi', 'group');
 
 spm_mkdir(opt.roi.dir);
 
-hemi = {'lh', 'rh'};
+hemi = {'L', 'H'};
 
 for iHemi = 1:numel(hemi)
 

demos/roi/neurosynth_left_right_rois.m

@@ -0,0 +1,26 @@
+% (C) Copyright 2021 CPP ROI developers
+
+% small demo to show how to create and rename ROIs that come from neurosynth
+% and how to only keep the data from one hemisphere of an image.
+
+run ../../initCppRoi;
+
+gunzip(fullfile('inputs', '*.gz'));
+zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
+
+zMap = renameNeuroSynth(zMap);
+roiImage = thresholdToMask(zMap, 5);
+
+% keep only one hemisphere and appends a 'hs--[hemisphere label]'
+leftRoiImage = keepHemisphere(roiImage, 'L');
+rightRoiImage = keepHemisphere(roiImage, 'R');
+
+% change the label entity and remove the hs one
+leftRoiImage = renameFile(leftRoiImage, ...
+                          struct('entities', struct( ...
+                                                    'label', 'ns left motion', ...
+                                                    'hemi', '')));
+rightRoiImage = renameFile(rightRoiImage, ...
+                           struct('entities', struct( ...
+                                                     'label', 'ns right motion', ...
+                                                     'hemi', '')));