Merge branch 'main' into update-canon-phantoms

.github/workflows/phantoms.yaml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - main
+      - switch-phantoms-to-s3
   pull_request:
     branches:
       - main
@@ -66,6 +67,18 @@ jobs:
             brew install dcm2niix
           fi
 
+      - name: Debug
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
+
+      - name: Check dcm2niix is installed and on path
+        if: runner.os != 'Windows'
+        run:
+          dcm2niix -h 
+
       - name: Install dcm2niix windows
         if: runner.os == 'Windows'
         run: |
@@ -84,7 +97,6 @@ jobs:
         run: |
           cd pypet2bids
           pip install .
-          pip install gdown
 
       - name: Install Poetry Build Package
         run: |
@@ -99,9 +111,9 @@ jobs:
       - name: Install BIDS Validator
         run: npm install -g bids-validator
 
-      - name: Collect Phantoms from Google Drive
+      - name: Collect Phantoms
         if: ${{ steps.cache-phantoms.outputs.cache-hit != 'true' }} && ${{ !env.ACT }}
-        run: gdown ${{ secrets.ZIPPED_OPEN_NEURO_PET_PHANTOMS_URL }} -O PHANTOMS.zip
+        run: wget -O PHANTOMS.zip https://openneuropet.s3.amazonaws.com/US-sourced-OpenNeuroPET-Phantoms.zip
 
       - name: Decompress phantoms windows
         if: steps.cache-phantoms.outputs.cache-hit != 'true' && !env.ACT && runner.os == 'Windows'

.github/workflows/python.yaml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - main
+      - switch-phantoms-to-s3
   workflow_call:
   workflow_dispatch:
     inputs:
@@ -18,8 +19,7 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     env:
-      ECAT_TEST_FOLDER: "cimbi36"
-      REAL_TEST_ECAT_PATH: cimbi36/Gris_102_19_2skan-2019.04.30.13.04.41_em_3d.v
+      REAL_ECAT_TEST_PATH: ${{ github.workspace }}/OpenNeuroPET-Phantoms/sourcedata/SiemensHRRT-JHU/Hoffman.v
       SMALLER_ECAT_PATH: ${{ github.workspace }}/ecat_validation/ECAT7_multiframe.v.gz
       TEST_ECAT_PATH: ${{ github.workspace }}/ecat_validation/ECAT7_multiframe.v
       OUTPUT_NIFTI_PATH: ${{ github.workspace}}/pypet2bids/tests/ECAT7_multiframe.nii
@@ -36,41 +36,49 @@ jobs:
       - name: Checkout Repo
         uses: actions/checkout@v2
 
-      - name: Cache ECAT
-        id: cache-ecat
+      - name: Cache Phantoms
+        id: cache-phantoms
         uses: actions/cache@v2
         with:
-          path: cimbi36
-          key: ${{ runner.os }}-ecats
+          path: US-sourced-OpenNeuroPET-Phantoms.zip
+          key: ${{ runner.os }}-phantoms
 
       - name: Set up python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
 
       - name: Install dependencies
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: |
           cd pypet2bids
-          pip3 install .
+          python -m pip install --upgrade pip
+          pip install poetry
+          poetry install --with dev
 
-      - name: Install gdown and collect Ecat from Google Drive
-        if: steps.cache-ecat.outputs.cache-hit != 'true'
-        run: "python3 -m pip install gdown && gdown ${{ secrets.CIMBI_ECAT_ON_GOOGLE_DRIVE }} -O ecat_test"
+      - name: Collect ECAT and other phantoms
+        if: steps.cache-phantoms.outputs.cache-hit != 'true'
+        run: "wget https://openneuropet.s3.amazonaws.com/US-sourced-OpenNeuroPET-Phantoms.zip"
 
-      - name: Decompress dataset
-        if: steps.cache-ecat.outputs.cache-hit != 'true'
-        run: "tar xvzf ecat_test && rm ecat_test"
+      - name: Decompress ECAT and other phantoms
+        run: "unzip US-sourced-OpenNeuroPET-Phantoms.zip"
+
+      - name: Debug
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
 
       - name: Test CLI --help
         run: |
           cd pypet2bids/
-          python3 -m pypet2bids.ecat_cli --help
+          poetry run python3 -m pypet2bids.ecat_cli --help
 
       - name: Test CLI Ecat Dump
         run: |
           cd pypet2bids/
-          python3 -m pypet2bids.ecat_cli ../${{ env.REAL_TEST_ECAT_PATH }} --dump
+          poetry run python3 -m pypet2bids.ecat_cli ${{ env.REAL_ECAT_TEST_PATH }} --dump
 
       # the larger real data file uses too much ram for the github runner, we use the small file for
       # heavy io operations instead
@@ -79,9 +87,9 @@ jobs:
           gzip -d ${{ env.SMALLER_ECAT_PATH }}
       
       - name: Test ecatread
-        run: "cd pypet2bids/ && python3 -m tests.test_ecatread"
+        run: "cd pypet2bids/ && poetry run python3 -m tests.test_ecatread"
 
       - name: Run All Other Python Tests w/ Pytest
         run: |
           cd pypet2bids
-          pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/
+          poetry run pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/

.github/workflows/readthedocs.yaml

@@ -0,0 +1,23 @@
+name: readthedocs/actions
+on:
+  pull_request_target:
+    types: [opened, synchronize, reopened]
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        type: boolean
+        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+        required: false
+        default: false
+
+permissions:
+  pull-requests: write
+
+jobs:
+  pull-request-links:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Preview RTD
+      uses: readthedocs/actions/preview@v1
+      with:
+        project-slug: "pet2bids"

.gitignore

@@ -57,3 +57,13 @@ D:\\BIDS*
 # test data
 *OpenNeuroPET-Phantoms*
 **PHANTOMS.zip
+ecat_validation/ECAT7_multiframe.v
+variables.env
+ecat_testing/matlab/
+ecat_testing/steps/
+ecat_testing/**/*.nii*
+*osem*
+*fbp*
+
+matlab/SiemensHRRTparameters.txt
+

.readthedocs.yaml

@@ -14,27 +14,22 @@ submodules:
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
   jobs:
     post_create_environment:
+      - cp -r metadata pypet2bids/pypet2bids/
       # install poetry
-      # https://python-poetry.org/docs/#osx--linux--bashonwindows-install-instructions
-      - curl -sSL https://install.python-poetry.org | python3 -
-      # Tell poetry to not use a virtual environment
-      - $HOME/.local/bin/poetry config virtualenvs.create false
+      - pip install poetry
+      - poetry config virtualenvs.create false
       # just use poetry to export a requirements.txt as that worked much better than the previous attempts
-      - cd pypet2bids && $HOME/.local/bin/poetry export --with dev --without-hashes -o requirements.txt
+      - cd pypet2bids && poetry lock && poetry export --without-hashes --with dev --format=requirements.txt > requirements.txt
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py
 
-# If using Sphinx, optionally build your docs in additional formats such as PDF
-# formats:
-#    - pdf
-
 # Optionally declare the Python requirements required to build your docs
 python:
    install:

CITATION.cff

@@ -31,11 +31,17 @@ authors:
 - family-names: "Ganz-Benjaminsen"
   given-names: "Melanie"
   orcid: "https://orcid.org/0000-0002-9120-8098"
+- family-names: "Bilgel"
+  given-names: "Murat"
+  orcid: "https://orcid.org/0000-0001-5042-7422"
+- family-names: "Eierud"
+  given-names: "Cyrus"
+  orcid: "https://orcid.org/0000-0002-9942-676X"
 - family-names: "Pernet"
   given-names: "Cyril"
   orcid: "https://orcid.org/0000-0003-4010-4632"
 title: "PET2BIDS"
-version: 1.0.0
+version: 1.3.20240502
 url: "https://github.com/openneuropet/PET2BIDS"
 date-released: 2022-10-01
 license: MIT

JOSS_metadata/persons_info.txt

@@ -21,3 +21,5 @@
 0000-0002-9120-8098  Melanie Ganz-Benjaminse  Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
 
 0000-0003-4010-4632  Cyril Pernet  Neurobiology Research Unit, Rigshospitalet, Copenhagen, Denmark
+
+0000-0001-5042-7422  Murat Bilgel  National Institute on Aging Intramural Research Program, Baltimore, MD, USA

Makefile

@@ -43,3 +43,47 @@ installpackage:
 
 testphantoms:
 	@scripts/testphantoms
+
+html:
+	@cd docs && make html
+
+installdependencies:
+	@cd pypet2bids; \
+	python -m pip install --upgrade pip; \
+	pip install poetry; \
+	poetry install --with dev
+
+collectphantoms:
+ifeq (, $(wildcard ./PHANTOMS.zip))
+	@wget -O PHANTOMS.zip https://openneuropet.s3.amazonaws.com/US-sourced-OpenNeuroPET-Phantoms.zip
+else
+	@echo "PHANTOMS.zip already exists"
+endif
+
+decompressphantoms:
+	@unzip -o PHANTOMS.zip
+
+testecatcli:
+	@cd pypet2bids; \
+	poetry run python -m pypet2bids.ecat_cli --help; \
+	poetry run python -m pypet2bids.ecat_cli ../OpenNeuroPET-Phantoms/sourcedata/SiemensHRRT-JHU/Hoffman.v --dump
+
+testecatread:
+	@cd pypet2bids; \
+	export TEST_ECAT_PATH="../OpenNeuroPET-Phantoms/sourcedata/SiemensHRRT-JHU/Hoffman.v"; \
+	export READ_ECAT_SAVE_AS_MATLAB="$$PWD/tests/ECAT7_multiframe.mat"; \
+	export NIBABEL_READ_ECAT_SAVE_AS_MATLAB="$$PWD/tests/ECAT7_multiframe.nibabel.mat"; \
+	poetry run python3 -m tests.test_ecatread
+
+testotherpython:
+	cd pypet2bids; \
+	export TEST_DICOM_IMAGE_FOLDER="../OpenNeuroPET-Phantoms/sourcedata/SiemensBiographPETMR-NIMH/AC_TOF"; \
+	poetry run pytest --ignore=tests/test_write_ecat.py tests/ -vvv
+
+pythongithubworkflow: installdependencies collectphantoms decompressphantoms testecatread testecatcli testotherpython
+	@echo finished running python tests
+
+black:
+	@for file in `find pypet2bids/ -name "*.py"`; do \
+		black $$file; \
+	done