junifer 0.0.7.dev192__tar.gz → 0.0.7.dev217__tar.gz

junifer-0.0.7.dev217/.github/workflows/ci.yml

@@ -0,0 +1,86 @@
+name: Run Tests
+
+on:
+  push:
+    paths:
+      - 'junifer/**'
+      - '.github/workflows/**'
+      - 'tox.ini'
+      - 'pyproject.toml'
+  pull_request:
+    paths:
+      - 'junifer/**'
+      - '.github/workflows/**'
+      - 'tox.ini'
+      - 'pyproject.toml'
+  workflow_dispatch: {}
+
+jobs:
+  run-tests:
+    # https://github.com/actions/setup-python/issues/1013#issuecomment-2642078401
+    runs-on: ubuntu-22.04
+    # Use custom CI image
+    container: ghcr.io/juaml/junifer-ci:main
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    steps:
+      - run: df -h
+      - name: Clean runner
+        run: |
+          rm -rf /usr/share/dotnet \
+                 /usr/local/lib/android \
+                 /opt/ghc \
+                 /opt/hostedtoolcache
+      - run: df -h
+      - name: Check ANTs
+        run: |
+          echo "Using ANTs : $(antsRegistration --version)"
+      - name: Check AFNI
+        run: |
+          echo "Using AFNI : $(afni --version)"
+      - name: Check FSL
+        run: |
+          echo "Using FSL : $(flirt -version)"
+      - name: Install system dependencies
+        # actions/checkout fails to identify Git as it's not in the CI image
+        run: |
+          apt-get -qq update
+          apt-get -qq install -y \
+          git \
+          git-annex \
+          make \
+          jq
+      - name: Copy junifer-data directory
+        run: |
+          mkdir -p $HOME/junifer_data/v4
+          cp -ar /root/junifer_data/v4/. $HOME/junifer_data/v4/
+      - name: Checkout repository
+        uses: actions/checkout@v5
+        with:
+          submodules: true
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install tox tox-gh-actions
+      - name: Configure Git for DataLad
+        run: |
+          git config --global user.email "junifer-runner@github.com"
+          git config --global user.name "GitHub Runner"
+      - name: Test with tox
+        # https://github.com/actions/checkout/issues/1169#issuecomment-2291682583
+        run: |
+          git config --system --add safe.directory $(pwd)
+          tox
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          flags: junifer
+        if: success() && matrix.python-version == 3.12

junifer-0.0.7.dev217/.github/workflows/docker-ci-publish.yml

@@ -0,0 +1,69 @@
+name: Docker for CI
+
+on:
+  push:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-ci" ]
+  pull_request:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-ci" ]
+  workflow_dispatch: {}
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}-ci
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+    steps:
+      - run: df -h
+      - name: Clean runner
+        run: |
+          sudo rm -rf /usr/share/dotnet \
+                 /usr/local/lib/android \
+                 /opt/ghc \
+                 /opt/hostedtoolcache
+          sudo docker image prune --all --force
+          sudo docker builder prune -a
+      - run: df -h
+      - name: Checkout repository
+        uses: actions/checkout@v5
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@v3.10.0
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3.11.1
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3.5.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5.8.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v6.18.0
+        with:
+          context: .
+          file: Dockerfile-ci
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

junifer-0.0.7.dev217/.github/workflows/docker-docs-publish.yml

@@ -0,0 +1,69 @@
+name: Docker for docs
+
+on:
+  push:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-docs" ]
+  pull_request:
+    branches: [ "main" ]
+    paths: [ "Dockerfile-docs" ]
+  workflow_dispatch: {}
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}-docs
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+    steps:
+      - run: df -h
+      - name: Clean runner
+        run: |
+          rm -rf /usr/share/dotnet \
+                 /usr/local/lib/android \
+                 /opt/ghc \
+                 /opt/hostedtoolcache
+          docker image prune --all --force
+          docker builder prune -a
+      - run: df -h
+      - name: Checkout repository
+        uses: actions/checkout@v5
+      - name: Install cosign
+        if: github.event_name != 'pull_request'
+        uses: sigstore/cosign-installer@v3.10.0
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3.11.1
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3.5.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5.8.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v6.18.0
+        with:
+          context: .
+          file: Dockerfile-docs
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+      - name: Sign the published Docker image
+        if: ${{ github.event_name != 'pull_request' }}
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}

{junifer-0.0.7.dev192 → junifer-0.0.7.dev217}/Dockerfile-ci

@@ -1,6 +1,6 @@
 # syntax=docker/dockerfile:1
 
-FROM python:3.12-slim
+FROM python:3.12-slim-bookworm
 
 LABEL org.opencontainers.image.source=https://github.com/juaml/junifer
 LABEL org.opencontainers.image.description="Junifer CI container image"
@@ -60,14 +60,13 @@ ENV PATH="/opt/afni/bin:$PATH"
 # Patch gsl
 RUN ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.23
 
-# disabled as standard github runner fails to install due to insufficient space on device
-# # Add FSL
-# RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | \
-#     python - -d /opt/fsl/ --skip_registration
-# # Set env vars for FSL
-# ENV FSLDIR=/opt/fsl \
-#     FSLOUTPUTTYPE=NIFTI_GZ \
-#     PATH="/opt/fsl/share/fsl/bin:$PATH"
+# Add FSL
+RUN curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py | \
+    python - -d /opt/fsl/ --skip_registration
+# Set env vars for FSL
+ENV FSLDIR=/opt/fsl \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    PATH="/opt/fsl/share/fsl/bin:$PATH"
 
 # Clean apt cache
 RUN apt-get autoremove --purge && apt-get clean

{junifer-0.0.7.dev192 → junifer-0.0.7.dev217}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev192
+Version: 0.0.7.dev217
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

junifer-0.0.7.dev217/docs/changes/newsfragments/462.feature

@@ -0,0 +1 @@
+Enable :class:`.SpaceWarper` to warp data from native space to template spaces via both FSL and ANTs by `Synchon Mandal`_

junifer-0.0.7.dev217/docs/changes/newsfragments/467.misc

@@ -0,0 +1 @@
+Disable FSL installation for ``junifer-ci`` Docker image build with ``junifer-data`` v4 by `Synchon Mandal`_

junifer-0.0.7.dev217/docs/changes/newsfragments/468.misc

@@ -0,0 +1 @@
+Pin ``junifer-ci`` Docker image to ``python:3.12-slim-bookworm`` and re-enable FSL installation by `Synchon Mandal`_

{junifer-0.0.7.dev192 → junifer-0.0.7.dev217}/junifer/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.7.dev192'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev192')
+__version__ = version = '0.0.7.dev217'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev217')
 
-__commit_id__ = commit_id = 'g61f12e356'
+__commit_id__ = commit_id = 'g0925af82f'

{junifer-0.0.7.dev192 → junifer-0.0.7.dev217}/junifer/preprocess/warping/_ants_warper.py

@@ -180,27 +180,74 @@ class ANTsWarper:
 
         # Template space warping
         else:
+            input_space = input["space"]
             logger.debug(
-                f"Using ANTs to warp data from {input['space']} to {reference}"
+                f"Using ANTs to warp data from {input_space} space "
+                f"to {reference} space"
             )
 
-            # Get xfm file
-            xfm_file_path = get_xfm(src=input["space"], dst=reference)
-            # Get template space image
-            template_space_img = get_template(
-                space=reference,
-                target_img=input["data"],
-                extra_input=None,
-            )
-            # Save template
-            template_space_img_path = (
-                element_tempdir / f"{reference}_T1w.nii.gz"
-            )
-            nib.save(template_space_img, template_space_img_path)
+            # Native to MNI
+            if input_space == "native":
+                # Get warp file path
+                xfm_file_path = None
+                for entry in extra_input["Warp"]:
+                    if entry["src"] == "native" and entry["dst"] == reference:
+                        xfm_file_path = entry["path"]
+                if xfm_file_path is None:
+                    raise_error(
+                        klass=RuntimeError,
+                        msg="Could not find correct warp file path",
+                    )
+
+                # Use ResampleImage if input data resolution and reference
+                # resolution don't match
+                input_res = np.min(input["data"].header.get_zooms()[:3])
+                ref_res = np.min(
+                    input["reference"]["data"].header.get_zooms()[:3]
+                )
+                logger.debug(f"Input resolution: {input_res}")
+                logger.debug(f"Reference resolution: {ref_res}")
+                if input_res != ref_res:
+                    # Create a tempfile for resampled reference output
+                    ref_path = (
+                        element_tempdir
+                        / f"resampled_reference-{reference}.nii.gz"
+                    )
+                    # Set ResampleImage command
+                    resample_image_cmd = [
+                        "ResampleImage",
+                        "3",  # image dimension
+                        f"{input['reference']['path'].resolve()}",
+                        f"{ref_path.resolve()}",
+                        f"{input_res}x{input_res}x{input_res}",
+                        "0",  # option for spacing and not size
+                        "3 3",  # Lanczos windowed sinc
+                    ]
+                    # Call ResampleImage
+                    run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
+                else:
+                    logger.debug(
+                        "Reference resolution matches input resolution"
+                    )
+                    ref_path = input["reference"]["path"]
+
+            # MNI to MNI
+            else:
+                # Get xfm file
+                xfm_file_path = get_xfm(src=input_space, dst=reference)
+                # Get template space image in correct resolution
+                template_space_img = get_template(
+                    space=reference,
+                    target_img=input["data"],
+                    extra_input=None,
+                )
+                # Save template
+                ref_path = element_tempdir / f"{reference}_T1w.nii.gz"
+                nib.save(template_space_img, ref_path)
 
             # Create a tempfile for warped output
             warped_output_path = element_tempdir / (
-                f"warped_data_from_{input['space']}_to_{reference}.nii.gz"
+                f"warped_data_from_{input_space}_to_{reference}.nii.gz"
             )
 
             # Set antsApplyTransforms command
@@ -210,7 +257,7 @@ class ANTsWarper:
                 "-e 3",
                 "-n LanczosWindowedSinc",
                 f"-i {input['path'].resolve()}",
-                f"-r {template_space_img_path.resolve()}",
+                f"-r {ref_path.resolve()}",
                 f"-t {xfm_file_path.resolve()}",
                 f"-o {warped_output_path.resolve()}",
             ]
@@ -226,18 +273,20 @@ class ANTsWarper:
                     "data": nib.load(warped_output_path),
                     # Update warped input's space
                     "space": reference,
-                    # Save reference path
-                    "reference": {"path": template_space_img_path},
+                    # Save resampled reference path or overwrite original
+                    # keeping it same
+                    "reference": {"path": ref_path},
                     # Keep pre-warp space for further operations
-                    "prewarp_space": input["space"],
+                    "prewarp_space": input_space,
                 }
             )
 
             # Check for data type's mask and warp if found
             if input.get("mask") is not None:
+                logger.debug("Warping associated mask")
                 # Create a tempfile for warped mask output
                 apply_transforms_mask_out_path = element_tempdir / (
-                    f"warped_mask_from_{input['space']}_to_{reference}.nii.gz"
+                    f"warped_mask_from_{input_space}_to_{reference}.nii.gz"
                 )
                 # Set antsApplyTransforms command
                 apply_transforms_mask_cmd = [
@@ -246,8 +295,8 @@ class ANTsWarper:
                     "-e 3",
                     "-n 'GenericLabel[NearestNeighbor]'",
                     f"-i {input['mask']['path'].resolve()}",
-                    # use resampled reference
-                    f"-r {input['reference']['path'].resolve()}",
+                    # use resampled reference or original
+                    f"-r {ref_path.resolve()}",
                     f"-t {xfm_file_path.resolve()}",
                     f"-o {apply_transforms_mask_out_path.resolve()}",
                 ]