Merge branch 'main-arkiev'

nipype · Mar 24, 2024 · 0da818e · 0da818e
2 parents 2d2595d + 71947e6
commit 0da818e
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Showing 2 changed files with 46 additions and 11 deletions.
diff --git a/.github/workflows/pythonpackage.yaml b/.github/workflows/pythonpackage.yaml
@@ -28,12 +28,12 @@ jobs:
         - '--editable git+https://github.com/nipype/pydra.git#egg=pydra'
     steps:
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')    
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install build dependencies
@@ -86,12 +86,12 @@ jobs:
         sudo cp /opt/FastSurfer/fastsurfer_env_gpu.yml /fastsurfer/fastsurfer_env_gpu.yml
         sudo cp -R /opt/FastSurfer/* /fastsurfer/ && rm -rf /opt/FastSurfer
     - name: Checkout Repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
     - name: Revert version to most recent tag on upstream update
       if: github.event_name == 'repository_dispatch'
       run: git checkout $(git tag -l | tail -n 1 | awk -F post '{print $1}')
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install build dependencies
@@ -116,7 +116,7 @@ jobs:
       matrix:
         python-version: ['3.11']
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
         fetch-depth: 0
@@ -130,7 +130,7 @@ jobs:
         git commit -am"added auto-generated version to make new tag for package version"
         git tag ${TAG}post${POST}    
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install build tools
@@ -139,7 +139,7 @@ jobs:
       run: python -m build
     - name: Check distributions
       run: twine check dist/*
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: distributions
         path: dist/

diff --git a/pydra/tasks/fastsurfer/v1/__init__.py b/pydra/tasks/fastsurfer/v1/__init__.py
@@ -2,12 +2,13 @@
 from pydra.engine import ShellCommandTask
 import typing as ty
 from pathlib import Path
-from fileformats.generic import File
+from fileformats.generic import File, Directory
+from fileformats.medimage import NiftiGz, MghGz
 
 input_fields = [
     (
         "subjects_dir",
-        ty.Any,
+        Path,
         {
             "help_string": "Subjects directory",
             "argstr": "--sd {subjects_dir}",
@@ -207,7 +208,41 @@
     name="Input", fields=input_fields, bases=(specs.ShellSpec,)
 )
 
-output_fields = []
+def norm_img_path(subjects_dir: Path):
+    return Path(subjects_dir) / "FS_outputs" / "mri" / "norm.mgz"
+
+def aparcaseg_img_path(subjects_dir: Path):
+    return Path(subjects_dir) / "FS_outputs" / "mri" / "aparc+aseg.orig.mgz"
+
+def subject_dir_path(subjects_dir: Path) -> Path:
+    return Path(subjects_dir) / "FS_outputs" 
+
+output_fields = [
+    (
+        "subject_dir_output",
+        Directory,
+        {
+            "help_string": "subject directory path",
+            "callable": subject_dir_path,
+        },
+    ),
+    ( 
+        "norm_img", 
+        MghGz,
+        {
+            "help_string": "norm image",
+            "callable": norm_img_path,
+        },
+    ),
+    (
+        "aparcaseg_img",
+        MghGz,
+        {
+            "help_string": "aparc+aseg image",
+            "callable": aparcaseg_img_path,
+        },
+    )
+]
 fastsurfer_output_spec = specs.SpecInfo(
     name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
 )
@@ -219,7 +254,7 @@ class fastsurfer(ShellCommandTask):
     -------
 
     >>> from fileformats.generic import File
-    >>> from pydra.tasks.fastsurfer.auto.fast_surfer import fast_surfer
+    >>> from pydra.tasks.fastsurfer.v1.fast_surfer import fast_surfer
 
     """