Fix runs and update to uv

.github/workflows/run_pytest.yaml

@@ -14,14 +14,12 @@ jobs:
   test_with_pytest:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Install Poetry
-        run: pipx install poetry
-      - uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-          cache: poetry
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+      - name: Set up Python
+        run: uv python install 3.11
       - name: Install dependencies
-        run: poetry install
+        run: uv sync --extra dev
       - name: Run Tests
-        run: poetry run pytest tests/
+        run: uv run pytest tests/

petutils/petutils.py

@@ -93,7 +93,7 @@ def collect_anat_and_pet(bids_data: Union[pathlib.Path, BIDSLayout], suffixes=["
         mapped_pet_to_anat[subject] = {}
     for subject in subjects:
         pet_files = bids_data.get(subject=subject, suffix="pet")
-        anat_files = [a.path for a in bids_data.get("anat",suffix=suffixes, subject=subject, extension=["nii", "nii.gz"])]
+        anat_files = [a.path for a in bids_data.get(suffix=suffixes, subject=subject, extension=["nii", "nii.gz"])]
         # for each pet image file we create an entry our mapping dictionary
         for entry in pet_files:
             if type(entry) is BIDSImageFile:

pyproject.toml

@@ -1,21 +1,26 @@
-[tool.poetry]
+[project]
 name = "petutils"
-version = "0.1.0"
+version = "0.2.0"
 description = ""
-authors = ["Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>"]
 readme = "README.md"
-packages = [{include = "petutils"}]
+requires-python = ">=3.9"
+authors = [
+    { name = "Anthony Galassi", email = "28850131+bendhouseart@users.noreply.github.com" }
+]
+dependencies = [
+    "pybids>=0.16.3",
+    "nipype>=1.8.6",
+]
 
-[tool.poetry.dependencies]
-python = "^3.9"
-pybids = "^0.16.3"
-nipype = "^1.8.6"
-
-
-[tool.poetry.group.dev.dependencies]
-ipython = "^8.16.1"
-pytest = "^7.4.2"
+[project.optional-dependencies]
+dev = [
+    "ipython>=8.16.1",
+    "pytest>=7.4.2",
+]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["petutils"]

tests/conftest.py

@@ -2,6 +2,7 @@
 import pytest
 import shutil
 import tempfile
+import os
 
 # our first steps to testing are to build the different types of bids datasets that we expect to encounter
 # these are:
@@ -114,3 +115,166 @@ def anat_in_each_session_folder(tmpdir):
             / file.name.replace("ses-baseline_", "ses-second_"),
         )
     return dest_dir
+
+#5 - test dataset with multi run pet scans
+@pytest.fixture
+def multi_run_pet_scans(tmpdir):
+    dest_dir = pathlib.Path(tmpdir) / "multi_run_pet_scans"
+    shutil.copytree(data_dir, dest_dir)
+
+    runs = ["01", "02"]
+
+    for run in runs:
+        shutil.copy(
+            dest_dir / "sub-01" / "ses-baseline" / "pet" / "sub-01_ses-baseline_pet.nii.gz",
+            dest_dir / "sub-01" / "ses-baseline" / "pet" / f"sub-01_ses-baseline_run-{run}_pet.nii.gz",
+        )
+        shutil.copy(
+            dest_dir / "sub-01" / "ses-baseline" / "pet" / "sub-01_ses-baseline_pet.json",
+            dest_dir / "sub-01" / "ses-baseline" / "pet" / f"sub-01_ses-baseline_run-{run}_pet.json",
+        )
+
+    os.remove(dest_dir / "sub-01" / "ses-baseline" / "pet" / "sub-01_ses-baseline_pet.nii.gz")
+    os.remove(dest_dir/ "sub-01" / "ses-baseline" / "pet" / "sub-01_ses-baseline_pet.json")
+
+    return dest_dir
+
+# Helper function to convert single run PET scans to multi-run
+def convert_to_multi_run(dest_dir):
+    """Convert all single-run PET scans in a directory to multi-run (run-01, run-02)"""
+    runs = ["01", "02"]
+
+    # Find all PET files without run entities
+    for pet_file in dest_dir.glob("**/pet/*_pet.nii.gz"):
+        if "run-" not in pet_file.name:
+            # Create run-01 and run-02 versions
+            for run in runs:
+                new_name = pet_file.name.replace("_pet.nii.gz", f"_run-{run}_pet.nii.gz")
+                shutil.copy(pet_file, pet_file.parent / new_name)
+            # Remove original
+            os.remove(pet_file)
+
+    # Do the same for JSON sidecars
+    for json_file in dest_dir.glob("**/pet/*_pet.json"):
+        if "run-" not in json_file.name:
+            for run in runs:
+                new_name = json_file.name.replace("_pet.json", f"_run-{run}_pet.json")
+                shutil.copy(json_file, json_file.parent / new_name)
+            os.remove(json_file)
+
+# 1 - Multi-run version
+@pytest.fixture
+def anat_in_no_session_folder_multi_run(tmpdir):
+    dest_dir = pathlib.Path(tmpdir) / "anat_in_subject_folder_multi_run"
+    shutil.copytree(data_dir, dest_dir)
+
+    original_anat_folder = (
+        dest_dir / "sub-01" / "ses-baseline" / "anat"
+    )
+    subject_folder = dest_dir / "sub-01"
+    # now we move the anatomical folder in the first session of our test data into the subject level folder
+    shutil.move(original_anat_folder, subject_folder)
+
+    inherited_anat_folder = subject_folder / "anat"
+
+    # and next remove the ses- entities from the files in the newly created anat folder
+    for file in inherited_anat_folder.glob("sub-01_ses-baseline_*"):
+        shutil.move(
+            file,
+            pathlib.Path(tmpdir)
+            / "anat_in_subject_folder_multi_run"
+            / "sub-01"
+            / "anat"
+            / file.name.replace("ses-baseline_", ""),
+        )
+
+    # Convert to multi-run
+    convert_to_multi_run(dest_dir)
+
+    return dest_dir
+
+# 2 - Multi-run version
+@pytest.fixture
+def anat_in_first_session_folder_multi_run(tmpdir):
+    dest_dir = pathlib.Path(tmpdir) / "anat_in_first_session_folder_multi_run"
+    shutil.copytree(data_dir, dest_dir)
+
+    # Convert to multi-run
+    convert_to_multi_run(dest_dir)
+
+    return dest_dir
+
+# 3 - Multi-run version
+@pytest.fixture
+def anat_in_first_session_folder_multi_sessions_multi_run(tmpdir):
+    dest_dir = pathlib.Path (tmpdir) / "anat_in_first_session_folder_multi_sessions_multi_run"
+    shutil.copytree(data_dir, dest_dir)
+
+    # create a second session
+    second_session_folder = (
+        dest_dir / "sub-01" / "ses-second"
+    )
+    second_session_folder.mkdir(parents=True, exist_ok=True)
+
+    shutil.copytree(
+        dest_dir / "sub-01" / "ses-baseline",
+        second_session_folder,
+        dirs_exist_ok=True,
+    )
+
+    # replace the ses- entities in the files in the newly created second session folder
+    for file in second_session_folder.glob("pet/*"):
+        shutil.move(
+            file,
+            second_session_folder
+            / "pet"
+            / file.name.replace("ses-baseline_", "ses-second_"),
+        )
+
+    # remove anat in second session folder
+    shutil.rmtree(second_session_folder / "anat")
+
+    # Convert to multi-run
+    convert_to_multi_run(dest_dir)
+
+    return dest_dir
+
+# 4 - Multi-run version
+@pytest.fixture
+def anat_in_each_session_folder_multi_run(tmpdir):
+    dest_dir = pathlib.Path(tmpdir) / "anat_in_each_session_folder_multi_run"
+    shutil.copytree(data_dir, dest_dir)
+
+    # create a second session
+    second_session_folder = (
+        dest_dir / "sub-01" / "ses-second"
+    )
+    second_session_folder.mkdir(parents=True, exist_ok=True)
+
+    shutil.copytree(
+        dest_dir / "sub-01" / "ses-baseline",
+        second_session_folder,
+        dirs_exist_ok=True,
+    )
+
+    # replace the ses- entities in the files in the newly created second session folder
+    for file in second_session_folder.glob("pet/*"):
+        shutil.move(
+            file,
+            second_session_folder
+            / "pet"
+            / file.name.replace("ses-baseline_", "ses-second_"),
+        )
+
+    for file in second_session_folder.glob("anat/*"):
+        shutil.move(
+            file,
+            second_session_folder
+            / "anat"
+            / file.name.replace("ses-baseline_", "ses-second_"),
+        )
+
+    # Convert to multi-run
+    convert_to_multi_run(dest_dir)
+
+    return dest_dir

tests/test_pet_utils.py

@@ -82,4 +82,127 @@ def test_anat_in_each_session_folder(anat_in_each_session_folder):
             assert len(pet_image.parts) == len(anat_image.parts)
             assert re.search(r"ses-[^_|\/]*", str(anat_image))[0]  == re.search(r"ses-[^_|\/]*", str(pet_image))[0]
             assert re.search(r"nii|(.gz)", str(anat_image)) is not None
-
+
+def test_multi_run_pet_scans(multi_run_pet_scans):
+    subprocess.run(["tree", multi_run_pet_scans])
+    a_and_p = collect_anat_and_pet(multi_run_pet_scans)
+    for subject in a_and_p.keys():
+        for pet_image, anat_image in a_and_p[subject].items():
+            pet_image = pathlib.Path(pet_image)
+            anat_image = pathlib.Path(anat_image)
+            assert len(pet_image.parts) == len(anat_image.parts)
+            assert re.search(r"ses-[^_|\/]*", str(anat_image))[0]  == re.search(r"ses-[^_|\/]*", str(pet_image))[0]
+            assert re.search(r"nii|(.gz)", str(anat_image)) is not None
+
+# Multi-run versions of all tests
+def test_anat_in_no_session_folder_multi_run(anat_in_no_session_folder_multi_run):
+    subprocess.run(["tree", anat_in_no_session_folder_multi_run])
+    a_and_p = collect_anat_and_pet(anat_in_no_session_folder_multi_run)
+
+    # Track number of runs detected
+    run_count = 0
+
+    # check that for each pet file, there is a corresponding inherited anat file from the subject level
+    for subject in a_and_p.keys():
+        for pet_image, anat_image in a_and_p[subject].items():
+            pet_image = pathlib.Path(pet_image)
+            anat_image = pathlib.Path(anat_image)
+            # check that the pet image is at least a subfolder deeper than the anat image
+            assert len(pet_image.parts) > len(anat_image.parts)
+            assert re.search(r"ses-", str(anat_image)) is None
+            assert re.search(r"ses-", str(pet_image)) is not None
+            assert re.search(r"nii|(.gz)", str(anat_image)) is not None
+            # Verify run entity exists in PET filename
+            assert re.search(r"run-\d+", str(pet_image)) is not None
+            run_count += 1
+
+    # Should have at least 2 runs (run-01 and run-02)
+    assert run_count >= 2
+
+def test_anat_in_first_session_folder_multi_run(anat_in_first_session_folder_multi_run):
+    subprocess.run(["tree", anat_in_first_session_folder_multi_run])
+    a_and_p = collect_anat_and_pet(anat_in_first_session_folder_multi_run)
+
+    for subject in a_and_p.keys():
+        set_of_anat_images = set()
+        set_of_pet_images = set()
+        anat_exists_in_one_session_folder = False
+        run_count = 0
+
+        for pet_image, anat_image in a_and_p[subject].items():
+            pet_image = pathlib.Path(pet_image)
+            anat_image = pathlib.Path(anat_image)
+
+            # add images to the set
+            set_of_anat_images.add(str(anat_image))
+            set_of_pet_images.add(str(pet_image))
+
+            # check that at least one session contains both a pet and an anat image
+            if re.search(r"ses-[^_|\/]*", str(anat_image))[0]  == re.search(r"ses-[^_|\/]*", str(pet_image))[0]:
+                anat_exists_in_one_session_folder = True
+
+            # Verify run entity exists in PET filename
+            assert re.search(r"run-\d+", str(pet_image)) is not None
+            run_count += 1
+
+        assert anat_exists_in_one_session_folder is True
+        assert len(set_of_anat_images) == 1
+        # Should have multiple PET images due to runs
+        assert len(set_of_pet_images) >= 2
+        assert run_count >= 2
+
+def test_anat_in_first_session_folder_multi_sessions_multi_run(anat_in_first_session_folder_multi_sessions_multi_run):
+    subprocess.run(["tree", anat_in_first_session_folder_multi_sessions_multi_run])
+    a_and_p = collect_anat_and_pet(anat_in_first_session_folder_multi_sessions_multi_run)
+
+    for subject in a_and_p.keys():
+        set_of_anat_images = set()
+        set_of_pet_images = set()
+        anat_exists_in_one_session_folder = False
+        run_count = 0
+
+        for pet_image, anat_image in a_and_p[subject].items():
+            pet_image = pathlib.Path(pet_image)
+            anat_image = pathlib.Path(anat_image)
+
+            # add images to the set
+            set_of_anat_images.add(str(anat_image))
+            set_of_pet_images.add(str(pet_image))
+
+            # check that at least one session contains both a pet and an anat image
+            if re.search(r"ses-[^_|\/]*", str(anat_image))[0]  == re.search(r"ses-[^_|\/]*", str(pet_image))[0]:
+                anat_exists_in_one_session_folder = True
+
+            # Verify run entity exists in PET filename
+            assert re.search(r"run-\d+", str(pet_image)) is not None
+            run_count += 1
+
+        print("!"*100)
+        print(set_of_pet_images)
+        assert anat_exists_in_one_session_folder is True
+        assert len(set_of_anat_images) == 1
+        # Should have even more PET images (multiple sessions × multiple runs)
+        assert len(set_of_pet_images) >= 4  # 2 sessions × 2 runs
+        assert run_count >= 4
+
+def test_anat_in_each_session_folder_multi_run(anat_in_each_session_folder_multi_run):
+    subprocess.run(["tree", anat_in_each_session_folder_multi_run])
+    a_and_p = collect_anat_and_pet(anat_in_each_session_folder_multi_run)
+
+    run_count = 0
+
+    # check that for each pet file, there is a corresponding anat file in the same session
+    for subject in a_and_p.keys():
+        for pet_image, anat_image in a_and_p[subject].items():
+            pet_image = pathlib.Path(pet_image)
+            anat_image = pathlib.Path(anat_image)
+            # check that the pet image is at the same folder depth as the anat image
+            assert len(pet_image.parts) == len(anat_image.parts)
+            assert re.search(r"ses-[^_|\/]*", str(anat_image))[0]  == re.search(r"ses-[^_|\/]*", str(pet_image))[0]
+            assert re.search(r"nii|(.gz)", str(anat_image)) is not None
+            # Verify run entity exists in PET filename
+            assert re.search(r"run-\d+", str(pet_image)) is not None
+            run_count += 1
+
+    # Should have multiple runs across sessions
+    assert run_count >= 4  # 2 sessions × 2 runs