dcccpy 0.1.8__tar.gz → 0.2.0__tar.gz

{dcccpy-0.1.8/src/dcccpy.egg-info → dcccpy-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcccpy
-Version: 0.1.8
+Version: 0.2.0
 Summary: Python wrapper for the DCCCcore PET biomarker command-line tool
 Author: DCCCSlicer contributors
 License-Expression: CC-BY-NC-ND-4.0
@@ -17,17 +17,17 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Requires-Dist: nibabel>=5
 Provides-Extra: linux-runtime
-Requires-Dist: dcccpy-linux-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "linux-runtime"
-Requires-Dist: dcccpy-linux-arm64-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "linux-runtime"
+Requires-Dist: dcccpy-linux-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "linux-runtime"
+Requires-Dist: dcccpy-linux-arm64-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "linux-runtime"
 Provides-Extra: windows-runtime
-Requires-Dist: dcccpy-windows-runtime==0.1.1; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "windows-runtime"
+Requires-Dist: dcccpy-windows-runtime==0.1.2; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "windows-runtime"
 Provides-Extra: macos-runtime
-Requires-Dist: dcccpy-macos-runtime==0.1.1; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "macos-runtime"
+Requires-Dist: dcccpy-macos-runtime==0.1.2; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "macos-runtime"
 Provides-Extra: runtime
-Requires-Dist: dcccpy-linux-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "runtime"
-Requires-Dist: dcccpy-linux-arm64-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "runtime"
-Requires-Dist: dcccpy-windows-runtime==0.1.1; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "runtime"
-Requires-Dist: dcccpy-macos-runtime==0.1.1; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "runtime"
+Requires-Dist: dcccpy-linux-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "runtime"
+Requires-Dist: dcccpy-linux-arm64-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "runtime"
+Requires-Dist: dcccpy-windows-runtime==0.1.2; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "runtime"
+Requires-Dist: dcccpy-macos-runtime==0.1.2; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "runtime"
 
 # dcccpy
 
@@ -109,6 +109,7 @@ Common helpers mirror `DCCCcore` subcommands:
 dcccpy.centiloid("amyloid.nii", suvr=True)
 dcccpy.centaurz("tau.nii", report_detailed_regions=True)
 dcccpy.fillstates("fdg.nii", tracer="fdg")
+dcccpy.adni_pet_core("fdg.nii", tracer="fdg")
 dcccpy.normalize("pet.nii", iterative=True)
 dcccpy.pet_motion_correct(
     "dynamic_pet.nii.gz",
@@ -134,8 +135,17 @@ Each helper returns `DCCCResult` with:
 ```bash
 dcccpy --help
 dcccpy centiloid --input amyloid_pet.nii --output result.nii
+dcccpy adni-pet-core --input fdg.nii --output fdg_adni.nii --tracer fdg
 ```
 
+`adni_pet_core` deliberately has no default tracer. Use `abeta`, `tau`, or
+`fdg`; FDG selects ADNI's iterative masked global-mean normalization, while
+Aβ and tau retain cerebellar gray normalization.
+
+Downloaded ADNI preprocessed FDG DICOMs can differ slightly from the exact
+published iteration. See the repository's
+[ADNI FDG compatibility note](../../docs/adni-fdg-preprocessing-validation.md).
+
 ## Runtime lookup
 
 At runtime, `dcccpy` looks for `DCCCcore` in this order:
@@ -179,7 +189,7 @@ the calculation again.
 Release wheels should vendor the matching `DCCCcore` runtime tree before build:
 
 ```bash
-python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-x64
+python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-x64
 python -m build --wheel
 ```
 
@@ -187,7 +197,7 @@ The Linux ARM64 runtime package uses the corresponding release asset:
 
 ```bash
 cd python/dcccpy-linux-arm64-runtime
-python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-arm64
+python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-arm64
 python -m build --wheel
 ```
 
@@ -205,7 +215,7 @@ The preferred distribution layout is:
 
 ## Packaging note
 
-The runtime wheels use a PyPI-size profile for DCCCcore version 4.3.0. They omit the
+The runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
 `fast_and_acc` registration model/config and the ADAD decoupler ONNX ensemble,
 while keeping the default spatial normalization model and assets needed by
 common Centiloid/CenTauR/CenTauRz workflows.

{dcccpy-0.1.8 → dcccpy-0.2.0}/README.md

@@ -78,6 +78,7 @@ Common helpers mirror `DCCCcore` subcommands:
 dcccpy.centiloid("amyloid.nii", suvr=True)
 dcccpy.centaurz("tau.nii", report_detailed_regions=True)
 dcccpy.fillstates("fdg.nii", tracer="fdg")
+dcccpy.adni_pet_core("fdg.nii", tracer="fdg")
 dcccpy.normalize("pet.nii", iterative=True)
 dcccpy.pet_motion_correct(
     "dynamic_pet.nii.gz",
@@ -103,8 +104,17 @@ Each helper returns `DCCCResult` with:
 ```bash
 dcccpy --help
 dcccpy centiloid --input amyloid_pet.nii --output result.nii
+dcccpy adni-pet-core --input fdg.nii --output fdg_adni.nii --tracer fdg
 ```
 
+`adni_pet_core` deliberately has no default tracer. Use `abeta`, `tau`, or
+`fdg`; FDG selects ADNI's iterative masked global-mean normalization, while
+Aβ and tau retain cerebellar gray normalization.
+
+Downloaded ADNI preprocessed FDG DICOMs can differ slightly from the exact
+published iteration. See the repository's
+[ADNI FDG compatibility note](../../docs/adni-fdg-preprocessing-validation.md).
+
 ## Runtime lookup
 
 At runtime, `dcccpy` looks for `DCCCcore` in this order:
@@ -148,7 +158,7 @@ the calculation again.
 Release wheels should vendor the matching `DCCCcore` runtime tree before build:
 
 ```bash
-python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-x64
+python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-x64
 python -m build --wheel
 ```
 
@@ -156,7 +166,7 @@ The Linux ARM64 runtime package uses the corresponding release asset:
 
 ```bash
 cd python/dcccpy-linux-arm64-runtime
-python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-arm64
+python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-arm64
 python -m build --wheel
 ```
 
@@ -174,7 +184,7 @@ The preferred distribution layout is:
 
 ## Packaging note
 
-The runtime wheels use a PyPI-size profile for DCCCcore version 4.3.0. They omit the
+The runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
 `fast_and_acc` registration model/config and the ADAD decoupler ONNX ensemble,
 while keeping the default spatial normalization model and assets needed by
 common Centiloid/CenTauR/CenTauRz workflows.

{dcccpy-0.1.8 → dcccpy-0.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dcccpy"
-version = "0.1.8"
+version = "0.2.0"
 description = "Python wrapper for the DCCCcore PET biomarker command-line tool"
 readme = "README.md"
 requires-python = ">=3.9"
@@ -31,16 +31,16 @@ Issues = "https://github.com/tctco/DCCCSlicer/issues"
 
 [project.optional-dependencies]
 linux-runtime = [
-  "dcccpy-linux-runtime==0.1.1; sys_platform == 'linux' and platform_machine == 'x86_64'",
-  "dcccpy-linux-arm64-runtime==0.1.1; sys_platform == 'linux' and platform_machine == 'aarch64'",
+  "dcccpy-linux-runtime==0.1.2; sys_platform == 'linux' and platform_machine == 'x86_64'",
+  "dcccpy-linux-arm64-runtime==0.1.2; sys_platform == 'linux' and platform_machine == 'aarch64'",
 ]
-windows-runtime = ["dcccpy-windows-runtime==0.1.1; sys_platform == 'win32' and platform_machine == 'AMD64'"]
-macos-runtime = ["dcccpy-macos-runtime==0.1.1; sys_platform == 'darwin' and platform_machine == 'arm64'"]
+windows-runtime = ["dcccpy-windows-runtime==0.1.2; sys_platform == 'win32' and platform_machine == 'AMD64'"]
+macos-runtime = ["dcccpy-macos-runtime==0.1.2; sys_platform == 'darwin' and platform_machine == 'arm64'"]
 runtime = [
-  "dcccpy-linux-runtime==0.1.1; sys_platform == 'linux' and platform_machine == 'x86_64'",
-  "dcccpy-linux-arm64-runtime==0.1.1; sys_platform == 'linux' and platform_machine == 'aarch64'",
-  "dcccpy-windows-runtime==0.1.1; sys_platform == 'win32' and platform_machine == 'AMD64'",
-  "dcccpy-macos-runtime==0.1.1; sys_platform == 'darwin' and platform_machine == 'arm64'",
+  "dcccpy-linux-runtime==0.1.2; sys_platform == 'linux' and platform_machine == 'x86_64'",
+  "dcccpy-linux-arm64-runtime==0.1.2; sys_platform == 'linux' and platform_machine == 'aarch64'",
+  "dcccpy-windows-runtime==0.1.2; sys_platform == 'win32' and platform_machine == 'AMD64'",
+  "dcccpy-macos-runtime==0.1.2; sys_platform == 'darwin' and platform_machine == 'arm64'",
 ]
 
 [project.scripts]

{dcccpy-0.1.8 → dcccpy-0.2.0}/src/dcccpy/core.py

@@ -409,9 +409,15 @@ def normalize(
 def adni_pet_core(
     input: object,
     output: str | os.PathLike[str] | None = None,
+    *,
+    tracer: str,
     **kwargs: object,
 ) -> DCCCResult:
-    return _spatial_command("adni-pet-core", input, output, **kwargs)
+    """Run tracer-specific ADNI PET Core preprocessing."""
+
+    extra_args = list(kwargs.pop("extra_args", ()))
+    extra_args.extend(["--tracer", tracer])
+    return _spatial_command("adni-pet-core", input, output, extra_args=extra_args, **kwargs)
 
 
 def rigid(

{dcccpy-0.1.8 → dcccpy-0.2.0}/src/dcccpy/runtime.py

@@ -12,7 +12,7 @@ from pathlib import Path
 from typing import Iterable
 
 
-DCCCCORE_VERSION = "4.3.0"
+DCCCCORE_VERSION = "4.4.0"
 RELEASE_REPO = "tctco/DCCCSlicer"
 
 

{dcccpy-0.1.8 → dcccpy-0.2.0/src/dcccpy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dcccpy
-Version: 0.1.8
+Version: 0.2.0
 Summary: Python wrapper for the DCCCcore PET biomarker command-line tool
 Author: DCCCSlicer contributors
 License-Expression: CC-BY-NC-ND-4.0
@@ -17,17 +17,17 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 Requires-Dist: nibabel>=5
 Provides-Extra: linux-runtime
-Requires-Dist: dcccpy-linux-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "linux-runtime"
-Requires-Dist: dcccpy-linux-arm64-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "linux-runtime"
+Requires-Dist: dcccpy-linux-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "linux-runtime"
+Requires-Dist: dcccpy-linux-arm64-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "linux-runtime"
 Provides-Extra: windows-runtime
-Requires-Dist: dcccpy-windows-runtime==0.1.1; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "windows-runtime"
+Requires-Dist: dcccpy-windows-runtime==0.1.2; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "windows-runtime"
 Provides-Extra: macos-runtime
-Requires-Dist: dcccpy-macos-runtime==0.1.1; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "macos-runtime"
+Requires-Dist: dcccpy-macos-runtime==0.1.2; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "macos-runtime"
 Provides-Extra: runtime
-Requires-Dist: dcccpy-linux-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "runtime"
-Requires-Dist: dcccpy-linux-arm64-runtime==0.1.1; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "runtime"
-Requires-Dist: dcccpy-windows-runtime==0.1.1; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "runtime"
-Requires-Dist: dcccpy-macos-runtime==0.1.1; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "runtime"
+Requires-Dist: dcccpy-linux-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "x86_64") and extra == "runtime"
+Requires-Dist: dcccpy-linux-arm64-runtime==0.1.2; (sys_platform == "linux" and platform_machine == "aarch64") and extra == "runtime"
+Requires-Dist: dcccpy-windows-runtime==0.1.2; (sys_platform == "win32" and platform_machine == "AMD64") and extra == "runtime"
+Requires-Dist: dcccpy-macos-runtime==0.1.2; (sys_platform == "darwin" and platform_machine == "arm64") and extra == "runtime"
 
 # dcccpy
 
@@ -109,6 +109,7 @@ Common helpers mirror `DCCCcore` subcommands:
 dcccpy.centiloid("amyloid.nii", suvr=True)
 dcccpy.centaurz("tau.nii", report_detailed_regions=True)
 dcccpy.fillstates("fdg.nii", tracer="fdg")
+dcccpy.adni_pet_core("fdg.nii", tracer="fdg")
 dcccpy.normalize("pet.nii", iterative=True)
 dcccpy.pet_motion_correct(
     "dynamic_pet.nii.gz",
@@ -134,8 +135,17 @@ Each helper returns `DCCCResult` with:
 ```bash
 dcccpy --help
 dcccpy centiloid --input amyloid_pet.nii --output result.nii
+dcccpy adni-pet-core --input fdg.nii --output fdg_adni.nii --tracer fdg
 ```
 
+`adni_pet_core` deliberately has no default tracer. Use `abeta`, `tau`, or
+`fdg`; FDG selects ADNI's iterative masked global-mean normalization, while
+Aβ and tau retain cerebellar gray normalization.
+
+Downloaded ADNI preprocessed FDG DICOMs can differ slightly from the exact
+published iteration. See the repository's
+[ADNI FDG compatibility note](../../docs/adni-fdg-preprocessing-validation.md).
+
 ## Runtime lookup
 
 At runtime, `dcccpy` looks for `DCCCcore` in this order:
@@ -179,7 +189,7 @@ the calculation again.
 Release wheels should vendor the matching `DCCCcore` runtime tree before build:
 
 ```bash
-python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-x64
+python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-x64
 python -m build --wheel
 ```
 
@@ -187,7 +197,7 @@ The Linux ARM64 runtime package uses the corresponding release asset:
 
 ```bash
 cd python/dcccpy-linux-arm64-runtime
-python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-arm64
+python scripts/vendor_dccccore.py --version 4.4.0 --release-platform ubuntu-latest-arm64
 python -m build --wheel
 ```
 
@@ -205,7 +215,7 @@ The preferred distribution layout is:
 
 ## Packaging note
 
-The runtime wheels use a PyPI-size profile for DCCCcore version 4.3.0. They omit the
+The runtime wheels use a PyPI-size profile for DCCCcore version 4.4.0. They omit the
 `fast_and_acc` registration model/config and the ADAD decoupler ONNX ensemble,
 while keeping the default spatial normalization model and assets needed by
 common Centiloid/CenTauR/CenTauRz workflows.

{dcccpy-0.1.8 → dcccpy-0.2.0}/src/dcccpy.egg-info/requires.txt

@@ -3,31 +3,31 @@ nibabel>=5
 [linux-runtime]
 
 [linux-runtime:sys_platform == "linux" and platform_machine == "aarch64"]
-dcccpy-linux-arm64-runtime==0.1.1
+dcccpy-linux-arm64-runtime==0.1.2
 
 [linux-runtime:sys_platform == "linux" and platform_machine == "x86_64"]
-dcccpy-linux-runtime==0.1.1
+dcccpy-linux-runtime==0.1.2
 
 [macos-runtime]
 
 [macos-runtime:sys_platform == "darwin" and platform_machine == "arm64"]
-dcccpy-macos-runtime==0.1.1
+dcccpy-macos-runtime==0.1.2
 
 [runtime]
 
 [runtime:sys_platform == "darwin" and platform_machine == "arm64"]
-dcccpy-macos-runtime==0.1.1
+dcccpy-macos-runtime==0.1.2
 
 [runtime:sys_platform == "linux" and platform_machine == "aarch64"]
-dcccpy-linux-arm64-runtime==0.1.1
+dcccpy-linux-arm64-runtime==0.1.2
 
 [runtime:sys_platform == "linux" and platform_machine == "x86_64"]
-dcccpy-linux-runtime==0.1.1
+dcccpy-linux-runtime==0.1.2
 
 [runtime:sys_platform == "win32" and platform_machine == "AMD64"]
-dcccpy-windows-runtime==0.1.1
+dcccpy-windows-runtime==0.1.2
 
 [windows-runtime]
 
 [windows-runtime:sys_platform == "win32" and platform_machine == "AMD64"]
-dcccpy-windows-runtime==0.1.1
+dcccpy-windows-runtime==0.1.2

{dcccpy-0.1.8 → dcccpy-0.2.0}/tests/test_core.py

@@ -142,7 +142,7 @@ def test_dccccore_path_can_disable_auto_download(tmp_path: Path, monkeypatch: py
 
 
 def test_dccccore_path_auto_downloads_to_cache(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
-    asset_root = tmp_path / "asset" / "DCCCcore-4.3.0-ubuntu-latest-x64"
+    asset_root = tmp_path / "asset" / "DCCCcore-4.4.0-ubuntu-latest-x64"
     asset_root.mkdir(parents=True)
     exe = asset_root / "DCCCcore"
     exe.write_text("#!/usr/bin/env sh\nprintf 'fake dccccore\\n'\n")
@@ -150,7 +150,7 @@ def test_dccccore_path_auto_downloads_to_cache(tmp_path: Path, monkeypatch: pyte
 
     archive = tmp_path / "DCCCcore.zip"
     with zipfile.ZipFile(archive, "w") as zf:
-        zf.write(exe, "DCCCcore-4.3.0-ubuntu-latest-x64/DCCCcore")
+        zf.write(exe, "DCCCcore-4.4.0-ubuntu-latest-x64/DCCCcore")
 
     monkeypatch.delenv("DCCCPY_DCCCCORE", raising=False)
     monkeypatch.setenv("DCCCPY_AUTO_DOWNLOAD", "1")
@@ -186,10 +186,10 @@ def test_linux_arm64_release_platform() -> None:
     assert release_platform("linux-arm64") == "ubuntu-latest-arm64"
 
 
-def test_default_release_targets_dccccore_430() -> None:
-    assert DCCCCORE_VERSION == "4.3.0"
+def test_default_release_targets_dccccore_440() -> None:
+    assert DCCCCORE_VERSION == "4.4.0"
     assert release_url(platform_name="ubuntu-latest-x64").endswith(
-        "/releases/download/v4.3.0/DCCCcore-4.3.0-ubuntu-latest-x64.zip"
+        "/releases/download/v4.4.0/DCCCcore-4.4.0-ubuntu-latest-x64.zip"
     )
 
 
@@ -262,6 +262,37 @@ def test_pet_motion_correct_forwards_optional_outputs(
     ]
 
 
+def test_adni_pet_core_requires_and_forwards_tracer(
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    fake_args = tmp_path / "args.txt"
+    fake_exe = make_fake_dccccore(tmp_path)
+    input_path = tmp_path / "pet.nii"
+    output_path = tmp_path / "adni.nii"
+    input_path.write_text("fake PET")
+    monkeypatch.setenv("DCCCPY_DCCCCORE", str(fake_exe))
+    monkeypatch.setenv("DCCCPY_FAKE_ARGS", str(fake_args))
+
+    result = dcccpy.adni_pet_core(input_path, output_path, tracer="fdg")
+
+    assert result.returncode == 0
+    assert fake_args.read_text().splitlines() == [
+        "adni-pet-core",
+        "--input",
+        str(input_path),
+        "--output",
+        str(output_path),
+        "--tracer",
+        "fdg",
+    ]
+
+
+def test_adni_pet_core_python_api_has_no_default_tracer() -> None:
+    with pytest.raises(TypeError, match="tracer"):
+        dcccpy.adni_pet_core("pet.nii")
+
+
 def test_run_adds_macos_security_hint_for_blocked_runtime(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,