Fix Windows NIfTI paths and release dcccpy 0.1.7

localizer/src/core/common/PathUtils.cpp

@@ -22,6 +22,14 @@ namespace Common::path {
 
 namespace {
 
+#ifdef _WIN32
+bool containsNonAscii(const std::string& value) {
+    return std::any_of(value.begin(), value.end(), [](unsigned char ch) {
+        return ch > 0x7F;
+    });
+}
+#endif
+
 std::string normalizeDirectory(const std::filesystem::path& directory) {
     if (directory.empty()) {
         return {};
@@ -103,6 +111,15 @@ std::string toUtf8(const std::filesystem::path& value) {
 
 std::string legacyFileName(const std::filesystem::path& value) {
 #ifdef _WIN32
+    const std::string utf8Path = toUtf8(value);
+    // ITK selects an ImageIO from the filename extension. Windows 8.3 paths
+    // collapse a compound NIfTI extension such as .nii.gz to .GZ, so keep
+    // ordinary ASCII paths intact and only fall back to a short path when it
+    // is needed for a non-ASCII filename.
+    if (!containsNonAscii(utf8Path)) {
+        return utf8Path;
+    }
+
     if (const std::wstring shortPath = shortPathForExistingPath(value); !shortPath.empty()) {
         return wideToUtf8(shortPath);
     }

python/dcccpy/README.md

@@ -79,6 +79,12 @@ dcccpy.centiloid("amyloid.nii", suvr=True)
 dcccpy.centaurz("tau.nii", report_detailed_regions=True)
 dcccpy.fillstates("fdg.nii", tracer="fdg")
 dcccpy.normalize("pet.nii", iterative=True)
+dcccpy.pet_motion_correct(
+    "dynamic_pet.nii.gz",
+    "averaged_pet.nii.gz",
+    save_corrected_dynamic="corrected.nii.gz",
+    motion_output="motion.tsv",
+)
 dcccpy.run(["centiloid", "--input", "a.nii", "--output", "b.nii"])
 ```
 
@@ -142,15 +148,15 @@ the calculation again.
 Release wheels should vendor the matching `DCCCcore` runtime tree before build:
 
 ```bash
-python scripts/vendor_dccccore.py --version 4.2.4 --release-platform ubuntu-latest-x64
+python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-x64
 python -m build --wheel
 ```
 
 The Linux ARM64 runtime package uses the corresponding release asset:
 
 ```bash
 cd python/dcccpy-linux-arm64-runtime
-python scripts/vendor_dccccore.py --version 4.2.4 --release-platform ubuntu-latest-arm64
+python scripts/vendor_dccccore.py --version 4.3.0 --release-platform ubuntu-latest-arm64
 python -m build --wheel
 ```
 

python/dcccpy/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "dcccpy"
-version = "0.1.6"
+version = "0.1.7"
 description = "Python wrapper for the DCCCcore PET biomarker command-line tool"
 readme = "README.md"
 requires-python = ">=3.9"

python/dcccpy/scripts/vendor_dccccore.py

@@ -15,7 +15,7 @@
 
 
 REPO = "tctco/DCCCSlicer"
-DEFAULT_VERSION = "4.2.4"
+DEFAULT_VERSION = "4.3.0"
 DEFAULT_RELEASE_PLATFORM = "ubuntu-latest-x64"
 DEFAULT_VENDOR_PLATFORM = "linux-x86_64"
 

python/dcccpy/src/dcccpy/__init__.py

@@ -13,6 +13,7 @@
     fillstates,
     normalize,
     parse_metrics,
+    pet_motion_correct,
     rigid,
     run,
     suvr,
@@ -36,6 +37,7 @@
     "fillstates",
     "normalize",
     "parse_metrics",
+    "pet_motion_correct",
     "rigid",
     "run",
     "suvr",

python/dcccpy/src/dcccpy/core.py

@@ -420,3 +420,42 @@ def rigid(
     **kwargs: object,
 ) -> DCCCResult:
     return _spatial_command("rigid", input, output, **kwargs)
+
+
+def pet_motion_correct(
+    input: object,
+    output: str | os.PathLike[str] | None = None,
+    *,
+    save_corrected_dynamic: str | os.PathLike[str] | None = None,
+    motion_output: str | os.PathLike[str] | None = None,
+    check: bool = True,
+    executable: str | os.PathLike[str] | None = None,
+) -> DCCCResult:
+    """Rigidly align a multi-frame PET image and return its averaged 3D output."""
+
+    input_path, actual_output, temp_dir = _prepare_io(input, output)
+    args = [
+        "pet-motion-correct",
+        "--input",
+        input_path,
+        "--output",
+        os.fspath(actual_output),
+    ]
+    if save_corrected_dynamic is not None:
+        corrected_path = _resolve_user_path(save_corrected_dynamic)
+        args.extend(["--save-corrected-dynamic", os.fspath(corrected_path)])
+    if motion_output is not None:
+        motion_path = _resolve_user_path(motion_output)
+        args.extend(["--motion-output", os.fspath(motion_path)])
+
+    result = run(args, check=check, executable=executable, output=actual_output)
+    return DCCCResult(
+        args=result.args,
+        returncode=result.returncode,
+        stdout=result.stdout,
+        stderr=result.stderr,
+        output=actual_output,
+        temp_dir=temp_dir,
+        executable=result.executable,
+        metrics=result.metrics,
+    )

python/dcccpy/src/dcccpy/runtime.py

@@ -12,7 +12,7 @@
 from typing import Iterable
 
 
-DCCCCORE_VERSION = "4.2.4"
+DCCCCORE_VERSION = "4.3.0"
 RELEASE_REPO = "tctco/DCCCSlicer"
 
 

python/dcccpy/tests/test_core.py

@@ -9,7 +9,14 @@
 import pytest
 
 import dcccpy
-from dcccpy.runtime import DCCCcoreNotFoundError, dccccore_path, find_existing_dccccore, release_platform
+from dcccpy.runtime import (
+    DCCCCORE_VERSION,
+    DCCCcoreNotFoundError,
+    dccccore_path,
+    find_existing_dccccore,
+    release_platform,
+    release_url,
+)
 
 
 def make_fake_dccccore(tmp_path: Path) -> Path:
@@ -135,15 +142,15 @@ 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-4.2.4-ubuntu-latest-x64"
+    asset_root = tmp_path / "asset" / "DCCCcore-4.3.0-ubuntu-latest-x64"
     asset_root.mkdir(parents=True)
     exe = asset_root / "DCCCcore"
     exe.write_text("#!/usr/bin/env sh\nprintf 'fake dccccore\\n'\n")
     exe.chmod(0o755)
 
     archive = tmp_path / "DCCCcore.zip"
     with zipfile.ZipFile(archive, "w") as zf:
-        zf.write(exe, "DCCCcore-4.2.4-ubuntu-latest-x64/DCCCcore")
+        zf.write(exe, "DCCCcore-4.3.0-ubuntu-latest-x64/DCCCcore")
 
     monkeypatch.delenv("DCCCPY_DCCCCORE", raising=False)
     monkeypatch.setenv("DCCCPY_AUTO_DOWNLOAD", "1")
@@ -179,6 +186,13 @@ 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"
+    assert release_url(platform_name="ubuntu-latest-x64").endswith(
+        "/releases/download/v4.3.0/DCCCcore-4.3.0-ubuntu-latest-x64.zip"
+    )
+
+
 def test_find_existing_dccccore_checks_linux_arm64_runtime_package(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
@@ -211,6 +225,43 @@ def test_cli_forwards_raw_args(tmp_path: Path, monkeypatch: pytest.MonkeyPatch,
     assert "Metric: Centiloid" in capsys.readouterr().out
 
 
+def test_pet_motion_correct_forwards_optional_outputs(
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
+    fake_args = tmp_path / "args.txt"
+    fake_exe = make_fake_dccccore(tmp_path)
+    input_path = tmp_path / "dynamic.nii.gz"
+    output_path = tmp_path / "average.nii.gz"
+    corrected_path = tmp_path / "corrected.nii.gz"
+    motion_path = tmp_path / "motion.tsv"
+    input_path.write_text("fake dynamic PET")
+    monkeypatch.setenv("DCCCPY_DCCCCORE", str(fake_exe))
+    monkeypatch.setenv("DCCCPY_FAKE_ARGS", str(fake_args))
+
+    result = dcccpy.pet_motion_correct(
+        input_path,
+        output_path,
+        save_corrected_dynamic=corrected_path,
+        motion_output=motion_path,
+    )
+
+    assert result.returncode == 0
+    assert result.output == output_path
+    assert output_path.exists()
+    assert fake_args.read_text().splitlines() == [
+        "pet-motion-correct",
+        "--input",
+        str(input_path),
+        "--output",
+        str(output_path),
+        "--save-corrected-dynamic",
+        str(corrected_path),
+        "--motion-output",
+        str(motion_path),
+    ]
+
+
 def test_run_adds_macos_security_hint_for_blocked_runtime(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,