Merge pull request #106 from bilgelm/speedup2

fix nibabel dataobj access for speed up; enable nesma test; ignore jinja2 safety issue

noxfile.py

@@ -143,7 +143,14 @@ def safety(session: Session) -> None:
     """Scan dependencies for insecure packages."""
     requirements = session.poetry.export_requirements()
     session.install("safety")
-    session.run("safety", "check", "--full-report", f"--file={requirements}")
+    session.run(
+        "safety",
+        "check",
+        "--full-report",
+        f"--file={requirements}",
+        "--ignore",
+        "70612",
+    )
 
 
 @session(python=python_versions)

src/dynamicpet/temporalobject/temporalimage.py

@@ -81,7 +81,7 @@ def __init__(
     @property
     def dataobj(self) -> NDArray[np.double]:
         """Get dataobj of image."""
-        return np.asarray(self.img.dataobj, dtype=np.double)
+        return self.img.get_fdata()  # np.asarray(self.img.dataobj, dtype=np.double)
 
     @property
     def num_voxels(self) -> int:

tests/test_main.py

@@ -146,7 +146,6 @@ def test_denoise_hyprlr(images: dict[str, Path]) -> None:
     assert os.path.isfile(outputdir / "pet_hyprlr.json")
 
 
-@pytest.mark.skip(reason="current NESMA implementation is too slow")
 def test_denoise_nesma(images: dict[str, Path]) -> None:
     """Test denoise in __main__.py."""
     from dynamicpet.__main__ import denoise