Configurable resampling interpolator (#55)

Allow setting the resampling interpolator for preprocessing.

Dependency updates:
*
[`requirements_dev.txt`](diffhunk://#diff-c9c796259f3852b51b531b79cbf07820145088d4f108fb006ab44b15f0b15934L1-R7):
Updated versions of `flake8`, `tox`, `pytest`, `pytest-cov`, `mypy`,
`build`, and `twine`.
*
[`setup.py`](diffhunk://#diff-60f61ab7a8d1910d86d9fda2261620314edcae5894d5aaa236b821c7256badd7L8-R8):
Incremented the version number from `2.1.8` to `2.1.9`.

Interpolation settings:
*
[`src/picai_prep/preprocessing.py`](diffhunk://#diff-f6c4c6e211631a6dba78bcca09d032a3147c3d8b4949bdca958e80dee0b93833R39-R48):
Added `scan_interpolator` and `lbl_interpolator` attributes to the
`PreprocessingSettings` class.
*
[`src/picai_prep/preprocessing.py`](diffhunk://#diff-f6c4c6e211631a6dba78bcca09d032a3147c3d8b4949bdca958e80dee0b93833R80):
Modified the `resample_img` function to accept an `interpolation`
parameter and use it if provided.
[[1]](diffhunk://#diff-f6c4c6e211631a6dba78bcca09d032a3147c3d8b4949bdca958e80dee0b93833R80)
[[2]](diffhunk://#diff-f6c4c6e211631a6dba78bcca09d032a3147c3d8b4949bdca958e80dee0b93833L110-R117)
*
[`src/picai_prep/preprocessing.py`](diffhunk://#diff-f6c4c6e211631a6dba78bcca09d032a3147c3d8b4949bdca958e80dee0b93833L257-R270):
Updated the `resample_to_first_scan` and `resample_spacing` methods to
use the new interpolation settings from `PreprocessingSettings`.
[[1]](diffhunk://#diff-f6c4c6e211631a6dba78bcca09d032a3147c3d8b4949bdca958e80dee0b93833L257-R270)
[[2]](diffhunk://#diff-f6c4c6e211631a6dba78bcca09d032a3147c3d8b4949bdca958e80dee0b93833L275-R288)

requirements_dev.txt

@@ -1,7 +1,7 @@
-flake8==3.9.2
-tox==3.24.3
-pytest==6.2.5
-pytest-cov==2.12.1
-mypy===0.910
-build
-twine
+flake8==7.1.1
+tox==4.18.1
+pytest==8.3.2
+pytest-cov==5.0.0
+mypy===1.11.2
+build==1.2.2
+twine==5.1.1

setup.py

@@ -5,7 +5,7 @@
         long_description = fh.read()
 
     setuptools.setup(
-        version='2.1.8',
+        version='2.1.9',
         author_email='[email protected]',
         long_description=long_description,
         long_description_content_type="text/markdown",

src/picai_prep/preprocessing.py

@@ -36,12 +36,16 @@ class PreprocessingSettings():
     - physical_size: size in mm of the target image (z, y, x)
     - crop_only: only crop to specified size (i.e., do not pad)
     - align_segmentation: whether to align the scans using the centroid of the provided segmentation
+    - scan_interpolator: interpolation method for scans
+    - lbl_interpolator: interpolation method for labels
     """
     matrix_size: Optional[Iterable[int]] = None
     spacing: Optional[Iterable[float]] = None
     physical_size: Optional[Iterable[float]] = None
     crop_only: bool = False
     align_segmentation: Optional[sitk.Image] = None
+    scan_interpolator: int = sitk.sitkBSpline
+    lbl_interpolator: int = sitk.sitkNearestNeighbor
 
     def __post_init__(self):
         if self.physical_size is None and self.spacing is not None and self.matrix_size is not None:
@@ -73,6 +77,7 @@ def resample_img(
     out_spacing: Iterable[float] = (2.0, 2.0, 2.0),
     out_size: Optional[Iterable[int]] = None,
     is_label: bool = False,
+    interpolation = None,
     pad_value: Optional[Union[float, int]] = 0.,
 ) -> sitk.Image:
     """
@@ -107,7 +112,9 @@ def resample_img(
     resample.SetOutputOrigin(image.GetOrigin())
     resample.SetTransform(sitk.Transform())
     resample.SetDefaultPixelValue(pad_value)
-    if is_label:
+    if interpolation is not None:
+        resample.SetInterpolator(interpolation)
+    elif is_label:
         resample.SetInterpolator(sitk.sitkNearestNeighbor)
     else:
         resample.SetInterpolator(sitk.sitkBSpline)
@@ -254,13 +261,13 @@ def resample_to_first_scan(self):
         # set up resampler to resolution, field of view, etc. of first scan
         resampler = sitk.ResampleImageFilter()  # default linear
         resampler.SetReferenceImage(self.scans[0])
-        resampler.SetInterpolator(sitk.sitkBSpline)
+        resampler.SetInterpolator(self.settings.scan_interpolator)
 
         # resample other images
         self.scans[1:] = [resampler.Execute(scan) for scan in self.scans[1:]]
 
         # resample annotation
-        resampler.SetInterpolator(sitk.sitkNearestNeighbor)
+        resampler.SetInterpolator(self.settings.lbl_interpolator)
         if self.lbl is not None:
             self.lbl = resampler.Execute(self.lbl)
 
@@ -272,13 +279,13 @@ def resample_spacing(self, spacing: Optional[Iterable[float]] = None):
 
         # resample scans to target resolution
         self.scans = [
-            resample_img(scan, out_spacing=spacing, is_label=False)
+            resample_img(scan, out_spacing=spacing, interpolation=self.settings.scan_interpolator)
             for scan in self.scans
         ]
 
         # resample annotation to target resolution
         if self.lbl is not None:
-            self.lbl = resample_img(self.lbl, out_spacing=spacing, is_label=True)
+            self.lbl = resample_img(self.lbl, out_spacing=spacing, interpolation=self.settings.lbl_interpolator)
 
     def centre_crop_or_pad(self):
         """Centre crop and/or pad scans and label"""