fixed up extras hooks signatures

ArcanaFramework · Dec 6, 2023 · cdbe8bb · cdbe8bb
1 parent 33795f8
commit cdbe8bb
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Showing 4 changed files with 13 additions and 12 deletions.
diff --git a/extras/fileformats/extras/medimage/dicom.py b/extras/fileformats/extras/medimage/dicom.py
@@ -19,14 +19,14 @@ def dicom_read_array(collection: DicomCollection):
 
 
 @MedicalImage.vox_sizes.register
-def dicom_vox_sizes(collection: DicomCollection):
+def dicom_vox_sizes(collection: DicomCollection) -> ty.Tuple[float, float, float]:
     return tuple(
         collection.metadata["PixelSpacing"] + [collection.metadata["SliceThickness"]]
     )
 
 
 @MedicalImage.dims.register
-def dicom_dims(collection: DicomCollection):
+def dicom_dims(collection: DicomCollection) -> ty.Tuple[int, int, int]:
     return tuple(
         (
             collection.metadata["Rows"],
@@ -37,12 +37,12 @@ def dicom_dims(collection: DicomCollection):
 
 
 @DicomCollection.series_number.register
-def dicom_series_number(collection: DicomCollection):
+def dicom_series_number(collection: DicomCollection) -> str:
     return str(collection.metadata["SeriesNumber"])
 
 
 @FileSet.generate_sample_data.register
-def dicom_dir_generate_sample_data(dcmdir: DicomDir, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]) -> ty.Iterable[Path]:
+def dicom_dir_generate_sample_data(dcmdir: DicomDir, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None) -> ty.Iterable[Path]:
     dcm_dir = medimages4tests.dummy.dicom.mri.t1w.siemens.skyra.syngo_d13c.get_image()
     # Set series number to random value to make it different
     if isinstance(seed, Random):
@@ -60,7 +60,7 @@ def dicom_dir_generate_sample_data(dcmdir: DicomDir, dest_dir: Path, seed: ty.Un
 
 
 @FileSet.generate_sample_data.register
-def dicom_set_generate_sample_data(dcm_series: DicomSeries, dest_dir: Path, seed: int, stem: ty.Optional[str]) -> ty.Iterable[Path]:
+def dicom_set_generate_sample_data(dcm_series: DicomSeries, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None) -> ty.Iterable[Path]:
     rng = Random(seed)
     dicom_dir = dicom_dir_generate_sample_data(dcm_series, dest_dir=mkdtemp(), seed=rng, stem=None)[0]
     stem = gen_filename(rng, stem=stem)

diff --git a/extras/fileformats/extras/medimage/nifti.py b/extras/fileformats/extras/medimage/nifti.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 import typing as ty
+from random import Random
 import nibabel
 from fileformats.core import FileSet
 from fileformats.core.utils import gen_filename
@@ -31,7 +32,7 @@ def nifti_dims(nifti: Nifti):
 
 @FileSet.generate_sample_data.register
 def nifti_generate_sample_data(
-    nifti: Nifti1, dest_dir: Path, seed: int, stem: ty.Optional[str]
+    nifti: Nifti1, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
 ) -> ty.Iterable[Path]:
     return medimages4tests.dummy.nifti.get_image(
         out_file=dest_dir / gen_filename(seed, file_type=Nifti1, stem=stem)
@@ -40,7 +41,7 @@ def nifti_generate_sample_data(
 
 @FileSet.generate_sample_data.register
 def nifti_gz_generate_sample_data(
-    nifti: NiftiGz, dest_dir: Path, seed: int, stem: ty.Optional[str]
+    nifti: NiftiGz, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
 ) -> ty.Iterable[Path]:
     return medimages4tests.dummy.nifti.get_image(
         out_file=dest_dir / gen_filename(seed, file_type=NiftiGz, stem=stem),
@@ -50,14 +51,14 @@ def nifti_gz_generate_sample_data(
 
 @FileSet.generate_sample_data.register
 def nifti_gz_x_generate_sample_data(
-    nifti: NiftiGzX, dest_dir: Path, seed: int, stem: ty.Optional[str]
+    nifti: NiftiGzX, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
 ) -> ty.Iterable[Path]:
     return medimages4tests.mri.neuro.t1w.get_image()
 
 
 @FileSet.generate_sample_data.register
 def nifti_x_generate_sample_data(
-    nifti: NiftiX, dest_dir: Path, seed: int, stem: ty.Optional[str]
+    nifti: NiftiX, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
 ) -> ty.Iterable[Path]:
     nifti_gz_x = NiftiGzX(medimages4tests.mri.neuro.t1w.get_image())
     return NiftiX.convert(nifti_gz_x)
diff --git a/fileformats/medimage/base.py b/fileformats/medimage/base.py
@@ -26,11 +26,11 @@ def read_array(self):
         raise NotImplementedError
 
     @hook.extra
-    def vox_sizes(self) -> ty.Tuple[float]:
+    def vox_sizes(self) -> ty.Tuple[float, float, float]:
         """The length of the voxels along each dimension"""
         raise NotImplementedError
 
     @hook.extra
-    def dims(self) -> ty.Tuple[int]:
+    def dims(self) -> ty.Tuple[int, int, int]:
         """The dimensions of the image"""
         raise NotImplementedError
diff --git a/fileformats/medimage/dicom.py b/fileformats/medimage/dicom.py
@@ -26,7 +26,7 @@ def __len__(self):
         return len(self.contents)
 
     @hook.extra
-    def series_number(self):
+    def series_number(self) -> str:
         raise NotImplementedError
 
     @cached_property