debugged extras hooks signatures

extras/fileformats/extras/medimage/dicom.py

@@ -11,7 +11,7 @@
 
 
 @MedicalImage.read_array.register
-def dicom_read_array(collection: DicomCollection):
+def dicom_read_array(collection: DicomCollection) -> np.ndarray:
     image_stack = []
     for dcm_file in collection.contents:
         image_stack.append(pydicom.dcmread(dcm_file).pixel_array)

extras/fileformats/extras/medimage/diffusion.py

@@ -1,14 +1,14 @@
 import numpy as np
-from fileformats.medimage.diffusion import DwiEncoding, Bval, Bvec
+from fileformats.medimage import DwiEncoding, Bval, Bvec
 
 
 @Bval.read_array.register
-def bval_read_array(bval: Bval):
+def bval_read_array(bval: Bval) -> np.ndarray:  # noqa
     return np.asarray([float(ln) for ln in bval.read_contents().split()])
 
 
 @DwiEncoding.read_array.register
-def bvec_read_array(bvec: Bvec):
+def bvec_read_array(bvec: Bvec) -> np.ndarray:  # noqa
     bvals = bvec.b_values_file.read_array()
     directions = np.asarray(
         [[float(x) for x in ln.split()] for ln in bvec.read_contents().splitlines()]

extras/fileformats/extras/medimage/nifti.py

@@ -2,32 +2,33 @@
 import typing as ty
 from random import Random
 import nibabel
+import numpy as np
 from fileformats.core import FileSet
 from fileformats.core.utils import gen_filename
 from fileformats.medimage import MedicalImage, Nifti, NiftiGz, Nifti1, NiftiGzX, NiftiX
 import medimages4tests.dummy.nifti
 
 
 @FileSet.read_metadata.register
-def nifti_read_metadata(nifti: Nifti):
+def nifti_read_metadata(nifti: Nifti) -> ty.Mapping[str, ty.Any]:
     return dict(nibabel.load(nifti.fspath).header)
 
 
 @MedicalImage.read_array.register
-def nifti_data_array(nifti: Nifti):
+def nifti_data_array(nifti: Nifti) -> np.ndarray:  # noqa
     return nibabel.load(nifti.fspath).get_data()
 
 
 @MedicalImage.vox_sizes.register
-def nifti_vox_sizes(nifti: Nifti):
+def nifti_vox_sizes(nifti: Nifti) -> ty.Tuple[float, float, float]:
     # FIXME: This won't work for 4-D files
-    return nifti.metadata["pixdim"][1:4]
+    return tuple(float(d) for d in nifti.metadata["pixdim"][1:4])
 
 
 @MedicalImage.dims.register
-def nifti_dims(nifti: Nifti):
+def nifti_dims(nifti: Nifti) -> ty.Tuple[int, int, int]:
     # FIXME: This won't work for 4-D files
-    return nifti.metadata["dim"][1:4]
+    return tuple(int(d) for d in nifti.metadata["dim"][1:4])
 
 
 @FileSet.generate_sample_data.register

fileformats/medimage/base.py

@@ -19,7 +19,7 @@ class MedicalImage(FileSet):
     binary = True
 
     @hook.extra
-    def read_array(self):
+    def read_array(self) -> "numpy.ndarray":  # noqa
         """
         Returns the binary data of the image in a numpy array
         """

fileformats/medimage/diffusion.py

@@ -10,21 +10,21 @@ class DwiEncoding(File):
     iana_mime: ty.Optional[str] = None
 
     @hook.extra
-    def read_array(self):
+    def read_array(self) -> "numpy.ndarray":  # noqa
         "Both the gradient direction and weighting combined into a single Nx4 array"
         raise NotImplementedError
 
     @property
-    def array(self):
+    def array(self) -> "numpy.ndarray":  # noqa
         return self.read_array()
 
     @property
-    def directions(self):
+    def directions(self) -> "numpy.ndarray":  # noqa
         "gradient direction and weighting combined into a single Nx4 array"
         return self.array[:, :3]
 
     @property
-    def b_values(self):
+    def b_values(self) -> "numpy.ndarray":  # noqa
         "the b-value weighting"
         return self.array[:, 3]
 
@@ -34,7 +34,7 @@ class Bval(File):
     ext = ".bval"
 
     @hook.extra
-    def read_array(self):
+    def read_array(self) -> "numpy.ndarray":  # noqa
         raise NotImplementedError