Merge pull request #27 from ArcanaFramework/develop

Adding ITK supported formats

fileformats/medimage/__init__.py

@@ -1,5 +1,6 @@
 from ._version import __version__  # noqa: F401
 from .base import MedicalImage  # noqa: F401
+
 # import Dicom to alias to the medimage namespace it here as well
 from fileformats.application import Dicom  # noqa: F401
 from .misc import (  # noqa: F401
@@ -28,7 +29,8 @@
     DicomCollection,
     DicomDir,
     DicomSeries,
-    # SiemensDicomDir,
+    # Vnd_Siemens_Vision,
+    # Vnd_Siemens_VisionDir,
 )
 from .raw import (  # noqa: F401
     Kspace,
@@ -43,9 +45,7 @@
     Vnd_Siemens_Biograph128Vision_Vr20b_PetCountRate,
     Vnd_Siemens_Biograph128Vision_Vr20b_PetNormalisation,
 )
-from .surface import (
-    Gifti  # noqa: F401
-)
+from .surface import Gifti  # noqa: F401
 from .contents.imaging.modality import (  # noqa: F401
     ImagingModality,
     CombinedModalities,
@@ -89,10 +89,18 @@
     RG,
     US,
 )
-from .contents.imaging.derivatives import (
-    Derivative,
-    Mask
+from .contents.imaging.derivatives import Derivative, Mask  # noqa: F401
+from .contents.anatomical_entity.material_anatomical_entity.anatomical_structure import (  # noqa: F401
+    Brain,
+    SpinalCord,
+)
+from .itk import (  # noqa: F401
+    GDCM,
+    GIPL,
+    VTK,
+    PGM,
+    MetaImage,
+    Nrrd,
+    NrrdGz,
+    ItkSupported,
 )
-from .contents.anatomical_entity.material_anatomical_entity.anatomical_structure import (
-    Brain, SpinalCord
-)

fileformats/medimage/dicom.py

@@ -1,5 +1,4 @@
 import typing as ty
-from operator import itemgetter
 from collections import defaultdict, Counter
 from pathlib import Path
 from functools import cached_property
@@ -40,8 +39,10 @@ class DicomDir(DicomCollection, DirectoryContaining[Dicom]):
 class DicomSeries(DicomCollection, SetOf[Dicom]):
     @classmethod
     def from_paths(
-        cls, fspaths: ty.Iterable[Path], common_ok: bool = False,
-        selected_keys: ty.Optional[ty.Sequence[str]] = None
+        cls,
+        fspaths: ty.Iterable[Path],
+        common_ok: bool = False,
+        selected_keys: ty.Optional[ty.Sequence[str]] = None,
     ) -> ty.Tuple[ty.Set["DicomSeries"], ty.Set[Path]]:
         """Separates a list of DICOM files into separate series from the file-system
         paths
@@ -67,7 +68,10 @@ def from_paths(
         for dicom in dicoms:
             dicom.select_metadata(selected_keys)
             series_dict[
-                (str(dicom.metadata["StudyInstanceUID"]), str(dicom.metadata["SeriesNumber"]))
+                (
+                    str(dicom.metadata["StudyInstanceUID"]),
+                    str(dicom.metadata["SeriesNumber"]),
+                )
             ].append(dicom)
         return set([cls(s) for s in series_dict.values()]), remaining
 
@@ -83,14 +87,18 @@ def dicom_collection_read_metadata(
     # We use the "contents" property implementation in TypeSet instead of the overload
     # in DicomCollection because we don't want the metadata to be read ahead of the
     # the `select_metadata` call below
-    base_class = TypedSet if isinstance(collection, DicomSeries) else DirectoryContaining
+    base_class = (
+        TypedSet if isinstance(collection, DicomSeries) else DirectoryContaining
+    )
     for dicom in base_class.contents.fget(collection):
         dicom.select_metadata(selected_keys)
         for key, val in dicom.metadata.items():
             try:
                 prev_val = collated[key]
             except KeyError:
-                collated[key] = val  # Insert initial value (should only happen on first iter)
+                collated[key] = (
+                    val  # Insert initial value (should only happen on first iter)
+                )
                 key_repeats.update([key])
             else:
                 if key in varying_keys:
@@ -103,3 +111,11 @@ def dicom_collection_read_metadata(
                 else:
                     key_repeats.update([key])
     return collated
+
+
+# class Vnd_Siemens_Vision(Dicom):
+#     ext = ".ima"
+
+
+# class Vnd_Siemens_VisionDir(DicomDir):
+#     content_types = (Vnd_Siemens_Vision,)

fileformats/medimage/itk.py

@@ -0,0 +1,49 @@
+import typing as ty
+from fileformats.core.mixin import WithMagicNumber
+from fileformats.image import (
+    RasterImage,
+    VectorImage,
+    Bitmap,
+    Jpeg,
+    Tiff,
+)
+from fileformats.application import Dicom, Gzip
+from .nifti import Nifti1, NiftiGz
+
+
+class GDCM(Dicom):
+    pass
+
+
+class GIPL(RasterImage):
+    ext = ".gipl"
+
+
+class VTK(VectorImage):
+    ext = ".vtk"
+
+
+class PGM(RasterImage):
+    ext = ".pgm"
+
+
+class MetaImage(RasterImage):
+    ext = ".mhd"
+
+
+class Nrrd(WithMagicNumber, RasterImage):
+
+    ext = ".nrrd"
+    alternate_exts = (".nhdr",)
+    magic_number = b"NRRD"
+
+
+class NrrdGz(Gzip[Nrrd]):
+
+    ext = ".nrrd.gz"
+    alternate_exts = (".nhdr.gz",)
+
+
+ItkSupported = ty.Union[
+    Nifti1, NiftiGz, Dicom, Bitmap, Tiff, Jpeg, GIPL, MetaImage, Nrrd, NrrdGz, PGM, VTK
+]