updated to use validated_property decorator

.codespell-ignorewords

@@ -1,2 +1,3 @@
 nd
 te
+ptd

.pre-commit-config.yaml

@@ -37,4 +37,9 @@ repos:
                     --non-interactive,
                 ]
             exclude: tests
-            additional_dependencies: [pytest, fileformats, pydicom, nibabel, attrs]
+            additional_dependencies:
+            - fileformats>=0.13.0
+            - pytest
+            - pydicom
+            - nibabel
+            - attrs

fileformats/medimage/base.py

@@ -1,5 +1,4 @@
 import sys
-import typing
 import typing as ty
 import logging
 from fileformats.core import extra, FileSet, mtime_cached_property
@@ -31,14 +30,12 @@
 
 class MedicalImage(WithClassifiers, FileSet):
 
-    iana_mime: ty.Optional[str] = None
     INCLUDE_HDR_KEYS: ty.Optional[ty.Tuple[str, ...]] = None
     IGNORE_HDR_KEYS: ty.Optional[ty.Tuple[str, ...]] = None
     binary = True
     classifiers_attr_name = "image_contents"
     image_contents = ()
     allowed_classifiers = (ContentsClassifier,)
-    multiple_classifiers = True
     exclusive_classifiers = (ImagingModality, AnatomicalEntity, Derivative)
 
     @extra

fileformats/medimage/diffusion.py

@@ -1,8 +1,8 @@
 import typing
-from fileformats.core import extra
+from fileformats.core import extra, validated_property
 from fileformats.core.typing import TypeAlias
 from fileformats.core.mixin import WithAdjacentFiles
-from fileformats.generic import File
+from fileformats.generic import BinaryFile
 from .nifti import NiftiGzX, NiftiGz, Nifti1, NiftiX
 
 
@@ -14,10 +14,7 @@
 )  # In Py<3.9 this is problematic "numpy.typing.NDArray[numpy.floating[typing.Any]]"
 
 
-class DwiEncoding(File):
-
-    iana_mime: typing.Optional[str] = None
-
+class DwiEncoding:
     @extra
     def read_array(self) -> EncodingArrayType:
         "Both the gradient direction and weighting combined into a single Nx4 array"
@@ -35,7 +32,7 @@ def b_values(self) -> EncodingArrayType:
         return self.array()[:, 3]
 
 
-class Bval(File):
+class Bval(BinaryFile):
 
     ext = ".bval"
 
@@ -44,19 +41,19 @@ def read_array(self) -> EncodingArrayType:
         raise NotImplementedError
 
 
-class Bvec(WithAdjacentFiles, DwiEncoding):
+class Bvec(WithAdjacentFiles, DwiEncoding, BinaryFile):
     """FSL-style diffusion encoding, in two separate files"""
 
     ext = ".bvec"
 
-    @property
+    @validated_property
     def b_values_file(self) -> Bval:
         return Bval(self.select_by_ext(Bval))
 
 
 # NIfTI file format gzipped with BIDS side car
 class WithBvec(WithAdjacentFiles):
-    @property
+    @validated_property
     def encoding(self) -> Bvec:
         return Bvec(self.select_by_ext(Bvec))  # type: ignore[attr-defined]
 

fileformats/medimage/misc.py

@@ -1,5 +1,6 @@
 from fileformats.application import Gzip
-from fileformats.generic import File
+from fileformats.generic import BinaryFile
+from fileformats.core import validated_property
 from fileformats.core.mixin import WithSeparateHeader, WithMagicVersion
 from .base import MedicalImage
 from fileformats.core.exceptions import FormatMismatchError
@@ -10,18 +11,18 @@
 # ==================
 
 
-class AnalyzeHeader(File):
+class AnalyzeHeader(BinaryFile):
 
     ext = ".hdr"
 
 
-class Analyze(WithSeparateHeader, MedicalImage, File):
+class Analyze(WithSeparateHeader, MedicalImage, BinaryFile):
 
     ext = ".img"
     header_type = AnalyzeHeader
 
 
-class Mgh(WithMagicVersion, File):
+class Mgh(WithMagicVersion, BinaryFile):
     """
     FreeSurfer 4-dimensional brain images
 
@@ -31,7 +32,7 @@ class Mgh(WithMagicVersion, File):
     ext = ".mgh"
     magic_pattern = rb"(....)"  # First integer is the version string
 
-    @property
+    @validated_property
     def _is_supported_version(self) -> None:
         assert isinstance(self.version, str)
         if int(self.version) != 1:

fileformats/medimage/nifti.py

@@ -1,23 +1,22 @@
-import typing as ty
-from fileformats.generic import File
+from fileformats.generic import BinaryFile
+from fileformats.core import validated_property
 from fileformats.core.mixin import WithSideCars, WithMagicNumber, WithAdjacentFiles
 from fileformats.application import Json
 from fileformats.application.archive import BaseGzip
 from .base import MedicalImage
 
 
-class Nifti(MedicalImage, File):
+class Nifti(MedicalImage, BinaryFile):
 
     ext: str = ".nii"
-    iana_mime: ty.Optional[str] = None
 
 
 class WithBids(WithSideCars):
 
     primary_type = Nifti
     side_car_types = (Json,)
 
-    @property
+    @validated_property
     def json_file(self) -> Json:
         return Json(self.select_by_ext(Json))  # type: ignore[attr-defined]
 
@@ -61,6 +60,6 @@ class NiftiWithDataFile(WithAdjacentFiles, Nifti1):
     magic_number = "6E693100"
     alternate_exts = (".hdr",)
 
-    @property
+    @validated_property
     def data_file(self) -> NiftiDataFile:
         return NiftiDataFile(self.select_by_ext(NiftiDataFile))

fileformats/medimage/raw/mri/__init__.py

@@ -1,14 +1,14 @@
-from fileformats.generic import File
+from fileformats.generic import BinaryFile
 
 
-class Kspace(File):
+class Kspace(BinaryFile):
 
     binary = True
     # iana_mime = None
     pass
 
 
-class Rda(File):
+class Rda(BinaryFile):
     """MRS format"""
 
     ext = ".rda"

fileformats/medimage/raw/pet/base.py

@@ -1,32 +1,21 @@
-from fileformats.generic import File
+from fileformats.generic import BinaryFile
 
 
-class PetRawData(File):
-
-    binary = True
-    # iana_mime = None
-    pass
+class PetRawData(BinaryFile):
+    """Base class for raw PET data files"""
 
 
 class PetListMode(PetRawData):
     "raw projection data"
-    # iana_mime = None
-    pass
 
 
 class PetSinogram(PetRawData):
     "histogrammed projection data in a reconstruction-friendly format"
-    # iana_mime = None
-    pass
 
 
 class PetCountRate(PetRawData):
     "number of prompt/random/single events per unit time"
-    # iana_mime = None
-    pass
 
 
 class PetNormalisation(PetRawData):
     "normalisation scan or the current cross calibration factor"
-    # iana_mime = None
-    pass

fileformats/medimage/raw/pet/siemens.py

@@ -1,6 +1,6 @@
 import io
 from fileformats.generic import TypedSet
-from fileformats.core.decorators import mtime_cached_property
+from fileformats.core import mtime_cached_property, validated_property
 from fileformats.core.mixin import WithMagicNumber
 from .base import (
     PetRawData,
@@ -32,10 +32,10 @@ class Vnd_Siemens_Biograph128Vision_Vr20b_PetRawData(WithMagicNumber, PetRawData
     def dicom_header_size(self) -> int:
         with self.open() as f:
             f.seek(self.dcm_hdr_size_int_offset, io.SEEK_END)
-            dcm_hdr_size_bytes: bytes = f.read(self.sizeof_dcm_hdr_size_int)  # type: ignore[assignment]
+            dcm_hdr_size_bytes: bytes = f.read(self.sizeof_dcm_hdr_size_int)
             return int.from_bytes(dcm_hdr_size_bytes, "little")
 
-    @property
+    @validated_property
     def dicom_header_offset(self) -> int:
         dcm_hdr_size: int = self.dicom_header_size
         return -dcm_hdr_size + self.dcm_hdr_size_int_offset

fileformats/medimage/surface.py

@@ -1,11 +1,9 @@
-import typing as ty
 from fileformats.core import FileSet
 from fileformats.application import Xml
 
 
 class SurfaceMesh(FileSet):
-
-    iana_mime: ty.Optional[str] = None
+    ...
 
 
 class Gifti(SurfaceMesh, Xml):

pyproject.toml

@@ -77,4 +77,4 @@ doctests = true
 per-file-ignores = ["__init__.py:F401"]
 max-line-length = 88
 select = "C,E,F,W,B,B950"
-extend-ignore = ['E203', 'E501', 'E129', 'W503']
+extend-ignore = ['E203', 'E501', 'E129', 'W503', 'E701']