updated fileformats to match core refactor

Author: tclose

.DS_Store

@@ -1,4 +1,4 @@
-from fileformats.core import hook
+from fileformats.core import converter
 from fileformats.medimage.base import MedicalImage
 
 from fileformats.medimage_mrtrix3 import (
@@ -16,7 +16,7 @@
     in_out_file_kwargs = {}
 
 
-@hook.converter(
+@converter(
     source_format=MedicalImage,
     target_format=MrtrixImage,
     out_ext=MrtrixImage.ext,
@@ -40,7 +40,7 @@ def mrconvert(name, out_ext: str, **kwargs):
     return MrConvert(name=name, out_file="out" + out_ext, **kwargs)
 
 
-@hook.converter(
+@converter(
     source_format=MedicalImage,
     target_format=MrtrixImageHeader,
     out_ext=MrtrixImageHeader.ext,

related-packages/.DS_Store

@@ -1,9 +1,10 @@
 import numpy as np
+from fileformats.core import extra_implementation
 from fileformats.medimage import DwiEncoding
 from fileformats.medimage_mrtrix3 import BFile
 
 
-@DwiEncoding.read_array.register
+@extra_implementation(DwiEncoding.read_array)
 def bfile_read_array(bfile: BFile) -> np.ndarray:
     return np.asarray(
         [[float(x) for x in ln.split()] for ln in bfile.read_contents().splitlines()]

related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/converters.py

@@ -4,12 +4,12 @@
 from pathlib import Path
 import numpy as np
 from medimages4tests.dummy.nifti import get_image as get_dummy_nifti
-from fileformats.core import FileSet, SampleFileGenerator
+from fileformats.core import FileSet, SampleFileGenerator, extra_implementation
 from fileformats.medimage import MedicalImage, Nifti1
 from fileformats.medimage_mrtrix3 import ImageFormat
 
 
-@FileSet.generate_sample_data.register
+@extra_implementation(FileSet.generate_sample_data)
 def generate_mrtrix_sample_data(
     mif: ImageFormat,
     generator: SampleFileGenerator,
@@ -20,7 +20,7 @@ def generate_mrtrix_sample_data(
     return mif.fspaths
 
 
-@MedicalImage.read_array.register
+@extra_implementation(MedicalImage.read_array)
 def mrtrix_read_array(mif: ImageFormat) -> np.ndarray:
     raise NotImplementedError(
         "Need to work out how to use the metadata to read the array in the correct order"

related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py

@@ -3,11 +3,11 @@
 import math
 from pathlib import Path
 import typing as ty
-from fileformats.core import FileSet, SampleFileGenerator
+from fileformats.core import FileSet, SampleFileGenerator, extra_implementation
 from fileformats.medimage_mrtrix3 import Tracks
 
 
-@FileSet.generate_sample_data.register
+@extra_implementation(FileSet.generate_sample_data)
 def generate_tracks_sample_data(
     tracks: Tracks,
     generator: SampleFileGenerator,

related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/image.py

@@ -1,4 +1,3 @@
-from fileformats.core import hook
 from fileformats.core.mixin import WithAdjacentFiles
 from fileformats.medimage import DwiEncoding, Nifti1, NiftiGz, NiftiX, NiftiGzX
 from .image import ImageFormat, ImageHeader, ImageFormatGz
@@ -12,7 +11,6 @@ class BFile(DwiEncoding):
 
 # NIfTI file format gzipped with BIDS side car
 class WithBFile(WithAdjacentFiles):
-    @hook.required
     @property
     def encoding(self) -> BFile:
         return BFile(self.select_by_ext(BFile))
@@ -35,12 +33,12 @@ class NiftiGzXB(WithBFile, NiftiGzX):
 
 
 class ImageFormatB(WithBFile, ImageFormat):
-    pass
+    iana_mime = "application/x-mrtrix-image-format.b"
 
 
 class ImageFormatGzB(WithBFile, ImageFormatGz):
-    pass
+    iana_mime = "application/x-mrtrix-image-format+gzip.b"
 
 
 class ImageHeaderB(WithBFile, ImageHeader):
-    pass
+    iana_mime = "application/x-mrtrix-image-header.b"

related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/tracks.py

@@ -1,6 +1,4 @@
-import typing as ty
 from pathlib import Path
-from fileformats.core import hook
 from fileformats.generic import File
 from fileformats.application import Gzip
 from fileformats.core.mixin import WithMagicNumber
@@ -81,8 +79,9 @@ def dims(self):
 class ImageFormat(BaseMrtrixImage):
 
     ext = ".mif"
+    iana_mime = "application/x-mrtrix-image-format"
 
-    @hook.check
+    @property
     def check_data_file(self):
         if self.data_fspath != self.fspath:
             raise FormatMismatchError(
@@ -97,15 +96,15 @@ def data_file(self):
 
 class ImageFormatGz(Gzip[ImageFormat]):
 
-    iana_mime = "application/x-image-format-gz"
+    iana_mime = "application/x-mrtrix-image-format-gz"
     ext = ".mif.gz"
 
 
 class ImageHeader(BaseMrtrixImage):
 
     ext = ".mih"
+    iana_mime = "application/x-mrtrix-image-header"
 
-    @hook.required
     @property
     def data_file(self):
         return ImageDataFile(self.data_fspath)