Merge pull request #23 from tclose/mif-gz-converter

added converter between mrtrix and mrtrix-gz

Author: tclose

related-packages/fileformats-extras/conftest.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 import tempfile
 import pytest
-from fileformats.medimage import DicomDir
+from fileformats.medimage import DicomDir, Nifti
 
 # Set DEBUG logging for unittests
 
@@ -43,3 +43,10 @@ def dummy_dwi_dicom():
     import medimages4tests.dummy.dicom.mri.dwi.siemens.skyra.syngo_d13c as module
 
     return DicomDir(module.get_image())
+
+
+@pytest.fixture(scope="session")
+def dummy_nifti():
+    import medimages4tests.dummy.nifti as module
+
+    return Nifti(module.get_image())

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

@@ -4,6 +4,7 @@
 from fileformats.medimage_mrtrix3 import (
     ImageFormat as MrtrixImage,
     ImageHeader as MrtrixImageHeader,
+    ImageFormatGz as MrtrixImageGz,
 )
 
 try:
@@ -16,6 +17,18 @@
     in_out_file_kwargs = {}
 
 
+@converter(
+    source_format=MedicalImage,
+    target_format=MrtrixImageGz,
+    out_ext=MrtrixImageGz.ext,
+    **in_out_file_kwargs,
+)
+@converter(
+    source_format=MedicalImage,
+    target_format=MrtrixImageHeader,
+    out_ext=MrtrixImageHeader.ext,
+    **in_out_file_kwargs,
+)
 @converter(
     source_format=MedicalImage,
     target_format=MrtrixImage,
@@ -40,25 +53,25 @@ def mrconvert(name, out_ext: str, **kwargs):
     return MrConvert(name=name, out_file="out" + out_ext, **kwargs)
 
 
-@converter(
-    source_format=MedicalImage,
-    target_format=MrtrixImageHeader,
-    out_ext=MrtrixImageHeader.ext,
-    **in_out_file_kwargs,
-)
-def mrconvert2(name, out_ext: str, **kwargs):
-    """Initiate an MRConvert task with the output file extension set
+# @converter(
+#     source_format=MedicalImage,
+#     target_format=MrtrixImageHeader,
+#     out_ext=MrtrixImageHeader.ext,
+#     **in_out_file_kwargs,
+# )
+# def mrconvert2(name, out_ext: str, **kwargs):
+#     """Initiate an MRConvert task with the output file extension set
 
-    Parameters
-    ----------
-    name : str
-        name of the converter task
-    out_ext : str
-        extension of the output file, used by MRConvert to determine the desired format
+#     Parameters
+#     ----------
+#     name : str
+#         name of the converter task
+#     out_ext : str
+#         extension of the output file, used by MRConvert to determine the desired format
 
-    Returns
-    -------
-    pydra.ShellCommandTask
-        the converter task
-    """
-    return MrConvert(name=name, out_file="out" + out_ext, **kwargs)
+#     Returns
+#     -------
+#     pydra.ShellCommandTask
+#         the converter task
+#     """
+#     return MrConvert(name=name, out_file="out" + out_ext, **kwargs)

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

@@ -1,13 +1,25 @@
 import os
+import sys
 from unittest import mock
 import typing as ty
 from pathlib import Path
 import numpy as np
+import numpy.typing
 from medimages4tests.dummy.nifti import get_image as get_dummy_nifti
 from fileformats.core import FileSet, SampleFileGenerator, extra_implementation
 from fileformats.medimage import MedicalImage, Nifti1
 from fileformats.medimage_mrtrix3 import ImageFormat
 
+if sys.version_info >= (3, 9):
+    from typing import TypeAlias
+else:
+    from typing_extensions import TypeAlias
+
+
+DataArrayType: TypeAlias = (
+    "numpy.typing.NDArray[ty.Union[np.floating[ty.Any], np.integer[ty.Any]]]"
+)
+
 
 @extra_implementation(FileSet.generate_sample_data)
 def generate_mrtrix_sample_data(
@@ -21,7 +33,7 @@ def generate_mrtrix_sample_data(
 
 
 @extra_implementation(MedicalImage.read_array)
-def mrtrix_read_array(mif: ImageFormat) -> np.ndarray:
+def mrtrix_read_array(mif: ImageFormat) -> DataArrayType:
     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/tests/test_converters.py

@@ -1,5 +1,5 @@
 from fileformats.medimage import NiftiBvec
-from fileformats.medimage_mrtrix3 import ImageFormat, ImageHeader
+from fileformats.medimage_mrtrix3 import ImageFormat, ImageHeader, ImageFormatGz
 
 
 # @pytest.mark.xfail(reason="not sure what the reason is at this stage, might be bug in Pydra")
@@ -15,3 +15,9 @@ def test_dicom_to_mrtrix_image(dummy_dwi_dicom):
 
 def test_dicom_to_mrtrix_image_header(dummy_dwi_dicom):
     ImageHeader.convert(dummy_dwi_dicom)
+
+
+def test_mif_to_mifgz(dummy_nifti):
+    mif = ImageFormat.convert(dummy_nifti)
+    mif_gz = ImageFormatGz.convert(mif)
+    ImageFormat.convert(mif_gz)

related-packages/fileformats/fileformats/medimage_mrtrix3/__init__.py

@@ -13,3 +13,23 @@
     ImageHeaderB,
 )
 from .track import Tracks
+
+
+__all__ = [
+    "__version__",
+    "ImageIn",
+    "ImageOut",
+    "BFile",
+    "Tracks",
+    "NiftiB",
+    "NiftiGzB",
+    "NiftiGzXB",
+    "NiftiXB",
+    "ImageFormatB",
+    "ImageFormatGzB",
+    "ImageHeaderB",
+    "ImageFormat",
+    "ImageFormatGz",
+    "ImageHeader",
+    "ImageDataFile",
+]

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

@@ -2,7 +2,7 @@
 import typing as ty
 from fileformats.core import FileSet, extra_implementation
 from fileformats.generic import File
-from fileformats.application import Gzip
+from fileformats.application.archive import BaseGzip
 from fileformats.core.mixin import WithMagicNumber
 from fileformats.core.exceptions import FormatMismatchError
 import fileformats.medimage
@@ -61,8 +61,9 @@ def data_file(self):
         return self
 
 
-class ImageFormatGz(Gzip[ImageFormat]):
+class ImageFormatGz(fileformats.medimage.MedicalImage, BaseGzip):
 
+    archived_type = ImageFormat
     iana_mime = "application/x-mrtrix-image-format-gz"
     ext = ".mif.gz"
 

related-packages/fileformats/fileformats/medimage_mrtrix3/in_out.py

@@ -1,3 +1,4 @@
+import sys
 import typing as ty
 from fileformats.application import Dicom
 from fileformats.medimage import (
@@ -10,6 +11,10 @@
     Mgh,
     MghGz,
     Analyze,
+    NiftiBvec,
+    NiftiGzBvec,
+    NiftiXBvec,
+    NiftiGzXBvec,
 )
 from .image import ImageFormat, ImageHeader, ImageFormatGz
 from .dwi import (
@@ -22,8 +27,13 @@
     ImageHeaderB,
 )
 
+if sys.version_info >= (3, 9):
+    from typing import TypeAlias
+else:
+    from typing_extensions import TypeAlias
 
-ImageIn = ty.Union[
+
+ImageIn: TypeAlias = ty.Union[
     ImageFormat,
     ImageFormatGz,
     ImageHeader,
@@ -37,12 +47,16 @@
     NiftiX,
     Nifti1,
     Nifti2,
+    NiftiB,
+    NiftiGzB,
+    NiftiGzXB,
+    NiftiXB,
     Mgh,
     MghGz,
     Analyze,
 ]
 
-ImageOut = ty.Union[
+ImageOut: TypeAlias = ty.Union[
     ImageFormat,
     ImageFormatGz,
     ImageHeader,
@@ -54,6 +68,14 @@
     NiftiX,
     Nifti1,
     Nifti2,
+    NiftiB,
+    NiftiGzB,
+    NiftiGzXB,
+    NiftiXB,
+    NiftiBvec,
+    NiftiGzBvec,
+    NiftiXBvec,
+    NiftiGzXBvec,
     Mgh,
     MghGz,
     Analyze,