added in mrtrix formats into fileformats-mrtrix

Author: tclose

lib/mrtrix3/app.py

@@ -1212,9 +1212,9 @@ def escape_id(id_: str) -> str:
         "from pathlib import Path  # noqa: F401\n"
         "from fileformats.generic import FsObject, File, Directory  # noqa: F401\n"
         "from fileformats.medimage import MrtrixTrack  # noqa: F401\n"
+        "from fileformats.mrtrix3 import ImageIn, ImageOut  # noqa: F401\n"
         "from pydra.engine.task import ShellCommandTask \n"
         "from pydra.engine import specs\n"
-        "from pydra.tasks.mrtrix3.fileformats import ImageIn, ImageOut  # noqa: F401\n"
     )
 
     text += f"input_fields = {inputs_str}\n"

pydra/fileformats-mrtrix3/fileformats/mrtrix3/__init__.py

@@ -1,2 +1,7 @@
 from ._version import __version__
 
+from .image import ImageFormat, ImageHeader, ImageIn, ImageOut
+from .dwi import (
+    Bfile, NiftiB, NiftiGzB, NiftiGzXB, NiftiXB
+)
+from .track import TrackFile

pydra/fileformats-mrtrix3/fileformats/mrtrix3/dwi.py

@@ -0,0 +1,36 @@
+from fileformats.core import mark
+from fileformats.core.mixin import WithAdjacentFiles
+from fileformats.generic import File
+from fileformats.medimage import DwiEncoding
+
+
+class Bfile(DwiEncoding):
+    """MRtrix-style diffusion encoding, all in one file"""
+
+    ext = ".b"
+
+
+# NIfTI file format gzipped with BIDS side car
+class WithBfile(WithAdjacentFiles):
+    @mark.required
+    @property
+    def encoding(self) -> Bfile:
+        return Bfile(self.select_by_ext(Bfile))
+
+
+class NiftiB(WithBfile, Nifti1):
+    iana_mime = "application/x-nifti2+b"
+
+
+class NiftiGzB(WithBfile, NiftiGz):
+    iana_mime = "application/x-nifti2+gzip.b"
+
+
+class NiftiXB(WithBfile, NiftiX):
+    iana_mime = "application/x-nifti2+json.b"
+
+
+class NiftiGzXB(WithBfile, NiftiGzX):
+    iana_mime = "application/x-nifti2+gzip.json.b"
+
+

…ts-mrtrix3/fileformats/mrtrix3/images.py …ats-mrtrix3/fileformats/mrtrix3/image.pypydra/fileformats-mrtrix3/fileformats/mrtrix3/images.py renamed to pydra/fileformats-mrtrix3/fileformats/mrtrix3/image.py pydra/fileformats-mrtrix3/fileformats/mrtrix3/images.py renamed to pydra/fileformats-mrtrix3/fileformats/mrtrix3/image.py

@@ -104,28 +104,29 @@ class ImageDataFile(File):
     ext = ".dat"
 
 
-SupportedImageIn = ty.Union[
+ImageIn = ty.Union[
+    ImageFormat,
+    ImageHeader,
+    fileformats.misc.Dicom,
     fileformats.medimage.DicomDir,
     fileformats.medimage.NiftiGzX,
     fileformats.medimage.NiftiGz,
     fileformats.medimage.NiftiX,
     fileformats.medimage.Nifti1,
     fileformats.medimage.Nifti2,
-    ImageFormat,
-    ImageHeader,
     fileformats.medimage.MGH,
     fileformats.medimage.MGHZip,
     fileformats.medimage.Analyze,
 ]
 
-SupportedImageOut = ty.Union[
+ImageOut = ty.Union[
+    ImageFormat,
+    ImageHeader,
     fileformats.medimage.NiftiGzX,
     fileformats.medimage.NiftiGz,
     fileformats.medimage.NiftiX,
     fileformats.medimage.Nifti1,
     fileformats.medimage.Nifti2,
-    ImageFormat,
-    ImageHeader,
     fileformats.medimage.MGH,
     fileformats.medimage.MGHZip,
     fileformats.medimage.Analyze,

pydra/fileformats-mrtrix3/fileformats/mrtrix3/track.py

@@ -0,0 +1,6 @@
+from fileformats.generic import File
+
+
+class TrackFile(File):
+
+    ext = ".tck"