adding generators for contrast-specific nifti files

extras/fileformats/extras/medimage/nifti.py

@@ -9,14 +9,18 @@
     NiftiGz,
     Nifti1,
     NiftiGzX,
+    NiftiGzXBvec,
+    NiftiXBvec,
     NiftiX,
     T1w,
-    Mri,
     Fmri,
+    Dmri,
     Brain,
 )
 import medimages4tests.dummy.nifti
 import medimages4tests.mri.neuro.t1w
+import medimages4tests.mri.neuro.dwi
+import medimages4tests.mri.neuro.bold
 
 
 @FileSet.read_metadata.register
@@ -67,17 +71,15 @@ def t1w_nifti_gz_x_generate_sample_data(
     nifti: NiftiGzX[T1w],
     generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    return medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir)
+    return _get_t1w_nifti_gz_x(generator)
 
 
 @FileSet.generate_sample_data.register
 def t1w_nifti_x_generate_sample_data(
     nifti: NiftiX[T1w],
     generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    nifti_gz_x = NiftiGzX(
-        medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir)
-    )
+    nifti_gz_x = NiftiGzX(_get_t1w_nifti_gz_x(generator))
     return NiftiX.convert(nifti_gz_x)
 
 
@@ -86,17 +88,15 @@ def t1w_brain_nifti_gz_x_generate_sample_data(
     nifti: NiftiGzX[T1w, Brain],
     generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    return medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir)
+    return _get_t1w_nifti_gz_x(generator)
 
 
 @FileSet.generate_sample_data.register
 def t1w_brain_nifti_x_generate_sample_data(
     nifti: NiftiX[T1w, Brain],
     generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    nifti_gz_x = NiftiGzX(
-        medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir)
-    )
+    nifti_gz_x = NiftiGzX(_get_t1w_nifti_gz_x(generator))
     return NiftiX.convert(nifti_gz_x)
 
 
@@ -105,15 +105,85 @@ def fmri_brain_nifti_gz_x_generate_sample_data(
     nifti: NiftiGzX[Fmri, Brain],
     generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    return medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir)
+    return _get_fmri_nifti_gz_x(generator)
 
 
 @FileSet.generate_sample_data.register
 def fmri_brain_nifti_x_generate_sample_data(
     nifti: NiftiX[Fmri, Brain],
     generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    nifti_gz_x = NiftiGzX(
-        medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir)
-    )
+    nifti_gz_x = NiftiGzX(_get_fmri_nifti_gz_x(generator))
     return NiftiX.convert(nifti_gz_x)
+
+
+@FileSet.generate_sample_data.register
+def fmri_nifti_gz_x_generate_sample_data(
+    nifti: NiftiGzX[Fmri],
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
+    return _get_fmri_nifti_gz_x(generator)
+
+
+@FileSet.generate_sample_data.register
+def fmri_nifti_x_generate_sample_data(
+    nifti: NiftiX[Fmri],
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
+    nifti_gz_x = NiftiGzX(_get_fmri_nifti_gz_x(generator))
+    return NiftiX.convert(nifti_gz_x)
+
+
+@FileSet.generate_sample_data.register
+def dmri_brain_nifti_gz_x_generate_sample_data(
+    nifti: NiftiGzXBvec[Dmri, Brain],
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
+    return _get_dmri_nifti_gz_x(generator)
+
+
+@FileSet.generate_sample_data.register
+def dmri_brain_nifti_x_generate_sample_data(
+    nifti: NiftiXBvec[Dmri, Brain],
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
+    nifti_gz_x = NiftiGzX(_get_dmri_nifti_gz_x(generator))
+    return NiftiX.convert(nifti_gz_x)
+
+
+@FileSet.generate_sample_data.register
+def dmri_nifti_gz_x_generate_sample_data(
+    nifti: NiftiGzXBvec[Dmri],
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
+    return _get_dmri_nifti_gz_x(generator)
+
+
+@FileSet.generate_sample_data.register
+def dmri_nifti_x_generate_sample_data(
+    nifti: NiftiXBvec[Dmri],
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
+    nifti_gz_x = NiftiGzXBvec(_get_dmri_nifti_gz_x(generator))
+    return NiftiX.convert(nifti_gz_x)
+
+
+def _get_t1w_nifti_gz_x(generator: SampleFileGenerator) -> ty.Iterable[Path]:
+    sample = generator.seed if generator.seed else "ds004130-ON01016"
+    return medimages4tests.mri.neuro.t1w.get_image(
+        out_dir=generator.dest_dir, sample=sample
+    )
+
+
+def _get_fmri_nifti_gz_x(generator: SampleFileGenerator) -> ty.Iterable[Path]:
+    sample = generator.seed if generator.seed else "ds002014-01"
+    return medimages4tests.mri.neuro.bold.get_image(
+        out_dir=generator.dest_dir, sample=sample
+    )
+
+
+def _get_dmri_nifti_gz_x(generator: SampleFileGenerator) -> ty.Iterable[Path]:
+    sample = generator.seed if generator.seed else "ds004024-CON031"
+    return medimages4tests.mri.neuro.dwi.get_image(
+        out_dir=generator.dest_dir, sample=sample
+    )

extras/fileformats/extras/medimage/tests/test_generators.py

@@ -0,0 +1,16 @@
+from fileformats.medimage import NiftiGzX, NiftiGzXBvec, T1w, Dmri, Fmri
+
+
+def test_t1w_generator():
+    img = NiftiGzX[T1w].sample()
+    assert len(img.dims()) == 3
+
+
+def test_fmri_generator():
+    img = NiftiGzX[Fmri].sample()
+    assert len(img.dims()) == 3
+
+
+def test_dmri_generator():
+    img = NiftiGzXBvec[Dmri].sample()
+    assert len(img.dims()) == 4

fileformats/medimage/__init__.py

@@ -78,6 +78,7 @@
     Mri,
     Pet,
     Dti,
+    Dmri,
     Fmri,
     Cr,
     Ct,

fileformats/medimage/contents/property/imaging_procedure/cross_sectional_procedure/mr_procedure/__init__.py

@@ -1,5 +1,5 @@
 from .. import CrossSectionalProcedure
-from fileformats.medimage.contents.imaging.modality import MagneticResonanceImaging
+from .....imaging.modality import MagneticResonanceImaging
 
 
 class MrProcedure(CrossSectionalProcedure, MagneticResonanceImaging):