Merge pull request #24 from ArcanaFramework/syntax-updates

update to match changes in fileformats base

conftest.py

@@ -11,6 +11,12 @@
     set_input_validator(True)
 from fileformats.medimage.dicom import DicomDir
 
+try:
+    import pydra.tasks.mrtrix3.v3_0
+except ImportError:
+    OLD_MRTRIX_VERSION = True
+else:
+    OLD_MRTRIX_VERSION = False
 
 # Set DEBUG logging for unittests
 

extras/fileformats/extras/medimage/dicom.py

@@ -5,7 +5,7 @@
 import pydicom
 import numpy as np
 from fileformats.core import FileSet
-from fileformats.core.utils import gen_filename
+from fileformats.core.utils import SampleFileGenerator
 from fileformats.medimage import MedicalImage, DicomCollection, DicomDir, DicomSeries
 import medimages4tests.dummy.dicom.mri.t1w.siemens.skyra.syngo_d13c
 
@@ -42,15 +42,13 @@ def dicom_series_number(collection: DicomCollection) -> str:
 
 
 @FileSet.generate_sample_data.register
-def dicom_dir_generate_sample_data(dcmdir: DicomDir, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None) -> ty.Iterable[Path]:
+def dicom_dir_generate_sample_data(
+    dcmdir: DicomDir,
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
     dcm_dir = medimages4tests.dummy.dicom.mri.t1w.siemens.skyra.syngo_d13c.get_image()
-    # Set series number to random value to make it different
-    if isinstance(seed, Random):
-        rng = seed
-    else:
-        rng = Random(seed)
-    series_number = rng.randint(1, SERIES_NUMBER_RANGE)
-    dest = Path(dest_dir) / gen_filename(seed_or_rng=seed, stem=stem)
+    series_number = generator.rng.randint(1, SERIES_NUMBER_RANGE)
+    dest = generator.generate_fspath(DicomDir)
     dest.mkdir()
     for dcm_file in dcm_dir.iterdir():
         dcm = pydicom.dcmread(dcm_file)
@@ -60,13 +58,16 @@ def dicom_dir_generate_sample_data(dcmdir: DicomDir, dest_dir: Path, seed: ty.Un
 
 
 @FileSet.generate_sample_data.register
-def dicom_series_generate_sample_data(dcm_series: DicomSeries, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None) -> ty.Iterable[Path]:
-    rng = Random(seed)
-    dicom_dir = dicom_dir_generate_sample_data(dcm_series, dest_dir=mkdtemp(), seed=rng, stem=None)[0]
-    stem = gen_filename(rng, stem=stem)
+def dicom_series_generate_sample_data(
+    dcm_series: DicomSeries,
+    generator: SampleFileGenerator,
+) -> ty.Iterable[Path]:
+    dicom_dir: Path = dicom_dir_generate_sample_data(dcm_series, generator=generator)[0]
+    stem = generator.generate_fspath().stem
     fspaths = []
     for i, dicom_file in enumerate(dicom_dir.iterdir(), start=1):
-        fspaths.append(dicom_file.rename(dest_dir / f"{stem}-{i}.dcm"))
+        fspaths.append(dicom_file.rename(generator.dest_dir / f"{stem}-{i}.dcm"))
+    dicom_dir.rmdir()
     return fspaths
 
 

extras/fileformats/extras/medimage/nifti.py

@@ -4,7 +4,7 @@
 import nibabel
 import numpy as np
 from fileformats.core import FileSet
-from fileformats.core.utils import gen_filename
+from fileformats.core.utils import SampleFileGenerator
 from fileformats.medimage import MedicalImage, Nifti, NiftiGz, Nifti1, NiftiGzX, NiftiX
 import medimages4tests.dummy.nifti
 
@@ -33,33 +33,37 @@ def nifti_dims(nifti: Nifti) -> ty.Tuple[int, int, int]:
 
 @FileSet.generate_sample_data.register
 def nifti_generate_sample_data(
-    nifti: Nifti1, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
+    nifti: Nifti1,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     return medimages4tests.dummy.nifti.get_image(
-        out_file=dest_dir / gen_filename(seed, file_type=Nifti1, stem=stem)
+        out_file=generator.generate_fspath(file_type=Nifti1)
     )
 
 
 @FileSet.generate_sample_data.register
 def nifti_gz_generate_sample_data(
-    nifti: NiftiGz, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
+    nifti: NiftiGz,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
     return medimages4tests.dummy.nifti.get_image(
-        out_file=dest_dir / gen_filename(seed, file_type=NiftiGz, stem=stem),
+        out_file=generator.generate_fspath(file_type=NiftiGz),
         compressed=True,
     )
 
 
 @FileSet.generate_sample_data.register
 def nifti_gz_x_generate_sample_data(
-    nifti: NiftiGzX, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
+    nifti: NiftiGzX,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    return medimages4tests.mri.neuro.t1w.get_image()
+    return medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir)
 
 
 @FileSet.generate_sample_data.register
 def nifti_x_generate_sample_data(
-    nifti: NiftiX, dest_dir: Path, seed: ty.Union[int, Random] = 0, stem: ty.Optional[str] = None
+    nifti: NiftiX,
+    generator: SampleFileGenerator,
 ) -> ty.Iterable[Path]:
-    nifti_gz_x = NiftiGzX(medimages4tests.mri.neuro.t1w.get_image())
+    nifti_gz_x = NiftiGzX(medimages4tests.mri.neuro.t1w.get_image(out_dir=generator.dest_dir))
     return NiftiX.convert(nifti_gz_x)

extras/fileformats/extras/medimage/tests/test_dicom_metadata.py

@@ -1,19 +1,23 @@
+import pytest
 from fileformats.medimage import DicomSeries, DicomDir
+from conftest import OLD_MRTRIX_VERSION
 
 
+@pytest.mark.xfail(condition=OLD_MRTRIX_VERSION, reason="Old MRtrix version")
 def test_dicom_series_metadata(tmp_path):
     series = DicomSeries.sample(tmp_path)
 
     # Check series number is not a list
-    assert not isinstance(series["SeriesNumber"], list)
+    assert not isinstance(series.metadata["SeriesNumber"], list)
     # check the SOP Instance ID has been converted into a list
-    assert isinstance(series["SOPInstanceUID"], list)
+    assert isinstance(series.metadata["SOPInstanceUID"], list)
 
 
+@pytest.mark.xfail(condition=OLD_MRTRIX_VERSION, reason="Old MRtrix version")
 def test_dicom_dir_metadata(tmp_path):
     series = DicomDir.sample(tmp_path)
 
     # Check series number is not a list
-    assert not isinstance(series["SeriesNumber"], list)
+    assert not isinstance(series.metadata["SeriesNumber"], list)
     # check the SOP Instance ID has been converted into a list
-    assert isinstance(series["SOPInstanceUID"], list)
+    assert isinstance(series.metadata["SOPInstanceUID"], list)

extras/fileformats/extras/medimage/tests/test_neuro_converters.py

@@ -2,10 +2,10 @@
 from fileformats.medimage import (
     NiftiGzX,
     NiftiGzXBvec,
-    NiftiBvec,
     Analyze,
 )
 from logging import getLogger
+from conftest import OLD_MRTRIX_VERSION
 
 
 logger = getLogger("fileformats")
@@ -27,6 +27,7 @@ def test_dicom_to_nifti_select_echo(dummy_magfmap_dicom):
     assert nifti_gz_x_e2.metadata["EchoNumber"] == 2
 
 
+@pytest.mark.xfail(condition=OLD_MRTRIX_VERSION, reason="Old MRtrix version")
 def test_dicom_to_nifti_select_suffix(dummy_mixedfmap_dicom):
 
     nifti_gz_x_ph = NiftiGzX.convert(dummy_mixedfmap_dicom, file_postfix="_ph")
@@ -42,6 +43,7 @@ def test_dicom_to_nifti_select_suffix(dummy_mixedfmap_dicom):
     assert list(nifti_gz_x_real.dims()) == [256, 256, 60]
 
 
+@pytest.mark.xfail(condition=OLD_MRTRIX_VERSION, reason="Old MRtrix version")
 def test_dicom_to_nifti_with_extract_volume(dummy_dwi_dicom):
 
     nifti_gz_x_e1 = NiftiGzX.convert(dummy_dwi_dicom, extract_volume=30)
@@ -57,6 +59,7 @@ def test_dicom_to_nifti_with_jq_edit(dummy_t1w_dicom):
     assert nifti_gz_x.metadata["EchoTime"] == 2.07
 
 
+@pytest.mark.xfail(condition=OLD_MRTRIX_VERSION, reason="Old MRtrix version")
 def test_dicom_to_niftix_with_fslgrad(dummy_dwi_dicom):
 
     logger.debug("Performing FSL grad conversion")
@@ -74,12 +77,13 @@ def test_dicom_to_niftix_with_fslgrad(dummy_dwi_dicom):
     assert all(abs(1 - m) < 1e5 for m in bvec_mags)
 
 
-# @pytest.mark.skip("Mrtrix isn't installed in test environment yet")
+@pytest.mark.xfail(condition=OLD_MRTRIX_VERSION, reason="Old MRtrix version")
 def test_dicom_to_nifti_as_4d(dummy_t1w_dicom):
 
     nifti_gz_x_e1 = NiftiGzX.convert(dummy_t1w_dicom, to_4d=True)
     assert nifti_gz_x_e1.metadata["dim"][0] == 4
 
 
+@pytest.mark.xfail(condition=OLD_MRTRIX_VERSION, reason="Old MRtrix version")
 def test_dicom_to_analyze(dummy_t1w_dicom):
     Analyze.convert(dummy_t1w_dicom)

fileformats/medimage/dicom.py

@@ -67,7 +67,7 @@ def from_paths(
         for dicom in dicoms:
             dicom.select_metadata(selected_keys)
             series_dict[
-                (str(dicom["StudyInstanceUID"]), str(dicom["SeriesNumber"]))
+                (str(dicom.metadata["StudyInstanceUID"]), str(dicom.metadata["SeriesNumber"]))
             ].append(dicom)
         return set([cls(s) for s in series_dict.values()]), remaining
 

fileformats/medimage/tests/test_dicom.py

@@ -34,6 +34,6 @@ def test_dicom_series_metadata(tmp_path):
     series = DicomSeries.sample(tmp_path)
 
     # Check series number is not a list
-    assert not isinstance(series["SeriesNumber"], list)
+    assert not isinstance(series.metadata["SeriesNumber"], list)
     # check the SOP Instance ID has been converted into a list
-    assert isinstance(series["SOPInstanceUID"], list)
+    assert isinstance(series.metadata["SOPInstanceUID"], list)