def test_save(self):
filepath = get_testdata_file("MR_small.dcm")
dr = DicomReader(group_by=None)
mv_base = dr.load(filepath)[0]
out_dir = os.path.join(self.data_dirpath, "test_save_sort_by")
dw = DicomWriter()
dw.save(mv_base, out_dir, sort_by="InstanceNumber")
mv2 = dr.load(filepath)[0]
assert mv2.is_identical(mv_base)
out_dir = os.path.join(self.data_dirpath, "test_save_no_headers")
mv = MedicalVolume(np.ones((10, 10, 10)), np.eye(4))
dw = DicomWriter()
with self.assertRaises(ValueError):
dw.save(mv, out_dir)
def test_save_different_bits(self):
"""Test writing volume where bit depth has changed."""
filepath = get_testdata_file("MR_small.dcm")
dr = DicomReader(group_by=None)
mv_base = dr.load(filepath)[0]
arr = (np.random.rand(*mv_base.shape) > 0.5).astype(np.uint8) * 255
mv = mv_base._partial_clone(volume=arr)
dw = DicomWriter()
out_dir = os.path.join(self.data_dirpath, "test_write_different_bits")
dw.save(mv, dir_path=out_dir)
dr = DicomReader(group_by=None)
mv2 = dr.load(out_dir)[0]
assert mv2.is_identical(mv)
def from_dicom(
cls,
dir_or_files,
group_by=None,
ignore_ext: bool = False,
num_workers: int = 0,
verbose: bool = False,
**kwargs,
):
"""Load scan from dicom files.
Args:
dir_or_files (str): The path to dicom directory or files.
group_by: DICOM field tag name or tag number used to group dicoms. Defaults
to scan's ``__DEFAULT_SPLIT_BY__``.
ignore_ext (bool, optional): If `True`, ignore extension (`.dcm`)
when loading dicoms from directory.
num_workers (int, optional): Number of workers to use for loading.
verbose (bool, optional): If ``True``, enable verbose logging for dicom loading.
kwargs: Other keywords required to construct scan.
Returns:
The scan.
"""
dr = DicomReader(num_workers, verbose)
if group_by is None:
group_by = cls.__DEFAULT_SPLIT_BY__
volumes = dr.load(dir_or_files, group_by, ignore_ext)
if isinstance(dir_or_files, (str, Path, os.PathLike)):
dir_or_files = os.path.abspath(dir_or_files)
else:
dir_or_files = type(dir_or_files)(
[os.path.abspath(x) for x in dir_or_files])
scan = cls(volumes, **kwargs)
scan._from_file_args = {
"dir_or_files": dir_or_files,
"ignore_ext": ignore_ext,
"group_by": group_by,
"_type": "dicom",
}
return scan
def test_init_params(self):
"""Test reading/writing works with passing values to constructor."""
dp = ututils.get_scan_dirpath("qdess")
# Echo 1 only
fp = ututils.get_read_paths(dp, self.data_format)[0]
e1_expected = self.dr.load(fp, group_by=None, sort_by="InstanceNumber", ignore_ext=False)[0]
dr = DicomReader(group_by=None, sort_by="InstanceNumber", ignore_ext=False)
e1 = dr.load(fp)[0]
e1_expected.orientation
assert e1.is_identical(e1_expected)
write_path = os.path.join(ututils.get_write_path(dp, self.data_format), "out-init-params")
dw = DicomWriter(fname_fmt="I%05d.dcm", sort_by="InstanceNumber")
dw.save(e1_expected, write_path, sort_by="InstanceNumber")
files = [_f for _f in os.listdir(write_path) if _f.endswith(".dcm")]
assert len(files) == e1_expected.shape[-1]
def test_load_pydicom_data(self):
filepath = get_testdata_file("MR_small.dcm")
dr = DicomReader(group_by=None)
mv = dr.load(filepath)[0]
# CT does not have EchoNumbers field in header.
with self.assertRaises(KeyError):
dr.load(get_testdata_file("CT_small.dcm"), group_by="EchoNumbers")
with self.assertRaises(KeyError):
dr.load(get_testdata_file("CT_small.dcm"), sort_by="EchoNumbers")
# Multiprocessing
dr_mp = DicomReader(group_by=None, num_workers=1)
mv2 = dr_mp.load(filepath)[0]
assert mv2.is_identical(mv)
dr_mp = DicomReader(group_by=None, num_workers=1, verbose=True)
mv2 = dr_mp.load(filepath)[0]
assert mv2.is_identical(mv)
# sort by
mv2 = dr.load(filepath, sort_by="InstanceNumber")[0]
assert mv2.is_identical(mv)