def test_default_finder(self):
finder = odil.VRFinder()
data_set = odil.DataSet()
data_set.add(odil.registry.BitsAllocated, [8])
vr = finder(
odil.Tag(0x7fe0, 0x0010), data_set,
odil.registry.ExplicitVRLittleEndian)
self.assertEqual(vr, odil.VR.OB)
def test_convert_element_required(self):
bruker_data_set = {}
dicom_data_set = odil.DataSet()
generator = dicomifier.bruker_to_dicom.FrameIndexGenerator(
bruker_data_set)
frame_index = [0]
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(
tag, odil.DataSet(), odil.registry.ImplicitVRLittleEndian)
with self.assertRaises(Exception) as context:
val = dicomifier.bruker_to_dicom.convert.convert_element(
bruker_data_set, dicom_data_set, "VisuSubjectName",
"PatientName", 1, None, None, frame_index, generator,
vr_finder_function)
self.assertTrue("PatientName must be present" in context.exception)
def test_convert_element_getter(self):
bruker_data_set = {}
dicom_data_set = odil.DataSet()
generator = dicomifier.bruker_to_dicom.FrameIndexGenerator(
bruker_data_set)
frame_index = [0]
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(
tag, odil.DataSet(), odil.registry.ImplicitVRLittleEndian)
val = dicomifier.bruker_to_dicom.convert.convert_element(
bruker_data_set, dicom_data_set, None, "PixelPresentation", 1,
lambda d, g, i: ["MONOCHROME"], None, frame_index, generator,
vr_finder_function)
self.assertEqual(val, ["MONOCHROME"])
dicom_val = list(dicom_data_set.as_string("PixelPresentation"))
self.assertEqual(["MONOCHROME"], dicom_val)
def test_convert_element_getter_none(self):
bruker_data_set = {"VisuSubjectName": ["Mouse^Mickey"]}
dicom_data_set = odil.DataSet()
generator = dicomifier.bruker_to_dicom.FrameIndexGenerator(
bruker_data_set)
frame_index = [0]
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(
tag, odil.DataSet(), odil.registry.ImplicitVRLittleEndian)
val = dicomifier.bruker_to_dicom.convert.convert_element(
bruker_data_set, dicom_data_set, "VisuSubjectName", "PatientName",
1, None, None, frame_index, generator, vr_finder_function)
# Check first the returned value of the convert_element function
self.assertEqual(val, ["Mouse^Mickey"])
# Check then the content of the dicom_data_set (should contain the correct value...)
dicom_val = list(dicom_data_set.as_string("PatientName"))
self.assertEqual(["Mouse^Mickey"], dicom_val)
def test_convert_element_setter_dict(self):
bruker_data_set = {"VisuSubjectSex": ["MALE"]}
dicom_data_set = odil.DataSet()
generator = dicomifier.bruker_to_dicom.FrameIndexGenerator(
bruker_data_set)
frame_index = [0]
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(
tag, odil.DataSet(), odil.registry.ImplicitVRLittleEndian)
val = dicomifier.bruker_to_dicom.convert.convert_element(
bruker_data_set, dicom_data_set, "VisuSubjectSex", "PatientSex", 1,
None, {
"MALE": "M",
"FEMALE": "F",
"UNDEFINED": "O",
"UNKNOWN": "O",
None: None
}, frame_index, generator, vr_finder_function)
self.assertEqual(val, ["M"])
dicom_val = list(dicom_data_set.as_string("PatientSex"))
self.assertEqual(["M"], dicom_val)
def test_convert_element_getter_frame_index(self):
bruker_data_set = {
# Only two group, with each one a different Echo Time
"VisuFGOrderDesc": [[2, "FG_SLICE", "", 0, 1]],
"VisuGroupDepVals": [["VisuAcqEchoTime", 0]],
"VisuAcqEchoTime": [10., 20.]
}
dicom_data_set = odil.DataSet()
generator = dicomifier.bruker_to_dicom.FrameIndexGenerator(
bruker_data_set)
frame_index = [1]
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(
tag, odil.DataSet(), odil.registry.ImplicitVRLittleEndian)
val = dicomifier.bruker_to_dicom.convert.convert_element(
bruker_data_set, dicom_data_set, "VisuAcqEchoTime", "EchoTime", 1,
None, None, frame_index, generator, vr_finder_function)
self.assertEqual(val, [20.])
dicom_val = list(dicom_data_set.as_real("EchoTime"))
self.assertEqual([20.], dicom_val)
def test_convert_element_setter_function(self):
bruker_data_set = {
# Here we make a simple example with only one frame => only one position
"VisuCorePosition": [-20., -20., -2.]
}
dicom_data_set = odil.DataSet()
generator = dicomifier.bruker_to_dicom.FrameIndexGenerator(
bruker_data_set)
frame_index = [0]
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(
tag, odil.DataSet(), odil.registry.ImplicitVRLittleEndian)
val = dicomifier.bruker_to_dicom.convert.convert_element(
bruker_data_set, dicom_data_set, "VisuCorePosition",
"ImagePositionPatient", 1,
lambda d, g, i: numpy.reshape(d["VisuCorePosition"],
(-1, 3)), lambda x: x[0].tolist(),
frame_index, generator, vr_finder_function)
self.assertEqual(val, [-20., -20., -2.])
dicom_val = list(dicom_data_set.as_real("ImagePositionPatient"))
self.assertEqual([-20., -20., -2.], dicom_val)
def enhanced_mr_image_storage(bruker_data_set, transfer_syntax):
""" Convert bruker_data_set into dicom_data_set by using the correct transfer_syntax
This function will create one data_set per reconstruction (multiFrame format)
:param bruker_data_set: Json dataSet containing bruker information
:param transfer_syntax: Wanted transfer syntax for the conversion
"""
if int(bruker_data_set.get("VisuCoreDim", [0])[0]) == 3:
to_2d(bruker_data_set)
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(tag, helper, transfer_syntax)
helper = odil.DataSet()
generator = FrameIndexGenerator(bruker_data_set)
dicom_data_set = odil.DataSet()
number_of_frames = generator._get_frames_count()
dicom_data_set.add("SpecificCharacterSet", ["ISO_IR 192"])
shared = [odil.DataSet()]
dicom_data_set.add(odil.registry.SharedFunctionalGroupsSequence, shared)
per_frame = [odil.DataSet() for x in range(number_of_frames) ]
# Modules factory
modules = [
patient.Patient,
study.GeneralStudy, study.PatientStudy,
series.GeneralSeries + [(None, "Modality", 1, lambda d,g,i: ["MR"], None)] ,
frame_of_reference.FrameOfReference,
equipment.GeneralEquipment, equipment.EnhancedGeneralEquipment,
image.MutliFrameFunctionalGroups,
image.MultiFrameDimension,
image.AcquisitionContext,
image.EnhancedMRImage,
image.MRPulseSequence,
image.SOPCommon + [(None, "SOPClassUID", 1, lambda d,g,i: [odil.registry.EnhancedMRImageStorage], None)],
image.ImagePixel,
]
framegroups = [
fg.PixelMeasures,
fg.FrameContent,
fg.PlanePosition,
fg.PlaneOrientation,
fg.FrameAnatomy,
fg.PixelValueTransformation,
fg.MRImageFrameType,
fg.MRTimingAndRelatedParameters,
fg.MREcho,
fg.MRModifier,
fg.MRImagingModifier,
fg.MRFOVGeometry,
fg.MRAverages
]
if "FG_DIFFUSION" in [x[1] for x in generator.frame_groups]:
framegroups.append(fg.MRDiffusion)
# parse here classical modules
for i, frame_index in enumerate(generator):
for bruker_name, dicom_name, type_, getter, setter in itertools.chain(*modules):
value = convert_element(
bruker_data_set, dicom_data_set,
bruker_name, dicom_name, type_, getter, setter,
frame_index, generator, vr_finder_function
)
if dicom_name in ["BitsAllocated", "PixelRepresentation"]:
helper.add(getattr(odil.registry, dicom_name), value)
# parse here frame groups
for frame_g in framegroups :
fg_modules = frame_g.values()
d = odil.DataSet()
for bruker_name, dicom_name, type_, getter, setter in itertools.chain(*fg_modules):
value = convert_element(
bruker_data_set, d,
bruker_name, dicom_name, type_, getter, setter,
frame_index, generator, vr_finder_function
)
per_frame[i].add(next(iter(frame_g.keys()))[0], [d])
dicom_data_set.add(odil.registry.PerFrameFunctionalGroupsSequence, per_frame)
regroup_shared_data(dicom_data_set, framegroups)
pixel_data_list = []
for i, frame_index in enumerate(generator):
pixel_data_list.append(
image._get_pixel_data(bruker_data_set, generator, frame_index)[0]
)
dicom_data_set.add(
odil.registry.PixelData, [b"".join(pixel_data_list)],
vr_finder_function("PixelData"))
# Add the raw Bruker meta-data, convert paths to Unicode if needed
paths = [
x.decode() if hasattr(x, "decode") else x
for x in bruker_data_set["reco_files"]
]
bruker_files = { os.path.basename(x): open(x).read() for x in paths }
dicom_data_set.add("EncapsulatedDocument", [json.dumps(bruker_files)])
dicom_data_set.add("MIMETypeOfEncapsulatedDocument", ["application/json"])
return [dicom_data_set]
def mr_image_storage(bruker_data_set, transfer_syntax):
""" Function to convert specific burker images into dicom
:param bruker_data_set: bruker data set to convert
:param transfer_syntax: target transfer syntax
"""
if int(bruker_data_set.get("VisuCoreDim", [0])[0]) == 3:
to_2d(bruker_data_set)
dicom_data_sets = []
modules = [
patient.Patient, study.GeneralStudy, study.PatientStudy,
series.GeneralSeries +
[(None, "Modality", 1, lambda d, g, i: ["MR"], None)],
frame_of_reference.FrameOfReference, equipment.GeneralEquipment,
image.GeneralImage, image.ImagePlane, image.ImagePixel, image.MRImage,
[(None, "PixelValueTransformationSequence", 1,
lambda bruker_data_set, generator, frame_index: [
convert_elements(bruker_data_set, odil.DataSet(
), image.PixelValueTransformation, frame_index, generator,
vr_finder_function)
], None)],
[(None, "MRDiffusionSequence", 3,
lambda bruker_data_set, generator, frame_index: [
convert_elements(bruker_data_set, odil.DataSet(
), image.MRDiffusion, frame_index, generator, vr_finder_function)
] if "FG_DIFFUSION" in [x[1]
for x in generator.frame_groups] else None,
None)], image.SOPCommon +
[(None, "SOPClassUID", 1,
lambda d, g, i: [odil.registry.MRImageStorage], None)]
]
vr_finder_object = odil.VRFinder()
vr_finder_function = lambda tag: vr_finder_object(tag, helper,
transfer_syntax)
helper = odil.DataSet()
generator = FrameIndexGenerator(bruker_data_set)
for frame_index in generator:
dicom_data_set = odil.DataSet()
dicom_data_set.add("SpecificCharacterSet", ["ISO_IR 192"])
for bruker_name, dicom_name, type_, getter, setter in itertools.chain(
*modules):
value = convert_element(bruker_data_set, dicom_data_set,
bruker_name, dicom_name, type_, getter,
setter, frame_index, generator,
vr_finder_function)
for name in ["BitsAllocated", "PixelRepresentation"]:
if dicom_name == name:
helper.add(getattr(odil.registry, name), value)
# FIXME: storing the Bruker meta-data in all instances is rather
# inefficient. It can amount to over 50 % of the total size of the
# DICOM file
# dict_files = {}
# path_list = bruker_data_set["reco_files"]
# for path in path_list:
# dict_files[os.path.basename(path)] = open(path).read()
# reco_files_tag = odil.Tag("67890010")
# dicom_data_set.add(reco_files_tag, [json.dumps(dict_files)], odil.VR.OB)
dicom_data_sets.append(dicom_data_set)
return dicom_data_sets
