def test_construct_rgb_slide_single_specimen(self):
bits_allocated = 8
photometric_interpretation = 'RGB'
coordinate_system = 'SLIDE'
specimen_description = SpecimenDescription(
specimen_id=self._specimen_identifier,
specimen_uid=self._specimen_uid)
instance = SCImage(
pixel_array=self._rgb_pixel_array,
photometric_interpretation=photometric_interpretation,
bits_allocated=bits_allocated,
coordinate_system=coordinate_system,
study_instance_uid=self._study_instance_uid,
series_instance_uid=self._series_instance_uid,
sop_instance_uid=self._sop_instance_uid,
series_number=self._series_number,
instance_number=self._instance_number,
manufacturer=self._manufacturer,
container_identifier=self._container_identifier,
specimen_descriptions=[specimen_description])
assert instance.BitsAllocated == bits_allocated
assert instance.SamplesPerPixel == 3
assert instance.PlanarConfiguration == 0
assert instance.PhotometricInterpretation == photometric_interpretation
assert instance.StudyInstanceUID == self._study_instance_uid
assert instance.SeriesInstanceUID == self._series_instance_uid
assert instance.SOPInstanceUID == self._sop_instance_uid
assert instance.SeriesNumber == self._series_number
assert instance.InstanceNumber == self._instance_number
assert instance.Manufacturer == self._manufacturer
assert instance.ContainerIdentifier == self._container_identifier
assert len(instance.ContainerTypeCodeSequence) == 1
assert len(instance.IssuerOfTheContainerIdentifierSequence) == 0
assert len(instance.SpecimenDescriptionSequence) == 1
specimen_item = instance.SpecimenDescriptionSequence[0]
assert specimen_item.SpecimenIdentifier == self._specimen_identifier
assert specimen_item.SpecimenUID == self._specimen_uid
assert instance.AccessionNumber is None
assert instance.PatientName is None
assert instance.PatientSex is None
assert instance.StudyTime is None
assert instance.StudyTime is None
assert instance.PixelData == self._rgb_pixel_array.tobytes()
with pytest.raises(AttributeError):
instance.Laterality
instance.PatientOrientation
def test_construct_rgb_patient_missing_parameter(self):
with pytest.raises(TypeError):
bits_allocated = 8
photometric_interpretation = 'RGB'
coordinate_system = 'PATIENT'
SCImage(
pixel_array=self._rgb_pixel_array,
photometric_interpretation=photometric_interpretation,
bits_allocated=bits_allocated,
coordinate_system=coordinate_system,
study_instance_uid=self._study_instance_uid,
series_instance_uid=self._series_instance_uid,
sop_instance_uid=self._sop_instance_uid,
series_number=self._series_number,
instance_number=self._instance_number,
manufacturer=self._manufacturer,
)
def test_construct_rgb_slide_single_specimen_missing_parameter_1(self):
bits_allocated = 8
photometric_interpretation = 'RGB'
coordinate_system = 'SLIDE'
with pytest.raises(TypeError):
SCImage(
pixel_array=self._rgb_pixel_array,
photometric_interpretation=photometric_interpretation,
bits_allocated=bits_allocated,
coordinate_system=coordinate_system,
study_instance_uid=self._study_instance_uid,
series_instance_uid=self._series_instance_uid,
sop_instance_uid=self._sop_instance_uid,
series_number=self._series_number,
instance_number=self._instance_number,
manufacturer=self._manufacturer,
container_identifier=self._container_identifier,
)
def test_construct_rgb_patient(self):
bits_allocated = 8
photometric_interpretation = 'RGB'
coordinate_system = 'PATIENT'
instance = SCImage(
pixel_array=self._rgb_pixel_array,
photometric_interpretation=photometric_interpretation,
bits_allocated=bits_allocated,
coordinate_system=coordinate_system,
study_instance_uid=self._study_instance_uid,
series_instance_uid=self._series_instance_uid,
sop_instance_uid=self._sop_instance_uid,
series_number=self._series_number,
instance_number=self._instance_number,
manufacturer=self._manufacturer,
patient_orientation=self._patient_orientation,
laterality=self._laterality)
assert instance.BitsAllocated == bits_allocated
assert instance.SamplesPerPixel == 3
assert instance.PlanarConfiguration == 0
assert instance.PhotometricInterpretation == photometric_interpretation
assert instance.StudyInstanceUID == self._study_instance_uid
assert instance.SeriesInstanceUID == self._series_instance_uid
assert instance.SOPInstanceUID == self._sop_instance_uid
assert instance.SeriesNumber == self._series_number
assert instance.InstanceNumber == self._instance_number
assert instance.Manufacturer == self._manufacturer
assert instance.Laterality == self._laterality
assert instance.PatientOrientation == self._patient_orientation
assert instance.AccessionNumber is None
assert instance.PatientName is None
assert instance.PatientSex is None
assert instance.StudyTime is None
assert instance.StudyTime is None
assert instance.PixelData == self._rgb_pixel_array.tobytes()
with pytest.raises(AttributeError):
instance.ContainerIdentifier
instance.SpecimenDescriptionSequence
instance.ContainerTypeCodeSequence
instance.IssuerOfTheContainerIdentifierSequence
def test_rgb_rle(self):
bits_allocated = 8 # RLE requires multiple of 8 bits
photometric_interpretation = 'RGB'
coordinate_system = 'PATIENT'
frame = np.random.randint(0, 256, size=(256, 256, 3), dtype=np.uint8)
instance = SCImage(
pixel_array=frame,
photometric_interpretation=photometric_interpretation,
bits_allocated=bits_allocated,
coordinate_system=coordinate_system,
study_instance_uid=self._study_instance_uid,
series_instance_uid=self._series_instance_uid,
sop_instance_uid=self._sop_instance_uid,
series_number=self._series_number,
instance_number=self._instance_number,
manufacturer=self._manufacturer,
patient_orientation=self._patient_orientation,
transfer_syntax_uid=RLELossless)
assert instance.file_meta.TransferSyntaxUID == RLELossless
assert np.array_equal(self.get_array_after_writing(instance), frame)