text:
from collections import defaultdict
from io import BytesIO
import unittest
from pathlib import Path

import numpy as np
import pytest

from pydicom.data import get_testdata_file, get_testdata_files
from pydicom.datadict import tag_for_keyword
from pydicom.filereader import dcmread
from pydicom.sr.codedict import codes
from pydicom.uid import (
    ExplicitVRLittleEndian,
    ImplicitVRLittleEndian,
    RLELossless,
    JPEG2000Lossless
)

from highdicom import (
    AlgorithmIdentificationSequence,
    PlanePositionSequence,
    PixelMeasuresSequence,
    PlaneOrientationSequence,
    UID,
)
from highdicom.enum import CoordinateSystemNames
from highdicom.seg import (
    segread,
    DimensionIndexSequence,
    SegmentationTypeValues,
    SegmentAlgorithmTypeValues,
    Segmentation,
    SegmentDescription,
    SegmentsOverlapValues,
    SegmentationFractionalTypeValues,
)
from highdicom.seg.utils import iter_segments
from highdicom.sr.coding import CodedConcept

class TestAlgorithmIdentificationSequence(unittest.TestCase):

    def setUp(self):
        super().setUp()
        self._name = 'verydeepneuralnetwork'
        self._version = '1.0'
        self._family = codes.DCM.ArtificialIntelligence
        self._source = 'me'
        self._parameters = {'one': '1', 'two': '2'}

    def test_construction(self):
        seq = AlgorithmIdentificationSequence(
            self._name,
            self._family,
            self._version
        )
        assert len(seq) == 1
        item = seq[0]
        assert item.AlgorithmName == self._name
        assert item.AlgorithmVersion == self._version
        assert len(item.AlgorithmFamilyCodeSequence) == 1
        assert item.AlgorithmFamilyCodeSequence[0] == self._family
        with pytest.raises(AttributeError):
            item.AlgorithmSource
        with pytest.raises(AttributeError):
            item.AlgorithmParameters

        assert seq.name == self._name
        assert seq.version == self._version
        assert seq.family == self._family
        assert seq.source is None
        assert seq.parameters is None

    def test_construction_missing_required_argument(self):
        with pytest.raises(TypeError):
            AlgorithmIdentificationSequence(
                name=self._name,
                family=self._family
            )

    def test_construction_missing_required_argument_2(self):
        with pytest.raises(TypeError):
            AlgorithmIdentificationSequence(
                name=self._name,
                source=self._source
            )

    def test_construction_missing_required_argument_3(self):
        with pytest.raises(TypeError):
            AlgorithmIdentificationSequence(
                family=self._family,
                source=self._source
            )

    def test_construction_optional_argument(self):
        seq = AlgorithmIdentificationSequence(
            name=self._name,
            family=self._family,
            version=self._version,
            source=self._source
        )
        assert len(seq) == 1
        item = seq[0]
        assert item.AlgorithmSource == self._source
        with pytest.raises(AttributeError):
            item.AlgorithmParameters

        assert seq.source == self._source

    def test_construction_optional_argument_2(self):
        seq = AlgorithmIdentificationSequence(
            name=self._name,
            family=self._family,
            version=self._version,
            parameters=self._parameters
        )
        assert len(seq) == 1
        item = seq[0]
        parsed_params = ','.join([
            '='.join([key, value])
            for key, value in self._parameters.items()
        ])
        assert item.AlgorithmParameters == parsed_params
        assert seq.parameters == self._parameters
        with pytest.raises(AttributeError):
            item.AlgorithmSource

    def test_malformed_params(self):
        seq = AlgorithmIdentificationSequence(
            self._name,
            self._family,
            self._version
        )
        seq[0].AlgorithmParameters = 'some invalid parameters'
        with pytest.raises(ValueError):
            seq.parameters

class TestSegmentDescription(unittest.TestCase):

    def setUp(self):
        super().setUp()
        self._segment_number = 1
        self._invalid_segment_number = 0
        self._segment_label = 'segment #1'
        self._segmented_property_category = \
            codes.SCT.MorphologicallyAbnormalStructure
        self._segmented_property_type = codes.SCT.Neoplasm
        self._segment_algorithm_type = \
            SegmentAlgorithmTypeValues.AUTOMATIC
        self._algorithm_identification = AlgorithmIdentificationSequence(
            name='bla',
            family=codes.DCM.ArtificialIntelligence,
            version='v1'
        )
        self._tracking_id = 'segment #1'
        self._tracking_uid = UID()
        self._anatomic_region = codes.SCT.Thorax
        self._anatomic_structure = codes.SCT.Lung

    def test_construction(self):
        item = SegmentDescription(
            self._segment_number,
            self._segment_label,
            self._segmented_property_category,
            self._segmented_property_type,
            self._segment_algorithm_type,
            self._algorithm_identification
        )
        assert item.SegmentNumber == self._segment_number
        assert item.SegmentLabel == self._segment_label
        assert item.SegmentedPropertyCategoryCodeSequence[0] == \
            self._segmented_property_category
        assert item.SegmentedPropertyTypeCodeSequence[0] == \
            self._segmented_property_type
        assert item.SegmentAlgorithmType == self._segment_algorithm_type.value
        assert item.SegmentAlgorithmName == \
            self._algorithm_identification[0].AlgorithmName
        assert len(item.SegmentationAlgorithmIdentificationSequence) == 1
        with pytest.raises(AttributeError):
            item.TrackingID
            item.TrackingUID
            item.AnatomicRegionSequence
            item.PrimaryAnatomicStructureSequence

        assert item.segment_number == self._segment_number
        assert item.segment_label == self._segment_label
        assert isinstance(item.segmented_property_category, CodedConcept)
        property_category = item.segmented_property_category
        assert property_category == self._segmented_property_category
        assert isinstance(item.segmented_property_type, CodedConcept)
        assert item.segmented_property_type == self._segmented_property_type
        assert isinstance(item.algorithm_type, SegmentAlgorithmTypeValues)
        algo_type = item.algorithm_type
        assert algo_type == SegmentAlgorithmTypeValues(
            self._segment_algorithm_type
        )
        algo_id = item.algorithm_identification
        assert isinstance(algo_id, AlgorithmIdentificationSequence)

        assert item.tracking_id is None
        assert item.tracking_uid is None
        assert len(item.anatomic_regions) == 0
        assert len(item.primary_anatomic_structures) == 0

    def test_construction_invalid_segment_number(self):
        with pytest.raises(ValueError):
            SegmentDescription(
                self._invalid_segment_number,
                self._segment_label,
                self._segmented_property_category,
                self._segmented_property_type,
                self._segment_algorithm_type,
                self._algorithm_identification
            )

    def test_construction_missing_required_argument(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                segmented_property_category=self._segmented_property_category,
                segmented_property_type=self._segmented_property_type,
                algorithm_type=self._segment_algorithm_type,
                algorithm_identification=self._algorithm_identification
            )

    def test_construction_missing_required_argument_2(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                segment_number=self._segment_number,
                segmented_property_category=self._segmented_property_category,
                segmented_property_type=self._segmented_property_type,
                algorithm_type=self._segment_algorithm_type,
                algorithm_identification=self._algorithm_identification
            )

    def test_construction_missing_required_argument_3(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                segment_number=self._segment_number,
                segment_label=self._segment_label,
                segmented_property_type=self._segmented_property_type,
                algorithm_type=self._segment_algorithm_type,
                algorithm_identification=self._algorithm_identification
            )

    def test_construction_missing_required_argument_4(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                segment_number=self._segment_number,
                segment_label=self._segment_label,
                segmented_property_category=self._segmented_property_category,
                algorithm_type=self._segment_algorithm_type,
                algorithm_identification=self._algorithm_identification
            )

    def test_construction_missing_required_argument_5(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                segment_number=self._segment_number,
                segment_label=self._segment_label,
                segmented_property_category=self._segmented_property_category,
                segmented_property_type=self._segmented_property_type,
                algorithm_identification=self._algorithm_identification
            )

    def test_construction_missing_required_argument_6(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                segment_number=self._segment_number,
                segment_label=self._segment_label,
                segmented_property_category=self._segmented_property_category,
                segmented_property_type=self._segmented_property_type,
                algorithm_type=self._segment_algorithm_type
            )

    def test_construction_no_algo_id_manual_seg(self):
        # Omitting the algo id should not give an error if the segmentation
        # type is MANUAL
        item = SegmentDescription(
            segment_number=self._segment_number,
            segment_label=self._segment_label,
            segmented_property_category=self._segmented_property_category,
            segmented_property_type=self._segmented_property_type,
            algorithm_type=SegmentAlgorithmTypeValues.MANUAL
        )
        assert item.algorithm_identification is None

    def test_construction_optional_argument(self):
        item = SegmentDescription(
            segment_number=self._segment_number,
            segment_label=self._segment_label,
            segmented_property_category=self._segmented_property_category,
            segmented_property_type=self._segmented_property_type,
            algorithm_type=self._segment_algorithm_type,
            algorithm_identification=self._algorithm_identification,
            tracking_id=self._tracking_id,
            tracking_uid=self._tracking_uid,
        )
        assert item.TrackingID == self._tracking_id
        assert item.TrackingUID == self._tracking_uid
        assert item.tracking_id == self._tracking_id
        assert item.tracking_uid == self._tracking_uid
        with pytest.raises(AttributeError):
            item.AnatomicRegionSequence
        with pytest.raises(AttributeError):
            item.PrimaryAnatomicStructureSequence

    def test_construction_optional_argument_2(self):
        item = SegmentDescription(
            segment_number=self._segment_number,
            segment_label=self._segment_label,
            segmented_property_category=self._segmented_property_category,
            segmented_property_type=self._segmented_property_type,
            algorithm_type=self._segment_algorithm_type,
            algorithm_identification=self._algorithm_identification,
            anatomic_regions=[self._anatomic_region],
            primary_anatomic_structures=[self._anatomic_structure]
        )
        assert len(item.AnatomicRegionSequence) == 1
        assert item.AnatomicRegionSequence[0] == self._anatomic_region
        assert len(item.anatomic_regions) == 1
        assert all(
            isinstance(el, CodedConcept) for el in item.anatomic_regions
        )
        assert item.anatomic_regions[0] == self._anatomic_region

        assert len(item.PrimaryAnatomicStructureSequence) == 1
        assert item.PrimaryAnatomicStructureSequence[0] == \
            self._anatomic_structure
        assert len(item.primary_anatomic_structures) == 1
        assert all(
            isinstance(el, CodedConcept)
            for el in item.primary_anatomic_structures
        )
        assert item.primary_anatomic_structures[0] == self._anatomic_structure

        with pytest.raises(AttributeError):
            item.TrackingID
        with pytest.raises(AttributeError):
            item.TrackingUID

    def test_construction_mismatched_ids(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                self._segment_number,
                self._segment_label,
                self._segmented_property_category,
                self._segmented_property_type,
                self._segment_algorithm_type,
                self._algorithm_identification,
                tracking_id=self._tracking_id,
            )

    def test_construction_mismatched_ids_2(self):
        with pytest.raises(TypeError):
            SegmentDescription(
                self._segment_number,
                self._segment_label,
                self._segmented_property_category,
                self._segmented_property_type,
                self._segment_algorithm_type,
                self._algorithm_identification,
                tracking_uid=self._tracking_uid,
            )

class TestPixelMeasuresSequence(unittest.TestCase):

    def setUp(self):
        super().setUp()
        self._pixel_spacing = (0.5, 0.5)
        self._slice_thickness = 0.3
        self._spacing_between_slices = 0.7

    def test_construction(self):
        seq = PixelMeasuresSequence(
            self._pixel_spacing,
            self._slice_thickness
        )
        assert len(seq) == 1
        item = seq[0]
        assert item.PixelSpacing == list(self._pixel_spacing)
        assert item.SliceThickness == self._slice_thickness
        with pytest.raises(AttributeError):
            self.SpacingBetweenSlices

    def test_construction_missing_required_attribute(self):
        with pytest.raises(TypeError):
            PixelMeasuresSequence(
                pixel_spacing=self._pixel_spacing
            )

    def test_construction_missing_required_attribute_2(self):
        with pytest.raises(TypeError):
            PixelMeasuresSequence(
                slice_thickness=self._slice_thickness
            )

    def test_construction_optional_attribute(self):
        seq = PixelMeasuresSequence(
            pixel_spacing=self._pixel_spacing,
            slice_thickness=self._slice_thickness,
            spacing_between_slices=self._spacing_between_slices
        )
        item = seq[0]
        assert item.SpacingBetweenSlices == self._spacing_between_slices

class TestPlanePositionSequence(unittest.TestCase):

    def setUp(self):
        super().setUp()
        self._image_position = (1.0, 2.0, 3.0)
        self._pixel_matrix_position = (20, 10)

    def test_construction_1(self):
        seq = PlanePositionSequence(
            coordinate_system=CoordinateSystemNames.PATIENT,
            image_position=self._image_position
        )
        assert len(seq) == 1
        item = seq[0]
        assert item.ImagePositionPatient == list(self._image_position)
        with pytest.raises(AttributeError):
            item.XOffsetInSlideCoordinateSystem

    def test_construction_2(self):
        seq = PlanePositionSequence(
            coordinate_system=CoordinateSystemNames.SLIDE,
            image_position=self._image_position,
            pixel_matrix_position=self._pixel_matrix_position
        )
        assert len(seq) == 1
        item = seq[0]
        assert item.XOffsetInSlideCoordinateSystem == self._image_position[0]
        assert item.YOffsetInSlideCoordinateSystem == self._image_position[1]
        assert item.ZOffsetInSlideCoordinateSystem == self._image_position[2]
        assert item.RowPositionInTotalImagePixelMatrix == \
            self._pixel_matrix_position[1]
        assert item.ColumnPositionInTotalImagePixelMatrix == \
            self._pixel_matrix_position[0]
        with pytest.raises(AttributeError):
            item.ImagePositionPatient

    def test_construction_missing_required_argument(self):
        with pytest.raises(TypeError):
            PlanePositionSequence(
                coordinate_system=CoordinateSystemNames.SLIDE,
                image_position=self._image_position
            )

    def test_construction_missing_required_argument_2(self):
        with pytest.raises(TypeError):
            PlanePositionSequence(
                coordinate_system=CoordinateSystemNames.SLIDE,
                pixel_matrix_position=self._pixel_matrix_position
            )

    def test_construction_missing_required_argument_3(self):
        with pytest.raises(TypeError):
            PlanePositionSequence(
                coordinate_system=CoordinateSystemNames.PATIENT
            )

    def test_construction_missing_required_argument_4(self):
        with pytest.raises(TypeError):
            PlanePositionSequence(
                pixel_matrix_position=self._pixel_matrix_position
            )

class TestPlaneOrientationSequence(unittest.TestCase):

    def setUp(self):
        super().setUp()
        self._image_orientation = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0)

    def test_construction(self):
        seq = PlaneOrientationSequence(
            'PATIENT',
            self._image_orientation
        )
        assert len(seq) == 1
        item = seq[0]
        assert item.ImageOrientationPatient == list(self._image_orientation)
        with pytest.raises(AttributeError):
            item.ImageOrientationSlide

    def test_construction_2(self):
        seq = PlaneOrientationSequence(
            'SLIDE',
            self._image_orientation
        )
        assert len(seq) == 1
        item = seq[0]
        assert item.ImageOrientationSlide == list(self._image_orientation)
        with pytest.raises(AttributeError):
            item.ImageOrientationPatient

    def test_construction_missing_required_attribute(self):
        with pytest.raises(TypeError):
            PlaneOrientationSequence(
                image_orientation=self._image_orientation
            )

    def test_construction_missing_required_attribute_2(self):
        with pytest.raises(TypeError):
            PlaneOrientationSequence(
                coordinate_system='PATIENT'
            )

    def test_construction_wrong_attribute_enumated_value(self):
        with pytest.raises(ValueError):
            PlaneOrientationSequence(
                coordinate_system='OTHER',
                image_orientation=self._image_orientation
            )

class TestDimensionIndexSequence(unittest.TestCase):

    def setUp(self):
        super().setUp()

    def test_construction(self):
        seq = DimensionIndexSequence(
            coordinate_system='PATIENT'
        )
        assert len(seq) == 2
        assert seq[0].DimensionIndexPointer == 0x0062000B
        assert seq[0].FunctionalGroupPointer == 0x0062000A
        assert seq[1].DimensionIndexPointer == 0x00200032
        assert seq[1].FunctionalGroupPointer == 0x00209113

    def test_construction_2(self):
        seq = DimensionIndexSequence(
            coordinate_system='SLIDE'
        )
        assert len(seq) == 6
        assert seq[0].DimensionIndexPointer == 0x0062000B
        assert seq[0].FunctionalGroupPointer == 0x0062000A
        assert seq[1].DimensionIndexPointer == 0x0048021E
        assert seq[1].FunctionalGroupPointer == 0x0048021A
        assert seq[2].DimensionIndexPointer == 0x0048021F
        assert seq[2].FunctionalGroupPointer == 0x0048021A
        assert seq[3].DimensionIndexPointer == 0x0040072A
        assert seq[3].FunctionalGroupPointer == 0x0048021A
        assert seq[4].DimensionIndexPointer == 0x0040073A
        assert seq[4].FunctionalGroupPointer == 0x0048021A
        assert seq[5].DimensionIndexPointer == 0x0040074A
        assert seq[5].FunctionalGroupPointer == 0x0048021A

class TestSegmentation(unittest.TestCase):

    def setUp(self):
        super().setUp()
        file_path = Path(__file__)
        data_dir = file_path.parent.parent.joinpath('data')
        self._segmented_property_category = \
            codes.SCT.MorphologicallyAbnormalStructure
        self._segmented_property_type = codes.SCT.Neoplasm
        self._segment_descriptions = [
            SegmentDescription(
                segment_number=1,
                segment_label='Segment #1',
                segmented_property_category=self._segmented_property_category,
                segmented_property_type=self._segmented_property_type,
                algorithm_type=SegmentAlgorithmTypeValues.AUTOMATIC.value,
                algorithm_identification=AlgorithmIdentificationSequence(
                    name='bla',
                    family=codes.DCM.ArtificialIntelligence,
                    version='v1'
                )
            ),
        ]
        self._additional_segment_descriptions = [
            SegmentDescription(
                segment_number=2,
                segment_label='Segment #2',
                segmented_property_category=self._segmented_property_category,
                segmented_property_type=self._segmented_property_type,
                algorithm_type=SegmentAlgorithmTypeValues.AUTOMATIC.value,
                algorithm_identification=AlgorithmIdentificationSequence(
                    name='foo',
                    family=codes.DCM.ArtificialIntelligence,
                    version='v1'
                )
            ),
        ]
        self._both_segment_descriptions = (
            self._segment_descriptions + self._additional_segment_descriptions
        )
        self._additional_segment_descriptions_no4 = [
            SegmentDescription(
                segment_number=4,
                segment_label='Segment #4',
                segmented_property_category=self._segmented_property_category,
                segmented_property_type=self._segmented_property_type,
                algorithm_type=SegmentAlgorithmTypeValues.AUTOMATIC.value,
                algorithm_identification=AlgorithmIdentificationSequence(
                    name='foo',
                    family=codes.DCM.ArtificialIntelligence,
                    version='v1'
                )
            ),
        ]
        self._series_instance_uid = UID()
        self._series_number = 1
        self._sop_instance_uid = UID()
        self._instance_number = 1
        self._manufacturer = 'FavoriteManufacturer'
        self._manufacturer_model_name = 'BestModel'
        self._software_versions = 'v1.0'
        self._device_serial_number = '1-2-3'
        self._content_description = 'Test Segmentation'
        self._content_creator_name = 'Robo^Doc'
        self._content_label = 'MY_SEG'

        # A single CT image
        self._ct_image = dcmread(
            str(data_dir.joinpath('test_files', 'ct_image.dcm'))
        )
        self._ct_pixel_array = np.zeros(
            self._ct_image.pixel_array.shape,
            dtype=bool
        )
        self._ct_pixel_array[1:5, 10:15] = True

        # A microscopy image
        self._sm_image = dcmread(
            str(data_dir.joinpath('test_files', 'sm_image.dcm'))
        )
        # Override te existing ImageOrientationSlide to make the frame ordering
        # simpler for the tests
        self._sm_pixel_array = np.zeros(
            self._sm_image.pixel_array.shape[:3],  # remove colour channel axis
            dtype=bool
        )
        self._sm_pixel_array[2:3, 1:5, 7:9] = True

        # A series of single frame CT images
        ct_series = [
            dcmread(f)
            for f in get_testdata_files('dicomdirtests/77654033/CT2/*')
        ]
        # Ensure the frames are in the right spatial order
        # (only 3rd dimension changes)
        self._ct_series = sorted(
            ct_series,
            key=lambda x: x.ImagePositionPatient[2]
        )
        self._ct_series_mask_array = np.zeros(
            (len(self._ct_series), ) + self._ct_series[0].pixel_array.shape,
            dtype=bool
        )
        nonempty_slice = slice(1, 3)
        self._ct_series_mask_array[nonempty_slice, 1:5, 7:9] = True
        self._ct_series_nonempty = self._ct_series[nonempty_slice]

        # An enhanced (multiframe) CT image
        self._ct_multiframe = dcmread(get_testdata_file('eCT_Supplemental.dcm'))
        self._ct_multiframe_mask_array = np.zeros(
            self._ct_multiframe.pixel_array.shape,
            dtype=bool
        )
        self._ct_multiframe_mask_array[:, 100:200, 200:400] = True

    @staticmethod
    def sort_frames(sources, mask):
        src = sources[0]
        if hasattr(src, 'ImageOrientationSlide'):
            coordinate_system = CoordinateSystemNames.SLIDE
        else:
            coordinate_system = CoordinateSystemNames.PATIENT
        dim_index = DimensionIndexSequence(coordinate_system)
        if hasattr(src, 'NumberOfFrames'):
            plane_positions = dim_index.get_plane_positions_of_image(src)
        else:
            plane_positions = dim_index.get_plane_positions_of_series(sources)
        _, index = dim_index.get_index_values(plane_positions)
        return mask[index, ...]

    @staticmethod
    def remove_empty_frames(mask):
        # Remove empty frames from an array
        return np.stack([
            frame for frame in mask if np.sum(frame) > 0
        ])

    @staticmethod
    def get_array_after_writing(instance):
        # Write DICOM object to buffer, read it again and reconstruct the mask
        with BytesIO() as fp:
            instance.save_as(fp)
            fp.seek(0)
            instance_reread = dcmread(fp)

        return instance_reread.pixel_array

    @staticmethod
    def check_dimension_index_vals(seg):
        # Function to apply some checks (necessary but not sufficient for
        # correctness) to ensure that the dimension indices are correct
        is_patient_coord_system = hasattr(
            seg.PerFrameFunctionalGroupsSequence[0],
            'PlanePositionSequence'
        )
        if is_patient_coord_system:
            # Build up the mapping from index to value
            index_mapping = defaultdict(list)
            for f in seg.PerFrameFunctionalGroupsSequence:
                posn_index = f.FrameContentSequence[0].DimensionIndexValues[1]
                # This is not general, but all the tests run here use axial
                # images so just check the z coordinate
                posn_val = f.PlanePositionSequence[0].ImagePositionPatient[2]
                index_mapping[posn_index].append(posn_val)

            # Check that each index value found references a unique value
            for values in index_mapping.values():
                assert [v == values[0] for v in values]

            # Check that the indices are monotonically increasing from 1
            expected_keys = range(1, len(index_mapping) + 1)
            assert set(index_mapping.keys()) == set(expected_keys)

            # Check that values are sorted
            old_v = float('-inf')
            for k in expected_keys:
                assert index_mapping[k][0] > old_v
                old_v = index_mapping[k][0]
        else:
            # Build up the mapping from index to value
            for dim_kw, dim_ind in zip([
                'ColumnPositionInTotalImagePixelMatrix',
                'RowPositionInTotalImagePixelMatrix'
            ], [1, 2]):
                index_mapping = defaultdict(list)
                for f in seg.PerFrameFunctionalGroupsSequence:
                    content_item = f.FrameContentSequence[0]
                    posn_index = content_item.DimensionIndexValues[dim_ind]
                    # This is not general, but all the tests run here use axial
                    # images so just check the z coordinate
                    posn_item = f.PlanePositionSlideSequence[0]
                    posn_val = getattr(posn_item, dim_kw)
                    index_mapping[posn_index].append(posn_val)

                # Check that each index value found references a unique value
                for values in index_mapping.values():
                    assert [v == values[0] for v in values]

                # Check that the indices are monotonically increasing from 1
                expected_keys = range(1, len(index_mapping) + 1)
                assert set(index_mapping.keys()) == set(expected_keys)

                # Check that values are sorted
                old_v = float('-inf')
                for k in expected_keys:
                    assert index_mapping[k][0] > old_v
                    old_v = index_mapping[k][0]

    def test_construction(self):
        instance = Segmentation(
            [self._ct_image],
            self._ct_pixel_array,
            SegmentationTypeValues.FRACTIONAL.value,
            self._segment_descriptions,
            self._series_instance_uid,
            self._series_number,
            self._sop_instance_uid,
            self._instance_number,
            self._manufacturer,
            self._manufacturer_model_name,
            self._software_versions,
            self._device_serial_number,
            content_label=self._content_label
        )
        assert instance.SeriesInstanceUID == self._series_instance_uid
        assert instance.SeriesNumber == self._series_number
        assert instance.SOPInstanceUID == self._sop_instance_uid
        assert instance.InstanceNumber == self._instance_number
        assert instance.Manufacturer == self._manufacturer
        assert instance.ManufacturerModelName == self._manufacturer_model_name
        assert instance.SoftwareVersions == self._software_versions
        assert instance.DeviceSerialNumber == self._device_serial_number
        assert instance.Modality == 'SEG'
        assert instance.file_meta.TransferSyntaxUID == '1.2.840.10008.1.2.1'
        assert instance.PatientID == self._ct_image.PatientID
        assert instance.AccessionNumber == self._ct_image.AccessionNumber
        assert instance.LossyImageCompression == '00'
        assert instance.BitsAllocated == 8
        assert instance.HighBit == 7
        assert instance.BitsStored == 8
        assert instance.ImageType == ['DERIVED', 'PRIMARY']
        assert instance.SamplesPerPixel == 1
        assert instance.PhotometricInterpretation == 'MONOCHROME2'
        assert instance.PixelRepresentation == 0
        assert instance.SegmentationType == 'FRACTIONAL'
        assert instance.SegmentationFractionalType == 'PROBABILITY'
        assert instance.MaximumFractionalValue == 255
        assert instance.ContentLabel == self._content_label
        assert instance.ContentDescription is None
        assert instance.ContentCreatorName is None
        with pytest.raises(AttributeError):
            instance.LossyImageCompressionRatio
        with pytest.raises(AttributeError):
            instance.LossyImageCompressionMethod
        with pytest.raises(AttributeError):
            instance.ImageOrientationSlide
        with pytest.raises(AttributeError):
            instance.TotalPixelMatrixOriginSequence
        with pytest.raises(AttributeError):
            instance.TotalPixelMatrixRows
        with pytest.raises(AttributeError):
            instance.TotalPixelMatrixColumns
        assert len(instance.SegmentSequence) == 1
        assert instance.SegmentSequence[0].SegmentNumber == 1
        assert len(instance.SourceImageSequence) == 1
        assert len(instance.DimensionIndexSequence) == 2
        ref_item = instance.SourceImageSequence[0]
        assert ref_item.ReferencedSOPInstanceUID == \
            self._ct_image.SOPInstanceUID
        assert instance.Rows == self._ct_image.pixel_array.shape[0]
        assert instance.Columns == self._ct_image.pixel_array.shape[1]
        assert len(instance.SharedFunctionalGroupsSequence) == 1
        shared_item = instance.SharedFunctionalGroupsSequence[0]
        assert len(shared_item.PixelMeasuresSequence) == 1
        pm_item = shared_item.PixelMeasuresSequence[0]
        assert pm_item.PixelSpacing == self._ct_image.PixelSpacing
        assert pm_item.SliceThickness == self._ct_image.SliceThickness
        assert len(shared_item.PlaneOrientationSequence) == 1
        po_item = shared_item.PlaneOrientationSequence[0]
        assert po_item.ImageOrientationPatient == \
            self._ct_image.ImageOrientationPatient
        assert len(instance.DimensionOrganizationSequence) == 1
        assert len(instance.DimensionIndexSequence) == 2
        assert instance.NumberOfFrames == 1
        assert len(instance.PerFrameFunctionalGroupsSequence) == 1
        frame_item = instance.PerFrameFunctionalGroupsSequence[0]
        assert len(frame_item.SegmentIdentificationSequence) == 1
        assert len(frame_item.FrameContentSequence) == 1
        assert len(frame_item.DerivationImageSequence) == 1
        assert len(frame_item.PlanePositionSequence) == 1
        frame_content_item = frame_item.FrameContentSequence[0]
        assert len(frame_content_item.DimensionIndexValues) == 2
        for i, frame_item in enumerate(
            instance.PerFrameFunctionalGroupsSequence, 1
        ):
            frame_content_item = frame_item.FrameContentSequence[0]
            # The slice location index values should be consecutive, starting
            # at 1
            assert frame_content_item.DimensionIndexValues[1] == i
        for derivation_image_item in frame_item.DerivationImageSequence:
            assert len(derivation_image_item.SourceImageSequence) == 1
        assert SegmentsOverlapValues[instance.SegmentsOverlap] == \
            SegmentsOverlapValues.NO
        with pytest.raises(AttributeError):
            frame_item.PlanePositionSlideSequence
        self.check_dimension_index_vals(instance)

    def test_construction_2(self):
        instance = Segmentation(
            [self._sm_image],
            self._sm_pixel_array,
            SegmentationTypeValues.FRACTIONAL.value,
            self._segment_descriptions,
            self._series_instance_uid,
            self._series_number,
            self._sop_instance_uid,
            self._instance_number,
            self._manufacturer,
            self._manufacturer_model_name,
            self._software_versions,
            self._device_serial_number
        )
        assert instance.PatientID == self._sm_image.PatientID
        assert instance.AccessionNumber == self._sm_image.AccessionNumber
        assert instance.ContainerIdentifier == \
            self._sm_image.ContainerIdentifier
        assert instance.SpecimenDescriptionSequence[0].SpecimenUID == \
            self._sm_image.SpecimenDescriptionSequence[0].SpecimenUID
        assert len(instance.SegmentSequence) == 1
        assert instance.SegmentSequence[0].SegmentNumber == 1
        assert len(instance.SourceImageSequence) == 1
        ref_item = instance.SourceImageSequence[0]
        assert ref_item.ReferencedSOPInstanceUID == \
            self._sm_image.SOPInstanceUID
        assert instance.Rows == self._sm_image.pixel_array.shape[1]
        assert instance.Columns == self._sm_image.pixel_array.shape[2]
        assert instance.TotalPixelMatrixRows == \
            self._sm_image.TotalPixelMatrixRows
        assert instance.TotalPixelMatrixColumns == \
            self._sm_image.TotalPixelMatrixColumns
        assert len(instance.SharedFunctionalGroupsSequence) == 1
        shared_item = instance.SharedFunctionalGroupsSequence[0]
        assert len(shared_item.PixelMeasuresSequence) == 1
        pm_item = shared_item.PixelMeasuresSequence[0]
        src_shared_item = self._sm_image.SharedFunctionalGroupsSequence[0]
        src_pm_item = src_shared_item.PixelMeasuresSequence[0]
        assert pm_item.PixelSpacing == src_pm_item.PixelSpacing
        assert pm_item.SliceThickness == src_pm_item.SliceThickness
        assert len(shared_item.PlaneOrientationSequence) == 1
        assert instance.ImageOrientationSlide == \
            self._sm_image.ImageOrientationSlide
        assert instance.TotalPixelMatrixOriginSequence == \
            self._sm_image.TotalPixelMatrixOriginSequence
        assert len(instance.DimensionOrganizationSequence) == 1
        assert len(instance.DimensionIndexSequence) == 6

        # Number of frames should be number of frames in the segmentation mask
        # that are non-empty, due to sparsity
        num_frames = (self._sm_pixel_array.sum(axis=(1, 2)) > 0).sum()
        assert instance.NumberOfFrames == num_frames
        assert len(instance.PerFrameFunctionalGroupsSequence) == num_frames
        frame_item = instance.PerFrameFunctionalGroupsSequence[0]
        assert len(frame_item.SegmentIdentificationSequence) == 1
        assert len(frame_item.DerivationImageSequence) == 1
        assert len(frame_item.FrameContentSequence) == 1
        assert len(frame_item.PlanePositionSlideSequence) == 1
        frame_content_item = frame_item.FrameContentSequence[0]
        assert len(frame_content_item.DimensionIndexValues) == 6
        for derivation_image_item in frame_item.DerivationImageSequence:
            assert len(derivation_image_item.SourceImageSequence) == 1
            source_image_item = derivation_image_item.SourceImageSequence[0]
            assert hasattr(source_image_item, 'ReferencedFrameNumber')
        assert SegmentsOverlapValues[instance.SegmentsOverlap] == \
            SegmentsOverlapValues.NO
        with pytest.raises(AttributeError):
            frame_item.PlanePositionSequence
        self.check_dimension_index_vals(instance)

    def test_construction_3(self):
        # Segmentation instance from a series of single-frame CT images
        instance = Segmentation(
            self._ct_series,
            self._ct_series_mask_array,
            SegmentationTypeValues.FRACTIONAL.value,
            self._segment_descriptions,
            self._series_instance_uid,
            self._series_number,
            self._sop_instance_uid,
            self._instance_number,
            self._manufacturer,
            self._manufacturer_model_name,
            self._software_versions,
            self._device_serial_number
        )
        src_im = self._ct_series_nonempty[0]
        assert instance.PatientID == src_im.PatientID
        assert instance.AccessionNumber == src_im.AccessionNumber
        assert len(instance.SegmentSequence) == 1
        assert instance.SegmentSequence[0].SegmentNumber == 1
        assert len(instance.SourceImageSequence) == len(self._ct_series)
        ref_item = instance.SourceImageSequence[1]
        assert ref_item.ReferencedSOPInstanceUID == src_im.SOPInstanceUID
        assert instance.Rows == src_im.pixel_array.shape[0]
        assert instance.Columns == src_im.pixel_array.shape[1]
        assert len(instance.SharedFunctionalGroupsSequence) == 1
        shared_item = instance.SharedFunctionalGroupsSequence[0]
        assert len(shared_item.PixelMeasuresSequence) == 1
        pm_item = shared_item.PixelMeasuresSequence[0]
        assert pm_item.PixelSpacing == src_im.PixelSpacing
        assert pm_item.SliceThickness == src_im.SliceThickness
        assert len(shared_item.PlaneOrientationSequence) == 1
        po_item = shared_item.PlaneOrientationSequence[0]
        assert po_item.ImageOrientationPatient == \
            src_im.ImageOrientationPatient
        assert len(instance.DimensionOrganizationSequence) == 1
        assert len(instance.DimensionIndexSequence) == 2
        n_frames = len(self._ct_series_nonempty)
        assert instance.NumberOfFrames == n_frames
        assert len(instance.PerFrameFunctionalGroupsSequence) == n_frames
        for i, (frame_item, src_ins) in enumerate(
            zip(
                instance.PerFrameFunctionalGroupsSequence,
                self._ct_series_nonempty
            ),
            1
        ):
            assert len(frame_item.SegmentIdentificationSequence) == 1
            assert len(frame_item.FrameContentSequence) == 1
            assert len(frame_item.DerivationImageSequence) == 1
            assert len(frame_item.PlanePositionSequence) == 1
            frame_content_item = frame_item.FrameContentSequence[0]
            # The slice location index values should be consecutive, starting
            # at 1
            assert frame_content_item.DimensionIndexValues[1] == i
            assert len(frame_content_item.DimensionIndexValues) == 2
            for derivation_image_item in frame_item.DerivationImageSequence:
                assert len(derivation_image_item.SourceImageSequence) == 1
                source_image_item = derivation_image_item.SourceImageSequence[0]
                assert source_image_item.ReferencedSOPClassUID == \
                    src_ins.SOPClassUID
                assert source_image_item.ReferencedSOPInstanceUID == \
                    src_ins.SOPInstanceUID
                assert hasattr(
                    source_image_item,
                    'PurposeOfReferenceCodeSequence'
                )
        uid_to_plane_position = {}
        for fm in instance.PerFrameFunctionalGroupsSequence:
            src_img_item = fm.DerivationImageSequence[0].SourceImageSequence[0]
            uid_to_plane_position[src_img_item.ReferencedSOPInstanceUID] = \
                fm.PlanePositionSequence[0].ImagePositionPatient
        source_uid_to_plane_position = {
            dcm.SOPInstanceUID: dcm.ImagePositionPatient
            for dcm in self._ct_series
            if dcm.SOPInstanceUID in uid_to_plane_position
        }
        assert source_uid_to_plane_position == uid_to_plane_position
        assert SegmentsOverlapValues[instance.SegmentsOverlap] == \
            SegmentsOverlapValues.NO
        with pytest.raises(AttributeError):
            frame_item.PlanePositionSlideSequence
        self.check_dimension_index_vals(instance)

    def test_construction_4(self):
        # Segmentation instance from an enhanced (multi-frame) CT image
        instance = Segmentation(
            [self._ct_multiframe],
            self._ct_multiframe_mask_array,
            SegmentationTypeValues.FRACTIONAL.value,
            self._segment_descriptions,
            self._series_instance_uid,
            self._series_number,
            self._sop_instance_uid,
            self._instance_number,
            self._manufacturer,
            self._manufacturer_model_name,
            self._software_versions,
            self._device_serial_number
        )
        assert instance.PatientID == self._ct_multiframe.PatientID
        assert instance.AccessionNumber == self._ct_multiframe.AccessionNumber
        assert len(instance.SegmentSequence) == 1
        assert instance.SegmentSequence[0].SegmentNumber == 1
        assert len(instance.SourceImageSequence) == 1
        ref_item = instance.SourceImageSequence[0]
        assert ref_item.ReferencedSOPInstanceUID == \
            self._ct_multiframe.SOPInstanceUID
        assert instance.NumberOfFrames == \
            self._ct_multiframe.pixel_array.shape[0]
        assert instance.Rows == self._ct_multiframe.pixel_array.shape[1]
        assert instance.Columns == self._ct_multiframe.pixel_array.shape[2]
        assert len(instance.SharedFunctionalGroupsSequence) == 1
        shared_item = instance.SharedFunctionalGroupsSequence[0]
        src_shared_item = self._ct_multiframe.SharedFunctionalGroupsSequence[0]
        assert len(shared_item.PixelMeasuresSequence) == 1
        pm_item = shared_item.PixelMeasuresSequence[0]
        assert pm_item.PixelSpacing == \
            src_shared_item.PixelMeasuresSequence[0].PixelSpacing
        assert pm_item.SliceThickness == \
            src_shared_item.PixelMeasuresSequence[0].SliceThickness
        assert len(shared_item.PlaneOrientationSequence) == 1
        po_item = shared_item.PlaneOrientationSequence[0]
        assert po_item.ImageOrientationPatient == \
            src_shared_item.PlaneOrientationSequence[0].ImageOrientationPatient
        assert len(instance.DimensionOrganizationSequence) == 1
        assert len(instance.DimensionIndexSequence) == 2
        assert len(instance.PerFrameFunctionalGroupsSequence) == \
            self._ct_multiframe.NumberOfFrames
        frame_item = instance.PerFrameFunctionalGroupsSequence[0]
        assert len(frame_item.SegmentIdentificationSequence) == 1
        assert len(frame_item.FrameContentSequence) == 1
        assert len(frame_item.DerivationImageSequence) == 1
        assert len(frame_item.PlanePositionSequence) == 1
        frame_content_item = frame_item.FrameContentSequence[0]
        assert len(frame_content_item.DimensionIndexValues) == 2
        for derivation_image_item in frame_item.DerivationImageSequence:
            assert len(derivation_image_item.SourceImageSequence) == 1
            source_image_item = derivation_image_item.SourceImageSequence[0]
            assert source_image_item.ReferencedSOPClassUID == \
                self._ct_multiframe.SOPClassUID
            assert source_image_item.ReferencedSOPInstanceUID == \
                self._ct_multiframe.SOPInstanceUID
            assert hasattr(source_image_item, 'PurposeOfReferenceCodeSequence')
        for i, (src_fm, seg_fm) in enumerate(
                zip(
                    self._ct_multiframe.PerFrameFunctionalGroupsSequence,
                    instance.PerFrameFunctionalGroupsSequence
                )
            ):
            assert src_fm.PlanePositionSequence[0].ImagePositionPatient == \
                seg_fm.PlanePositionSequence[0].ImagePositionPatient
            derivation_image_item = seg_fm.DerivationImageSequence[0]
            source_image_item = derivation_image_item.SourceImageSequence[0]
            assert source_image_item.ReferencedFrameNumber == i + 1
            assert source_image_item.ReferencedSOPInstanceUID == \
                self._ct_multiframe.SOPInstanceUID
        assert SegmentsOverlapValues[instance.SegmentsOverlap] == \
            SegmentsOverlapValues.NO
        with pytest.raises(AttributeError):
            frame_item.PlanePositionSlideSequence
        self.check_dimension_index_vals(instance)

    def test_construction_5(self):
        # Segmentation instance from a series of single-frame CT images
        # with empty frames kept in
        instance = Segmentation(
            self._ct_series,
            self._ct_series_mask_array,
            SegmentationTypeValues.FRACTIONAL.value,
            self._segment_descriptions,
            self._series_instance_uid,
            self._series_number,
            self._sop_instance_uid,
            self._instance_number,
            self._manufacturer,
            self._manufacturer_model_name,
            self._software_versions,
            self._device_serial_number,
            omit_empty_frames=False
        )
        src_im = self._ct_series[0]
        assert instance.PatientID == src_im.PatientID
        assert instance.AccessionNumber == src_im.AccessionNumber
        assert len(instance.SegmentSequence) == 1
        assert instance.SegmentSequence[0].SegmentNumber == 1
        assert len(instance.SourceImageSequence) == len(self._ct_series)
        ref_item = instance.SourceImageSequence[0]
        assert ref_item.ReferencedSOPInstanceUID == src_im.SOPInstanceUID
        assert instance.Rows == src_im.pixel_array.shape[0]
        assert instance.Columns == src_im.pixel_array.shape[1]
        assert len(instance.SharedFunctionalGroupsSequence) == 1
        shared_item = instance.SharedFunctionalGroupsSequence[0]
        assert len(shared_item.PixelMeasuresSequence) == 1
        pm_item = shared_item.PixelMeasuresSequence[0]
        assert pm_item.PixelSpacing == src_im.PixelSpacing
        assert pm_item.SliceThickness == src_im.SliceThickness
        assert len(shared_item.PlaneOrientationSequence) == 1
        po_item = shared_item.PlaneOrientationSequence[0]
        assert po_item.ImageOrientationPatient == \
            src_im.ImageOrientationPatient
        assert len(instance.DimensionOrganizationSequence) == 1
        assert len(instance.DimensionIndexSequence) == 2
        assert instance.NumberOfFrames == 4
        assert len(instance.PerFrameFunctionalGroupsSequence) == 4
        frame_item = instance.PerFrameFunctionalGroupsSequence[0]
        assert len(frame_item.SegmentIdentificationSequence) == 1
        assert len(frame_item.FrameContentSequence) == 1
        assert len(frame_item.DerivationImageSequence) == 1
        assert len(frame_item.PlanePositionSequence) == 1
        for i, (frame_item, src_ins) in enumerate(
            zip(instance.PerFrameFunctionalGroupsSequence, self._ct_series),
            1
        ):
            frame_content_item = frame_item.FrameContentSequence[0]
            # The slice location index values should be consecutive, starting
            # at 1
            assert frame_content_item.DimensionIndexValues[1] == i
            assert len(frame_content_item.DimensionIndexValues) == 2
            for derivation_image_item in frame_item.DerivationImageSequence:
                assert len(derivation_image_item.SourceImageSequence) == 1
                source_image_item = derivation_image_item.SourceImageSequence[0]
                assert source_image_item.ReferencedSOPClassUID == \
                    src_ins.SOPClassUID
                assert source_image_item.ReferencedSOPInstanceUID == \
                    src_ins.SOPInstanceUID
                assert hasattr(
                    source_image_item,
                    'PurposeOfReferenceCodeSequence'
                )
        uid_to_plane_position = {}
        for fm in instance.PerFrameFunctionalGroupsSequence:
            src_img_item = fm.DerivationImageSequence[0].SourceImageSequence[0]
            uid_to_plane_position[src_img_item.ReferencedSOPInstanceUID] = \
                fm.PlanePositionSequence[0].ImagePositionPatient
        source_uid_to_plane_position = {
            dcm.SOPInstanceUID: dcm.ImagePositionPatient
            for dcm in self._ct_series
            if dcm.SOPInstanceUID in uid_to_plane_position
        }
        assert source_uid_to_plane_position == uid_to_plane_position
        assert SegmentsOverlapValues[instance.SegmentsOverlap] == \
            SegmentsOverlapValues.NO
        with pytest.raises(AttributeError):
            frame_item.PlanePositionSlideSequence
        self.check_dimension_index_vals(instance)

    def test_pixel_types(self):
        # A series of tests on different types of image
        tests = [
            ([self._ct_image], self._ct_pixel_array),
            ([self._sm_image], self._sm_pixel_array),
            (self._ct_series, self._ct_series_mask_array),
            ([self._ct_multiframe], self._ct_multiframe_mask_array),
        ]

        for sources, mask in tests:

            # Two segments, overlapping
            multi_segment_overlap = np.stack([mask, mask], axis=-1)
            if multi_segment_overlap.ndim == 3:
                multi_segment_overlap = multi_segment_overlap[np.newaxis, ...]

            # Two segments non-overlapping
            multi_segment_exc = np.stack([mask, 1 - mask], axis=-1)
            if multi_segment_exc.ndim == 3:
                multi_segment_exc = multi_segment_exc[np.newaxis, ...]
            additional_mask = 1 - mask

            # Find the expected encodings for the masks
            if mask.ndim > 2:
                # Expected encoding of the mask
                expected_encoding = self.sort_frames(
                    sources,
                    mask
                )
                expected_encoding = self.remove_empty_frames(
                    expected_encoding
                )

                # Expected encoding of the complement
                expected_encoding_comp = self.sort_frames(
                    sources,
                    additional_mask
                )
                expected_encoding_comp = self.remove_empty_frames(
                    expected_encoding_comp
                )

                # Expected encoding of the multi segment arrays
                expected_enc_overlap = np.concatenate(
                    [expected_encoding, expected_encoding],
                    axis=0
                )
                expected_enc_exc = np.concatenate(
                    [expected_encoding, expected_encoding_comp],
                    axis=0
                )
                expected_encoding = expected_encoding.squeeze()
            else:
                expected_encoding = mask

                # Expected encoding of the multi segment arrays
                expected_enc_overlap = np.stack(
                    [expected_encoding, expected_encoding],
                    axis=0
                )
                expected_enc_exc = np.stack(
                    [expected_encoding, 1 - expected_encoding],
                    axis=0
                )

            # Test instance creation for different pixel types and transfer
            # syntaxes
            valid_transfer_syntaxes = [
                ExplicitVRLittleEndian,
                ImplicitVRLittleEndian,
                RLELossless,
                JPEG2000Lossless
            ]

            max_fractional_value = 255
            for transfer_syntax_uid in valid_transfer_syntaxes:
                for pix_type in [np.bool_, np.uint8, np.uint16, np.float_]:
                    instance = Segmentation(
                        sources,
                        mask.astype(pix_type),
                        SegmentationTypeValues.FRACTIONAL.value,
                        self._segment_descriptions,
                        self._series_instance_uid,
                        self._series_number,
                        self._sop_instance_uid,
                        self._instance_number,
                        self._manufacturer,
                        self._manufacturer_model_name,
                        self._software_versions,
                        self._device_serial_number,
                        max_fractional_value=max_fractional_value,
                        transfer_syntax_uid=transfer_syntax_uid
                    )

                    # Ensure the recovered pixel array matches what is expected
                    if pix_type in (np.bool_, np.float_):
                        assert np.array_equal(
                            self.get_array_after_writing(instance),
                            expected_encoding * max_fractional_value
                        ), f'{sources[0].Modality} {transfer_syntax_uid}'
                    else:
                        assert np.array_equal(
                            self.get_array_after_writing(instance),
                            expected_encoding
                        ), f'{sources[0].Modality} {transfer_syntax_uid}'
                    self.check_dimension_index_vals(instance)

                    # Multi-segment (exclusive)
                    instance = Segmentation(
                        sources,
                        multi_segment_exc.astype(pix_type),
                        SegmentationTypeValues.FRACTIONAL.value,
                        self._both_segment_descriptions,
                        self._series_instance_uid,
                        self._series_number,
                        self._sop_instance_uid,
                        self._instance_number,
                        self._manufacturer,
                        self._manufacturer_model_name,
                        self._software_versions,
                        self._device_serial_number,
                        max_fractional_value=1,
                        transfer_syntax_uid=transfer_syntax_uid
                    )
                    if pix_type == np.float_:
                        assert (
                            instance.SegmentsOverlap ==
                            SegmentsOverlapValues.UNDEFINED.value
                        )
                    else:
                        assert (
                            instance.SegmentsOverlap ==
                            SegmentsOverlapValues.NO.value
                        )

                    assert np.array_equal(
                        self.get_array_after_writing(instance),
                        expected_enc_exc
                    ), f'{sources[0].Modality} {transfer_syntax_uid}'
                    self.check_dimension_index_vals(instance)

                    # Multi-segment (overlapping)
                    instance = Segmentation(
                        sources,
                        multi_segment_overlap.astype(pix_type),
                        SegmentationTypeValues.FRACTIONAL.value,
                        self._both_segment_descriptions,
                        self._series_instance_uid,
                        self._series_number,
                        self._sop_instance_uid,
                        self._instance_number,
                        self._manufacturer,
                        self._manufacturer_model_name,
                        self._software_versions,
                        self._device_serial_number,
                        max_fractional_value=1,
                        transfer_syntax_uid=transfer_syntax_uid
                    )
                    if pix_type == np.float_:
                        assert (
                            instance.SegmentsOverlap ==
                            SegmentsOverlapValues.UNDEFINED.value
                        )
                    else:
                        assert (
                            instance.SegmentsOverlap ==
                            SegmentsOverlapValues.YES.value
                        )

                    assert np.array_equal(
                        self.get_array_after_writing(instance),
                        expected_enc_overlap
                    ), f'{sources[0].Modality} {transfer_syntax_uid}'
                    self.check_dimension_index_vals(instance)

        for sources, mask in tests:
            # Two segments, overlapping
            multi_segment_overlap = np.stack([mask, mask], axis=-1)
            if multi_segment_overlap.ndim == 3:
                multi_segment_overlap = multi_segment_overlap[np.newaxis, ...]

            # Two segments non-overlapping
            multi_segment_exc = np.stack([mask, 1 - mask], axis=-1)

            if multi_segment_exc.ndim == 3:
                multi_segment_exc = multi_segment_exc[np.newaxis, ...]
            additional_mask = 1 - mask

            additional_mask = (1 - mask)
            # Find the expected encodings for the masks
            if mask.ndim > 2:
                # Expected encoding of the mask
                expected_encoding = self.sort_frames(
                    sources,
                    mask
                )
                expected_encoding = self.remove_empty_frames(
                    expected_encoding
                )

                # Expected encoding of the complement
                expected_encoding_comp = self.sort_frames(
                    sources,
                    additional_mask
                )
                expected_encoding_comp = self.remove_empty_frames(
                    expected_encoding_comp
                )

                # Expected encoding of the multi segment arrays
                expected_enc_overlap = np.concatenate(
                    [expected_encoding, expected_encoding],
                    axis=0
                )
                expected_enc_exc = np.concatenate(
                    [expected_encoding, expected_encoding_comp],
                    axis=0
                )
                expected_encoding = expected_encoding.squeeze()
            else:
                expected_encoding = mask

                # Expected encoding of the multi segment arrays
                expected_enc_overlap = np.stack(
                    [expected_encoding, expected_encoding],
                    axis=0
                )
                expected_enc_exc = np.stack(
                    [expected_encoding, 1 - expected_encoding],
                    axis=0
                )

            valid_transfer_syntaxes = [
                ExplicitVRLittleEndian,
                ImplicitVRLittleEndian,
            ]

            for transfer_syntax_uid in valid_transfer_syntaxes:
                for pix_type in [np.bool_, np.uint8, np.uint16, np.float_]:
                    instance = Segmentation(
                        sources,
                        mask.astype(pix_type),
                        SegmentationTypeValues.BINARY.value,
                        self._segment_descriptions,
                        self._series_instance_uid,
                        self._series_number,
                        self._sop_instance_uid,
                        self._instance_number,
                        self._manufacturer,
                        self._manufacturer_model_name,
                        self._software_versions,
                        self._device_serial_number,
                        max_fractional_value=1,
                        transfer_syntax_uid=transfer_syntax_uid
                    )

                    # Ensure the recovered pixel array matches what is expected
                    assert np.array_equal(
                        self.get_array_after_writing(instance),
                        expected_encoding
                    ), f'{sources[0].Modality} {transfer_syntax_uid}'
                    self.check_dimension_index_vals(instance)

                    # Multi-segment (exclusive)
                    instance = Segmentation(
                        sources,
                        multi_segment_exc.astype(pix_type),
                        SegmentationTypeValues.BINARY.value,
                        self._both_segment_descriptions,
                        self._series_instance_uid,
                        self._series_number,
                        self._sop_instance_uid,
                        self._instance_number,
                        self._manufacturer,
                        self._manufacturer_model_name,
                        self._software_versions,
                        self._device_serial_number,
                        max_fractional_value=1,
                        transfer_syntax_uid=transfer_syntax_uid
                    )
                    assert (
                        instance.SegmentsOverlap ==
                        SegmentsOverlapValues.NO.value
                    )

                    assert np.array_equal(
                        self.get_array_after_writing(instance),
                        expected_enc_exc
                    ), f'{sources[0].Modality} {transfer_syntax_uid}'
                    self.check_dimension_index_vals(instance)

                    # Multi-segment (overlapping)
                    instance = Segmentation(
                        sources,
                        multi_segment_overlap.astype(pix_type),
                        SegmentationTypeValues.BINARY.value,
                        self._both_segment_descriptions,
                        self._series_instance_uid,
                        self._series_number,
                        self._sop_instance_uid,
                        self._instance_number,
                        self._manufacturer,
                        self._manufacturer_model_name,
                        self._software_versions,
                        self._device_serial_number,
                        max_fractional_value=1,
                        transfer_syntax_uid=transfer_syntax_uid
                    )
                    assert (
                        instance.SegmentsOverlap ==
                        SegmentsOverlapValues.YES.value
                    )

                    assert np.array_equal(
                        self.get_array_after_writing(instance),
                        expected_enc_overlap
                    ), f'{sources[0].Modality} {transfer_syntax_uid}'
                    self.check_dimension_index_vals(instance)

    def test_odd_number_pixels(self):
        # Test that an image with an odd number of pixels per frame is encoded
        # properly Including when additional segments are subsequently added

        # Create an instance with an odd number of pixels in each frame
        # Based on the single frame CT image
        odd_instance = self._ct_image
        r = 9
        c = 9
        odd_pixels = np.random.randint(
            256,
            size=(r, c),
            dtype=np.uint16
        )

        odd_instance.PixelData = odd_pixels.flatten().tobytes()
        odd_instance.Rows = r
        odd_instance.Columns = c

        odd_mask = np.random.randint(
            2,
            size=odd_pixels.shape,
            dtype=bool
        )

        instance = Segmentation(
            [odd_instance],
            odd_mask,
            SegmentationTypeValues.BINARY.value,
            segment_descriptions=self._segment_descriptions,
            series_instance_uid=self._series_instance_uid,
            series_number=self._series_number,
            sop_instance_uid=self._sop_instance_uid,
            instance_number=self._instance_number,
            manufacturer=self._manufacturer,
            manufacturer_model_name=self._manufacturer_model_name,
            software_versions=self._software_versions,
            device_serial_number=self._device_serial_number
        )

        assert np.array_equal(self.get_array_after_writing(instance), odd_mask)
        self.check_dimension_index_vals(instance)

        additional_odd_mask = np.random.randint(
            2,
            size=odd_pixels.shape,
            dtype=bool
        )
        two_segment_mask = np.stack(
            [odd_mask, additional_odd_mask],
            axis=-1
        )[np.newaxis, ...]
        expected_encoding = np.stack(
            [odd_mask, additional_odd_mask],
            axis=0
        )

        instance = Segmentation(
            [odd_instance],
            two_segment_mask,
            SegmentationTypeValues.BINARY.value,
            segment_descriptions=self._both_segment_descriptions,
            series_instance_uid=self._series_instance_uid,
            series_number=self._series_number,
            sop_instance_uid=self._sop_instance_uid,
            instance_number=self._instance_number,
            manufacturer=self._manufacturer,
            manufacturer_model_name=self._manufacturer_model_name,
            software_versions=self._software_versions,
            device_serial_number=self._device_serial_number
        )

        assert np.array_equal(
            self.get_array_after_writing(instance),
            expected_encoding
        )
        self.check_dimension_index_vals(instance)

    def test_multi_segments(self):
        # Test that the multi-segment encoding is behaving as expected

        # Create an example mask with two segments
        multi_segment_mask = np.zeros(
            self._ct_image.pixel_array.shape,
            dtype=np.uint8
        )
        multi_segment_mask[1:5, 10:15] = 1
        multi_segment_mask[5:7, 1:5] = 2

        # Create another example mask with two segments,
        # where one is empty
        multi_segment_mask_empty = np.zeros(
            self._ct_image.pixel_array.shape,
            dtype=np.uint8
        )
        multi_segment_mask_empty[5:7, 1:5] = 2

        for mask in [multi_segment_mask, multi_segment_mask_empty]:
            # The expected encoding splits into two channels stacked down axis 0
            if len(np.unique(mask)) > 2:
                expected_encoding = np.stack([
                    mask == i for i in np.arange(1, len(np.unique(mask)))
                ])
            else:
                expected_encoding = (mask > 0).astype(mask.dtype)

            all_segment_descriptions = (
                self._segment_descriptions +
                self._additional_segment_descriptions
            )
            instance = Segmentation(
                [self._ct_image],
                mask,
                SegmentationTypeValues.BINARY.value,
                all_segment_descriptions,
                self._series_instance_uid,
                self._series_number,
                self._sop_instance_uid,
                self._instance_number,
                self._manufacturer,
                self._manufacturer_model_name,
                self._software_versions,
                self._device_serial_number,
                max_fractional_value=1
            )

            assert len(instance.SegmentSequence) == 2
            assert instance.SegmentSequence[0].SegmentNumber == 1
            assert instance.SegmentSequence[1].SegmentNumber == 2

            # Ensure the recovered pixel array matches what is expected
            assert np.array_equal(
                self.get_array_after_writing(instance),
                expected_encoding
            )
            self.check_dimension_index_vals(instance)

    def test_construction_empty_source_image(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[],  # empty
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._segment_descriptions
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_invalid_content_label(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._segment_descriptions
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number,
                content_label='invalid-content-label'
            )

    def test_construction_mixed_source_series(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=self._ct_series + [self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._additional_segment_descriptions  # seg num 2
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_wrong_number_of_segments(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array[..., np.newaxis],
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._both_segment_descriptions
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_stacked_label_map(self):
        # A 4D integer cannot have non-binary values
        mask = np.zeros(
            (1, self._ct_image.Rows, self._ct_image.Columns, 2),
            dtype=np.uint8
        )
        mask[0, 0, 0, 0] = 2  # disallowed
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=mask,
                segmentation_type=SegmentationTypeValues.BINARY.value,
                segment_descriptions=(
                    self._both_segment_descriptions
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_segment_numbers_start_wrong(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._additional_segment_descriptions  # seg num 2
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_empty_invalid_floats(self):
        # Floats outside the range 0.0 to 1.0 are invalid
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],  # empty
                pixel_array=self._ct_pixel_array.astype(np.float_) * 2,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._segment_descriptions
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_empty_invalid_floats_binary(self):
        # Cannot use floats other than 0.0 and 1.0 when encoding as BINARY
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array.astype(np.float_) * 0.5,
                segmentation_type=SegmentationTypeValues.BINARY.value,
                segment_descriptions=(
                    self._segment_descriptions
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_empty_invalid_dtype(self):
        # Cannot use signed integers
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array.astype(np.int16),
                segmentation_type=SegmentationTypeValues.BINARY.value,
                segment_descriptions=(
                    self._segment_descriptions
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_wrong_segment_order(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._additional_segment_descriptions +  # seg 2
                    self._segment_descriptions               # seg 1
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_duplicate_segment_number(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._segment_descriptions +
                    self._segment_descriptions  # duplicate
                ),
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_non_described_segment(self):
        with pytest.raises(ValueError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=(self._ct_pixel_array * 3).astype(np.uint8),
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=(
                    self._segment_descriptions +
                    self._additional_segment_descriptions
                ),  # two segments, value of 3 in pixel array
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute(self):
        with pytest.raises(TypeError):
            Segmentation(
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_2(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_3(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_4(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_5(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_6(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_7(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_8(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_9(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                software_versions=self._software_versions,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_10(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                device_serial_number=self._device_serial_number
            )

    def test_construction_missing_required_attribute_11(self):
        with pytest.raises(TypeError):
            Segmentation(
                source_images=[self._ct_image],
                pixel_array=self._ct_pixel_array,
                segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
                segment_descriptions=self._segment_descriptions,
                series_instance_uid=self._series_instance_uid,
                series_number=self._series_number,
                sop_instance_uid=self._sop_instance_uid,
                instance_number=self._instance_number,
                manufacturer=self._manufacturer,
                manufacturer_model_name=self._manufacturer_model_name,
                software_versions=self._software_versions
            )

    def test_construction_optional_arguments(self):
        fractional_type = 'OCCUPANCY'
        max_fractional_value = 100
        content_description = 'bla bla bla'
        content_creator_name = 'Family^Given'
        series_description = 'My First Segmentation'
        instance = Segmentation(
            source_images=[self._ct_image],
            pixel_array=self._ct_pixel_array,
            segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
            segment_descriptions=self._segment_descriptions,
            series_instance_uid=self._series_instance_uid,
            series_number=self._series_number,
            sop_instance_uid=self._sop_instance_uid,
            instance_number=self._instance_number,
            manufacturer=self._manufacturer,
            manufacturer_model_name=self._manufacturer_model_name,
            software_versions=self._software_versions,
            device_serial_number=self._device_serial_number,
            fractional_type=fractional_type,
            max_fractional_value=max_fractional_value,
            content_description=content_description,
            content_creator_name=content_creator_name,
            series_description=series_description,
        )
        assert instance.SegmentationFractionalType == fractional_type
        assert instance.MaximumFractionalValue == max_fractional_value
        assert instance.ContentDescription == content_description
        assert instance.ContentCreatorName == content_creator_name
        assert instance.SeriesDescription == series_description
        self.check_dimension_index_vals(instance)

    def test_construction_optional_arguments_2(self):
        pixel_spacing = (0.5, 0.5)
        slice_thickness = 0.3
        pixel_measures = PixelMeasuresSequence(
            pixel_spacing=pixel_spacing,
            slice_thickness=slice_thickness,
            spacing_between_slices=0.7
        )
        image_orientation = (-1.0, 0.0, 0.0, 0.0, -1.0, 0.0)
        plane_orientation = PlaneOrientationSequence(
            coordinate_system=CoordinateSystemNames.PATIENT,
            image_orientation=image_orientation
        )
        plane_positions = [
            PlanePositionSequence(
                coordinate_system=CoordinateSystemNames.PATIENT,
                image_position=(0.0, 0.0, 0.0)
            ),
        ]
        instance = Segmentation(
            source_images=[self._ct_image],
            pixel_array=self._ct_pixel_array,
            segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
            segment_descriptions=self._segment_descriptions,
            series_instance_uid=self._series_instance_uid,
            series_number=self._series_number,
            sop_instance_uid=self._sop_instance_uid,
            instance_number=self._instance_number,
            manufacturer=self._manufacturer,
            manufacturer_model_name=self._manufacturer_model_name,
            software_versions=self._software_versions,
            device_serial_number=self._device_serial_number,
            pixel_measures=pixel_measures,
            plane_orientation=plane_orientation,
            plane_positions=plane_positions
        )
        shared_item = instance.SharedFunctionalGroupsSequence[0]
        assert len(shared_item.PixelMeasuresSequence) == 1
        pm_item = shared_item.PixelMeasuresSequence[0]
        assert pm_item.PixelSpacing == list(pixel_spacing)
        assert pm_item.SliceThickness == slice_thickness
        assert len(shared_item.PlaneOrientationSequence) == 1
        po_item = shared_item.PlaneOrientationSequence[0]
        assert po_item.ImageOrientationPatient == list(image_orientation)
        self.check_dimension_index_vals(instance)

    def test_construction_optional_arguments_3(self):
        pixel_spacing = (0.5, 0.5)
        slice_thickness = 0.3
        pixel_measures = PixelMeasuresSequence(
            pixel_spacing=pixel_spacing,
            slice_thickness=slice_thickness
        )
        image_orientation = (-1.0, 0.0, 0.0, 0.0, -1.0, 0.0)
        plane_orientation = PlaneOrientationSequence(
            coordinate_system=CoordinateSystemNames.SLIDE,
            image_orientation=image_orientation
        )
        plane_positions = [
            PlanePositionSequence(
                coordinate_system=CoordinateSystemNames.SLIDE,
                image_position=(i * 1.0, i * 1.0, 1.0),
                pixel_matrix_position=(i * 1, i * 1)
            )
            for i in range(self._sm_image.pixel_array.shape[0])
        ]
        instance = Segmentation(
            source_images=[self._sm_image],
            pixel_array=self._sm_pixel_array,
            segmentation_type=SegmentationTypeValues.FRACTIONAL.value,
            segment_descriptions=self._segment_descriptions,
            series_instance_uid=self._series_instance_uid,
            series_number=self._series_number,
            sop_instance_uid=self._sop_instance_uid,
            instance_number=self._instance_number,
            manufacturer=self._manufacturer,
            manufacturer_model_name=self._manufacturer_model_name,
            software_versions=self._software_versions,
            device_serial_number=self._device_serial_number,
            pixel_measures=pixel_measures,
            plane_orientation=plane_orientation,
            plane_positions=plane_positions
        )
        shared_item = instance.SharedFunctionalGroupsSequence[0]
        assert len(shared_item.PixelMeasuresSequence) == 1
        pm_item = shared_item.PixelMeasuresSequence[0]
        assert pm_item.PixelSpacing == list(pixel_spacing)
        assert pm_item.SliceThickness == slice_thickness
        assert len(shared_item.PlaneOrientationSequence) == 1
        po_item = shared_item.PlaneOrientationSequence[0]
        assert po_item.ImageOrientationSlide == list(image_orientation)
        self.check_dimension_index_vals(instance)

class TestSegmentationParsing(unittest.TestCase):
    def setUp(self):
        self._sm_control_seg_ds = dcmread(
            'data/test_files/seg_image_sm_control.dcm'
        )
        self._sm_control_seg = Segmentation.from_dataset(
            self._sm_control_seg_ds
        )

        self._ct_binary_seg_ds = dcmread(
            'data/test_files/seg_image_ct_binary.dcm'
        )
        self._ct_binary_seg = Segmentation.from_dataset(
            self._ct_binary_seg_ds
        )

        self._ct_binary_overlap_seg_ds = dcmread(
            'data/test_files/seg_image_ct_binary_overlap.dcm'
        )
        self._ct_binary_overlap_seg = Segmentation.from_dataset(
            self._ct_binary_overlap_seg_ds
        )

        self._ct_binary_fractional_seg_ds = dcmread(
            'data/test_files/seg_image_ct_binary_fractional.dcm'
        )
        self._ct_binary_fractional_seg = Segmentation.from_dataset(
            self._ct_binary_fractional_seg_ds
        )

        self._ct_true_fractional_seg_ds = dcmread(
            'data/test_files/seg_image_ct_true_fractional.dcm'
        )
        self._ct_true_fractional_seg = Segmentation.from_dataset(
            self._ct_true_fractional_seg_ds
        )
        self._ct_segs = [
            self._ct_binary_seg,
            self._ct_binary_fractional_seg,
            self._ct_true_fractional_seg
        ]

    def test_from_dataset(self):
        assert isinstance(self._sm_control_seg, Segmentation)

    def test_segread(self):
        seg = segread('data/test_files/seg_image_ct_true_fractional.dcm')
        assert isinstance(seg, Segmentation)
        seg = segread('data/test_files/seg_image_ct_binary_overlap.dcm')
        assert isinstance(seg, Segmentation)
        seg = segread('data/test_files/seg_image_sm_numbers.dcm')
        assert isinstance(seg, Segmentation)

    def test_properties(self):
        # SM segs
        seg_type = self._sm_control_seg.segmentation_type
        assert seg_type == SegmentationTypeValues.BINARY
        assert self._sm_control_seg.segmentation_fractional_type is None
        assert self._sm_control_seg.number_of_segments == 20
        assert self._sm_control_seg.segment_numbers == range(1, 21)

        assert len(self._sm_control_seg.segmented_property_categories) == 1
        seg_category = self._sm_control_seg.segmented_property_categories[0]
        assert seg_category == codes.SCT.Tissue
        seg_property = self._sm_control_seg.segmented_property_types[0]
        assert seg_property == codes.SCT.ConnectiveTissue

        # CT segs
        for seg in self._ct_segs:
            seg_type = seg.segmentation_type
            assert seg.number_of_segments == 1
            assert seg.segment_numbers == range(1, 2)

            assert len(seg.segmented_property_categories) == 1
            seg_category = seg.segmented_property_categories[0]
            assert seg_category == codes.SCT.Tissue
            seg_property = seg.segmented_property_types[0]
            assert seg_property == codes.SCT.Bone

        seg_type = self._ct_binary_seg.segmentation_type
        assert seg_type == SegmentationTypeValues.BINARY
        seg_type = self._ct_binary_fractional_seg.segmentation_type
        assert seg_type == SegmentationTypeValues.FRACTIONAL
        seg_type = self._ct_true_fractional_seg.segmentation_type
        assert seg_type == SegmentationTypeValues.FRACTIONAL

        frac_type = self._ct_binary_fractional_seg.segmentation_fractional_type
        assert frac_type == SegmentationFractionalTypeValues.PROBABILITY
        frac_type = self._ct_true_fractional_seg.segmentation_fractional_type
        assert frac_type == SegmentationFractionalTypeValues.PROBABILITY

    def test_get_source_image_uids(self):
        uids = self._sm_control_seg.get_source_image_uids()
        assert len(uids) == 1
        ins_uids = uids[0]
        assert len(ins_uids) == 3
        assert all(isinstance(uid, UID) for uid in ins_uids)

    def test_get_segment_description(self):
        desc1 = self._sm_control_seg.get_segment_description(1)
        desc20 = self._sm_control_seg.get_segment_description(20)
        assert isinstance(desc1, SegmentDescription)
        assert desc1.segment_number == 1
        assert isinstance(desc20, SegmentDescription)
        assert desc20.segment_number == 20

    def test_get_segment_numbers_no_filters(self):
        seg_nums = self._sm_control_seg.get_segment_numbers()
        assert seg_nums == list(self._sm_control_seg.segment_numbers)

    def test_get_segment_numbers_with_filters(self):
        desc1 = self._sm_control_seg.get_segment_description(1)

        seg_nums = self._sm_control_seg.get_segment_numbers(
            tracking_id=desc1.tracking_id
        )
        assert seg_nums == [1]

        seg_nums = self._sm_control_seg.get_segment_numbers(
            tracking_uid=desc1.tracking_uid
        )
        assert seg_nums == [1]

        # All segments match these filters
        seg_nums = self._sm_control_seg.get_segment_numbers(
            segmented_property_category=codes.SCT.Tissue,
            segmented_property_type=codes.SCT.ConnectiveTissue,
            algorithm_type=SegmentAlgorithmTypeValues.AUTOMATIC
        )
        assert seg_nums == list(self._sm_control_seg.segment_numbers)

    def test_get_tracking_ids(self):
        desc1 = self._sm_control_seg.get_segment_description(1)

        tracking_id_tuples = self._sm_control_seg.get_tracking_ids()
        n_segs = self._sm_control_seg.number_of_segments
        assert len(tracking_id_tuples) == n_segs
        ids, uids = zip(*tracking_id_tuples)
        assert desc1.tracking_id in ids
        assert desc1.tracking_uid in uids

    def test_get_tracking_ids_with_filters(self):
        desc1 = self._sm_control_seg.get_segment_description(1)

        # All segments in this test image match these filters
        tracking_id_tuples = self._sm_control_seg.get_tracking_ids(
            segmented_property_category=codes.SCT.Tissue,
            segmented_property_type=codes.SCT.ConnectiveTissue,
            algorithm_type=SegmentAlgorithmTypeValues.AUTOMATIC
        )
        n_segs = self._sm_control_seg.number_of_segments
        assert len(tracking_id_tuples) == n_segs
        ids, uids = zip(*tracking_id_tuples)
        assert desc1.tracking_id in ids
        assert desc1.tracking_uid in uids

    def test_get_tracking_ids_with_filters_2(self):
        # No segments in this test image match these filters
        tracking_id_tuples = self._sm_control_seg.get_tracking_ids(
            segmented_property_category=codes.SCT.Tissue,
            segmented_property_type=codes.SCT.Lung,
        )
        assert len(tracking_id_tuples) == 0

    def test_get_pixels_by_source_frames(self):
        source_sop_uid = self._sm_control_seg.get_source_image_uids()[0][-1]

        source_frames_valid = [1, 2, 4, 5]
        pixels = self._sm_control_seg.get_pixels_by_source_frame(
            source_sop_instance_uid=source_sop_uid,
            source_frame_numbers=source_frames_valid
        )

        out_shape = (
            len(source_frames_valid),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns,
            self._sm_control_seg.number_of_segments
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_invalid_source_frames(self):
        source_sop_uid = self._sm_control_seg.get_source_image_uids()[0][-1]

        # (frame 3 has no segment)
        source_frames_invalid = [1, 3, 4, 5]
        with pytest.raises(ValueError):
            self._sm_control_seg.get_pixels_by_source_frame(
                source_sop_instance_uid=source_sop_uid,
                source_frame_numbers=source_frames_invalid
            )

    def test_get_pixels_by_invalid_source_frames_with_assert(self):
        source_sop_uid = self._sm_control_seg.get_source_image_uids()[0][-1]

        # (frame 3 has no segment)
        source_frames_invalid = [1, 3, 4, 5]
        pixels = self._sm_control_seg.get_pixels_by_source_frame(
            source_sop_instance_uid=source_sop_uid,
            source_frame_numbers=source_frames_invalid,
            assert_missing_frames_are_empty=True
        )

        out_shape = (
            len(source_frames_invalid),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns,
            self._sm_control_seg.number_of_segments
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_source_frames_with_segments(self):
        source_sop_uid = self._sm_control_seg.get_source_image_uids()[0][-1]

        source_frames_valid = [1, 2, 4, 5]
        segments_valid = [1, 20]
        pixels = self._sm_control_seg.get_pixels_by_source_frame(
            source_sop_instance_uid=source_sop_uid,
            source_frame_numbers=source_frames_valid,
            segment_numbers=segments_valid
        )

        out_shape = (
            len(source_frames_valid),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns,
            len(segments_valid)
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_source_frames_with_invalid_segments(self):
        source_sop_uid = self._sm_control_seg.get_source_image_uids()[0][-1]

        source_frames_valid = [1, 2, 4, 5]
        segments_invalid = [1, 21]  # 21 > 20
        with pytest.raises(ValueError):
            self._sm_control_seg.get_pixels_by_source_frame(
                source_sop_instance_uid=source_sop_uid,
                source_frame_numbers=source_frames_valid,
                segment_numbers=segments_invalid
            )

    def test_get_pixels_by_source_frames_combine(self):
        source_sop_uid = self._sm_control_seg.get_source_image_uids()[0][-1]

        source_frames_valid = [1, 2, 4, 5]
        # These segments match the above frames for this test image
        segments_valid = [6, 7, 8, 9]
        pixels = self._sm_control_seg.get_pixels_by_source_frame(
            source_sop_instance_uid=source_sop_uid,
            source_frame_numbers=source_frames_valid,
            segment_numbers=segments_valid,
            combine_segments=True
        )

        out_shape = (
            len(source_frames_valid),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns
        )
        assert pixels.shape == out_shape
        assert np.all(np.unique(pixels) == np.array([0] + segments_valid))

        pixels = self._sm_control_seg.get_pixels_by_source_frame(
            source_sop_instance_uid=source_sop_uid,
            source_frame_numbers=source_frames_valid,
            segment_numbers=segments_valid,
            combine_segments=True,
            relabel=True
        )
        assert pixels.shape == out_shape
        assert np.all(np.unique(pixels) == np.arange(len(segments_valid) + 1))

    def test_get_default_dimension_index_pointers(self):
        ptrs = self._sm_control_seg.get_default_dimension_index_pointers()
        assert len(ptrs) == 5

    def test_are_dimension_indices_unique(self):
        ptrs = self._sm_control_seg.get_default_dimension_index_pointers()
        assert self._sm_control_seg.are_dimension_indices_unique(ptrs)

        ptr_kws = [
            'ColumnPositionInTotalImagePixelMatrix',
            'RowPositionInTotalImagePixelMatrix'
        ]
        ptrs = [tag_for_keyword(kw) for kw in ptr_kws]
        assert self._sm_control_seg.are_dimension_indices_unique(ptrs)

        ptr_kws = [
            'XOffsetInSlideCoordinateSystem',
            'YOffsetInSlideCoordinateSystem'
        ]
        ptrs = [tag_for_keyword(kw) for kw in ptr_kws]
        assert self._sm_control_seg.are_dimension_indices_unique(ptrs)

        ptr_kws = [
            'ZOffsetInSlideCoordinateSystem'
        ]
        ptrs = [tag_for_keyword(kw) for kw in ptr_kws]
        assert not self._sm_control_seg.are_dimension_indices_unique(ptrs)

    def test_are_dimension_indices_unique_invalid_ptrs(self):
        ptr_kws = [
            'ImagePositionPatient'
        ]
        ptrs = [tag_for_keyword(kw) for kw in ptr_kws]
        with pytest.raises(KeyError):
            self._sm_control_seg.are_dimension_indices_unique(ptrs)

    def test_get_pixels_by_dimension_index_values(self):
        ind_values = [
            (1, 1, 5, 5, 1),
            (2, 1, 4, 5, 1),
            (3, 1, 3, 5, 1)
        ]
        pixels = self._sm_control_seg.get_pixels_by_dimension_index_values(
            dimension_index_values=ind_values,
        )

        out_shape = (
            len(ind_values),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns,
            self._sm_control_seg.number_of_segments
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_dimension_index_values_subset(self):
        ptr_kws = [
            'ColumnPositionInTotalImagePixelMatrix',
            'RowPositionInTotalImagePixelMatrix'
        ]
        ptrs = [tag_for_keyword(kw) for kw in ptr_kws]

        ind_values = [
            (1, 1),
            (2, 1),
            (3, 1)
        ]
        pixels = self._sm_control_seg.get_pixels_by_dimension_index_values(
            dimension_index_values=ind_values,
            dimension_index_pointers=ptrs
        )

        out_shape = (
            len(ind_values),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns,
            self._sm_control_seg.number_of_segments
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_dimension_index_values_missing(self):
        ind_values = [
            (1, 1, 4, 5, 1),
        ]
        with pytest.raises(RuntimeError):
            self._sm_control_seg.get_pixels_by_dimension_index_values(
                dimension_index_values=ind_values,
            )

        pixels = self._sm_control_seg.get_pixels_by_dimension_index_values(
            dimension_index_values=ind_values,
            assert_missing_frames_are_empty=True
        )

        out_shape = (
            len(ind_values),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns,
            self._sm_control_seg.number_of_segments
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_dimension_index_values_with_segments(self):
        ind_values = [
            (1, 1, 5, 5, 1),
            (2, 1, 4, 5, 1),
            (3, 1, 3, 5, 1)
        ]
        segments = [1, 6, 11]
        pixels = self._sm_control_seg.get_pixels_by_dimension_index_values(
            dimension_index_values=ind_values,
            segment_numbers=segments
        )

        out_shape = (
            len(ind_values),
            self._sm_control_seg.Rows,
            self._sm_control_seg.Columns,
            len(segments)
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_dimension_index_values_invalid(self):
        ind_values = [
            (1, 1, 5, 5, 1),
            (2, 1, 4, 5, 1),
            (3, 1, 3, 5, 1)
        ]
        ptrs = [tag_for_keyword('ImagePositionPatient')]

        # Invalid pointers
        with pytest.raises(KeyError):
            self._sm_control_seg.get_pixels_by_dimension_index_values(
                dimension_index_values=ind_values,
                dimension_index_pointers=ptrs
            )
        # Invalid values
        with pytest.raises(ValueError):
            self._sm_control_seg.get_pixels_by_dimension_index_values(
                dimension_index_values=[(-1, 1, 1, 1, 1)],
            )
        # Empty values
        with pytest.raises(ValueError):
            self._sm_control_seg.get_pixels_by_dimension_index_values(
                dimension_index_values=[],
            )
        # Empty pointers
        with pytest.raises(ValueError):
            self._sm_control_seg.get_pixels_by_dimension_index_values(
                dimension_index_values=ind_values,
                dimension_index_pointers=[]
            )
        # Empty segment numbers
        with pytest.raises(ValueError):
            self._sm_control_seg.get_pixels_by_dimension_index_values(
                dimension_index_values=ind_values,
                segment_numbers=[]
            )
        # Invalid segment numbers
        with pytest.raises(ValueError):
            self._sm_control_seg.get_pixels_by_dimension_index_values(
                dimension_index_values=ind_values,
                segment_numbers=[-1]
            )

    def test_get_pixels_by_source_instances(self):
        all_source_sop_uids = [
            tup[-1] for tup in self._ct_binary_seg.get_source_image_uids()
        ]
        source_sop_uids = all_source_sop_uids[1:3]

        pixels = self._ct_binary_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_binary_seg.Rows,
            self._ct_binary_seg.Columns,
            self._ct_binary_seg.number_of_segments
        )
        assert pixels.shape == out_shape

        pixels = self._ct_binary_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
            combine_segments=True
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_binary_seg.Rows,
            self._ct_binary_seg.Columns,
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_source_instances_with_segments(self):
        all_source_sop_uids = [
            tup[-1] for tup in self._ct_binary_seg.get_source_image_uids()
        ]
        source_sop_uids = all_source_sop_uids[1:3]
        segment_numbers = [1]

        pixels = self._ct_binary_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
            segment_numbers=segment_numbers
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_binary_seg.Rows,
            self._ct_binary_seg.Columns,
            len(segment_numbers)
        )
        assert pixels.shape == out_shape

    def test_get_pixels_by_source_instances_invalid(self):
        all_source_sop_uids = [
            tup[-1] for tup in self._ct_binary_seg.get_source_image_uids()
        ]
        source_sop_uids = all_source_sop_uids[1:3]

        # Empty SOP uids
        with pytest.raises(ValueError):
            self._ct_binary_seg.get_pixels_by_source_instance(
                source_sop_instance_uids=[],
            )
        # Empty SOP uids
        with pytest.raises(KeyError):
            self._ct_binary_seg.get_pixels_by_source_instance(
                source_sop_instance_uids=['1.2.3.4'],
            )
        # Empty segments
        with pytest.raises(ValueError):
            self._ct_binary_seg.get_pixels_by_source_instance(
                source_sop_instance_uids=source_sop_uids,
                segment_numbers=[]
            )
        # Invalid segments
        with pytest.raises(ValueError):
            self._ct_binary_seg.get_pixels_by_source_instance(
                source_sop_instance_uids=source_sop_uids,
                segment_numbers=[0]
            )

    def test_get_pixels_by_source_instances_binary_fractional(self):
        all_source_sop_uids = [
            tup[-1] for tup in
            self._ct_binary_fractional_seg.get_source_image_uids()
        ]
        source_sop_uids = all_source_sop_uids[1:3]

        pixels = self._ct_binary_fractional_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_binary_fractional_seg.Rows,
            self._ct_binary_fractional_seg.Columns,
            self._ct_binary_fractional_seg.number_of_segments
        )
        assert pixels.shape == out_shape
        assert np.all(np.unique(pixels) == np.array([0.0, 1.0]))

        pixels = self._ct_binary_fractional_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
            combine_segments=True
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_binary_fractional_seg.Rows,
            self._ct_binary_fractional_seg.Columns,
        )
        assert pixels.shape == out_shape
        assert np.all(np.unique(pixels) == np.array([0.0, 1.0]))

    def test_get_pixels_by_source_instances_true_fractional(self):
        all_source_sop_uids = [
            tup[-1] for tup in
            self._ct_true_fractional_seg.get_source_image_uids()
        ]
        source_sop_uids = all_source_sop_uids[1:3]

        pixels = self._ct_true_fractional_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_true_fractional_seg.Rows,
            self._ct_true_fractional_seg.Columns,
            self._ct_true_fractional_seg.number_of_segments
        )
        assert pixels.shape == out_shape
        assert pixels.max() <= 1.0
        assert pixels.min() >= 0.0
        assert len(np.unique(pixels)) > 2

        # Without fractional rescaling
        pixels = self._ct_true_fractional_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
            rescale_fractional=False
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_true_fractional_seg.Rows,
            self._ct_true_fractional_seg.Columns,
            self._ct_true_fractional_seg.number_of_segments
        )
        assert pixels.shape == out_shape
        assert pixels.max() == 128
        assert len(np.unique(pixels)) > 2

        # Can't combine segments with a true fractional segmentation
        with pytest.raises(ValueError):
            self._ct_true_fractional_seg.get_pixels_by_source_instance(
                source_sop_instance_uids=source_sop_uids,
                combine_segments=True
            )

    def test_get_pixels_by_source_instances_overlap(self):
        all_source_sop_uids = [
            tup[-1] for tup in
            self._ct_binary_overlap_seg.get_source_image_uids()
        ]
        source_sop_uids = all_source_sop_uids

        pixels = self._ct_binary_overlap_seg.get_pixels_by_source_instance(
            source_sop_instance_uids=source_sop_uids,
        )

        out_shape = (
            len(source_sop_uids),
            self._ct_binary_overlap_seg.Rows,
            self._ct_binary_overlap_seg.Columns,
            self._ct_binary_overlap_seg.number_of_segments
        )
        assert pixels.shape == out_shape

        with pytest.raises(RuntimeError):
            self._ct_binary_overlap_seg.get_pixels_by_source_instance(
                source_sop_instance_uids=source_sop_uids,
                combine_segments=True
            )

class TestSegUtilities(unittest.TestCase):

    def setUp(self):
        super().setUp()
        file_path = Path(__file__)
        data_dir = file_path.parent.parent.joinpath('data')
        self._ct_image = dcmread(
            str(data_dir.joinpath('test_files', 'ct_image.dcm'))
        )
        self._sm_image = dcmread(
            str(data_dir.joinpath('test_files', 'sm_image.dcm'))
        )

    def test_iter_segments_ct_single_frame(self):
        seg_dataset = dcmread(
            'data/test_files/seg_image_ct_binary_single_frame.dcm'
        )

        generator = iter_segments(seg_dataset)
        items = list(generator)
        assert len(items) == 1
        item_segment_1 = items[0]
        assert item_segment_1[0].shape == (1, 128, 128)
        seg_id_item_1 = item_segment_1[1][0].SegmentIdentificationSequence[0]
        assert seg_id_item_1.ReferencedSegmentNumber == 1
        assert item_segment_1[2].SegmentNumber == 1

    def test_iter_segments_ct_single_frame_2_segments(self):
        image_dataset = self._ct_image
        mask = np.zeros(
            self._ct_image.pixel_array.shape,
            dtype=np.uint8
        )
        mask[1:5, 10:15] = 1
        mask[5:7, 1:5] = 2
        algorithm_identification = AlgorithmIdentificationSequence(
            name='test',
            version='v1.0',
            family=codes.cid7162.ArtificialIntelligence
        )
        segment_descriptions = [
            SegmentDescription(
                segment_number=1,
                segment_label='tumor tissue',
                segmented_property_category=codes.cid7150.Tissue,
                segmented_property_type=codes.SCT.Neoplasm,
                algorithm_type=SegmentAlgorithmTypeValues.AUTOMATIC,
                algorithm_identification=algorithm_identification,
                tracking_uid=UID(),
                tracking_id='first segment'
            ),
            SegmentDescription(
                segment_number=2,
                segment_label='connective tissue',
                segmented_property_category=codes.cid7150.Tissue,
                segmented_property_type=codes.cid7166.ConnectiveTissue,
                algorithm_type=SegmentAlgorithmTypeValues.AUTOMATIC,
                algorithm_identification=algorithm_identification,
                tracking_uid=UID(),
                tracking_id='second segment'
            ),
        ]

        seg_dataset = Segmentation(
            source_images=[image_dataset],
            pixel_array=mask,
            segmentation_type=SegmentationTypeValues.BINARY,
            segment_descriptions=segment_descriptions,
            series_instance_uid=UID(),
            series_number=2,
            sop_instance_uid=UID(),
            instance_number=1,
            manufacturer='Manufacturer',
            manufacturer_model_name='Manufacturer Model',
            software_versions='v1',
            device_serial_number='Device XYZ'
        )

        generator = iter_segments(seg_dataset)
        items = list(generator)
        assert len(items) == 2
        item_segment_1 = items[0]
        assert np.squeeze(item_segment_1[0]).shape == mask.shape
        seg_id_item_1 = item_segment_1[1][0].SegmentIdentificationSequence[0]
        assert seg_id_item_1.ReferencedSegmentNumber == 1
        assert item_segment_1[2].SegmentNumber == 1
        item_segment_2 = items[1]
        assert np.squeeze(item_segment_2[0]).shape == mask.shape
        seg_id_item_2 = item_segment_2[1][0].SegmentIdentificationSequence[0]
        assert seg_id_item_2.ReferencedSegmentNumber == 2
        assert item_segment_2[2].SegmentNumber == 2

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