def __init__(self,
patch_pattern,
dataset_origin,
subtypes=None,
is_binary=None):
self.is_binary = is_binary
self.patch_pattern = utils.create_patch_pattern(patch_pattern)
self.CategoryEnum = utils.create_category_enum(is_binary, subtypes)
self.dataset_origin = dataset_origin
def test_create_patch_id_for_tcga(self):
path = '/path/to/patch/TCGA-A5-A0GH-01Z-00-DX1.22005F4A-0E77-4FCB-B57A-9944866263AE/Necrosis/41984_45056_d_256.png'
patch_pattern = utils.create_patch_pattern(
'slide/annotation')
patch_id = utils.create_patch_id(path, patch_pattern)
assert patch_id == 'TCGA-A5-A0GH-01Z-00-DX1.22005F4A-0E77-4FCB-B57A-9944866263AE/Necrosis/41984_45056_d_256'
slide_id = utils.get_slide_by_patch_id(patch_id, patch_pattern)
assert slide_id == 'TCGA-A5-A0GH-01Z-00-DX1.22005F4A-0E77-4FCB-B57A-9944866263AE'
patient_id = utils.get_patient_by_slide_id(slide_id, dataset_origin='tcga')
assert patient_id == 'TCGA-A5-A0GH'
CategoryEnum = utils.create_category_enum(True)
label = utils.get_label_by_patch_id(patch_id, patch_pattern, CategoryEnum,
is_binary=True)
assert label.name == 'Normal'
def test_group_paths_1(self):
patch_pattern = 'annotation/subtype/slide/patch_size/magnification'
patch_pattern = utils.create_patch_pattern(patch_pattern)
patch_ids = [
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/20/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/20/2_2.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/10/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/256/20/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/256/10/0_0.png',
'/path/to/rootdir/Tumor/POLE/VOA-1000B/256/10/0_0.png']
actual = utils.group_paths(patch_ids, patch_pattern, include=['patch_size'])
# print(actual)
expected = {
'512/0_0': [
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/20/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/10/0_0.png'
],
'512/2_2': [
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/20/2_2.png',
],
'256/0_0': [
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/256/20/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/256/10/0_0.png',
'/path/to/rootdir/Tumor/POLE/VOA-1000B/256/10/0_0.png'
]
}
list(map(lambda v: v.sort(), actual.values()))
list(map(lambda v: v.sort(), expected.values()))
assert actual == expected
# return
actual = utils.group_paths(patch_ids, patch_pattern,
exclude=['patch_size', 'magnification'])
expected = {
'Stroma/MMRd/VOA-1000A/0_0': [
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/20/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/10/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/256/20/0_0.png',
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/256/10/0_0.png'
],
'Stroma/MMRd/VOA-1000A/2_2': [
'/path/to/rootdir/Stroma/MMRd/VOA-1000A/512/20/2_2.png'
],
'Tumor/POLE/VOA-1000B/0_0': [
'/path/to/rootdir/Tumor/POLE/VOA-1000B/256/10/0_0.png'
]
}
list(map(lambda v: v.sort(), actual.values()))
list(map(lambda v: v.sort(), expected.values()))
assert actual == expected
def test_create_subtype_patient_slide_patch_dict(self):
tumor__VOA_1234__VOA_1234A = [
'/path/to/patch/Tumor/CC/VOA-1234A/0_0.png',
'/path/to/patch/Tumor/CC/VOA-1234A/1_0.png',
'/path/to/patch/Tumor/CC/VOA-1234A/2_0.png'
]
normal__VOA_1234__VOA_1234A = [
'/path/to/patch/Stroma/CC/VOA-1234A/3_0.png',
'/path/to/patch/Necrosis/CC/VOA-1234A/4_0.png',
'/path/to/patch/Other/CC/VOA-1234A/5_0.png'
]
tumor__VOA_1234__VOA_1234B = [
'/path/to/patch/Tumor/CC/VOA-1234B/6_0.png',
'/path/to/patch/Tumor/CC/VOA-1234B/7_0.png',
'/path/to/patch/Tumor/CC/VOA-1234B/8_0.png'
]
normal__VOA_1234__VOA_1234B = [
'/path/to/patch/Stroma/CC/VOA-1234B/9_0.png',
'/path/to/patch/Necrosis/CC/VOA-1234B/10_0.png',
'/path/to/patch/Other/CC/VOA-1234B/11_0.png'
]
tumor__VOA_5678__VOA_5678A = [
'/path/to/patch/Tumor/CC/VOA-5678A/6_0.png',
'/path/to/patch/Tumor/CC/VOA-5678A/7_0.png',
'/path/to/patch/Tumor/CC/VOA-5678A/8_0.png'
]
patch_paths = []
patch_paths.extend(tumor__VOA_1234__VOA_1234A)
patch_paths.extend(tumor__VOA_1234__VOA_1234B)
patch_paths.extend(normal__VOA_1234__VOA_1234A)
patch_paths.extend(tumor__VOA_5678__VOA_5678A)
patch_paths.extend(normal__VOA_1234__VOA_1234B)
random.shuffle(patch_paths)
patch_pattern = utils.create_patch_pattern(
'annotation/subtype/slide')
CategoryEnum = utils.create_category_enum(True)
subtype_patient_slide_patch_dict = utils.create_subtype_patient_slide_patch_dict(
patch_paths, patch_pattern, CategoryEnum, is_binary=True)
assert set(tumor__VOA_1234__VOA_1234A) == \
set(subtype_patient_slide_patch_dict['Tumor']['1234']['VOA-1234A'])
assert set(normal__VOA_1234__VOA_1234A) == \
set(subtype_patient_slide_patch_dict['Normal']['1234']['VOA-1234A'])
assert set(tumor__VOA_1234__VOA_1234B) == \
set(subtype_patient_slide_patch_dict['Tumor']['1234']['VOA-1234B'])
assert set(normal__VOA_1234__VOA_1234B) == \
set(subtype_patient_slide_patch_dict['Normal']['1234']['VOA-1234B'])
assert set(tumor__VOA_5678__VOA_5678A) == \
set(subtype_patient_slide_patch_dict['Tumor']['5678']['VOA-5678A'])
def test_create_patch_id_2(self):
path = '/path/to/dir/to/patch/Necrosis/VOA-1234A/1234_5687.png'
patch_pattern = utils.create_patch_pattern(
'annotation/slide')
patch_id = utils.create_patch_id(path, patch_pattern)
assert patch_id == 'Necrosis/VOA-1234A/1234_5687'
slide_id = utils.get_slide_by_patch_id(patch_id, patch_pattern)
assert slide_id == 'VOA-1234A'
patient_id = utils.get_patient_by_slide_id(slide_id, dataset_origin='ovcare')
assert patient_id == '1234'
CategoryEnum = utils.create_category_enum(True)
label = utils.get_label_by_patch_id(patch_id, patch_pattern, CategoryEnum,
is_binary=True)
assert label.name == 'Normal'
def test_create_subtype_patient_slide_patch_dict_for_tcga(self):
tumor__TCGA_PG_A6IB__DX4 = [
'/path/to/patch/TCGA-PG-A6IB-01Z-00-DX4.631A44B6-43E0-4481-AF1F-3EB484784672/Tumor/1_0.png',
'/path/to/patch/TCGA-PG-A6IB-01Z-00-DX4.631A44B6-43E0-4481-AF1F-3EB484784672/Tumor/2_0.png'
]
tumor__TCGA_PG_A6IB__DX1 = [
'/path/to/patch/TCGA-PG-A6IB-01Z-00-DX1.575AC6BD-6ABA-468D-9A46-DC61BD92269C/Tumor/3_0.png'
]
normal__TCGA_PG_A6IB__DX4 = [
'/path/to/patch/TCGA-PG-A6IB-01Z-00-DX4.631A44B6-43E0-4481-AF1F-3EB484784672/Stroma/2_0.png',
'/path/to/patch/TCGA-PG-A6IB-01Z-00-DX4.631A44B6-43E0-4481-AF1F-3EB484784672/Stroma/3_0.png'
]
tumor__TCGA_AX_A1CC__DX2 = [
'/path/to/patch/TCGA-AX-A1CC-01Z-00-DX2.9DBD4FAD-5E16-450D-8B8F-CCDD34A211F1/Tumor/1_0.png',
'/path/to/patch/TCGA-AX-A1CC-01Z-00-DX2.9DBD4FAD-5E16-450D-8B8F-CCDD34A211F1/Tumor/2_0.png'
]
normal__TCGA_AX_A1CC__DX2 = [
'/path/to/patch/TCGA-AX-A1CC-01Z-00-DX2.9DBD4FAD-5E16-450D-8B8F-CCDD34A211F1/Necrosis/2_0.png'
]
patch_paths = []
patch_paths.extend(tumor__TCGA_PG_A6IB__DX4)
patch_paths.extend(tumor__TCGA_PG_A6IB__DX1)
patch_paths.extend(normal__TCGA_PG_A6IB__DX4)
patch_paths.extend(tumor__TCGA_AX_A1CC__DX2)
patch_paths.extend(normal__TCGA_AX_A1CC__DX2)
random.shuffle(patch_paths)
patch_pattern = utils.create_patch_pattern(
'slide/annotation')
CategoryEnum = utils.create_category_enum(True)
subtype_patient_slide_patch_dict = utils.create_subtype_patient_slide_patch_dict(
patch_paths, patch_pattern, CategoryEnum,
is_binary=True, dataset_origin='tcga')
assert set(tumor__TCGA_PG_A6IB__DX4) == \
set(subtype_patient_slide_patch_dict['Tumor']['TCGA-PG-A6IB']['TCGA-PG-A6IB-01Z-00-DX4.631A44B6-43E0-4481-AF1F-3EB484784672'])
assert set(tumor__TCGA_PG_A6IB__DX1) == \
set(subtype_patient_slide_patch_dict['Tumor']['TCGA-PG-A6IB']['TCGA-PG-A6IB-01Z-00-DX1.575AC6BD-6ABA-468D-9A46-DC61BD92269C'])
assert set(normal__TCGA_PG_A6IB__DX4) == \
set(subtype_patient_slide_patch_dict['Normal']['TCGA-PG-A6IB']['TCGA-PG-A6IB-01Z-00-DX4.631A44B6-43E0-4481-AF1F-3EB484784672'])
assert set(tumor__TCGA_AX_A1CC__DX2) == \
set(subtype_patient_slide_patch_dict['Tumor']['TCGA-AX-A1CC']['TCGA-AX-A1CC-01Z-00-DX2.9DBD4FAD-5E16-450D-8B8F-CCDD34A211F1'])
assert set(normal__TCGA_AX_A1CC__DX2) == \
set(subtype_patient_slide_patch_dict['Normal']['TCGA-AX-A1CC']['TCGA-AX-A1CC-01Z-00-DX2.9DBD4FAD-5E16-450D-8B8F-CCDD34A211F1'])
def test_create_patch_id_for_nonmultiscale(self):
path = '/path/to/patch/Stroma/LGSC/VOA-1234A/10/1234_5687.png'
patch_pattern = utils.create_patch_pattern(
'annotation/subtype/slide/magnification')
patch_id = utils.create_patch_id(path, patch_pattern)
assert patch_id == 'Stroma/LGSC/VOA-1234A/10/1234_5687'
slide_id = utils.get_slide_by_patch_id(patch_id, patch_pattern)
assert slide_id == 'VOA-1234A'
patient_id = utils.get_patient_by_slide_id(slide_id, dataset_origin='ovcare')
assert patient_id == '1234'
subtypes={'CC': 0, 'EC': 1, 'HGSC': 2, 'LGSC': 3, 'MC': 4}
CategoryEnum = utils.create_category_enum(False,
subtypes=subtypes)
label = utils.get_label_by_patch_id(patch_id, patch_pattern, CategoryEnum)
assert label.name == 'LGSC'
CategoryEnum = utils.create_category_enum(True)
label = utils.get_label_by_patch_id(patch_id, patch_pattern, CategoryEnum,
is_binary=True)
assert label.name == 'Normal'
def test_count_subtype(self):
input_src = [
'/path/to/patch/Tumor/CC/VOA-1234A/0_0.png',
'/path/to/patch/Tumor/CC/VOA-1234A/1_0.png',
'/path/to/patch/Tumor/EC/VOA-1234A/2_0.png',
'/path/to/patch/Stroma/EC/VOA-5678A/3_0.png',
'/path/to/patch/Necrosis/HGSC/VOA-5678A/4_0.png',
'/path/to/patch/Other/HGSC/VOA-5678A/5_0.png',
'/path/to/patch/MucinousBorderlineTumor/MC/VOA-2000C/6_0.png',
]
subtypes={'CC': 0, 'EC': 1, 'HGSC': 2, 'LGSC': 3, 'MC': 4}
random.shuffle(input_src)
patch_pattern = utils.create_patch_pattern(
'annotation/subtype/slide')
CategoryEnum = utils.create_category_enum(True,
subtypes=subtypes)
count = utils.count_subtype(input_src, patch_pattern, CategoryEnum,
is_binary=True)
np.testing.assert_array_equal(count, np.array([4,3]))
CategoryEnum = utils.create_category_enum(False,
subtypes=subtypes)
count = utils.count_subtype(input_src, patch_pattern, CategoryEnum,
is_binary=False)
np.testing.assert_array_equal(count, np.array([2,2,2,0,1]))