def test_simple_mask(self):
mask_array = np.zeros((10, 20, 20), dtype=np.uint8)
mask_array[3:7, 6:14, 6:14] = 1
prop = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.NO,
max_holes_size=0,
save_components=False,
clip_to_mask=False,
)
new_mask = calculate_mask(prop, mask_array, None, (1, 1, 1))
assert np.all(new_mask == mask_array)
mask_array2 = np.copy(mask_array)
mask_array2[4:6, 8:12, 8:12] = 2
new_mask = calculate_mask(prop, mask_array2, None, (1, 1, 1))
assert np.all(new_mask == mask_array)
prop2 = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.NO,
max_holes_size=0,
save_components=True,
clip_to_mask=False,
)
new_mask = calculate_mask(prop2, mask_array2, None, (1, 1, 1))
assert np.all(new_mask == mask_array2)
def test_fill_holes_components(self):
mask_base_array = np.zeros((20, 30, 30), dtype=np.uint8)
mask_base_array[4:16, 6:15, 6:24] = 1
mask_base_array[4:16, 15:24, 6:24] = 2
res_mask1 = (mask_base_array > 0).astype(np.uint8)
res_mask2 = np.copy(mask_base_array)
mask_base_array[6:14, 8:12, 8:22] = 0
mask_base_array[6:14, 18:22, 8:22] = 0
prop1 = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.R3D,
max_holes_size=0,
save_components=False,
clip_to_mask=False,
)
prop2 = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.R3D,
max_holes_size=0,
save_components=True,
clip_to_mask=False,
)
new_mask = calculate_mask(prop1, mask_base_array, None, (1, 1, 1))
assert np.all(new_mask == res_mask1)
new_mask = calculate_mask(prop2, mask_base_array, None, (1, 1, 1))
assert np.all(new_mask == res_mask2)
mask_base_array[6:14, 14:16, 8:22] = 0
res_mask2[6:14, 14:16, 8:22] = 0
new_mask = calculate_mask(prop1, mask_base_array, None, (1, 1, 1))
assert np.all(new_mask == res_mask1)
new_mask = calculate_mask(prop2, mask_base_array, None, (1, 1, 1))
assert np.all(new_mask == res_mask2)
def test_fill_holes(self):
mask_base_array = np.zeros((1, 20, 30, 30), dtype=np.uint8)
mask_base_array[:, 4:16, 8:22, 8:22] = 1
mask1_array = np.copy(mask_base_array)
mask1_array[:, 4:16, 10:15, 10:15] = 0
prop = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.R2D,
max_holes_size=0,
save_components=False,
clip_to_mask=False,
)
new_mask = calculate_mask(prop, mask1_array, None, (1, 1, 1))
assert np.all(mask_base_array == new_mask)
prop = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.R3D,
max_holes_size=0,
save_components=False,
clip_to_mask=False,
)
new_mask = calculate_mask(prop, mask1_array, None, (1, 1, 1))
assert np.all(mask1_array == new_mask)
mask2_array = np.copy(mask1_array)
mask2_array[:, 5:15, 10:15, 17:20] = 0
new_mask = calculate_mask(prop, mask2_array, None, (1, 1, 1))
assert np.all(mask1_array == new_mask)
def test_fill_holes_size(self):
mask_base_array = np.zeros((1, 20, 20, 40), dtype=np.uint8)
mask_base_array[0, 2:18, 2:18, 4:36] = 1
mask_base_array[0, 4:16, 4:16, 6:18] = 0
mask1_array = np.copy(mask_base_array)
mask1_array[0, 6:14, 6:14, 24:32] = 0
prop1 = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.R2D,
max_holes_size=70,
save_components=False,
clip_to_mask=False,
)
prop2 = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.R3D,
max_holes_size=530,
save_components=True,
clip_to_mask=False,
)
new_mask = calculate_mask(prop1, mask_base_array, None, (1, 1, 1))
assert np.all(new_mask == mask_base_array)
new_mask = calculate_mask(prop2, mask_base_array, None, (1, 1, 1))
assert np.all(new_mask == mask_base_array)
def test_reversed_mask(self):
mask_base_array = np.zeros((30, 30, 30), dtype=np.uint8)
mask_base_array[10:20, 10:20, 10:20] = 1
mask2_array = np.copy(mask_base_array)
mask2_array[13:17, 13:17, 13:17] = 0
prop1 = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=-0,
fill_holes=RadiusType.NO,
max_holes_size=0,
save_components=False,
clip_to_mask=False,
reversed_mask=False,
)
prop2 = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=-0,
fill_holes=RadiusType.NO,
max_holes_size=0,
save_components=False,
clip_to_mask=False,
reversed_mask=True,
)
new_mask1 = calculate_mask(prop1, mask_base_array, mask2_array,
(1, 1, 1))
new_mask2 = calculate_mask(prop2, mask_base_array, mask2_array,
(1, 1, 1))
assert np.all(new_mask1 == mask_base_array)
assert np.all(new_mask2 == (mask_base_array == 0))
def test_single(self):
mask = np.zeros((10, 10, 10), dtype=np.uint8)
mask[2:8, 2:8, 2:8] = 1
mask2 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.NO, -1, False, True),
mask, None, (1, 1, 1))
assert np.all(mask2 == mask)
mask3 = np.copy(mask)
mask3[mask > 0] = 2
mask2 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.NO, -1, False, True),
mask, None, (1, 1, 1))
assert np.all(mask2 == mask)
def test_dilate(self):
mask = np.zeros((1, 10, 10, 10), dtype=np.uint8)
mask[0, 2:8, 2:8, 2:8] = 1
mask2 = calculate_mask(
MaskProperty(RadiusType.R3D, -1, RadiusType.NO, -1, False, True),
mask, None, (1, 1, 1))
mask3 = np.zeros((1, 10, 10, 10), dtype=np.uint8)
mask3[0, 3:7, 3:7, 3:7] = 1
assert np.all(mask2 == mask3)
mask2 = calculate_mask(
MaskProperty(RadiusType.R2D, -1, RadiusType.NO, -1, False, True),
mask, None, (1, 1, 1))
mask3 = np.zeros((1, 10, 10, 10), dtype=np.uint8)
mask3[0, 2:8, 3:7, 3:7] = 1
assert np.all(mask2 == mask3)
def test_mask_property_combinations(self, dilate, radius, fill_holes,
max_holes_size, save_components,
clip_to_mask, reversed_mask, old_mask):
mask = np.zeros((1, 6, 6, 15), dtype=np.uint8)
im = Image(data=mask.copy(),
image_spacing=(3, 1, 1),
file_path="",
axes_order="TZYX")
mask[:, 1:-1, 1:-1, 2:5] = 1
mask[:, 2:-2, 2:-2, 3:4] = 0
mask[:, 1:-1, 1:-1, 6:9] = 2
mask[:, 2:-2, 2:-2, 7:8] = 0
mask[:, 1:-1, 1:-1, 10:13] = 3
mask[:, 2:-2, 2:-2, 11:12] = 0
mask = im.fit_mask_to_image(mask)
assert np.all(np.unique(mask.flat) == [0, 1, 2, 3])
_old_mask = np.zeros(mask.shape,
dtype=mask.dtype) if old_mask else None
mp = MaskProperty(
dilate=dilate,
dilate_radius=radius,
fill_holes=fill_holes,
max_holes_size=max_holes_size,
save_components=save_components,
clip_to_mask=clip_to_mask,
reversed_mask=reversed_mask,
)
mask1 = calculate_mask(mp,
mask,
_old_mask,
im.spacing,
time_axis=im.time_pos)
assert mask1.shape == mask.shape
def test_save_component_fill_holes_problematic(self):
mask = np.zeros((12, 12, 12), dtype=np.uint8)
mask[2:7, 2:-2, 2:-2] = 3
mask[7:-2, 2:-2, 2:-2] = 2
mask[4:-4, 4:-4, 4:-4] = 1
mask2 = np.copy(mask)
mask2[5, 5, 5] = 0
mask2[3, 3, 3] = 0
mask1 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.R2D, -1, True, True),
mask2, None, (1, 1, 1))
assert np.all(mask == mask1)
mask1 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.R3D, -1, True, True),
mask2, None, (1, 1, 1))
assert np.all(mask == mask1)
def calculate_pipeline(image: Image, mask: typing.Optional[np.ndarray],
pipeline: SegmentationPipeline, report_fun):
history = []
report_fun("max", 2 * len(pipeline.mask_history) + 1)
for i, el in enumerate(pipeline.mask_history):
result, _ = calculate_segmentation_step(el.segmentation, image, mask)
segmentation = image.fit_array_to_image(result.roi)
report_fun("step", 2 * i + 1)
new_mask = calculate_mask(
mask_description=el.mask_property,
segmentation=segmentation,
old_mask=mask,
spacing=image.spacing,
time_axis=image.time_pos,
)
segmentation_parameters = {
"algorithm_name": el.segmentation.name,
"values": el.segmentation.values
}
history.append(
HistoryElement.create(segmentation, mask, segmentation_parameters,
el.mask_property))
report_fun("step", 2 * i + 2)
mask = image.fit_array_to_image(new_mask)
result, text = calculate_segmentation_step(pipeline.segmentation, image,
mask)
report_fun("step", 2 * len(pipeline.mask_history) + 1)
return PipelineResult(result.roi, result.additional_layers, mask, history,
text)
def step_mask_create(self, operation: MaskCreate,
children: List[CalculationTree]):
"""
Create mask from current segmentation state using definition
:param MaskCreate operation: mask create description.
:param List[CalculationTree] children: list of nodes to iterate over after perform segmentation
"""
mask = calculate_mask(
mask_description=operation.mask_property,
segmentation=self.segmentation,
old_mask=self.mask,
spacing=self.image.spacing,
time_axis=self.image.time_pos,
)
if operation.name in self.reused_mask:
self.mask_dict[operation.name] = mask
history_element = HistoryElement.create(
self.segmentation,
self.mask,
self.algorithm_parameters,
operation.mask_property,
)
backup = self.mask, self.history
self.mask = mask
self.history.append(history_element)
self.iterate_over(children)
self.mask, self.history = backup
def test_fil_holes_2d(self):
mask = np.zeros((10, 10, 10), dtype=np.uint8)
mask[2:8, 2:8, 2:8] = 1
mask2 = np.copy(mask)
mask2[:, 4:6, 4:6] = 0
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.R2D, -1, False, True),
mask2, None, (1, 1, 1))
assert np.all(mask3 == mask)
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.R2D, 3, False, True),
mask2, None, (1, 1, 1))
assert np.all(mask3 == mask2)
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.R2D, 4, False, True),
mask2, None, (1, 1, 1))
assert np.all(mask3 == mask)
def test_dilate_spacing_positive(self):
mask_base_array = np.zeros((1, 30, 30, 30), dtype=np.uint8)
mask_base_array[:, 10:20, 10:20, 10:20] = 1
prop1 = MaskProperty(
dilate=RadiusType.R3D,
dilate_radius=1,
fill_holes=RadiusType.NO,
max_holes_size=70,
save_components=False,
clip_to_mask=False,
)
prop2 = MaskProperty(
dilate=RadiusType.R3D,
dilate_radius=2,
fill_holes=RadiusType.NO,
max_holes_size=70,
save_components=False,
clip_to_mask=False,
)
prop3 = MaskProperty(
dilate=RadiusType.R3D,
dilate_radius=3,
fill_holes=RadiusType.NO,
max_holes_size=70,
save_components=False,
clip_to_mask=False,
)
res_array1 = np.zeros((30, 30, 30), dtype=np.uint8)
res_array1[10:20, 9:21, 9:21] = 1
new_mask = calculate_mask(prop1, mask_base_array, None, (3, 1, 1))
assert np.all(new_mask[0] == res_array1)
res_array2 = np.zeros((30, 30, 30), dtype=np.uint8)
res_array2[10:20, 8:22, 8:22] = 1
res_array2[(9, 20), 9:21, 9:21] = 1
res_array2[:, (8, 21, 8, 21), (8, 8, 21, 21)] = 0
new_mask = calculate_mask(prop2, mask_base_array, None, (3, 1, 1))
assert np.all(new_mask[0] == res_array2)
res_array3 = np.zeros((30, 30, 30), dtype=np.uint8)
res_array3[(9, 20), 8:22, 9:21] = 1
res_array3[(9, 9, 20, 20), 9:21, (8, 21, 8, 21)] = 1
res_array3[10:20, 7:23, 9:21] = 1
res_array3[10:20, 8:22, (8, 21)] = 1
res_array3[10:20, 9:21, (7, 22)] = 1
new_mask = calculate_mask(prop3, mask_base_array, None, (3, 1, 1))
assert np.all(new_mask == res_array3)
def test_fil_holes_3d_torus(self):
mask = np.zeros((1, 10, 10, 10), dtype=np.uint8)
mask[0, 2:8, 2:8, 2:8] = 1
mask[0, :, 4:6, 4:6] = 0
mask2 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.R3D, -1, False, True),
mask, None, (1, 1, 1))
assert np.all(mask2 == mask)
def test_reverse(self):
mask = np.zeros((10, 10, 10), dtype=np.uint8)
mask[3:7, 3:7, 3:7] = 1
mask2 = np.ones((10, 10, 10), dtype=np.uint8)
mask2[mask > 0] = 0
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.NO, -1, False, True,
True), mask, None, (1, 1, 1))
assert np.all(mask3 == mask2)
def test_chose_components(self):
mask = np.zeros((12, 12, 12), dtype=np.uint8)
mask[2:7, 2:-2, 2:-2] = 3
mask[7:-2, 2:-2, 2:-2] = 2
mask[4:-4, 4:-4, 4:-4] = 1
mask1 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.R2D, -1, True, True),
mask, None, (1, 1, 1), [1, 3])
assert np.all(np.unique(mask1) == [0, 1, 3])
def test_save_components(self):
mask = np.zeros((10, 10, 10), dtype=np.uint8)
mask[2:8, 2:8, 2:8] = 1
mask2 = np.copy(mask)
mask2[2:8, 4:6, 4:6] = 2
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.NO, -1, False, True),
mask2, None, (1, 1, 1))
assert np.all(mask3 == mask)
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.NO, -1, True, True),
mask2, None, (1, 1, 1))
assert np.all(mask3 == mask2)
mask4 = np.copy(mask2)
mask4[mask4 == 2] = 3
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.NO, -1, True, True),
mask4, None, (1, 1, 1))
assert np.all(mask3 == mask4)
def test_clip(self):
mask = np.zeros((10, 10, 10), dtype=np.uint8)
mask[3:7, 3:7, 3:7] = 1
mask2 = calculate_mask(
MaskProperty(RadiusType.R3D, 1, RadiusType.NO, -1, False, True),
mask, mask, (1, 1, 1))
assert np.all(mask == mask2)
mask2[:, 4:6, 4:6] = 0
mask3 = calculate_mask(
MaskProperty(RadiusType.R3D, 1, RadiusType.NO, -1, False, True),
mask, mask2, (1, 1, 1))
assert np.all(mask3 == mask2)
mask2[:] = 0
mask2[4:6, 4:6, 4:6] = 1
mask3 = calculate_mask(
MaskProperty(RadiusType.NO, 0, RadiusType.NO, -1, False, True,
True), mask2, mask, (1, 1, 1))
mask[mask2 == 1] = 0
assert np.all(mask3 == mask)
def test_pipeline_manual(image, algorithm_parameters, mask_property):
algorithm = analysis_algorithm_dict[
algorithm_parameters["algorithm_name"]]()
algorithm.set_image(image)
algorithm.set_parameters(**algorithm_parameters["values"])
result = algorithm.calculation_run(lambda x, y: None)
mask = calculate_mask(mask_property, result.roi, None, image.spacing)
algorithm_parameters["values"]["channel"] = 1
algorithm.set_parameters(**algorithm_parameters["values"])
algorithm.set_mask(mask)
result2 = algorithm.calculation_run(lambda x, y: None)
assert np.max(result2.roi) == 2
def test_time_axis(self, time):
mask = np.zeros((time, 6, 6, 6), dtype=np.uint8)
mask[:, 1:-1, 1:-1, 2:5] = 1
mask[:, 2:-2, 2:-2, 3:4] = 0
mp = MaskProperty(
dilate=RadiusType.NO,
dilate_radius=0,
fill_holes=RadiusType.NO,
max_holes_size=-1,
save_components=False,
clip_to_mask=False,
)
mask1 = calculate_mask(mp, mask, None, (1, 1, 1))
assert mask1.shape == mask.shape
def test_dilate_spacing_negative(self, radius):
mask_base_array = np.zeros((1, 30, 30, 30), dtype=np.uint8)
mask_base_array[:, 10:20, 5:25, 5:25] = 1
res_array1 = np.zeros((1, 30, 30, 30), dtype=np.uint8)
s = slice(10, 20) if radius == -1 else slice(11, 19)
res_array1[:, s, 5 - radius:25 + radius, 5 - radius:25 + radius] = 1
prop1 = MaskProperty(
dilate=RadiusType.R3D,
dilate_radius=radius,
fill_holes=RadiusType.NO,
max_holes_size=70,
save_components=False,
clip_to_mask=False,
)
new_mask = calculate_mask(prop1, mask_base_array, None, (3, 1, 1))
assert np.all(new_mask == res_array1)
def calculate_mask_from_project(
mask_description: MaskProperty, project: ProjectInfoBase, components: Optional[List[int]] = None
) -> np.ndarray:
"""
Function for calculate mask base on MaskProperty.
This function calls :py:func:`calculate_mask` with arguments from project.
:param MaskProperty mask_description: information how calculate mask
:param ProjectInfoBase project: project with information about segmentation
:param Optional[List[int]] components: If present inform which components
should be used when calculation mask, otherwise use all.
:return: new mask
:rtype: np.ndarray
"""
try:
time_axis = project.image.time_pos
except AttributeError:
time_axis = None
return calculate_mask(
mask_description, project.roi_info.roi, project.mask, project.image.spacing, components, time_axis
)
def create_mask(self):
if self.roi_select.value is None:
return
layer_name = self.name.text()
self.settings.set("mask_create_name", layer_name)
mask_property = self.mask_widget.get_mask_property()
if mask_property.clip_to_mask and self.mask_select.value is None:
warnings.warn("Select base mask", RuntimeWarning)
return
base_mask = None if self.mask_select.value is None else self.mask_select.value.data
scale = np.array(self.roi_select.value.scale)
mask = np.array(calculate_mask(mask_property, self.roi_select.value.data, base_mask, scale[-3:]))
if layer_name in self.viewer.layers:
self.viewer.layers[layer_name].data = mask
else:
self.viewer.add_labels(
mask,
scale=scale[-int(mask.ndim) :],
name=layer_name,
)
self.settings.dump()
def test_dilate(self, radius_type, radius, time):
mask_base_array = np.zeros((time, 30, 30, 30), dtype=np.uint8)
mask_base_array[:, 10:20, 10:20, 10:20] = 1
prop1 = MaskProperty(
dilate=radius_type,
dilate_radius=radius,
fill_holes=RadiusType.NO,
max_holes_size=70,
save_components=False,
clip_to_mask=False,
)
res_array1 = np.zeros((1, 30, 30, 30), dtype=np.uint8)
slices: List[Union[int, slice]] = [slice(None)] * 4
for i in range(1, 4):
slices[i] = slice(10 - radius, 20 + radius)
if radius_type == RadiusType.R2D:
slices[1] = slice(10, 20)
res_array1[tuple(slices)] = 1
if radius_type == RadiusType.R3D:
res_array1[:, (9, 9, 9, 9), (9, 9, 20, 20), (9, 20, 20, 9)] = 0
res_array1[:, (20, 20, 20, 20), (9, 9, 20, 20), (9, 20, 20, 9)] = 0
new_mask = calculate_mask(prop1, mask_base_array, None, (1, 1, 1))
assert np.all(new_mask == res_array1)