def test_create(self, mask_prop):
roi_info = ROIInfo(np.zeros((10, 10), dtype=np.uint8))
elem = HistoryElement.create(roi_info, None, {}, mask_prop)
assert elem.mask_property == mask_prop
assert elem.roi_extraction_parameters == {}
param = {"a": 1, "b": 2}
elem2 = HistoryElement.create(roi_info, None, param, mask_prop)
assert elem2.roi_extraction_parameters == param
roi_info2, mask = elem2.get_roi_info_and_mask()
assert np.all(roi_info2.roi == 0)
assert mask is None
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)
roi_info = result.roi_info.fit_to_image(image)
report_fun("step", 2 * i + 1)
new_mask = calculate_mask(
mask_description=el.mask_property,
roi=roi_info.roi,
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(roi_info, 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_info, result.additional_layers, mask,
history, text)
def create_history_element_from_project(project_info: ProjectTuple,
mask_property: MaskProperty):
return HistoryElement.create(
roi_info=project_info.roi_info,
mask=project_info.mask,
roi_extraction_parameters=project_info.algorithm_parameters,
mask_property=mask_property,
)
def create_history_element_from_segmentation_tuple(project_info: MaskProjectTuple, mask_property: MaskProperty):
return HistoryElement.create(
roi_info=project_info.roi_info,
mask=project_info.mask,
roi_extraction_parameters={
"selected": project_info.selected_components,
"parameters": project_info.roi_extraction_parameters,
},
mask_property=mask_property,
)
def test_mask(self, mask_prop):
mask = np.zeros((10, 10), dtype=np.uint8)
mask[1:-1, 1:-1] = 2
mask2 = np.copy(mask)
mask2[2:-2, 2:-2] = 4
roi_info = ROIInfo(mask2)
elem = HistoryElement.create(roi_info, mask, {}, mask_prop)
roi_info2, mask2 = elem.get_roi_info_and_mask()
assert np.all(mask == mask2)
assert np.all(roi_info.roi == roi_info2.roi)
def test_base_settings_history(self, tmp_path, qtbot, monkeypatch):
settings = base_settings.BaseSettings(tmp_path)
assert settings.history_size() == 0
assert settings.history_redo_size() == 0
hist_elem = HistoryElement({"a": 1}, None, MaskProperty.simple_mask(),
BytesIO())
hist_elem2 = HistoryElement({"a": 2}, None, MaskProperty.simple_mask(),
BytesIO())
hist_elem3 = HistoryElement({"a": 3}, None, MaskProperty.simple_mask(),
BytesIO())
settings.add_history_element(hist_elem)
assert settings.history_size() == 1
assert settings.history_redo_size() == 0
settings.add_history_element(hist_elem2)
assert settings.history_size() == 2
assert settings.history_redo_size() == 0
assert settings.history_pop().roi_extraction_parameters["a"] == 2
assert settings.history_current_element(
).roi_extraction_parameters["a"] == 1
assert settings.history_next_element(
).roi_extraction_parameters["a"] == 2
assert settings.history_redo_size() == 1
assert settings.history_size() == 1
assert len(settings.get_history()) == 1
assert settings.get_history()[-1].roi_extraction_parameters["a"] == 1
settings.add_history_element(hist_elem3)
settings.history_pop()
settings.history_redo_clean()
assert settings.history_redo_size() == 0
settings.history_pop()
assert settings.history_pop() is None
assert settings.history_size() == 0
assert settings.history_redo_size() == 1
settings.set_history([hist_elem, hist_elem2])
assert settings.get_history()[-1].roi_extraction_parameters["a"] == 2
assert settings.history_size() == 2
assert settings.history_redo_size() == 0
settings.history_pop()
monkeypatch.setattr(settings, "cmp_history_element", lambda x, y: True)
settings.add_history_element(hist_elem3)
def test_annotations(self, mask_prop):
data = np.zeros((10, 10), dtype=np.uint8)
data[1:5, 1:5] = 1
data[5:-1, 1:5] = 2
data[1:5, 5:-1] = 3
data[5:-1, 5:-1] = 4
annotations = {1: "a", 2: "b", 3: "c", 4: "d"}
roi_info = ROIInfo(data, annotations=annotations)
elem = HistoryElement.create(roi_info, None, {}, mask_prop)
roi_info2, mask2 = elem.get_roi_info_and_mask()
assert mask2 is None
assert np.all(roi_info2.roi == roi_info.roi)
def test_additional(self, mask_prop):
data = np.zeros((10, 10), dtype=np.uint8)
data[1:-1, 1:-1] = 2
alternative = {}
for i in range(4):
alternative_array = np.copy(data)
alternative_array[alternative_array > 0] = i + 2
alternative[f"add{i}"] = alternative_array
roi_info = ROIInfo(data, alternative=alternative)
elem = HistoryElement.create(roi_info, None, {}, mask_prop)
roi_info2, mask2 = elem.get_roi_info_and_mask()
assert np.all(roi_info2.roi == roi_info.roi)
assert mask2 is None
assert len(roi_info.alternative) == 4
assert set(roi_info.alternative) == {f"add{i}" for i in range(4)}
for i in range(4):
arr = roi_info.alternative[f"add{i}"]
assert np.all(arr[arr > 0] == i + 2)
def perform_roi_info_history_test(
self, project, save_path, mask_property, save_method: Type[SaveBase], load_method: Type[LoadBase]
):
alt1 = np.copy(project.roi_info.roi)
alt1[alt1 > 0] += 3
roi_info = ROIInfo(
roi=project.roi_info.roi, annotations={i: f"a{i}" for i in range(1, 5)}, alternative={"test": alt1}
)
history = []
for i in range(3):
alt2 = np.copy(alt1)
alt2[alt2 > 0] = i + 5
roi_info2 = ROIInfo(
roi=project.roi_info.roi,
annotations={i: f"a{i}_{j}" for j in range(1, 5)},
alternative={f"test{i}": alt2},
)
history.append(
HistoryElement.create(
roi_info2, alt1, {"algorithm_name": f"task_{i}", "values": {"a": 1}}, mask_property
)
)
proj = dataclasses.replace(project, roi_info=roi_info, history=history)
save_method.save(save_path / "data.tgz", proj, SaveROI.get_default_values())
proj2: ProjectInfoBase = load_method.load([save_path / "data.tgz"])
assert np.all(proj2.roi_info.roi == project.roi_info.roi)
assert set(proj2.roi_info.annotations) == {1, 2, 3, 4}
assert proj2.roi_info.annotations == {i: f"a{i}" for i in range(1, 5)}
assert "test" in proj2.roi_info.alternative
assert np.all(proj2.roi_info.alternative["test"] == alt1)
assert len(proj2.history) == 3
for i in range(3):
roi_info3, mask2 = proj2.history[i].get_roi_info_and_mask()
assert np.all(mask2 == alt1)
assert set(roi_info3.alternative) == {f"test{i}"}
assert np.all(roi_info3.alternative[f"test{i}"][alt1 > 0] == i + 5)
assert np.all(roi_info3.alternative[f"test{i}"][alt1 == 0] == 0)
assert roi_info3.annotations == {i: f"a{i}_{j}" for j in range(1, 5)}
assert proj2.history[i].roi_extraction_parameters == {"algorithm_name": f"task_{i}", "values": {"a": 1}}