def test_save_segmentation(self, tmpdir, data_test_dir):
seg = LoadROIImage.load(
[os.path.join(data_test_dir, "test_nucleus_1_1.seg")], metadata={"default_spacing": (1, 1, 1)}
)
SaveROI.save(os.path.join(tmpdir, "segmentation.seg"), seg, {"relative_path": False})
assert os.path.exists(os.path.join(tmpdir, "segmentation.seg"))
os.makedirs(os.path.join(tmpdir, "seg_save"))
save_components(
seg.image,
seg.selected_components,
os.path.join(tmpdir, "seg_save"),
seg.roi_info,
SaveComponents.get_default_values(),
)
assert os.path.isdir(os.path.join(tmpdir, "seg_save"))
assert len(glob(os.path.join(tmpdir, "seg_save", "*"))) == 4
seg2 = LoadROI.load([os.path.join(tmpdir, "segmentation.seg")])
assert seg2 is not None
save_components(
seg.image,
[],
os.path.join(tmpdir, "seg_save2"),
seg.roi_info,
SaveComponents.get_default_values(),
)
assert os.path.isdir(os.path.join(tmpdir, "seg_save2"))
assert len(glob(os.path.join(tmpdir, "seg_save2", "*"))) == 8
def test_load_seg_with_image(self, data_test_dir):
seg = LoadROIImage.load(
[os.path.join(data_test_dir, "test_nucleus_1_1.seg")], metadata={"default_spacing": (1, 1, 1)}
)
assert isinstance(seg.image, Image)
assert seg.selected_components == [1, 3]
assert isinstance(seg.roi, np.ndarray)
seg.image.fit_array_to_image(seg.roi)
assert os.path.basename(seg.image.file_path) == "test_nucleus.tif"
def test_save_segmentation_without_image(self, tmpdir, data_test_dir):
seg = LoadROIImage.load(
[os.path.join(data_test_dir, "test_nucleus_1_1.seg")], metadata={"default_spacing": (1, 1, 1)}
)
seg_clean = dataclasses.replace(seg, image=None, roi=reduce_array(seg.roi))
SaveROI.save(os.path.join(tmpdir, "segmentation.seg"), seg_clean, {"relative_path": False})
SaveROI.save(
os.path.join(tmpdir, "segmentation1.seg"),
seg_clean,
{"relative_path": False, "spacing": (210 * 10 ** -6, 70 * 10 ** -6, 70 * 10 ** -6)},
)
def run_calculation(self):
while not self.queue.empty():
task: BatchTask = self.queue.get()
if isinstance(task.data, str):
file_path = task.data
if path.splitext(task.data)[1] == ".seg":
project_tuple = LoadROIImage.load([task.data])
else:
project_tuple = LoadStackImage.load([task.data])
elif isinstance(task.data, MaskProjectTuple):
project_tuple: MaskProjectTuple = task.data
file_path = project_tuple.image.file_path
else:
continue
try:
name = path.basename(file_path)
blank = get_mask(project_tuple.roi, project_tuple.mask, project_tuple.selected_components)
algorithm: StackAlgorithm = mask_algorithm_dict[task.parameters.algorithm]()
algorithm.set_image(project_tuple.image)
algorithm.set_mask(blank)
algorithm.set_parameters(**task.parameters.values)
if isinstance(task.save_prefix, tuple):
self.range_signal.emit(0, algorithm.get_steps_num() + 1)
else:
self.range_signal.emit(0, algorithm.get_steps_num())
# noinspection PyTypeChecker
segmentation = algorithm.calculation_run(partial(self.progress_info, name))
state2 = StackSettings.transform_state(
project_tuple, segmentation.roi_info, defaultdict(lambda: segmentation.parameters), []
)
if isinstance(task.save_prefix, tuple):
self.progress_info(name, "saving", algorithm.get_steps_num())
name = path.splitext(path.basename(file_path))[0] + ".seg"
re_end = re.compile(r"(.*_version)(\d+)\.seg$")
while path.exists(path.join(task.save_prefix[0], name)):
match = re_end.match(name)
if match:
num = int(match.group(2)) + 1
name = match.group(1) + str(num) + ".seg"
else:
name = path.splitext(path.basename(file_path))[0] + "_version1.seg"
SaveROI.save(path.join(task.save_prefix[0], name), state2, parameters=task.save_prefix[1])
else:
self.multiple_result.emit(state2)
except Exception as e: # pylint: disable=W0703
self.error_signal.emit(f"Exception occurred during proceed {file_path}. Exception info {e}")
self.index += 1
self.index = 0
self.execution_done.emit()
def test_load_segmentation_image(self, data_test_dir, stack_settings):
pi = LoadROIImage.load(
[os.path.join(data_test_dir, "test_nucleus.seg")])
assert isinstance(pi, MaskProjectTuple)
stack_settings.set_project_info(pi)
assert pi.image is not None