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(self, data_test_dir):
seg = LoadROI.load([os.path.join(data_test_dir, "test_nucleus_1_1.seg")])
assert isinstance(seg.image, str)
assert seg.selected_components == [1, 3]
assert os.path.exists(os.path.join(data_test_dir, seg.image))
assert len(seg.roi_extraction_parameters) == 4
assert os.path.basename(seg.image) == "test_nucleus.tif"
def test_load_old_seg(self, data_test_dir):
"""
For PartSeg 0.9.4 and older
"""
seg = LoadROI.load([os.path.join(data_test_dir, "test_nucleus.seg")])
assert isinstance(seg.image, str)
assert seg.selected_components == [1, 3]
assert os.path.exists(os.path.join(data_test_dir, seg.image))
assert os.path.basename(seg.image) == "test_nucleus.tif"
def test_load_project_with_history(self, tmp_path, stack_segmentation1, mask_property):
image_location = tmp_path / "test1.tif"
SaveAsTiff.save(image_location, stack_segmentation1)
seg2 = dataclasses.replace(
stack_segmentation1,
history=[create_history_element_from_segmentation_tuple(stack_segmentation1, mask_property)],
selected_components=[1],
mask=stack_segmentation1.roi_info.roi,
image=stack_segmentation1.image.substitute(file_path=image_location),
file_path=image_location,
)
SaveROI.save(tmp_path / "test1.seg", seg2, {"relative_path": False})
res = LoadROI.load([tmp_path / "test1.seg"])
assert res.image == str(image_location)
assert res.mask is not None
assert len(res.history) == 1
assert res.history[0].mask_property == mask_property
cmp_dict = {str(k): v for k, v in stack_segmentation1.roi_extraction_parameters.items()}
assert str(res.history[0].roi_extraction_parameters["parameters"]) == str(cmp_dict)
def test_loading_new_segmentation(self, tmpdir, data_test_dir):
image_data = LoadStackImage.load([os.path.join(data_test_dir, "test_nucleus.tif")])
algorithm = ThresholdAlgorithm()
algorithm.set_image(image_data.image)
param = algorithm.get_default_values()
param["channel"] = 0
algorithm.set_parameters(**param)
res = algorithm.calculation_run(lambda x, y: None)
num = np.max(res.roi) + 1
data_dict = {str(i): deepcopy(res.parameters) for i in range(1, num)}
to_save = MaskProjectTuple(
file_path=image_data.image.file_path,
image=image_data.image,
mask=None,
roi_info=res.roi_info,
selected_components=list(range(1, num)),
roi_extraction_parameters=data_dict,
)
SaveROI.save(os.path.join(tmpdir, "segmentation2.seg"), to_save, {"relative_path": False})
seg2 = LoadROI.load([os.path.join(tmpdir, "segmentation2.seg")])
assert seg2 is not None
def napari_get_reader(path: str):
for extension in LoadROI.get_extensions():
if path.endswith(extension):
return functools.partial(partseg_loader, LoadROI)
def load_segmentation(self):
dial = PLoadDialog(
{
LoadROI.get_name(): LoadROI,
LoadROIParameters.get_name(): LoadROIParameters,
LoadROIFromTIFF.get_name(): LoadROIFromTIFF,
},
settings=self.settings,
path="io.open_segmentation_directory",
)
if not dial.exec_():
return
load_property = dial.get_result()
def exception_hook(exception):
mess = QMessageBox(self)
if isinstance(
exception, ValueError
) and exception.args[0] == "Segmentation do not fit to image":
mess.warning(self, "Open error",
"Segmentation do not fit to image")
elif isinstance(exception, MemoryError):
mess.warning(self, "Open error",
"Not enough memory to read this image")
elif isinstance(exception, IOError):
mess.warning(self, "Open error",
"Some problem with reading from disc")
elif isinstance(exception, WrongFileTypeException):
mess.warning(
self,
"Open error",
"No needed files inside archive. Most probably you choose file from segmentation analysis",
)
else:
raise exception
dial = ExecuteFunctionDialog(
load_property.load_class.load,
[load_property.load_location],
text="Load segmentation",
exception_hook=exception_hook,
)
if not dial.exec_():
return
result = dial.get_result()
if result is None:
QMessageBox.critical(self, "Data Load fail",
"Fail of loading data")
return
if result.roi is not None:
try:
self.settings.set_project_info(dial.get_result())
return
except ValueError as e:
if e.args != (ROI_NOT_FIT, ):
raise
self.segmentation_dialog.set_additional_text(
"Segmentation do not fit to image, maybe you would lie to load parameters only."
)
except HistoryProblem:
QMessageBox().warning(
self,
"Load Problem",
"You set to save selected components when loading "
"another segmentation but history is incomatybile",
)
else:
self.segmentation_dialog.set_additional_text("")
self.segmentation_dialog.set_parameters_dict(
result.roi_extraction_parameters)
self.segmentation_dialog.show()