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 get_mask(segmentation: typing.Optional[np.ndarray], mask: typing.Optional[np.ndarray], selected: typing.List[int]):
"""
Calculate mask base on segmentation, current mask and list of chosen components.
:param typing.Optional[np.ndarray] segmentation: segmentation array
:param typing.Optional[np.ndarray] mask: current mask
:param typing.List[int] selected: list of selected components
:return: new mask
:rtype: typing.Optional[np.ndarray]
"""
if segmentation is None or len(selected) == 0:
return None if mask is None else mask
segmentation = reduce_array(segmentation, selected)
if mask is None:
resp = np.ones(segmentation.shape, dtype=np.uint8)
else:
resp = np.copy(mask)
resp[segmentation > 0] = 0
return resp
def transform_state(
state: SegmentationTuple,
new_segmentation_data: np.ndarray,
segmentation_parameters: typing.Dict,
list_of_components: typing.List[int],
save_chosen: bool = True,
) -> SegmentationTuple:
if list_of_components is None:
list_of_components = []
if segmentation_parameters is None:
segmentation_parameters = defaultdict(lambda: None)
segmentation_count = 0 if state.segmentation is None else len(
np.unique(state.segmentation.flat))
new_segmentation_count = 0 if new_segmentation_data is None else len(
np.unique(new_segmentation_data.flat))
segmentation_dtype = minimal_dtype(segmentation_count +
new_segmentation_count)
if save_chosen and state.segmentation is not None:
segmentation = reduce_array(state.segmentation,
state.selected_components,
dtype=segmentation_dtype)
components_parameters_dict = {}
for i, val in enumerate(sorted(state.selected_components), 1):
components_parameters_dict[i] = state.segmentation_parameters[
val]
base_chose = list(range(1, len(state.selected_components) + 1))
else:
segmentation = None
base_chose = []
components_parameters_dict = {}
if new_segmentation_data is not None:
state.image.fit_array_to_image(new_segmentation_data)
num = np.max(new_segmentation_data)
if segmentation is not None:
new_segmentation = np.copy(new_segmentation_data)
new_segmentation[segmentation > 0] = 0
new_segmentation = reduce_array(new_segmentation,
dtype=segmentation_dtype)
segmentation[new_segmentation > 0] = new_segmentation[
new_segmentation > 0] + len(base_chose)
components_size = np.bincount(new_segmentation.flat)
base_index = len(base_chose) + 1
chosen_components = base_chose[:]
components_list = base_chose[:]
for i, val in enumerate(components_size[1:], 1):
if val > 0:
if i in list_of_components:
chosen_components.append(base_index)
components_list.append(base_index)
components_parameters_dict[
base_index] = segmentation_parameters[i]
base_index += 1
return dataclasses.replace(
state,
segmentation=segmentation,
selected_components=chosen_components,
segmentation_parameters=components_parameters_dict,
)
else:
for i in range(1, num + 1):
components_parameters_dict[i] = segmentation_parameters[i]
return dataclasses.replace(
state,
segmentation=new_segmentation_data,
selected_components=list_of_components,
segmentation_parameters=components_parameters_dict,
)
else:
return dataclasses.replace(
state,
segmentation=segmentation,
selected_components=base_chose,
segmentation_parameters=components_parameters_dict,
)
def load_stack_segmentation(file_data: typing.Union[str, Path],
range_changed=None,
step_changed=None):
if range_changed is None:
range_changed = empty_fun
if step_changed is None:
step_changed = empty_fun
range_changed(0, 7)
tar_file = open_tar_file(file_data)[0]
try:
if check_segmentation_type(tar_file) != SegmentationType.mask:
raise WrongFileTypeException()
files = tar_file.getnames()
step_changed(1)
metadata = load_metadata(
tar_file.extractfile("metadata.json").read().decode("utf8"))
step_changed(2)
if "segmentation.npy" in files:
segmentation_file_name = "segmentation.npy"
segmentation_load_fun = np.load
else:
segmentation_file_name = "segmentation.tif"
segmentation_load_fun = TiffImageReader.read_image
segmentation_buff = BytesIO()
segmentation_tar = tar_file.extractfile(
tar_file.getmember(segmentation_file_name))
segmentation_buff.write(segmentation_tar.read())
step_changed(3)
segmentation_buff.seek(0)
segmentation = segmentation_load_fun(segmentation_buff)
if isinstance(segmentation, Image):
spacing = segmentation.spacing
segmentation = segmentation.get_channel(0)
else:
spacing = None
segmentation = reduce_array(segmentation)
step_changed(4)
if "mask.tif" in tar_file.getnames():
mask = tifffile.imread(tar_to_buff(tar_file, "mask.tif"))
if np.max(mask) == 1:
mask = mask.astype(np.bool)
else:
mask = None
step_changed(5)
history = []
try:
history_buff = tar_file.extractfile(
tar_file.getmember("history/history.json")).read()
history_json = load_metadata(history_buff)
for el in history_json:
history_buffer = BytesIO()
history_buffer.write(
tar_file.extractfile(
f"history/arrays_{el['index']}.npz").read())
history_buffer.seek(0)
history.append(
HistoryElement(
segmentation_parameters=el["segmentation_parameters"],
mask_property=el["mask_property"],
arrays=history_buffer,
))
except KeyError:
pass
step_changed(6)
finally:
if isinstance(file_data, (str, Path)):
tar_file.close()
return SegmentationTuple(
file_path=file_data if isinstance(file_data, str) else "",
image=metadata["base_file"] if "base_file" in metadata else None,
segmentation=segmentation,
selected_components=metadata["components"],
mask=mask,
segmentation_parameters=metadata["parameters"]
if "parameters" in metadata else None,
history=history,
spacing=([10**-9] + list(spacing)) if spacing is not None else None,
)
def transform_state(
cls,
state: MaskProjectTuple,
new_roi_info: ROIInfo,
new_roi_extraction_parameters: typing.Dict[
int, typing.Optional[ROIExtractionProfile]],
list_of_components: typing.List[int],
save_chosen: bool = True,
) -> MaskProjectTuple:
"""
:param MaskProjectTuple state: state to be transformed
:param ROIInfo new_roi_info: roi description
:param typing.Dict[int, typing.Optional[ROIExtractionProfile]] new_roi_extraction_parameters:
Parameters used to extract roi
:param typing.List[int] list_of_components: list of components from new_roi which should be selected
:param bool save_chosen: if save currently selected components
:return: new state
"""
# TODO Refactor
if not save_chosen or state.roi_info.roi is None or len(
state.selected_components) == 0:
return dataclasses.replace(
state,
roi_info=new_roi_info,
selected_components=list_of_components,
roi_extraction_parameters={
i: new_roi_extraction_parameters[i]
for i in new_roi_info.bound_info
},
)
if list_of_components is None:
list_of_components = []
if new_roi_extraction_parameters is None:
new_roi_extraction_parameters = defaultdict(lambda: None)
segmentation_count = len(state.roi_info.bound_info)
new_segmentation_count = len(new_roi_info.bound_info)
segmentation_dtype = minimal_dtype(segmentation_count +
new_segmentation_count)
roi_base = reduce_array(state.roi_info.roi,
state.selected_components,
dtype=segmentation_dtype)
annotation_base = {
i: state.roi_info.annotations.get(x)
for i, x in enumerate(state.selected_components, start=1)
}
alternative_base = {
name: cls._clip_data_array(roi_base, array)
for name, array in state.roi_info.alternative.items()
}
components_parameters_dict = {
i: state.roi_extraction_parameters[val]
for i, val in enumerate(sorted(state.selected_components), 1)
}
base_chose = list(annotation_base.keys())
if new_segmentation_count == 0:
return dataclasses.replace(
state,
roi_info=ROIInfo(roi=roi_base,
annotations=annotation_base,
alternative=alternative_base),
selected_components=base_chose,
roi_extraction_parameters=components_parameters_dict,
)
new_segmentation = np.copy(new_roi_info.roi)
new_segmentation[roi_base > 0] = 0
left_component_list = np.unique(new_segmentation.flat)
if left_component_list[0] == 0:
left_component_list = left_component_list[1:]
new_segmentation = reduce_array(new_segmentation,
dtype=segmentation_dtype)
roi_base[new_segmentation >
0] = new_segmentation[new_segmentation > 0] + len(base_chose)
for name, array in new_roi_info.alternative.items():
if name in alternative_base:
alternative_base[name][new_segmentation > 0] = array[
new_segmentation > 0]
else:
alternative_base[name] = cls._clip_data_array(
new_segmentation, array)
for i, el in enumerate(left_component_list, start=len(base_chose) + 1):
annotation_base[i] = new_roi_info.annotations.get(el)
if el in list_of_components:
base_chose.append(i)
components_parameters_dict[i] = new_roi_extraction_parameters[el]
roi_info = ROIInfo(roi=roi_base,
annotations=annotation_base,
alternative=alternative_base)
return dataclasses.replace(
state,
roi_info=roi_info,
selected_components=base_chose,
roi_extraction_parameters=components_parameters_dict,
)
