def _auto_find_minimisation_square_sum(self):
num_cors = self.view.get_number_of_cors()
if num_cors is None:
return
self.do_clear_all_cors()
selected_row, slice_indices = self.model.get_slice_indices(num_cors)
if self.model.has_results:
initial_cor = []
for slc in slice_indices:
initial_cor.append(self.model.data_model.get_cor_from_regression(slc))
else:
initial_cor = self.view.rotation_centre
def _completed_finding_cors(task: TaskWorkerThread):
cors = task.result
for slice_idx, cor in zip(slice_indices, cors):
self.view.add_cor_table_row(selected_row, slice_idx, cor)
self.do_cor_fit()
self.view.set_correlate_buttons_enabled(True)
self.view.set_correlate_buttons_enabled(False)
start_async_task_view(self.view, self.model.auto_find_minimisation_sqsum, _completed_finding_cors, {
'slices': slice_indices,
'recon_params': self.view.recon_params(),
'initial_cor': initial_cor
})
def _auto_find_correlation(self):
def completed(task: TaskWorkerThread):
cor, tilt = task.result
self._set_precalculated_cor_tilt(cor, tilt)
start_async_task_view(self.view, self.model.auto_find_correlation,
completed)
def _auto_find_correlation(self):
if not self.model.images.has_proj180deg():
self.view.show_status_message(
"Unable to correlate 0 and 180 because the dataset doesn't have a 180 "
"projection set. Please load a 180 projection manually.")
return
self.recon_is_running = True
def completed(task: TaskWorkerThread):
if task.result is None and task.error is not None:
selected_stack = self.view.main_window.get_images_from_stack_uuid(
self.view.stackSelector.current())
self.view.warn_user(
"Failure!",
f"Finding the COR failed, likely caused by the selected stack's 180 "
f"degree projection being a different shape. \n\n "
f"Error: {str(task.error)} "
f"\n\n Suggestion: Use crop coordinates to resize the 180 degree projection to "
f"({selected_stack.height}, {selected_stack.width})")
else:
cor, tilt = task.result
self._set_precalculated_cor_tilt(cor, tilt)
self.view.set_correlate_buttons_enabled(True)
self.recon_is_running = False
self.view.set_correlate_buttons_enabled(False)
start_async_task_view(self.view,
self.model.auto_find_correlation,
completed,
tracker=self.async_tracker)
def do_reconstruct_volume(self):
if not self.model.has_results:
raise ValueError(
"Fit is not performed on the data, therefore the CoR cannot be found for each slice."
)
start_async_task_view(self.view, self.model.run_full_recon,
self._on_volume_recon_done,
{'recon_params': self.view.recon_params()})
def save(self):
kwargs = {
'stack_uuid': self.view.save_dialogue.selected_stack,
'output_dir': self.view.save_dialogue.save_path(),
'name_prefix': self.view.save_dialogue.name_prefix(),
'image_format': self.view.save_dialogue.image_format(),
'overwrite': self.view.save_dialogue.overwrite()
}
start_async_task_view(self.view, self.model.do_saving,
self._on_save_done, kwargs)
def load_stack(self, **kwargs):
if kwargs:
raise NotImplementedError(
"Converting from kwargs to LoadParameters not implemented")
par = self.view.load_dialogue.get_parameters()
if par.sample.input_path == "":
raise ValueError("No sample path provided")
start_async_task_view(self.view, self.model.do_load_stack,
self._on_stack_load_done, {'parameters': par})
def do_apply_filter(self, stacks: List['StackVisualiserView'], post_filter: Callable[[Any], None]):
"""
Applies the selected filter to the selected stack.
"""
if len(stacks) == 0:
raise ValueError('No stack selected')
# Get auto parameters
# Generate sub-stack and run filter
apply_func = partial(self.apply_to_stacks, stacks)
start_async_task_view(self.presenter.view, apply_func, post_filter)
def load_dataset(self, par: Optional[LoadingParameters] = None) -> None:
if par is None and self.view.load_dialogue is not None:
par = self.view.load_dialogue.get_parameters()
if par is None:
return
if par.sample.input_path == "":
raise ValueError("No sample path provided")
start_async_task_view(self.view, self.model.do_load_dataset,
self._on_dataset_load_done, {'parameters': par})
def save(self) -> None:
assert isinstance(self.view.save_dialogue, MWSaveDialog)
kwargs = {
'images_id': self.view.save_dialogue.selected_stack,
'output_dir': self.view.save_dialogue.save_path(),
'name_prefix': self.view.save_dialogue.name_prefix(),
'image_format': self.view.save_dialogue.image_format(),
'overwrite': self.view.save_dialogue.overwrite(),
'pixel_depth': self.view.save_dialogue.pixel_depth()
}
start_async_task_view(self.view, self.model.do_images_saving,
self._on_save_done, kwargs)
def do_apply_filter(self, stack_view, stack_presenter,
post_filter: Callable[[Any], None]):
"""
Applies the selected filter to the selected stack.
"""
if not stack_presenter:
raise ValueError('No stack selected')
# Get auto parameters
stack_params = get_parameters_from_stack(stack_presenter,
self.params_needed_from_stack)
apply_func = partial(self.apply_filter, stack_presenter.images,
stack_params)
start_async_task_view(stack_view, apply_func, post_filter)
def _get_reconstruct_slice(
self, cor, slice_idx: int, call_back: Callable[[TaskWorkerThread],
None]) -> None:
# If no COR is provided and there are regression results then calculate
# the COR for the selected preview slice
cor = self.model.get_me_a_cor(cor)
start_async_task_view(self.view,
self.model.run_preview_recon,
call_back, {
'slice_idx': slice_idx,
'cor': cor,
'recon_params': self.view.recon_params()
},
tracker=self.async_tracker)
def _auto_find_correlation(self):
def completed(task: TaskWorkerThread):
if task.result is None and task.error is not None:
selected_stack = self.view.main_window.get_images_from_stack_uuid(self.view.stackSelector.current())
self.view.warn_user(
"Failure!", f"Finding the COR failed, likely caused by the selected stack's 180 "
f"degree projection being a different shape. \n\n "
f"Error: {str(task.error)} "
f"\n\n Suggestion: Use crop coordinates to resize the 180 degree projection to "
f"({selected_stack.height}, {selected_stack.width})")
else:
cor, tilt = task.result
self._set_precalculated_cor_tilt(cor, tilt)
self.view.set_correlate_buttons_enabled(True)
self.view.set_correlate_buttons_enabled(False)
start_async_task_view(self.view, self.model.auto_find_correlation, completed)
def load_image_stack(self, file_path: str) -> None:
start_async_task_view(self.view, self.model.load_images,
self._on_stack_load_done,
{'file_path': file_path})
