def __init__(self, view: 'ReconstructWindowView', main_window):
super(ReconstructWindowPresenter, self).__init__(view)
self.view = view
self.model = ReconstructWindowModel(self.view.cor_table_model)
self.allowed_recon_kwargs: Dict[str, List[str]] = self.model.load_allowed_recon_kwargs()
self.restricted_arg_widgets: Dict[str, List[QWidget]] = {
'filter_name': [self.view.filterName, self.view.filterNameLabel],
'num_iter': [self.view.numIter, self.view.numIterLabel],
}
self.main_window = main_window
def __init__(self, view: 'ReconstructWindowView', main_window):
super().__init__(view)
self.view = view
self.model = ReconstructWindowModel(self.view.cor_table_model)
self.allowed_recon_kwargs: Dict[
str, List[str]] = self.model.load_allowed_recon_kwargs()
self.restricted_arg_widgets: Dict[str, List[QWidget]] = {
'filter_name': [self.view.filterName, self.view.filterNameLabel],
'num_iter': [self.view.numIter, self.view.numIterLabel],
'alpha': [self.view.alphaSpinbox, self.view.alphaLabel],
}
self.main_window = main_window
self.recon_is_running = False
self.async_tracker: Set[Any] = set()
class ReconstructWindowPresenter(BasePresenter):
ERROR_STRING = "COR/Tilt finding failed: {}"
view: 'ReconstructWindowView'
def __init__(self, view: 'ReconstructWindowView', main_window):
super(ReconstructWindowPresenter, self).__init__(view)
self.view = view
self.model = ReconstructWindowModel(self.view.cor_table_model)
self.allowed_recon_kwargs: Dict[str, List[str]] = self.model.load_allowed_recon_kwargs()
self.restricted_arg_widgets: Dict[str, List[QWidget]] = {
'filter_name': [self.view.filterName, self.view.filterNameLabel],
'num_iter': [self.view.numIter, self.view.numIterLabel],
}
self.main_window = main_window
def notify(self, notification, slice_idx=None):
try:
if notification == Notifications.RECONSTRUCT_VOLUME:
self.do_reconstruct_volume()
elif notification == Notifications.RECONSTRUCT_PREVIEW_SLICE:
self.do_preview_reconstruct_slice()
elif notification == Notifications.RECONSTRUCT_STACK_SLICE:
self.do_stack_reconstruct_slice()
elif notification == Notifications.RECONSTRUCT_USER_CLICK:
self.do_preview_reconstruct_slice(slice_idx=slice_idx)
elif notification == Notifications.COR_FIT:
self.do_cor_fit()
elif notification == Notifications.CLEAR_ALL_CORS:
self.do_clear_all_cors()
elif notification == Notifications.REMOVE_SELECTED_COR:
self.do_remove_selected_cor()
elif notification == Notifications.CALCULATE_CORS_FROM_MANUAL_TILT:
self.do_calculate_cors_from_manual_tilt()
elif notification == Notifications.ALGORITHM_CHANGED:
self.do_algorithm_changed()
elif notification == Notifications.UPDATE_PROJECTION:
self.do_update_projection()
elif notification == Notifications.ADD_COR:
self.do_add_cor()
elif notification == Notifications.REFINE_COR:
self._do_refine_selected_cor()
elif notification == Notifications.REFINE_ITERS:
self._do_refine_iterations()
elif notification == Notifications.AUTO_FIND_COR_CORRELATE:
self._auto_find_correlation()
elif notification == Notifications.AUTO_FIND_COR_MINIMISE:
self._auto_find_minimisation_square_sum()
except Exception as err:
self.show_error(err, traceback.format_exc())
def do_algorithm_changed(self):
alg_name = self.view.algorithm_name
allowed_args = self.allowed_recon_kwargs[alg_name]
for arg, widgets in self.restricted_arg_widgets.items():
if arg in allowed_args:
for widget in widgets:
widget.show()
else:
for widget in widgets:
widget.hide()
with BlockQtSignals([self.view.filterName, self.view.numIter]):
self.view.set_filters_for_recon_tool(self.model.get_allowed_filters(alg_name))
self.do_preview_reconstruct_slice()
self.view.change_refine_iterations()
def set_stack_uuid(self, uuid):
stack = self.view.get_stack_visualiser(uuid)
if self.model.is_current_stack(stack):
return
self.view.reset_image_recon_preview()
self.view.clear_cor_table()
self.model.initial_select_data(stack)
self.view.rotation_centre = self.model.last_cor.value
self.view.pixel_size = self.get_pixel_size_from_images()
self.do_update_projection()
self.do_preview_reconstruct_slice(refresh_recon_slice_histogram=True)
def set_preview_projection_idx(self, idx):
self.model.preview_projection_idx = idx
self.do_update_projection()
def set_preview_slice_idx(self, idx):
self.model.preview_slice_idx = idx
self.do_update_projection()
self.do_preview_reconstruct_slice()
def set_row(self, row):
self.model.selected_row = row
def get_pixel_size_from_images(self):
if self.model.images is not None and self.model.images.pixel_size is not None:
return self.model.images.pixel_size
else:
return 0.
def do_update_projection(self):
images = self.model.images
if images is not None:
img_data = images.projection(self.model.preview_projection_idx)
self.view.update_projection(img_data, self.model.preview_slice_idx, self.model.tilt_angle)
def _find_next_free_slice_index(self) -> int:
slice_index = self.model.preview_slice_idx
max_slice = self.model.images.height
column = self.view.cor_table_model.getColumn(0)
for index in range(slice_index + 1, max_slice):
if index not in column:
return index
for index in range(0, slice_index):
if index not in column:
return index
raise RuntimeError("No free slice indexes to add to the COR Table")
def do_add_cor(self):
row = self.model.selected_row
cor = self.model.get_me_a_cor()
slice_index = self._find_next_free_slice_index()
self.view.add_cor_table_row(row, slice_index, cor.value)
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 _get_reconstruct_slice(self, cor, slice_idx: Optional[int]) -> Optional[Images]:
# 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)
return self.model.run_preview_recon(slice_idx, cor, self.view.recon_params())
def _get_slice_index(self, slice_idx: Optional[int]):
if slice_idx is None:
slice_idx = self.model.preview_slice_idx
else:
self.model.preview_slice_idx = slice_idx
return slice_idx
def do_preview_reconstruct_slice(self,
cor=None,
slice_idx: Optional[int] = None,
refresh_recon_slice_histogram: bool = False):
if self.model.images is None:
return
slice_idx = self._get_slice_index(slice_idx)
self.view.update_sinogram(self.model.images.sino(slice_idx))
images = None
try:
images = self._get_reconstruct_slice(cor, slice_idx)
except Exception as err:
self.view.show_error_dialog(f"Encountered error while trying to reconstruct: {str(err)}. "
f"Check your COR table values for invalid values!")
if images is not None:
self.view.update_recon_preview(images.data[0], refresh_recon_slice_histogram)
def do_stack_reconstruct_slice(self, cor=None, slice_idx: Optional[int] = None):
slice_idx = self._get_slice_index(slice_idx)
images = None
try:
images = self._get_reconstruct_slice(cor, slice_idx)
except ValueError as err:
self.view.show_error_dialog(f"Encountered error while trying to reconstruct: {str(err)}")
if images is not None:
self.view.show_recon_volume(images)
def _do_refine_selected_cor(self):
slice_idx = self.model.preview_slice_idx
dialog = CORInspectionDialogView(self.view, self.model.images, slice_idx, self.model.last_cor,
self.view.recon_params(), False)
res = dialog.exec()
LOG.debug('COR refine dialog result: {}'.format(res))
if res == CORInspectionDialogView.Accepted:
new_cor = dialog.optimal_rotation_centre
LOG.debug('New optimal rotation centre: {}'.format(new_cor))
self.model.data_model.set_cor_at_slice(slice_idx, new_cor.value)
self.model.last_cor = new_cor
# Update reconstruction preview with new COR
self.do_preview_reconstruct_slice(new_cor, slice_idx)
def _do_refine_iterations(self):
slice_idx = self.model.preview_slice_idx
dialog = CORInspectionDialogView(self.view, self.model.images, slice_idx, self.model.last_cor,
self.view.recon_params(), True)
res = dialog.exec()
LOG.debug('COR refine iteration result: {}'.format(res))
if res == CORInspectionDialogView.Accepted:
new_iters = dialog.optimal_iterations
LOG.debug('New optimal iterations: {}'.format(new_iters))
self.view.num_iter = new_iters
def do_cor_fit(self):
self.model.do_fit()
self.view.set_results(*self.model.get_results())
self.do_update_projection()
self.do_preview_reconstruct_slice()
def _on_volume_recon_done(self, task):
self.view.show_recon_volume(task.result)
def do_clear_all_cors(self):
self.view.clear_cor_table()
self.model.reset_selected_row()
def do_remove_selected_cor(self):
self.view.remove_selected_cor()
def set_last_cor(self, cor):
self.model.last_cor = ScalarCoR(cor)
def do_calculate_cors_from_manual_tilt(self):
cor = ScalarCoR(self.view.rotation_centre)
tilt = Degrees(self.view.tilt)
self._set_precalculated_cor_tilt(cor, tilt)
def _set_precalculated_cor_tilt(self, cor: ScalarCoR, tilt: Degrees):
self.model.set_precalculated(cor, tilt)
self.view.set_results(*self.model.get_results())
for idx, point in enumerate(self.model.data_model.iter_points()):
self.view.set_table_point(idx, point.slice_index, point.cor)
self.do_update_projection()
self.do_preview_reconstruct_slice()
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 _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 proj_180_degree_shape_matches_images(self, images):
return self.model.proj_180_degree_shape_matches_images(images)
class ReconstructWindowPresenter(BasePresenter):
ERROR_STRING = "COR/Tilt finding failed: {}"
view: 'ReconstructWindowView'
def __init__(self, view: 'ReconstructWindowView', main_window):
super(ReconstructWindowPresenter, self).__init__(view)
self.view = view
self.model = ReconstructWindowModel(self.view.cor_table_model)
self.allowed_recon_kwargs: Dict[
str, List[str]] = self.model.load_allowed_recon_kwargs()
self.restricted_arg_widgets: Dict[str, List[QWidget]] = {
'filter_name': [self.view.filterName, self.view.filterNameLabel],
'num_iter': [self.view.numIter, self.view.numIterLabel],
}
self.main_window = main_window
def notify(self, notification, slice_idx=None):
try:
if notification == Notifications.RECONSTRUCT_VOLUME:
self.do_reconstruct_volume()
elif notification == Notifications.RECONSTRUCT_SLICE:
self.do_reconstruct_slice()
elif notification == Notifications.RECONSTRUCT_USER_CLICK:
self.do_reconstruct_slice(slice_idx=slice_idx)
elif notification == Notifications.COR_FIT:
self.do_cor_fit()
elif notification == Notifications.CLEAR_ALL_CORS:
self.do_clear_all_cors()
elif notification == Notifications.REMOVE_SELECTED_COR:
self.do_remove_selected_cor()
elif notification == Notifications.CALCULATE_CORS_FROM_MANUAL_TILT:
self.do_calculate_cors_from_manual_tilt()
elif notification == Notifications.ALGORITHM_CHANGED:
self.do_algorithm_changed()
elif notification == Notifications.UPDATE_PROJECTION:
self.do_update_projection()
elif notification == Notifications.ADD_COR:
self.do_add_cor()
elif notification == Notifications.REFINE_COR:
self._do_refine_selected_cor()
elif notification == Notifications.AUTO_FIND_COR:
self.do_auto_find_cor()
except Exception as err:
self.show_error(err, traceback.format_exc())
def do_algorithm_changed(self):
alg_name = self.view.algorithm_name
allowed_args = self.allowed_recon_kwargs[alg_name]
for arg, widgets in self.restricted_arg_widgets.items():
if arg in allowed_args:
for widget in widgets:
widget.show()
else:
for widget in widgets:
widget.hide()
with BlockQtSignals([self.view.filterName, self.view.numIter]):
self.view.set_filters_for_recon_tool(
self.model.get_allowed_filters(alg_name))
self.do_reconstruct_slice()
def set_stack_uuid(self, uuid):
stack = self.view.get_stack_visualiser(uuid)
if self.model.is_current_stack(stack):
return
self.view.reset_image_recon_preview()
self.view.clear_cor_table()
self.model.initial_select_data(stack)
self.view.rotation_centre = self.model.last_cor.value
self.do_update_projection()
self.do_reconstruct_slice()
def set_preview_projection_idx(self, idx):
self.model.preview_projection_idx = idx
self.do_update_projection()
def set_preview_slice_idx(self, idx):
self.model.preview_slice_idx = idx
self.do_update_projection()
self.do_reconstruct_slice()
def set_row(self, row):
self.model.selected_row = row
def do_update_projection(self):
images = self.model.images
if images is not None:
img_data = images.projection(self.model.preview_projection_idx)
self.view.update_projection(img_data, self.model.preview_slice_idx,
self.model.tilt_angle)
def do_add_cor(self):
row = self.model.selected_row
cor = self.model.get_me_a_cor()
self.view.add_cor_table_row(row, self.model.preview_slice_idx,
cor.value)
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 do_reconstruct_slice(self,
cor=None,
slice_idx=None,
refresh_recon_slice_histogram=True):
if slice_idx is None:
slice_idx = self.model.preview_slice_idx
else:
self.model.preview_slice_idx = slice_idx
# 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)
self.view.update_sinogram(self.model.images.sino(slice_idx))
try:
data = self.model.run_preview_recon(slice_idx, cor,
self.view.recon_params())
self.view.update_recon_preview(data, refresh_recon_slice_histogram)
except ValueError as err:
self.view.show_error_dialog(
f"Encountered error while trying to reconstruct: {str(err)}")
def _do_refine_selected_cor(self):
slice_idx = self.model.preview_slice_idx
dialog = CORInspectionDialogView(self.view, self.model.images,
slice_idx, self.model.last_cor,
self.view.recon_params())
res = dialog.exec()
LOG.debug('COR refine dialog result: {}'.format(res))
if res == CORInspectionDialogView.Accepted:
new_cor = dialog.optimal_rotation_centre
LOG.debug('New optimal rotation centre: {}'.format(new_cor))
self.model.data_model.set_cor_at_slice(slice_idx, new_cor.value)
self.model.last_cor = new_cor
# Update reconstruction preview with new COR
self.do_reconstruct_slice(new_cor, slice_idx)
def do_cor_fit(self):
self.model.do_fit()
self.view.set_results(*self.model.get_results())
self.do_update_projection()
self.do_reconstruct_slice()
def _on_volume_recon_done(self, task):
self.view.show_recon_volume(task.result)
def do_clear_all_cors(self):
self.view.clear_cor_table()
self.model.reset_selected_row()
def do_remove_selected_cor(self):
self.view.remove_selected_cor()
def set_last_cor(self, cor):
self.model.last_cor = ScalarCoR(cor)
def do_calculate_cors_from_manual_tilt(self):
cor = ScalarCoR(self.view.rotation_centre)
tilt = Degrees(self.view.tilt)
self._set_precalculated_cor_tilt(cor, tilt)
def _set_precalculated_cor_tilt(self, cor: ScalarCoR, tilt: Degrees):
self.model.set_precalculated(cor, tilt)
self.view.set_results(*self.model.get_results())
for idx, point in enumerate(self.model.data_model.iter_points()):
self.view.set_table_point(idx, point.slice_index, point.cor)
self.do_update_projection()
self.do_reconstruct_slice()
def do_auto_find_cor(self):
if self.model.images is None:
return
method = self.view.get_auto_cor_method()
if method == AutoCorMethod.CORRELATION:
self._auto_find_correlation()
else:
self._auto_find_minimisation_square_sum()
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_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()
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
})