def acquire_ov(base_dir, selection, sem, stage, ovm, cs, queue, trigger):
# Update current xy position:
stage.get_xy()
queue.put('UPDATE XY')
trigger.s.emit()
success = True
if selection == -1: # acquire all OVs
start, end = 0, ovm.get_number_ov()
else:
start, end = selection, selection + 1 # acquire only one OV
# Acquisition loop:
for i in range(start, end):
queue.put(
utils.format_log_entry('3VIEW: Moving stage to OV %d position.' %
i))
trigger.s.emit()
# Move to OV stage coordinates:
stage.move_to_xy(cs.get_ov_centre_s(i))
# Check to see if error ocurred:
if stage.get_error_state() > 0:
success = False
stage.reset_error_state()
if success:
# update stage position in GUI:
queue.put('UPDATE XY')
trigger.s.emit()
# Set specified OV frame settings:
sem.apply_frame_settings(ovm.get_ov_size_selector(i),
ovm.get_ov_pixel_size(i),
ovm.get_ov_dwell_time(i))
save_path = base_dir + '\\workspace\\OV' + str(i).zfill(3) + '.bmp'
queue.put(utils.format_log_entry('SEM: Acquiring OV %d.' % i))
trigger.s.emit()
# Indicate the overview being acquired in the viewport
queue.put('ACQ IND OV' + str(i))
trigger.s.emit()
success = sem.acquire_frame(save_path)
# Remove indicator colour
queue.put('ACQ IND OV' + str(i))
trigger.s.emit()
# Show updated OV:
queue.put('MV UPDATE OV' + str(i))
trigger.s.emit()
if success:
ovm.update_ov_file_list(i, save_path)
if not success:
break # leave loop if error has occured
if success:
queue.put('OV SUCCESS')
trigger.s.emit()
else:
queue.put('OV FAILURE')
trigger.s.emit()
def _add_to_main_log(self, msg):
"""Add entry to the log in the main window"""
msg = utils.format_log_entry(msg)
self.main_controls_trigger.transmit(msg)
def acquire_ov(base_dir, selection, sem, stage, ovm, img_inspector,
main_controls_trigger, viewport_trigger):
# Update current XY stage position
stage.get_xy()
success = True
if selection == -1:
# acquire all OVs
start = 0
end = ovm.number_ov
else:
# acquire only one OV
start = selection
end = selection + 1
# Acquisition loop
for ov_index in range(start, end):
if not ovm[ov_index].active:
continue
main_controls_trigger.transmit(
utils.format_log_entry('STAGE: Moving to OV %d position.' %
ov_index))
# Move to OV stage coordinates
stage.move_to_xy(ovm[ov_index].centre_sx_sy)
# Check to see if error ocurred
if stage.error_state != Error.none:
stage.reset_error_state()
sleep(1)
# Try again
stage.move_to_xy(ovm[ov_index].centre_sx_sy)
if stage.error_state != Error.none:
stage.reset_error_state()
main_controls_trigger.transmit(
utils.format_log_entry(
'STAGE: Second attempt to move to OV %d position failed.'
% ov_index))
success = False
if success:
# Update stage position in Main Controls GUI and Viewport
main_controls_trigger.transmit('UPDATE XY')
sleep(0.1)
main_controls_trigger.transmit('DRAW VP')
# Use custom focus settings for this OV if available
ov_wd = ovm[ov_index].wd_stig_xy[0]
if ov_wd > 0:
sem.set_wd(ov_wd)
stig_x, stig_y = ovm[ov_index].wd_stig_xy[1:3]
sem.set_stig_xy(stig_x, stig_y)
main_controls_trigger.transmit(
utils.format_log_entry(
'SEM: Using specified ' +
utils.format_wd_stig(ov_wd, stig_x, stig_y)))
# Set specified OV frame settings
sem.apply_frame_settings(ovm[ov_index].frame_size_selector,
ovm[ov_index].pixel_size,
ovm[ov_index].dwell_time)
save_path = os.path.join(base_dir, 'workspace',
'OV' + str(ov_index).zfill(3) + '.bmp')
main_controls_trigger.transmit(
utils.format_log_entry('SEM: Acquiring OV %d.' % ov_index))
# Indicate the overview being acquired in the viewport
viewport_trigger.transmit('ACQ IND OV' + str(ov_index))
success = sem.acquire_frame(save_path)
# Remove indicator colour
viewport_trigger.transmit('ACQ IND OV' + str(ov_index))
_, _, _, load_error, _, grab_incomplete = (
img_inspector.load_and_inspect(save_path))
if load_error or grab_incomplete:
# Try again
sleep(0.5)
main_controls_trigger.transmit(
utils.format_log_entry(
'SEM: Second attempt: Acquiring OV %d.' % ov_index))
viewport_trigger.transmit('ACQ IND OV' + str(ov_index))
success = sem.acquire_frame(save_path)
viewport_trigger.transmit('ACQ IND OV' + str(ov_index))
sleep(1)
_, _, _, load_error, _, grab_incomplete = (
img_inspector.load_and_inspect(save_path))
if load_error or grab_incomplete:
success = False
if load_error:
cause = 'load error'
elif grab_incomplete:
cause = 'grab incomplete'
else:
cause = 'acquisition error'
main_controls_trigger.transmit(
utils.format_log_entry(
f'SEM: Second attempt to acquire OV {ov_index} '
f'failed ({cause}).'))
if success:
ovm[ov_index].vp_file_path = save_path
# Show updated OV
viewport_trigger.transmit('DRAW VP')
if not success:
break # leave loop if error has occured
if success:
viewport_trigger.transmit('REFRESH OV SUCCESS')
else:
viewport_trigger.transmit('REFRESH OV FAILURE')
def add_to_main_log(self, msg):
"""Add entry to the log in the main window"""
msg = utils.format_log_entry(msg)
# Send entry to main window via queue and trigger:
self.queue.put(msg)
self.trigger.s.emit()