import logging
log = logging.getLogger(__name__)
[docs]def initialize(ip_address='10.0.0.1'):
"""Initialize connection to microscope."""
import autoscript_sdb_microscope_client
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect(ip_address)
microscope.imaging.set_active_view(2) # the ion beam view
return microscope
[docs]def patterning_engine(microscope):
"""Start Autoscript toolkit patterning engine."""
import autoscript_toolkit.drift_correction as dc_toolkit
dcp_engine = dc_toolkit.DcPatterningEngine(microscope)
return dcp_engine
[docs]def reset_patterning_state(microscope):
"""Reset patterning state"""
from autoscript_sdb_microscope_client.enumerations import BeamType
microscope.patterning.clear_patterns()
microscope.patterning.set_default_application_file('Si')
microscope.patterning.set_default_beam_type(BeamType.ION)
microscope.patterning.mode = 'Serial'
return microscope
[docs]def create_milling_patterns(microscope, roi_coordinates, settings):
"""Creates Autoscript milling patterns from a list of coordinates.
Parameters
----------
microscope : Autoscript microscope object.
roi_coordinates : list of lists
[center_x, center_y, roi_width, roi_height, depth, theta]
settings : dict
User input settings from config yml file.
Returns
-------
patterns
List containing the Autoscript milling patterns.
"""
import autoscript_core # need this for the ApplicationServerException
print('Creating milling ROIs...')
microscope = reset_patterning_state(microscope)
milling_patterns = []
for coords in roi_coordinates:
center_x, center_y, roi_width, roi_height, depth, theta = coords
try:
pattern = microscope.patterning.create_cleaning_cross_section(
center_x, center_y, roi_width, roi_height, depth)
pattern.overlap_x = settings['ion_beam_overlap']
pattern.overlap_y = settings['ion_beam_overlap']
pattern.rotation = theta
except autoscript_core.common.ApplicationServerException:
log.warn('Cannot create autoscript milling pattern because '
'it is outside of the field of view')
microscope = reset_patterning_state(microscope)
return []
milling_patterns.append(pattern)
return milling_patterns