def microscope():
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect("localhost")
microscope.beams.ion_beam.scanning.rotation.value = 0.0
return microscope
def test__validate_scanning_rotation(rotation):
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect("localhost")
microscope.beams.ion_beam.scanning.rotation.value = rotation
_validate_scanning_rotation(microscope)
microscope.beams.ion_beam.scanning.rotation.value = 0.0
def test__validate_scanning_rotation_invalid(invalid_rotation):
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect("localhost")
microscope.beams.ion_beam.scanning.rotation.value = invalid_rotation
with pytest.raises(ValueError):
_validate_scanning_rotation(microscope)
microscope.beams.ion_beam.scanning.rotation.value = 0.0
def initialize(ip_address="localhost"):
"""Initialize autoscript for the FIBSEM microscope.
Parameters
----------
ip_address : str, optional
The ip address of the microscope, by default 'localhost'.
Use 'localhost' to connect to Autoscript offline.
Returns
-------
Autoscript microscope instance
"""
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect(ip_address)
microscope = reset_beam_shift(microscope)
microscope.imaging.set_active_view(2) # the ion beam view
return microscope
def test_mock_adorned():
pytest.importorskip(
"autoscript_sdb_microscope_client", reason="Autoscript is not available."
)
import autolamella.autoscript
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect("localhost")
expected = microscope.imaging.get_image()
output = autolamella.data.mock_adorned_image()
assert np.allclose(output.data, expected.data)
assert np.isclose(
output.metadata.binary_result.pixel_size.x,
expected.metadata.binary_result.pixel_size.x,
)
assert np.isclose(
output.metadata.binary_result.pixel_size.y,
expected.metadata.binary_result.pixel_size.y,
)
def microscope():
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect("localhost")
return microscope
def initialize(ip_address='10.0.0.1'):
"""Initialize connection to FIBSEM microscope with Autoscript."""
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect(ip_address)
return microscope
import numpy as np
import pytest
from piescope.data.mocktypes import MockAdornedImage
import piescope.fibsem
autoscript = pytest.importorskip("autoscript_sdb_microscope_client",
reason="Autoscript is not available.")
try:
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect("localhost")
except Exception as e:
pytest.skip(
"AutoScript cannot connect to localhost, skipping all AutoScript tests.",
allow_module_level=True)
def test_initialize():
"""Test connecting to the microscope offline with localhost."""
microscope = piescope.fibsem.initialize("localhost")
@pytest.fixture
def microscope():
from autoscript_sdb_microscope_client import SdbMicroscopeClient
microscope = SdbMicroscopeClient()
microscope.connect("localhost")
return microscope
