def test_coverage_ROA(self):
"""Acquire a megafield (ROA), which does not match an integer multiple of fields.
Check that the acquired ROA exceeds the requested ROA."""
x_fields = 3
y_fields = 4
self.multibeam.resolution.value = (6400, 6400) # don't change
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
# some extra pixels (< 1 field) to be added to the ROA
x_margin, y_margin = (res_x / 10, res_y / 20)
coordinates = (0, 0,
res_x * px_size_x * x_fields + x_margin * px_size_x,
res_y * px_size_y * y_fields + y_margin * px_size_y) # in m
roc_2 = fastem.FastEMROC("roc_2", coordinates)
roc_3 = fastem.FastEMROC("roc_3", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name,
coordinates,
roc_2,
roc_3,
self.asm,
self.multibeam,
self.descanner,
self.mppc)
path_storage = os.path.join(datetime.today().strftime('%Y-%m-%d'), "test_project_field_indices")
f = fastem.acquire(roa, path_storage, self.scanner, self.multibeam, self.descanner, self.mppc, self.stage,
self.ccd, self.beamshift, self.lens)
data, e = f.result()
self.assertIsNone(e) # check no exceptions were returned
# check data returned contains the correct number of field images
# expect plus 1 field in x and y respectively
self.assertEqual(len(data), (x_fields + 1) * (y_fields + 1))
self.assertIsInstance(data[(0, 0)], model.DataArray)
def test_progress_ROA(self):
"""Check if some progress is reported between the field images acquired for the ROA (megafield)."""
x_fields = 2
y_fields = 3
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
coordinates = (0, 0, res_x * px_size_x * x_fields, res_y * px_size_y * y_fields) # in m
roc_2 = fastem.FastEMROC("roc_2", coordinates)
roc_3 = fastem.FastEMROC("roc_3", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name,
coordinates,
roc_2,
roc_3,
self.asm,
self.multibeam,
self.descanner,
self.mppc)
path_storage = os.path.join(datetime.today().strftime('%Y-%m-%d'), "test_project_progress")
self.updates = 0 # updated in callback on_progress_update
f = fastem.acquire(roa, path_storage, self.scanner, self.multibeam, self.descanner, self.mppc, self.stage,
self.ccd, self.beamshift, self.lens)
f.add_update_callback(self.on_progress_update) # callback executed every time f.set_progress is called
f.add_done_callback(self.on_done) # callback executed when f.set_result is called (via bindFuture)
data, e = f.result()
self.assertIsNone(e) # check no exceptions were returned
self.assertIsInstance(data[(0, 0)], model.DataArray)
self.assertTrue(self.done)
self.assertGreaterEqual(self.updates, 6) # at least one update per field
def test_calculate_field_indices(self):
"""Check that the correct number and order of field indices is returned and that row and column are in the
correct order."""
x_fields = 3
y_fields = 2
self.multibeam.resolution.value = (6400, 6400) # don't change
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
coordinates = (0, 0, res_x * px_size_x * x_fields, res_y * px_size_y * y_fields) # in m, don't change
roc_2 = fastem.FastEMROC("roc_2", coordinates)
roc_3 = fastem.FastEMROC("roc_3", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name,
coordinates,
roc_2,
roc_3,
self.asm,
self.multibeam,
self.descanner,
self.mppc)
expected_indices = [(0, 0), (1, 0), (2, 0), (0, 1), (1, 1), (2, 1)] # (col, row)
field_indices = roa._calculate_field_indices()
self.assertListEqual(expected_indices, field_indices)
def test_stage_movement(self):
"""Test that the stage move corresponds to one field image (excluding over-scanned pixels)."""
x_fields = 2
y_fields = 3
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
# FIXME: This test does not consider yet, that ROA coordinates need to be transformed into the
# correct coordinate system. Replace role='stage' with role='stage-scan' when function available.
# Note: Do not change those values; _calculate_field_indices handles floating point errors the same way
# as an ROA that does not match an integer number of field indices by just adding an additional row or column
# of field images.
xmin = -0.002 # top corner coordinate of ROA in stage coordinates in meter
ymin = +0.001 # left corner coordinate of ROA in stage coordinates in meter
xmax = xmin + res_x * px_size_x * x_fields
ymax = ymin + res_y * px_size_y * y_fields
coordinates = (xmin, ymin, xmax, ymax) # in m
roc_2 = fastem.FastEMROC("roc_2", coordinates)
roc_3 = fastem.FastEMROC("roc_3", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name,
coordinates,
roc_2,
roc_3,
self.asm,
self.multibeam,
self.descanner,
self.mppc)
path_storage = os.path.join(datetime.today().strftime('%Y-%m-%d'), "test_project_stage_move")
f = fastem.acquire(roa, path_storage, self.scanner, self.multibeam, self.descanner, self.mppc, self.stage,
self.ccd, self.beamshift, self.lens)
data, e = f.result()
self.assertIsNone(e) # check no exceptions were returned
# total expected stage movement in x and y during the acquisition
# half a field to start at center of first field image
exp_move_x = res_x / 2. * px_size_x + res_x * px_size_x * (x_fields - 1)
exp_move_y = res_y / 2. * px_size_y + res_y * px_size_y * (y_fields - 1)
# FIXME Needs to be updated when role="stage" is replaced with role="stage-scan"
# In role="stage" coordinate system:
# Move in the positive x direction, because the second field should be right of the first.
# Move in the negative y direction, because the second field should be below the first.
exp_position = (xmin + exp_move_x, ymax - exp_move_y)
# get the last stage position (it is the center of the last field)
cur_position = (self.stage.position.value['x'], self.stage.position.value['y'])
# check stage position is matching expected position (Note: stage accuracy is ~ TODO fix decimal accordingly)
numpy.testing.assert_almost_equal(exp_position, cur_position, decimal=6)
def test_estimate_acquisition_time(self):
"""Check that the estimated time for one ROA (megafield) is calculated correctly."""
# Use float for number of fields, in order to not end up with additional fields scanned and thus an
# incorrectly estimated roa acquisition time.
x_fields = 2.9
y_fields = 3.2
n_fields = math.ceil(x_fields) * math.ceil(y_fields)
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
coordinates = (0, 0, res_x * px_size_x * x_fields, res_y * px_size_y * y_fields) # in m
roc_2 = fastem.FastEMROC("roc_2", coordinates)
roc_3 = fastem.FastEMROC("roc_3", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
for dwell_time in [400e-9, 1e-6, 10e-6]:
self.multibeam.dwellTime.value = dwell_time
roa = fastem.FastEMROA(roa_name,
coordinates,
roc_2,
roc_3,
self.asm,
self.multibeam,
self.descanner,
self.mppc)
cell_res = self.mppc.cellCompleteResolution.value
flyback = self.descanner.physicalFlybackTime.value # extra time per line scan
# calculate expected roa (megafield) acquisition time
# (number of pixels per line * dwell time + flyback time) * number of lines * number of cells in x and y
estimated_line_time = cell_res[0] * dwell_time
# Remainder of the line scan time, part which is not a whole multiple of the descan periods.
remainder_scanning_time = estimated_line_time % self.descanner.clockPeriod.value
if remainder_scanning_time is not 0:
# Adjusted the flyback time if there is a remainder of scanning time by adding one setpoint to ensure
# the line scan time is equal to a whole multiple of the descanner clock period
flyback = flyback + (self.descanner.clockPeriod.value - remainder_scanning_time)
# Round to prevent floating point errors
estimated_line_time = numpy.round(estimated_line_time + flyback, 9)
# The estimated ROA time is the line time multiplied with the cell resolution and the number of fields.
# Additionally, 1.5s overhead per field image and the first field image is acquired twice.
estimated_roa_acq_time = (estimated_line_time * cell_res[1] + 1.5) * (n_fields + 1)
# get roa acquisition time
roa_acq_time = estimate_acquisition_time(roa)
self.assertAlmostEqual(estimated_roa_acq_time, roa_acq_time)
def test_acquire_ROA(self):
"""Acquire a small mega field image with ROA matching integer multiple of single field size."""
x_fields = 2
y_fields = 3
self.multibeam.resolution.value = (6400, 6400) # don't change
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
# Note: Do not change those values; _calculate_field_indices handles floating point errors the same way
# as an ROA that does not match an integer number of field indices by just adding an additional row or column
# of field images.
top = -0.002 # top corner coordinate of ROA in stage coordinates in meter
left = +0.001 # left corner coordinate of ROA in stage coordinates in meter
coordinates = (top, left, top + res_x * px_size_x * x_fields,
left + res_y * px_size_y * y_fields) # in m
roc = fastem.FastEMROC("roc_name", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name, coordinates, roc, self.asm,
self.multibeam, self.descanner, self.mppc)
path_storage = os.path.join(datetime.today().strftime('%Y-%m-%d'),
"test_project_megafield")
f = fastem.acquire(roa, path_storage, self.scanner, self.multibeam,
self.descanner, self.mppc, self.stage, self.ccd,
self.beamshift, self.lens)
data, e = f.result()
self.assertIsNone(e) # check no exceptions were returned
# check data returned contains the correct number of field images
self.assertEqual(len(data), x_fields * y_fields)
self.assertIsInstance(data[(0, 0)], model.DataArray)
def test_estimate_acquisition_time(self):
"""Check that the estimated time for one ROA (megafield) is calculated correctly."""
# Use float for number of fields, in order to not end up with additional fields scanned and thus an
# incorrectly estimated roa acquisition time.
x_fields = 2.9
y_fields = 3.2
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
coordinates = (0, 0, res_x * px_size_x * x_fields,
res_y * px_size_y * y_fields) # in m
roc = fastem.FastEMROC("roc_name", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name, coordinates, roc, self.asm,
self.multibeam, self.descanner, self.mppc)
cell_res = self.mppc.cellCompleteResolution.value
dwell_time = self.multibeam.dwellTime.value
flyback = self.descanner.physicalFlybackTime.value # extra time per line scan
# calculate expected roa (megafield) acquisition time
# (number of pixels per line * dwell time + flyback time) * number of lines * number of cells in x and y
estimated_roa_acq_time = (cell_res[0] * dwell_time + flyback) * cell_res[1] \
* math.ceil(x_fields) * math.ceil(y_fields)
# get roa acquisition time
roa_acq_time = roa.estimate_acquisition_time()
self.assertAlmostEqual(estimated_roa_acq_time, roa_acq_time)
def test_cancel_ROA(self):
"""Test if it is possible to cancel between field images acquired for one ROA."""
x_fields = 2
y_fields = 3
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
coordinates = (0, 0, res_x * px_size_x * x_fields, res_y * px_size_y * y_fields) # in m
roc_2 = fastem.FastEMROC("roc_2", coordinates)
roc_3 = fastem.FastEMROC("roc_3", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name,
coordinates,
roc_2,
roc_3,
self.asm,
self.multibeam,
self.descanner,
self.mppc)
path_storage = os.path.join(datetime.today().strftime('%Y-%m-%d'), "test_project_cancel")
self.end = None # updated in callback on_progress_update
self.updates = 0 # updated in callback on_progress_update
self.done = False # updated in callback on_done
f = fastem.acquire(roa, path_storage, self.scanner, self.multibeam, self.descanner, self.mppc, self.stage,
self.ccd, self.beamshift, self.lens)
f.add_update_callback(self.on_progress_update) # callback executed every time f.set_progress is called
f.add_done_callback(self.on_done) # callback executed when f.set_result is called (via bindFuture)
time.sleep(1) # make sure it's started
self.assertTrue(f.running())
f.cancel()
with self.assertRaises(CancelledError):
f.result(timeout=5) # add timeout = 5s in case cancellation error was not raised
self.assertGreaterEqual(self.updates, 3) # at least one update at cancellation
self.assertLessEqual(self.end, time.time())
self.assertTrue(self.done)
self.assertTrue(f.cancelled())
def test_stage_movement(self):
"""Test that the stage move corresponds to one field image (excluding over-scanned pixels)."""
x_fields = 2
y_fields = 3
res_x, res_y = self.multibeam.resolution.value # single field size
px_size_x, px_size_y = self.multibeam.pixelSize.value
# FIXME: It is not clear in which coordinate system the coordinates of the ROA are!!!
# Note: the coordinates are in the stage coordinate system with role='stage' and not role='stage-scan'.
# However, for fast em acquisitions we use stage-scan, which scans along the multiprobe axes.
# FIXME: This test does not consider yet, that ROA coordinates need to be transformed into the
# correct coordinate system. Replace role='stage' with role='stage-scan' when function available.
# Note: Do not change those values; _calculate_field_indices handles floating point errors the same way
# as an ROA that does not match an integer number of field indices by just adding an additional row or column
# of field images.
top = -0.002 # top corner coordinate of ROA in stage coordinates in meter
left = +0.001 # left corner coordinate of ROA in stage coordinates in meter
coordinates = (top, left, top + res_x * px_size_x * x_fields,
left + res_y * px_size_y * y_fields) # in m
roc = fastem.FastEMROC("roc_name", coordinates)
roa_name = time.strftime("test_megafield_id-%Y-%m-%d-%H-%M-%S")
roa = fastem.FastEMROA(roa_name, coordinates, roc, self.asm,
self.multibeam, self.descanner, self.mppc)
path_storage = os.path.join(datetime.today().strftime('%Y-%m-%d'),
"test_project_stage_move")
f = fastem.acquire(roa, path_storage, self.multibeam, self.descanner,
self.mppc, self.stage)
data, e = f.result()
self.assertIsNone(e) # check no exceptions were returned
# total expected stage movement in x and y during the acquisition
# half a field to start at center of first field image
exp_move_x = res_x / 2. * px_size_x + res_x * px_size_x * (x_fields -
1)
exp_move_y = res_y / 2. * px_size_y + res_y * px_size_y * (y_fields -
1)
# TODO these comments are true, when stage is replaced with stage-scan
# Move in the negative x direction, because the second field should be right of the first.
# Move in positive y direction, because the second field should be bottom of the first.
exp_position = (top - exp_move_x, left + exp_move_y)
# get the last stage position (it is the center of the last field)
cur_position = (self.stage.position.value['x'],
self.stage.position.value['y'])
# check stage position is matching expected position (Note: stage accuracy is ~ TODO fix decimal accordingly)
numpy.testing.assert_almost_equal(exp_position,
cur_position,
decimal=6)
