def _on_fine_align(self, event):
"""
Called when the "Fine alignment" button is clicked
"""
self._pause()
main_data = self._main_data_model
main_data.is_acquiring.value = True
logging.debug("Starting overlay procedure")
f = align.FindOverlay(self.OVRL_REPETITION,
main_data.fineAlignDwellTime.value,
self.OVRL_MAX_DIFF,
main_data.ebeam,
main_data.ccd,
main_data.sed,
skew=True)
logging.debug("Overlay procedure is running...")
self._acq_future = f
# Transform Fine alignment button into cancel
self._tab_panel.btn_fine_align.Bind(wx.EVT_BUTTON, self._on_cancel)
self._tab_panel.btn_fine_align.Label = "Cancel"
# Set up progress bar
self._tab_panel.lbl_fine_align.Hide()
self._tab_panel.gauge_fine_align.Show()
self._sizer.Layout()
self._faf_connector = ProgressiveFutureConnector(
f, self._tab_panel.gauge_fine_align)
f.add_done_callback(self._on_fa_done)
def test_find_overlay(self):
"""
Test FindOverlay
"""
escan = self.ebeam
detector = self.sed
ccd = self.ccd
f = align.FindOverlay((7, 7), 0.1, 1e-06, escan, ccd, detector)
t, md = f.result()
def test_find_overlay_failure(self):
"""
Test FindOverlay failure due to low maximum allowed difference
"""
escan = self.ebeam
detector = self.sed
ccd = self.ccd
f = align.FindOverlay((9, 9), 1e-06, 1e-08, escan, ccd, detector)
with self.assertRaises(ValueError):
f.result()
def acquire(self):
"""
Runs the find overlay procedure
returns Future that will have as a result an empty DataArray with
the correction metadata
"""
# Just calls the FindOverlay function and return its future
ovrl_future = align.FindOverlay(self.repetition.value,
self.dwellTime.value, OVRL_MAX_DIFF,
self._emitter, self._ccd,
self._detector)
return _FutureOverlayWrapper(ovrl_future)
def test_find_overlay_failure(self):
"""
Test FindOverlay failure due to low maximum allowed difference
"""
f = align.FindOverlay((6, 6),
1e-6,
1e-08,
self.ebeam,
self.ccd,
self.sed,
skew=True)
with self.assertRaises(ValueError):
f.result()
def test_find_overlay(self):
"""
Test FindOverlay
"""
f = align.FindOverlay((4, 4),
0.1,
10e-06,
self.ebeam,
self.ccd,
self.sed,
skew=True)
t, (opt_md, sem_md) = f.result()
self.assertEqual(len(t), 5)
self.assertIn(model.MD_PIXEL_SIZE_COR, opt_md)
self.assertIn(model.MD_SHEAR_COR, sem_md)
def test_find_overlay_cancelled(self):
"""
Test FindOverlay cancellation
"""
escan = self.ebeam
detector = self.sed
ccd = self.ccd
f = align.FindOverlay((9, 9), 1e-06, 1e-07, escan, ccd, detector)
time.sleep(0.04) # Cancel almost after the half grid is scanned
f.cancel()
self.assertTrue(f.cancelled())
self.assertTrue(f.done())
with self.assertRaises(futures.CancelledError):
f.result()
def test_find_overlay_cancelled(self):
"""
Test FindOverlay cancellation
"""
f = align.FindOverlay((6, 6),
10e-06,
1e-07,
self.ebeam,
self.ccd,
self.sed,
skew=True)
time.sleep(0.04) # Cancel almost after the half grid is scanned
f.cancel()
self.assertTrue(f.cancelled())
self.assertTrue(f.done())
with self.assertRaises(futures.CancelledError):
f.result()
def test_bad_mag(self):
self._prepare_hardware(ccd_img="overlay_4_4_test_1.tiff")
# original mag was 35 (SEM pxs size = 432e-9 m), which was incorrect by x2
for mag in (30, 40, 70, 1000):
self.ebeam.magnification.value = mag
f = align.FindOverlay((4, 4),
0.001,
10e-06,
self.ebeam,
self.ccd,
self.sed,
skew=True)
t, (opt_md, sem_md) = f.result()
self.assertEqual(len(t), 5)
self.assertIn(model.MD_PIXEL_SIZE_COR, opt_md)
self.assertIn(model.MD_SHEAR_COR, sem_md)
def test_ratio_3_4(self):
"""
Try also (unsual) 3:4
"""
ebeam_kwargs = {
"max_res": [3072, 4096],
"hfw_nomag": 0.132,
}
# SEM mag = 150x ~ SEM pxs size = 288e-9 m
self._prepare_hardware(ebeam_kwargs, 150, "overlay_4_4_test_2.tiff")
f = align.FindOverlay((4, 4),
0.001,
10e-06,
self.ebeam,
self.ccd,
self.sed,
skew=True)
t, (opt_md, sem_md) = f.result()
self.assertEqual(len(t), 5)
self.assertIn(model.MD_PIXEL_SIZE_COR, opt_md)
self.assertIn(model.MD_SHEAR_COR, sem_md)
def test_ratio_4_3(self):
"""
Test FindOverlay when the SEM image ratio is not 1:1 (but 4:3)
"""
ebeam_kwargs = {
"max_res": [4096, 3072],
"hfw_nomag": 0.177,
}
# SEM mag = 150x ~ SEM pxs size = 288e-9 m
self._prepare_hardware(ebeam_kwargs, 150, "overlay_4_4_test_2.tiff")
f = align.FindOverlay((4, 4),
0.001,
10e-06,
self.ebeam,
self.ccd,
self.sed,
skew=True)
t, (opt_md, sem_md) = f.result()
self.assertEqual(len(t), 5)
self.assertIn(model.MD_PIXEL_SIZE_COR, opt_md)
self.assertIn(model.MD_SHEAR_COR, sem_md)
def _DoDelphiCalibration(future, main_data, overview_pressure, vacuum_pressure,
vented_pressure):
"""
It performs all the calibration steps for Delphi including the lens alignment,
the conversion metadata update and the fine alignment.
future (model.ProgressiveFuture): Progressive future provided by the wrapper
main_data (odemis.gui.model.MainGUIData)
overview_pressure (float): NavCam pressure value
vacuum_pressure (float): Pressure under vacuum
vented_pressure (float): Pressure when vented
returns (tuple of floats): Hole top
(tuple of floats): Hole bottom
(tuple of floats): Stage translation
(tuple of floats): Stage scale
(tuple of floats): Stage rotation
(tuple of floats): Image scale
(tuple of floats): Image rotation
(tuple of floats): Resolution-related shift slope
(tuple of floats): Resolution-related shift intercept
(tuple of floats): HFW-related shift slope
(tuple of floats): Spot shift percentage
raises:
CancelledError() if cancelled
"""
logging.debug("Delphi calibration...")
try:
if future._delphi_calib_state == CANCELLED:
raise CancelledError()
try:
# Move to the overview position first
f = main_data.chamber.moveAbs({"pressure": overview_pressure})
f.result()
# Clear all the previous calibration
logging.debug("Clear all the previous calibration...")
main_data.stage.updateMetadata({
model.MD_POS_COR: (0, 0),
model.MD_PIXEL_SIZE_COR: (1, 1),
model.MD_ROTATION_COR: 0
})
# We need access to the separate sem and optical stages, which form
# the "stage". They are not found in the model, but we can find them
# as children of stage (on the DELPHI), and distinguish them by
# their role.
sem_stage = None
opt_stage = None
logging.debug("Find SEM and optical stages...")
for c in main_data.stage.children.value:
if c.role == "sem-stage":
sem_stage = c
elif c.role == "align":
opt_stage = c
if not sem_stage or not opt_stage:
raise KeyError("Failed to find SEM and optical stages")
# Reference the (optical) stage
logging.debug("Reference the (optical) stage...")
f = opt_stage.reference({"x", "y"})
f.result()
logging.debug("Reference the focus...")
f = main_data.focus.reference({"z"})
f.result()
# SEM stage to (0,0)
logging.debug("Move to the center of SEM stage...")
f = sem_stage.moveAbs({"x": 0, "y": 0})
f.result()
# Calculate offset approximation
try:
logging.debug("Starting lens alignment...")
f = aligndelphi.LensAlignment(main_data.overview_ccd,
sem_stage)
position = f.result()
logging.debug("SEM position after lens alignment: %s",
position)
except Exception:
raise IOError("Lens alignment failed.")
# Update progress of the future
future.set_end_time(time.time() + 14 * 60)
# Just to check if move makes sense
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
# Move to SEM
f = main_data.chamber.moveAbs({"pressure": vacuum_pressure})
f.result()
# Lens to a good optical focus position
logging.debug("Move focus to a good initial level...")
f = main_data.focus.moveAbs({"z": DELPHI_OPT_GOOD_FOCUS})
f.result()
# Update progress of the future
logging.debug("Try to update the remaining time...")
future.set_end_time(time.time() + 12.5 * 60)
# Compute stage calibration values
try:
logging.debug("Starting conversion update...")
f = aligndelphi.UpdateConversion(main_data.ccd,
main_data.bsd,
main_data.ebeam,
sem_stage,
opt_stage,
main_data.ebeam_focus,
main_data.focus,
main_data.stage,
first_insertion=True,
sem_position=position)
htop, hbot, hole_focus, strans, srot, sscale, resa, resb, hfwa, spotshift = f.result(
)
except Exception:
raise IOError("Conversion update failed.")
# Update progress of the future
logging.debug("Try to update the remaining time...")
future.set_end_time(time.time() + 60)
# Run the optical fine alignment
# TODO: reuse the exposure time
f = align.FindOverlay(
(4, 4),
0.5, # s, dwell time
10e-06, # m, maximum difference allowed
main_data.ebeam,
main_data.ccd,
main_data.bsd)
trans_val, cor_md = f.result()
iscale = cor_md[model.MD_PIXEL_SIZE_COR]
irot = cor_md[model.MD_ROTATION_COR]
return htop, hbot, strans, sscale, srot, iscale, irot, resa, resb, hfwa, spotshift
except Exception:
raise IOError("Delphi calibration failed.")
finally:
with future._delphi_calib_lock:
if future._delphi_calib_state == CANCELLED:
raise CancelledError()
future._delphi_calib_state = FINISHED
def man_calib(logpath):
escan = None
detector = None
ccd = None
# find components by their role
for c in model.getComponents():
if c.role == "e-beam":
escan = c
elif c.role == "bs-detector":
detector = c
elif c.role == "ccd":
ccd = c
elif c.role == "sem-stage":
sem_stage = c
elif c.role == "align":
opt_stage = c
elif c.role == "ebeam-focus":
ebeam_focus = c
elif c.role == "overview-focus":
navcam_focus = c
elif c.role == "focus":
focus = c
elif c.role == "overview-ccd":
overview_ccd = c
elif c.role == "chamber":
chamber = c
if not all([escan, detector, ccd]):
logging.error("Failed to find all the components")
raise KeyError("Not all components found")
hw_settings = aligndelphi.list_hw_settings(escan, ccd)
try:
# Get pressure values
pressures = chamber.axes["pressure"].choices
vacuum_pressure = min(pressures.keys())
vented_pressure = max(pressures.keys())
if overview_ccd:
for p, pn in pressures.items():
if pn == "overview":
overview_pressure = p
break
else:
raise IOError("Failed to find the overview pressure in %s" %
(pressures, ))
calibconf = get_calib_conf()
shid, sht = chamber.sampleHolder.value
calib_values = calibconf.get_sh_calib(shid)
if calib_values is None:
first_hole = second_hole = offset = resa = resb = hfwa = scaleshift = (
0, 0)
scaling = iscale = iscale_xy = (1, 1)
rotation = irot = ishear = 0
hole_focus = aligndelphi.SEM_KNOWN_FOCUS
opt_focus = aligndelphi.OPTICAL_KNOWN_FOCUS
print "\033[1;31mCalibration values missing! All the steps will be performed anyway...\033[1;m"
force_calib = True
else:
first_hole, second_hole, hole_focus, opt_focus, offset, scaling, rotation, iscale, irot, iscale_xy, ishear, resa, resb, hfwa, scaleshift = calib_values
force_calib = False
print "\033[1;36m"
print "**Delphi Manual Calibration steps**"
print "1.Sample holder hole detection"
print " Current values: 1st hole: " + str(first_hole)
print " 2st hole: " + str(second_hole)
print " hole focus: " + str(hole_focus)
print "2.Twin stage calibration"
print " Current values: offset: " + str(offset)
print " scaling: " + str(scaling)
print " rotation: " + str(rotation)
print " optical focus: " + str(opt_focus)
print "3.Fine alignment"
print " Current values: scale: " + str(iscale)
print " rotation: " + str(irot)
print " scale-xy: " + str(iscale_xy)
print " shear: " + str(ishear)
print "4.SEM image calibration"
print " Current values: resolution-a: " + str(resa)
print " resolution-b: " + str(resb)
print " hfw-a: " + str(hfwa)
print " spot shift: " + str(scaleshift)
print '\033[1;m'
print "\033[1;33mNote that you should not perform any stage move during the process. \nInstead, you may zoom in/out while focusing.\033[1;m"
print "\033[1;30mNow initializing, please wait...\033[1;m"
# Move to the overview position first
f = chamber.moveAbs({"pressure": overview_pressure})
f.result()
# Reference the (optical) stage
f = opt_stage.reference({"x", "y"})
f.result()
f = focus.reference({"z"})
f.result()
# SEM stage to (0,0)
f = sem_stage.moveAbs({"x": 0, "y": 0})
f.result()
# Calculate offset approximation
try:
f = aligndelphi.LensAlignment(overview_ccd, sem_stage, logpath)
position = f.result()
except IOError as ex:
if not force_calib:
position = (offset[0] * scaling[0], offset[1] * scaling[1])
else:
position = (0, 0)
logging.warning(
"Failed to locate the optical lens (%s), will used previous value %s",
ex, position)
# Just to check if move makes sense
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
# Move to SEM
f = chamber.moveAbs({"pressure": vacuum_pressure})
f.result()
# Set basic e-beam settings
escan.spotSize.value = 2.7
escan.accelVoltage.value = 5300 # V
# Detect the holes/markers of the sample holder
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to execute the sample holder hole detection? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
# Move Phenom sample stage next to expected hole position
sem_stage.moveAbsSync(aligndelphi.SHIFT_DETECTION)
ebeam_focus.moveAbsSync({"z": hole_focus})
# Set the FoV to almost 2mm
escan.horizontalFoV.value = escan.horizontalFoV.range[1]
msg = "\033[1;34mPlease turn on the SEM stream and focus the SEM image. Then turn off the stream and press Enter ...\033[1;m"
raw_input(msg)
print "\033[1;30mTrying to detect the holes/markers, please wait...\033[1;m"
try:
hole_detectionf = aligndelphi.HoleDetection(
detector,
escan,
sem_stage,
ebeam_focus,
manual=True,
logpath=logpath)
new_first_hole, new_second_hole, new_hole_focus = hole_detectionf.result(
)
print '\033[1;36m'
print "Values computed: 1st hole: " + str(new_first_hole)
print " 2st hole: " + str(new_second_hole)
print " hole focus: " + str(new_hole_focus)
print '\033[1;m'
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to update the calibration file with these values? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
first_hole, second_hole, hole_focus = new_first_hole, new_second_hole, new_hole_focus
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
break
except IOError:
print "\033[1;31mSample holder hole detection failed.\033[1;m"
else:
break
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
f = opt_stage.moveAbs({"x": 0, "y": 0})
f.result()
if hole_focus is not None:
good_focus = hole_focus - aligndelphi.GOOD_FOCUS_OFFSET
else:
good_focus = aligndelphi.SEM_KNOWN_FOCUS - aligndelphi.GOOD_FOCUS_OFFSET
f = ebeam_focus.moveAbs({"z": good_focus})
f.result()
# Set min fov
# We want to be as close as possible to the center when we are zoomed in
escan.horizontalFoV.value = escan.horizontalFoV.range[0]
pure_offset = None
# Start with the best optical focus known so far
f = focus.moveAbs({"z": opt_focus})
f.result()
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to execute the twin stage calibration? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
# Configure CCD and e-beam to write CL spots
ccd.binning.value = (1, 1)
ccd.resolution.value = ccd.resolution.range[1]
ccd.exposureTime.value = 900e-03
escan.scale.value = (1, 1)
escan.resolution.value = (1, 1)
escan.translation.value = (0, 0)
if not escan.rotation.readonly:
escan.rotation.value = 0
escan.shift.value = (0, 0)
escan.dwellTime.value = 5e-06
detector.data.subscribe(_discard_data)
print "\033[1;34mPlease turn on the Optical stream, set Power to 0 Watt and focus the image so you have a clearly visible spot.\033[1;m"
print "\033[1;34mUse the up and down arrows or the mouse to move the optical focus and right and left arrows to move the SEM focus. Then turn off the stream and press Enter ...\033[1;m"
if not force_calib:
print "\033[1;33mIf you cannot see the whole source background (bright circle) you may try to move to the already known offset position. \nTo do this press the R key at any moment.\033[1;m"
rollback_pos = (offset[0] * scaling[0],
offset[1] * scaling[1])
else:
rollback_pos = None
ar = ArrowFocus(sem_stage, focus, ebeam_focus,
ccd.depthOfField.value,
escan.depthOfField.value)
ar.focusByArrow(rollback_pos)
detector.data.unsubscribe(_discard_data)
print "\033[1;30mFine alignment in progress, please wait...\033[1;m"
try:
# TODO: the first point (at 0,0) isn't different from the next 4 points,
# excepted it might be a little harder to focus.
# => use the same code for all of them
align_offsetf = aligndelphi.AlignAndOffset(
ccd, detector, escan, sem_stage, opt_stage, focus,
logpath)
align_offset = align_offsetf.result()
new_opt_focus = focus.position.value.get('z')
def ask_user_to_focus(n):
detector.data.subscribe(_discard_data)
msg = (
"\033[1;34mAbout to calculate rotation and scaling (%d/4). "
"Please turn on the Optical stream, "
"set Power to 0 Watt and focus the image using the mouse "
"so you have a clearly visible spot. \n"
"If you do not see a spot nor the source background, "
"move the sem-stage from the command line by steps of 200um "
"in x and y until you can see the source background at the center. \n"
"Then turn off the stream and press Enter ...\033[1;m"
% (n + 1, ))
raw_input(msg) # TODO: use ArrowFocus() too?
print "\033[1;30mCalculating rotation and scaling (%d/4), please wait...\033[1;m" % (
n + 1, )
detector.data.unsubscribe(_discard_data)
f = aligndelphi.RotationAndScaling(
ccd,
detector,
escan,
sem_stage,
opt_stage,
focus,
align_offset,
manual=ask_user_to_focus,
logpath=logpath)
acc_offset, new_rotation, new_scaling = f.result()
# Offset is divided by scaling, since Convert Stage applies scaling
# also in the given offset
pure_offset = acc_offset
new_offset = ((acc_offset[0] / new_scaling[0]),
(acc_offset[1] / new_scaling[1]))
print '\033[1;36m'
print "Values computed: offset: " + str(new_offset)
print " scaling: " + str(new_scaling)
print " rotation: " + str(new_rotation)
print " optical focus: " + str(
new_opt_focus)
print '\033[1;m'
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to update the calibration file with these values? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
offset, scaling, rotation, opt_focus = new_offset, new_scaling, new_rotation, new_opt_focus
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
break
except IOError:
print "\033[1;31mTwin stage calibration failed.\033[1;m"
else:
break
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to execute the fine alignment? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
# Return to the center so fine alignment can be executed just after calibration
f = opt_stage.moveAbs({"x": 0, "y": 0})
f.result()
if pure_offset is not None:
f = sem_stage.moveAbs({
"x": pure_offset[0],
"y": pure_offset[1]
})
f.result()
elif offset is not None:
f = sem_stage.moveAbs({
"x": offset[0] * scaling[0],
"y": offset[1] * scaling[1]
})
f.result()
else:
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
f = focus.moveAbs({"z": opt_focus})
f.result()
f = ebeam_focus.moveAbs({"z": good_focus})
f.result()
# Run the optical fine alignment
# TODO: reuse the exposure time
# Configure e-beam to write CL spots
escan.horizontalFoV.value = escan.horizontalFoV.range[0]
escan.scale.value = (1, 1)
escan.resolution.value = (1, 1)
escan.translation.value = (0, 0)
if not escan.rotation.readonly:
escan.rotation.value = 0
escan.shift.value = (0, 0)
escan.dwellTime.value = 5e-06
detector.data.subscribe(_discard_data)
print "\033[1;34mPlease turn on the Optical stream, set Power to 0 Watt and focus the image so you have a clearly visible spot.\033[1;m"
print "\033[1;34mUse the up and down arrows or the mouse to move the optical focus and right and left arrows to move the SEM focus. Then turn off the stream and press Enter ...\033[1;m"
ar = ArrowFocus(sem_stage, focus, ebeam_focus,
ccd.depthOfField.value,
escan.depthOfField.value)
ar.focusByArrow()
detector.data.unsubscribe(_discard_data)
# restore CCD settings (as the GUI/user might have changed them)
ccd.binning.value = (1, 1)
ccd.resolution.value = ccd.resolution.range[1]
ccd.exposureTime.value = 900e-03
# Center (roughly) the spot on the CCD
f = spot.CenterSpot(ccd, sem_stage, escan, spot.ROUGH_MOVE,
spot.STAGE_MOVE, detector.data)
dist, vect = f.result()
if dist is None:
logging.warning(
"Failed to find a spot, twin stage calibration might have failed"
)
print "\033[1;30mFine alignment in progress, please wait...\033[1;m"
try:
escan.horizontalFoV.value = 80e-06
f = align.FindOverlay(
(4, 4),
0.5, # s, dwell time
10e-06, # m, maximum difference allowed
escan,
ccd,
detector,
skew=True,
bgsub=True)
trans_val, cor_md = f.result()
trans_md, skew_md = cor_md
new_iscale = trans_md[model.MD_PIXEL_SIZE_COR]
new_irot = -trans_md[model.MD_ROTATION_COR] % (2 * math.pi)
new_ishear = skew_md[model.MD_SHEAR_COR]
new_iscale_xy = skew_md[model.MD_PIXEL_SIZE_COR]
print '\033[1;36m'
print "Values computed: scale: " + str(new_iscale)
print " rotation: " + str(new_irot)
print " scale-xy: " + str(new_iscale_xy)
print " shear: " + str(new_ishear)
print '\033[1;m'
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to update the calibration file with these values? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
iscale, irot, iscale_xy, ishear = new_iscale, new_irot, new_iscale_xy, new_ishear
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
break
except ValueError:
print "\033[1;31mFine alignment failed.\033[1;m"
else:
break
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to execute the SEM image calibration? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
# Resetting shift parameters, to not take them into account during calib
blank_md = dict.fromkeys(aligndelphi.MD_CALIB_SEM, (0, 0))
escan.updateMetadata(blank_md)
# We measure the shift in the area just behind the hole where there
# are always some features plus the edge of the sample carrier. For
# that reason we use the focus measured in the hole detection step
f = sem_stage.moveAbs(aligndelphi.SHIFT_DETECTION)
f.result()
f = ebeam_focus.moveAbs({"z": hole_focus})
f.result()
try:
# Compute spot shift percentage
print "\033[1;30mSpot shift measurement in progress, please wait...\033[1;m"
f = aligndelphi.ScaleShiftFactor(detector, escan, logpath)
new_scaleshift = f.result()
# Compute resolution-related values.
print "\033[1;30mCalculating resolution shift, please wait...\033[1;m"
resolution_shiftf = aligndelphi.ResolutionShiftFactor(
detector, escan, logpath)
new_resa, new_resb = resolution_shiftf.result()
# Compute HFW-related values
print "\033[1;30mCalculating HFW shift, please wait...\033[1;m"
hfw_shiftf = aligndelphi.HFWShiftFactor(
detector, escan, logpath)
new_hfwa = hfw_shiftf.result()
print '\033[1;36m'
print "Values computed: resolution-a: " + str(new_resa)
print " resolution-b: " + str(new_resb)
print " hfw-a: " + str(new_hfwa)
print " spot shift: " + str(new_scaleshift)
print '\033[1;m'
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
msg = "\033[1;35mDo you want to update the calibration file with these values? [Y/n]\033[1;m"
ans = raw_input(msg)
if ans in YES_CHARS:
resa, resb, hfwa, scaleshift = new_resa, new_resb, new_hfwa, new_scaleshift
calibconf.set_sh_calib(shid, first_hole, second_hole,
hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot,
iscale_xy, ishear, resa, resb,
hfwa, scaleshift)
break
except IOError:
print "\033[1;31mSEM image calibration failed.\033[1;m"
else:
break
# Update calibration file
print "\033[1;30mUpdating calibration file is done\033[1;m"
finally:
print "\033[1;30mCalibration ended, now ejecting sample, please wait...\033[1;m"
# Eject the sample holder
f = chamber.moveAbs({"pressure": vented_pressure})
aligndelphi.restore_hw_settings(escan, ccd, hw_settings)
# Store the final version of the calibration file
try:
shutil.copy(calibconf.file_path, logpath)
except Exception:
logging.info("Failed to log calibration file", exc_info=True)
f.result()
def man_calib(logpath):
escan = None
detector = None
ccd = None
# find components by their role
for c in model.getComponents():
if c.role == "e-beam":
escan = c
elif c.role == "bs-detector":
detector = c
elif c.role == "ccd":
ccd = c
elif c.role == "sem-stage":
sem_stage = c
elif c.role == "align":
opt_stage = c
elif c.role == "ebeam-focus":
ebeam_focus = c
elif c.role == "overview-focus":
navcam_focus = c
elif c.role == "focus":
focus = c
elif c.role == "overview-ccd":
overview_ccd = c
elif c.role == "chamber":
chamber = c
if not all([escan, detector, ccd]):
logging.error("Failed to find all the components")
raise KeyError("Not all components found")
hw_settings = aligndelphi.list_hw_settings(escan, ccd)
try:
# Get pressure values
pressures = chamber.axes["pressure"].choices
vacuum_pressure = min(pressures.keys())
vented_pressure = max(pressures.keys())
if overview_ccd:
for p, pn in pressures.items():
if pn == "overview":
overview_pressure = p
break
else:
raise IOError("Failed to find the overview pressure in %s" % (pressures,))
calibconf = get_calib_conf()
shid, sht = chamber.sampleHolder.value
calib_values = calibconf.get_sh_calib(shid)
if calib_values is None:
first_hole = second_hole = offset = resa = resb = hfwa = scaleshift = (0, 0)
scaling = iscale = iscale_xy = (1, 1)
rotation = irot = ishear = 0
hole_focus = aligndelphi.SEM_KNOWN_FOCUS
opt_focus = aligndelphi.OPTICAL_KNOWN_FOCUS
print_col(ANSI_RED, "Calibration values missing! All the steps will be performed anyway...")
force_calib = True
else:
first_hole, second_hole, hole_focus, opt_focus, offset, scaling, rotation, iscale, irot, iscale_xy, ishear, resa, resb, hfwa, scaleshift = calib_values
force_calib = False
print_col(ANSI_CYAN,
"**Delphi Manual Calibration steps**\n"
"1.Sample holder hole detection\n"
" Current values: 1st hole: " + str(first_hole) + "\n"
" 2st hole: " + str(second_hole) + "\n"
" hole focus: " + str(hole_focus) + "\n"
"2.SEM image calibration\n"
" Current values: resolution-a: " + str(resa) + "\n"
" resolution-b: " + str(resb) + "\n"
" hfw-a: " + str(hfwa) + "\n"
" spot shift: " + str(scaleshift) + "\n"
"3.Twin stage calibration\n"
" Current values: offset: " + str(offset) + "\n"
" scaling: " + str(scaling) + "\n"
" rotation: " + str(rotation) + "\n"
" optical focus: " + str(opt_focus) + "\n"
"4.Fine alignment\n"
" Current values: scale: " + str(iscale) + "\n"
" rotation: " + str(irot) + "\n"
" scale-xy: " + str(iscale_xy) + "\n"
" shear: " + str(ishear))
print_col(ANSI_YELLOW,
"Note that you should not perform any stage move during the process.\n"
"Instead, you may zoom in/out while focusing.")
print_col(ANSI_BLACK, "Now initializing, please wait...")
# Move to the overview position first
f = chamber.moveAbs({"pressure": overview_pressure})
f.result()
# Reference the (optical) stage
f = opt_stage.reference({"x", "y"})
f.result()
f = focus.reference({"z"})
f.result()
# SEM stage to (0,0)
f = sem_stage.moveAbs({"x": 0, "y": 0})
f.result()
# Calculate offset approximation
try:
f = aligndelphi.LensAlignment(overview_ccd, sem_stage, logpath)
position = f.result()
except IOError as ex:
if not force_calib:
position = (offset[0] * scaling[0], offset[1] * scaling[1])
else:
position = (0, 0)
logging.warning("Failed to locate the optical lens (%s), will used previous value %s",
ex, position)
# Just to check if move makes sense
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
# Move to SEM
f = chamber.moveAbs({"pressure": vacuum_pressure})
f.result()
# Set basic e-beam settings
escan.spotSize.value = 2.7
escan.accelVoltage.value = 5300 # V
# Without automatic blanker, the background subtraction doesn't work
if (model.hasVA(escan, "blanker") and # For simulator
None in escan.blanker.choices and
escan.blanker.value is not None):
logging.warning("Blanker set back to automatic")
escan.blanker.value = None
# Detect the holes/markers of the sample holder
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to execute the sample holder hole detection? [Y/n]")
if ans in YES_CHARS:
# Move Phenom sample stage next to expected hole position
sem_stage.moveAbsSync(aligndelphi.SHIFT_DETECTION)
ebeam_focus.moveAbsSync({"z": hole_focus})
# Set the FoV to almost 2mm
escan.horizontalFoV.value = escan.horizontalFoV.range[1]
input_col(ANSI_BLUE,
"Please turn on the SEM stream and focus the SEM image. Then turn off the stream and press Enter...")
print_col(ANSI_BLACK,"Trying to detect the holes/markers, please wait...")
try:
hole_detectionf = aligndelphi.HoleDetection(detector, escan, sem_stage,
ebeam_focus, manual=True, logpath=logpath)
new_first_hole, new_second_hole, new_hole_focus = hole_detectionf.result()
print_col(ANSI_CYAN,
"Values computed: 1st hole: " + str(new_first_hole) + "\n"
" 2st hole: " + str(new_second_hole) + "\n"
" hole focus: " + str(new_hole_focus))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]")
if ans in YES_CHARS:
first_hole, second_hole, hole_focus = new_first_hole, new_second_hole, new_hole_focus
calibconf.set_sh_calib(shid, first_hole, second_hole, hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot, iscale_xy, ishear,
resa, resb, hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except IOError:
print_col(ANSI_RED, "Sample holder hole detection failed.")
else:
break
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to execute the SEM image calibration? [Y/n]")
if ans in YES_CHARS:
# Resetting shift parameters, to not take them into account during calib
blank_md = dict.fromkeys(aligndelphi.MD_CALIB_SEM, (0, 0))
escan.updateMetadata(blank_md)
# We measure the shift in the area just behind the hole where there
# are always some features plus the edge of the sample carrier. For
# that reason we use the focus measured in the hole detection step
sem_stage.moveAbsSync(aligndelphi.SHIFT_DETECTION)
ebeam_focus.moveAbsSync({"z": hole_focus})
try:
# Compute spot shift percentage
print_col(ANSI_BLACK, "Spot shift measurement in progress, please wait...")
f = aligndelphi.ScaleShiftFactor(detector, escan, logpath)
new_scaleshift = f.result()
# Compute resolution-related values.
print_col(ANSI_BLACK, "Calculating resolution shift, please wait...")
resolution_shiftf = aligndelphi.ResolutionShiftFactor(detector, escan, logpath)
new_resa, new_resb = resolution_shiftf.result()
# Compute HFW-related values
print_col(ANSI_BLACK, "Calculating HFW shift, please wait...")
hfw_shiftf = aligndelphi.HFWShiftFactor(detector, escan, logpath)
new_hfwa = hfw_shiftf.result()
print_col(ANSI_CYAN,
"Values computed: resolution-a: " + str(new_resa) + "\n"
" resolution-b: " + str(new_resb) + "\n"
" hfw-a: " + str(new_hfwa) + "\n"
" spot shift: " + str(new_scaleshift))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]")
if ans in YES_CHARS:
resa, resb, hfwa, scaleshift = new_resa, new_resb, new_hfwa, new_scaleshift
calibconf.set_sh_calib(shid, first_hole, second_hole, hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot, iscale_xy, ishear,
resa, resb, hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except IOError:
print_col(ANSI_RED, "SEM image calibration failed.")
else:
break
# Update the SEM metadata to have the spots already at corrected place
escan.updateMetadata({
model.MD_RESOLUTION_SLOPE: resa,
model.MD_RESOLUTION_INTERCEPT: resb,
model.MD_HFW_SLOPE: hfwa,
model.MD_SPOT_SHIFT: scaleshift
})
f = sem_stage.moveAbs({"x": position[0], "y": position[1]})
f.result()
f = opt_stage.moveAbs({"x": 0, "y": 0})
f.result()
if hole_focus is not None:
good_focus = hole_focus - aligndelphi.GOOD_FOCUS_OFFSET
else:
good_focus = aligndelphi.SEM_KNOWN_FOCUS - aligndelphi.GOOD_FOCUS_OFFSET
f = ebeam_focus.moveAbs({"z": good_focus})
f.result()
# Set min fov
# We want to be as close as possible to the center when we are zoomed in
escan.horizontalFoV.value = escan.horizontalFoV.range[0]
pure_offset = None
# Start with the best optical focus known so far
f = focus.moveAbs({"z": opt_focus})
f.result()
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to execute the twin stage calibration? [Y/n]")
if ans in YES_CHARS:
# Configure CCD and e-beam to write CL spots
ccd.binning.value = ccd.binning.clip((4, 4))
ccd.resolution.value = ccd.resolution.range[1]
ccd.exposureTime.value = 900e-03
escan.scale.value = (1, 1)
escan.resolution.value = (1, 1)
escan.translation.value = (0, 0)
if not escan.rotation.readonly:
escan.rotation.value = 0
escan.shift.value = (0, 0)
escan.dwellTime.value = 5e-06
detector.data.subscribe(_discard_data)
print_col(ANSI_BLUE,
"Please turn on the Optical stream, set Power to 0 Watt "
"and focus the image so you have a clearly visible spot.\n"
"Use the up and down arrows or the mouse to move the "
"optical focus and right and left arrows to move the SEM focus. "
"Then turn off the stream and press Enter...")
if not force_calib:
print_col(ANSI_YELLOW,
"If you cannot see the whole source background (bright circle) "
"you may try to move to the already known offset position. \n"
"To do this press the R key at any moment and use I to go back "
"to the initial position.")
rollback_pos = (offset[0] * scaling[0], offset[1] * scaling[1])
else:
rollback_pos = None
ar = ArrowFocus(sem_stage, focus, ebeam_focus, ccd.depthOfField.value, 10e-6)
ar.focusByArrow(rollback_pos)
detector.data.unsubscribe(_discard_data)
print_col(ANSI_BLACK, "Twin stage calibration starting, please wait...")
try:
# TODO: the first point (at 0,0) isn't different from the next 4 points,
# excepted it might be a little harder to focus.
# => use the same code for all of them
align_offsetf = aligndelphi.AlignAndOffset(ccd, detector, escan, sem_stage,
opt_stage, focus, logpath)
align_offset = align_offsetf.result()
new_opt_focus = focus.position.value.get('z')
# If the offset is large, it can prevent the SEM stage to follow
# the optical stage. If it's really large (eg > 1mm) it will
# even prevent from going to the calibration locations.
# So warn about this, as soon as we detect it. It could be
# caused either due to a mistake in the offset detection, or
# because the reference switch of the optical axis is not
# centered (enough) on the axis. In such case, a technician
# should open the sample holder and move the reference switch.
# Alternatively, we could try to be more clever and support
# the range of the tmcm axes to be defined per sample
# holder, and set some asymmetric range (to reflect the fact
# that 0 is not at the center).
for a, trans in zip(("x", "y"), align_offset):
# SEM pos = Opt pos + offset
rng_sem = sem_stage.axes[a].range
rng_opt = opt_stage.axes[a].range
if (rng_opt[0] + trans < rng_sem[0] or
rng_opt[1] + trans > rng_sem[1]):
logging.info("Stage align offset = %s, which could cause "
"moves on the SEM stage out of range (on axis %s)",
align_offset, a)
input_col(ANSI_RED,
"Twin stage offset on axis %s is %g mm, which could cause moves out of range.\n"
"Check that the reference switch in the sample holder is properly at the center." %
(a, trans * 1e3))
def ask_user_to_focus(n):
detector.data.subscribe(_discard_data)
input_col(ANSI_BLUE,
"About to calculate rotation and scaling (%d/4). " % (n + 1,) +
"Please turn on the Optical stream, "
"set Power to 0 Watt and focus the image using the mouse "
"so you have a clearly visible spot. \n"
"If you do not see a spot nor the source background, "
"move the sem-stage from the command line by steps of 200um "
"in x and y until you can see the source background at the center. \n"
"Then turn off the stream and press Enter...")
# TODO: use ArrowFocus() too?
print_col(ANSI_BLACK, "Calculating rotation and scaling (%d/4), please wait..." % (n + 1,))
detector.data.unsubscribe(_discard_data)
f = aligndelphi.RotationAndScaling(ccd, detector, escan, sem_stage,
opt_stage, focus, align_offset,
manual=ask_user_to_focus, logpath=logpath)
acc_offset, new_rotation, new_scaling = f.result()
# Offset is divided by scaling, since Convert Stage applies scaling
# also in the given offset
pure_offset = acc_offset
new_offset = ((acc_offset[0] / new_scaling[0]), (acc_offset[1] / new_scaling[1]))
print_col(ANSI_CYAN,
"Values computed: offset: " + str(new_offset) + "\n"
" scaling: " + str(new_scaling) + "\n"
" rotation: " + str(new_rotation) + "\n"
" optical focus: " + str(new_opt_focus))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]")
if ans in YES_CHARS:
offset, scaling, rotation, opt_focus = new_offset, new_scaling, new_rotation, new_opt_focus
calibconf.set_sh_calib(shid, first_hole, second_hole, hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot, iscale_xy, ishear,
resa, resb, hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except IOError:
print_col(ANSI_RED, "Twin stage calibration failed.")
else:
break
while True:
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to execute the fine alignment? [Y/n]")
if ans in YES_CHARS:
# Return to the center so fine alignment can be executed just after calibration
f = opt_stage.moveAbs({"x": 0, "y": 0})
f.result()
if pure_offset is not None:
f = sem_stage.moveAbs({"x":pure_offset[0], "y":pure_offset[1]})
f.result()
elif offset is not None:
f = sem_stage.moveAbs({"x":offset[0] * scaling[0], "y":offset[1] * scaling[1]})
f.result()
else:
f = sem_stage.moveAbs({"x":position[0], "y":position[1]})
f.result()
f = focus.moveAbs({"z": opt_focus})
f.result()
f = ebeam_focus.moveAbs({"z": good_focus})
f.result()
# Run the optical fine alignment
# TODO: reuse the exposure time
# Configure e-beam to write CL spots
escan.horizontalFoV.value = escan.horizontalFoV.range[0]
escan.scale.value = (1, 1)
escan.resolution.value = (1, 1)
escan.translation.value = (0, 0)
if not escan.rotation.readonly:
escan.rotation.value = 0
escan.shift.value = (0, 0)
escan.dwellTime.value = 5e-06
detector.data.subscribe(_discard_data)
print_col(ANSI_BLUE,
"Please turn on the Optical stream, set Power to 0 Watt "
"and focus the image so you have a clearly visible spot.\n"
"Use the up and down arrows or the mouse to move the "
"optical focus and right and left arrows to move the SEM focus. "
"Then turn off the stream and press Enter...")
ar = ArrowFocus(sem_stage, focus, ebeam_focus, ccd.depthOfField.value, 10e-6)
ar.focusByArrow()
detector.data.unsubscribe(_discard_data)
print_col(ANSI_BLACK, "Fine alignment in progress, please wait...")
# restore CCD settings (as the GUI/user might have changed them)
ccd.binning.value = (1, 1)
ccd.resolution.value = ccd.resolution.range[1]
ccd.exposureTime.value = 900e-03
# Center (roughly) the spot on the CCD
f = spot.CenterSpot(ccd, sem_stage, escan, spot.ROUGH_MOVE, spot.STAGE_MOVE, detector.data)
dist, vect = f.result()
if dist is None:
logging.warning("Failed to find a spot, twin stage calibration might have failed")
try:
escan.horizontalFoV.value = 80e-06
f = align.FindOverlay((4, 4),
0.5, # s, dwell time
10e-06, # m, maximum difference allowed
escan,
ccd,
detector,
skew=True,
bgsub=True)
trans_val, cor_md = f.result()
trans_md, skew_md = cor_md
new_iscale = trans_md[model.MD_PIXEL_SIZE_COR]
new_irot = -trans_md[model.MD_ROTATION_COR] % (2 * math.pi)
new_ishear = skew_md[model.MD_SHEAR_COR]
new_iscale_xy = skew_md[model.MD_PIXEL_SIZE_COR]
print_col(ANSI_CYAN,
"Values computed: scale: " + str(new_iscale) + "\n"
" rotation: " + str(new_irot) + "\n"
" scale-xy: " + str(new_iscale_xy) + "\n"
" shear: " + str(new_ishear))
ans = "Y" if force_calib else None
while ans not in YES_NO_CHARS:
ans = input_col(ANSI_MAGENTA,
"Do you want to update the calibration file with these values? [Y/n]")
if ans in YES_CHARS:
iscale, irot, iscale_xy, ishear = new_iscale, new_irot, new_iscale_xy, new_ishear
calibconf.set_sh_calib(shid, first_hole, second_hole, hole_focus, opt_focus, offset,
scaling, rotation, iscale, irot, iscale_xy, ishear,
resa, resb, hfwa, scaleshift)
print_col(ANSI_BLACK, "Calibration file is updated.")
break
except ValueError:
print_col(ANSI_RED, "Fine alignment failed.")
else:
break
except Exception:
logging.exception("Unexpected failure during calibration")
finally:
print_col(ANSI_BLACK, "Calibration ended, now ejecting sample, please wait...")
# Eject the sample holder
f = chamber.moveAbs({"pressure": vented_pressure})
aligndelphi.restore_hw_settings(escan, ccd, hw_settings)
# Store the final version of the calibration file in the log folder
try:
shutil.copy(calibconf.file_path, logpath)
except Exception:
logging.info("Failed to log calibration file", exc_info=True)
ans = input_col(ANSI_MAGENTA, "Press Enter to close")
f.result()
