def start_sem(self):
main_data = self.main_app.main_data
sem_stream = stream.SEMStream(
"Secondary electrons survey",
main_data.sed,
main_data.sed.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=get_local_vas(main_data.ebeam),
detvas=get_local_vas(main_data.sed),
)
self.start(sem_stream)
def start_sem(self):
main_data = self.main_app.main_data
sem_stream = stream.SEMStream(
"Secondary electrons survey",
main_data.sed,
main_data.sed.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=get_local_vas(main_data.ebeam),
detvas=get_local_vas(main_data.sed),
)
self.start(sem_stream)
def addst(self):
main_data = self.main_app.main_data
stctrl = self._tab.streambar_controller
axes = stctrl._filter_axes(
{"filter": ("band", main_data.light_filter)})
# TODO: special live stream?
ar_stream = ARSettingsStream(
"CL intensity on CCD",
main_data.ccd,
main_data.ccd.data,
main_data.ebeam,
sstage=main_data.scan_stage,
opm=main_data.opm,
axis_map=axes,
detvas=get_local_vas(main_data.ccd, main_data.hw_settings_config),
)
# TODO: Allow very large binning on the CCD
# Make sure the binning is not crazy (especially can happen if CCD is shared for spectrometry)
if model.hasVA(ar_stream, "detBinning"):
b = ar_stream.detBinning.value
if b[0] != b[1] or b[0] > 16:
ar_stream.detBinning.value = ar_stream.detBinning.clip((1, 1))
ar_stream.detResolution.value = ar_stream.detResolution.range[
1]
# Create the equivalent MDStream
sem_stream = self._tab.tab_data_model.semStream
sem_cl_stream = SEMCLCCDStream("SEM CLi CCD", [sem_stream, ar_stream])
return stctrl._addRepStream(ar_stream, sem_cl_stream)
def addst(self):
main_data = self.main_app.main_data
# TODO: special live stream?
ar_stream = ARSettingsStream(
"CL intensity on CCD",
main_data.ccd,
main_data.ccd.data,
main_data.ebeam,
sstage=main_data.scan_stage,
opm=main_data.opm,
detvas=get_local_vas(main_data.ccd, main_data.hw_settings_config),
)
# TODO: Allow very large binning on the CCD
# Make sure the binning is not crazy (especially can happen if CCD is shared for spectrometry)
if model.hasVA(ar_stream, "detBinning"):
b = ar_stream.detBinning.value
if b[0] != b[1] or b[0] > 16:
ar_stream.detBinning.value = ar_stream.detBinning.clip((1, 1))
ar_stream.detResolution.value = ar_stream.detResolution.range[1]
# Create the equivalent MDStream
sem_stream = self._tab.tab_data_model.semStream
sem_cl_stream = SEMCLCCDStream("SEM CLi CCD", [sem_stream, ar_stream])
stctrl = self._tab.streambar_controller
return stctrl._addRepStream(ar_stream, sem_cl_stream,
axes={"band": main_data.light_filter}
)
def addSpectrum(self, name, detector):
"""
name (str): name of the stream
detector (DigitalCamera): spectrometer to acquire the spectrum
"""
logging.debug("Adding spectrum stream for %s", detector.name)
main_data = self.main_app.main_data
stctrl = self._tab.streambar_controller
spg = stctrl._getAffectingSpectrograph(detector)
axes = {
"wavelength": ("wavelength", spg),
"grating": ("grating", spg),
"slit-in": ("slit-in", spg),
}
# Also add light filter for the spectrum stream if it affects the detector
for fw in (main_data.cl_filter, main_data.light_filter):
if fw is None:
continue
if detector.name in fw.affects.value:
axes["filter"] = ("band", fw)
break
axes = stctrl._filter_axes(axes)
if model.hasVA(main_data.ebeam, "blanker"):
blanker = main_data.ebeam.blanker
else:
logging.warning(
"E-beam doesn't support blanker, but trying to use a BlankerSpectrum stream"
)
blanker = None
spec_stream = BlSpectrumSettingsStream(
name,
detector,
detector.data,
main_data.ebeam,
sstage=main_data.scan_stage,
opm=main_data.opm,
axis_map=axes,
detvas=get_local_vas(detector, main_data.hw_settings_config),
blanker=blanker)
stctrl._set_default_spectrum_axes(spec_stream)
# Create the equivalent MDStream
sem_stream = self._tab.tab_data_model.semStream
sem_spec_stream = BlSEMSpectrumMDStream("SEM " + name,
[sem_stream, spec_stream])
ret = stctrl._addRepStream(spec_stream, sem_spec_stream)
# Force the ROI to full FoV, as for the alignment with the SEM image, we need to have always a full image
spec_stream.roi.value = (0, 0, 1, 1)
return ret
def start_fluo(self):
main_data = self.main_app.main_data
fluo_stream = stream.FluoStream(
"Filtered colour",
main_data.ccd,
main_data.ccd.data,
main_data.light,
main_data.light_filter,
focuser=main_data.focus,
emtvas={"power"},
detvas=get_local_vas(main_data.ccd),
)
self.start(fluo_stream)
def start_fluo(self):
main_data = self.main_app.main_data
fluo_stream = stream.FluoStream(
"Filtered colour",
main_data.ccd,
main_data.ccd.data,
main_data.light,
main_data.light_filter,
focuser=main_data.focus,
emtvas={"power"},
detvas=get_local_vas(main_data.ccd),
)
self.start(fluo_stream)
def addSpectrum(self, name, detector):
"""
name (str): name of the stream
detector (DigitalCamera): spectrometer to acquire the spectrum
"""
logging.debug("Adding spectrum stream for %s", detector.name)
main_data = self.main_app.main_data
stctrl = self._tab.streambar_controller
spg = stctrl._getAffectingSpectrograph(detector)
axes = {
"wavelength": ("wavelength", spg),
"grating": ("grating", spg),
"slit-in": ("slit-in", spg),
}
# Also add light filter for the spectrum stream if it affects the detector
for fw in (main_data.cl_filter, main_data.light_filter):
if fw is None:
continue
if detector.name in fw.affects.value:
axes["filter"] = ("band", fw)
break
axes = stctrl._filter_axes(axes)
spec_stream = LASpectrumSettingsStream(
name,
detector,
detector.data,
main_data.ebeam,
l2=self._lens2,
analyzer=main_data.pol_analyzer,
sstage=main_data.scan_stage,
opm=main_data.opm,
axis_map=axes,
detvas=get_local_vas(detector, main_data.hw_settings_config),
)
stctrl._set_default_spectrum_axes(spec_stream)
# Create the equivalent MDStream
sem_stream = self._tab.tab_data_model.semStream
sem_spec_stream = LASEMSpectrumMDStream("SEM " + name,
[sem_stream, spec_stream])
return stctrl._addRepStream(spec_stream, sem_spec_stream)
def addSpectrum(self, name, detector):
"""
name (str): name of the stream
detector (DigitalCamera): spectrometer to acquire the spectrum
"""
logging.debug("Adding spectrum stream for %s", detector.name)
main_data = self.main_app.main_data
stctrl = self._tab.streambar_controller
spg = stctrl._getAffectingSpectrograph(detector)
spec_stream = LASpectrumSettingsStream(
name,
detector,
detector.data,
main_data.ebeam,
l2=self._lens2,
analyzer=main_data.pol_analyzer,
sstage=main_data.scan_stage,
opm=main_data.opm,
detvas=get_local_vas(detector, main_data.hw_settings_config),
)
# Create the equivalent MDStream
sem_stream = self._tab.tab_data_model.semStream
sem_spec_stream = LASEMSpectrumMDStream("SEM " + name,
[sem_stream, spec_stream])
# TODO: all the axes, including the filter band should be local. The
# band should be set to the pass-through by default
axes = {
"wavelength": spg,
"grating": spg,
"slit-in": spg,
}
# Also add light filter for the spectrum stream if it affects the detector
for fw in (main_data.cl_filter, main_data.light_filter):
if fw is None:
continue
if detector.name in fw.affects.value:
axes["band"] = fw
return stctrl._addRepStream(spec_stream, sem_spec_stream, axes=axes)
def addSpectrum(self, name, detector):
"""
name (str): name of the stream
detector (DigitalCamera): spectrometer to acquire the spectrum
"""
logging.debug("Adding spectrum stream for %s", detector.name)
main_data = self.main_app.main_data
stctrl = self._tab.streambar_controller
spg = stctrl._getAffectingSpectrograph(detector)
spec_stream = LASpectrumSettingsStream(
name,
detector,
detector.data,
main_data.ebeam,
l2=self._lens2,
analyzer=main_data.pol_analyzer,
sstage=main_data.scan_stage,
opm=main_data.opm,
detvas=get_local_vas(detector, main_data.hw_settings_config),
)
# Create the equivalent MDStream
sem_stream = self._tab.tab_data_model.semStream
sem_spec_stream = LASEMSpectrumMDStream("SEM " + name,
[sem_stream, spec_stream])
# TODO: all the axes, including the filter band should be local. The
# band should be set to the pass-through by default
axes = {"wavelength": spg,
"grating": spg,
"slit-in": spg,
}
# Also add light filter for the spectrum stream if it affects the detector
for fw in (main_data.cl_filter, main_data.light_filter):
if fw is None:
continue
if detector.name in fw.affects.value:
axes["band"] = fw
return stctrl._addRepStream(spec_stream, sem_spec_stream, axes=axes)
def __init__(self, microscope, main_app):
super(QuickCLPlugin, self).__init__(microscope, main_app)
# Can only be used with a SPARC with CL detector (or monochromator)
if not microscope:
return
main_data = self.main_app.main_data
if not main_data.ebeam or not (main_data.cld
or main_data.monochromator):
return
self.conf = get_acqui_conf()
self.filename = model.StringVA("")
self.filename.subscribe(self._on_filename)
self.expectedDuration = model.VigilantAttribute(1,
unit="s",
readonly=True)
self.hasDatabar = model.BooleanVA(False)
# Only put the VAs that do directly define the image as local, everything
# else should be global. The advantage is double: the global VAs will
# set the hardware even if another stream (also using the e-beam) is
# currently playing, and if the VAs are changed externally, the settings
# will be displayed correctly (and not reset the values on next play).
emtvas = set()
hwemtvas = set()
for vaname in get_local_vas(main_data.ebeam,
main_data.hw_settings_config):
if vaname in ("resolution", "dwellTime", "scale"):
emtvas.add(vaname)
else:
hwemtvas.add(vaname)
self._sem_stream = stream.SEMStream(
"Secondary electrons",
main_data.sed,
main_data.sed.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
hwemtvas=hwemtvas,
hwdetvas=None,
emtvas=emtvas,
detvas=get_local_vas(main_data.sed, main_data.hw_settings_config),
)
# This stream is used both for rendering and acquisition.
# LiveCLStream is more or less like a SEMStream, but ensures the icon in
# the merge slider is correct, and provide a few extra.
if main_data.cld:
self._cl_stream = LiveCLStream(
"CL intensity",
main_data.cld,
main_data.cld.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=emtvas,
detvas=get_local_vas(main_data.cld,
main_data.hw_settings_config),
opm=main_data.opm,
)
# TODO: allow to type in the resolution of the CL?
# TODO: add the cl-filter axis (or reset it to pass-through?)
self.logScale = self._cl_stream.logScale
if hasattr(self._cl_stream, "detGain"):
self._cl_stream.detGain.subscribe(self._on_cl_gain)
# Update the acquisition time when it might change (ie, the scan settings
# change)
self._cl_stream.emtDwellTime.subscribe(self._update_exp_dur)
self._cl_stream.emtResolution.subscribe(self._update_exp_dur)
# Note: for now we don't really support SPARC with BOTH CL-detector and
# monochromator.
if main_data.monochromator:
self._mn_stream = LiveCLStream(
"Monochromator",
main_data.monochromator,
main_data.monochromator.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=emtvas,
detvas=get_local_vas(main_data.monochromator,
main_data.hw_settings_config),
opm=main_data.opm,
)
self._mn_stream.emtDwellTime.subscribe(self._update_exp_dur)
self._mn_stream.emtResolution.subscribe(self._update_exp_dur)
# spg = self._getAffectingSpectrograph(main_data.spectrometer)
# TODO: show axes
self._dlg = None
self.addMenu("Acquisition/Quick CL...\tF2", self.start)
def __init__(self, microscope, main_app):
super(QuickCLPlugin, self).__init__(microscope, main_app)
# Can only be used with a SPARC with CL detector (or monochromator)
if not microscope:
return
main_data = self.main_app.main_data
if not main_data.ebeam or not (main_data.cld or main_data.monochromator):
return
self.conf = get_acqui_conf()
self.filename = model.StringVA("")
self.filename.subscribe(self._on_filename)
self.expectedDuration = model.VigilantAttribute(1, unit="s", readonly=True)
self.hasDatabar = model.BooleanVA(False)
# Only put the VAs that do directly define the image as local, everything
# else should be global. The advantage is double: the global VAs will
# set the hardware even if another stream (also using the e-beam) is
# currently playing, and if the VAs are changed externally, the settings
# will be displayed correctly (and not reset the values on next play).
emtvas = set()
hwemtvas = set()
for vaname in get_local_vas(main_data.ebeam, main_data.hw_settings_config):
if vaname in ("resolution", "dwellTime", "scale"):
emtvas.add(vaname)
else:
hwemtvas.add(vaname)
self._sem_stream = stream.SEMStream(
"Secondary electrons",
main_data.sed,
main_data.sed.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
hwemtvas=hwemtvas,
hwdetvas=None,
emtvas=emtvas,
detvas=get_local_vas(main_data.sed, main_data.hw_settings_config),
)
# This stream is used both for rendering and acquisition.
# LiveCLStream is more or less like a SEMStream, but ensures the icon in
# the merge slider is correct, and provide a few extra.
if main_data.cld:
self._cl_stream = LiveCLStream(
"CL intensity",
main_data.cld,
main_data.cld.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=emtvas,
detvas=get_local_vas(main_data.cld, main_data.hw_settings_config),
opm=main_data.opm,
)
# TODO: allow to type in the resolution of the CL?
# TODO: add the cl-filter axis (or reset it to pass-through?)
self.logScale = self._cl_stream.logScale
if hasattr(self._cl_stream, "detGain"):
self._cl_stream.detGain.subscribe(self._on_cl_gain)
# Update the acquisition time when it might change (ie, the scan settings
# change)
self._cl_stream.emtDwellTime.subscribe(self._update_exp_dur)
self._cl_stream.emtResolution.subscribe(self._update_exp_dur)
# Note: for now we don't really support SPARC with BOTH CL-detector and
# monochromator.
if main_data.monochromator:
self._mn_stream = LiveCLStream(
"Monochromator",
main_data.monochromator,
main_data.monochromator.data,
main_data.ebeam,
focuser=main_data.ebeam_focus,
emtvas=emtvas,
detvas=get_local_vas(main_data.monochromator, main_data.hw_settings_config),
opm=main_data.opm,
)
self._mn_stream.emtDwellTime.subscribe(self._update_exp_dur)
self._mn_stream.emtResolution.subscribe(self._update_exp_dur)
# spg = self._getAffectingSpectrograph(main_data.spectrometer)
# TODO: show axes
self._dlg = None
self.addMenu("Acquisition/Quick CL...\tF2", self.start)