def start(self):
dlg = AcquisitionDialog(self, "Manually change the alignment",
text="Change the translation, rotation, and pixel size "
"of any stream. The display is immediately updated, "
"but you need to save the file (as a snapshot) for "
"the changes to be permanent.")
vah = VAHolder()
vah._subscribers = []
vaconf = OrderedDict()
tab_data = self.main_app.main_data.tab.value.tab_data_model
for i, stream in enumerate(tab_data.streams.value):
dlg.addStream(stream)
# Add 5 VAs for each stream, to modify the overlay metadata
poscor = stream.raw[0].metadata.get(model.MD_POS_COR, (0, 0))
rotation = stream.raw[0].metadata.get(model.MD_ROTATION_COR, 0)
scalecor = stream.raw[0].metadata.get(model.MD_PIXEL_SIZE_COR, (1, 1))
vatransx = model.FloatContinuous(-poscor[0], range=(-10e-6, 10e-6), unit="m")
vatransy = model.FloatContinuous(-poscor[1], range=(-10e-6, 10e-6), unit="m")
varot = model.FloatContinuous(rotation, range=(-math.pi, math.pi), unit="rad")
vascalex = model.FloatContinuous(scalecor[0], range=(0.5, 1.5))
vascaley = model.FloatContinuous(scalecor[1], range=(0.5, 1.5))
# Add the VAs to the holder, and to the vaconf mainly to force the order
setattr(vah, "%dTransX" % i, vatransx)
setattr(vah, "%dTransY" % i, vatransy)
setattr(vah, "%dRotation" % i, varot)
setattr(vah, "%dScaleX" % i, vascalex)
setattr(vah, "%dScaleY" % i, vascaley)
vaconf["%dTransX" % i] = {"label": "%s trans X" % stream.name.value}
vaconf["%dTransY" % i] = {"label": "%s trans Y" % stream.name.value}
vaconf["%dRotation" % i] = {"label": "%s rotation X" % stream.name.value}
vaconf["%dScaleX" % i] = {"label": "%s scale X" % stream.name.value}
vaconf["%dScaleY" % i] = {"label": "%s scale Y" % stream.name.value}
# Create listeners with information of the stream and dimension
va_on_transx = functools.partial(self._on_trans, stream, 0)
va_on_transy = functools.partial(self._on_trans, stream, 1)
va_on_rotation = functools.partial(self._on_rotation, stream)
va_on_scalex = functools.partial(self._on_scale, stream, 0)
va_on_scaley = functools.partial(self._on_scale, stream, 1)
# We hold a reference to the listeners to prevent automatic subscription
vah._subscribers.append(va_on_transx)
vah._subscribers.append(va_on_transy)
vah._subscribers.append(va_on_rotation)
vah._subscribers.append(va_on_scalex)
vah._subscribers.append(va_on_scaley)
vatransx.subscribe(va_on_transx)
vatransy.subscribe(va_on_transy)
varot.subscribe(va_on_rotation)
vascalex.subscribe(va_on_scalex)
vascaley.subscribe(va_on_scaley)
dlg.addSettings(vah, vaconf)
# TODO: add a 'reset' button
dlg.addButton("Done", None, face_colour='blue')
dlg.ShowModal()
def start(self):
dlg = AcquisitionDialog(self, "Remove spikes from CL data",
text="Change the threshold value to determine the sensitivity of the spike removal")
self._dlg = dlg
self.tab_data = self.main_app.main_data.tab.value.tab_data_model
# don't allow adding/removing streams
dlg.streambar_controller.to_static_mode()
for stream in self.tab_data.streams.value:
#there must be a better way to do this
if isinstance(stream, SpectrumStream):
# Check the stream is really _spectrum_ data, CTYX or TYX are not supported
raw_shape = stream.raw[0].shape # CTZYX
if numpy.prod(raw_shape[1:3]) > 1: # T * Z
logging.info("Skipping stream %s of shape %s, as it not a simple spectral stream",
stream.name, raw_shape)
continue
dlg.addStream(stream)
self._spec_stream = stream
break # Only one stream handled
else:
# if no spectral data is present spike removal cannot be done (for now)
box = wx.MessageDialog(self.main_app.main_frame,
"No spectral stream is present, so it's not possible to correct the data",
"No spectral stream", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
wx.CallAfter(dlg.viewport_l.canvas.fit_view_to_content) # async, to call after the stream is added
dlg.addSettings(self, conf=self.vaconf)
# TODO: add a 'reset' button
dlg.addButton("Close")
dlg.addButton("Correct", self.correct_data, face_colour='red')
dlg.addButton("Save", self.save, face_colour='blue')
self._update_save_button() # It'll be called _after_ the button is added
dlg.Size = (1000, 600) # Make it big enough to fit the view and the stream panel
dlg.ShowModal()
# The end
self._spec_stream = None # drop reference
dlg.Close()
self._dlg = None
if dlg: # If dlg hasn't been destroyed yet
dlg.Destroy()
def start(self):
"""
Called when the menu entry is selected
"""
main_data = self.main_app.main_data
# Stop the streams
tab_data = main_data.tab.value.tab_data_model
for s in tab_data.streams.value:
s.should_update.value = False
self.filename.value = self._get_new_filename()
self._update_exp_dur()
# Special CCD settings to get values as photon counting
if model.hasVA(self.ccd, "countConvert"):
self.ccd.countConvert.value = 2 # photons
dlg = AcquisitionDialog(
self, "Super-resolution acquisition",
"Acquires a series of shortly exposed images, "
"and store them in sequence.\n"
"Note, the advanced settings are only applied "
"after restarting the stream.")
dlg.addStream(self._stream)
dlg.addSettings(self, self.vaconf)
dlg.addButton("Close")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
dlg.Maximize()
ans = dlg.ShowModal()
# Make sure the stream is not playing anymore and CCD is back to normal
self._stream.should_update.value = False
if model.hasVA(self.ccd, "countConvert"):
try:
self.ccd.countConvert.value = 0 # normal
except Exception:
logging.exception("Failed to set back count convert mode")
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
dlg.Destroy()
def start(self):
"""
Called when the menu entry is selected
"""
main_data = self.main_app.main_data
# Stop the streams
tab_data = main_data.tab.value.tab_data_model
for s in tab_data.streams.value:
s.should_update.value = False
self.filename.value = self._get_new_filename()
self._update_exp_dur()
# Special CCD settings to get values as photon counting
if model.hasVA(self.ccd, "countConvert"):
self.ccd.countConvert.value = 2 # photons
dlg = AcquisitionDialog(self, "Super-resolution acquisition",
"Acquires a series of shortly exposed images, "
"and store them in sequence.\n"
"Note, the advanced settings are only applied "
"after restarting the stream.")
dlg.addStream(self._stream)
dlg.addSettings(self, self.vaconf)
dlg.addButton("Close")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
dlg.Maximize()
ans = dlg.ShowModal()
# Make sure the stream is not playing anymore and CCD is back to normal
self._stream.should_update.value = False
if model.hasVA(self.ccd, "countConvert"):
try:
self.ccd.countConvert.value = 0 # normal
except Exception:
logging.exception("Failed to set back count convert mode")
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
dlg.Destroy()
def start(self):
dlg = AcquisitionDialog(self, "Fancy Acquisition", "Enter everything")
dlg.addSettings(self, conf={"filename": {"control_type": CONTROL_SAVE_FILE}})
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
stream = FakeFluoStream("Fluo Stream")
dlg.addStream(stream)
stream = FakeFluoStream("Fluo Stream")
dlg.addStream(stream)
ans = dlg.ShowModal()
if ans == 0:
# Ignore errors about a missing analysis tab
try:
self.showAcquisition(self.filename.value)
except AttributeError:
pass
def start(self, st):
self._stream = st
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(self, "Timelapse acquisition",
"The same stream will be acquired multiple times, defined by the 'number of acquisitions'.\n"
"The time separating each acquisition is defined by the 'period'.\n")
dlg.addSettings(self, self.vaconf)
dlg.addStream(st)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
ans = dlg.ShowModal()
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
def start(self, st):
self._stream = st
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(
self, "Timelapse acquisition",
"The same stream will be acquired multiple times, defined by the 'number of acquisitions'.\n"
"The time separating each acquisition is defined by the 'period'.\n"
)
dlg.addSettings(self, self.vaconf)
dlg.addStream(st)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
ans = dlg.ShowModal()
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
def start(self):
dlg = AcquisitionDialog(self, "Fancy Acquisition", "Enter everything")
dlg.addSettings(self,
conf={"filename": {
"control_type": CONTROL_SAVE_FILE
}})
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
stream = FakeFluoStream("Fluo Stream")
dlg.addStream(stream)
stream = FakeFluoStream("Fluo Stream")
dlg.addStream(stream)
ans = dlg.ShowModal()
if ans == 1:
# Ignore errors about a missing analysis tab
try:
self.showAcquisition(self.filename.value)
except AttributeError:
pass
def start(self):
dlg = AcquisitionDialog(
self,
"Merging channels to RGB image",
text="Insert 3 R, G, B files so that they are assigned the tints \n"
"and are merged to an RGB image.")
# remove the play overlay from the viewport
dlg.viewport_l.canvas.remove_view_overlay(
dlg.viewport_l.canvas.play_overlay)
self._dlg = dlg
dlg.addStream(None)
dlg.Size = (1000, 600)
dlg.addSettings(self, self.vaconf)
dlg.addButton("Cancel", None)
dlg.addButton("Add", self._updateViewer, face_colour='blue')
dlg.pnl_gauge.Hide()
dlg.ShowModal() # Blocks until the window is closed
# Destroy the dialog and reset the VAs and subscribers
dlg.Destroy()
self.filenameR.value = " "
self.filenameG.value = " "
self.filenameB.value = " "
self.redShiftX.value = 0
self.redShiftY.value = 0
self.greenShiftX.value = 0
self.greenShiftY.value = 0
self.blueShiftX.value = 0
self.blueShiftY.value = 0
self.cropBottom.value = 0
self._subscribers = []
self._dlg = None
self._raw_orig = {}
def start(self):
# Fail if the live tab is not selected
tab = self.main_app.main_data.tab.value
if tab.name not in ("secom_live", "sparc_acqui", "cryosecom-localization"):
box = wx.MessageDialog(self.main_app.main_frame,
"ZStack acquisition must be done from the acquisition stream.",
"ZStack acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
# On SPARC, fail if no ROI selected
if hasattr(tab.tab_data_model, "roa") and tab.tab_data_model.roa.value == UNDEFINED_ROI:
box = wx.MessageDialog(self.main_app.main_frame,
"You need to select a region of acquisition.",
"Z stack acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
# Stop the stream(s) playing to not interfere with the acquisition
tab.streambar_controller.pauseStreams()
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(self, "Z Stack acquisition",
"The same streams will be acquired multiple times at different Z positions, defined starting from Z start, with a step size.\n")
self._dlg = dlg
dlg.addSettings(self, self.vaconf)
ss = self._get_live_streams(tab.tab_data_model)
for s in ss:
if isinstance(s, (ARStream, SpectrumStream, MonochromatorSettingsStream)):
# TODO: instead of hard-coding the list, a way to detect the type
# of live image?
logging.info("Not showing stream %s, for which the live image is not spatial", s)
dlg.addStream(s, index=None)
else:
dlg.addStream(s)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
# Connect zstart with the actual focus position
self.zstart.subscribe(self._on_zstart)
self.focus.position.subscribe(self._on_focus_pos, init=True)
# Update acq time when streams are added/removed
dlg.view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
dlg.hidden_view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
# TODO: update the acquisition time whenever a setting changes
# TODO: disable "acquire" button if no stream selected
# TODO: also display the repetition and axis settings for the SPARC streams.
ans = dlg.ShowModal()
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
self.focus.position.unsubscribe(self._on_focus_pos)
self.zstart.unsubscribe(self._on_zstart)
# Don't hold references
self._acq_streams = None
if dlg: # If dlg hasn't been destroyed yet
dlg.Destroy()
def start(self):
# Fail if the live tab is not selected
tab = self.main_app.main_data.tab.value
if tab.name not in ("secom_live", "sparc_acqui"):
box = wx.MessageDialog(self.main_app.main_frame,
"Timelapse acquisition must be done from the acquisition stream.",
"Timelapse acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
# On SPARC, fail if no ROI selected
try:
if tab.tab_data_model.semStream.roi.value == UNDEFINED_ROI:
box = wx.MessageDialog(self.main_app.main_frame,
"You need to select a region of acquisition.",
"Timelapse acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
except AttributeError:
pass # Not a SPARC
# Stop the stream(s) playing to not interfere with the acquisition
tab.streambar_controller.pauseStreams()
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(self, "Timelapse acquisition",
"The same streams will be acquired multiple times, defined by the 'number of acquisitions'.\n"
"The time separating each acquisition is defined by the 'period'.\n")
self._dlg = dlg
dlg.addSettings(self, self.vaconf)
ss = self._get_live_streams(tab.tab_data_model)
for s in ss:
if isinstance(s, (ARStream, SpectrumStream, MonochromatorSettingsStream)):
# TODO: instead of hard-coding the list, a way to detect the type
# of live image?
logging.info("Not showing stream %s, for which the live image is not spatial", s)
dlg.addStream(s, index=None)
else:
dlg.addStream(s)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
# Force to re-check the minimum period time
self.period.value = self.period.value
# Update acq time when streams are added/removed
dlg.view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
dlg.hidden_view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
# TODO: update the acquisition time whenever a setting changes
# TODO: disable "acquire" button if no stream selected
# TODO: also display the repetition and axis settings for the SPARC streams.
ans = dlg.ShowModal()
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
dlg.Destroy()
def show_dlg(self):
# TODO: if there is a chamber, only allow if there is vacuum
# Fail if the live tab is not selected
self._tab = self.main_app.main_data.tab.value
if self._tab.name not in ("secom_live", "sparc_acqui"):
box = wx.MessageDialog(self.main_app.main_frame,
"Tiled acquisition must be done from the acquisition stream.",
"Tiled acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
self._tab.streambar_controller.pauseStreams()
# If no ROI is selected, select entire area
try:
if self._tab.tab_data_model.semStream.roi.value == UNDEFINED_ROI:
self._tab.tab_data_model.semStream.roi.value = (0, 0, 1, 1)
except AttributeError:
pass # Not a SPARC
# Disable drift correction (on SPARC)
if hasattr(self._tab.tab_data_model, "driftCorrector"):
self._tab.tab_data_model.driftCorrector.roi.value = UNDEFINED_ROI
ss = self._get_live_streams()
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(self, "Tiled acquisition",
"Acquire a large area by acquiring the streams multiple "
"times over a grid.")
self._dlg = dlg
# don't allow adding/removing streams
self._dlg.streambar_controller.to_static_mode()
dlg.addSettings(self, self.vaconf)
for s in ss:
if isinstance(s, (ARStream, SpectrumStream, MonochromatorSettingsStream)):
# TODO: instead of hard-coding the list, a way to detect the type
# of live image?
logging.info("Not showing stream %s, for which the live image is not spatial", s)
dlg.addStream(s, index=None)
else:
dlg.addStream(s, index=0)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
# Update acq time and area when streams are added/removed. Add stream settings
# to subscribed vas.
dlg.view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
dlg.view.stream_tree.flat.subscribe(self._update_total_area, init=True)
dlg.view.stream_tree.flat.subscribe(self._on_streams_change, init=True)
# Default fineAlign to True if it's possible
# Use live streams to make the decision since visible streams might not be initialized yet
# TODO: the visibility of the streams seems to be reset when the plugin is started,
# a stream that is invisible in the main panel becomes visible. This should be fixed.
if self._can_fine_align(ss):
self.fineAlign.value = True
self._ovrl_stream = self._create_overlay_stream(ss)
# This looks tautologic, but actually, it forces the setter to check the
# value is within range, and will automatically reduce it if necessary.
self.nx.value = self.nx.value
self.ny.value = self.ny.value
self._memory_check()
# TODO: disable "acquire" button if no stream selected.
ans = dlg.ShowModal()
if ans == 0 or ans == wx.ID_CANCEL:
logging.info("Tiled acquisition cancelled")
self.ft.cancel()
elif ans == 1:
logging.info("Tiled acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
# Don't hold references
self._unsubscribe_vas()
dlg.Destroy()
self._dlg = None
def start(self):
dlg = AcquisitionDialog(
self,
"Manually change the alignment",
text="Change the translation, rotation, and pixel size "
"of any stream. The display is immediately updated, "
"but you need to save the file (as a snapshot) for "
"the changes to be permanent.")
self._dlg = dlg
vah = VAHolder()
vah._subscribers = []
vaconf = OrderedDict()
tab_data = self.main_app.main_data.tab.value.tab_data_model
if not tab_data.streams.value:
box = wx.MessageDialog(
self.main_app.main_frame,
"No stream is present, so it's not possible to modify the alignment.",
"No stream", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
for i, stream in enumerate(tab_data.streams.value):
dlg.addStream(stream)
# Add 5 VAs for each stream, to modify the overlay metadata
poscor = stream.raw[0].metadata.get(model.MD_POS_COR, (0, 0))
rotation = stream.raw[0].metadata.get(model.MD_ROTATION_COR, 0)
scalecor = stream.raw[0].metadata.get(model.MD_PIXEL_SIZE_COR,
(1, 1))
shear = stream.raw[0].metadata.get(model.MD_SHEAR_COR, 0)
vatransx = model.FloatContinuous(-poscor[0],
range=(-10e-6, 10e-6),
unit="m")
vatransy = model.FloatContinuous(-poscor[1],
range=(-10e-6, 10e-6),
unit="m")
varot = model.FloatContinuous(rotation,
range=(-math.pi, math.pi),
unit="rad")
vascalex = model.FloatContinuous(scalecor[0], range=(0.5, 1.5))
vascaley = model.FloatContinuous(scalecor[1], range=(0.5, 1.5))
vashear = model.FloatContinuous(shear, range=(-1, 1))
# Add the VAs to the holder, and to the vaconf mainly to force the order
setattr(vah, "%dTransX" % i, vatransx)
setattr(vah, "%dTransY" % i, vatransy)
setattr(vah, "%dRotation" % i, varot)
setattr(vah, "%dScaleX" % i, vascalex)
setattr(vah, "%dScaleY" % i, vascaley)
setattr(vah, "%dShear" % i, vashear)
vaconf["%dTransX" % i] = {
"label": "%s trans X" % stream.name.value
}
vaconf["%dTransY" % i] = {
"label": "%s trans Y" % stream.name.value
}
vaconf["%dRotation" % i] = {
"label": "%s rotation" % stream.name.value
}
vaconf["%dScaleX" % i] = {
"label": "%s scale X" % stream.name.value
}
vaconf["%dScaleY" % i] = {
"label": "%s scale Y" % stream.name.value
}
vaconf["%dShear" % i] = {"label": "%s shear" % stream.name.value}
# Create listeners with information of the stream and dimension
va_on_transx = functools.partial(self._on_trans, stream, 0)
va_on_transy = functools.partial(self._on_trans, stream, 1)
va_on_rotation = functools.partial(self._on_rotation, stream)
va_on_scalex = functools.partial(self._on_scale, stream, 0)
va_on_scaley = functools.partial(self._on_scale, stream, 1)
va_on_shear = functools.partial(self._on_shear, stream)
# We hold a reference to the listeners to prevent automatic subscription
vah._subscribers.append(va_on_transx)
vah._subscribers.append(va_on_transy)
vah._subscribers.append(va_on_rotation)
vah._subscribers.append(va_on_scalex)
vah._subscribers.append(va_on_scaley)
vah._subscribers.append(va_on_shear)
vatransx.subscribe(va_on_transx)
vatransy.subscribe(va_on_transy)
varot.subscribe(va_on_rotation)
vascalex.subscribe(va_on_scalex)
vascaley.subscribe(va_on_scaley)
vashear.subscribe(va_on_shear)
dlg.addSettings(vah, vaconf)
# TODO: add a 'reset' button
dlg.addButton("Done", None, face_colour='blue')
dlg.ShowModal()
# The end
dlg.Destroy()
vah._subscribers = []
self._dlg = None
def start(self):
# Fail if the live tab is not selected
tab = self.main_app.main_data.tab.value
if tab.name not in ("secom_live", "sparc_acqui"):
box = wx.MessageDialog(self.main_app.main_frame,
"ZStack acquisition must be done from the acquisition stream.",
"ZStack acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
# On SPARC, fail if no ROI selected
if hasattr(tab.tab_data_model, "roa") and tab.tab_data_model.roa.value == UNDEFINED_ROI:
box = wx.MessageDialog(self.main_app.main_frame,
"You need to select a region of acquisition.",
"Z stack acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
# Stop the stream(s) playing to not interfere with the acquisition
tab.streambar_controller.pauseStreams()
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(self, "Z Stack acquisition",
"The same streams will be acquired multiple times at different Z positions, defined starting from Z start, with a step size.\n")
self._dlg = dlg
dlg.addSettings(self, self.vaconf)
ss = self._get_live_streams(tab.tab_data_model)
for s in ss:
if isinstance(s, (ARStream, SpectrumStream, MonochromatorSettingsStream)):
# TODO: instead of hard-coding the list, a way to detect the type
# of live image?
logging.info("Not showing stream %s, for which the live image is not spatial", s)
dlg.addStream(s, index=None)
else:
dlg.addStream(s)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
# Update acq time when streams are added/removed
dlg.view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
dlg.hidden_view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
# TODO: update the acquisition time whenever a setting changes
# TODO: disable "acquire" button if no stream selected
# TODO: also display the repetition and axis settings for the SPARC streams.
ans = dlg.ShowModal()
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
# Don't hold references
self._acq_streams = None
if dlg: # If dlg hasn't been destroyed yet
dlg.Destroy()
def start(self):
"""
Displays the plugin window.
"""
self._update_filename()
str_ctrl = self.main_app.main_data.tab.value.streambar_controller
str_ctrl.pauseStreams()
dlg = AcquisitionDialog(
self, "CL acquisition",
"Acquires a CCD image for each e-beam spot.\n")
self._dlg = dlg
self._survey_stream = self._get_sem_survey()
dlg.SetSize((1500, 1000))
# Hack to force the canvas to have a region of acquisition (ROA) and anchor region (drift) overlay.
dlg._dmodel.tool.choices = {
TOOL_NONE,
TOOL_ROA,
TOOL_RO_ANCHOR,
}
dlg._dmodel.roa = self._secom_cl_stream.roi # region of acquisition selected (x_tl, y_tl, x_br, y_br)
dlg._dmodel.fovComp = self.main_data.ebeam # size (x, y) of sem image for given magnification
dlg._dmodel.driftCorrector = self._driftCorrector
dlg.viewport_l.canvas.view = None
dlg.viewport_l.canvas.setView(dlg.view, dlg._dmodel)
dlg.viewport_r.canvas.allowed_modes = {}
dlg.viewport_r.canvas.view = None
dlg.viewport_r.canvas.setView(dlg.view_r, dlg._dmodel)
self.repetition = self._secom_cl_stream.repetition # ebeam positions to acquire
self.repetition.subscribe(self._on_rep, init=True)
self.pixelSize = self._secom_cl_stream.pixelSize # pixel size per ebeam pos
self.roi_margin = self._secom_cl_stream.roi_margin
self.period = self._driftCorrector.period # time between to drift corrections
self.tool = dlg._dmodel.tool # tools to select ROA and anchor region for drift correction
self._driftCorrector.roi.subscribe(self._on_dc_roi, init=True)
# subscribe to update estimated acquisition time
self.repetition.subscribe(self._update_exp_dur, init=True)
self.period.subscribe(self._update_exp_dur)
self._driftCorrector.roi.subscribe(self._update_exp_dur)
dlg.addSettings(self, self.vaconf)
dlg.addStream(self._survey_stream)
dlg.addStream(self._optical_stream)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self._acquire, face_colour='blue')
ans = dlg.ShowModal()
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
self._dlg = None
self._survey_stream = None
dlg.Destroy()
def start(self):
# Fail if the live tab is not selected
tab = self.main_app.main_data.tab.value
if tab.name not in ("secom_live", "sparc_acqui"):
box = wx.MessageDialog(
self.main_app.main_frame,
"Timelapse acquisition must be done from the acquisition stream.",
"Timelapse acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
# On SPARC, fail if no ROI selected
try:
if tab.tab_data_model.semStream.roi.value == UNDEFINED_ROI:
box = wx.MessageDialog(
self.main_app.main_frame,
"You need to select a region of acquisition.",
"Timelapse acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
except AttributeError:
pass # Not a SPARC
# Stop the stream(s) playing to not interfere with the acquisition
tab.streambar_controller.pauseStreams()
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(
self, "Timelapse acquisition",
"The same streams will be acquired multiple times, defined by the 'number of acquisitions'.\n"
"The time separating each acquisition is defined by the 'period'.\n"
)
self._dlg = dlg
dlg.addSettings(self, self.vaconf)
ss = self._get_live_streams(tab.tab_data_model)
for s in ss:
if isinstance(
s,
(ARStream, SpectrumStream, MonochromatorSettingsStream)):
# TODO: instead of hard-coding the list, a way to detect the type
# of live image?
logging.info(
"Not showing stream %s, for which the live image is not spatial",
s)
dlg.addStream(s, index=None)
else:
dlg.addStream(s)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
# Force to re-check the minimum period time
self.period.value = self.period.value
# Update acq time when streams are added/removed
dlg.view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
dlg.hidden_view.stream_tree.flat.subscribe(self._update_exp_dur,
init=True)
# TODO: update the acquisition time whenever a setting changes
# TODO: disable "acquire" button if no stream selected
# TODO: also display the repetition and axis settings for the SPARC streams.
ans = dlg.ShowModal()
if ans == 0:
logging.info("Acquisition cancelled")
elif ans == 1:
logging.info("Acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
dlg.view.stream_tree.flat.unsubscribe(self._update_exp_dur)
dlg.Destroy()
def show_dlg(self):
# TODO: if there is a chamber, only allow if there is vacuum
# Fail if the live tab is not selected
self._tab = self.main_app.main_data.tab.value
if self._tab.name not in ("secom_live", "sparc_acqui"):
box = wx.MessageDialog(
self.main_app.main_frame,
"Tiled acquisition must be done from the acquisition tab.",
"Tiled acquisition not possible", wx.OK | wx.ICON_STOP)
box.ShowModal()
box.Destroy()
return
self._tab.streambar_controller.pauseStreams()
# If no ROI is selected, select entire area
try:
if self._tab.tab_data_model.semStream.roi.value == UNDEFINED_ROI:
self._tab.tab_data_model.semStream.roi.value = (0, 0, 1, 1)
except AttributeError:
pass # Not a SPARC
# Disable drift correction (on SPARC)
if hasattr(self._tab.tab_data_model, "driftCorrector"):
self._tab.tab_data_model.driftCorrector.roi.value = UNDEFINED_ROI
ss = self._get_live_streams()
self.filename.value = self._get_new_filename()
dlg = AcquisitionDialog(
self, "Tiled acquisition",
"Acquire a large area by acquiring the streams multiple "
"times over a grid.")
self._dlg = dlg
# don't allow adding/removing streams
self._dlg.streambar_controller.to_static_mode()
dlg.addSettings(self, self.vaconf)
for s in ss:
if isinstance(
s,
(ARStream, SpectrumStream, MonochromatorSettingsStream)):
# TODO: instead of hard-coding the list, a way to detect the type
# of live image?
logging.info(
"Not showing stream %s, for which the live image is not spatial",
s)
dlg.addStream(s, index=None)
else:
dlg.addStream(s, index=0)
dlg.addButton("Cancel")
dlg.addButton("Acquire", self.acquire, face_colour='blue')
# Update acq time and area when streams are added/removed. Add stream settings
# to subscribed vas.
dlg.view.stream_tree.flat.subscribe(self._update_exp_dur, init=True)
dlg.view.stream_tree.flat.subscribe(self._update_total_area, init=True)
dlg.view.stream_tree.flat.subscribe(self._on_streams_change, init=True)
# Default fineAlign to True if it's possible
# Use live streams to make the decision since visible streams might not be initialized yet
# TODO: the visibility of the streams seems to be reset when the plugin is started,
# a stream that is invisible in the main panel becomes visible. This should be fixed.
if self._can_fine_align(ss):
self.fineAlign.value = True
self._ovrl_stream = self._create_overlay_stream(ss)
# This looks tautologic, but actually, it forces the setter to check the
# value is within range, and will automatically reduce it if necessary.
self.nx.value = self.nx.value
self.ny.value = self.ny.value
self._memory_check()
# TODO: disable "acquire" button if no stream selected.
ans = dlg.ShowModal()
if ans == 0 or ans == wx.ID_CANCEL:
logging.info("Tiled acquisition cancelled")
self.ft.cancel()
elif ans == 1:
logging.info("Tiled acquisition completed")
else:
logging.warning("Got unknown return code %s", ans)
# Don't hold references
self._unsubscribe_vas()
dlg.Destroy()
self._dlg = None
