def setUpClass(cls):
super(GridPanelTestCase, cls).setUpClass()
# Make the Panels look like ViewPorts
v = StreamView("everything")
f = cls.frame
for vp in (f.red, f.blue, f.purple, f.brown, f.yellow, f.green):
vp.view = v
def __init__(self, plugin, title, text=None):
"""
Creates a modal window. The return code is the button number that was
last pressed before closing the window.
plugin (Plugin): The plugin creating this dialog
title (str): The title of the window
text (None or str): If provided, it is displayed at the top of the window
"""
super(AcquisitionDialog, self).__init__(plugin.main_app.main_frame)
logging.debug("Creating acquisition dialog for %s",
plugin.__class__.__name__)
self.plugin = plugin
self.SetTitle(title)
if text is not None:
self.lbl_description = AutoWrapStaticText(self.pnl_desc, "")
self.lbl_description.SetBackgroundColour(
self.pnl_desc.GetBackgroundColour())
self.lbl_description.SetForegroundColour(gui.FG_COLOUR_MAIN)
self.pnl_desc.GetSizer().Add(self.lbl_description,
flag=wx.EXPAND | wx.ALL,
border=10)
self.lbl_description.SetLabel(text)
self._acq_future_connector = None
self.buttons = [] # The buttons
self.current_future = None
self.btn_cancel.Bind(wx.EVT_BUTTON, self._cancel_future)
self.setting_controller = SettingsController(self.fp_settings,
"No settings defined")
# Create a minimal model for use in the streambar controller
self._dmodel = MicroscopyGUIData(plugin.main_app.main_data)
self.hidden_view = StreamView("Plugin View Hidden")
self.view = MicroscopeView("Plugin View left")
self.viewport_l.setView(self.view, self._dmodel)
self.view_r = MicroscopeView("Plugin View right")
self.viewport_r.setView(self.view_r, self._dmodel)
self.spectrum_view = MicroscopeView("Plugin View spectrum")
self.spectrum_viewport.setView(self.spectrum_view, self._dmodel)
self._dmodel.focussedView.value = self.view
self._dmodel.views.value = [self.view, self.view_r, self.spectrum_view]
self._viewports = (self.viewport_l, self.viewport_r,
self.spectrum_viewport)
self.streambar_controller = StreamBarController(self._dmodel,
self.pnl_streams,
ignore_view=True)
self.Fit()
def __init__(self, parent, orig_tab_data):
xrcfr_acq.__init__(self, parent)
self.conf = get_acqui_conf()
for n in presets:
self.cmb_presets.Append(n)
# TODO: record and reuse the preset used?
self.cmb_presets.Select(0)
self.filename = model.StringVA(create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count))
self.filename.subscribe(self._onFilename, init=True)
# The name of the last file that got written to disk (used for auto viewing on close)
self.last_saved_file = None
# True when acquisition occurs
self.acquiring = False
# a ProgressiveFuture if the acquisition is going on
self.acq_future = None
self._acq_future_connector = None
self._main_data_model = orig_tab_data.main
# duplicate the interface, but with only one view
self._tab_data_model = self.duplicate_tab_data_model(orig_tab_data)
# Create a new settings controller for the acquisition dialog
self._settings_controller = SecomSettingsController(
self,
self._tab_data_model,
highlight_change=True # also adds a "Reset" context menu
)
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
self._hidden_view = StreamView("Plugin View Hidden")
self.streambar_controller = StreamBarController(self._tab_data_model,
self.pnl_secom_streams,
static=True,
ignore_view=True)
# The streams currently displayed are the one visible
self.add_all_streams()
# The list of streams ready for acquisition (just used as a cache)
self._acq_streams = {}
# FIXME: pass the fold_panels
# Compute the preset values for each preset
self._preset_values = {} # dict string -> dict (SettingEntries -> value)
self._orig_entries = get_global_settings_entries(self._settings_controller)
for sc in self.streambar_controller.stream_controllers:
self._orig_entries += get_local_settings_entries(sc)
self._orig_settings = preset_as_is(self._orig_entries) # to detect changes
for n, preset in presets.items():
self._preset_values[n] = preset(self._orig_entries)
# Presets which have been confirmed on the hardware
self._presets_confirmed = set() # (string)
self.start_listening_to_va()
# If it could be possible to do fine alignment, allow the user to choose
if self._can_fine_align(self._tab_data_model.streams.value):
self.chkbox_fine_align.Show()
# Set to True to make it the default, but will be automatically
# disabled later if the current visible streams don't allow it.
self.chkbox_fine_align.Value = True
for s in self._tab_data_model.streams.value:
if isinstance(s, EMStream):
em_det = s.detector
em_emt = s.emitter
elif isinstance(s, OpticalStream) and not isinstance(s, ScannedFluoStream):
opt_det = s.detector
self._ovrl_stream = stream.OverlayStream("Fine alignment", opt_det, em_emt, em_det,
opm=self._main_data_model.opm)
self._ovrl_stream.dwellTime.value = self._main_data_model.fineAlignDwellTime.value
else:
self.chkbox_fine_align.Show(False)
self.chkbox_fine_align.Value = False
self._prev_fine_align = self.chkbox_fine_align.Value
# make sure the view displays the same thing as the one we are
# duplicating
self._view.view_pos.value = orig_view.view_pos.value
self._view.mpp.value = orig_view.mpp.value
self._view.merge_ratio.value = orig_view.merge_ratio.value
# attach the view to the viewport
self.pnl_view_acq.canvas.fit_view_to_next_image = False
self.pnl_view_acq.setView(self._view, self._tab_data_model)
# The TOOL_ROA is not present because we don't allow the user to change
# the ROA), so we need to explicitly request the canvas to show the ROA.
if hasattr(self._tab_data_model, "roa") and self._tab_data_model.roa is not None:
cnvs = self.pnl_view_acq.canvas
self.roa_overlay = RepetitionSelectOverlay(cnvs, self._tab_data_model.roa,
self._tab_data_model.fovComp)
cnvs.add_world_overlay(self.roa_overlay)
self.Bind(wx.EVT_CHAR_HOOK, self.on_key)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self.btn_change_file.Bind(wx.EVT_BUTTON, self.on_change_file)
self.btn_secom_acquire.Bind(wx.EVT_BUTTON, self.on_acquire)
self.cmb_presets.Bind(wx.EVT_COMBOBOX, self.on_preset)
self.Bind(wx.EVT_CLOSE, self.on_close)
# on_streams_changed is compatible because it doesn't use the args
self.chkbox_fine_align.Bind(wx.EVT_CHECKBOX, self.on_streams_changed)
self.on_preset(None) # will force setting the current preset
# To update the estimated time when streams are removed/added
self._view.stream_tree.flat.subscribe(self.on_streams_changed)
self._hidden_view.stream_tree.flat.subscribe(self.on_streams_changed)
class AcquisitionDialog(xrcfr_acq):
""" Wrapper class responsible for additional initialization of the
Acquisition Dialog created in XRCed
"""
# TODO: share more code with cont.acquisition
def __init__(self, parent, orig_tab_data):
xrcfr_acq.__init__(self, parent)
self.conf = get_acqui_conf()
for n in presets:
self.cmb_presets.Append(n)
# TODO: record and reuse the preset used?
self.cmb_presets.Select(0)
self.filename = model.StringVA(create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count))
self.filename.subscribe(self._onFilename, init=True)
# The name of the last file that got written to disk (used for auto viewing on close)
self.last_saved_file = None
# True when acquisition occurs
self.acquiring = False
# a ProgressiveFuture if the acquisition is going on
self.acq_future = None
self._acq_future_connector = None
self._main_data_model = orig_tab_data.main
# duplicate the interface, but with only one view
self._tab_data_model = self.duplicate_tab_data_model(orig_tab_data)
# Create a new settings controller for the acquisition dialog
self._settings_controller = SecomSettingsController(
self,
self._tab_data_model,
highlight_change=True # also adds a "Reset" context menu
)
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
self._hidden_view = StreamView("Plugin View Hidden")
self.streambar_controller = StreamBarController(self._tab_data_model,
self.pnl_secom_streams,
static=True,
ignore_view=True)
# The streams currently displayed are the one visible
self.add_all_streams()
# The list of streams ready for acquisition (just used as a cache)
self._acq_streams = {}
# FIXME: pass the fold_panels
# Compute the preset values for each preset
self._preset_values = {} # dict string -> dict (SettingEntries -> value)
self._orig_entries = get_global_settings_entries(self._settings_controller)
for sc in self.streambar_controller.stream_controllers:
self._orig_entries += get_local_settings_entries(sc)
self._orig_settings = preset_as_is(self._orig_entries) # to detect changes
for n, preset in presets.items():
self._preset_values[n] = preset(self._orig_entries)
# Presets which have been confirmed on the hardware
self._presets_confirmed = set() # (string)
self.start_listening_to_va()
# If it could be possible to do fine alignment, allow the user to choose
if self._can_fine_align(self._tab_data_model.streams.value):
self.chkbox_fine_align.Show()
# Set to True to make it the default, but will be automatically
# disabled later if the current visible streams don't allow it.
self.chkbox_fine_align.Value = True
for s in self._tab_data_model.streams.value:
if isinstance(s, EMStream):
em_det = s.detector
em_emt = s.emitter
elif isinstance(s, OpticalStream) and not isinstance(s, ScannedFluoStream):
opt_det = s.detector
self._ovrl_stream = stream.OverlayStream("Fine alignment", opt_det, em_emt, em_det,
opm=self._main_data_model.opm)
self._ovrl_stream.dwellTime.value = self._main_data_model.fineAlignDwellTime.value
else:
self.chkbox_fine_align.Show(False)
self.chkbox_fine_align.Value = False
self._prev_fine_align = self.chkbox_fine_align.Value
# make sure the view displays the same thing as the one we are
# duplicating
self._view.view_pos.value = orig_view.view_pos.value
self._view.mpp.value = orig_view.mpp.value
self._view.merge_ratio.value = orig_view.merge_ratio.value
# attach the view to the viewport
self.pnl_view_acq.canvas.fit_view_to_next_image = False
self.pnl_view_acq.setView(self._view, self._tab_data_model)
# The TOOL_ROA is not present because we don't allow the user to change
# the ROA), so we need to explicitly request the canvas to show the ROA.
if hasattr(self._tab_data_model, "roa") and self._tab_data_model.roa is not None:
cnvs = self.pnl_view_acq.canvas
self.roa_overlay = RepetitionSelectOverlay(cnvs, self._tab_data_model.roa,
self._tab_data_model.fovComp)
cnvs.add_world_overlay(self.roa_overlay)
self.Bind(wx.EVT_CHAR_HOOK, self.on_key)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self.btn_change_file.Bind(wx.EVT_BUTTON, self.on_change_file)
self.btn_secom_acquire.Bind(wx.EVT_BUTTON, self.on_acquire)
self.cmb_presets.Bind(wx.EVT_COMBOBOX, self.on_preset)
self.Bind(wx.EVT_CLOSE, self.on_close)
# on_streams_changed is compatible because it doesn't use the args
self.chkbox_fine_align.Bind(wx.EVT_CHECKBOX, self.on_streams_changed)
self.on_preset(None) # will force setting the current preset
# To update the estimated time when streams are removed/added
self._view.stream_tree.flat.subscribe(self.on_streams_changed)
self._hidden_view.stream_tree.flat.subscribe(self.on_streams_changed)
def start_listening_to_va(self):
# Get all the VA's from the stream and subscribe to them for changes.
for entry in self._orig_entries:
if hasattr(entry, "vigilattr"):
entry.vigilattr.subscribe(self.on_setting_change)
def stop_listening_to_va(self):
for entry in self._orig_entries:
if hasattr(entry, "vigilattr"):
entry.vigilattr.unsubscribe(self.on_setting_change)
def duplicate_tab_data_model(self, orig):
"""
Duplicate a MicroscopyGUIData and adapt it for the acquisition window
The streams will be shared, but not the views
orig (MicroscopyGUIData)
return (MicroscopyGUIData)
"""
# TODO: we'd better create a new view and copy the streams
new = copy.copy(orig) # shallow copy
new.streams = model.ListVA(orig.streams.value) # duplicate
# create view (which cannot move or focus)
view = guimodel.MicroscopeView("All")
# differentiate it (only one view)
new.views = model.ListVA()
new.views.value.append(view)
new.focussedView = model.VigilantAttribute(view)
new.viewLayout = model.IntEnumerated(guimodel.VIEW_LAYOUT_ONE,
choices={guimodel.VIEW_LAYOUT_ONE})
new.tool = model.IntEnumerated(TOOL_NONE, choices={TOOL_NONE})
return new
def add_all_streams(self):
"""
Add all the streams present in the interface model to the stream panel.
"""
# the order the streams are added should not matter on the display, so
# it's ok to not duplicate the streamTree literally
# go through all the streams available in the interface model
for s in self._tab_data_model.streams.value:
if isinstance(s, NON_SPATIAL_STREAMS):
v = self._hidden_view
else:
v = self._view
self.streambar_controller.addStream(s, add_to_view=v)
def remove_all_streams(self):
"""
Remove the streams we added to the view on creation
Must be called in the main GUI thread
"""
# Ensure we don't update the view after the window is destroyed
self.streambar_controller.clear()
# TODO: need to have a .clear() on the settings_controller to clean up?
self._settings_controller = None
self._acq_streams = {} # also empty the cache
gc.collect() # To help reclaiming some memory
def get_acq_streams(self):
"""
return (list of Streams): the streams to be acquired
"""
# Only acquire the streams which are displayed
streams = self._view.getStreams() + self._hidden_view.getStreams()
# Add the overlay stream if requested, and folds all the streams
if streams and self.chkbox_fine_align.Value:
streams.append(self._ovrl_stream)
self._acq_streams = acqmng.foldStreams(streams, self._acq_streams)
return self._acq_streams
def find_current_preset(self):
"""
find the name of the preset identical to the current settings (not
including "Custom")
returns (string): name of the preset
raises KeyError: if no preset can be found
"""
# check each preset
for n, settings in self._preset_values.items():
# compare each value between the current and proposed
different = False
for entry, value in settings.items():
if entry.vigilattr.value != value:
different = True
break
if not different:
return n
raise KeyError()
def _can_fine_align(self, streams):
"""
Return True if with the given streams it would make sense to fine align
streams (iterable of Stream)
return (bool): True if at least a SEM and an optical stream are present
"""
# check for a SEM stream
for s in streams:
if isinstance(s, EMStream):
break
else:
return False
# check for an optical stream
# TODO: allow it also for ScannedFluoStream once fine alignment is supported
# on confocal SECOM.
for s in streams:
if isinstance(s, OpticalStream) and not isinstance(s, ScannedFluoStream):
break
else:
return False
return True
@wxlimit_invocation(0.1)
def update_setting_display(self):
if not self:
return
# if gauge was left over from an error => now hide it
if self.acquiring:
self.gauge_acq.Show()
return
elif self.gauge_acq.IsShown():
self.gauge_acq.Hide()
self.Layout()
# Enable/disable Fine alignment check box
streams = self._view.getStreams() + self._hidden_view.getStreams()
can_fa = self._can_fine_align(streams)
if self.chkbox_fine_align.Enabled:
self._prev_fine_align = self.chkbox_fine_align.Value
self.chkbox_fine_align.Enable(can_fa)
# Uncheck if disabled, otherwise put same as previous value
self.chkbox_fine_align.Value = (can_fa and self._prev_fine_align)
self.update_acquisition_time()
# update highlight
for se, value in self._orig_settings.items():
se.highlight(se.vigilattr.value != value)
def on_streams_changed(self, val):
"""
When the list of streams to acquire has changed
"""
self.update_setting_display()
def on_setting_change(self, _=None):
self.update_setting_display()
# check presets and fall-back to custom
try:
preset_name = self.find_current_preset()
logging.debug("Detected preset %s", preset_name)
except KeyError:
# should not happen with the current preset_no_change
logging.exception("Couldn't match any preset")
preset_name = u"Custom"
wx.CallAfter(self.cmb_presets.SetValue, preset_name)
def update_acquisition_time(self):
"""
Must be called in the main GUI thread.
"""
streams = self.get_acq_streams()
if streams:
acq_time = acqmng.estimateTime(streams)
acq_time = math.ceil(acq_time) # round a bit pessimisticly
txt = "The estimated acquisition time is {}."
txt = txt.format(units.readable_time(acq_time))
else:
txt = "No streams present."
self.lbl_acqestimate.SetLabel(txt)
@call_in_wx_main
def _onFilename(self, name):
""" updates the GUI when the filename is updated """
# decompose into path/file
path, base = os.path.split(name)
self.txt_destination.SetValue(str(path))
# show the end of the path (usually more important)
self.txt_destination.SetInsertionPointEnd()
self.txt_filename.SetValue(str(base))
def on_preset(self, evt):
preset_name = self.cmb_presets.GetValue()
try:
new_preset = self._preset_values[preset_name]
except KeyError:
logging.debug("Not changing settings for preset %s", preset_name)
return
logging.debug("Changing setting to preset %s", preset_name)
# TODO: presets should also be able to change the special stream settings
# (eg: accumulation/interpolation) when we have them
# apply the recorded values
apply_preset(new_preset)
# The hardware might not exactly apply the setting as computed in the
# preset. We need the _exact_ same value to find back which preset is
# currently selected. So update the values the first time.
if preset_name not in self._presets_confirmed:
for se in new_preset.keys():
new_preset[se] = se.vigilattr.value
self._presets_confirmed.add(preset_name)
self.update_setting_display()
def on_key(self, evt):
""" Dialog key press handler. """
if evt.GetKeyCode() == wx.WXK_ESCAPE:
self.Close()
else:
evt.Skip()
def on_change_file(self, evt):
"""
Shows a dialog to change the path, name, and format of the acquisition
file.
returns nothing, but updates .filename and .conf
"""
fn = create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count)
new_name = ShowAcquisitionFileDialog(self, fn)
if new_name is not None:
self.filename.value = new_name
self.conf.fn_ptn, self.conf.fn_count = guess_pattern(new_name)
logging.debug("Generated filename pattern '%s'", self.conf.fn_ptn)
# It means the user wants to do a new acquisition
self.btn_secom_acquire.SetLabel("START")
self.last_saved_file = None
def terminate_listeners(self):
"""
Disconnect all the connections to the streams.
Must be called in the main GUI thread.
"""
# stop listening to events
self._view.stream_tree.flat.unsubscribe(self.on_streams_changed)
self._hidden_view.stream_tree.flat.unsubscribe(self.on_streams_changed)
self.stop_listening_to_va()
self.remove_all_streams()
def on_close(self, evt):
""" Close event handler that executes various cleanup actions
"""
if self.acq_future:
# TODO: ask for confirmation before cancelling?
# What to do if the acquisition is done while asking for
# confirmation?
msg = "Cancelling acquisition due to closing the acquisition window"
logging.info(msg)
self.acq_future.cancel()
self.terminate_listeners()
self.EndModal(wx.ID_CANCEL)
def _view_file(self):
"""
Called to open the file which was just acquired
Must be called in the main GUI thread.
"""
self.terminate_listeners()
self.EndModal(wx.ID_OPEN)
logging.debug("My return code is %d", self.GetReturnCode())
def _pause_settings(self):
""" Pause the settings of the GUI and save the values for restoring them later """
self._settings_controller.pause()
self._settings_controller.enable(False)
self.streambar_controller.pause()
self.streambar_controller.enable(False)
def _resume_settings(self):
""" Resume the settings of the GUI and save the values for restoring them later """
self._settings_controller.enable(True)
self._settings_controller.resume()
self.streambar_controller.enable(True)
self.streambar_controller.resume()
def on_acquire(self, evt):
""" Start the actual acquisition """
if self.last_saved_file: # This means the button is actually "View"
self._view_file()
return
logging.info("Acquire button clicked, starting acquisition")
self.acquiring = True
self.btn_secom_acquire.Disable()
# disable estimation time updates during acquisition
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
# Freeze all the settings so that it's not possible to change anything
self._pause_settings()
self.gauge_acq.Show()
self.Layout() # to put the gauge at the right place
# For now, always indicate the best quality (even if the preset is set
# to "live")
if self._main_data_model.opm:
self._main_data_model.opm.setAcqQuality(path.ACQ_QUALITY_BEST)
# Note: It should never be possible to reach here with no streams
streams = self.get_acq_streams()
v_streams = self._view.getStreams() # visible streams
for s in streams:
# Add extra viewable streams to view. However, do not add incompatible streams.
if s not in v_streams and not isinstance(s, NON_SPATIAL_STREAMS):
self._view.addStream(s)
# Update the filename in the streams
if hasattr(s, "filename"):
pathname, base = os.path.split(self.filename.value)
s.filename.value = base
self.acq_future = acqmng.acquire(streams, self._main_data_model.settings_obs)
self._acq_future_connector = ProgressiveFutureConnector(self.acq_future,
self.gauge_acq,
self.lbl_acqestimate)
self.acq_future.add_done_callback(self.on_acquisition_done)
self.btn_cancel.SetLabel("Cancel")
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_cancel)
def on_cancel(self, evt):
""" Handle acquisition cancel button click """
if not self.acq_future:
logging.warning("Tried to cancel acquisition while it was not started")
return
logging.info("Cancel button clicked, stopping acquisition")
self.acq_future.cancel()
self.acquiring = False
self.btn_cancel.SetLabel("Close")
# all the rest will be handled by on_acquisition_done()
@call_in_wx_main
def on_acquisition_done(self, future):
""" Callback called when the acquisition is finished (either successfully or cancelled) """
if self._main_data_model.opm:
self._main_data_model.opm.setAcqQuality(path.ACQ_QUALITY_FAST)
# bind button back to direct closure
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self._resume_settings()
self.acquiring = False
# re-enable estimation time updates
self._view.lastUpdate.subscribe(self.on_streams_changed)
self.acq_future = None # To avoid holding the ref in memory
self._acq_future_connector = None
try:
data, exp = future.result(1) # timeout is just for safety
self.conf.fn_count = update_counter(self.conf.fn_count)
except CancelledError:
# put back to original state:
# re-enable the acquire button
self.btn_secom_acquire.Enable()
# hide progress bar (+ put pack estimated time)
self.update_acquisition_time()
self.gauge_acq.Hide()
self.Layout()
return
except Exception:
# We cannot do much: just warn the user and pretend it was cancelled
logging.exception("Acquisition failed")
self.btn_secom_acquire.Enable()
self.lbl_acqestimate.SetLabel("Acquisition failed.")
self.lbl_acqestimate.Parent.Layout()
# leave the gauge, to give a hint on what went wrong.
return
# Handle the case acquisition failed "a bit"
if exp:
logging.warning("Acquisition failed (after %d streams): %s",
len(data), exp)
# save result to file
self.lbl_acqestimate.SetLabel("Saving file...")
self.lbl_acqestimate.Parent.Layout()
try:
thumb = acqmng.computeThumbnail(self._view.stream_tree, future)
filename = self.filename.value
exporter = dataio.get_converter(self.conf.last_format)
exporter.export(filename, data, thumb)
logging.info("Acquisition saved as file '%s'.", filename)
# Allow to see the acquisition
self.btn_secom_acquire.SetLabel("VIEW")
self.last_saved_file = filename
except Exception:
logging.exception("Saving acquisition failed")
self.btn_secom_acquire.Enable()
self.lbl_acqestimate.SetLabel("Saving acquisition file failed.")
self.lbl_acqestimate.Parent.Layout()
return
if exp:
self.lbl_acqestimate.SetLabel("Acquisition failed (partially).")
else:
self.lbl_acqestimate.SetLabel("Acquisition completed.")
# As the action is complete, rename "Cancel" to "Close"
self.btn_cancel.SetLabel("Close")
self.lbl_acqestimate.Parent.Layout()
# Make sure the file is not overridden
self.btn_secom_acquire.Enable()
def __init__(self, parent, orig_tab_data):
xrcfr_acq.__init__(self, parent)
self.conf = get_acqui_conf()
for n in presets:
self.cmb_presets.Append(n)
# TODO: record and reuse the preset used?
self.cmb_presets.Select(0)
self.filename = model.StringVA(create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count))
self.filename.subscribe(self._onFilename, init=True)
# The name of the last file that got written to disk (used for auto viewing on close)
self.last_saved_file = None
# True when acquisition occurs
self.acquiring = False
# a ProgressiveFuture if the acquisition is going on
self.acq_future = None
self._acq_future_connector = None
self._main_data_model = orig_tab_data.main
# duplicate the interface, but with only one view
self._tab_data_model = self.duplicate_tab_data_model(orig_tab_data)
# Create a new settings controller for the acquisition dialog
self._settings_controller = SecomSettingsController(
self,
self._tab_data_model,
highlight_change=True # also adds a "Reset" context menu
)
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
self._hidden_view = StreamView("Plugin View Hidden")
self.streambar_controller = StreamBarController(self._tab_data_model,
self.pnl_secom_streams,
static=True,
ignore_view=True)
# The streams currently displayed are the one visible
self.add_all_streams()
# The list of streams ready for acquisition (just used as a cache)
self._acq_streams = {}
# FIXME: pass the fold_panels
# Compute the preset values for each preset
self._preset_values = {} # dict string -> dict (SettingEntries -> value)
self._orig_entries = get_global_settings_entries(self._settings_controller)
for sc in self.streambar_controller.stream_controllers:
self._orig_entries += get_local_settings_entries(sc)
self._orig_settings = preset_as_is(self._orig_entries) # to detect changes
for n, preset in presets.items():
self._preset_values[n] = preset(self._orig_entries)
# Presets which have been confirmed on the hardware
self._presets_confirmed = set() # (string)
self.start_listening_to_va()
# If it could be possible to do fine alignment, allow the user to choose
if self._can_fine_align(self._tab_data_model.streams.value):
self.chkbox_fine_align.Show()
# Set to True to make it the default, but will be automatically
# disabled later if the current visible streams don't allow it.
self.chkbox_fine_align.Value = True
for s in self._tab_data_model.streams.value:
if isinstance(s, EMStream):
em_det = s.detector
em_emt = s.emitter
elif isinstance(s, OpticalStream) and not isinstance(s, ScannedFluoStream):
opt_det = s.detector
self._ovrl_stream = stream.OverlayStream("Fine alignment", opt_det, em_emt, em_det,
opm=self._main_data_model.opm)
self._ovrl_stream.dwellTime.value = self._main_data_model.fineAlignDwellTime.value
else:
self.chkbox_fine_align.Show(False)
self.chkbox_fine_align.Value = False
self._prev_fine_align = self.chkbox_fine_align.Value
# make sure the view displays the same thing as the one we are
# duplicating
self._view.view_pos.value = orig_view.view_pos.value
self._view.mpp.value = orig_view.mpp.value
self._view.merge_ratio.value = orig_view.merge_ratio.value
# attach the view to the viewport
self.pnl_view_acq.canvas.fit_view_to_next_image = False
self.pnl_view_acq.setView(self._view, self._tab_data_model)
# The TOOL_ROA is not present because we don't allow the user to change
# the ROA), so we need to explicitly request the canvas to show the ROA.
if hasattr(self._tab_data_model, "roa") and self._tab_data_model.roa is not None:
cnvs = self.pnl_view_acq.canvas
self.roa_overlay = RepetitionSelectOverlay(cnvs, self._tab_data_model.roa,
self._tab_data_model.fovComp)
cnvs.add_world_overlay(self.roa_overlay)
self.Bind(wx.EVT_CHAR_HOOK, self.on_key)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self.btn_change_file.Bind(wx.EVT_BUTTON, self.on_change_file)
self.btn_secom_acquire.Bind(wx.EVT_BUTTON, self.on_acquire)
self.cmb_presets.Bind(wx.EVT_COMBOBOX, self.on_preset)
self.Bind(wx.EVT_CLOSE, self.on_close)
# on_streams_changed is compatible because it doesn't use the args
self.chkbox_fine_align.Bind(wx.EVT_CHECKBOX, self.on_streams_changed)
self.on_preset(None) # will force setting the current preset
# To update the estimated time when streams are removed/added
self._view.stream_tree.flat.subscribe(self.on_streams_changed)
self._hidden_view.stream_tree.flat.subscribe(self.on_streams_changed)
class AcquisitionDialog(xrcfr_acq):
""" Wrapper class responsible for additional initialization of the
Acquisition Dialog created in XRCed
"""
# TODO: share more code with cont.acquisition
def __init__(self, parent, orig_tab_data):
xrcfr_acq.__init__(self, parent)
self.conf = get_acqui_conf()
for n in presets:
self.cmb_presets.Append(n)
# TODO: record and reuse the preset used?
self.cmb_presets.Select(0)
self.filename = model.StringVA(create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count))
self.filename.subscribe(self._onFilename, init=True)
# The name of the last file that got written to disk (used for auto viewing on close)
self.last_saved_file = None
# True when acquisition occurs
self.acquiring = False
# a ProgressiveFuture if the acquisition is going on
self.acq_future = None
self._acq_future_connector = None
self._main_data_model = orig_tab_data.main
# duplicate the interface, but with only one view
self._tab_data_model = self.duplicate_tab_data_model(orig_tab_data)
# Create a new settings controller for the acquisition dialog
self._settings_controller = SecomSettingsController(
self,
self._tab_data_model,
highlight_change=True # also adds a "Reset" context menu
)
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
self._hidden_view = StreamView("Plugin View Hidden")
self.streambar_controller = StreamBarController(self._tab_data_model,
self.pnl_secom_streams,
static=True,
ignore_view=True)
# The streams currently displayed are the one visible
self.add_all_streams()
# The list of streams ready for acquisition (just used as a cache)
self._acq_streams = {}
# FIXME: pass the fold_panels
# Compute the preset values for each preset
self._preset_values = {} # dict string -> dict (SettingEntries -> value)
self._orig_entries = get_global_settings_entries(self._settings_controller)
for sc in self.streambar_controller.stream_controllers:
self._orig_entries += get_local_settings_entries(sc)
self._orig_settings = preset_as_is(self._orig_entries) # to detect changes
for n, preset in presets.items():
self._preset_values[n] = preset(self._orig_entries)
# Presets which have been confirmed on the hardware
self._presets_confirmed = set() # (string)
self.start_listening_to_va()
# If it could be possible to do fine alignment, allow the user to choose
if self._can_fine_align(self._tab_data_model.streams.value):
self.chkbox_fine_align.Show()
# Set to True to make it the default, but will be automatically
# disabled later if the current visible streams don't allow it.
self.chkbox_fine_align.Value = True
for s in self._tab_data_model.streams.value:
if isinstance(s, EMStream):
em_det = s.detector
em_emt = s.emitter
elif isinstance(s, OpticalStream) and not isinstance(s, ScannedFluoStream):
opt_det = s.detector
self._ovrl_stream = stream.OverlayStream("Fine alignment", opt_det, em_emt, em_det,
opm=self._main_data_model.opm)
self._ovrl_stream.dwellTime.value = self._main_data_model.fineAlignDwellTime.value
else:
self.chkbox_fine_align.Show(False)
self.chkbox_fine_align.Value = False
self._prev_fine_align = self.chkbox_fine_align.Value
# make sure the view displays the same thing as the one we are
# duplicating
self._view.view_pos.value = orig_view.view_pos.value
self._view.mpp.value = orig_view.mpp.value
self._view.merge_ratio.value = orig_view.merge_ratio.value
# attach the view to the viewport
self.pnl_view_acq.canvas.fit_view_to_next_image = False
self.pnl_view_acq.setView(self._view, self._tab_data_model)
# The TOOL_ROA is not present because we don't allow the user to change
# the ROA), so we need to explicitly request the canvas to show the ROA.
if hasattr(self._tab_data_model, "roa") and self._tab_data_model.roa is not None:
cnvs = self.pnl_view_acq.canvas
self.roa_overlay = RepetitionSelectOverlay(cnvs, self._tab_data_model.roa,
self._tab_data_model.fovComp)
cnvs.add_world_overlay(self.roa_overlay)
self.Bind(wx.EVT_CHAR_HOOK, self.on_key)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self.btn_change_file.Bind(wx.EVT_BUTTON, self.on_change_file)
self.btn_secom_acquire.Bind(wx.EVT_BUTTON, self.on_acquire)
self.cmb_presets.Bind(wx.EVT_COMBOBOX, self.on_preset)
self.Bind(wx.EVT_CLOSE, self.on_close)
# on_streams_changed is compatible because it doesn't use the args
self.chkbox_fine_align.Bind(wx.EVT_CHECKBOX, self.on_streams_changed)
self.on_preset(None) # will force setting the current preset
# To update the estimated time when streams are removed/added
self._view.stream_tree.flat.subscribe(self.on_streams_changed)
self._hidden_view.stream_tree.flat.subscribe(self.on_streams_changed)
def start_listening_to_va(self):
# Get all the VA's from the stream and subscribe to them for changes.
for entry in self._orig_entries:
if hasattr(entry, "vigilattr"):
entry.vigilattr.subscribe(self.on_setting_change)
def stop_listening_to_va(self):
for entry in self._orig_entries:
if hasattr(entry, "vigilattr"):
entry.vigilattr.unsubscribe(self.on_setting_change)
def duplicate_tab_data_model(self, orig):
"""
Duplicate a MicroscopyGUIData and adapt it for the acquisition window
The streams will be shared, but not the views
orig (MicroscopyGUIData)
return (MicroscopyGUIData)
"""
# TODO: we'd better create a new view and copy the streams
new = copy.copy(orig) # shallow copy
new.streams = model.ListVA(orig.streams.value) # duplicate
# create view (which cannot move or focus)
view = guimodel.MicroscopeView("All")
# differentiate it (only one view)
new.views = model.ListVA()
new.views.value.append(view)
new.focussedView = model.VigilantAttribute(view)
new.viewLayout = model.IntEnumerated(guimodel.VIEW_LAYOUT_ONE,
choices={guimodel.VIEW_LAYOUT_ONE})
new.tool = model.IntEnumerated(TOOL_NONE, choices={TOOL_NONE})
return new
def add_all_streams(self):
"""
Add all the streams present in the interface model to the stream panel.
"""
# the order the streams are added should not matter on the display, so
# it's ok to not duplicate the streamTree literally
# go through all the streams available in the interface model
for s in self._tab_data_model.streams.value:
if isinstance(s, NON_SPATIAL_STREAMS):
v = self._hidden_view
else:
v = self._view
self.streambar_controller.addStream(s, add_to_view=v)
def remove_all_streams(self):
""" Remove the streams we added to the view on creation """
# Ensure we don't update the view after the window is destroyed
self.streambar_controller.clear()
# TODO: need to have a .clear() on the settings_controller to clean up?
self._settings_controller = None
self._acq_streams = {} # also empty the cache
gc.collect() # To help reclaiming some memory
def get_acq_streams(self):
"""
return (list of Streams): the streams to be acquired
"""
# Only acquire the streams which are displayed
streams = self._view.getStreams() + self._hidden_view.getStreams()
# Add the overlay stream if requested, and folds all the streams
if streams and self.chkbox_fine_align.Value:
streams.append(self._ovrl_stream)
self._acq_streams = acq.foldStreams(streams, self._acq_streams)
return self._acq_streams
def find_current_preset(self):
"""
find the name of the preset identical to the current settings (not
including "Custom")
returns (string): name of the preset
raises KeyError: if no preset can be found
"""
# check each preset
for n, settings in self._preset_values.items():
# compare each value between the current and proposed
different = False
for entry, value in settings.items():
if entry.vigilattr.value != value:
different = True
break
if not different:
return n
raise KeyError()
def _can_fine_align(self, streams):
"""
Return True if with the given streams it would make sense to fine align
streams (iterable of Stream)
return (bool): True if at least a SEM and an optical stream are present
"""
# check for a SEM stream
for s in streams:
if isinstance(s, EMStream):
break
else:
return False
# check for an optical stream
# TODO: allow it also for ScannedFluoStream once fine alignment is supported
# on confocal SECOM.
for s in streams:
if isinstance(s, OpticalStream) and not isinstance(s, ScannedFluoStream):
break
else:
return False
return True
@wxlimit_invocation(0.1)
def update_setting_display(self):
if not self:
return
# if gauge was left over from an error => now hide it
if self.acquiring:
self.gauge_acq.Show()
elif self.gauge_acq.IsShown():
self.gauge_acq.Hide()
self.Layout()
# Enable/disable Fine alignment check box
streams = self._view.getStreams() + self._hidden_view.getStreams()
can_fa = self._can_fine_align(streams)
if self.chkbox_fine_align.Enabled:
self._prev_fine_align = self.chkbox_fine_align.Value
self.chkbox_fine_align.Enable(can_fa)
# Uncheck if disabled, otherwise put same as previous value
self.chkbox_fine_align.Value = (can_fa and self._prev_fine_align)
self.update_acquisition_time()
# update highlight
for se, value in self._orig_settings.items():
se.highlight(se.vigilattr.value != value)
def on_streams_changed(self, val):
"""
When the list of streams to acquire has changed
"""
self.update_setting_display()
def on_setting_change(self, _=None):
self.update_setting_display()
# check presets and fall-back to custom
try:
preset_name = self.find_current_preset()
logging.debug("Detected preset %s", preset_name)
except KeyError:
# should not happen with the current preset_no_change
logging.exception("Couldn't match any preset")
preset_name = u"Custom"
self.cmb_presets.SetValue(preset_name)
def update_acquisition_time(self):
streams = self.get_acq_streams()
if streams:
acq_time = acq.estimateTime(streams)
acq_time = math.ceil(acq_time) # round a bit pessimisticly
txt = "The estimated acquisition time is {}."
txt = txt.format(units.readable_time(acq_time))
else:
txt = "No streams present."
self.lbl_acqestimate.SetLabel(txt)
def _onFilename(self, name):
""" updates the GUI when the filename is updated """
# decompose into path/file
path, base = os.path.split(name)
self.txt_destination.SetValue(unicode(path))
# show the end of the path (usually more important)
self.txt_destination.SetInsertionPointEnd()
self.txt_filename.SetValue(unicode(base))
def on_preset(self, evt):
preset_name = self.cmb_presets.GetValue()
try:
new_preset = self._preset_values[preset_name]
except KeyError:
logging.debug("Not changing settings for preset %s", preset_name)
return
logging.debug("Changing setting to preset %s", preset_name)
# TODO: presets should also be able to change the special stream settings
# (eg: accumulation/interpolation) when we have them
# apply the recorded values
apply_preset(new_preset)
# The hardware might not exactly apply the setting as computed in the
# preset. We need the _exact_ same value to find back which preset is
# currently selected. So update the values the first time.
if preset_name not in self._presets_confirmed:
for se in new_preset.keys():
new_preset[se] = se.vigilattr.value
self._presets_confirmed.add(preset_name)
self.update_setting_display()
def on_key(self, evt):
""" Dialog key press handler. """
if evt.GetKeyCode() == wx.WXK_ESCAPE:
self.Close()
else:
evt.Skip()
def on_change_file(self, evt):
"""
Shows a dialog to change the path, name, and format of the acquisition
file.
returns nothing, but updates .filename and .conf
"""
fn = create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count)
new_name = ShowAcquisitionFileDialog(self, fn)
if new_name is not None:
self.filename.value = new_name
self.conf.fn_ptn, self.conf.fn_count = guess_pattern(new_name)
logging.debug("Generated filename pattern '%s'", self.conf.fn_ptn)
# It means the user wants to do a new acquisition
self.btn_secom_acquire.SetLabel("START")
self.last_saved_file = None
def terminate_listeners(self):
# stop listening to events
self._view.stream_tree.flat.unsubscribe(self.on_streams_changed)
self._hidden_view.stream_tree.flat.unsubscribe(self.on_streams_changed)
self.stop_listening_to_va()
self.remove_all_streams()
def on_close(self, evt):
""" Close event handler that executes various cleanup actions
"""
if self.acq_future:
# TODO: ask for confirmation before cancelling?
# What to do if the acquisition is done while asking for
# confirmation?
msg = "Cancelling acquisition due to closing the acquisition window"
logging.info(msg)
self.acq_future.cancel()
self.terminate_listeners()
self.EndModal(wx.ID_CANCEL)
def _view_file(self):
"""
Called to open the file which was just acquired
"""
self.terminate_listeners()
self.EndModal(wx.ID_OPEN)
logging.debug("My return code is %d", self.GetReturnCode())
def _pause_settings(self):
""" Pause the settings of the GUI and save the values for restoring them later """
self._settings_controller.pause()
self._settings_controller.enable(False)
self.streambar_controller.pause()
self.streambar_controller.enable(False)
def _resume_settings(self):
""" Resume the settings of the GUI and save the values for restoring them later """
self._settings_controller.enable(True)
self._settings_controller.resume()
self.streambar_controller.enable(True)
self.streambar_controller.resume()
def on_acquire(self, evt):
""" Start the actual acquisition """
if self.last_saved_file: # This means the button is actually "View"
self._view_file()
return
logging.info("Acquire button clicked, starting acquisition")
self.acquiring = True
self.btn_secom_acquire.Disable()
# disable estimation time updates during acquisition
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
# Freeze all the settings so that it's not possible to change anything
self._pause_settings()
self.gauge_acq.Show()
self.Layout() # to put the gauge at the right place
# For now, always indicate the best quality (even if the preset is set
# to "live")
if self._main_data_model.opm:
self._main_data_model.opm.setAcqQuality(path.ACQ_QUALITY_BEST)
# Note: It should never be possible to reach here with no streams
streams = self.get_acq_streams()
v_streams = self._view.getStreams() # visible streams
for s in streams:
# Add extra viewable streams to view. However, do not add incompatible streams.
if s not in v_streams and not isinstance(s, NON_SPATIAL_STREAMS):
self._view.addStream(s)
# Update the filename in the streams
if hasattr(s, "filename"):
pathname, base = os.path.split(self.filename.value)
s.filename.value = base
self.acq_future = acq.acquire(streams)
self._acq_future_connector = ProgressiveFutureConnector(self.acq_future,
self.gauge_acq,
self.lbl_acqestimate)
self.acq_future.add_done_callback(self.on_acquisition_done)
self.btn_cancel.SetLabel("Cancel")
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_cancel)
def on_cancel(self, evt):
""" Handle acquisition cancel button click """
if not self.acq_future:
logging.warning("Tried to cancel acquisition while it was not started")
return
logging.info("Cancel button clicked, stopping acquisition")
self.acq_future.cancel()
self.acquiring = False
self.btn_cancel.SetLabel("Close")
# all the rest will be handled by on_acquisition_done()
@call_in_wx_main
def on_acquisition_done(self, future):
""" Callback called when the acquisition is finished (either successfully or cancelled) """
if self._main_data_model.opm:
self._main_data_model.opm.setAcqQuality(path.ACQ_QUALITY_FAST)
# bind button back to direct closure
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self._resume_settings()
self.acquiring = False
# re-enable estimation time updates
self._view.lastUpdate.subscribe(self.on_streams_changed)
self.acq_future = None # To avoid holding the ref in memory
self._acq_future_connector = None
try:
data, exp = future.result(1) # timeout is just for safety
self.conf.fn_count = update_counter(self.conf.fn_count)
except CancelledError:
# put back to original state:
# re-enable the acquire button
self.btn_secom_acquire.Enable()
# hide progress bar (+ put pack estimated time)
self.update_acquisition_time()
self.gauge_acq.Hide()
self.Layout()
return
except Exception:
# We cannot do much: just warn the user and pretend it was cancelled
logging.exception("Acquisition failed")
self.btn_secom_acquire.Enable()
self.lbl_acqestimate.SetLabel("Acquisition failed.")
self.lbl_acqestimate.Parent.Layout()
# leave the gauge, to give a hint on what went wrong.
return
# Handle the case acquisition failed "a bit"
if exp:
logging.warning("Acquisition failed (after %d streams): %s",
len(data), exp)
# save result to file
self.lbl_acqestimate.SetLabel("Saving file...")
self.lbl_acqestimate.Parent.Layout()
try:
thumb = acq.computeThumbnail(self._view.stream_tree, future)
filename = self.filename.value
exporter = dataio.get_converter(self.conf.last_format)
exporter.export(filename, data, thumb)
logging.info("Acquisition saved as file '%s'.", filename)
# Allow to see the acquisition
self.btn_secom_acquire.SetLabel("VIEW")
self.last_saved_file = filename
except Exception:
logging.exception("Saving acquisition failed")
self.btn_secom_acquire.Enable()
self.lbl_acqestimate.SetLabel("Saving acquisition file failed.")
self.lbl_acqestimate.Parent.Layout()
return
if exp:
self.lbl_acqestimate.SetLabel("Acquisition failed (partially).")
else:
self.lbl_acqestimate.SetLabel("Acquisition completed.")
# As the action is complete, rename "Cancel" to "Close"
self.btn_cancel.SetLabel("Close")
self.lbl_acqestimate.Parent.Layout()
# Make sure the file is not overridden
self.btn_secom_acquire.Enable()