class OverviewAcquisitionDialog(xrcfr_overview_acq):
"""
Class used to control the cryo-secom overview dialog
"""
def __init__(self, parent, orig_tab_data):
xrcfr_overview_acq.__init__(self, parent)
self.conf = get_acqui_conf()
# True when acquisition occurs
self.acquiring = False
self.data = None
# 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)
# The pattern to use for storing each tile file individually
# None disables storing them
self.filename_tiles = create_filename(self.conf.last_path, "{datelng}-{timelng}-overview",
".ome.tiff")
# Create a new settings controller for the acquisition dialog
self._settings_controller = LocalizationSettingsController(
self,
self._tab_data_model,
highlight_change=True # also adds a "Reset" context menu
)
self.zsteps = model.IntContinuous(1, range=(1, 51))
self._zsteps_vac = VigilantAttributeConnector(self.zsteps, self.zstack_steps, events=wx.EVT_SLIDER)
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
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_streams()
# The list of streams ready for acquisition (just used as a cache)
self._acq_streams = {}
# Compute the preset values for each preset
self._orig_entries = get_global_settings_entries(self._settings_controller)
self._orig_settings = preset_as_is(self._orig_entries)
for sc in self.streambar_controller.stream_controllers:
self._orig_entries += get_local_settings_entries(sc)
self.start_listening_to_va()
# 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)
self.Bind(wx.EVT_CHAR_HOOK, self.on_key)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self.btn_secom_acquire.Bind(wx.EVT_BUTTON, self.on_acquire)
self.Bind(wx.EVT_CLOSE, self.on_close)
# on_streams_changed is compatible because it doesn't use the args
# To update the estimated time when streams are removed/added
self._view.stream_tree.flat.subscribe(self.on_streams_changed)
# Set parameters for tiled acq
self.overlap = 0.2
try:
# Use the stage range, which can be overridden by the MD_POS_ACTIVE_RANGE,
# which can be overridden by MD_OVERVIEW_RANGE.
# Note: this last one might be temporary, until we have a RoA tool provided in the GUI.
stage_rng = {
"x": self._main_data_model.stage.axes["x"].range,
"y": self._main_data_model.stage.axes["y"].range
}
stage_md = self._main_data_model.stage.getMetadata()
if model.MD_POS_ACTIVE_RANGE in stage_md:
stage_rng.update(stage_md[model.MD_POS_ACTIVE_RANGE])
if model.MD_OVERVIEW_RANGE in stage_md:
stage_rng.update(stage_md[model.MD_OVERVIEW_RANGE])
# left, bottom, right, top
self.area = (stage_rng["x"][0], stage_rng["y"][0], stage_rng["x"][1], stage_rng["y"][1])
except (KeyError, IndexError):
raise ValueError("Failed to find stage.MD_POS_ACTIVE_RANGE with x and y range")
# Note: It should never be possible to reach here with no streams
streams = self.get_acq_streams()
for s in streams:
self._view.addStream(s)
self.update_acquisition_time()
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)
self.zsteps.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)
self.zsteps.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)
"""
data_model = AcquisitionWindowData(orig.main)
data_model.streams.value.extend(orig.streams.value)
# create view (which cannot move or focus)
view = guimodel.MicroscopeView("All")
data_model.views.value = [view]
data_model.focussedView.value = view
return data_model
def add_streams(self):
"""
Add live streams
"""
# go through all the streams available in the interface model
for s in self._tab_data_model.streams.value:
if not isinstance(s, LiveStream):
continue
self.streambar_controller.addStream(s, add_to_view=self._view)
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()
return streams
@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()
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()
def update_acquisition_time(self, acq_time=999):
"""
Must be called in the main GUI thread.
"""
if not self.acquiring:
streams = self.get_acq_streams()
if not streams:
acq_time = 0
else:
acq_time = stitching.estimateTiledAcquisitionTime(streams,
self._main_data_model.stage,
self.area, self.overlap,
zlevels=self._get_zstack_levels())
txt = "The estimated acquisition time is {}."
txt = txt.format(units.readable_time(acq_time))
self.lbl_acqestimate.SetLabel(txt)
def on_key(self, evt):
""" Dialog key press handler. """
if evt.GetKeyCode() == wx.WXK_ESCAPE:
self.Close()
else:
evt.Skip()
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.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()
# Set the streambar controller to None so it wouldn't be a listener to stream.remove
self.streambar_controller = None
self.EndModal(wx.ID_CANCEL)
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 _get_zstack_levels(self):
"""
Calculate the zstack levels from the current focus position and zsteps value
:returns (list(float) or None) zstack levels for zstack acquisition
"""
focus_value = self._main_data_model.focus.position.value['z']
# Clip zsteps value to allowed range
zsteps = self.zsteps.value
if zsteps == 1:
return None
# Create focus zlevels from the given zsteps number
zlevels = numpy.linspace(focus_value - (zsteps / 2 * ZSTEP), focus_value + (zsteps / 2 * ZSTEP), zsteps).tolist()
return zlevels
def _fit_view_to_area(self):
center = ((self.area[0] + self.area[2]) / 2,
(self.area[1] + self.area[3]) / 2)
self._view.view_pos.value = center
fov = (self.area[2] - self.area[0], self.area[3] - self.area[1])
self.pnl_view_acq.set_mpp_from_fov(fov)
def on_acquire(self, evt):
""" Start the actual acquisition """
logging.info("Acquire button clicked, starting acquisition")
acq_streams = self.get_acq_streams()
if not acq_streams:
logging.info("No stream to acquire, ending immediately")
self.on_close(evt) # Nothing to do, so it's the same as closing the window
self.acquiring = True
# Adjust view FoV to the whole area, so that it's possible to follow the acquisition
self._fit_view_to_area()
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
if self._main_data_model.opm:
self._main_data_model.opm.setAcqQuality(path.ACQ_QUALITY_BEST)
zlevels = self._get_zstack_levels()
logging.info("Acquisition tiles logged at %s", self.filename_tiles)
self.acq_future = stitching.acquireTiledArea(acq_streams, self._main_data_model.stage, area=self.area,
overlap=self.overlap,
settings_obs=self._main_data_model.settings_obs,
log_path=self.filename_tiles, zlevels=zlevels,
weaver=WEAVER_COLLAGE_REVERSE)
self._acq_future_connector = ProgressiveFutureConnector(self.acq_future,
self.gauge_acq,
self.lbl_acqestimate)
# TODO: Build-up the complete image during the acquisition, so that the
# progress can be followed live.
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 """
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:
# TODO: Add code for getting the data from the acquisition future
self.data = 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
self.terminate_listeners()
self.EndModal(wx.ID_OPEN)
class AcquisitionDialog(xrcfr_plugin):
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()
@call_in_wx_main
def addSettings(self, objWithVA, conf=None):
"""
Adds settings as one widget on a line for each VigilantAttribute (VA) in
the given object. Each setting entry created is added to setting_controller.entries.
objWithVA (object): an object with VAs.
conf (None or dict of str->config): allows to override the automatic
selection of the VA widget. See odemis.gui.conf.data for documentation.
raise:
LookupError: if no VA is found on the objWithVA
"""
vas = getVAs(objWithVA)
if not vas:
raise LookupError("No VAs found!")
if not conf:
conf = {}
vas_names = util.sorted_according_to(list(vas.keys()),
list(conf.keys()))
for name in vas_names:
va = vas[name]
self.setting_controller.add_setting_entry(name,
va,
None,
conf=conf.get(
name, None))
self.Layout()
@call_in_wx_main
def addButton(self, label, callback=None, face_colour='def'):
"""
Add a button at the bottom right of the window. If some buttons are already
present, they are shifted to the left.
label (str): text on the button,
callback (None or callable): the function to be called when the button
is pressed (with the dialog as argument). If callback is None,
pressing the button will close the window and the button number will
be the return code of the dialog.
"""
btnid = len(self.buttons)
btn = ImageTextButton(self.pnl_buttons,
label=label,
height=48,
style=wx.ALIGN_CENTER,
face_colour=face_colour)
self.buttons.append(btn)
sizer = self.pnl_buttons.GetSizer()
sizer.Add(btn, proportion=1, flag=wx.ALL, border=10)
if callback is not None and callable(callback):
# Wrap the callback, to run in a separate thread, so it doesn't block
# the GUI.
def button_callback_wrapper(evt, btnid=btnid):
# TODO: disable the button while the callback is running, so that
# it's not possible for the user to press twice in a row and cause
# the code to run twice simultaneously (without very explicitly
# allowing that).
try:
self.SetReturnCode(btnid)
logging.info("Button '%s' handled by %s, %s", label,
self.plugin.__class__.__name__, callback)
t = threading.Thread(target=callback,
args=(self, ),
name="Callback for button %s" %
(label, ))
t.start()
except Exception:
logging.exception(
"Error when processing button %s of plugin %s", label,
self.plugin)
btn.Bind(wx.EVT_BUTTON, button_callback_wrapper)
else:
btn.Bind(wx.EVT_BUTTON, partial(self.on_close, btnid))
self.pnl_buttons.Layout()
@call_in_wx_main
def addStream(self, stream, index=0):
"""
Adds a stream to the viewport, and a stream entry to the stream panel.
It also ensures the panel box and viewport are shown.
Note: If this method is not called, the stream panel and viewports are hidden.
stream (Stream or None): Stream to be added. Use None to force a viewport
to be seen without adding a stream.
index (0, 1, 2, or None): Index of the viewport to add the stream. 0 = left,
1 = right, 2 = spectrum viewport. If None, it will not show the stream
on any viewport (and it will be added to the .hidden_view)
"""
need_layout = False
if index is None:
v = self.hidden_view
else:
viewport = self._viewports[index]
v = self._dmodel.views.value[index]
assert viewport.view is v
if not viewport.IsShown():
viewport.Show()
need_layout = True
if stream:
if not self.fp_streams.IsShown():
self.fp_streams.Show()
need_layout = True
self.streambar_controller.addStream(stream, add_to_view=v)
if need_layout:
self.Layout()
self.Update()
@call_in_wx_main
def showProgress(self, future):
"""
Shows a progress bar, based on the status of the progressive future given.
As long as the future is not finished, the buttons are disabled.
future (None or Future): The progressive future to show the progress with
the progress bar. If future is None, it will hide the progress bar.
If future is cancellable, show a cancel button next to the progress bar.
"""
if future is not None and not future.cancelled():
self.current_future = future
self.enable_buttons(False)
self.pnl_gauge.Show(future is not None)
self.Layout()
if self.current_future is None:
self._acq_future_connector = None
return
else:
if hasattr(self.current_future, "add_update_callback"):
self._acq_future_connector = ProgressiveFutureConnector(
self.current_future, self.gauge_progress, self.lbl_gauge)
else:
# TODO: just pulse the gauge at a "good" frequency (need to use a timer)
self.gauge_progress.Pulse()
# If the future is cancellable (ie, has task_canceller), allow to
# press the "cancel" button, which will call cancel() on the future.
# TODO: if there is already a "cancel" button in the window, use it
# instead a providing another one.
if hasattr(self.current_future, 'task_canceller'):
self.btn_cancel.Enable()
else:
self.btn_cancel.Disable()
future.add_done_callback(self._on_future_done)
@call_in_wx_main
def setAcquisitionInfo(self, text=None, lvl=logging.INFO):
"""
Displays acquisition info above progress bar.
text (str or None): text to be displayed. If None is passed, the acquisition
label will be hidden, so no empty space is displayed.
lvl (int, from logging.*): log level, which selects the display colour.
Options: logging.INFO, logging.WARNING, logging.ERROR
"""
if text is None:
self.pnl_info.Hide()
else:
self.lbl_acquisition_info.SetLabel(text)
if lvl >= logging.ERROR:
self.lbl_acquisition_info.SetForegroundColour(FG_COLOUR_ERROR)
elif lvl >= logging.WARNING:
self.lbl_acquisition_info.SetForegroundColour(
FG_COLOUR_WARNING)
else:
self.lbl_acquisition_info.SetForegroundColour(FG_COLOUR_MAIN)
self.pnl_info.Show()
self.Layout()
@call_in_wx_main
def pauseSettings(self):
""" Pause the settings widgets. They will be disabled and the value frozen even when the VAs are changed """
self.setting_controller.pause()
self.streambar_controller.pause()
@call_in_wx_main
def resumeSettings(self):
""" unpause the settings widgets. They will be re-enabled and the value unfrozen """
self.setting_controller.resume()
self.streambar_controller.resume()
@call_in_wx_main
def enable_buttons(self, enable):
""" Enable or disable all the buttons in the button panel """
for btn in self.pnl_buttons.GetChildren():
btn.Enable(enable)
def _cancel_future(self, _):
""" Cancel the future if it's there and running """
if self.current_future is not None and not self.current_future.cancelled(
):
if self.current_future.cancel():
logging.debug("Future cancelled")
else:
logging.debug("Failed to cancel future")
@call_in_wx_main
def _on_future_done(self, _):
""" When the future finishes, reset the progress bar and enable the buttons """
self.gauge_progress.SetValue(0)
self.lbl_gauge.SetLabel("")
self.btn_cancel.Disable()
self.enable_buttons(True)
def on_close(self, btnid, _):
logging.debug("Closing window")
self.streambar_controller.clear()
self.EndModal(btnid)
@call_in_wx_main
def Close(self, *args, **kwargs):
"""
Request to close the window.
Make sure to call .Destroy() when not using the dialog anymore.
"""
# save the return code, as Close() automatically sets it to wx.ID_CANCEL
# but we want to keep the value potentially set by the button.
rc = self.ReturnCode
logging.debug("Closing acquisition dialog")
super(AcquisitionDialog, self).Close(*args, **kwargs)
self.ReturnCode = rc
logging.debug("Dialog closed")
@call_in_wx_main
def EndModal(self, retCode):
"""
Request to close the window, and pass a specific return code.
Make sure to call .Destroy() when not using the dialog anymore.
retCode (int)
"""
super(AcquisitionDialog, self).EndModal(retCode)
@call_in_wx_main
def Destroy(self, *args, **kwargs):
"""
Discards entirely the dialog. It's free'd from the memory.
Note: in most cases, if it's still opened, it get closed, but it seems
that with some version of wxPython, it causes a crash, so better call
Close() first.
"""
self.streambar_controller.clear()
logging.debug("Destroying acquisition dialog")
super(AcquisitionDialog, self).Destroy(*args, **kwargs)
logging.debug("Dialog destroyed")
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()
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(self._get_default_filename())
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
# 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
)
# To turn on/off the fan
self._orig_fan_speed = None
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
self.streambar_controller = StreamBarController(self._tab_data_model,
self.pnl_secom_streams)
# The streams currently displayed are the one visible
self.add_all_streams()
# FIXME: pass the fold_panels
# Compute the preset values for each preset
self._preset_values = {} # dict string -> dict (SettingEntries -> value)
orig_entries = get_global_settings_entries(self._settings_controller)
for sc in self.streambar_controller.stream_controllers:
orig_entries += get_local_settings_entries(sc)
self._orig_settings = preset_as_is(orig_entries) # to detect changes
for n, preset in presets.items():
self._preset_values[n] = preset(orig_entries)
# Presets which have been confirmed on the hardware
self._presets_confirmed = set() # (string)
# 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):
opt_det = s.detector
self._ovrl_stream = stream.OverlayStream("Fine alignment", opt_det, em_emt, em_det)
if self._main_data_model.role == "delphi":
self._main_data_model.fineAlignDwellTime.value = 0.5
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)
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
# TODO: use the presets VAs and subscribe to each of them, instead of
# using pub/sub messages
pub.subscribe(self.on_setting_change, 'setting.changed')
# TODO: we should actually listen to the stream tree, but it's not
# currently possible. => listen to .flat once it's there
# Currently just use view.lastUpdate which should be "similar"
# (but doesn't work if the stream contains no image)
self._view.lastUpdate.subscribe(self.on_streams_changed)
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})
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:
self._view.addStream(s) # Add first to the view, so "visible" button is correct
self.streambar_controller.add_acquisition_stream_cont(s)
# listen to changes in local VAs
local_vas = set(s.emt_vas.values()) | set(s.det_vas.values())
for lva in local_vas:
lva.subscribe(self.on_setting_change)
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()
for s in list(self._tab_data_model.streams.value): # copy, as it's modified by stream cont
# Stop listening to changes in local VAs
local_vas = set(s.emt_vas.values()) | set(s.det_vas.values())
for lva in local_vas:
lva.unsubscribe(self.on_setting_change)
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
for s in streams:
if isinstance(s, OpticalStream):
break
else:
return False
return True
@wxlimit_invocation(0.1)
def update_setting_display(self):
# if gauge was left over from an error => now hide it
if self.gauge_acq.IsShown():
self.gauge_acq.Hide()
self.Layout()
# Enable/disable Fine alignment check box
streams = self._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._view.getStreams()
if streams:
if self.chkbox_fine_align.Value:
streams.append(self._ovrl_stream)
acq_time = acq.estimateTime(streams)
acq_time = math.ceil(acq_time) # round a bit pessimistically
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 _get_default_filename(self):
"""
Return a good default filename
"""
# TODO: check the file doesn't yet exist (if the computer clock is
# correct it's unlikely)
return os.path.join(
self.conf.last_path,
u"%s%s" % (time.strftime("%Y%m%d-%H%M%S"), self.conf.last_extension)
)
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.
# TODO: this should not be necessary once the settings only change the
# stream settings, and not directly the hardware.
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
"""
new_name = ShowAcquisitionFileDialog(self, self.filename.value)
if new_name is not None:
self.filename.value = new_name
# It means the user wants to do a new acquisition
self.btn_secom_acquire.SetLabel("START")
self.last_saved_file = None
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.remove_all_streams()
# stop listening to events
pub.unsubscribe(self.on_setting_change, 'setting.changed')
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
self.EndModal(wx.ID_CANCEL)
def _view_file(self):
"""
Called to open the file which was just acquired
"""
self.remove_all_streams()
# stop listening to events
pub.unsubscribe(self.on_setting_change, 'setting.changed')
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
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 _set_fan(self, enable):
"""
Turn on/off the fan of the CCD
enable (boolean): True to turn on/restore the fan, and False to turn if off
"""
if model.hasVA(self._main_data_model.ccd, "fanSpeed"):
return
fs = self._main_data_model.ccd.fanSpeed
if enable:
if self._orig_fan_speed is not None:
fs.value = max(fs.value, self._orig_fan_speed)
else:
self._orig_fan_speed = fs.value
fs.value = 0
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.btn_secom_acquire.Disable()
# disable estimation time updates during acquisition
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
# TODO: 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
# start acquisition + connect events to callback
streams = self._view.getStreams()
# Add the overlay stream if the fine alignment check box is checked
if self.chkbox_fine_align.Value:
streams.append(self._ovrl_stream)
# Turn off the fan to avoid vibrations (in all acquisitions)
self._set_fan(False)
# It should never be possible to reach here with no streams
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.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) """
self._set_fan(True) # Turn the fan back on
# bind button back to direct closure
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self._resume_settings()
# re-enable estimation time updates
self._view.lastUpdate.subscribe(self.on_streams_changed)
try:
data, exp = future.result(1) # timeout is just for safety
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.error("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()
class OverviewAcquisitionDialog(xrcfr_overview_acq):
"""
Class used to control the overview acquisition dialog
The data acquired is stored in a file, with predefined name, available on
.filename and it is opened (as pyramidal data) in .data .
"""
def __init__(self, parent, orig_tab_data):
xrcfr_overview_acq.__init__(self, parent)
self.conf = get_acqui_conf()
# True when acquisition occurs
self.acquiring = False
self.data = None
# 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)
# Store the final image as {datelng}-{timelng}-overview
# The pattern to store them in a sub folder, with the name xxxx-overview-tiles/xxx-overview-NxM.ome.tiff
# The pattern to use for storing each tile file individually
# None disables storing them
save_dir = self.conf.last_path
if isinstance(orig_tab_data, guimodel.CryoGUIData):
save_dir = self.conf.pj_last_path
self.filename = create_filename(save_dir,
"{datelng}-{timelng}-overview",
".ome.tiff")
assert self.filename.endswith(".ome.tiff")
dirname, basename = os.path.split(self.filename)
tiles_dir = os.path.join(dirname,
basename[:-len(".ome.tiff")] + "-tiles")
self.filename_tiles = os.path.join(tiles_dir, basename)
# Create a new settings controller for the acquisition dialog
self._settings_controller = LocalizationSettingsController(
self,
self._tab_data_model,
)
self.zsteps = model.IntContinuous(1, range=(1, 51))
# The depth of field is an indication of how far the focus needs to move
# to see the current in-focus position out-of-focus. So it's a good default
# value for the zstep size. We use 2x to "really" see something else.
# Typically, it's about 1 µm.
dof = self._main_data_model.ccd.depthOfField.value
self.zstep_size = model.FloatContinuous(2 * dof,
range=(1e-9, 100e-6),
unit="m")
self._zstep_size_vac = VigilantAttributeConnector(
self.zstep_size, self.zstep_size_ctrl, events=wx.EVT_COMMAND_ENTER)
self.tiles_nx = model.IntContinuous(5, range=(1, 1000))
self.tiles_ny = model.IntContinuous(5, range=(1, 1000))
self._zsteps_vac = VigilantAttributeConnector(self.zsteps,
self.zstack_steps,
events=wx.EVT_SLIDER)
self._tiles_n_vacx = VigilantAttributeConnector(
self.tiles_nx, self.tiles_number_x, events=wx.EVT_COMMAND_ENTER)
self._tiles_n_vacy = VigilantAttributeConnector(
self.tiles_ny, self.tiles_number_y, events=wx.EVT_COMMAND_ENTER)
self.area = None # None or 4 floats: left, top, right, bottom positions of the acquisition area (in m)
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
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_streams()
# The list of streams ready for acquisition (just used as a cache)
self._acq_streams = {}
# Find every setting, and listen to it
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.start_listening_to_va()
# 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)
self.Bind(wx.EVT_CHAR_HOOK, self.on_key)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self.btn_secom_acquire.Bind(wx.EVT_BUTTON, self.on_acquire)
self.Bind(wx.EVT_CLOSE, self.on_close)
# Set parameters for tiled acq
self.overlap = 0.2
try:
# Use the stage range, which can be overridden by the MD_POS_ACTIVE_RANGE.
# Note: this last one might be temporary, until we have a RoA tool provided in the GUI.
self._tiling_rng = {
"x": self._main_data_model.stage.axes["x"].range,
"y": self._main_data_model.stage.axes["y"].range
}
stage_md = self._main_data_model.stage.getMetadata()
if model.MD_POS_ACTIVE_RANGE in stage_md:
self._tiling_rng.update(stage_md[model.MD_POS_ACTIVE_RANGE])
except (KeyError, IndexError):
raise ValueError(
"Failed to find stage.MD_POS_ACTIVE_RANGE with x and y range")
# Note: It should never be possible to reach here with no streams
streams = self.get_acq_streams()
for s in streams:
self._view.addStream(s)
# To update the estimated time & area when streams are removed/added
self._view.stream_tree.flat.subscribe(self.on_streams_changed,
init=True)
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)
self.zsteps.subscribe(self.on_setting_change)
self.tiles_nx.subscribe(self.on_tiles_number)
self.tiles_ny.subscribe(self.on_tiles_number)
def stop_listening_to_va(self):
for entry in self._orig_entries:
if hasattr(entry, "vigilattr"):
entry.vigilattr.unsubscribe(self.on_setting_change)
self.zsteps.unsubscribe(self.on_setting_change)
self.tiles_nx.unsubscribe(self.on_tiles_number)
self.tiles_ny.unsubscribe(self.on_tiles_number)
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)
"""
data_model = AcquisitionWindowData(orig.main)
data_model.streams.value.extend(orig.streams.value)
# create view (which cannot move or focus)
view = guimodel.MicroscopeView("All")
data_model.views.value = [view]
data_model.focussedView.value = view
return data_model
def add_streams(self):
"""
Add live streams
"""
# go through all the streams available in the interface model
for s in self._tab_data_model.streams.value:
if not isinstance(s, LiveStream):
continue
self.streambar_controller.addStream(s, add_to_view=self._view)
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()
return streams
def update_area_size(self):
"""
Calculates the requested tiling area size, based on the tiles number
"""
# get smallest fov
fovs = [self.get_fov(s) for s in self.get_acq_streams()]
if not fovs:
# fall back to a small fov (default)
self.fov = DEFAULT_FOV
else:
# smallest fov
self.fov = (min(f[0] for f in fovs), min(f[1] for f in fovs))
nx = self.tiles_nx.value
ny = self.tiles_ny.value
# these formulas for w and h have to match the ones used in the 'stitching' module.
w = nx * self.fov[0] * (1 - self.overlap)
h = ny * self.fov[1] * (1 - self.overlap)
pos = self._tab_data_model.main.stage.position.value
# Note the area can accept LTRB or LBRT.
self.area = self.clip_tiling_area_to_range(w, h, pos, self._tiling_rng)
if self.area is None:
# there is no intersection
logging.warning(
"Couldn't find intersection between stage pos %s and tiling range %s"
% (pos, self._tiling_rng))
@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()
# Some settings can affect the FoV. Also, adding/removing the stream with
# the smallest FoV would also affect the area.
self.update_area_size()
# Disable acquisition button if no area
self.btn_secom_acquire.Enable(self.area is not None)
if self.area is None:
self.area_size_txt.SetLabel("Invalid stage position")
return
area_size = self.area[2] - self.area[0], self.area[3] - self.area[1]
area_size_str = util.readable_str(area_size, unit="m", sig=3)
self.area_size_txt.SetLabel(area_size_str)
self.update_acquisition_time()
def on_streams_changed(self, _=None):
"""
When the list of streams to acquire has changed
"""
self.update_setting_display()
def on_tiles_number(self, _=None):
"""
Called when the user enters values for the tiles number in the GUI.
"""
self.update_setting_display()
def on_setting_change(self, _=None):
self.update_setting_display()
def update_acquisition_time(self):
"""
Must be called in the main GUI thread.
"""
if self.acquiring:
return
if not self.area:
logging.debug(
"Unknown acquisition area, cannot estimate acquisition time")
return
streams = self.get_acq_streams()
if not streams:
acq_time = 0
else:
zlevels = self._get_zstack_levels()
focus_mtd = FocusingMethod.MAX_INTENSITY_PROJECTION if zlevels else FocusingMethod.NONE
acq_time = stitching.estimateTiledAcquisitionTime(
streams,
self._main_data_model.stage,
self.area,
self.overlap,
zlevels=zlevels,
focusing_method=focus_mtd)
txt = "The estimated acquisition time is {}."
txt = txt.format(units.readable_time(acq_time))
self.lbl_acqestimate.SetLabel(txt)
def get_fov(self, s):
try:
return s.guessFoV()
except (NotImplementedError, AttributeError):
raise TypeError(
"Unsupported Stream %s, it doesn't have a .guessFoV()" % (s, ))
@staticmethod
def clip_tiling_area_to_range(w, h, pos, tiling_rng):
"""
Finds the intersection between the requested tiling area and the tiling range.
w (float): width of the tiling area
h (float): height of the tiling area
pos (dict -> float): current position of the stage
tiling_rng (dict -> list): the tiling range along x and y axes as
(xmin, ymin, xmax, ymax), or (xmin, ymax, xmax, ymin)
return (None or tuple of 4 floats): None if there is no intersection, or
the rectangle representing the intersection as (xmin, ymin, xmax, ymax).
"""
area_req = (pos["x"] - w / 2, pos["y"] - h / 2, pos["x"] + w / 2,
pos["y"] + h / 2)
# clip the tiling area, if needed (or find the intersection between the active range and the requested area)
return rect_intersect(area_req,
(tiling_rng["x"][0], tiling_rng["y"][1],
tiling_rng["x"][1], tiling_rng["y"][0]))
def on_key(self, evt):
""" Dialog key press handler. """
if evt.GetKeyCode() == wx.WXK_ESCAPE:
self.Close()
else:
evt.Skip()
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.stop_listening_to_va()
self.remove_all_streams()
# Set the streambar controller to None so it wouldn't be a listener to stream.remove
self.streambar_controller = None
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 _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 _get_zstack_levels(self):
"""
Calculate the zstack levels from the current focus position and zsteps value
:returns (list(float) or None) zstack levels for zstack acquisition.
return None if only one zstep is requested.
"""
zsteps = self.zsteps.value
if zsteps == 1:
return None
# Clip zsteps value to allowed range
focus_value = self._main_data_model.focus.position.value['z']
focus_range = self._main_data_model.focus.axes['z'].range
zmin = focus_value - (zsteps / 2 * self.zstep_size.value)
zmax = focus_value + (zsteps / 2 * self.zstep_size.value)
if (zmax - zmin) > (focus_range[1] - focus_range[0]):
# Corner case: it'd be larger than the entire range => limit to the entire range
zmin = focus_range[0]
zmax = focus_range[1]
if zmax > focus_range[1]:
# Too high => shift down
zmax -= zmax - focus_range[1]
zmin -= zmax - focus_range[1]
if zmin < focus_range[0]:
# Too low => shift up
zmin += focus_range[0] - zmin
zmax += focus_range[0] - zmin
# Create focus zlevels from the given zsteps number
zlevels = numpy.linspace(zmin, zmax, zsteps).tolist()
return zlevels
def _fit_view_to_area(self):
if self.area is None:
logging.warning("Unknown area, cannot fit view")
return
center = ((self.area[0] + self.area[2]) / 2,
(self.area[1] + self.area[3]) / 2)
self._view.view_pos.value = center
fov = (self.area[2] - self.area[0], self.area[3] - self.area[1])
self.pnl_view_acq.set_mpp_from_fov(fov)
def on_acquire(self, evt):
""" Start the actual acquisition """
logging.info("Acquire button clicked, starting acquisition")
acq_streams = self.get_acq_streams()
if not acq_streams:
logging.info("No stream to acquire, ending immediately")
self.on_close(
evt) # Nothing to do, so it's the same as closing the window
self.acquiring = True
# Adjust view FoV to the whole area, so that it's possible to follow the acquisition
self._fit_view_to_area()
self.btn_secom_acquire.Disable()
# 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
if self._main_data_model.opm:
self._main_data_model.opm.setAcqQuality(path.ACQ_QUALITY_BEST)
zlevels = self._get_zstack_levels()
focus_mtd = FocusingMethod.MAX_INTENSITY_PROJECTION if zlevels else FocusingMethod.NONE
if self.filename_tiles:
logging.info("Acquisition tiles logged at %s", self.filename_tiles)
os.makedirs(os.path.dirname(self.filename_tiles))
self.acq_future = stitching.acquireTiledArea(
acq_streams,
self._main_data_model.stage,
area=self.area,
overlap=self.overlap,
settings_obs=self._main_data_model.settings_obs,
log_path=self.filename_tiles,
weaver=WEAVER_COLLAGE_REVERSE,
zlevels=zlevels,
focusing_method=focus_mtd)
self._acq_future_connector = ProgressiveFutureConnector(
self.acq_future, self.gauge_acq, self.lbl_acqestimate)
# TODO: Build-up the complete image during the acquisition, so that the
# progress can be followed live.
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 """
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
self.acq_future = None # To avoid holding the ref in memory
self._acq_future_connector = None
try:
data = 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
# Now store the data (as pyramidal data), and open it again (but now it's
# backed with the persistent storage.
try:
exporter = dataio.find_fittest_converter(self.filename)
if exporter.CAN_SAVE_PYRAMID:
exporter.export(self.filename, data, pyramid=True)
else:
logging.warning(
"File format doesn't support saving image in pyramidal form"
)
exporter.export(self.filename)
self.data = exporter.open_data(self.filename).content
except Exception:
# We cannot do much: just warn the user and pretend it was cancelled
logging.exception("Storage failed")
self.btn_secom_acquire.Enable()
self.lbl_acqestimate.SetLabel("Storage failed.")
self.lbl_acqestimate.Parent.Layout()
return
self.terminate_listeners()
self.EndModal(wx.ID_OPEN)
class AcquisitionDialog(xrcfr_plugin):
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.
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)
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.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()
@call_in_wx_main
def addSettings(self, objWithVA, conf=None):
"""
Adds settings as one widget on a line for each VigilantAttribute (VA) in
the given object. Each setting entry created is added to setting_controller.entries.
objWithVA (object): an object with VAs.
conf (None or dict of str->config): allows to override the automatic
selection of the VA widget. See odemis.gui.conf.data for documentation.
raise:
LookupError: if no VA is found on the objWithVA
"""
vas = getVAs(objWithVA)
if not vas:
raise LookupError("No VAs found!")
if not conf:
conf = {}
vas_names = util.sorted_according_to(vas.keys(), conf.keys())
for name in vas_names:
va = vas[name]
self.setting_controller.add_setting_entry(name, va, None,
conf=conf.get(name, None))
self.Layout()
@call_in_wx_main
def addButton(self, label, callback=None, face_colour='def'):
"""
Add a button at the bottom right of the window. If some buttons are already
present, they are shifted to the left.
label (str): text on the button,
callback (None or callable): the function to be called when the button
is pressed (with the dialog as argument). If callback is None,
pressing the button will close the window and the button number will
be the return code of the dialog.
"""
btnid = len(self.buttons)
btn = ImageTextButton(self.pnl_buttons, label=label, height=48,
style=wx.ALIGN_CENTER, face_colour=face_colour)
self.buttons.append(btn)
sizer = self.pnl_buttons.GetSizer()
sizer.Add(btn, proportion=1, flag=wx.ALL | wx.ALIGN_RIGHT, border=10)
if callback is not None and callable(callback):
# Wrap the callback, to run in a separate thread, so it doesn't block
# the GUI.
def button_callback_wrapper(evt, btnid=btnid):
# TODO: disable the button while the callback is running, so that
# it's not possible for the user to press twice in a row and cause
# the code to run twice simultaneously (without very explicitly
# allowing that).
try:
self.SetReturnCode(btnid)
t = threading.Thread(target=callback, args=(self,),
name="Callback for button %s" % (label,))
t.start()
except Exception:
logging.exception("Error when processing button %s of plugin %s",
label, self.plugin)
btn.Bind(wx.EVT_BUTTON, button_callback_wrapper)
else:
btn.Bind(wx.EVT_BUTTON, partial(self.on_close, btnid))
self.pnl_buttons.Layout()
@call_in_wx_main
def addStream(self, stream, index=0):
"""
Adds a stream to the viewport, and a stream entry to the stream panel.
It also ensures the panel box and viewport are shown.
Note: If this method is not called, the stream panel and viewports are hidden.
stream (Stream or None): Stream to be added. Use None to force a viewport
to be seen without adding a stream.
index (0, 1, 2, or None): Index of the viewport to add the stream. 0 = left,
1 = right, 2 = spectrum viewport. If None, it will not show the stream
on any viewport (and it will be added to the .hidden_view)
"""
need_layout = False
if index is None:
v = self.hidden_view
else:
viewport = self._viewports[index]
v = self._dmodel.views.value[index]
assert viewport.view is v
if not viewport.IsShown():
viewport.Show()
need_layout = True
if stream:
if not self.fp_streams.IsShown():
self.fp_streams.Show()
need_layout = True
self.streambar_controller.addStream(stream, add_to_view=v)
if need_layout:
self.Layout()
self.Update()
@call_in_wx_main
def showProgress(self, future):
"""
Shows a progress bar, based on the status of the progressive future given.
As long as the future is not finished, the buttons are disabled.
future (None or Future): The progressive future to show the progress with
the progress bar. If future is None, it will hide the progress bar.
If future is cancellable, show a cancel button next to the progress bar.
"""
if future is not None and not future.cancelled():
self.current_future = future
self.enable_buttons(False)
self.pnl_gauge.Show(future is not None)
self.Layout()
if self.current_future is None:
self._acq_future_connector = None
return
else:
if hasattr(self.current_future, "add_update_callback"):
self._acq_future_connector = ProgressiveFutureConnector(self.current_future,
self.gauge_progress,
self.lbl_gauge)
else:
# TODO: just pulse the gauge at a "good" frequency (need to use a timer)
self.gauge_progress.Pulse()
# If the future is cancellable (ie, has task_canceller), allow to
# press the "cancel" button, which will call cancel() on the future.
# TODO: if there is already a "cancel" button in the window, use it
# instead a providing another one.
if hasattr(self.current_future, 'task_canceller'):
self.btn_cancel.Enable()
else:
self.btn_cancel.Disable()
future.add_done_callback(self._on_future_done)
@call_in_wx_main
def setAcquisitionInfo(self, text=None, lvl=logging.INFO):
"""
Displays acquisition info above progress bar.
text (str or None): text to be displayed. If None is passed, the acquisition
label will be hidden, so no empty space is displayed.
lvl (int, from logging.*): log level, which selects the display colour.
Options: logging.INFO, logging.WARNING, logging.ERROR
"""
if text is None:
self.pnl_info.Hide()
else:
self.lbl_acquisition_info.SetLabel(text)
if lvl >= logging.ERROR:
self.lbl_acquisition_info.SetForegroundColour(FG_COLOUR_ERROR)
elif lvl >= logging.WARNING:
self.lbl_acquisition_info.SetForegroundColour(FG_COLOUR_WARNING)
else:
self.lbl_acquisition_info.SetForegroundColour(FG_COLOUR_MAIN)
self.pnl_info.Show()
self.Layout()
def pauseSettings(self):
""" Pause the settings widgets. They will be disabled and the value frozen even when the VAs are changed """
self.setting_controller.pause()
self.setting_controller.enable(False)
self.streambar_controller.pause()
self.streambar_controller.enable(False)
def resumeSettings(self):
""" unpause the settings widgets. They will be re-enabled and the value unfrozen """
self.setting_controller.enable(True)
self.setting_controller.resume()
self.streambar_controller.enable(True)
self.streambar_controller.resume()
@call_in_wx_main
def enable_buttons(self, enable):
""" Enable or disable all the buttons in the button panel """
for btn in self.pnl_buttons.GetChildren():
btn.Enable(enable)
def _cancel_future(self, _):
""" Cancel the future if it's there and running """
if self.current_future is not None and not self.current_future.cancelled():
if self.current_future.cancel():
logging.debug("Future cancelled")
else:
logging.debug("Failed to cancel future")
@call_in_wx_main
def _on_future_done(self, _):
""" When the future finishes, reset the progress bar and enable the buttons """
self.gauge_progress.SetValue(0)
self.lbl_gauge.SetLabel("")
self.btn_cancel.Disable()
self.enable_buttons(True)
def on_close(self, btnid, _):
logging.debug("Closing window")
self.streambar_controller.clear()
self.EndModal(btnid)
@call_in_wx_main
def Close(self, *args, **kwargs):
"""
Request to close the window.
Make sure to call .Destroy() when not using the dialog anymore.
"""
# save the return code, as Close() automatically sets it to wx.ID_CANCEL
# but we want to keep the value potentially set by the button.
rc = self.ReturnCode
logging.debug("Closing acquisition dialog")
super(AcquisitionDialog, self).Close(*args, **kwargs)
self.ReturnCode = rc
logging.debug("Dialog closed")
@call_in_wx_main
def EndModal(self, retCode):
"""
Request to close the window, and pass a specific return code.
Make sure to call .Destroy() when not using the dialog anymore.
retCode (int)
"""
super(AcquisitionDialog, self).EndModal(retCode)
@call_in_wx_main
def Destroy(self, *args, **kwargs):
"""
Discards entirely the dialog. It's free'd from the memory.
Note: in most cases, if it's still opened, it get closed, but it seems
that with some version of wxPython, it causes a crash, so better call
Close() first.
"""
self.streambar_controller.clear()
logging.debug("Destroying acquisition dialog")
super(AcquisitionDialog, self).Destroy(*args, **kwargs)
logging.debug("Dialog destroyed")
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(self._get_default_filename())
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
# 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
)
# To turn on/off the fan
self._orig_fan_speed = None
self._orig_fan_temp = None
orig_view = orig_tab_data.focussedView.value
self._view = self._tab_data_model.focussedView.value
self.streambar_controller = StreamBarController(
self._tab_data_model, self.pnl_secom_streams)
# The streams currently displayed are the one visible
self.add_all_streams()
# FIXME: pass the fold_panels
# Compute the preset values for each preset
self._preset_values = {
} # dict string -> dict (SettingEntries -> value)
orig_entries = get_global_settings_entries(self._settings_controller)
for sc in self.streambar_controller.stream_controllers:
orig_entries += get_local_settings_entries(sc)
self._orig_settings = preset_as_is(orig_entries) # to detect changes
for n, preset in presets.items():
self._preset_values[n] = preset(orig_entries)
# Presets which have been confirmed on the hardware
self._presets_confirmed = set() # (string)
# 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):
opt_det = s.detector
self._ovrl_stream = stream.OverlayStream("Fine alignment", opt_det,
em_emt, em_det)
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)
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
# TODO: use the presets VAs and subscribe to each of them, instead of
# using pub/sub messages
pub.subscribe(self.on_setting_change, 'setting.changed')
# TODO: we should actually listen to the stream tree, but it's not
# currently possible. => listen to .flat once it's there
# Currently just use view.lastUpdate which should be "similar"
# (but doesn't work if the stream contains no image)
self._view.lastUpdate.subscribe(self.on_streams_changed)
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})
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:
self._view.addStream(
s) # Add first to the view, so "visible" button is correct
self.streambar_controller.add_acquisition_stream_cont(s)
# listen to changes in local VAs
local_vas = set(s.emt_vas.values()) | set(s.det_vas.values())
for lva in local_vas:
lva.subscribe(self.on_setting_change)
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()
for s in list(self._tab_data_model.streams.value
): # copy, as it's modified by stream cont
# Stop listening to changes in local VAs
local_vas = set(s.emt_vas.values()) | set(s.det_vas.values())
for lva in local_vas:
lva.unsubscribe(self.on_setting_change)
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
for s in streams:
if isinstance(s, OpticalStream):
break
else:
return False
return True
@wxlimit_invocation(0.1)
def update_setting_display(self):
# if gauge was left over from an error => now hide it
if self.gauge_acq.IsShown():
self.gauge_acq.Hide()
self.Layout()
# Enable/disable Fine alignment check box
streams = self._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._view.getStreams()
if streams:
if self.chkbox_fine_align.Value:
streams.append(self._ovrl_stream)
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 _get_default_filename(self):
"""
Return a good default filename
"""
# TODO: check the file doesn't yet exist (if the computer clock is
# correct it's unlikely)
return os.path.join(
self.conf.last_path, u"%s%s" %
(time.strftime("%Y%m%d-%H%M%S"), self.conf.last_extension))
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
"""
new_name = ShowAcquisitionFileDialog(self, self.filename.value)
if new_name is not None:
self.filename.value = new_name
# It means the user wants to do a new acquisition
self.btn_secom_acquire.SetLabel("START")
self.last_saved_file = None
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.remove_all_streams()
# stop listening to events
pub.unsubscribe(self.on_setting_change, 'setting.changed')
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
self.EndModal(wx.ID_CANCEL)
def _view_file(self):
"""
Called to open the file which was just acquired
"""
self.remove_all_streams()
# stop listening to events
pub.unsubscribe(self.on_setting_change, 'setting.changed')
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
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 _set_fan(self, enable):
"""
Turn on/off the fan of the CCD
enable (boolean): True to turn on/restore the fan, and False to turn if off
"""
if not model.hasVA(self._main_data_model.ccd, "fanSpeed"):
return
fs = self._main_data_model.ccd.fanSpeed
if enable:
if self._orig_fan_speed is not None:
fs.value = max(fs.value, self._orig_fan_speed)
else:
self._orig_fan_speed = fs.value
fs.value = 0
# Raise targetTemperature to max/ambient to avoid the fan from
# automatically starting again. (Some hardware have this built-in when
# the current temperature is too high compared to the target)
if model.hasVA(self._main_data_model.ccd, "targetTemperature"):
temp = self._main_data_model.ccd.targetTemperature
if enable:
if self._orig_fan_temp is not None:
temp.value = min(temp.value, self._orig_fan_temp)
else:
self._orig_fan_temp = temp.value
# TODO: handle choices
try:
temp.value = min(temp.range[1],
25) # don't set above ambient temperature
except Exception:
logging.warning(
"Failed to change targetTemperature when disabling fan",
exc_info=True)
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.btn_secom_acquire.Disable()
# disable estimation time updates during acquisition
self._view.lastUpdate.unsubscribe(self.on_streams_changed)
# TODO: 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
# start acquisition + connect events to callback
streams = self._view.getStreams()
# Add the overlay stream if the fine alignment check box is checked
if self.chkbox_fine_align.Value:
streams.append(self._ovrl_stream)
# Turn off the fan to avoid vibrations (in all acquisitions)
self._set_fan(False)
# It should never be possible to reach here with no streams
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.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) """
self._set_fan(True) # Turn the fan back on
# bind button back to direct closure
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_close)
self._resume_settings()
# 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
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()
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()