def update_acquisition_time(self):
if self._ellipsis_animator:
# cancel if there is an ellipsis animator updating the status message
self._ellipsis_animator.cancel()
self._ellipsis_animator = None
# Don't update estimated time if acquisition is running (as we are
# sharing the label with the estimated time-to-completion).
if self._main_data_model.is_acquiring.value:
return
lvl = None # icon status shown
if self._main_data_model.is_preparing.value:
txt = u"Optical path is being reconfigured…"
self._ellipsis_animator = EllipsisAnimator(txt,
self.lbl_acqestimate)
self._ellipsis_animator.start()
lvl = logging.INFO
elif self._roa.value == UNDEFINED_ROI:
# TODO: update the default text to be the same
txt = u"Region of acquisition needs to be selected"
lvl = logging.WARN
else:
streams = self._tab_data_model.acquisitionView.getStreams()
acq_time = acq.estimateTime(streams)
acq_time = math.ceil(acq_time) # round a bit pessimistic
txt = u"Estimated time is {}."
txt = txt.format(units.readable_time(acq_time))
logging.debug("Updating status message %s, with level %s", txt, lvl)
self.lbl_acqestimate.SetLabel(txt)
self._show_status_icons(lvl)
def update_acquisition_time(self):
if self._ellipsis_animator:
# cancel if there is an ellipsis animator updating the status message
self._ellipsis_animator.cancel()
self._ellipsis_animator = None
# Don't update estimated time if acquisition is running (as we are
# sharing the label with the estimated time-to-completion).
if self._main_data_model.is_acquiring.value:
return
lvl = None # icon status shown
if self._main_data_model.is_preparing.value:
txt = u"Optical path is being reconfigured…"
self._ellipsis_animator = EllipsisAnimator(txt, self.lbl_acqestimate)
self._ellipsis_animator.start()
lvl = logging.INFO
elif self._roa.value == UNDEFINED_ROI:
# TODO: update the default text to be the same
txt = u"Region of acquisition needs to be selected"
lvl = logging.WARN
else:
streams = self._tab_data_model.acquisitionStreams
acq_time = acq.estimateTime(streams)
acq_time = math.ceil(acq_time) # round a bit pessimistic
txt = u"Estimated time is {}."
txt = txt.format(units.readable_time(acq_time))
logging.debug("Updating status message %s, with level %s", txt, lvl)
self.lbl_acqestimate.SetLabel(txt)
self._show_status_icons(lvl)
class SparcAcquiController(object):
"""
Takes care of the acquisition button and process on the Sparc acquisition
tab.
"""
def __init__(self, tab_data, tab_panel, streambar_controller):
"""
tab_data (MicroscopyGUIData): the representation of the microscope GUI
tab_panel: (wx.Frame): the frame which contains the 4 viewports
stream_ctrl (StreamBarController): controller to pause/resume the streams
"""
self._tab_data_model = tab_data
self._main_data_model = tab_data.main
self._tab_panel = tab_panel
self._streambar_controller = streambar_controller
# For file selection
self.conf = conf.get_acqui_conf()
# TODO: this should be the date at which the user presses the acquire
# button (or when the last settings were changed)!
# At least, we must ensure it's a new date after the acquisition
# is done.
# Filename to save the acquisition
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)
# For acquisition
# a ProgressiveFuture if the acquisition is going on
self.btn_acquire = self._tab_panel.btn_sparc_acquire
self.btn_change_file = self._tab_panel.btn_sparc_change_file
self.btn_cancel = self._tab_panel.btn_sparc_cancel
self.acq_future = None
self.gauge_acq = self._tab_panel.gauge_sparc_acq
self.lbl_acqestimate = self._tab_panel.lbl_sparc_acq_estimate
self.bmp_acq_status_warn = self._tab_panel.bmp_acq_status_warn
self.bmp_acq_status_info = self._tab_panel.bmp_acq_status_info
self._acq_future_connector = None
# TODO: share an executor with the whole GUI.
self._executor = futures.ThreadPoolExecutor(max_workers=2)
# Link buttons
self.btn_acquire.Bind(wx.EVT_BUTTON, self.on_acquisition)
self.btn_change_file.Bind(wx.EVT_BUTTON, self.on_change_file)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_cancel)
self.gauge_acq.Hide()
self._tab_panel.Parent.Layout()
# Animator for messages containing ellipsis character
self._ellipsis_animator = None
# TODO: we need to be informed if the user closes suddenly the window
# self.Bind(wx.EVT_CLOSE, self.on_close)
self._roa = tab_data.semStream.roi
# Listen to change of streams to update the acquisition time
self._prev_streams = set() # set of streams already listened to
tab_data.streams.subscribe(self._onStreams, init=True)
# also listen to .semStream, which is not in .streams
for va in self._get_settings_vas(tab_data.semStream):
va.subscribe(self._onAnyVA)
# Extra options affecting the acquisitions globally
tab_data.pcdActive.subscribe(self._onAnyVA)
# TODO: should also listen to the VAs of the leeches on semStream
tab_data.useScanStage.subscribe(self._onAnyVA)
self._roa.subscribe(self._onROA, init=True)
# Listen to preparation state
self._main_data_model.is_preparing.subscribe(self.on_preparation)
def __del__(self):
self._executor.shutdown(wait=False)
# black list of VAs name which are known to not affect the acquisition time
VAS_NO_ACQUSITION_EFFECT = ("image", "autoBC", "intensityRange",
"histogram", "is_active", "should_update",
"status", "name", "tint")
def _get_settings_vas(self, stream):
"""
Find all the VAs of a stream which can potentially affect the acquisition time
return (set of VAs)
"""
nvas = model.getVAs(stream) # name -> va
vas = set()
# remove some VAs known to not affect the acquisition time
for n, va in nvas.items():
if n not in self.VAS_NO_ACQUSITION_EFFECT:
vas.add(va)
return vas
def _onFilename(self, name):
""" updates the GUI when the filename is updated """
# decompose into path/file
path, base = os.path.split(name)
self._tab_panel.txt_destination.SetValue(unicode(path))
# show the end of the path (usually more important)
self._tab_panel.txt_destination.SetInsertionPointEnd()
self._tab_panel.txt_filename.SetValue(unicode(base))
def _onROA(self, roi):
""" updates the acquire button according to the acquisition ROI """
self.check_acquire_button()
self.update_acquisition_time() # to update the message
def on_preparation(self, is_preparing):
self.check_acquire_button()
self.update_acquisition_time()
def check_acquire_button(self):
self.btn_acquire.Enable(
self._roa.value != UNDEFINED_ROI
and not self._main_data_model.is_preparing.value)
def _onStreams(self, streams):
"""
Called when streams are added/deleted. Used to listen to settings change
and update the acquisition time.
"""
streams = set(streams)
# remove subscription for streams that were deleted
for s in (self._prev_streams - streams):
for va in self._get_settings_vas(s):
va.unsubscribe(self._onAnyVA)
# add subscription for new streams
for s in (streams - self._prev_streams):
for va in self._get_settings_vas(s):
va.subscribe(self._onAnyVA)
self._prev_streams = streams
self.update_acquisition_time() # to update the message
def _onAnyVA(self, val):
"""
Called whenever a VA which might affect the acquisition is modified
"""
self.update_acquisition_time() # to update the message
def update_fn_suggestion(self):
"""
When the filename counter is updated in a plugin, the suggested name for
the main acquisition needs to be updated
"""
self.filename.value = create_filename(self.conf.last_path,
self.conf.fn_ptn,
self.conf.last_extension,
self.conf.fn_count)
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
"""
# Update .filename with new filename instead of input name so the right
# time is used
fn = create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count)
new_name = ShowAcquisitionFileDialog(self._tab_panel, 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)
@wxlimit_invocation(1) # max 1/s
def update_acquisition_time(self):
if self._ellipsis_animator:
# cancel if there is an ellipsis animator updating the status message
self._ellipsis_animator.cancel()
self._ellipsis_animator = None
# Don't update estimated time if acquisition is running (as we are
# sharing the label with the estimated time-to-completion).
if self._main_data_model.is_acquiring.value:
return
lvl = None # icon status shown
if self._main_data_model.is_preparing.value:
txt = u"Optical path is being reconfigured…"
self._ellipsis_animator = EllipsisAnimator(txt,
self.lbl_acqestimate)
self._ellipsis_animator.start()
lvl = logging.INFO
elif self._roa.value == UNDEFINED_ROI:
# TODO: update the default text to be the same
txt = u"Region of acquisition needs to be selected"
lvl = logging.WARN
else:
streams = self._tab_data_model.acquisitionStreams
acq_time = acq.estimateTime(streams)
acq_time = math.ceil(acq_time) # round a bit pessimistic
txt = u"Estimated time is {}."
txt = txt.format(units.readable_time(acq_time))
logging.debug("Updating status message %s, with level %s", txt, lvl)
self.lbl_acqestimate.SetLabel(txt)
self._show_status_icons(lvl)
def _show_status_icons(self, lvl):
# update status icon to show the logging level
self.bmp_acq_status_info.Show(lvl in (logging.INFO, logging.DEBUG))
self.bmp_acq_status_warn.Show(lvl == logging.WARN)
self._tab_panel.Layout()
def _pause_streams(self):
"""
Freeze the streams settings and ensure no stream is playing
"""
self._streambar_controller.pauseStreams()
self._streambar_controller.pause()
self._streambar_controller.enable(False)
def _resume_streams(self):
"""
Resume (unfreeze) the stream settings
"""
self._streambar_controller.enable(True)
self._streambar_controller.resume()
def _reset_acquisition_gui(self,
text=None,
level=None,
keep_filename=False):
"""
Set back every GUI elements to be ready for the next acquisition
text (None or str): a (error) message to display instead of the
estimated acquisition time
level (None or logging.*): logging level of the text, shown as an icon.
If None, no icon is shown.
keep_filename (bool): if True, will not update the filename
"""
self.btn_cancel.Hide()
self.btn_acquire.Enable()
self._tab_panel.Layout()
self._resume_streams()
if not keep_filename:
self.conf.fn_count = update_counter(self.conf.fn_count)
# Update filename even if keep_filename is True (but don't update counter). This
# ensures that the time is always up to date.
self.filename.value = create_filename(self.conf.last_path,
self.conf.fn_ptn,
self.conf.last_extension,
self.conf.fn_count)
if text is not None:
self.lbl_acqestimate.SetLabel(text)
self._show_status_icons(level)
else:
self.update_acquisition_time()
def _show_acquisition(self, data, acqfile):
"""
Show the acquired data (saved into a file) in the analysis tab.
data (list of DataFlow): all the raw data acquired
acqfile (File): file object to which the data was saved
"""
# get the analysis tab
analysis_tab = self._main_data_model.getTabByName("analysis")
analysis_tab.display_new_data(acqfile.name, data)
# show the new tab
self._main_data_model.tab.value = analysis_tab
def on_acquisition(self, evt):
"""
Start the acquisition (really)
Similar to win.acquisition.on_acquire()
"""
# Time-resolved data cannot be saved in .ome.tiff format for now
# OME-TIFF wants to save each time data on a separate "page", which causes too many pages.
has_temporal = False
for s in self._tab_data_model.streams.value:
if (isinstance(s, ScannedTemporalSettingsStream)
or isinstance(s, ScannedTCSettingsStream)
or isinstance(s, TemporalSpectrumSettingsStream)):
has_temporal = True
if (self.conf.last_format == 'TIFF' or self.conf.last_format
== 'Serialized TIFF') and has_temporal:
raise NotImplementedError("Cannot save temporal data in %s format, data format must be HDF5." \
% self.conf.last_format)
self._pause_streams()
self.btn_acquire.Disable()
self.btn_cancel.Enable()
self._main_data_model.is_acquiring.value = True
self.gauge_acq.Show()
self.btn_cancel.Show()
self._show_status_icons(None)
self._tab_panel.Layout() # to put the gauge at the right place
# start acquisition + connect events to callback
self.acq_future = acq.acquire(self._tab_data_model.acquisitionStreams)
self._acq_future_connector = ProgressiveFutureConnector(
self.acq_future, self.gauge_acq, self.lbl_acqestimate)
self.acq_future.add_done_callback(self.on_acquisition_done)
def on_cancel(self, evt):
"""
Called during acquisition when pressing the cancel button
"""
if not self.acq_future:
msg = "Tried to cancel acquisition while it was not started"
logging.warning(msg)
return
self.acq_future.cancel()
# self._main_data_model.is_acquiring.value = False
# all the rest will be handled by on_acquisition_done()
def _export_to_file(self, acq_future):
"""
return (list of DataArray, filename): data exported and filename
"""
streams = list(self._tab_data_model.acquisitionStreams)
st = acq.stream.StreamTree(streams=streams)
thumb = acq.computeThumbnail(st, acq_future)
data, exp = acq_future.result()
filename = self.filename.value
if data:
exporter = dataio.get_converter(self.conf.last_format)
exporter.export(filename, data, thumb)
logging.info(u"Acquisition saved as file '%s'.", filename)
else:
logging.debug("Not saving into file '%s' as there is no data",
filename)
return data, exp, filename
@call_in_wx_main
def on_acquisition_done(self, future):
"""
Callback called when the acquisition is finished (either successfully or
cancelled)
"""
self.btn_cancel.Disable()
self._main_data_model.is_acquiring.value = False
self.acq_future = None # To avoid holding the ref in memory
self._acq_future_connector = None
try:
data, exp = future.result()
except CancelledError:
# hide progress bar (+ put pack estimated time)
self.gauge_acq.Hide()
# don't change filename => we can reuse it
self._reset_acquisition_gui(keep_filename=True)
return
except Exception as exp:
# leave the gauge, to give a hint on what went wrong.
logging.exception("Acquisition failed")
self._reset_acquisition_gui("Acquisition failed (see log panel).",
level=logging.WARNING,
keep_filename=True)
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...")
# on big acquisitions, it can take ~20s
sf = self._executor.submit(self._export_to_file, future)
sf.add_done_callback(self.on_file_export_done)
@call_in_wx_main
def on_file_export_done(self, future):
"""
Callback called when the acquisition is finished (either successfully or
cancelled)
"""
# hide progress bar
self.gauge_acq.Hide()
try:
data, exp, filename = future.result()
except Exception:
logging.exception("Saving acquisition failed")
self._reset_acquisition_gui(
"Saving acquisition file failed (see log panel).",
level=logging.WARNING)
return
if exp is None:
# Needs to be done before changing tabs as it will play again the stream
# (and they will be immediately be stopped when changing tab).
self._reset_acquisition_gui()
# TODO: we should add the file to the list of recently-used files
# cf http://pyxdg.readthedocs.org/en/latest/recentfiles.html
# display in the analysis tab
self._show_acquisition(data, open(filename))
else:
self._reset_acquisition_gui("Acquisition failed (see log panel).",
level=logging.WARNING,
keep_filename=(not data))
class SparcAcquiController(object):
"""
Takes care of the acquisition button and process on the Sparc acquisition
tab.
"""
def __init__(self, tab_data, tab_panel, streambar_controller):
"""
tab_data (MicroscopyGUIData): the representation of the microscope GUI
tab_panel: (wx.Frame): the frame which contains the 4 viewports
stream_ctrl (StreamBarController): controller to pause/resume the streams
"""
self._tab_data_model = tab_data
self._main_data_model = tab_data.main
self._tab_panel = tab_panel
self._streambar_controller = streambar_controller
# For file selection
self.conf = conf.get_acqui_conf()
# TODO: this should be the date at which the user presses the acquire
# button (or when the last settings were changed)!
# At least, we must ensure it's a new date after the acquisition
# is done.
# Filename to save the acquisition
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)
# For acquisition
# a ProgressiveFuture if the acquisition is going on
self.btn_acquire = self._tab_panel.btn_sparc_acquire
self.btn_change_file = self._tab_panel.btn_sparc_change_file
self.btn_cancel = self._tab_panel.btn_sparc_cancel
self.acq_future = None
self.gauge_acq = self._tab_panel.gauge_sparc_acq
self.lbl_acqestimate = self._tab_panel.lbl_sparc_acq_estimate
self.bmp_acq_status_warn = self._tab_panel.bmp_acq_status_warn
self.bmp_acq_status_info = self._tab_panel.bmp_acq_status_info
self._acq_future_connector = None
# TODO: share an executor with the whole GUI.
self._executor = futures.ThreadPoolExecutor(max_workers=2)
# Link buttons
self.btn_acquire.Bind(wx.EVT_BUTTON, self.on_acquisition)
self.btn_change_file.Bind(wx.EVT_BUTTON, self.on_change_file)
self.btn_cancel.Bind(wx.EVT_BUTTON, self.on_cancel)
self.gauge_acq.Hide()
self._tab_panel.Parent.Layout()
# Animator for messages containing ellipsis character
self._ellipsis_animator = None
# TODO: we need to be informed if the user closes suddenly the window
# self.Bind(wx.EVT_CLOSE, self.on_close)
self._roa = tab_data.semStream.roi
# Listen to change of streams to update the acquisition time
self._prev_streams = set() # set of streams already listened to
tab_data.streams.subscribe(self._onStreams, init=True)
# also listen to .semStream, which is not in .streams
for va in self._get_settings_vas(tab_data.semStream):
va.subscribe(self._onAnyVA)
# Extra options affecting the acquisitions globally
tab_data.pcdActive.subscribe(self._onAnyVA)
# TODO: should also listen to the VAs of the leeches on semStream
tab_data.useScanStage.subscribe(self._onAnyVA)
self._roa.subscribe(self._onROA, init=True)
# Listen to preparation state
self._main_data_model.is_preparing.subscribe(self.on_preparation)
def __del__(self):
self._executor.shutdown(wait=False)
# black list of VAs name which are known to not affect the acquisition time
VAS_NO_ACQUSITION_EFFECT = ("image", "autoBC", "intensityRange", "histogram",
"is_active", "should_update", "status", "name", "tint")
def _get_settings_vas(self, stream):
"""
Find all the VAs of a stream which can potentially affect the acquisition time
return (set of VAs)
"""
nvas = model.getVAs(stream) # name -> va
vas = set()
# remove some VAs known to not affect the acquisition time
for n, va in nvas.items():
if n not in self.VAS_NO_ACQUSITION_EFFECT:
vas.add(va)
return vas
def _onFilename(self, name):
""" updates the GUI when the filename is updated """
# decompose into path/file
path, base = os.path.split(name)
self._tab_panel.txt_destination.SetValue(unicode(path))
# show the end of the path (usually more important)
self._tab_panel.txt_destination.SetInsertionPointEnd()
self._tab_panel.txt_filename.SetValue(unicode(base))
def _onROA(self, roi):
""" updates the acquire button according to the acquisition ROI """
self.check_acquire_button()
self.update_acquisition_time() # to update the message
def on_preparation(self, is_preparing):
self.check_acquire_button()
self.update_acquisition_time()
def check_acquire_button(self):
self.btn_acquire.Enable(self._roa.value != UNDEFINED_ROI and
not self._main_data_model.is_preparing.value)
def _onStreams(self, streams):
"""
Called when streams are added/deleted. Used to listen to settings change
and update the acquisition time.
"""
streams = set(streams)
# remove subscription for streams that were deleted
for s in (self._prev_streams - streams):
for va in self._get_settings_vas(s):
va.unsubscribe(self._onAnyVA)
# add subscription for new streams
for s in (streams - self._prev_streams):
for va in self._get_settings_vas(s):
va.subscribe(self._onAnyVA)
self._prev_streams = streams
self.update_acquisition_time() # to update the message
def _onAnyVA(self, val):
"""
Called whenever a VA which might affect the acquisition is modified
"""
self.update_acquisition_time() # to update the message
def update_fn_suggestion(self):
"""
When the filename counter is updated in a plugin, the suggested name for
the main acquisition needs to be updated
"""
self.filename.value = create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count)
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
"""
# Update .filename with new filename instead of input name so the right
# time is used
fn = create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count)
new_name = ShowAcquisitionFileDialog(self._tab_panel, 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)
@wxlimit_invocation(1) # max 1/s
def update_acquisition_time(self):
if self._ellipsis_animator:
# cancel if there is an ellipsis animator updating the status message
self._ellipsis_animator.cancel()
self._ellipsis_animator = None
# Don't update estimated time if acquisition is running (as we are
# sharing the label with the estimated time-to-completion).
if self._main_data_model.is_acquiring.value:
return
lvl = None # icon status shown
if self._main_data_model.is_preparing.value:
txt = u"Optical path is being reconfigured…"
self._ellipsis_animator = EllipsisAnimator(txt, self.lbl_acqestimate)
self._ellipsis_animator.start()
lvl = logging.INFO
elif self._roa.value == UNDEFINED_ROI:
# TODO: update the default text to be the same
txt = u"Region of acquisition needs to be selected"
lvl = logging.WARN
else:
streams = self._tab_data_model.acquisitionStreams
acq_time = acq.estimateTime(streams)
acq_time = math.ceil(acq_time) # round a bit pessimistic
txt = u"Estimated time is {}."
txt = txt.format(units.readable_time(acq_time))
logging.debug("Updating status message %s, with level %s", txt, lvl)
self.lbl_acqestimate.SetLabel(txt)
self._show_status_icons(lvl)
def _show_status_icons(self, lvl):
# update status icon to show the logging level
self.bmp_acq_status_info.Show(lvl in (logging.INFO, logging.DEBUG))
self.bmp_acq_status_warn.Show(lvl == logging.WARN)
self._tab_panel.Layout()
def _pause_streams(self):
"""
Freeze the streams settings and ensure no stream is playing
"""
self._streambar_controller.pauseStreams()
self._streambar_controller.pause()
self._streambar_controller.enable(False)
def _resume_streams(self):
"""
Resume (unfreeze) the stream settings
"""
self._streambar_controller.enable(True)
self._streambar_controller.resume()
def _reset_acquisition_gui(self, text=None, level=None, keep_filename=False):
"""
Set back every GUI elements to be ready for the next acquisition
text (None or str): a (error) message to display instead of the
estimated acquisition time
level (None or logging.*): logging level of the text, shown as an icon.
If None, no icon is shown.
keep_filename (bool): if True, will not update the filename
"""
self.btn_cancel.Hide()
self.btn_acquire.Enable()
self._tab_panel.Layout()
self._resume_streams()
if not keep_filename:
self.conf.fn_count = update_counter(self.conf.fn_count)
# Update filename even if keep_filename is True (but don't update counter). This
# ensures that the time is always up to date.
self.filename.value = create_filename(self.conf.last_path, self.conf.fn_ptn,
self.conf.last_extension, self.conf.fn_count)
if text is not None:
self.lbl_acqestimate.SetLabel(text)
self._show_status_icons(level)
else:
self.update_acquisition_time()
def _show_acquisition(self, data, acqfile):
"""
Show the acquired data (saved into a file) in the analysis tab.
data (list of DataFlow): all the raw data acquired
acqfile (File): file object to which the data was saved
"""
# get the analysis tab
analysis_tab = self._main_data_model.getTabByName("analysis")
analysis_tab.display_new_data(acqfile.name, data)
# show the new tab
self._main_data_model.tab.value = analysis_tab
def on_acquisition(self, evt):
"""
Start the acquisition (really)
Similar to win.acquisition.on_acquire()
"""
# Time-resolved data cannot be saved in .ome.tiff format for now
# OME-TIFF wants to save each time data on a separate "page", which causes too many pages.
has_temporal = False
for s in self._tab_data_model.streams.value:
if (isinstance(s, ScannedTemporalSettingsStream) or
isinstance(s, ScannedTCSettingsStream) or
isinstance(s, TemporalSpectrumSettingsStream)):
has_temporal = True
if (self.conf.last_format == 'TIFF' or self.conf.last_format == 'Serialized TIFF') and has_temporal:
raise NotImplementedError("Cannot save temporal data in %s format, data format must be HDF5." \
% self.conf.last_format)
self._pause_streams()
self.btn_acquire.Disable()
self.btn_cancel.Enable()
self._main_data_model.is_acquiring.value = True
self.gauge_acq.Show()
self.btn_cancel.Show()
self._show_status_icons(None)
self._tab_panel.Layout() # to put the gauge at the right place
# start acquisition + connect events to callback
self.acq_future = acq.acquire(self._tab_data_model.acquisitionStreams)
self._acq_future_connector = ProgressiveFutureConnector(self.acq_future,
self.gauge_acq,
self.lbl_acqestimate)
self.acq_future.add_done_callback(self.on_acquisition_done)
def on_cancel(self, evt):
"""
Called during acquisition when pressing the cancel button
"""
if not self.acq_future:
msg = "Tried to cancel acquisition while it was not started"
logging.warning(msg)
return
self.acq_future.cancel()
# self._main_data_model.is_acquiring.value = False
# all the rest will be handled by on_acquisition_done()
def _export_to_file(self, acq_future):
"""
return (list of DataArray, filename): data exported and filename
"""
streams = list(self._tab_data_model.acquisitionStreams)
st = acq.stream.StreamTree(streams=streams)
thumb = acq.computeThumbnail(st, acq_future)
data, exp = acq_future.result()
if data:
filename = self.filename.value
exporter = dataio.get_converter(self.conf.last_format)
exporter.export(filename, data, thumb)
logging.info(u"Acquisition saved as file '%s'.", filename)
else:
logging.debug("Not saving into file '%s' as there is no data", filename)
return data, exp, filename
@call_in_wx_main
def on_acquisition_done(self, future):
"""
Callback called when the acquisition is finished (either successfully or
cancelled)
"""
self.btn_cancel.Disable()
self._main_data_model.is_acquiring.value = False
self.acq_future = None # To avoid holding the ref in memory
self._acq_future_connector = None
try:
data, exp = future.result()
except CancelledError:
# hide progress bar (+ put pack estimated time)
self.gauge_acq.Hide()
# don't change filename => we can reuse it
self._reset_acquisition_gui(keep_filename=True)
return
except Exception as exp:
# leave the gauge, to give a hint on what went wrong.
logging.exception("Acquisition failed")
self._reset_acquisition_gui("Acquisition failed (see log panel).",
level=logging.WARNING,
keep_filename=True)
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...")
# on big acquisitions, it can take ~20s
sf = self._executor.submit(self._export_to_file, future)
sf.add_done_callback(self.on_file_export_done)
@call_in_wx_main
def on_file_export_done(self, future):
"""
Callback called when the acquisition is finished (either successfully or
cancelled)
"""
# hide progress bar
self.gauge_acq.Hide()
try:
data, exp, filename = future.result()
except Exception:
logging.exception("Saving acquisition failed")
self._reset_acquisition_gui("Saving acquisition file failed (see log panel).",
level=logging.WARNING)
return
if exp is None:
# Needs to be done before changing tabs as it will play again the stream
# (and they will be immediately be stopped when changing tab).
self._reset_acquisition_gui()
# TODO: we should add the file to the list of recently-used files
# cf http://pyxdg.readthedocs.org/en/latest/recentfiles.html
# display in the analysis tab
self._show_acquisition(data, open(filename))
else:
self._reset_acquisition_gui("Acquisition failed (see log panel).",
level=logging.WARNING,
keep_filename=(not data))
