def _on_current_feature_changes(self, feature):
"""
Update the feature panel controls when the current feature VA is modified
:param feature: (CryoFeature or None) the newly selected current feature
"""
if self._feature_name_va_connector:
self._feature_name_va_connector.disconnect()
if self._feature_status_va_connector:
self._feature_status_va_connector.disconnect()
if self._feature_z_va_connector:
self._feature_z_va_connector.disconnect()
def enable_feature_ctrls(enable):
self._panel.cmb_feature_status.Enable(enable)
self._panel.ctrl_feature_z.Enable(enable)
self._panel.btn_use_current_z.Enable(enable)
self._panel.btn_go_to_feature.Enable(enable)
if not feature:
enable_feature_ctrls(False)
self._panel.cmb_features.SetValue("No Feature Selected")
self._panel.cmb_feature_status.SetValue("Not Selected")
return
save_features(self._tab.conf.pj_last_path,
self._tab_data_model.main.features)
enable_feature_ctrls(True)
# Set feature list with the current feature
index = self._tab_data_model.main.features.value.index(feature)
self._panel.cmb_features.SetSelection(index)
# Disconnect and reconnect the VA connectors to the newly selected feature
self._feature_name_va_connector = VigilantAttributeConnector(
feature.name,
self._panel.cmb_features,
events=wx.EVT_TEXT_ENTER,
va_2_ctrl=self._on_feature_name,
ctrl_2_va=self._on_cmb_feature_name_change,
)
self._feature_status_va_connector = VigilantAttributeConnector(
feature.status,
self._panel.cmb_feature_status,
events=wx.EVT_COMBOBOX,
ctrl_2_va=self._on_cmb_feature_status_change,
va_2_ctrl=self._on_feature_status)
# TODO: check, it seems that sometimes the EVT_TEXT_ENTER is first received
# by the VAC, before the widget itself, which prevents getting the right value.
self._feature_z_va_connector = VigilantAttributeConnector(
feature.pos,
self._panel.ctrl_feature_z,
events=wx.EVT_TEXT_ENTER,
ctrl_2_va=self._on_ctrl_feature_z_change,
va_2_ctrl=self._on_feature_pos)
def __init__(self, btn_ctrl, va, _):
self.btn = btn_ctrl
self.vac = VigilantAttributeConnector(va,
btn_ctrl,
self._va_to_btn,
self._btn_to_va,
events=wx.EVT_BUTTON)
def __init__(self, tab_data, main_frame, tab_prefix):
""" Binds the step and axis buttons to their appropriate
Vigilant Attributes in the model.ActuatorGUIData. It only connects the
buttons which exists with the actuators which exists.
tab_data (ActuatorGUIData): the data model of the tab
main_frame: (wx.Frame): the main frame of the GUI
tab_prefix (string): common prefix of the names of the buttons
"""
self._tab_data_model = tab_data
self._main_frame = main_frame
# Check which widgets and VAs exist. Bind the matching ones.
# Bind size steps (= sliders)
self._va_connectors = []
for an, ss in tab_data.stepsizes.items():
slider_name = tab_prefix + "slider_" + an
try:
slider = getattr(main_frame, slider_name)
except AttributeError:
continue
slider.SetRange(*ss.range)
vac = VigilantAttributeConnector(ss, slider, events=wx.EVT_SLIDER)
self._va_connectors.append(vac)
if not self._va_connectors:
logging.warning("No slider found for tab %s", tab_prefix)
# Bind buttons
self._btns = []
for actuator, axis in tab_data.axes:
for suffix, factor in [("m", -1), ("p", 1)]:
# something like "lens_align_btn_p_mirror_rz"
btn_name = "%sbtn_%s_%s_%s" % (tab_prefix, suffix, actuator,
axis)
try:
btn = getattr(main_frame, btn_name)
except AttributeError:
logging.debug("No button in GUI found for axis %s", axis)
continue
def btn_action(evt,
tab_data=tab_data,
actuator=actuator,
axis=axis,
factor=factor):
# Button events don't contain key state, so check ourselves
if wx.GetKeyState(wx.WXK_SHIFT):
factor /= 10
tab_data.step(actuator, axis, factor)
btn.Bind(wx.EVT_BUTTON, btn_action)
self._btns.append(btn)
tab_data.main.is_acquiring.subscribe(self._on_acquisition)
def __init__(self, tab_data, main_frame, btn_prefix):
""" Binds the 'hardware' buttons to their appropriate
Vigilant Attributes in the model.MainGUIData
tab_data (MicroscopyGUIData): the data model of the tab
main_frame: (wx.Frame): the main frame of the GUI
btn_prefix (string): common prefix of the names of the buttons
"""
main_data = tab_data.main
# Look for which buttons actually exist, and which VAs exist. Bind the
# fitting ones
self._callbacks = []
self._va_connectors = []
for btn_name, vaname in btn_to_va.items():
try:
btn = getattr(main_frame, btn_prefix + btn_name)
except AttributeError:
continue
try:
va = getattr(main_data, vaname)
except AttributeError:
# This microscope is not available
btn.Hide()
# TODO: need to update layout?
continue
logging.debug("Connecting button %s to %s", btn_name, vaname)
vac = VigilantAttributeConnector(
va,
btn,
lambda s, btn=btn: btn.SetToggle(s != model.STATE_OFF),
lambda btn=btn: model.STATE_ON
if btn.GetToggle() else model.STATE_OFF,
events=wx.EVT_BUTTON)
self._va_connectors.append(vac)
if not self._va_connectors:
logging.warning("No microscope button found in tab %s", btn_prefix)
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 __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 __init__(self, tab_data, tab_panel, tab_prefix):
""" Binds the step and axis buttons to their appropriate
Vigilant Attributes in the model.ActuatorGUIData. It only connects the
buttons which exists with the actuators which exists.
tab_data (ActuatorGUIData): the data model of the tab
tab_panel: (wx.Frame): the main frame of the GUI
tab_prefix (string): common prefix of the names of the buttons
"""
self._tab_data_model = tab_data
self._tab_panel = tab_panel
# Check which widgets and VAs exist. Bind the matching ones.
# Bind size steps (= sliders)
self._va_connectors = []
for an, ss in tab_data.stepsizes.items():
slider_name = tab_prefix + "slider_" + an
try:
slider = getattr(tab_panel, slider_name)
except AttributeError:
continue
slider.SetRange(*ss.range)
vac = VigilantAttributeConnector(ss, slider, events=wx.EVT_SLIDER)
self._va_connectors.append(vac)
if not self._va_connectors:
logging.warning("No slider found for tab %s", tab_prefix)
# Bind buttons
self._btns = []
for actuator, axis in tab_data.axes:
for suffix, factor in [("m", -1), ("p", 1)]:
# something like "lens_align_btn_p_mirror_rz"
btn_name = "%sbtn_%s_%s_%s" % (tab_prefix, suffix, actuator,
axis)
try:
btn = getattr(tab_panel, btn_name)
except AttributeError:
logging.debug("No button in GUI found for axis %s", axis)
continue
def btn_action(evt,
tab_data=tab_data,
actuator=actuator,
axis=axis,
factor=factor):
# Button events don't contain key state, so check ourselves
if wx.GetKeyState(wx.WXK_SHIFT):
factor /= 10
tab_data.step(actuator, axis, factor)
btn.Bind(wx.EVT_BUTTON, btn_action)
self._btns.append(btn)
# On SECOM, show the right aligner panel (X/Y or A/B)
if ("aligner", "x") in tab_data.axes:
tab_panel.pnl_xy_align.Show()
if ("aligner", "a") in tab_data.axes:
tab_panel.pnl_ab_align.Show()
# On SPARC, show the Yaw/Pitch only if available
if hasattr(tab_panel, 'pnl_sparc_rot'):
showrot = (("mirror", "ry") in tab_data.axes
or ("mirror", "rz") in tab_data.axes)
tab_panel.pnl_sparc_rot.Show(showrot)
# On SPARC, show the fiber aligner only if needed
if hasattr(tab_panel, 'pnl_fibaligner'):
showfib = ("fibaligner", "x") in tab_data.axes
tab_panel.pnl_fibaligner.Show(showfib)
tab_data.main.is_acquiring.subscribe(self._on_acquisition)