def on_plugin_enable(self):
super(SyringePumpPlugin, self).on_plugin_enable()
self.cleanup_plugin()
self.check_device_name_and_version()
if not self.initialized:
app = get_app()
self.tools_menu_item = gtk.MenuItem('Syringe pump controller')
app.main_window_controller.menu_tools.append(self.tools_menu_item)
self.tools_menu = gtk.Menu()
self.tools_menu.show()
self.tools_menu_item.set_submenu(self.tools_menu)
self.edit_config_menu_item = \
gtk.MenuItem("Edit configuration settings...")
self.tools_menu.append(self.edit_config_menu_item)
self.edit_config_menu_item.connect("activate",
self.on_edit_configuration)
self.edit_config_menu_item.show()
self.edit_config_menu_item.set_sensitive(False)
self.tools_menu_item.show()
self.edit_config_menu_item.set_sensitive(self.proxy != None)
if get_app().protocol:
self.on_step_run()
self._update_protocol_grid()
def on_experiment_log_changed(self, experiment_log):
# Reset number of completed DStat experiments for each step.
self.dstat_experiment_count_by_step = {}
self.dstat_experiment_data = None
app = get_app()
app_values = self.get_app_values()
calibrator_file = app_values.get('calibrator_file', '')
data = {'calibrator_file': calibrator_file}
if hasattr(app, 'experiment_log') and app.experiment_log:
app.experiment_log.metadata[self.name] = data
# copy the calibrator file to the experiment log directory
if calibrator_file:
if not path(calibrator_file).isfile():
logger.error('Calibration file (%s) does not exist.' %
calibrator_file)
else:
try:
output_path = path(app.experiment_log.get_log_path()) / self.name
if not output_path.isdir():
output_path.mkdir()
path(calibrator_file).copy2(output_path / 'calibrator.csv')
except:
logger.error('Could not copy calibration file to the '
'experiment log directory.' , exc_info=True)
def on_step_run(self):
""""
Handler called whenever a step is executed. Note that this signal
is only emitted in realtime mode or if a protocol is running.
Plugins that handle this signal must emit the on_step_complete
signal once they have completed the step. The protocol controller
will wait until all plugins have completed the current step before
proceeding.
return_value can be one of:
None
'Repeat' - repeat the step
or 'Fail' - unrecoverable error (stop the protocol)
"""
app = get_app()
logger.info('[SyringePumpPlugin] on_step_run(): step #%d',
app.protocol.current_step_number)
app_values = self.get_app_values()
options = self.get_step_options()
if (self.proxy != None and (app.realtime_mode or app.running)):
microsteps = self.proxy.microstep_setting
steps = (app_values['steps_per_microliter'] *
options['microliters'] * microsteps)
steps_per_second = (app_values['steps_per_microliter'] *
microsteps * options['microliters_per_min'] /
60.0)
self.proxy.move(steps, steps_per_second)
print 'move(steps=%d, steps_per_second=%d)' % (steps,
steps_per_second)
while self.proxy.steps_remaining:
gtk.main_iteration()
return_value = None
emit_signal('on_step_complete', [self.name, return_value])
def on_step_swapped(self, original_step_number, new_step_number):
logger.info(
'[DropBotPlugin] on_step_swapped():'
'original_step_number=%d, new_step_number=%d',
original_step_number, new_step_number)
self.on_step_options_changed(self.name,
get_app().protocol.current_step_number)
def get_label(self):
app = get_app()
vbox = app.main_window_controller.vbox2
main_window_children = vbox.get_children()
# Get reference to metadata label (or add it if necessary).
labels = [widget for widget in main_window_children
if isinstance(widget, gtk.Label) and (widget.props.name ==
'metadata')]
if labels:
# Metadata label has already been added. Use existing label.
label_metadata = labels[0]
else:
# Metadata label has not been added. Create new metadata label.
label_metadata = gtk.Label()
label_metadata.props.name = 'metadata'
label_metadata.set_alignment(0, .5) # Left, middle vertical align
vbox.pack_start(label_metadata, False, False, 0)
# Find position in main window `gtk.VBox` to insert metadata label
# (after first set of labels).
for i, child in enumerate(main_window_children):
if not isinstance(child, gtk.Label):
break
# Move metadata label to new position.
vbox.reorder_child(label_metadata, i)
# Display label
label_metadata.show()
return label_metadata
def edit_metadata(self):
from pygtkhelpers.schema import schema_dialog
app = get_app()
metadata = self.get_metadata()
schema = json.loads(self.get_app_values()['json_schema'])
video_config = json.loads(self.get_app_values().get('video_config',
'null'))
if video_config is None:
video_config = {}
device_name = video_config.get('device_name')
max_width = video_config.get('width', 320)
max_fps = video_config.get('framerate', 15)
try:
data = schema_dialog(schema, data=metadata,
device_name=device_name, max_width=max_width,
max_fps=max_fps, title='Edit metadata',
parent=app.main_window_controller.view)
except ValueError:
logger.info('Metadata edit cancelled.')
except KeyError:
logger.error('Error setting metadata scanner video config.',
exc_info=True)
else:
self.set_metadata(data)
def on_plugin_enable(self):
app = get_app()
self.parent = app.builder.get_object("vbox2")
self.window = gtk.ScrolledWindow()
self.window.show_all()
self.parent.add(self.window)
super(ProtocolGridController, self).on_plugin_enable()
def _create_accel_group(self, widget):
class FocusWrapper(object):
'''
This class allows for a function to be executed, restoring the
focused state of the protocol grid view if necessary.
'''
def __init__(self, controller, func):
self.controller = controller
self.func = func
def __call__(self):
focused = self.controller.widget.has_focus()
self.func()
if focused:
self.controller.widget.grab_focus()
app = get_app()
shortcuts = {
'<Control>c':
self.widget.copy_rows,
'<Control>x':
FocusWrapper(self, self.widget.cut_rows),
'Delete':
FocusWrapper(self, self.widget.delete_rows),
'<Control>v':
FocusWrapper(self, self.widget.paste_rows_after),
'<Control><Shift>v':
FocusWrapper(self, self.widget.paste_rows_before),
'<Control><Shift>i':
FocusWrapper(self, lambda: app.protocol.insert_step())
}
return get_accel_group(widget,
shortcuts,
enabled_widgets=[self.widget])
def _create_accel_group(self, widget):
class FocusWrapper(object):
'''
This class allows for a function to be executed, restoring the
focused state of the protocol grid view if necessary.
'''
def __init__(self, controller, func):
self.controller = controller
self.func = func
def __call__(self):
focused = self.controller.widget.has_focus()
self.func()
if focused:
self.controller.widget.grab_focus()
app = get_app()
shortcuts = {
'<Control>c': self.widget.copy_rows,
'<Control>x': FocusWrapper(self, self.widget.cut_rows),
'Delete': FocusWrapper(self, self.widget.delete_rows),
'<Control>v': FocusWrapper(self, self.widget.paste_rows_after),
'<Control><Shift>v': FocusWrapper(self,
self.widget.paste_rows_before),
'<Control><Shift>i': FocusWrapper(self, lambda:
app.protocol.insert_step())}
return get_accel_group(widget, shortcuts,
enabled_widgets=[self.widget])
def update_connection_status(self):
'''
Update connection status message and corresponding UI label.
.. versionchanged:: 0.14
Schedule update of control board status label in main GTK thread.
'''
self.connection_status = "Not connected"
app = get_app()
connected = self.control_board is not None
if connected:
properties = self.control_board.properties
version = self.control_board.hardware_version
n_channels = self.control_board.number_of_channels
id = self.control_board.id
uuid = self.control_board.uuid
self.connection_status = ('%s v%s (Firmware: %s, id: %s, uuid: '
'%s)\n'
'%d channels' %
(properties['display_name'], version,
properties['software_version'], id,
str(uuid)[:8], n_channels))
self.trigger("set-stats", self.connection_status)
# Schedule update of control board status label in main GTK thread.
gobject.idle_add(
app.main_window_controller.label_control_board_status.set_text,
self.connection_status)
def on_step_run(self):
'''
Handler called whenever a step is executed.
Plugins that handle this signal must emit the on_step_complete signal
once they have completed the step. The protocol controller will wait
until all plugins have completed the current step before proceeding.
.. versionchanged:: 2.2.2
Emit ``on_step_complete`` signal within thread-safe function, since
signal callbacks may use GTK.
'''
app = get_app()
if (app.realtime_mode or app.running) and self.gui_process is not None:
step_options = self.get_step_options()
if not step_options['video_enabled']:
command = 'disable_video'
else:
command = 'enable_video'
hub_execute(self.name, command)
# Call as thread-safe function, since signal callbacks may use GTK.
gtk_threadsafe(emit_signal)('on_step_complete', [self.name, None])
def on_app_options_changed(self, plugin_name):
app = get_app()
if plugin_name == self.name:
app_values = self.get_app_values()
reconnect = False
if self.control_board.connected():
for k, v in app_values.items():
if k == 'baud_rate' and self.control_board.baud_rate != v:
self.control_board.baud_rate = v
reconnect = True
if k == 'serial_port' and self.control_board.port != v:
reconnect = True
if reconnect:
self.connect()
self._update_protocol_grid()
elif plugin_name == app.name:
# Turn off all electrodes if we're not in realtime mode and not
# running a protocol.
if (self.control_board.connected() and not app.realtime_mode and
not app.running):
logger.info('Turning off all electrodes.')
self.control_board.set_state_of_all_channels(
np.zeros(self.control_board.number_of_channels())
)
def on_step_run(self):
"""
Handler called whenever a step is executed. Note that this signal
is only emitted in realtime mode or if a protocol is running.
Plugins that handle this signal must emit the on_step_complete
signal once they have completed the step. The protocol controller
will wait until all plugins have completed the current step before
proceeding.
return_value can be one of:
None
'Repeat' - repeat the step
or 'Fail' - unrecoverable error (stop the protocol)
"""
app = get_app()
if not app.running:
return
self.kill_running_step()
step_options = self.get_step_options()
try:
self.repeat_i = 0
self.step_start_time = datetime.now()
df_routes = self.get_routes()
self.route_controller.execute_routes(
df_routes, step_options['transition_duration_ms'],
trail_length=step_options['trail_length'],
on_complete=self.on_step_routes_complete,
on_error=self.on_error)
except:
self.on_error()
def _get_popup_menu(self, item, column_title, value, row_ids,
menu_items=None):
app = get_app()
if menu_items is None:
# Use list of tuples (menu label, callback) rather than a dict to
# allow ordering.
menu_items = []
def request_field_filter(*args, **kwargs):
from .field_filter_controller import FieldFilterController
ffc = FieldFilterController()
response = ffc.run(self.forms, self.enabled_fields_by_form_name)
if response == gtk.RESPONSE_OK:
self.emit('fields-filter-request',
ffc.enabled_fields_by_plugin)
# Add menu entry to select enabled fields for each plugin
menu_items += [('Select fields...', request_field_filter)]
# Add seperator
menu_items += [(None, None)]
menu_items += [('Insert', lambda x: app.protocol.insert_step())]
menu_items += [('Delete', self.delete_rows)]
menu_items += [('Cut', self.cut_rows)]
menu_items += [('Copy', self.copy_rows)]
menu_items += [('Paste before', self.paste_rows_before)]
menu_items += [('Paste after', self.paste_rows_after)]
# Add seperator
menu_items += [(None, None)]
return super(ProtocolGridView, self)._get_popup_menu(item,
column_title,
value, row_ids,
menu_items)
def set_electrode_states(self, electrode_states):
'''
Set the state of multiple electrodes.
Args:
electrode_states (pandas.Series) : State of electrodes, indexed by
electrode identifier (e.g., `"electrode001"`).
Returns:
(dict) : States of modified channels and electrodes, as well as the
total area of all actuated electrodes.
'''
app = get_app()
# Set the state of DMF device channels.
self.electrode_states = (electrode_states
.combine_first(self.electrode_states))
def notify(step_number):
emit_signal('on_step_options_changed', [self.name, step_number],
interface=IPlugin)
gtk.idle_add(notify, app.protocol.current_step_number)
result = self.get_state(electrode_states)
result['actuated_area'] = self.get_actuated_area(self.electrode_states)
return result
def on_plugin_enable(self):
app = get_app()
self.parent = app.builder.get_object("vbox2")
self.window = gtk.ScrolledWindow()
self.window.show_all()
self.parent.add(self.window)
super(ProtocolGridController, self).on_plugin_enable()
def get_actuated_area(self, electrode_states):
'''
Get area of actuated electrodes.
'''
app = get_app()
actuated_electrodes = electrode_states[electrode_states > 0].index
return app.dmf_device.electrode_areas.ix[actuated_electrodes].sum()
def on_plugin_enable(self):
'''
Handler called when plugin is enabled.
For example, when the MicroDrop application is **launched**, or when
the plugin is **enabled** from the plugin manager dialog.
'''
self.open_board_connection()
if not self.initialized:
app = get_app()
self.tools_menu_item = gtk.MenuItem("PMT-plugin")
app.main_window_controller.menu_tools.append(self.tools_menu_item)
self.tools_menu = gtk.Menu()
self.tools_menu_item.set_submenu(self.tools_menu)
self.edit_config_menu_item = \
gtk.MenuItem("Edit configuration settings...")
self.tools_menu.append(self.edit_config_menu_item)
self.edit_config_menu_item.connect("activate",
self.on_edit_configuration)
self.edit_config_menu_item.show()
self.initialized = True
# if we're connected to the board, display the menu
if self.board:
self.reset_board_state()
self.tools_menu.show()
self.tools_menu_item.show()
try:
super(MrBoxPeripheralBoardPlugin, self).on_plugin_enable()
except AttributeError:
pass
def on_flash_firmware(self, widget=None, data=None):
app = get_app()
try:
self.board.flash_firmware()
app.main_window_controller.info("Firmware updated successfully.",
"Firmware update")
except Exception, why:
logger.error("Problem flashing firmware. ""%s" % why)
def on_selection_changed(self, grid_view):
if self.selected_ids:
_L().debug('selected_ids=%s', self.selected_ids)
app = get_app()
_L().debug('current_step_number=%d',
app.protocol.current_step_number)
if app.protocol.current_step_number not in self.selected_ids:
app.protocol.goto_step(self.selected_ids[0])
def on_selection_changed(self, grid_view):
if self.selected_ids:
_L().debug('selected_ids=%s', self.selected_ids)
app = get_app()
_L().debug('current_step_number=%d',
app.protocol.current_step_number)
if app.protocol.current_step_number not in self.selected_ids:
app.protocol.goto_step(self.selected_ids[0])
def on_selection_changed(self, grid_view):
if self.selected_ids:
logger = _L()
app = get_app()
step_number = app.protocol_controller.protocol_state['step_number']
logger.debug('selected_ids=%s', self.selected_ids)
logger.debug('step number=%d', step_number)
if step_number not in self.selected_ids:
app.protocol_controller.goto_step(self.selected_ids[0])
def on_step_swapped(self, *args):
'''
.. versionchanged:: 2.1.3
Pass current step number to as argument to
:meth:`update_nearest_step_labels`.
'''
app = get_app()
step_i = app.protocol.current_step_number
self.update_nearest_step_labels(step_i)
def on_step_options_changed(self, plugin, step_number):
logger.info('[DropBotPlugin] on_step_options_changed(): %s step #%d',
plugin, step_number)
app = get_app()
if (app.protocol and not app.running and not app.realtime_mode
and (plugin == 'microdrop.gui.dmf_device_controller'
or plugin == self.name)
and app.protocol.current_step_number == step_number):
self.on_step_run()
def get_state(self, electrode_states):
app = get_app()
electrode_channels = (app.dmf_device.actuated_channels(electrode_states
.index))
channel_states = pd.Series(electrode_states.values,
index=electrode_channels)
return {'electrode_states': electrode_states,
'channel_states': channel_states}
def on_selection_changed(self, grid_view):
if self.selected_ids:
logging.debug('[ProtocolGridView].on_selection_changed: '
'selected_ids=%s', self.selected_ids)
app = get_app()
logging.debug('\tcurrent_step_number=%d',
app.protocol.current_step_number)
if app.protocol.current_step_number not in self.selected_ids:
app.protocol.goto_step(self.selected_ids[0])
def metadata(self):
'''
Add experiment index and experiment UUID to metadata.
'''
metadata = self._metadata.copy() if self._metadata else {}
app = get_app()
metadata['experiment_id'] = app.experiment_log.experiment_id
metadata['experiment_uuid'] = app.experiment_log.uuid
return metadata
def create_ui(self):
self.menu = gtk.MenuItem('E_xport 2.35+ protocol...')
self.menu.set_tooltip_text('Export protocol compatible with MicroDrop '
'2.35+.')
self.menu.show_all()
app = get_app()
# Add main DropBot menu to MicroDrop `Tools` menu.
app.main_window_controller.menu_tools.append(self.menu)
self.menu.connect('activate',
lambda menu_item: self._export_protocol())
def on_protocol_pause(self):
"""
Handler called when a protocol is paused.
"""
app = get_app()
self._kill_running_step()
if self.control_board and not app.realtime_mode:
# Turn off all electrodes
logger.debug('Turning off all electrodes.')
self.control_board.hv_output_enabled = False
def on_step_options_changed(self, plugin, step_number):
logger.debug('[OpenDropPlugin] on_step_options_changed(): %s '
'step #%d' % (plugin, step_number))
app = get_app()
app_values = self.get_app_values()
options = self.get_step_options(step_number)
if (app.protocol and not app.running and not app.realtime_mode and
(plugin == 'microdrop.gui.dmf_device_controller' or plugin ==
self.name) and app.protocol.current_step_number == step_number):
self.on_step_run()
def on_step_run(self):
"""
Handler called whenever a step is executed.
Plugins that handle this signal must emit the on_step_complete
signal once they have completed the step. The protocol controller
will wait until all plugins have completed the current step before
proceeding.
.. versionchanged:: 0.14
Schedule update of control board status label in main GTK thread.
"""
logger.debug('[DropBotPlugin] on_step_run()')
self._kill_running_step()
app = get_app()
options = self.get_step_options()
if (self.control_board and (app.realtime_mode or app.running)):
max_channels = self.control_board.number_of_channels
# All channels should default to off.
channel_states = np.zeros(max_channels, dtype=int)
# Set the state of any channels that have been set explicitly.
channel_states[self.channel_states.index.values.tolist(
)] = self.channel_states
emit_signal("set_frequency",
options['frequency'],
interface=IWaveformGenerator)
emit_signal("set_voltage",
options['voltage'],
interface=IWaveformGenerator)
if not self.control_board.hv_output_enabled:
self.control_board.hv_output_enabled = True
label = (
self.connection_status +
', Voltage: %.1f V' % self.control_board.measure_voltage())
# Schedule update of control board status label in main GTK thread.
gobject.idle_add(
app.main_window_controller.label_control_board_status.
set_markup, label)
self.control_board.set_state_of_channels(channel_states)
# if a protocol is running, wait for the specified minimum duration
if app.running:
logger.debug('[DropBotPlugin] on_step_run: '
'timeout_add(%d, _callback_step_completed)' %
options['duration'])
self.timeout_id = gobject.timeout_add(
options['duration'], self._callback_step_completed)
return
else:
self.step_complete()
def update_steps(self):
app = get_app()
num_steps = len(app.protocol.steps)
protocol = []
for i in range(num_steps):
protocol.append(self.get_step_options(i))
self.mqtt_client.publish('microdrop/droplet-planning-plugin/step-options',
json.dumps(protocol, cls=PandasJsonEncoder),
retain=True)
def on_protocol_run(self):
"""
Handler called when a protocol starts running.
"""
app = get_app()
if not self.control_board.connected():
logger.warning("Warning: no control board connected.")
elif (self.control_board.number_of_channels() <=
app.dmf_device.max_channel()):
logger.warning("Warning: currently connected board does not have "
"enough channels for this protocol.")
def on_protocol_pause(self):
"""
Handler called when a protocol is paused.
"""
app = get_app()
self._kill_running_step()
if self.control_board.connected() and not app.realtime_mode:
# Turn off all electrodes
logger.debug('Turning off all electrodes.')
self.control_board.set_state_of_all_channels(
np.zeros(self.control_board.number_of_channels()))
def update_steps(self):
app = get_app()
num_steps = len(app.protocol.steps)
protocol = []
for i in range(num_steps):
protocol.append(self.get_step_options(i))
self.mqtt_client.publish('microdrop/dmf-device-ui-plugin/step-options',
json.dumps(protocol, cls=PandasJsonEncoder),
retain=True)
def on_protocol_run(self):
"""
Handler called when a protocol starts running.
"""
app = get_app()
if not self.control_board:
logger.warning("Warning: no control board connected.")
elif (self.control_board.number_of_channels <=
app.dmf_device.max_channel()):
logger.warning("Warning: currently connected board does not have "
"enough channels for this protocol.")
def remove_labels(self):
'''
.. versionchanged:: 2.1.3
Wrap with :func:`gtk_threadsafe` decorator to ensure the code runs
in the main GTK thread.
'''
app = get_app()
for child_i in app.main_window_controller.box_step.get_children():
if any([child_i is self.label_most_recent_step_label,
child_i is self.label_next_step_label]):
app.main_window_controller.box_step.remove(child_i)
self.label_most_recent_step_label = None
self.label_next_step_label = None
def update_channel_states(self, channel_states):
# Update locally cached channel states with new modified states.
try:
self.channel_states = channel_states.combine_first(
self.channel_states)
except ValueError:
logging.info('channel_states: %s', channel_states)
logging.info('self.channel_states: %s', self.channel_states)
logging.info('', exc_info=True)
else:
app = get_app()
connected = self.control_board != None
if connected and (app.realtime_mode or app.running):
self.on_step_run()
def on_execute__save_channel_impedances(self, request):
data = decode_content_data(request)
impedance_structures = data.pop('impedance_structures')
output_path = data.pop('output_path')
try:
self.parent.save_channel_impedances(impedance_structures,
output_path, **data)
except Exception, error:
app = get_app()
if app.config.data.get('advanced_ui', False):
# Launch debugger to inspect state.
import pdb; pdb.set_trace()
raise
def update_grid(self, protocol=None):
app = get_app()
if protocol is None:
protocol = app.protocol
if protocol is None:
return
logging.debug('[ProtocolGridController].update_grid:')
logging.debug('[ProtocolGridController] plugin_fields=%s',
protocol.plugin_fields)
forms = emit_signal('get_step_form_class')
steps = protocol.steps
logging.debug('[ProtocolGridController] forms=%s steps=%s', forms,
steps)
if self.enabled_fields is None:
# Assign directly to _enabled_fields to avoid recursive call into
# update_grid()
self._enabled_fields = dict([(form_name,
set(form.field_schema_mapping
.keys()))
for form_name, form in forms.items()])
# The step ID column can be hidden by changing show_ids to False
combined_fields = ProtocolGridView(forms, self.enabled_fields,
show_ids=True)
combined_fields.connect('fields-filter-request',
self.set_fields_filter)
for i, step in enumerate(steps):
values = emit_signal('get_step_values', [i])
logging.debug('[ProtocolGridController] Step[%d]=%s values=%s',
i, step, values)
attributes = dict()
for form_name, form in combined_fields.forms.iteritems():
attr_values = values[form_name]
logging.debug('[CombinedRow] attr_values=%s' % attr_values)
attributes[form_name] = RowFields(**attr_values)
c = CombinedRow(combined_fields, attributes=attributes)
combined_fields.append(c)
if self.widget:
self.window.remove(self.widget)
del self.widget
self.widget = combined_fields
if self.widget:
self.widget.show_all()
self.widget.select_row(app.protocol.current_step_number)
self._register_shortcuts()
self.window.add(self.widget)
def on_step_run(self):
"""
Handler called whenever a step is executed.
Plugins that handle this signal must emit the on_step_complete
signal once they have completed the step. The protocol controller
will wait until all plugins have completed the current step before
proceeding.
"""
logger.debug('[OpenDropPlugin] on_step_run()')
self._kill_running_step()
app = get_app()
options = self.get_step_options()
dmf_options = app.dmf_device_controller.get_step_options()
logger.debug('[OpenDropPlugin] options=%s dmf_options=%s' %
(options, dmf_options))
app_values = self.get_app_values()
if (self.control_board.connected() and (app.realtime_mode or
app.running)):
state = dmf_options.state_of_channels
max_channels = self.control_board.number_of_channels()
if len(state) > max_channels:
state = state[0:max_channels]
elif len(state) < max_channels:
state = np.concatenate([state, np.zeros(max_channels -
len(state), int)])
assert(len(state) == max_channels)
emit_signal("set_frequency",
options['frequency'],
interface=IWaveformGenerator)
emit_signal("set_voltage", options['voltage'],
interface=IWaveformGenerator)
self.control_board.set_state_of_all_channels(state)
# if a protocol is running, wait for the specified minimum duration
if app.running:
logger.debug('[OpenDropPlugin] on_step_run: '
'timeout_add(%d, _callback_step_completed)' %
options['duration'])
self.timeout_id = gobject.timeout_add(
options['duration'], self._callback_step_completed)
return
else:
self.step_complete()
def set_metadata(self, data):
'''
Args
----
data (dict) : New metadata to replace existing metadata.
Emits `metadata-changed` signal with original and new metadata.
'''
app = get_app()
# Validate new metadata against schema.
jsonschema.validate(data, self.schema)
original_metadata = self.get_metadata()
app.experiment_log.metadata[self.name] = data
self.emit('metadata-changed', original_metadata,
app.experiment_log.metadata[self.name])
def create_ui(self):
self.menu = gtk.Menu()
self.menu_item = gtk.MenuItem(self.name)
self.video_config_menu = gtk.MenuItem('Set barcode scanner video config...')
self.video_config_menu.connect('activate', self.on_video_config_menu__activate)
self.metadata_menu = gtk.MenuItem('Edit experiment metadata...')
self.metadata_menu.connect('activate', self.on_metadata_menu__activate)
app = get_app()
if not hasattr(app, 'experiment_log') or app.experiment_log is None:
self.metadata_menu.set_sensitive(False)
self.menu.append(self.video_config_menu)
self.menu.append(self.metadata_menu)
self.menu.show_all()
self.menu_item.set_submenu(self.menu)
self.menu_item.show_all()
app.main_window_controller.menu_tools.append(self.menu_item)
def update_protocol(self, protocol):
app = get_app()
for i, s in enumerate(protocol):
step = app.protocol.steps[i]
prevData = step.get_data(self.plugin_name)
values = {}
for k, v in prevData.iteritems():
if k in s:
values[k] = s[k]
step.set_data(self.plugin_name, values)
emit_signal('on_step_options_changed', [self.plugin_name, i],
interface=IPlugin)
def update_connection_status(self):
self.connection_status = "Not connected"
app = get_app()
connected = self.control_board.connected()
if connected:
name = self.control_board.name()
version = self.control_board.hardware_version()
firmware = self.control_board.software_version()
n_channels = self.control_board.number_of_channels()
serial_number = self.control_board.serial_number
self.connection_status = ('%s v%s (Firmware: %s, S/N %03d)\n'
'%d channels' % (name, version, firmware, serial_number,
n_channels))
app.main_window_controller.label_control_board_status\
.set_text(self.connection_status)
def update_protocol(self, protocol):
app = get_app()
for i, s in enumerate(protocol):
step = app.protocol.steps[i]
prevData = step.get_data(self.plugin_name)
values = {}
for k,v in prevData.iteritems():
if k in s:
values[k] = s[k]
step.set_data(self.plugin_name, values)
emit_signal('on_step_options_changed', [self.plugin_name, i],
interface=IPlugin)
def on_plugin_enable(self):
self.connect()
if not self.initialized:
app = get_app()
self.tools_menu_item = gtk.MenuItem("DropBot DX")
app.main_window_controller.menu_tools.append(self.tools_menu_item)
self.tools_menu = gtk.Menu()
self.tools_menu.show()
self.tools_menu_item.set_submenu(self.tools_menu)
menu_item = gtk.MenuItem("Launch Dstat interface")
self.tools_menu.append(menu_item)
menu_item.connect("activate", self.on_launch_dstat_interface)
menu_item.show()
menu_item = gtk.MenuItem("Set step Dstat parameters file...")
self.tools_menu.append(menu_item)
menu_item.connect("activate", self.on_set_dstat_params_file)
menu_item.show()
self.edit_config_menu_item = \
gtk.MenuItem("Edit configuration settings...")
self.tools_menu.append(self.edit_config_menu_item)
self.edit_config_menu_item.connect("activate",
self.on_edit_configuration)
self.view_menu_item = gtk.MenuItem("DropBot DX")
app.main_window_controller.menu_view.append(self.view_menu_item)
self.view_menu = gtk.Menu()
self.view_menu.show()
self.view_menu_item.set_submenu(self.view_menu)
menu_item = gtk.MenuItem("View DStat results...")
self.view_menu.append(menu_item)
# Display DStat summary table in dialog.
menu_item.connect("activate", lambda *args:
dataframe_display_dialog
(self.dstat_summary_frame(unit='n'),
message='DStat result summary'))
menu_item.show()
self.initialized = True
self.tools_menu_item.show()
self.view_menu_item.show()
if self.connected():
self.edit_config_menu_item.show()
super(DropBotDxAccessoriesPlugin, self).on_plugin_enable()
def update_excel_results(self, launch=False):
'''
Update output Excel results file.
.. versionadded:: 0.19
Parameters
----------
launch : bool, optional
If ``True``, launch Excel spreadsheet after writing.
'''
app = get_app()
log_dir = app.experiment_log.get_log_path()
# Update Excel file with latest PMT results.
output_path = log_dir.joinpath('PMT_readings.xlsx')
data_files = list(log_dir.files('PMT_readings-*.ndjson'))
if not data_files:
logger.debug('No PMT readings files found.')
return
logger.info(TEMPLATE_PATH)
def _threadsafe_write_results():
logger.info(launch)
while True:
try:
_write_results(TEMPLATE_PATH, output_path, data_files)
if launch:
try:
output_path.launch()
except Exception:
pass
break
except IOError as e:
logger.info("I/O error({0}): {1}".format(e.errno, e.strerror))
response = yesno('Error writing PMT summary to Excel '
'spreadsheet output path: `%s`.\n\nTry '
'again?' %output_path)
if response == gtk.RESPONSE_NO:
break
# Schedule writing of results to occur in main GTK
# thread in case confirmation dialog needs to be
# displayed.
gobject.idle_add(_threadsafe_write_results)
def on_step_swapped(self, original_step_number, new_step_number):
'''
Handler called when a new step is activated/selected.
Parameters
----------
original_step_number : int
Step number of previously activated step.
new_step_number : int
Step number of newly activated step.
'''
# Step options have changed.
app = get_app()
if app.realtime_mode and not app.running:
# Apply step options.
options = self.get_step_options()
self.apply_step_options(options)
def on_step_run(self):
"""
Handler called whenever a step is executed.
Plugins that handle this signal must emit the on_step_complete
signal once they have completed the step. The protocol controller
will wait until all plugins have completed the current step before
proceeding.
"""
logger.debug('[TestPlugin] on_step_run()')
app = get_app()
if (self.proxy and app.realtime_mode or app.running):
options = self.get_step_options()
self.proxy.digital_write(pin=13, value=options['led_on'])
emit_signal('on_step_complete', [self.name, None])
def find_next_step_label(self, step_i):
'''
.. versionchanged:: 2.1.3
Add :data:`step_i` parameter.
Parameters
----------
step_i : int
Step number to find labels relative to.
'''
app = get_app()
for i in xrange(step_i + 1, len(app.protocol.steps)):
next_step_label = self.get_step_value('label', step_number=i)
if next_step_label:
return i, next_step_label
else:
return None, ''
def on_step_run(self):
"""
Handler called whenever a step is executed.
Plugins that handle this signal must emit the on_step_complete
signal once they have completed the step. The protocol controller
will wait until all plugins have completed the current step before
proceeding.
"""
logger.debug('[TestPlugin] on_step_run()')
app = get_app()
if (self.proxy and app.realtime_mode or app.running):
options = self.get_step_options()
self.proxy.digital_write(pin=13, value=options['led_on'])
emit_signal('on_step_complete', [self.name, None])
def update_connection_status(self):
self.connection_status = "Not connected"
app = get_app()
connected = self.control_board != None
if connected:
properties = self.control_board.properties
version = self.control_board.hardware_version
n_channels = self.control_board.number_of_channels
id = self.control_board.id
uuid = self.control_board.uuid
self.connection_status = (
'%s v%s (Firmware: %s, id: %s, uuid: %s)\n'
'%d channels' % (properties['display_name'],
version, properties['software_version'], id,
str(uuid)[:8], n_channels))
app.main_window_controller.label_control_board_status\
.set_text(self.connection_status)
def on_step_options_changed(self, plugin, step_number):
'''
Handler called when field values for the specified plugin and step.
Parameters
----------
plugin : str
Name of plugin.
step_number : int
Step index number.
'''
# Step options have changed.
app = get_app()
if all([plugin == self.plugin_name, app.realtime_mode,
step_number == app.protocol.current_step_number]):
# Apply step options.
options = self.get_step_options()
self.apply_step_options(options)
def on_plugin_enable(self):
super(DropBotDxPlugin, self).on_plugin_enable()
self.cleanup_plugin()
# Initialize 0MQ hub plugin and subscribe to hub messages.
self.plugin = DmfZmqPlugin(self,
self.name,
get_hub_uri(),
subscribe_options={zmq.SUBSCRIBE: ''})
# Initialize sockets.
self.plugin.reset()
# Periodically process outstanding message received on plugin sockets.
self.plugin_timeout_id = gtk.timeout_add(10, self.plugin.check_sockets)
self.check_device_name_and_version()
if get_app().protocol:
self.on_step_run()
self._update_protocol_grid()