class MqttPlugin(pmh.BaseMqttReactor, Plugin):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = __version__
plugin_name = get_plugin_info(ph.path(__file__).parent).plugin_name
def __init__(self):
super(MqttPlugin, self).__init__()
self.name = self.plugin_name
###########################################################################
# MicroDrop pyutilib plugin handlers
# ==================================
def on_plugin_disable(self):
"""
Handler called once the plugin instance is disabled.
"""
# Stop MQTT reactor.
self.stop()
def on_plugin_enable(self):
"""
Handler called once the plugin instance is enabled.
"""
# Start MQTT reactor.
self.start()
def __init__(self):
self.control_board = None
self.name = get_plugin_info(path(__file__).parent).plugin_name
self.connection_status = "Not connected"
self.current_frequency = None
self.timeout_id = None
self.channel_states = pd.Series()
self.plugin = None
self.plugin_timeout_id = None
def max_voltage(element, state):
"""Verify that the voltage is below a set maximum"""
service = get_service_instance_by_name(
get_plugin_info(path(__file__).parent).plugin_name)
if service.control_board and \
element.value > service.control_board.max_waveform_voltage:
return element.errors.append(
'Voltage exceeds the maximum value '
'(%d V).' % service.control_board.max_waveform_voltage)
else:
return True
def max_voltage(element, state):
"""Verify that the voltage is below a set maximum"""
service = get_service_instance_by_name(
get_plugin_info(path(__file__).parent).plugin_name)
if service.control_board.connected() and \
element.value > service.control_board.max_waveform_voltage:
return element.errors.append('Voltage exceeds the maximum value '
'(%d V).' %
service.control_board.max_waveform_voltage)
else:
return True
def check_frequency(element, state):
"""Verify that the frequency is within the valid range"""
service = get_service_instance_by_name(
get_plugin_info(path(__file__).parent).plugin_name)
if service.control_board and \
(element.value < service.control_board.min_waveform_frequency or \
element.value > service.control_board.max_waveform_frequency):
return element.errors.append(
'Frequency is outside of the valid range '
'(%.1f - %.1f Hz).' %
(service.control_board.min_waveform_frequency,
service.control_board.max_waveform_frequency))
else:
return True
def check_frequency(element, state):
"""Verify that the frequency is within the valid range"""
service = get_service_instance_by_name(
get_plugin_info(path(__file__).parent).plugin_name)
if service.control_board.connected() and \
(element.value < service.control_board.min_waveform_frequency or \
element.value > service.control_board.max_waveform_frequency):
return element.errors.append('Frequency is outside of the valid range '
'(%.1f - %.1f Hz).' %
(service.control_board.min_waveform_frequency,
service.control_board.max_waveform_frequency)
)
else:
return True
class EmqttdPlugin(Plugin):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = __version__
plugin_name = get_plugin_info(ph.path(__file__).parent).plugin_name
def __init__(self):
self.name = self.plugin_name
# Flag to indicate whether or not we started the `emqttd` service.
# Used to determine if we should **stop** the service when the plugin
# is disabled.
self.launched_service = False
def on_plugin_enable(self):
"""
Handler called once the plugin instance is enabled.
Note: if you inherit your plugin from AppDataController and don't
implement this handler, by default, it will automatically load all
app options from the config file. If you decide to overide the
default handler, you should call:
AppDataController.on_plugin_enable(self)
to retain this functionality.
"""
super(EmqttdPlugin, self).on_plugin_enable()
# Launch `emqttd` service (if not already running).
self.launched_service = emqttd_start()
def on_plugin_disable(self):
"""
Handler called once the plugin instance is disabled.
"""
if self.launched_service:
# We started the `emqttd` service, so stop it.
emqttd_stop()
class DmfDeviceUiPlugin(AppDataController, StepOptionsController, Plugin,
pmh.BaseMqttReactor):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = get_plugin_info(path(__file__).parent).version
plugin_name = get_plugin_info(path(__file__).parent).plugin_name
AppFields = Form.of(
String.named('video_config').using(default='',
optional=True,
properties={'show_in_gui': False}),
String.named('surface_alphas').using(default='',
optional=True,
properties={'show_in_gui':
False}),
String.named('canvas_corners').using(default='',
optional=True,
properties={'show_in_gui':
False}),
String.named('frame_corners').using(default='',
optional=True,
properties={'show_in_gui': False}),
Integer.named('x').using(default=None,
optional=True,
properties={'show_in_gui': False}),
Integer.named('y').using(default=None,
optional=True,
properties={'show_in_gui': False}),
Integer.named('width').using(default=400,
optional=True,
properties={'show_in_gui': False}),
Integer.named('height').using(default=500,
optional=True,
properties={'show_in_gui': False}))
StepFields = Form.of(
Boolean.named('video_enabled').using(default=True,
optional=True,
properties={'title': 'Video'}))
def __init__(self):
self.name = self.plugin_name
self.gui_process = None
self.gui_heartbeat_id = None
self._gui_enabled = False
self.alive_timestamp = None
self.should_terminate = False
pmh.BaseMqttReactor.__init__(self)
self.start()
def reset_gui(self):
py_exe = sys.executable
# Set allocation based on saved app values (i.e., remember window size
# and position from last run).
app_values = self.get_app_values()
allocation_args = ['-a', json.dumps(app_values)]
app = get_app()
if app.config.data.get('advanced_ui', False):
debug_args = ['-d']
else:
debug_args = []
self.gui_process = Popen(
[py_exe, '-m', 'dmf_device_ui.bin.device_view', '-n', self.name] +
allocation_args + debug_args + ['fixed', get_hub_uri()],
creationflags=CREATE_NEW_PROCESS_GROUP)
self.gui_process.daemon = False
self._gui_enabled = True
def keep_alive():
if not self._gui_enabled:
self.alive_timestamp = None
return False
elif self.gui_process.poll() == 0:
# GUI process has exited. Restart.
self.cleanup()
self.reset_gui()
return False
else:
self.alive_timestamp = datetime.now()
# Keep checking.
return True
# Go back to Undo 613 for working corners
self.step_video_settings = None
# Get current video settings from UI.
app_values = self.get_app_values()
# Convert JSON settings to 0MQ plugin API Python types.
ui_settings = self.json_settings_as_python(app_values)
self.set_ui_settings(ui_settings, default_corners=True)
self.gui_heartbeat_id = gobject.timeout_add(1000, keep_alive)
def cleanup(self):
if self.gui_heartbeat_id is not None:
gobject.source_remove(self.gui_heartbeat_id)
self.alive_timestamp = None
def get_schedule_requests(self, function_name):
"""
Returns a list of scheduling requests (i.e., ScheduleRequest instances)
for the function specified by function_name.
"""
if function_name == 'on_plugin_enable':
return [ScheduleRequest('droplet_planning_plugin', self.name)]
elif function_name == 'on_dmf_device_swapped':
# XXX Schedule `on_app_exit` handling before `device_info_plugin`,
# since `hub_execute` uses the `device_info_plugin` service to
# submit commands to through the 0MQ plugin hub.
return [ScheduleRequest('microdrop.device_info_plugin', self.name)]
elif function_name == 'on_app_exit':
# XXX Schedule `on_app_exit` handling before `device_info_plugin`,
# since `hub_execute` uses the `device_info_plugin` service to
# submit commands to through the 0MQ plugin hub.
return [ScheduleRequest(self.name, 'microdrop.device_info_plugin')]
return []
def on_app_exit(self):
self.should_terminate = True
self.mqtt_client.publish(
'microdrop/dmf-device-ui-plugin/get-video-settings',
json.dumps(None))
def json_settings_as_python(self, json_settings):
'''
Convert DMF device UI plugin settings from json format to Python types.
Python types are expected by DMF device UI plugin 0MQ command API.
Args
----
json_settings (dict) : DMF device UI plugin settings in
JSON-compatible format (i.e., only basic Python data types).
Returns
-------
(dict) : DMF device UI plugin settings in Python types expected by
DMF device UI plugin 0MQ commands.
'''
py_settings = {}
corners = dict([(k, json_settings.get(k))
for k in ('canvas_corners', 'frame_corners')])
if all(corners.values()):
# Convert CSV corners lists for canvas and frame to
# `pandas.DataFrame` instances
for k, v in corners.iteritems():
# Prepend `'df_'` to key to indicate the type as a data frame.
py_settings['df_' + k] = pd.read_csv(io.BytesIO(bytes(v)),
index_col=0)
for k in ('video_config', 'surface_alphas'):
if k in json_settings:
if not json_settings[k]:
py_settings[k] = pd.Series(None)
else:
py_settings[k] = pd.Series(json.loads(json_settings[k]))
return py_settings
def save_ui_settings(self, video_settings):
'''
Save specified DMF device UI 0MQ plugin settings to persistent
Microdrop configuration (i.e., settings to be applied when Microdrop is
launched).
Args
----
video_settings (dict) : DMF device UI plugin settings in
JSON-compatible format returned by `get_ui_json_settings`
method (i.e., only basic Python data types).
'''
app_values = self.get_app_values()
# Select subset of app values that are present in `video_settings`.
app_video_values = dict([(k, v) for k, v in app_values.iteritems()
if k in video_settings.keys()])
# If the specified video settings differ from app values, update
# app values.
if app_video_values != video_settings:
app_values.update(video_settings)
self.set_app_values(app_values)
def set_ui_settings(self, ui_settings, default_corners=False):
'''
Set DMF device UI settings from settings dictionary.
Args
----
ui_settings (dict) : DMF device UI plugin settings in format
returned by `json_settings_as_python` method.
'''
if 'video_config' in ui_settings:
msg = {}
msg['video_config'] = ui_settings['video_config'].to_json()
self.mqtt_client.publish(
'microdrop/dmf-device-ui-plugin/set-video-config',
payload=json.dumps(msg),
retain=True)
if 'surface_alphas' in ui_settings:
# TODO: Make Clear retained messages after exit
msg = {}
msg['surface_alphas'] = ui_settings['surface_alphas'].to_json()
self.mqtt_client.publish(
'microdrop/dmf-device-ui-plugin/set-surface-alphas',
payload=json.dumps(msg),
retain=True)
if all((k in ui_settings)
for k in ('df_canvas_corners', 'df_frame_corners')):
# TODO: Test With Camera
msg = {}
msg['df_canvas_corners'] = ui_settings[
'df_canvas_corners'].to_json()
msg['df_frame_corners'] = ui_settings['df_frame_corners'].to_json()
if default_corners:
self.mqtt_client.publish(
'microdrop/dmf-device-ui-plugin/'
'set-default-corners',
payload=json.dumps(msg),
retain=True)
else:
self.mqtt_client.publish(
'microdrop/dmf-device-ui-plugin/'
'set-corners',
payload=json.dumps(msg),
retain=True)
# #########################################################################
# # Plugin signal handlers
def on_connect(self, client, userdata, flags, rc):
self.mqtt_client.subscribe(
'microdrop/dmf-device-ui/get-video-settings')
self.mqtt_client.subscribe('microdrop/dmf-device-ui/update-protocol')
def on_message(self, client, userdata, msg):
if msg.topic == 'microdrop/dmf-device-ui/get-video-settings':
self.video_settings = json.loads(msg.payload)
self.save_ui_settings(self.video_settings)
if self.should_terminate:
self.mqtt_client.publish(
'microdrop/dmf-device-ui-plugin/terminate')
if msg.topic == 'microdrop/dmf-device-ui/update-protocol':
self.update_protocol(json.loads(msg.payload))
def on_plugin_disable(self):
self._gui_enabled = False
self.cleanup()
def on_plugin_enable(self):
super(DmfDeviceUiPlugin, self).on_plugin_enable()
self.reset_gui()
form = flatlandToDict(self.StepFields)
self.mqtt_client.publish('microdrop/dmf-device-ui-plugin/schema',
json.dumps(form),
retain=True)
defaults = {}
for k, v in form.iteritems():
defaults[k] = v['default']
# defaults = map(lambda (k,v): {k: v['default']}, form.iteritems())
self.mqtt_client.publish('microdrop/dmf-device-ui-plugin/step-options',
json.dumps([defaults], cls=PandasJsonEncoder),
retain=True)
def on_step_removed(self, step_number, step):
self.update_steps()
def on_step_options_changed(self, plugin, step_number):
self.update_steps()
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.
'''
app = get_app()
# TODO: Migrate video commands to mqtt!!
# 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']:
# hub_execute(self.name, 'disable_video',
# wait_func=lambda *args: refresh_gui(), timeout_s=5,
# silent=True)
# else:
# hub_execute(self.name, 'enable_video',
# wait_func=lambda *args: refresh_gui(), timeout_s=5,
# silent=True)
emit_signal('on_step_complete', [self.name, None])
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 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)
class ProtocolTranslatorPlugin(Plugin):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = __version__
plugin_name = get_plugin_info(ph.path(__file__).parent).plugin_name
def __init__(self):
self.menu = None
def on_plugin_enable(self):
@gtk_threadsafe
def init_ui():
if self.menu is None:
# Schedule initialization of menu user interface. Calling
# `create_ui()` directly is not thread-safe, since it includes GTK
# code.
self.create_ui()
else:
self.menu.show()
init_ui()
def on_plugin_disable(self):
if self.menu is not None:
self.menu.hide()
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())
@gtk_threadsafe
def _export_protocol(self):
app = get_app()
filter_ = gtk.FileFilter()
filter_.set_name(' MicroDrop protocols (*.json)')
filter_.add_pattern("*.json")
dialog = gtk.FileChooserDialog(
title="Export protocol",
action=gtk.FILE_CHOOSER_ACTION_SAVE,
buttons=(gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL, gtk.STOCK_SAVE,
gtk.RESPONSE_OK))
dialog.add_filter(filter_)
dialog.set_default_response(gtk.RESPONSE_OK)
dialog.set_current_name(app.protocol.name)
dialog.set_current_folder(
os.path.join(app.get_device_directory(), app.dmf_device.name,
"protocols"))
response = dialog.run()
try:
if response == gtk.RESPONSE_OK:
filename = ph.path(dialog.get_filename())
if filename.ext.lower() != '.json':
filename = filename + '.json'
logger = _L() # use logger with method context
try:
with open(filename, 'w') as output:
protocol_dict_to_json(upgrade_protocol(app.protocol),
ostream=output,
validate=False,
json_kwargs={'indent': 2})
except md.protocol.SerializationError, exception:
plugin_exception_counts = Counter(
[e['plugin'] for e in exception.exceptions])
logger.info('%s: `%s`', exception, exception.exceptions)
result = yesno(
'Error exporting data for the following '
'plugins: `%s`\n\n'
'Would you like to exclude this data and '
'export anyway?' %
', '.join(sorted(plugin_exception_counts.keys())))
if result == gtk.RESPONSE_YES:
# Delete plugin data that is causing serialization
# errors.
protocol = copy.deepcopy(app.protocol)
protocol.remove_exceptions(exception.exceptions,
inplace=True)
with open(filename, 'w') as output:
protocol_dict_to_json(upgrade_protocol(
app.protocol),
ostream=output,
validate=False,
json_kwargs={'indent': 2})
else:
# Abort export.
logger.warn('Export cancelled.')
return
logger.info('exported protocol to %s', filename)
app = get_app()
parent_window = app.main_window_controller.view
message = 'Exported protocol to:\n\n%s' % filename
ok_dialog = gtk.MessageDialog(parent=parent_window,
message_format=message,
type=gtk.MESSAGE_OTHER,
buttons=gtk.BUTTONS_OK)
# Increase default dialog size.
ok_dialog.set_size_request(450, 150)
ok_dialog.props.title = 'Export complete'
ok_dialog.props.use_markup = True
ok_dialog.run()
ok_dialog.destroy()
finally:
dialog.destroy()
class SyringePumpPlugin(Plugin, AppDataController, StepOptionsController):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = get_plugin_info(path(__file__).parent).version
plugin_name = get_plugin_info(path(__file__).parent).plugin_name
serial_ports_ = [port for port in get_serial_ports()]
if len(serial_ports_):
default_port_ = serial_ports_[0]
else:
default_port_ = None
'''
AppFields
---------
A flatland Form specifying application options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed AppDataController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the app options dialog
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently in the microdrop
config file, in a section named after this plugin's name attribute
'''
AppFields = Form.of(
Enum.named('serial_port').using(default=default_port_,
optional=True).valued(*serial_ports_),
Float.named('steps_per_microliter').using(optional=True, default=1.0),
)
'''
StepFields
---------
A flatland Form specifying the per step options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed StepOptionsController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the protocol grid view
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently for each step
'''
StepFields = Form.of(
Float.named('microliters_per_min').using(
optional=True,
default=60,
#validators=
#[ValueAtLeast(minimum=0),
# ValueAtMost(maximum=100000)]
),
Float.named('microliters').using(
optional=True,
default=10,
#validators=
#[ValueAtLeast(minimum=0),
# ValueAtMost(maximum=100000)]
),
)
def __init__(self):
self.name = self.plugin_name
self.proxy = None
self.initialized = False # Latch to, e.g., config menus, only once
def connect(self):
"""
Try to connect to the syring pump at the default serial
port selected in the Microdrop application options.
If unsuccessful, try to connect to the proxy on any
available serial port, one-by-one.
"""
from stepper_motor_controller import SerialProxy
if len(SyringePumpPlugin.serial_ports_):
app_values = self.get_app_values()
# try to connect to the last successful port
try:
self.proxy = SerialProxy(port=str(app_values['serial_port']))
except:
logger.warning(
'Could not connect to the syringe pump on port %s. '
'Checking other ports...',
app_values['serial_port'],
exc_info=True)
self.proxy = SerialProxy()
app_values['serial_port'] = self.proxy.port
self.set_app_values(app_values)
else:
raise Exception("No serial ports available.")
def check_device_name_and_version(self):
"""
Check to see if:
a) The connected device is a what we are expecting
b) The device firmware matches the host driver API version
In the case where the device firmware version does not match, display a
dialog offering to flash the device with the firmware version that
matches the host driver API version.
"""
try:
self.connect()
properties = self.proxy.properties
package_name = properties['package_name']
display_name = properties['display_name']
if package_name != self.proxy.host_package_name:
raise Exception("Device is not a %s" %
properties['display_name'])
host_software_version = self.proxy.host_software_version
remote_software_version = self.proxy.remote_software_version
# Reflash the firmware if it is not the right version.
if host_software_version != remote_software_version:
response = yesno("The %s firmware version (%s) "
"does not match the driver version (%s). "
"Update firmware?" %
(display_name, remote_software_version,
host_software_version))
if response == gtk.RESPONSE_YES:
self.on_flash_firmware()
except Exception, why:
logger.warning("%s" % why)
class DmfDeviceUiPlugin(AppDataController, StepOptionsController, Plugin):
"""
This class is automatically registered with the PluginManager.
.. versionchanged:: 2.10
Set default window size and position according to **screen size** *and*
**window titlebar size**. Also, force default window size if
``MICRODROP_FIRST_RUN`` environment variable is set to non-empty value.
"""
implements(IPlugin)
version = get_plugin_info(path(__file__).parent).version
plugin_name = get_plugin_info(path(__file__).parent).plugin_name
AppFields = Form.of(
String.named('video_config').using(default='',
optional=True,
properties={'show_in_gui': False}),
String.named('surface_alphas').using(default='',
optional=True,
properties={'show_in_gui':
False}),
String.named('canvas_corners').using(default='',
optional=True,
properties={'show_in_gui':
False}),
String.named('frame_corners').using(default='',
optional=True,
properties={'show_in_gui': False}),
Integer.named('x').using(default=.5 * SCREEN_WIDTH,
optional=True,
properties={'show_in_gui': False}),
Integer.named('y').using(default=SCREEN_TOP,
optional=True,
properties={'show_in_gui': False}),
Integer.named('width').using(default=.5 * SCREEN_WIDTH,
optional=True,
properties={'show_in_gui': False}),
Integer.named('height').using(default=SCREEN_HEIGHT -
1.5 * TITLEBAR_HEIGHT,
optional=True,
properties={'show_in_gui': False}))
StepFields = Form.of(
Boolean.named('video_enabled').using(default=True,
optional=True,
properties={'title': 'Video'}))
def __init__(self):
self.name = self.plugin_name
self.gui_process = None
self.gui_heartbeat_id = None
self._gui_enabled = False
self.alive_timestamp = None
def reset_gui(self):
'''
.. versionchanged:: 2.2.2
Use :func:`pygtkhelpers.gthreads.gtk_threadsafe` decorator around
function to wait for GUI process, rather than using
:func:`gobject.idle_add`, to make intention clear.
.. versionchanged:: 2.9
Refresh list of registered commands once device UI process has
started. The list of registered commands is used to dynamically
generate items in the device UI context menu.
'''
py_exe = sys.executable
# Set allocation based on saved app values (i.e., remember window size
# and position from last run).
app_values = self.get_app_values()
if os.environ.get('MICRODROP_FIRST_RUN'):
# Use default options for window allocation.
default_app_values = self.get_default_app_options()
for k in ('x', 'y', 'width', 'height'):
app_values[k] = default_app_values[k]
allocation_args = ['-a', json.dumps(app_values)]
app = get_app()
if app.config.data.get('advanced_ui', False):
debug_args = ['-d']
else:
debug_args = []
self.gui_process = Popen(
[py_exe, '-m', 'dmf_device_ui.bin.device_view', '-n', self.name] +
allocation_args + debug_args + ['fixed', get_hub_uri()],
creationflags=CREATE_NEW_PROCESS_GROUP)
self._gui_enabled = True
def keep_alive():
if not self._gui_enabled:
self.alive_timestamp = None
return False
elif self.gui_process.poll() == 0:
# GUI process has exited. Restart.
self.cleanup()
self.reset_gui()
return False
else:
self.alive_timestamp = datetime.now()
# Keep checking.
return True
self.step_video_settings = None
@gtk_threadsafe
def _wait_for_gui():
self.wait_for_gui_process()
# Get current video settings from UI.
app_values = self.get_app_values()
# Convert JSON settings to 0MQ plugin API Python types.
ui_settings = self.json_settings_as_python(app_values)
self.set_ui_settings(ui_settings, default_corners=True)
self.gui_heartbeat_id = gobject.timeout_add(1000, keep_alive)
# Refresh list of electrode and route commands.
hub_execute('microdrop.command_plugin', 'get_commands')
# Call as thread-safe function, since function uses GTK.
_wait_for_gui()
def cleanup(self):
'''
.. versionchanged:: 2.2.2
Catch any exception encountered during GUI process termination.
.. versionchanged:: 2.3.1
Use :func:`kill_process_tree` to terminate DMF device UI process.
This ensures any child processes of the UI process (e.g., video
input process) are also killed.
See also:
https://stackoverflow.com/a/44648162/345236
.. versionchanged:: 2.7
Only try to terminate the GUI process if it is still running.
'''
logger.info('Stop DMF device UI keep-alive timer')
if self.gui_heartbeat_id is not None:
# Stop keep-alive polling of device UI process.
gobject.source_remove(self.gui_heartbeat_id)
if self.gui_process is not None and self.gui_process.poll() is None:
logger.info('Terminate DMF device UI process')
try:
kill_process_tree(self.gui_process.pid)
logger.info('Close DMF device UI process `%s`',
self.gui_process.pid)
except Exception:
logger.info(
'Unexpected error closing DMF device UI process '
'`%s`',
self.gui_process.pid,
exc_info=True)
else:
logger.info('No active DMF device UI process')
self.alive_timestamp = None
def wait_for_gui_process(self, retry_count=20, retry_duration_s=1):
'''
.. versionchanged:: 2.7.2
Do not execute `refresh_gui()` while waiting for response from
`hub_execute()`.
'''
start = datetime.now()
for i in xrange(retry_count):
try:
hub_execute(self.name, 'ping', timeout_s=5, silent=True)
except Exception:
logger.debug('[wait_for_gui_process] failed (%d of %d)',
i + 1,
retry_count,
exc_info=True)
else:
logger.info('[wait_for_gui_process] success (%d of %d)', i + 1,
retry_count)
self.alive_timestamp = datetime.now()
return
for j in xrange(10):
time.sleep(retry_duration_s / 10.)
refresh_gui()
raise IOError('Timed out after %ss waiting for GUI process to connect '
'to hub.' % si_format(
(datetime.now() - start).total_seconds()))
def get_schedule_requests(self, function_name):
"""
Returns a list of scheduling requests (i.e., ScheduleRequest instances)
for the function specified by function_name.
.. versionchanged:: 2.3.3
Do not submit ``on_app_exit`` schedule request. This is no longer
necessary since ``hub_execute`` listening socket is no longer
closed by ``microdrop.device_info_plugin`` during ``on_app_exit``
callback.
.. versionadded:: 2.9
Enable _after_ command plugin and zmq hub plugin.
"""
if function_name == 'on_plugin_enable':
return [
ScheduleRequest(p, self.name)
for p in ('microdrop.zmq_hub_plugin',
'microdrop.command_plugin',
'droplet_planning_plugin')
]
return []
def on_app_exit(self):
logger.info('Get current video settings from DMF device UI plugin.')
json_settings = self.get_ui_json_settings()
self.save_ui_settings(json_settings)
self._gui_enabled = False
self.cleanup()
# #########################################################################
# # DMF device UI 0MQ plugin settings
def get_ui_json_settings(self):
'''
Get current video settings from DMF device UI plugin.
Returns
-------
(dict) : DMF device UI plugin settings in JSON-compatible format
(i.e., only basic Python data types).
.. versionchanged:: 2.7.2
Do not execute `refresh_gui()` while waiting for response from
`hub_execute()`.
'''
video_settings = {}
# Try to request video configuration.
try:
video_config = hub_execute(self.name,
'get_video_config',
timeout_s=2)
except IOError:
logger.warning('Timed out waiting for device window size and '
'position request.')
else:
if video_config is not None:
video_settings['video_config'] = video_config.to_json()
else:
video_settings['video_config'] = ''
# Try to request allocation to save in app options.
try:
data = hub_execute(self.name, 'get_corners', timeout_s=2)
except IOError:
logger.warning('Timed out waiting for device window size and '
'position request.')
else:
if data:
# Get window allocation settings (i.e., width, height, x, y).
# Replace `df_..._corners` with CSV string named `..._corners`
# (no `df_` prefix).
for k in ('df_canvas_corners', 'df_frame_corners'):
if k in data:
data['allocation'][k[3:]] = data.pop(k).to_csv()
video_settings.update(data['allocation'])
# Try to request surface alphas.
try:
surface_alphas = hub_execute(self.name,
'get_surface_alphas',
timeout_s=2)
except IOError:
logger.warning('Timed out waiting for surface alphas.')
else:
if surface_alphas is not None:
video_settings['surface_alphas'] = surface_alphas.to_json()
else:
video_settings['surface_alphas'] = ''
return video_settings
def get_ui_settings(self):
'''
Get current video settings from DMF device UI plugin.
Returns
-------
(dict) : DMF device UI plugin settings in Python types expected by
DMF device UI plugin 0MQ commands.
'''
json_settings = self.get_ui_json_settings()
return self.json_settings_as_python(json_settings)
def json_settings_as_python(self, json_settings):
'''
Convert DMF device UI plugin settings from json format to Python types.
Python types are expected by DMF device UI plugin 0MQ command API.
Args
----
json_settings (dict) : DMF device UI plugin settings in
JSON-compatible format (i.e., only basic Python data types).
Returns
-------
(dict) : DMF device UI plugin settings in Python types expected by
DMF device UI plugin 0MQ commands.
'''
py_settings = {}
corners = dict([(k, json_settings.get(k))
for k in ('canvas_corners', 'frame_corners')])
if all(corners.values()):
# Convert CSV corners lists for canvas and frame to
# `pandas.DataFrame` instances
for k, v in corners.iteritems():
# Prepend `'df_'` to key to indicate the type as a data frame.
py_settings['df_' + k] = pd.read_csv(io.BytesIO(bytes(v)),
index_col=0)
for k in ('video_config', 'surface_alphas'):
if k in json_settings:
if not json_settings[k]:
py_settings[k] = pd.Series(None)
else:
py_settings[k] = pd.Series(json.loads(json_settings[k]))
return py_settings
def save_ui_settings(self, video_settings):
'''
Save specified DMF device UI 0MQ plugin settings to persistent
Microdrop configuration (i.e., settings to be applied when Microdrop is
launched).
Args
----
video_settings (dict) : DMF device UI plugin settings in
JSON-compatible format returned by `get_ui_json_settings`
method (i.e., only basic Python data types).
'''
app_values = self.get_app_values()
# Select subset of app values that are present in `video_settings`.
app_video_values = dict([(k, v) for k, v in app_values.iteritems()
if k in video_settings.keys()])
# If the specified video settings differ from app values, update
# app values.
if app_video_values != video_settings:
app_values.update(video_settings)
self.set_app_values(app_values)
def set_ui_settings(self, ui_settings, default_corners=False):
'''
Set DMF device UI settings from settings dictionary.
Args
----
ui_settings (dict) : DMF device UI plugin settings in format
returned by `json_settings_as_python` method.
.. versionchanged:: 2.7.2
Do not execute `refresh_gui()` while waiting for response from
`hub_execute()`.
'''
if self.alive_timestamp is None or self.gui_process is None:
# Repeat until GUI process has started.
raise IOError('GUI process not ready.')
if 'video_config' in ui_settings:
hub_execute(self.name,
'set_video_config',
video_config=ui_settings['video_config'],
timeout_s=5)
if 'surface_alphas' in ui_settings:
hub_execute(self.name,
'set_surface_alphas',
surface_alphas=ui_settings['surface_alphas'],
timeout_s=5)
if all((k in ui_settings)
for k in ('df_canvas_corners', 'df_frame_corners')):
if default_corners:
hub_execute(self.name,
'set_default_corners',
canvas=ui_settings['df_canvas_corners'],
frame=ui_settings['df_frame_corners'],
timeout_s=5)
else:
hub_execute(self.name,
'set_corners',
df_canvas_corners=ui_settings['df_canvas_corners'],
df_frame_corners=ui_settings['df_frame_corners'],
timeout_s=5)
# #########################################################################
# # Plugin signal handlers
def on_plugin_disable(self):
self._gui_enabled = False
self.cleanup()
def on_plugin_enable(self):
super(DmfDeviceUiPlugin, self).on_plugin_enable()
self.reset_gui()
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 __init__(self):
self.control_board = OpenDropBoard()
self.name = get_plugin_info(path(__file__).parent).plugin_name
self.connection_status = "Not connected"
self.current_frequency = None
self.timeout_id = None
class DropletPlanningPlugin(Plugin, StepOptionsController, pmh.BaseMqttReactor):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = get_plugin_info(path(__file__).parent).version
plugin_name = get_plugin_info(path(__file__).parent).plugin_name
'''
StepFields
---------
A flatland Form specifying the per step options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed StepOptionsController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the protocol grid view
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently for each step
'''
StepFields = Form.of(
Integer.named('trail_length').using(default=1, optional=True,
validators=
[ValueAtLeast(minimum=1)]),
Integer.named('route_repeats').using(default=1, optional=True,
validators=
[ValueAtLeast(minimum=1)]),
Integer.named('repeat_duration_s').using(default=0, optional=True),
Integer.named('transition_duration_ms')
.using(optional=True, default=750,
validators=[ValueAtLeast(minimum=0)]))
def __init__(self,*args, **kwargs):
self.name = self.plugin_name
self.step_start_time = None
self.route_controller = None
pmh.BaseMqttReactor.__init__(self)
self.start()
def get_schedule_requests(self, function_name):
"""
Returns a list of scheduling requests (i.e., ScheduleRequest instances)
for the function specified by function_name.
"""
if function_name in ['on_step_run']:
# Execute `on_step_run` before control board.
return [ScheduleRequest(self.name, 'dmf_control_board_plugin')]
return []
def on_connect(self, client, userdata, flags, rc):
self.mqtt_client.subscribe("microdrop/dmf-device-ui/add-route")
self.mqtt_client.subscribe("microdrop/dmf-device-ui/get-routes")
self.mqtt_client.subscribe("microdrop/dmf-device-ui/clear-routes")
self.mqtt_client.subscribe('microdrop/dmf-device-ui/execute-routes')
self.mqtt_client.subscribe('microdrop/dmf-device-ui/update-protocol')
self.mqtt_client.subscribe("microdrop/mqtt-plugin/step-inserted")
def on_message(self, client, userdata, msg):
'''
Callback for when a ``PUBLISH`` message is received from the broker.
'''
logger.info('[on_message] %s: "%s"', msg.topic, msg.payload)
if msg.topic == 'microdrop/dmf-device-ui/add-route':
self.add_route(json.loads(msg.payload))
self.get_routes()
if msg.topic == 'microdrop/dmf-device-ui/get-routes':
self.get_routes()
if msg.topic == 'microdrop/dmf-device-ui/clear-routes':
data = json.loads(msg.payload)
if data:
self.clear_routes(electrode_id=data['electrode_id'])
else:
self.clear_routes()
if msg.topic == 'microdrop/dmf-device-ui/execute-routes':
self.execute_routes(json.loads(msg.payload))
if msg.topic == 'microdrop/dmf-device-ui/update-protocol':
self.update_protocol(json.loads(msg.payload))
if msg.topic == "microdrop/mqtt-plugin/step-inserted":
self.step_inserted(json.loads(msg.payload))
def on_plugin_enable(self):
self.route_controller = RouteController(self)
form = flatlandToDict(self.StepFields)
self.mqtt_client.publish('microdrop/droplet-planning-plugin/schema',
json.dumps(form),
retain=True)
defaults = {}
for k,v in form.iteritems():
defaults[k] = v['default']
self.mqtt_client.publish('microdrop/droplet-planning-plugin/step-options',
json.dumps([defaults], cls=PandasJsonEncoder),
retain=True)
def on_plugin_disable(self):
"""
Handler called once the plugin instance is disabled.
"""
pass
def on_app_exit(self):
"""
Handler called just before the Microdrop application exits.
"""
pass
###########################################################################
# Step event handler methods
def on_error(self, *args):
logger.error('Error executing routes.', exc_info=True)
# An error occurred while initializing Analyst remote control.
emit_signal('on_step_complete', [self.name, 'Fail'])
def on_protocol_pause(self):
self.kill_running_step()
def kill_running_step(self):
# Stop execution of any routes that are currently running.
if self.route_controller is not None:
self.route_controller.reset()
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 on_step_routes_complete(self, start_time, electrode_ids):
'''
Callback function executed when all concurrent routes for a step have
completed a single run.
If repeats are requested, either through repeat counts or a repeat
duration, *cycle* routes (i.e., routes that terminate at the start
electrode) will repeat as necessary.
'''
step_options = self.get_step_options()
step_duration_s = (datetime.now() -
self.step_start_time).total_seconds()
if ((step_options['repeat_duration_s'] > 0 and step_duration_s <
step_options['repeat_duration_s']) or
(self.repeat_i + 1 < step_options['route_repeats'])):
# Either repeat duration has not been met, or the specified number
# of repetitions has not been met. Execute another iteration of
# the routes.
self.repeat_i += 1
df_routes = self.get_routes()
self.route_controller.execute_routes(
df_routes, step_options['transition_duration_ms'],
trail_length=step_options['trail_length'],
cyclic=True, acyclic=False,
on_complete=self.on_step_routes_complete,
on_error=self.on_error)
else:
logger.info('Completed routes (%s repeats in %ss)', self.repeat_i +
1, si_format(step_duration_s))
# Transitions along all droplet routes have been processed.
# Signal step has completed and reset plugin step state.
emit_signal('on_step_complete', [self.name, None])
def on_step_options_swapped(self, plugin, old_step_number, step_number):
"""
Handler called when the step options are changed for a particular
plugin. This will, for example, allow for GUI elements to be
updated based on step specified.
Parameters:
plugin : plugin instance for which the step options changed
step_number : step number that the options changed for
"""
logger.info('[on_step_swapped] old step=%s, step=%s', old_step_number,
step_number)
self.kill_running_step()
def on_step_removed(self, step_number, step):
self.update_steps()
def on_step_options_changed(self, plugin, step_number):
self.update_steps()
def on_step_swapped(self, old_step_number, step_number):
"""
Handler called when the current step is swapped.
"""
logger.info('[on_step_swapped] old step=%s, step=%s', old_step_number,
step_number)
self.kill_running_step()
self.get_routes()
def on_step_inserted(self, step_number, *args):
self.step_inserted(step_number)
def step_inserted(self, step_number):
app = get_app()
logger.info('[on_step_inserted] current step=%s, created step=%s',
app.protocol.current_step_number, step_number)
self.clear_routes(step_number=step_number)
###########################################################################
# Step options dependent methods
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 add_route(self, electrode_ids):
'''
Add droplet route.
Args:
electrode_ids (list) : Ordered list of identifiers of electrodes on
route.
'''
drop_routes = self.get_routes()
route_i = (drop_routes.route_i.max() + 1
if drop_routes.shape[0] > 0 else 0)
drop_route = (pd.DataFrame(electrode_ids, columns=['electrode_i'])
.reset_index().rename(columns={'index': 'transition_i'}))
drop_route.insert(0, 'route_i', route_i)
drop_routes = drop_routes.append(drop_route, ignore_index=True)
self.set_routes(drop_routes)
return {'route_i': route_i, 'drop_routes': drop_routes}
def clear_routes(self, electrode_id=None, step_number=None):
'''
Clear all drop routes for protocol step that include the specified
electrode (identified by string identifier).
'''
step_options = self.get_step_options(step_number)
if electrode_id is None:
# No electrode identifier specified. Clear all step routes.
df_routes = RouteController.default_routes()
else:
df_routes = step_options['drop_routes']
# Find indexes of all routes that include electrode.
routes_to_clear = df_routes.loc[df_routes.electrode_i ==
electrode_id, 'route_i']
# Remove all routes that include electrode.
df_routes = df_routes.loc[~df_routes.route_i
.isin(routes_to_clear.tolist())].copy()
step_options['drop_routes'] = df_routes
self.set_step_values(step_options, step_number=step_number)
self.get_routes()
def get_routes(self, step_number=None):
step_options = self.get_step_options(step_number=step_number)
x = step_options.get('drop_routes',
RouteController.default_routes())
msg = json.dumps(x, cls=PandasJsonEncoder)
self.mqtt_client.publish('microdrop/droplet-planning-plugin/routes-set',
msg, retain=True)
return x
def execute_routes(self, data):
# TODO allow for passing of both electrode_id and route_i
# Currently electrode_id only
try:
df_routes = self.get_routes()
step_options = self.get_step_options()
if 'transition_duration_ms' in data:
transition_duration_ms = data['transition_duration_ms']
else:
transition_duration_ms = step_options['transition_duration_ms']
if 'trail_length' in data:
trail_length = data['trail_length']
else:
trail_length = step_options['trail_length']
if 'route_i' in data:
df_routes = df_routes.loc[df_routes.route_i == data['route_i']]
elif 'electrode_i' in data:
if data['electrode_i'] is not None:
routes_to_execute = df_routes.loc[df_routes.electrode_i ==
data['electrode_i'],
'route_i']
df_routes = df_routes.loc[df_routes.route_i
.isin(routes_to_execute
.tolist())].copy()
route_controller = RouteController(self)
route_controller.execute_routes(df_routes, transition_duration_ms,
trail_length=trail_length)
except:
logger.error(str(data), exc_info=True)
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 set_routes(self, df_routes, step_number=None):
step_options = self.get_step_options(step_number=step_number)
step_options['drop_routes'] = df_routes
self.set_step_values(step_options, step_number=step_number)
class TestPlugin(Plugin, AppDataController, StepOptionsController):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = get_plugin_info(path(__file__).parent).version
plugins_name = get_plugin_info(path(__file__).parent).plugin_name
'''
AppFields
---------
A flatland Form specifying application options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed AppDataController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the app options dialog
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently in the microdrop
config file, in a section named after this plugin's name attribute
'''
serial_ports_ = [port for port in serial_device.get_serial_ports()]
if len(serial_ports_):
default_port_ = serial_ports_[0]
else:
default_port_ = None
AppFields = Form.of(
Enum.named('serial_port').using(default=default_port_, optional=True)\
.valued(*serial_ports_),
)
'''
StepFields
---------
A flatland Form specifying the per step options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed StepOptionsController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the protocol grid view
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently for each step
'''
StepFields = Form.of(
Boolean.named('led_on').using(default=False, optional=True), )
def __init__(self):
self.name = self.plugins_name
self.proxy = None
def on_plugin_enable(self):
# We need to call AppDataController's on_plugin_enable() to update the
# application options data.
AppDataController.on_plugin_enable(self)
self.on_app_init()
app_values = self.get_app_values()
try:
self.proxy = SerialProxy(port=app_values['serial_port'])
self.proxy.pin_mode(pin=13, mode=1)
logger.info('Connected to %s on port %s',
self.proxy.properties.display_name,
app_values['serial_port'])
except Exception, e:
logger.error('Could not connect to base-node-rpc on port %s: %s.',
app_values['serial_port'], e)
if get_app().protocol:
pgc = get_service_instance(ProtocolGridController, env='microdrop')
pgc.update_grid()
class ElectrodeControllerPlugin(Plugin, AppDataController,
StepOptionsController):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = get_plugin_info(path(__file__).parent).version
plugin_name = get_plugin_info(path(__file__).parent).plugin_name
'''
AppFields
---------
A flatland Form specifying application options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed AppDataController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the app options dialog
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently in the microdrop
config file, in a section named after this plugin's name attribute
'''
AppFields = Form.of(
String.named('hub_uri').using(optional=True,
default='tcp://localhost:31000'),
)
def __init__(self):
self.name = self.plugin_name
self.plugin = None
self.plugin_timeout_id = None
def get_schedule_requests(self, function_name):
"""
Returns a list of scheduling requests (i.e., ScheduleRequest
instances) for the function specified by function_name.
"""
if function_name == 'on_plugin_enable':
return [ScheduleRequest('wheelerlab.zmq_hub_plugin', self.name)]
else:
return []
def on_plugin_enable(self):
"""
Handler called once the plugin instance is enabled.
Note: if you inherit your plugin from AppDataController and don't
implement this handler, by default, it will automatically load all
app options from the config file. If you decide to overide the
default handler, you should call:
AppDataController.on_plugin_enable(self)
to retain this functionality.
"""
super(ElectrodeControllerPlugin, self).on_plugin_enable()
app_values = self.get_app_values()
self.cleanup()
self.plugin = ElectrodeControllerZmqPlugin(self, self.name,
app_values['hub_uri'])
# Initialize sockets.
self.plugin.reset()
self.plugin_timeout_id = gobject.timeout_add(10,
self.plugin.check_sockets)
def cleanup(self):
if self.plugin_timeout_id is not None:
gobject.source_remove(self.plugin_timeout_id)
if self.plugin is not None:
self.plugin = None
def on_plugin_disable(self):
"""
Handler called once the plugin instance is disabled.
"""
self.cleanup()
def on_app_exit(self):
"""
Handler called just before the Microdrop application exits.
"""
self.cleanup()
def on_step_swapped(self, old_step_number, step_number):
if self.plugin is not None:
self.plugin.execute_async('wheelerlab.electrode_controller_plugin',
'get_channel_states')
class DropBotDxPlugin(Plugin, StepOptionsController, AppDataController):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
implements(IWaveformGenerator)
serial_ports_ = [port for port in get_serial_ports()]
if len(serial_ports_):
default_port_ = serial_ports_[0]
else:
default_port_ = None
AppFields = Form.of(
Enum.named('serial_port').using(default=default_port_,
optional=True).valued(*serial_ports_),
Float.named('default_duration').using(default=1000, optional=True),
Float.named('default_voltage').using(default=80, optional=True),
Float.named('default_frequency').using(default=10e3, optional=True),
)
version = get_plugin_info(path(__file__).parent).version
@property
def StepFields(self):
"""
Expose StepFields as a property to avoid breaking code that accesses
the StepFields member (vs through the get_step_form_class method).
"""
return self.get_step_form_class()
def __init__(self):
self.control_board = None
self.name = get_plugin_info(path(__file__).parent).plugin_name
self.connection_status = "Not connected"
self.current_frequency = None
self.timeout_id = None
self.channel_states = pd.Series()
self.plugin = None
self.plugin_timeout_id = None
def get_step_form_class(self):
"""
Override to set default values based on their corresponding app options.
"""
app = get_app()
app_values = self.get_app_values()
return Form.of(
Integer.named('duration').using(
default=app_values['default_duration'],
optional=True,
validators=[
ValueAtLeast(minimum=0),
]),
Float.named('voltage').using(
default=app_values['default_voltage'],
optional=True,
validators=[ValueAtLeast(minimum=0), max_voltage]),
Float.named('frequency').using(
default=app_values['default_frequency'],
optional=True,
validators=[ValueAtLeast(minimum=0), check_frequency]),
)
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 cleanup_plugin(self):
if self.plugin_timeout_id is not None:
gobject.source_remove(self.plugin_timeout_id)
if self.plugin is not None:
self.plugin = None
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()
def on_plugin_disable(self):
self.cleanup_plugin()
if get_app().protocol:
self.on_step_run()
self._update_protocol_grid()
def on_app_exit(self):
"""
Handler called just before the Microdrop application exits.
"""
self.cleanup_plugin()
try:
self.control_board.hv_output_enabled = False
except: # ignore any exceptions (e.g., if the board is not connected)
pass
def on_protocol_swapped(self, old_protocol, protocol):
self._update_protocol_grid()
def _update_protocol_grid(self):
pgc = get_service_instance(ProtocolGridController, env='microdrop')
if pgc.enabled_fields:
pgc.update_grid()
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:
for k, v in app_values.items():
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 and not app.realtime_mode
and not app.running):
logger.info('Turning off all electrodes.')
self.control_board.hv_output_enabled = False
def connect(self):
"""
Try to connect to the control board at the default serial port selected
in the Microdrop application options.
If unsuccessful, try to connect to the control board on any available
serial port, one-by-one.
"""
self.current_frequency = None
if len(DropBotDxPlugin.serial_ports_):
app_values = self.get_app_values()
# try to connect to the last successful port
try:
self.control_board = SerialProxy(
port=str(app_values['serial_port']))
except:
logger.warning(
'Could not connect to control board on port %s.'
' Checking other ports...',
app_values['serial_port'],
exc_info=True)
self.control_board = SerialProxy()
self.control_board.initialize_switching_boards()
app_values['serial_port'] = self.control_board.port
self.set_app_values(app_values)
else:
raise Exception("No serial ports available.")
def check_device_name_and_version(self):
"""
Check to see if:
a) The connected device is a OpenDrop
b) The device firmware matches the host driver API version
In the case where the device firmware version does not match, display a
dialog offering to flash the device with the firmware version that
matches the host driver API version.
"""
try:
self.connect()
name = self.control_board.properties['package_name']
if name != self.control_board.host_package_name:
raise Exception("Device is not a DropBot DX")
host_software_version = self.control_board.host_software_version
remote_software_version = self.control_board.remote_software_version
# Reflash the firmware if it is not the right version.
if host_software_version != remote_software_version:
response = yesno(
"The DropBot DX firmware version (%s) "
"does not match the driver version (%s). "
"Update firmware?" %
(remote_software_version, host_software_version))
if response == gtk.RESPONSE_YES:
self.on_flash_firmware()
except Exception, why:
logger.warning("%s" % why)
self.update_connection_status()
class DropletPlanningPlugin(Plugin, StepOptionsController):
"""
This class is automatically registered with the PluginManager.
.. versionchanged:: 2.4
Refactor to implement the `IElectrodeMutator` interface, which
delegates route execution to the
``microdrop.electrode_controller_plugin``.
.. versionchanged:: 2.5.2
Explicitly set human-readable title for ``repeat_duration_s`` step
field to ``"Repeat duration (s)"``.
"""
implements(IPlugin)
implements(IElectrodeMutator)
version = get_plugin_info(path(__file__).parent).version
plugin_name = get_plugin_info(path(__file__).parent).plugin_name
'''
StepFields
---------
A flatland Form specifying the per step options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed StepOptionsController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the protocol grid view
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently for each step
'''
StepFields = Form.of(
Integer.named('trail_length').using(
default=1, optional=True, validators=[ValueAtLeast(minimum=1)]),
Integer.named('route_repeats').using(
default=1, optional=True, validators=[ValueAtLeast(minimum=1)]),
Integer.named('repeat_duration_s').using(
default=0,
optional=True,
properties={'title': 'Repeat '
'duration (s)'}))
def __init__(self):
self.name = self.plugin_name
self._electrode_states = iter([])
self.plugin = None
self.executor = ThreadPoolExecutor(max_workers=1)
self._plugin_monitor_task = None
def get_schedule_requests(self, function_name):
"""
.. versionchanged:: 2.5
Enable _after_ command plugin and zmq hub to ensure command can be
registered.
.. versionchanged:: 2.5.3
Remove scheduling requests for deprecated `on_step_run()` method.
"""
if function_name == 'on_plugin_enable':
return [
ScheduleRequest('microdrop.zmq_hub_plugin', self.name),
ScheduleRequest('microdrop.command_plugin', self.name)
]
return []
def on_plugin_enable(self):
'''
.. versionchanged:: 2.5
- Use `zmq_plugin.plugin.watch_plugin()` to monitor ZeroMQ
interface in background thread.
- Register `clear_routes` commands with ``microdrop.command_plugin``.
'''
self.cleanup()
self.plugin = RouteControllerZmqPlugin(self, self.name, get_hub_uri())
self._plugin_monitor_task = watch_plugin(self.executor, self.plugin)
hub_execute_async('microdrop.command_plugin',
'register_command',
command_name='clear_routes',
namespace='global',
plugin_name=self.name,
title='Clear all r_outes')
hub_execute_async('microdrop.command_plugin',
'register_command',
command_name='clear_routes',
namespace='electrode',
plugin_name=self.name,
title='Clear electrode '
'_routes')
def on_plugin_disable(self):
"""
Handler called once the plugin instance is disabled.
"""
self.cleanup()
def on_app_exit(self):
"""
Handler called just before the Microdrop application exits.
"""
self.cleanup()
def cleanup(self):
if self.plugin is not None:
self.plugin = None
if self._plugin_monitor_task is not None:
self._plugin_monitor_task.cancel()
###########################################################################
# Step event handler methods
def get_electrode_states_request(self):
try:
return self._electrode_states.next()
except StopIteration:
return None
def on_step_options_swapped(self, plugin, old_step_number, step_number):
"""
Handler called when the step options are changed for a particular
plugin. This will, for example, allow for GUI elements to be
updated based on step specified.
Parameters
----------
plugin : plugin instance for which the step options changed
old_step_number : int
Previous step number.
step_number : int
Current step number that the options changed for.
"""
self.reset_electrode_states_generator()
def on_step_swapped(self, old_step_number, step_number):
"""
Handler called when the current step is swapped.
"""
self.reset_electrode_states_generator()
if self.plugin is not None:
self.plugin.execute_async(self.name, 'get_routes')
def on_step_inserted(self, step_number, *args):
self.clear_routes(step_number=step_number)
self._electrode_states = iter([])
###########################################################################
# Step options dependent methods
def add_route(self, electrode_ids):
'''
Add droplet route.
Args:
electrode_ids (list) : Ordered list of identifiers of electrodes on
route.
'''
drop_routes = self.get_routes()
route_i = (drop_routes.route_i.max() +
1 if drop_routes.shape[0] > 0 else 0)
drop_route = (pd.DataFrame(electrode_ids, columns=[
'electrode_i'
]).reset_index().rename(columns={'index': 'transition_i'}))
drop_route.insert(0, 'route_i', route_i)
drop_routes = drop_routes.append(drop_route, ignore_index=True)
self.set_routes(drop_routes)
return {'route_i': route_i, 'drop_routes': drop_routes}
def clear_routes(self, electrode_id=None, step_number=None):
'''
Clear all drop routes for protocol step that include the specified
electrode (identified by string identifier).
'''
step_options = self.get_step_options(step_number)
if electrode_id is None:
# No electrode identifier specified. Clear all step routes.
df_routes = RouteController.default_routes()
else:
df_routes = step_options['drop_routes']
# Find indexes of all routes that include electrode.
routes_to_clear = df_routes.loc[df_routes.electrode_i ==
electrode_id, 'route_i']
# Remove all routes that include electrode.
df_routes = df_routes.loc[~df_routes.route_i.
isin(routes_to_clear.tolist())].copy()
step_options['drop_routes'] = df_routes
self.set_step_values(step_options, step_number=step_number)
def get_routes(self, step_number=None):
step_options = self.get_step_options(step_number=step_number)
return step_options.get('drop_routes',
RouteController.default_routes())
def set_routes(self, df_routes, step_number=None):
step_options = self.get_step_options(step_number=step_number)
step_options['drop_routes'] = df_routes
self.set_step_values(step_options, step_number=step_number)
def reset_electrode_states_generator(self):
'''
Reset iterator over actuation states of electrodes in routes table.
'''
df_routes = self.get_routes()
step_options = self.get_step_options()
_L().debug('df_routes=%s\nstep_options=%s', df_routes, step_options)
self._electrode_states = \
electrode_states(df_routes,
trail_length=step_options['trail_length'],
repeats=step_options['route_repeats'],
repeat_duration_s=step_options
['repeat_duration_s'])
class ZmqHubPlugin(Plugin, AppDataController):
"""
This class is automatically registered with the PluginManager.
"""
implements(IPlugin)
version = get_plugin_info(path(__file__).parent).version
plugin_name = get_plugin_info(path(__file__).parent).plugin_name
'''
AppFields
---------
A flatland Form specifying application options for the current plugin.
Note that nested Form objects are not supported.
Since we subclassed AppDataController, an API is available to access and
modify these attributes. This API also provides some nice features
automatically:
-all fields listed here will be included in the app options dialog
(unless properties=dict(show_in_gui=False) is used)
-the values of these fields will be stored persistently in the microdrop
config file, in a section named after this plugin's name attribute
'''
AppFields = Form.of(
String.named('hub_uri').using(optional=True, default='tcp://*:31000'),
Enum.named('log_level').using(default='info', optional=True).valued(
'debug', 'info', 'warning', 'error', 'critical'),
)
def __init__(self):
self.name = self.plugin_name
self.hub_process = None
def on_plugin_enable(self):
"""
Handler called once the plugin instance is enabled.
Note: if you inherit your plugin from AppDataController and don't
implement this handler, by default, it will automatically load all
app options from the config file. If you decide to overide the
default handler, you should call:
AppDataController.on_plugin_enable(self)
to retain this functionality.
"""
super(ZmqHubPlugin, self).on_plugin_enable()
app_values = self.get_app_values()
self.hub_process = Process(target=run_hub,
args=(Hub(app_values['hub_uri'], self.name),
getattr(
logging,
app_values['log_level'].upper())))
self.hub_process.daemon = False
self.hub_process.start()
def on_plugin_disable(self):
"""
Handler called once the plugin instance is disabled.
"""
if self.hub_process is not None:
self.hub_process.terminate()
self.hub_process = None
def on_app_exit(self):
"""
Handler called just before the Microdrop application exits.
"""
if self.hub_process is not None:
self.hub_process.terminate()
self.hub_process = None
