def _onTimer(self):
self.last_sample_done = True
d = dict()
values = self.instrument.query_ascii_values('FETC:IMP?')
self.current_bias = float(self.instrument.query('BIAS:VOLT?'))
self.current_frequency = float(self.instrument.query('FREQ?'))
self.current_capacitance = values[0]
measurement_time = time() - self.start_time
d[self.output_channels[0]] = (dict({self.x_units[0] : self.sample_nr,
self.x_units[1] : measurement_time}),
dict({self.y_units[0] : self.current_capacitance,
self.y_units[1] : self.current_frequency,
self.y_units[2] : self.current_bias}))
self.sample_nr += 1
# logger.warning('_onTimer() time: %f, primed timer with: %f, ui: %f, sn: %f',\
# measurement_time,((self.update_interval * float(self.sample_nr)) - measurement_time) * 1000,
# self.update_interval, float(self.sample_nr))
if self.running:
Timer.singleShot(max(0, ((self.update_interval * float(self.sample_nr)) - measurement_time) * 1000), self._onTimer)
self.acquired_data.append(d)
if self.settings_changed:
self.settings_changed = False
self.instrument.write('VOLT ' + str(self.osc_level))
self.instrument.write('BIAS:VOLT ' + str(self.bias))
self.instrument.write('FUNC:IMP ' + str(self.mode))
self.instrument.write('FREQ ' + str(self.frequency))
def start(self):
self.button_label = 'Stop'
self.sample_nr = 1
self.running = True
self.instrument_init()
self.start_time = time()
Timer.singleShot(self.update_interval * 1000 - 200, self._onTimer)
def _start_stop_video(self):
"""Starts the video playing"""
if self.play_timer is None:
self.play_timer = Timer(500, self._next_frame_looped)
else:
self.play_timer.Stop()
self.play_timer = None
def _on_timer(self):
socks = dict(self.subscriber_poller.poll(POLL_TIMEOUT))
logger.info(socks)
if self.subscriber in socks and socks[self.subscriber] == zmq.POLLIN:
msg = self.subscriber.recv()
self.connect_timeout = 0
logger.info(msg.decode('UTF8'))
if msg.find('NEWCOL') != -1:
self.current_column = ({self.x_units[0]: 0},
{self.y_units[0]: int(msg.strip('NEWCOL '))})
elif msg.find('STOP') != -1:
if self.control_gasmixer:
if self.active_instrument.running is True:
self.active_instrument.start_stop = True
elif msg.find('START') != -1:
if self.control_gasmixer:
if self.active_instrument.running is False:
self.active_instrument.start_stop = True
else:
self.active_instrument.start_stop = True
self.active_instrument.start_stop = True
logger.info('Starting measurement')
elif msg.find('HEARTBEAT') != -1:
self.state = State.CONNECTED
self.running_label = 'GasMixer ' + State.strings[self.state]
self.timer = Timer.singleShot(0.01, self._on_timer)
return
self.connect_timeout += UPDATE_INTERVAL
if self.connect_timeout > CONNECT_TIMEOUT:
self.state = State.DISCONNECTED
self.running_label = 'GasMixer ' + State.strings[self.state]
self.timer = Timer.singleShot(UPDATE_INTERVAL, self._on_timer)
def _start_timer(self):
"""Called when the user selects "Start Timer" from the menu."""
if self.my_timer is None:
# First call, so create a Timer. It starts automatically.
self.my_timer = Timer(500, self._timer_task)
else:
self.my_timer.Start()
def __init__(self, setchannelName, port, connection, rpiADC):
self.channelName = setchannelName
self.x = ad.ADEvalBC()
self.port = port
self.connection = connection
self.rpiADC = rpiADC
self.wmLockTimer = Timer(1000, self.wmLock2)
self.wmLockTimer.Stop()
def __running_changed(self):
'''
'''
if self._running:
self.start_time = datetime.datetime.now()
self.timer = Timer(1000, self._run_time_update)
else:
self.timer.Stop()
def _reset(self):
if hasattr(self,'_timer'):
self._timer.Stop()
self._create_plot()
self._counter = Counter(self.tagger, self.channels, int(self.seconds_per_point*1e12), self.number_of_points)
self.time = self._counter.getIndex() * 1e-12
self.count_rate = self._counter.getData() / self.seconds_per_point
self._timer = Timer(100, self._refresh_data)
self._timer.Start()
def __init__(self, config, server):
HasTraits.__init__(self)
self.mayavi_view = PlotHead(self, config, server)
self.tail_data = np.zeros((2,3))
self.head_data = np.zeros((2,3))
self.reset = False
self.init_plot()
self.timer = Timer(2000, self.update_plot)
self.timer.Start()
def start(self, tasks):
"""This can be called to start timer and to define unfinished tasks
"""
self.tasks_all = tasks
self.start_time = time.time()
try:
self.timer.Start(1000)
except AttributeError:
self.timer = Timer(1000, self._timer_task)
def start_readout(self, interval=1.):
"""Starts readout process. GUI must be running for this to work...
"""
super(DSCUSBUILog, self).start_readout(interval)
try:
self.log_timer.Start(1000)
except AttributeError:
#self._timer_function()
self.log_timer = Timer(1000, self._log_timer_function)
def start_timer(self, interval=TIMER_INTERVAL):
"""Starts timer process. It updates status of the instrument with the
interval specified, collects data, etc, depending on the defined
update method
"""
self.logger.info('Starting readout.')
try:
self.timer.Start(interval * 1000)
except AttributeError:
self.timer = Timer(interval * 1000, self._update)
def start_readout(self, interval=1.):
"""Starts readout process. GUI must be running for this to work...
"""
try:
self.timer.Start(interval * 1000)
self.timer_fast.Start(self._interval_min * 1000)
except AttributeError:
#self._timer_function()
self.timer = Timer(interval * 1000, self._timer_function)
self.timer_fast = Timer(self._interval_min * 1000,
self._timer_fast_function)
def _watchFolderModeChanged(self):
eagle = self.view
eagle.oldFiles = []
if eagle.watchFolderBool:
if eagle.watchFolder == '' and os.path.isfile(eagle.selectedFile):
eagle.watchFolder = os.path.dirname(eagle.selectedFile)
eagle.oldFiles = self.getPNGFiles()
self.watchFolderTimer = Timer(2000., self.checkForNewFiles)
else:
if self.watchFolderTimer is not None:
self.watchFolderTimer.stop()
self.watchFolderTimer = None
def startTimers(self):
"""This timer object polls the experiment runner regularly polling at any time"""
#stop any previous timers
self.stopTimers()
#start timer
self.connectionTimer = Timer(self.connectionPollFrequency,
self.getStatus)
time.sleep(0.1)
self.statusStringTimer = Timer(self.statusStringFrequency,
self.updateStatusString)
time.sleep(0.1)
self.getCurrentTimer = Timer(self.getCurrentFrequency, self.getCurrent)
"""Menu action function to change logger level """
logger.info("timers started")
class MainWindow(ApplicationWindow):
""" The main application window. """
# The pyface Timer.
my_timer = Any()
# Count each time the timer task executes.
counter = Int
def __init__(self, **traits):
""" Creates a new application window. """
# Base class constructor.
super(MainWindow, self).__init__(**traits)
# Add a menu bar.
self.menu_bar_manager = MenuBarManager(
MenuManager(
Action(name='Start Timer', on_perform=self._start_timer),
Action(name='Stop Timer', on_perform=self._stop_timer),
Action(name='E&xit', on_perform=self.close),
name = '&File',
)
)
return
def _start_timer(self):
"""Called when the user selects "Start Timer" from the menu."""
if self.my_timer is None:
# First call, so create a Timer. It starts automatically.
self.my_timer = Timer(500, self._timer_task)
else:
self.my_timer.Start()
def _stop_timer(self):
"""Called when the user selecte "Stop Timer" from the menu."""
if self.my_timer is not None:
self.my_timer.Stop()
def _timer_task(self):
"""The method run periodically by the timer."""
self.counter += 1
print "counter = %d" % self.counter
def _start_timer(self):
# Start up the timer! We should do this only when the demo actually
# starts and not when the demo object is created.
# FIXME: close timer on exit.
self.timer_controller.view = self.view
self.timer_controller.model_view = self
self.timer = Timer(40, self.timer_controller.onTimer)
def run(self):
MayaviDaemon._viewers.append(self)
mlab.clf()
self.cellsource = self.setup_source(self.cellfname)
self.has_cell, bounds = self._examine_data(source=self.cellsource,
datatype="cell_data",
bounds=zeros((0, 6), 'l'))
self.facesource = self.setup_source(self.facefname)
self.has_face, bounds = self._examine_data(source=self.facesource,
datatype="point_data",
bounds=bounds)
boundsmin = bounds.min(axis=0)
boundsmax = bounds.max(axis=0)
bounds = (boundsmin[0], boundsmax[1], boundsmin[2], boundsmax[3],
boundsmin[4], boundsmax[5])
self.bounds = where(self.bounds == array((None, )), bounds,
self.bounds).astype(float)
self.view_data()
# Poll the lock file.
self.timer = Timer(1000 / self.fps, self.poll_file)
def _on_timer(self):
self.sample_number += 1
data = [self.sample_number, time() - self.start_time]
if self.derivative_resistance_enabled:
self.instrument.write('f2, msg2 = InitiatePulseTest(1)')
response = self.instrument.query('printbuffer(1, {:d}, smua.nvbuffer1)'
.format(self.derivative_resistance_voltage_points))
self.instrument.write('smua.nvbuffer1.clear()')
logger.info(response)
values = [float(n) for n in response.replace(',', '').split()]
filtered_response = savgol_filter(values, self.derivative_resistance_voltage_points, 2, 1,
2*self.derivative_resistance_voltage_span /
(self.derivative_resistance_voltage_points-1))
logger.info(1/filtered_response)
data.append(self.voltage)
data.append(values[self.derivative_resistance_voltage_points/2])
data.append(1/filtered_response[self.derivative_resistance_voltage_points/2])
self.actual_current = values[self.derivative_resistance_voltage_points/2] * 1000
self.actual_voltage = self.voltage
self.dispatch_data(data)
else:
resp = self.instrument.query('print(smua.measure.iv())')
values = [float(f) for f in resp.split()]
data.append(values[1])
data.append(values[0])
data.append(values[1]/values[0])
self.actual_voltage = values[1]
self.actual_current = values[0] * 1000
self.dispatch_data(data)
if self.running:
self.timer = Timer.singleShot(max(((self.sample_number+1) * self.sampling_interval -
(time()-self.start_time))*1000, 0.01),
self._on_timer)
def _create_window(self):
numpoints = 50
low = -5
high = 15.0
x = arange(low, high, (high - low) / numpoints)
container = OverlayPlotContainer(bgcolor="lightgray")
common_index = None
index_range = None
value_range = None
self.animated_plots = []
for i, color in enumerate(COLOR_PALETTE):
if not common_index:
animated_plot = AnimatedPlot(x, jn(i, x), color)
common_index = animated_plot.plot.index
index_range = animated_plot.plot.index_mapper.range
value_range = animated_plot.plot.value_mapper.range
else:
animated_plot = AnimatedPlot(common_index, jn(i, x), color)
animated_plot.plot.index_mapper.range = index_range
animated_plot.plot.value_mapper.range = value_range
container.add(animated_plot.plot)
self.animated_plots.append(animated_plot)
for i, a_plot in enumerate(self.animated_plots):
a_plot.plot.position = [
50 + (i % 3) * (PLOT_SIZE + 50),
50 + (i // 3) * (PLOT_SIZE + 50)
]
self.timer = Timer(100.0, self.onTimer)
self.container = container
return Window(self, -1, component=container)
def _configure_timer(self, event):
"""Creates, replaces, or destroys the autosave timer."""
if self._timer:
self._timer.Stop()
if self.autosave and self.saveObject:
self._timer = Timer(self.autosaveInterval * 1000, self._autosave)
else:
self._timer = None
def _make_play_timer(self):
scene = self.scene
if scene is None or scene.off_screen_rendering:
timer = NoUITimer(self.play_delay*1000, self._play_event)
else:
from pyface.timer.api import Timer
timer = Timer(self.play_delay*1000, self._play_event)
return timer
def __init__(self, num_frames, callable, millisec=40, figure=None, play=True, *args, **kwargs):
HasTraits.__init__(self)
self.delay = millisec
self._last_frame = num_frames - 1
self._callable = callable
if figure is None:
figure = mlab.gcf()
self._figure = figure
self._camera_interpolator = tvtk.CameraInterpolator(interpolation_type='spline')
self._t_keyframes = {}
self.render_to_frame = self._last_frame
self.timer = Timer(millisec, self._on_timer, *args, **kwargs)
if not play:
self.stop = True
self._internal_generator = None
self.current_frame = 0
self.on_trait_change(self._render, "render, current_frame", dispatch="ui")
def __init__(self, **traits):
super(Demo, self).__init__(**traits)
self._create_plot_component()
self.queue = Queue()
self.finish_event = threading.Event()
self.thread = threading.Thread(target=self.get_audio_data)
self.thread.start()
self.timer = Timer(10, self.on_timer)
self.win_func = np.hanning(NUM_SAMPLES + 1)[:NUM_SAMPLES]
class DSCUSBUILog(DSCUSBUI):
"""Same as :class:`.DSCUSBUI` except that it adds a logger facility. It
defines an :attr:`~.DSCUSBUILog.data` that hold the measured data.
Examples
--------
For a display with a logger ...
>>> dsc = DSCUSBUILog()
>>> ok = dsc.configure_traits() %(skip)s
"""
#: this holds the measured data
data = Instance(StructArrayData, ())
log_timer = Any
_data = []
#: set to False to stop writing to :attr:`~.DSCUSBUILog.data`
do_log = Bool(True, desc='whether logging is activated or not')
view = dscusbui_log_view
def _data_default(self):
return StructArrayData(width=420,
height=230,
dtype=[('time', 'float'), ('force', 'float'),
('temperature', 'float')])
def _timer_function(self):
value_temp = super(DSCUSBUILog, self)._timer_function()
if self.do_log and value_temp is not None:
value, temp = value_temp
self._data.append((time.time(), value, temp))
def _log_timer_function(self):
if len(self._data) != 0:
data, self._data = self._data, []
self.data.append(data)
def start_readout(self, interval=1.):
"""Starts readout process. GUI must be running for this to work...
"""
super(DSCUSBUILog, self).start_readout(interval)
try:
self.log_timer.Start(1000)
except AttributeError:
#self._timer_function()
self.log_timer = Timer(1000, self._log_timer_function)
def stop_readout(self):
"""Stops readout process
"""
super(DSCUSBUILog, self).stop_readout()
self.log_timer.Stop()
def start(self):
self.running = True
self.acq_start_time = time()
self.sample_nr = 0
self.instrument = SerialUtil.open(self.selected_device, self.visa_resource)
if self.instrument is None:
self.instrument = None
self.selected_device = ''
self.timer = Timer.singleShot(self.sampling_interval * 1000, self.add_data)
def __init__(self, millisec, callable, *args, **kwargs):
"""Constructor.
**Parameters**
:millisec: int specifying the delay in milliseconds
between calls to the callable.
:callable: callable function to call after the specified
delay.
:\*args: optional arguments to be passed to the callable.
:\*\*kwargs: optional keyword arguments to be passed to the callable.
"""
HasTraits.__init__(self)
self.delay = millisec
self.timer = Timer(millisec, callable, *args, **kwargs)
def main():
fname = 'output.vtk'
data = setup_data(fname)
view_data()
p = Pollster(fname, data)
timer = Timer(1000, p.poll_file)
mayavi2.savedtimerbug = timer
def run(self):
MayaviDaemon._viewers.append(self)
mlab.clf()
bounds = zeros((0, 6), 'l')
self.cellsource = self.setup_source(self.cellfname)
if self.cellsource is not None:
tmp = [out.cell_data.scalars for out in self.cellsource.outputs \
if out.cell_data.scalars is not None]
self.has_cell_scalars = (len(tmp) > 0)
tmp = [out.cell_data.vectors for out in self.cellsource.outputs \
if out.cell_data.vectors is not None]
self.has_cell_vectors = (len(tmp) > 0)
tmp = [out.cell_data.tensors for out in self.cellsource.outputs \
if out.cell_data.tensors is not None]
self.has_cell_tensors = (len(tmp) > 0)
bounds = concatenate((bounds,
[out.bounds for out in self.cellsource.outputs]),
axis=0)
self.facesource = self.setup_source(self.facefname)
if self.facesource is not None:
tmp = [out.point_data.scalars for out in self.facesource.outputs \
if out.point_data.scalars is not None]
self.has_face_scalars = (len(tmp) > 0)
tmp = [out.point_data.vectors for out in self.facesource.outputs \
if out.point_data.vectors is not None]
self.has_face_vectors = (len(tmp) > 0)
tmp = [out.point_data.tensors for out in self.facesource.outputs \
if out.point_data.tensors is not None]
self.has_face_tensors = (len(tmp) > 0)
bounds = concatenate((bounds,
[out.bounds for out in self.facesource.outputs]),
axis=0)
boundsmin = bounds.min(axis=0)
boundsmax = bounds.max(axis=0)
bounds = (boundsmin[0], boundsmax[1],
boundsmin[2], boundsmax[3],
boundsmin[4], boundsmax[5])
self.bounds = where(self.bounds == array((None,)),
bounds,
self.bounds).astype(float)
self.view_data()
# Poll the lock file.
self.timer = Timer(1000 / self.fps, self.poll_file)
def start(self):
self.button_label = "Stop"
self.sample_nr = 0
self.running = True
self.instrument_init()
self.start_time = time()
self.bias_table_current_row = 0
self._row_changed(0)
if self.timer is None:
self.timer = Timer(self.update_interval * 1000, self._onTimer)
else:
self.timer.Start(self.update_interval * 1000)
def start(self):
self.running = True
self.acq_start_time = time()
self.sample_nr = 0
self.instrument = SerialUtil.open(self.selected_device, self.visa_resource)
self.instrument_init()
if self.instrument is None:
# GenericPopupMessage(message ='Error opening ' + new).edit_traits()
self.instrument = None
self.selected_device = ''
self.timer = Timer.singleShot(self.sampling_interval * 1000, self.add_data)
def _start_timer(self, project):
"""
Resets the timer to work on auto-saving the current project.
"""
if self.timer is None:
if self.autosave_interval > 0:
# Timer needs the interval in millisecs
self.timer = Timer(self.autosave_interval * 60000,
self._auto_save, project)
return
def _autoRefresh_dialog(self):
"""when user clicks autorefresh in the menu this function calls the dialog
after user hits ok, it makes the choices of how to setup or stop the timer"""
logger.info("auto refresh dialog called")
if self.autoRefreshDialog is None:
self.autoRefreshDialog = plotObjects.autoRefreshDialog.AutoRefreshDialog(
)
self.autoRefreshDialog.configure_traits()
logger.info("dialog edit traits finished")
if self.autoRefreshDialog.autoRefreshBool:
if self.autoRefreshTimer is not None:
self.autoRefreshTimer.stop()
self.selectedLFP.autoRefreshObject = self.autoRefreshDialog #this gives it all the info it needs
self.autoRefreshTimer = Timer(
self.autoRefreshDialog.minutes * 60.0 * 1000.0,
self.selectedLFP.autoRefresh)
logger.info("started auto refresh timer to autorefresh")
else:
self.selectedLFP.autoRefreshObject = None
logger.info("stopping auto refresh")
if self.autoRefreshTimer is not None:
self.autoRefreshTimer.stop()
def __init__(self, **traits):
if USE_ZMQ is False:
return
super(GasMixerPanel, self).__init__(**traits)
self.context = zmq.Context.instance()
self.subscriber = self.context.socket(zmq.SUB)
self.subscriber.connect('tcp://localhost:5561')
self.subscriber.setsockopt(zmq.SUBSCRIBE, "")
self.subscriber_poller = zmq.Poller()
self.subscriber_poller.register(self.subscriber, zmq.POLLIN)
self.state = State.DISCONNECTED
self.timer = Timer.singleShot(UPDATE_INTERVAL, self._on_timer)
def _portname_changed(self, new):
if new is '':
return
if self.serialport != None:
self.serialport.close()
try:
self.serialport = serial.Serial(self.portname, 115200, timeout = 0.1)
except Exception as e:
logger.error(e)
return
#self.serialport.open()
self.serialport.flushInput()
self.timer = Timer.singleShot(self.sample_interval, self.add_data)
class BrownianMotionVisualization(HasTraits):
scene = Instance(MlabSceneModel, ())
plot = Instance(PipelineBase)
x = Array()
y = Array()
z = Array()
timer = Any()
timer_button = Button()
@on_trait_change('scene.activated')
def create_plot(self):
""" Wait before the scene is activated before trying to add data,
modules, filers into it.
"""
x, y, z = compute_positions()
self.plot = self.scene.mlab.points3d(x, y, z)
def _timer_button_fired(self):
if self.timer is None:
self.timer = Timer(100, self.update_plot)
else:
self.timer.stop()
self.timer = None
def update_plot(self):
""" Recompute the ball positions and redraw
"""
x, y, z = compute_positions()
self.plot.mlab_source.set(x=x, y=y, z=z)
# the layout of the dialog created
view = View(Item('scene', editor=SceneEditor(scene_class=MayaviScene),
height=250, width=300, show_label=False),
Item('timer_button', label = "Start/Stop animation",
show_label = False),
)
def add_data(self):
if not self.running:
return
self.timer = Timer.singleShot(500, self.add_data)
self.response_remainder = self.serial_response[-15:]
self.serial_response = bytearray(self.serialport.inWaiting())
self.serialport.readinto(self.serial_response)
d = self._parse_data(self.response_remainder +self.serial_response)
data_dict = dict()
if self.running is True:
for entry in d:
data_dict[self.output_channels[0]] = entry[0]
data_dict[self.output_channels[1]] = entry[1]
self.acquired_data.append(data_dict)
def start(self):
self.running = True
self.acq_start_time = time()
self.sample_nr = 0
if self.serialport is None:
try:
self.serialport = serial.Serial(self.portname, 57600, timeout = 0.2)
except Exception as e:
logger.error(e)
self.stop()
return
else:
self.serialport.open()
self.serialport.write('a')
self.timer = Timer.singleShot(900, self.add_data)
def add_data(self):
if not self.running:
return
b = bytearray(2)
self.sample_nr += 1
measurement_time = time() - self.acq_start_time
self.serialport.readinto(b)
d = dict()
for i, enabled in enumerate(self.enabled_channels):
d[self.output_channels[i]] = (dict({self.x_units[0]:self.sample_nr,
self.x_units[1]:measurement_time}),\
dict({self.y_units[0]:4.9*((b[0]*256 + b[1])/1024.0)}))
self.timer = Timer.singleShot(max(0, ((float(self.sample_nr)) - measurement_time) * 1000), self.add_data)
self.sensor_output_voltage = 4.9*((b[0]*256 + b[1])/1024.0)
self.acquired_data.append(d)
def main():
# Change this to suit your needs. Edit the file after running this
# script and the pipeline should be updated automatically.
fname = join(mayavi2.get_data_dir(abspath(dirname(__file__))),
'heart.vtk')
data = setup_data(fname)
view_data()
# Poll the file.
p = Pollster(fname, data)
timer = Timer(1000, p.poll_file)
# Keep a reference on the timer
mayavi2.savedtimerbug = timer
def create_mayavi(pipe):
def send_key_callback(widget, event):
"Send the key-presses to the process which created this mayavi viewer."
pipe.send(cPickle.dumps(("KEY_DOWN", widget.GetKeyCode())))
fig = mlab.figure()
fig.scene.interactor.add_observer("KeyPressEvent", send_key_callback)
time.sleep(1)
mayavi_app = Plotter(pipe)
from pyface.timer.api import Timer
from mayavi.scripts import mayavi2
timer = Timer(50, mayavi_app.check_and_process)
mayavi2.savedtimerbug = timer
def start(self):
self.running = True
self.acq_start_time = time()
if self.synced_acqusistion is True:
self.acqusition_task = CallbackTaskSynced()
else:
self.acqusition_task = CallbackTask()
channels = []
for i, enabled in enumerate(self.enabled_channels):
if enabled:
channels.append('ai' + str(i))
self.acqusition_task.setup('/' + self.selected_device,
channels, self.sampling_interval, self)
self.acqusition_task.StartTask()
self.timer = Timer(RENDER_INTERVAL_MS, self.handle_data)
self.timer.start()
def start(self):
self.running = True
self.acq_start_time = time()
self.sample_nr = 0
if self.serialport is None:
try:
self.serialport = serial.Serial(self.portname, 115200, timeout=0.045)
except Exception as e:
logger.error(e)
self.stop()
return
else:
self.serialport.open()
self.serial_handler = SerialHandler(self.serialport)
self.serial_handler.start()
self.timer = Timer.singleShot(self.sample_interval * 1000, self.add_data)
def __init__(self, Xmean, tris, components):
HasTraits.__init__(self)
self._components = components
self._max_component_index = len(components)
self._Xmean = Xmean
self.pd = tvtk.PolyData(points=Xmean, polys=tris)
self.pd.point_data.normals = compute_normals(
self.pd) # compute normals once for rest-shape (faster)
self.actor = tvtk.Actor(mapper=tvtk.PolyDataMapper(
input=self.pd, immediate_mode_rendering=True))
self.actor.mapper.lookup_table = tvtk.LookupTable(
hue_range=(0.45, 0.6),
saturation_range=(0., 0.8),
value_range=(.6, 1.),
)
self.scene.add_actor(self.actor)
self.timer = Timer(40, self.animate().next)
def add_data(self):
self.sample_nr += 1
measurement_time = time() - self.acq_start_time
if not self.running:
return
(nox_ppm, lambda_linear, oxygen_millivolt) = self._poll_queue()
self.serial_out = str(nox_ppm)
dict_data = dict()
for i, enabled in enumerate(self.enabled_channels):
dict_data[
self.output_channels[i]] = (
dict(
{self.x_units[0]: self.sample_nr, self.x_units[1]: measurement_time}),
dict({self.y_units[0]: nox_ppm}))
self.acquired_data.append(dict_data)
self.timer = Timer.singleShot(max(0, (self.sample_interval * self.sample_nr -
(time() - self.acq_start_time))*1000), self.add_data)
def _connect_fired(self):
if self.serial_handler is None:
self.serial_handler = SerialHandler(self.set_parameters_queue, self.get_parameters_queue,
self.selected_com_port)
if not self.serial_handler.open_port():
return
self.poll_timer = Timer(POLL_INTERVAL, self._poll_queue)
self.serial_handler.start()
self.connected = True
else:
self.start_stop(False)
self.serial_handler.exit_flag = True
self.serial_handler.join()
self.serial_handler = None
if self.poll_timer is not None:
self.poll_timer.stop()
self.connected = False
def __init__(self, Xmean, tris, components):
HasTraits.__init__(self)
self._components = components
self._max_component_index = len(components)
self._Xmean = Xmean
self.pd = tvtk.PolyData(points=Xmean, polys=tris)
self.normals = tvtk.PolyDataNormals(splitting=False)
configure_input_data(self.normals, self.pd)
mapper = tvtk.PolyDataMapper(immediate_mode_rendering=True)
self.actor = tvtk.Actor(mapper=mapper)
configure_input(self.actor.mapper, self.normals)
self.actor.mapper.lookup_table = tvtk.LookupTable(
hue_range=(0.45, 0.6),
saturation_range=(0., 0.8),
value_range=(.6, 1.),
)
self.scene.add_actor(self.actor)
self.timer = Timer(40, self.animate().next)
def start(self):
if self.timer is None:
self.timer = Timer(self.update_interval * 1000, self._onTimer)
else:
self.timer.Start(self.update_interval * 1000)
self.button_label = "Stop"
self.current_voltage = self.start_voltage
self.current_frequency = self.start_frequency
self.iteration = 0
self.running = True
self.bias = random.random_sample() - 0.5
self.measurement_info = {
"name": self.sweep_name,
"start_voltage": self.start_voltage,
"start_frequency": self.start_frequency,
"start_bias": self.bias,
}
if len(self.measurement_info["name"]) is 0:
self.measurement_info.pop("name")
def add_data(self):
if not self.running:
return
self.sample_nr += 1
try:
data = self.instrument.query('READ?')
except visa.VisaIOError:
data = self.acq_value
pass
self.acq_value = float(data)
logger.info(data)
self.measurement_time = time() - self.acq_start_time
d = dict()
for i, enabled in enumerate(self.enabled_channels):
d[self.output_channels[i]] = (dict({self.x_units[0]:self.sample_nr,
self.x_units[1]:self.measurement_time}),\
self._fix_output_dict(self.acq_value))
self.timer = Timer.singleShot(max(0,
((float(self.sample_nr) * self.sampling_interval) - self.measurement_time) * 1000),
self.add_data)
self.acquired_data.append(d)
def _set_parameters_fired(self):
enter = '\r\n'
if self.serialport.isOpen():
self.serialport.flushOutput()
self.serialport.read(self.serialport.inWaiting())
self.timer = None
self.serialport.write('A')
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(self.temperature) + enter)
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(0) + enter)
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(self.samples_per_sec) + enter)
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(self.max_cur_drain1) + enter)
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(self.min_cur_drain1) + enter)
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(self.max_cur_drain2) + enter)
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(self.min_cur_drain2) + enter)
sleep(0.1)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
self.serialport.write(str(0) + enter)
sleep(0.1)
# sleep(0.2)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
sleep(0.1)
self.serialport.write(enter)
logger.debug(bytearray(self.serialport.read(self.serialport.inWaiting())))
sleep(0.1)
self.timer = Timer.singleShot(500, self.add_data)
class PhysiologyController(Controller):
buffer_ = Any
iface_physiology = Any
buffer_raw = Any
buffer_proc = Any
buffer_ts = Any
buffer_ttl = Any
physiology_ttl_pipeline = Any
buffer_spikes = List(Any)
state = Enum('master', 'client')
process = Instance('tdt.DSPProject')
timer = Instance(Timer)
parent = Any
shell_variables = Dict
# These define what variables will be available in the Python shell. Right
# now we can't add various stuff such as the data and interface classes
# because they have not been created yet. I'm not sure how we can update
# the Python shell with new instances once the experiment has started
# running.
def _shell_variables_default(self):
return dict(controller=self, c=self)
def init(self, info):
self.setup_physiology()
self.model = info.object
if self.state == 'master':
self.process.start()
self.iface_physiology.trigger('A', 'high')
self.start()
def close(self, info, is_ok, from_parent=False):
return True
if self.state == 'client':
return from_parent
else:
# The function confirm returns an integer that represents the
# response that the user requested. YES is a constant (also
# imported from the same module as confirm) corresponding to the
# return value of confirm when the user presses the "yes" button on
# the dialog. If any other button (e.g. "no", "abort", etc.) is
# pressed, the return value will be something other than YES and we
# will assume that the user has requested not to quit the
# experiment.
if confirm(info.ui.control, 'OK to stop?') == YES:
self.stop(info)
return True
else:
return False
def setup_physiology(self):
# Load the circuit
circuit = join(get_config('RCX_ROOT'), 'physiology')
self.iface_physiology = self.process.load_circuit(circuit, 'RZ5')
# Initialize the buffers that will be spooling the data
self.buffer_raw = self.iface_physiology.get_buffer('craw',
'r', src_type='float32', dest_type='float32', channels=CHANNELS,
block_size=1048)
self.buffer_filt = self.iface_physiology.get_buffer('cfilt',
'r', src_type='int16', dest_type='float32', channels=CHANNELS,
block_size=1048)
self.buffer_ts = self.iface_physiology.get_buffer('trig/',
'r', src_type='int32', dest_type='int32', block_size=1)
self.buffer_ts_start = self.iface_physiology.get_buffer('trig/',
'r', src_type='int32', dest_type='int32', block_size=1)
self.buffer_ts_end = self.iface_physiology.get_buffer('trig\\',
'r', src_type='int32', dest_type='int32', block_size=1)
self.buffer_ttl = self.iface_physiology.get_buffer('TTL',
'r', src_type='int8', dest_type='int8', block_size=1)
for i in range(CHANNELS):
name = 'spike{}'.format(i+1)
buffer = self.iface_physiology.get_buffer(name, 'r',
block_size=SPIKE_SNIPPET_SIZE+2)
self.buffer_spikes.append(buffer)
@on_trait_change('model.data')
def update_data(self):
# Ensure that the data store has the correct sampling frequency
for i in range(CHANNELS):
data_spikes = self.model.data.spikes
for src, dest in zip(self.buffer_spikes, data_spikes):
dest.fs = src.fs
dest.snippet_size = SPIKE_SNIPPET_SIZE
self.model.data.raw.fs = self.buffer_raw.fs
self.model.data.processed.fs = self.buffer_filt.fs
self.model.data.ts.fs = self.iface_physiology.fs
self.model.data.epoch.fs = self.iface_physiology.fs
self.model.data.sweep.fs = self.buffer_ttl.fs
# Setup the pipeline
targets = [self.model.data.sweep]
self.physiology_ttl_pipeline = deinterleave_bits(targets)
def start(self):
self.timer = Timer(100, self.monitor_physiology)
def stop(self):
self.timer.stop()
self.process.stop()
def monitor_physiology(self):
# Acquire raw physiology data
waveform = self.buffer_raw.read()
self.model.data.raw.send(waveform)
# Acquire filtered physiology data
waveform = self.buffer_filt.read()
self.model.data.processed.send(waveform)
# Acquire sweep data
ttl = self.buffer_ttl.read()
self.physiology_ttl_pipeline.send(ttl)
# Get the timestamps
ts = self.buffer_ts.read().ravel()
self.model.data.ts.send(ts)
ends = self.buffer_ts_end.read().ravel()
starts = self.buffer_ts_start.read(len(ends)).ravel()
self.model.data.epoch.send(zip(starts, ends))
# Get the spikes. Each channel has a separate buffer for the spikes
# detected online. Need to add 2 to the snippet size to compensate for
# the extra samples provided with the snippet (the timestamp and the
# classifier).
snippet_shape = (-1, SPIKE_SNIPPET_SIZE+2)
for i in range(CHANNELS):
data = self.buffer_spikes[i].read().reshape(snippet_shape)
# First sample of each snippet is the timestamp (as a 32 bit
# integer) and last sample is the classifier (also as a 32 bit
# integer). The bits in between should be interpreted as 32-bit
# floating point values.
snip = data[:,1:-1]
ts = data[:,0].view('int32')
cl = data[:,-1].view('int32')
self.model.data.spikes[i].send(snip, ts, cl)
@on_trait_change('model.settings.spike_signs')
def set_spike_signs(self, value):
for ch, sign in enumerate(value):
name = 's_spike{}'.format(ch+1)
self.iface_physiology.set_tag(name, sign)
@on_trait_change('model.settings.spike_thresholds')
def set_spike_thresholds(self, value):
for ch, threshold in enumerate(value):
name = 'a_spike{}'.format(ch+1)
self.iface_physiology.set_tag(name, threshold)
@on_trait_change('model.settings.monitor_fc_highpass')
def set_monitor_fc_highpass(self, value):
self.iface_physiology.set_tag('FiltHP', value)
@on_trait_change('model.settings.monitor_fc_lowpass')
def set_monitor_fc_lowpass(self, value):
self.iface_physiology.set_tag('FiltLP', value)
@on_trait_change('model.settings.monitor_ch_1')
def set_monitor_ch_1(self, value):
self.iface_physiology.set_tag('ch1_out', value)
@on_trait_change('model.settings.monitor_ch_2')
def set_monitor_ch_2(self, value):
self.iface_physiology.set_tag('ch2_out', value)
@on_trait_change('model.settings.monitor_ch_3')
def set_monitor_ch_3(self, value):
self.iface_physiology.set_tag('ch3_out', value)
@on_trait_change('model.settings.monitor_gain_1')
def set_monitor_gain_1(self, value):
self.iface_physiology.set_tag('ch1_out_sf', value*1e3)
@on_trait_change('model.settings.monitor_gain_2')
def set_monitor_gain_2(self, value):
self.iface_physiology.set_tag('ch2_out_sf', value*1e3)
@on_trait_change('model.settings.monitor_gain_3')
def set_monitor_gain_3(self, value):
self.iface_physiology.set_tag('ch3_out_sf', value*1e3)
@on_trait_change('model.settings.diff_matrix')
def set_diff_matrix(self, value):
self.iface_physiology.set_coefficients('diff_map', value.ravel())
def load_settings(self, info):
instance = load_instance(PHYSIOLOGY_ROOT, PHYSIOLOGY_WILDCARD)
if instance is not None:
self.model.settings.copy_traits(instance)
def saveas_settings(self, info):
dump_instance(self.model.settings, PHYSIOLOGY_ROOT, PHYSIOLOGY_WILDCARD)
@on_trait_change('model.channel_mode')
def _channel_mode_changed(self, new):
if new == 'TDT':
offset = 0
elif new =='TBSI':
offset = 1
else:
offset = 2
self.iface_physiology.set_tag('ch_offset', offset*16+1)
class Boonton7200(HasTraits):
name = Unicode("Boonton7200")
measurement_info = Dict()
x_units = Dict({0: "SampleNumber", 1: "Time"})
y_units = Dict({0: "Capacitance"})
acquired_data = List(Dict)
start_stop = Event
running = Bool
output_channels = Dict({0: "cap", 1: "bias"})
enabled_channels = List(Bool)
timer = Instance(Timer)
timer_dormant = Bool(False)
update_interval = Float(0.5)
start_time = Float
# bias = Range(-10.0, 10.0, 0.0)
bias = Float(0.0)
current_capacitance = Float
current_bias = Float
sample_nr = Int(0)
start_stop = Event
button_label = Str("Start")
bias_low_limit = Float(-10.0) # Instrument supports -100V to +100V
bias_high_limit = Float(10.0)
bias_table = List(TableEntry)
bias_table_current_row = Int(0)
bias_table_enable = Bool(False)
stop_meas_after_last_row = Bool(False)
_available_devices_map = Dict(Unicode, Unicode)
selected_device = Str
visa_resource = Instance(visa.ResourceManager, ())
instrument = Instance(visa.Resource)
traits_view = View(
Item(
"selected_device",
label="Device",
editor=EnumEditor(name="_available_devices_map"),
enabled_when="not running",
),
Item("update_interval", enabled_when="not running"),
Item("bias", editor=RangeEditor(is_float=True, low_name="bias_low_limit", high_name="bias_high_limit")),
Group(
Item("current_capacitance", enabled_when="False"),
Item("current_bias", enabled_when="False"),
Item("sample_nr", enabled_when="False"),
label="Measurement",
show_border=True,
),
Group(
Item("bias_table_enable"),
Item("stop_meas_after_last_row"),
Item(
"bias_table",
show_label=False,
# label = 'right-click to edit',
editor=table_editor,
enabled_when="not running and bias_table_enable",
),
show_border=True,
),
Item("start_stop", label="Start/Stop Acqusistion", editor=ButtonEditor(label_value="button_label")),
handler=ViewHandler,
)
def instrument_init(self):
if self.instrument is not None:
self.instrument.write("BI" + str(self.bias))
def instrument_stop(self):
if self.instrument is not None:
pass
def start(self):
self.button_label = "Stop"
self.sample_nr = 0
self.running = True
self.instrument_init()
self.start_time = time()
self.bias_table_current_row = 0
self._row_changed(0)
if self.timer is None:
self.timer = Timer(self.update_interval * 1000, self._onTimer)
else:
self.timer.Start(self.update_interval * 1000)
def stop(self):
if self.timer is not None:
self.timer.Stop()
self.button_label = "Start"
self.running = False
self.timer_dormant = False
self.instrument_stop()
def _onTimer(self):
# self.timer.Stop()
self.timer_dormant = True
d = dict()
values = self.instrument.query_ascii_values("TM")
self.current_capacitance = values[0] * 1e-12
self.current_bias = values[2]
d[self.output_channels[0]] = (
dict({self.x_units[0]: self.sample_nr, self.x_units[1]: time() - self.start_time}),
dict({self.y_units[0]: self.current_capacitance}),
)
d[self.output_channels[1]] = (
dict({self.x_units[0]: self.sample_nr, self.x_units[1]: time() - self.start_time}),
dict({self.y_units[0]: self.bias}),
)
self.sample_nr += 1
# self.timer.Start(self.update_interval * 1000)
self.timer_dormant = False
self.acquired_data.append(d)
if self.bias_table_enable:
if self.bias_table_current_row < len(self.bias_table):
row_time = time() - self.row_start_time
self.bias_table[self.bias_table_current_row].remaining = int(
self.bias_table[self.bias_table_current_row].time - row_time
)
if self.bias_table[self.bias_table_current_row].remaining < 1:
self.bias_table_current_row += 1
self._row_changed(self.bias_table[self.bias_table_current_row - 1].time - row_time)
def _row_changed(self, remainder):
self.row_start_time = time() + remainder
# logging.getLogger(__name__).info('self.row_start_time: %f', self.row_start_time)
if self.bias_table_current_row >= len(self.bias_table):
if self.stop_meas_after_last_row:
self.start_stop = True
return
self.bias = self.bias_table[self.bias_table_current_row].bias
def _start_stop_fired(self):
if self.instrument is None:
return
if self.timer is None:
self.start()
return
if self.timer.isActive() or self.timer_dormant:
self.stop()
else:
self.start()
def _selected_device_changed(self, new):
logger.info("New instrument %s", new)
if self.instrument is not None:
self.instrument.close()
if new is not "":
self.instrument = SerialUtil.open(new, self.visa_resource, command="ID")
if self.instrument is None:
GenericPopupMessage(message="Error opening " + new).edit_traits()
self.instrument = None
self.selected_device = ""
def _selected_device_default(self):
try:
device = self._available_devices_map.items()[0][0]
except IndexError:
return ""
self._selected_device_changed(device)
return device
def _enabled_channels_default(self):
return [True, False]
def _bias_table_default(self):
return [TableEntry(time=10, bias=0.0, remaining=0), TableEntry(time=10, bias=0.5, remaining=0)]
def __available_devices_map_default(self):
try:
instruments_info = self.visa_resource.list_resources_info()
except visa.VisaIOError:
return {}
d = {}
candidates = [n for n in instruments_info.values() if n.resource_name.upper().startswith("GPIB")]
d.update(SerialUtil.probe(candidates, self.visa_resource, INSTRUMENT_IDENTIFIER, command="ID"))
return d
def _bias_changed(self, new):
if self.instrument is not None:
self.instrument.write("BI" + str(new))
def _timer_button_fired(self):
if self.timer is None:
self.timer = Timer(100, self.update_plot)
else:
self.timer.stop()
self.timer = None
class TemperatureControlPanel(HasTraits):
TIMING_UPDATE_INTERVAL = 500.0
pane_name = Str('Temperature control ')
pane_id = Str('sensorscience.unimeas.temperatur_control_pane')
output_channels = Dict({0:'temp_controller'})
y_units = Dict({0 : 'temp'})
enable = Bool(False)
loop_sequence = Bool(True)
poll_timer = Instance(Timer)
timing_timer = Instance(Timer)
table_entries = List(TableEntry)
current_row = Int(0)
current_temp = Float
actual_temp = Float
process_value = Float
adjusted_pv = Float
PID_out = Float
pwm_value = Int
max31865_ctrl = Int
max31865_error = Int
setpoint = Float
supply_voltage = Float
RT_resistance = Float
set_temp = Float
current_time = Float
row_start_time = Float
start_time = Float
running = False
connected = Bool(False)
save_detailed_log = Bool(False)
pid_P = Float(0)
pid_I = Float(0)
pid_D = Float(0)
pid_N = Float(0)
pwm_table_index = Int(0)
use_direct_pwm = Bool(False)
pwm_set_direct = Int(0)
use_direct_pv = Bool(False)
pv_set_direct = Int(0)
temp_setpoint = Float
resistance_setpoint = Float
supply_voltage_setpoint = Float(15.0)
RT_resistance_setpoint = Float(109.71)
temperature_table = Array
selected_com_port = Str
selected_pid_configuration = Str
available_pid_configurations = List(['Normal TO-8', 'M18 ceramic', 'L-A Cap'])
com_ports_list = List(Str)
connect = Button
connect_button_string = Str('Connect')
update_PID_values = Int(0)
set_parameters = Button
update_pid = Button
save = Button
load = Button
filename = File
set_parameters_queue = Instance(Queue.Queue)
get_parameters_queue = Instance(Queue.Queue)
serial_handler = Instance(SerialHandler)
traits_view = View(
HGroup(Item('selected_com_port', label='Com port',
editor=EnumEditor(name='com_ports_list'),
enabled_when='not running'),
Item('connect', editor=ButtonEditor(label_value='connect_button_string'),
show_label=False, enabled_when='selected_com_port != ""')),
Item('enable', label='Enable temp program', enabled_when='connected'),
Item('loop_sequence', label='Loop temperature sequence'),
Group(Item('table_entries', show_label=False, editor=table_editor,
enabled_when='True'
),
HGroup(Item('filename'), spring, Item('save', show_label=False),
Item('load', show_label=False)),
show_border=True,
),
Group(
HGroup(
VGroup(Item('actual_temp', style='readonly', format_str='%.2f'),
Item('process_value', style='readonly', format_str='%.2f'),
Item('adjusted_pv', style='readonly', format_str='%.2f'),
Item('setpoint', style='readonly', format_str='%.2f')),
spring,
VGroup(Item('pwm_value', style='readonly', format_str='%d'),
Item('max31865_ctrl', style='readonly', format_str='%#04x'),
Item('max31865_error', style='readonly', format_str='%#04x')),
spring,
VGroup(Item('PID_out', style='readonly', format_str='%.2f'),
Item('supply_voltage', style='readonly', format_str='%.2f'),
Item('RT_resistance', style='readonly', format_str='%.2f'))),
label='Diagnostic parameters', show_border=True,
),
HGroup(
Group(
VGroup(Item('temp_setpoint', format_str='%.1f')),
VGroup(Item('resistance_setpoint', format_str='%.1f')),
VGroup(Item('supply_voltage_setpoint', format_str='%.1f')),
VGroup(Item('RT_resistance_setpoint', format_str='%.1f')),
Item('set_parameters', enabled_when='connected'),
label='Adjustable parameters', show_border=True,
),
Group(
Item('selected_pid_configuration', label='PID adaption',
editor=EnumEditor(name='available_pid_configurations'),
enabled_when='True'),
VGroup(Item('pid_P', label='PID P', format_str='%.7f')),
VGroup(Item('pid_I', label='PID I', format_str='%.7f')),
VGroup(Item('pid_D', label='PID D', format_str='%.7f')),
VGroup(Item('pid_N', label='PID Nd', format_str='%.7f')),
VGroup(Item('pwm_table_index', label='tbl_idx')),
HGroup(Item('use_direct_pwm'), Item('pwm_set_direct', show_label=False)),
HGroup(Item('use_direct_pv'), Item('pv_set_direct', show_label=False)),
Item('update_pid', enabled_when='connected'),
Item('save_detailed_log', enabled_when='connected'),
label='PID parameters - Don\'t touch', show_border=True,
),
),
resizable=True, kind='live', handler=TemperatureControlHandler
)
def _set_parameters_queue_default(self):
return Queue.Queue(QUEUE_LENGHT)
def _get_parameters_queue_default(self):
return Queue.Queue(QUEUE_LENGHT)
def _temp_setpoint_changed(self, new):
self.resistance_setpoint = temp_to_resistance(new, self.RT_resistance_setpoint)
def _connected_changed(self, new):
if new is True:
self.connect_button_string = 'Disconnect'
self._selected_pid_configuration_changed(self.selected_pid_configuration)
self.update_PID_values = 3
else:
self.connect_button_string = 'Connect'
def _save_detailed_log_changed(self, new):
if new:
self.fh = open('templog_' + strftime("%y%m%d_%H%M%S") + '.csv', 'w')
self.csv_writer = csv.writer(self.fh,quoting=csv.QUOTE_NONNUMERIC)
self.csv_writer.writerow(['pv','pid_out','pwm','max31ctrl','max31err','sp', 'sv','RT_ref','pid_p','pid_i','pid_d','pid_n','time'])
self.log_start_time = time()
else:
self.fh.close()
def _RT_resistance_setpoint_changed(self, new):
self.resistance_setpoint = temp_to_resistance(self.temp_setpoint, new)
def _selected_pid_configuration_changed(self, new):
self.pid_P = PID_configurations[new]['P']
self.pid_I = PID_configurations[new]['I']
self.pid_D = PID_configurations[new]['D']
self.pid_N = PID_configurations[new]['N']
self.pwm_table_index = PID_configurations[new]['pwm_table_index']
def _selected_pid_configuration_default(self):
return 'Normal TO-8'
def _available_pid_configurations_default(self):
return PID_configurations.keys()
def _onTimer(self):
self.current_time = time() - self.start_time
index = int(np.floor(self.current_time))
if index >= len(self.temperature_table):
return
if self.temperature_table[index] is not self.current_temp:
self.current_temp = self.temperature_table[index]
if self.current_row >= len(self.table_entries):
return
time_left = self.table_entries[self.current_row].time + self.row_start_time - self.current_time
self.table_entries[self.current_row].remaining = int(time_left)
if self.table_entries[self.current_row].remaining < 1:
self.current_row += 1
self.row_changed(time_left)
def _poll_queue(self):
while not self.get_parameters_queue.empty():
try:
values = self.get_parameters_queue.get_nowait()
except Queue.Empty:
logger.error('No temp recieved from SerialHandler - Strange')
pass
self.get_parameters_queue.task_done()
self.actual_temp = resistance_to_temp(values[0], values[7])
self.process_value = values[0]
self.adjusted_pv = values[0]*(109.7/values[7])
self.PID_out = values[1]
self.pwm_value = values[2]
self.max31856_ctrl = values[3]
self.max31856_error = values[4]
self.setpoint = values[5]
self.supply_voltage = values[6]
self.RT_resistance = values[7]
if self.update_PID_values > 0:
self.update_PID_values -= 1
self.pid_P = values[8]
self.pid_I = values[9]
self.pid_D = values[10]
self.pid_N = values[11]
if self.save_detailed_log:
self.csv_writer.writerow(values)
def _table_entries_default(self):
return [TableEntry(time = 15, start_temp = 150, end_temp = 150, remaining = -1),
TableEntry(time = 15, start_temp = 350, end_temp = 350, remaining = -1),
TableEntry(time = 15, start_temp = 250, end_temp = 250, remaining = -1)]
# return [TableEntry(time = 700, start_temp = 50, end_temp = 650, remaining = -1),
# TableEntry(time = 200, start_temp = 650, end_temp = 650, remaining = -1),
# TableEntry(time = 1200, start_temp = 650, end_temp = 200, remaining = -1),
# TableEntry(time = 7300, start_temp = 200, end_temp = 200, remaining = -1),
# TableEntry(time = 1200, start_temp = 200, end_temp = 150, remaining = -1),
# TableEntry(time = 1200, start_temp = 150, end_temp = 150, remaining = -1),
# TableEntry(time = 750, start_temp = 150, end_temp = 650, remaining = -1),
# TableEntry(time = 120, start_temp = 650, end_temp = 50, remaining = -1),
# TableEntry(time = 700, start_temp = 50, end_temp = 650, remaining = -1),
# TableEntry(time = 200, start_temp = 650, end_temp = 650, remaining = -1),
# TableEntry(time = 1200, start_temp = 650, end_temp = 300, remaining = -1),
# TableEntry(time = 7300, start_temp = 300, end_temp = 300, remaining = -1),
# TableEntry(time = 1200, start_temp = 300, end_temp = 150, remaining = -1),
# TableEntry(time = 1200, start_temp = 150, end_temp = 150, remaining = -1),
# TableEntry(time = 750, start_temp = 150, end_temp = 650, remaining = -1),
# TableEntry(time = 120, start_temp = 650, end_temp = 50, remaining = -1),
# TableEntry(time = 700, start_temp = 50, end_temp = 650, remaining = -1),
# TableEntry(time = 200, start_temp = 650, end_temp = 650, remaining = -1),
# TableEntry(time = 1200, start_temp = 650, end_temp = 400, remaining = -1),
# TableEntry(time = 7300, start_temp = 400, end_temp = 400, remaining = -1),
# TableEntry(time = 1200, start_temp = 400, end_temp = 150, remaining = -1),
# TableEntry(time = 1200, start_temp = 150, end_temp = 150, remaining = -1),
# TableEntry(time = 750, start_temp = 150, end_temp = 650, remaining = -1),
# TableEntry(time = 120, start_temp = 650, end_temp = 50, remaining = -1),
# TableEntry(time = 700, start_temp = 50, end_temp = 650, remaining = -1),
# TableEntry(time = 200, start_temp = 650, end_temp = 650, remaining = -1),
# TableEntry(time = 1200, start_temp = 650, end_temp = 500, remaining = -1),
# TableEntry(time = 7300, start_temp = 500, end_temp = 500, remaining = -1),
# TableEntry(time = 1200, start_temp = 500, end_temp = 150, remaining = -1),
# TableEntry(time = 1200, start_temp = 150, end_temp = 150, remaining = -1),
# TableEntry(time = 750, start_temp = 150, end_temp = 650, remaining = -1),
# TableEntry(time = 120, start_temp = 650, end_temp = 50, remaining = -1),]
def start_stop(self, running):
if not self.enable:
return
if running:
if self.running:
return
self.start_time = time()
self.calculate_temperature_table()
for row in self.table_entries:
row.remaining = row.time
self.current_time = 0
self.current_row = 0
self.row_changed(time() - self.start_time)
self.current_temp = self.temperature_table[0]
self.timing_timer = Timer(self.TIMING_UPDATE_INTERVAL, self._onTimer)
else:
if not self.running:
return
if self.timing_timer is not None:
self.timing_timer.Stop()
self.running = running
def add_data(self, data):
pass
def get_data(self):
return {'time': 0}, {'temp': self.actual_temp}
def calculate_temperature_table(self):
self.temperature_table = np.array([])
for row in self.table_entries:
self.temperature_table = np.hstack((self.temperature_table,
np.linspace(row.start_temp, row.end_temp, row.time)))
def row_changed(self, remainder):
self.row_start_time = self.current_time + remainder
if self.current_row >= len(self.table_entries):
if self.loop_sequence:
self.start_time = time()
for row in self.table_entries:
row.remaining = row.time
self.current_time = 0
self.current_row = 0
self.row_changed(time() - self.start_time)
def _current_temp_changed(self, new):
self.temp_setpoint = new
if self.use_direct_pwm:
self.pwm_set_direct = int(new)
self._update_pid_fired()
return
self._set_parameters_fired()
def _com_ports_list_default(self):
import serial.tools.list_ports as lp
l = []
for p in lp.grep('Arduino'):
l.append(p[0])
return l
def _set_parameters_fired(self):
self.set_parameters_queue.put_nowait(struct.pack('<c5B5f', 's', 0, 0, 0, 0, self.pwm_table_index,
self.resistance_setpoint, self.supply_voltage_setpoint,
self.RT_resistance_setpoint, 0, 0))
def _update_pid_fired(self):
self.set_parameters_queue.put_nowait(struct.pack('<c4f', 'p', self.pid_P, self.pid_I, self.pid_D, self.pid_N))
self.set_parameters_queue.put_nowait(struct.pack('<c5B5f', 's', 0,
int(self.use_direct_pwm), int(self.use_direct_pv), self.pwm_set_direct, self.pwm_table_index, self.resistance_setpoint,
self.supply_voltage_setpoint, self.RT_resistance_setpoint, 0, self.pv_set_direct))
self.update_PID_values = 3
def _connect_fired(self):
if self.serial_handler is None:
self.serial_handler = SerialHandler(self.set_parameters_queue, self.get_parameters_queue,
self.selected_com_port)
if not self.serial_handler.open_port():
return
self.poll_timer = Timer(POLL_INTERVAL, self._poll_queue)
self.serial_handler.start()
self.connected = True
else:
self.start_stop(False)
self.serial_handler.exit_flag = True
self.serial_handler.join()
self.serial_handler = None
if self.poll_timer is not None:
self.poll_timer.stop()
self.connected = False
def _save_fired(self):
if self.filename is '':
GenericPopupMessage(message='No filename given').edit_traits()
return
filehandle = open(self.filename, "w", 1)
fieldnames = self.table_entries[0].trait_get().keys()
csv_writer = csv.DictWriter(filehandle, fieldnames=fieldnames, delimiter=',',
quotechar='"', quoting=csv.QUOTE_NONNUMERIC,
lineterminator='\n')
csv_writer.writeheader()
for row in self.table_entries:
csv_writer.writerow(row.trait_get())
filehandle.close()
def _load_fired(self):
if self.filename is '':
GenericPopupMessage(message='No filename given').edit_traits()
return
filehandle = open(self.filename, 'rU', 1)
reader = csv.DictReader(filehandle, lineterminator='\n')
self.table_entries = []
for row in reader:
self.table_entries.append(TableEntry(time = int(row['time']),
start_temp=int(row['start_temp']),
end_temp=int(row['end_temp']),
remaining=int(row['time'])))
filehandle.close()
def _set_temp_table_for_calibration(self):
pwms = [int(a) for a in np.hstack((np.linspace(0, 255, 256), np.linspace(255, 0, 256)))]
self.table_entries = [TableEntry(time = 60, start_temp = t, end_temp = t, remaining = -1) for t in pwms]
self.temp_setpoint = self.table_entries[0].start_temp - 1 # Make sure they are unequal
class NI6215(HasTraits):
"""Dummy instrument for generation of values (V, I, R) over time"""
""" 'IInstrument' interface ############################################# """
name = Unicode('NI-DAQmx')
measurement_info = Dict()
x_units = Dict({0:'SampleNumber', 1:'Time'})
y_units = Dict({0: 'Voltage'})
running = Bool(False)
output_channels = Dict({0:'ai00', 1:'ai01', 2:'ai02', 3:'ai03',
4:'ai04', 5:'ai05', 6:'ai06', 7:'ai07',
8:'ai08', 9:'ai09', 10:'ai10', 11:'ai11',
12:'ai12', 13:'ai13', 14:'ai14', 15:'ai15'})
enabled_channels = List(Bool)
CHANNEL_CELL_WIDTH = 25.0
sampling_interval = Range(0.05, 10, 1)
start_stop = Event
refresh_list = Button
ai0 =Bool(False)
ai1 =Bool(False)
ai2 =Bool(False)
ai3 =Bool(False)
ai4 =Bool(False)
ai5 =Bool(False)
ai6 =Bool(False)
ai7 =Bool(False)
ai8 =Bool(False)
ai9 =Bool(False)
ai10 =Bool(False)
ai11 =Bool(False)
ai12 =Bool(False)
ai13 =Bool(False)
ai14 =Bool(False)
ai15 =Bool(False)
button_label = Str('Start')
value_ai0 = Float
value_ai1 = Float
value_ai2 = Float
value_ai3 = Float
synced_acqusistion = Bool(False)
data_acquired = Bool(False)
data = List(Float)
output_unit = 0
timebase = 0
acqusition_task = Instance(Task)
acquired_data = List(Dict)
_available_devices_map = Dict(Unicode, Unicode)
selected_device = Str
parameter_group = Group(Item('sampling_interval', enabled_when='not running'),
show_border=True)
traits_view = View(parameter_group,
HGroup(Label('Device: '), Item('selected_device',
show_label=False,
editor=EnumEditor(name='_available_devices_map'),
enabled_when='not running'),
Item('refresh_list')),
HGroup(Label('Channels:'), spring,
VGroup(
HGroup(
Item('ai0', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai1', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai2', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai3', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH)),
HGroup(
Item('ai4', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai5', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai6', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai7', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH)),
HGroup(
Item('ai8', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai9', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai10', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai11', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH)),
HGroup(
Item('ai12', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai13', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai14', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH),
Item('ai15', enabled_when='not running', springy=True, width=CHANNEL_CELL_WIDTH)))),
HGroup(Item('value_ai0', style='readonly'),
Item('value_ai1', style='readonly'),
Item('value_ai2', style='readonly'),
Item('value_ai3', style='readonly')),
Item('synced_acqusistion', enabled_when='false'),
Item('start_stop', label='Start/Stop Acqusistion',
editor=ButtonEditor(label_value='button_label')),
handler=NI6215Handler)
def __init__(self):
self.logger = logging.getLogger(__name__)
self.on_trait_change(self.channel_changed, 'ai+')
self.ai0 = self.ai1 = self.ai2 = self.ai3 = True
def _enabled_channels_default(self):
return [False] * 16
def __available_devices_map_default(self):
s = str('000000000000000000000000000000000000000000000000000')
PyDAQmx.DAQmxGetSysDevNames(s, len(s))
(a, b, c) = s.partition('\x00')
devs = a.split(', ')
serial = c_uint32(0)
devices=[]
for d in devs:
if len(d) > 0:
PyDAQmx.DAQmxGetDevProductType(d, s, len(s))
(a, b, c) = s.partition('\x00')
if a.startswith('USB-'):
PyDAQmx.DAQmxGetDevSerialNum(d, serial)
devices.append((d, a + ' - ' + hex(serial.value)[2:-1].upper()))
if a.startswith('PCI-'):
PyDAQmx.DAQmxGetDevSerialNum(d, serial)
devices.append((d, a + ' - In computer'))
else:
break
retval = dict((device[0], device[1]) for device in devices)
self.logger.info('_available_devices_map_default %s', retval)
return retval
@on_trait_change('_available_devices_map')
def __available_devices_map_changed(self):
if self.selected_device not in self._available_devices_map.keys():
self.selected_device = self._available_devices_map.items()[0][0]
def _selected_device_default(self):
try:
device = self._available_devices_map.items()[0][0]
except IndexError:
return ''
return device
def _refresh_list_fired(self):
self._available_devices_map = self.__available_devices_map_default()
self.__available_devices_map_changed()
def add_data(self, data):
self.data = data
def handle_data(self):
if self.data_acquired is False:
return
self.data_acquired = False
if len(self.data) < 18:
return
d = dict()
for i, enabled in enumerate(self.enabled_channels):
d[self.output_channels[i]] = (dict({self.x_units[0]:self.data[0], self.x_units[1]:self.data[1], }),
dict({self.y_units[0]:self.data[i + 2]}))
self.acquired_data.append(d)
self.value_ai0 = self.data[2]
self.value_ai1 = self.data[3]
# self.timer = Timer.singleShot(RENDER_INTERVAL_MS, self.add_data)
def start(self):
self.running = True
self.acq_start_time = time()
if self.synced_acqusistion is True:
self.acqusition_task = CallbackTaskSynced()
else:
self.acqusition_task = CallbackTask()
channels = []
for i, enabled in enumerate(self.enabled_channels):
if enabled:
channels.append('ai' + str(i))
self.acqusition_task.setup('/' + self.selected_device,
channels, self.sampling_interval, self)
self.acqusition_task.StartTask()
self.timer = Timer(RENDER_INTERVAL_MS, self.handle_data)
self.timer.start()
def stop(self):
self.logger.info('stop()')
self.running = False
self.acqusition_task.StopTask()
self.acqusition_task.ClearTask()
def _start_stop_fired(self, old, new):
if self.running:
self.button_label = 'Start'
self.stop()
else:
self.button_label = 'Stop'
self.start()
def channel_changed(self, obj, name, new):
self.enabled_channels[int(name[2:])] = new
def start(self):
self.instrument.write('reset()')
self.instrument.write('digio.writeprotect = 0')
self.instrument.write('smua.measure.nplc = 5')
self.instrument.write('smua.measure.autozero = smua.AUTOZERO_ONCE')
self.instrument.write('smua.sense = smua.SENSE_REMOTE')
self.instrument.write('smua.source.autorangei = smua.AUTORANGE_OFF')
self.instrument.write('smua.source.autorangev = smua.AUTORANGE_OFF')
self.instrument.write('smua.measure.autorangei = smua.AUTORANGE_OFF')
self.instrument.write('smua.measure.autorangev = smua.AUTORANGE_OFF')
if self.constant_current_mode:
self.instrument.write('smua.source.func = smua.OUTPUT_DCAMPS')
self.instrument.write('smua.source.limitv = {:f}'.format(self.voltage_limit))
self.instrument.write('smua.source.leveli = {:f}'.format(self.current/1000))
self.instrument.write('smua.source.rangei = {:f}'.format(1.2*self.current/1000))
if self.voltage_range == 'Auto':
self.instrument.write('smua.measure.autorangev = smua.AUTORANGE_ON')
else:
self.instrument.write('smua.measure.rangev = ' + self.voltage_range)
self.instrument.write('display.smua.measure.func = smua.OUTPUT_DCVOLTS')
else:
self.instrument.write('smua.source.func = smua.OUTPUT_DCVOLTS')
self.instrument.write('smua.source.limiti = {:f}'.format(self.current_limit/1000))
self.instrument.write('smua.source.levelv = {:f}'.format(self.voltage))
self.instrument.write('smua.source.rangev = {:f}'.format(self.voltage*1.2))
if self.current_range == 'Auto':
self.instrument.write('smua.measure.autorangei = smua.AUTORANGE_ON')
else:
self.instrument.write('smua.measure.rangei = {:f}'.format(float(self.current_range)))
self.instrument.write('display.smua.measure.func = smua.OUTPUT_DCAMPS')
if self.derivative_resistance_enabled:
nplc = (0.25*(self.sampling_interval/self.derivative_resistance_voltage_points))/0.02
logger.info('NPLC=%f', nplc)
self.instrument.write('smua.measure.nplc = {:f}'.format(nplc))
self.instrument.write('smua.nvbuffer1.clear()')
self.instrument.write('smua.nvbuffer1.appendmode = 1')
self.instrument.write('smua.source.autorangei = smua.AUTORANGE_OFF')
self.instrument.write('smua.source.autorangev = smua.AUTORANGE_OFF')
self.instrument.write('smua.source.rangev = {:f}'.format(self.voltage +
self.derivative_resistance_voltage_span*1.2))
query = 'f1, msg1 = ConfigPulseVMeasureISweepLin(smua, {:f}, {:f}, {:f}, {:f}, {:f}, 0, {:d}, ' \
'smua.nvbuffer1, 1)'.format(self.voltage,
self.voltage - self.derivative_resistance_voltage_span,
self.voltage + self.derivative_resistance_voltage_span,
self.current_limit/1000,
0.5*(self.sampling_interval /
self.derivative_resistance_voltage_points),
self.derivative_resistance_voltage_points)
logger.info(query)
self.instrument.write(query)
response = self.instrument.query('print(f1, msg1)')
logger.info(response)
self.instrument.write('smua.source.output = smua.OUTPUT_ON')
self.running = True
self.start_time = time()
self.sample_number = 0
if self.running:
self.timer = Timer.singleShot(max(((self.sample_number+1) * self.sampling_interval -
(time()-self.start_time))*1000, 0.01),
self._on_timer)
def start(self):
self.timer = Timer(100, self.monitor_physiology)
class DummyIntervalInstrument(HasTraits):
# implements(IInstrument)
name = Unicode("DummyIntervalInstrument")
model = Unicode("DummyInterval")
# x_units = Dict
# y_units = Dict
x_units = Dict({0: "Voltage"})
y_units = Dict({0: "Current", 1: "Resistance"})
acquired_data = List(Dict)
start_stop = Event
running = Bool
output_channels = Dict({0: "IV", 1: "CF"})
measurement_info = Dict()
enabled_channels = List(Bool)
timer = Instance(Timer)
update_interval = Float(0.03)
start_voltage = Float(0)
stop_voltage = Float(5)
step_voltage = Float(0.05)
current_voltage = Float
current_current = Float
start_frequency = Float(20)
stop_frequency = Float(1e6)
step_frequency = Float(10000)
current_frequency = Float
current_capacitance = Float
use_log_steps = Bool(True)
iteration = Int(0)
start_stop = Event
button_label = Str("Start")
sweep_name = Str
bias = Float
measurement_mode = Int
traits_view = View(
Item("measurement_mode", editor=EnumEditor(name="output_channels"), enabled_when="not running"),
Group(
Item("start_voltage"),
Item("stop_voltage"),
Item("step_voltage"),
Item("current_voltage", enabled_when="False"),
Item("current_current", enabled_when="False"),
label="I/V",
show_border=True,
),
Group(
Item("start_frequency"),
Item("stop_frequency"),
Item("step_frequency"),
Item("use_log_steps"),
Item("current_frequency", enabled_when="False"),
Item("current_capacitance", enabled_when="False"),
label="C/F",
show_border=True,
),
Item("update_interval"),
Item("sweep_name"),
Item("start_stop", label="Start/Stop Acqusistion", editor=ButtonEditor(label_value="button_label")),
handler=DummyIntervalInstrumentHandler,
)
def start(self):
if self.timer is None:
self.timer = Timer(self.update_interval * 1000, self._onTimer)
else:
self.timer.Start(self.update_interval * 1000)
self.button_label = "Stop"
self.current_voltage = self.start_voltage
self.current_frequency = self.start_frequency
self.iteration = 0
self.running = True
self.bias = random.random_sample() - 0.5
self.measurement_info = {
"name": self.sweep_name,
"start_voltage": self.start_voltage,
"start_frequency": self.start_frequency,
"start_bias": self.bias,
}
if len(self.measurement_info["name"]) is 0:
self.measurement_info.pop("name")
def stop(self):
if self.timer is not None:
self.timer.Stop()
self.button_label = "Start"
self.running = False
def _onTimer(self):
d = dict()
self.current_current = self.current_voltage ** 1.3 + self.bias
self.current_capacitance = (self.current_frequency * (self.stop_frequency - self.current_frequency)) / 1e9
if self.measurement_mode is 0:
d[self.output_channels[self.measurement_mode]] = (
dict({self.x_units[0]: self.current_voltage}),
dict(
{
self.y_units[0]: self.current_current,
self.y_units[1]: self.current_voltage / self.current_current,
}
),
)
elif self.measurement_mode is 1:
d[self.output_channels[self.measurement_mode]] = (
dict({self.x_units[0]: self.current_frequency}),
dict({self.y_units[0]: self.current_capacitance}),
)
self.iteration += 1
self.current_voltage += self.step_voltage
# if self.use_log_steps:
self.current_frequency += self.step_frequency
self.acquired_data.append(d)
if self.current_voltage > self.stop_voltage:
self.start_stop = True
def _start_stop_fired(self):
if self.timer is None:
self.start()
return
if self.timer.isActive():
self.stop()
else:
self.start()
def _enabled_channels_default(self):
return [True, False]
def _measurement_mode_changed(self, new):
if new is 0:
self.x_units = {0: "Voltage"}
self.y_units = {0: "Current", 1: "Resistance"}
self.enabled_channels = [True, False]
elif new is 1:
self.x_units = {0: "Frequency"}
self.y_units = {0: "Capacitance"}
self.enabled_channels = [False, True]
def _measurement_mode_default(self):
return 0
def get_nr_of_samples(self):
if self.measurement_mode == 0:
return (self.stop_frequency - self.start_frequency) / self.step_frequency
elif self.measurement_mode == 1:
return (self.stop_voltage - self.start_voltage) / self.step_voltage
else:
return 1
