def __init__(self):
logging.debug('Initializing Cell Builder')
self.geometry = None
self.segment = None
section_diam_panel = neuron_utils.add_text_field_with_label(
'Section Diam', None)
section_length_panel = neuron_utils.add_text_field_with_label(
'Section Length', None)
segment_diam_panel = neuron_utils.add_text_field_with_label(
'Segment Diam', None)
# Get textfields from panels
self.section_diam = section_diam_panel.items[1]
self.section_length = section_length_panel.items[1]
self.segment_diam = segment_diam_panel.items[1]
self.save_button = neuron_utils.add_button('Save', self.modify_segment)
self.cellBuilderPanel = neuron_utils.add_panel(
'Cell Builder',
items=[
segment_diam_panel, section_diam_panel, section_length_panel,
self.save_button
],
widget_id='cellBuilderPanel',
position_x=955,
position_y=374,
width=340,
height=190)
self.cellBuilderPanel.register_to_event(
[GeppettoJupyterModelSync.events_controller._events['Select']],
self.updateValues)
self.cellBuilderPanel.on_close(self.close)
self.cellBuilderPanel.display()
def __init__(self):
logging.debug('Loading HNN')
neuron_utils.createProject(name='HNN')
import run
self.t_vec = h.Vector()
self.t_vec.record(h._ref_t)
neuron_utils.createStateVariable(id='time',
name='time',
units='ms',
python_variable={
"record_variable": self.t_vec,
"segment": None
})
neuron_geometries_utils.extractGeometries()
logging.debug('HNN loaded')
self.RunSimButton = neuron_utils.add_button('Run',
extraData={'commands': []})
self.StopSimButton = neuron_utils.add_button(
'Stop', extraData={'commands': []})
self.SetParams = neuron_utils.add_button('Set Parameters')
self.BasePanel = neuron_utils.add_panel(
'HNN Control',
items=[self.RunSimButton, self.StopSimButton, self.SetParams],
widget_id='hnnBasePanel')
self.BasePanel.on_close(self.close)
self.BasePanel.display()
def __init__(self):
logging.debug('Initializing Analysis panel')
self.analysis_button = neuron_utils.add_button('Plot',
self.run_analysis)
self.analysis_panel = neuron_utils.add_panel(
'Analysis',
items=[self.analysis_button],
widget_id='analysisPanel',
position_x=90,
position_y=250)
self.analysis_panel.display()
def __init__(self):
logging.debug('Initializing Samples panel')
self.items = []
self.items.append(neuron_utils.add_button('Single compartment Hodgkin-Huxley',
self.loadModule, extraData={'module': 'verysimple_cell', 'model': 'VerySimpleCell'}))
self.items.append(neuron_utils.add_button('Multi compartments Hodgkin-Huxley',
self.loadModule, extraData={'module': 'simple_cell', 'model': 'SimpleCell'}))
#self.items.append(neuron_utils.add_button('Simple network', self.loadModule, extraData = {'module': 'simple_network', 'model':'SimpleNetwork'}))
self.items.append(neuron_utils.add_button(
'Ring network', self.loadModule, extraData={'module': 'ring', 'model': 'Ring'}))
self.items.append(neuron_utils.add_button('CA3 Pyramidal', self.loadModule, extraData={
'module': 'CA3_pyramidal', 'model': 'CA3_pyramidal'}))
self.items.append(neuron_utils.add_button(
'PT Cell', self.loadModule, extraData={'module': 'PTcell', 'model': 'PTcell'}))
self.loadModelPanel = neuron_utils.add_panel(
'Sample NEURON Models', items=self.items, widget_id='loadModelPanel', position_x=108, position_y=125, width=287, properties={"closable":False})
self.loadModelPanel.on_close(self.close)
self.loadModelPanel.display()
def __init__(self):
logging.debug('Initializing Point Process')
# self.point_processes = None
self.current_point_process = None
drop_down_panel = neuron_utils.add_drop_down_with_label(
'Current Clamps', [{
'id': 'noSelection',
'value': 'No segment selected'
}])
delay_panel = neuron_utils.add_text_field_with_label('Delay', None)
duration_panel = neuron_utils.add_text_field_with_label(
'Duration', None)
amplitude_panel = neuron_utils.add_text_field_with_label(
'Amplitude', None)
i_panel = neuron_utils.add_text_field_with_label('i', None)
self.drop_down = drop_down_panel.items[1]
self.drop_down.on_change(self.update_drop_down_selection)
self.delay = delay_panel.items[1]
self.duration = duration_panel.items[1]
self.amplitude = amplitude_panel.items[1]
self.i = i_panel.items[1]
self.save_button = neuron_utils.add_button('Save',
self.create_current_clamp)
self.pointProcessPanel = neuron_utils.add_panel(
'Point Process',
items=[
drop_down_panel, delay_panel, duration_panel, amplitude_panel,
i_panel, self.save_button
],
widget_id='pointProcessPanel',
position_x=955,
position_y=69,
width=340,
height=277)
self.pointProcessPanel.register_to_event(
[GeppettoJupyterModelSync.events_controller._events['Select']],
self.updateValues)
self.pointProcessPanel.on_close(self.close)
self.pointProcessPanel.display()
def __init__(self):
logging.debug('Initializing Run Control')
self.initPanel = neuron_utils.add_text_field_and_button(
"Init",
'v_init',
True,
self.execute_neuron_command,
extraData={'commands': ['h.stdinit()']})
self.initRunButton = neuron_utils.add_button(
'Init & Run',
self.execute_neuron_command,
extraData={
'commands': [
'GeppettoJupyterModelSync.events_controller.triggerEvent("spin_logo")',
'GeppettoJupyterModelSync.current_experiment.status = "RUNNING"',
'h.run()',
'GeppettoJupyterModelSync.current_experiment.status = "COMPLETED"',
'import time;time.sleep(1.5);',
'GeppettoJupyterModelSync.events_controller.triggerEvent("experiment:doPlay")',
'GeppettoJupyterModelSync.events_controller.triggerEvent("stop_spin_logo")'
]
})
self.stopButton = neuron_utils.add_button('Stop')
self.stopButton.on_click(['h.stoprun = 1'])
self.continueTilPanel = neuron_utils.add_text_field_and_button(
"Continue til",
'runStopAt',
True,
self.execute_neuron_command,
extraData={
'commands': ['h.continuerun(runStopAt)', 'h.stoprun=1']
})
self.continueForPanel = neuron_utils.add_text_field_and_button(
"Continue for",
'runStopIn',
True,
self.execute_neuron_command,
extraData={
'commands': ['h.continuerun(t + runStopIn)', 'h.stoprun=1']
})
self.singleStepButton = neuron_utils.add_button(
'Single Step',
self.execute_neuron_command,
extraData={
'commands': [
'h.steprun()',
'GeppettoJupyterModelSync.events_controller.triggerEvent("experiment:doPlay")',
'GeppettoJupyterModelSync.events_controller.triggerEvent("experiment:update")'
]
})
self.timePanel = neuron_utils.add_text_field_and_button(
"t",
't',
False,
self.execute_neuron_command,
extraData={'commands': []})
self.stopPanel = neuron_utils.add_text_field_and_button(
"Tstop",
'tstop',
True,
self.execute_neuron_command,
extraData={'commands': ['h.tstop_changed()']})
self.dtPanel = neuron_utils.add_text_field_and_button(
"dt",
'dt',
True,
self.execute_neuron_command,
extraData={'commands': ['h.setdt()']})
self.pointsPlottedPanel = neuron_utils.add_text_field_and_button(
"Points plotted/ms",
'steps_per_ms',
True,
self.execute_neuron_command,
extraData={'commands': ['h.setdt()']})
self.scrnUpdateInvlPanel = neuron_utils.add_text_field_and_button(
"Scrn update invl",
'screen_update_invl',
True,
self.execute_neuron_command,
extraData={'commands': []})
self.realTimePanel = neuron_utils.add_text_field_and_button(
"Real Time",
'realtime',
False,
self.execute_neuron_command,
extraData={'commands': []})
self.runControlPanel = neuron_utils.add_panel(
'Run Control',
items=[
self.initPanel, self.initRunButton, self.stopButton,
self.continueTilPanel, self.continueForPanel,
self.singleStepButton, self.timePanel, self.stopPanel,
self.dtPanel, self.pointsPlottedPanel,
self.scrnUpdateInvlPanel, self.realTimePanel
],
widget_id='runControlPanel',
position_x=700,
position_y=150)
self.runControlPanel.on_close(self.close)
self.runControlPanel.display()