def beforeClicked(self, event, button: Button, graphId: int,
metadata: Metadata):
button.disabled = True
button.label = 'Working!'
UnlockedDocumentProxy(button.document).add_next_tick_callback(
partial(self.calculate_datapoints,
graphId=graphId,
button=button,
metadata=metadata))
def make_tab():
# Slider to select width of bin
pastdays_select = RangeSlider(start=0,
end=999,
value=(0, 999),
step=1,
title='Past Days',
sizing_mode="stretch_both")
# Slider to select buffer size
bufferdays_select = Slider(start=.01,
end=9,
value=0.01,
step=.1,
title='Buffer Size (days)',
sizing_mode="stretch_both")
# Re-read
refresh_button = Button(label="Time window and buffer are up to date",
button_type="success",
sizing_mode="stretch_both")
refresh_button.disabled = True
# read data
flights, available_carriers = read(pastdays_select, bufferdays_select)
# CheckboxGroup to select carrier to display
locationcodes = np.unique(
['.'.join(seedid.split('.')[:3]) for seedid in available_carriers])
selections = []
for locationcode in locationcodes[:maxnstation]:
matching = [s for s in available_carriers if locationcode in s]
active = [i for i, m in enumerate(matching)] # if "Z" == m[-1]]
selections += [
CheckboxButtonGroup(labels=matching,
active=active,
sizing_mode="stretch_both")
]
#selections += [MultiSelect(#title="Option:",
# value=matching,
# active=active)
# Find the initially selected carrieres
initial_carriers = [s.labels[i] for s in selections for i in s.active]
# Slider to select width of bin
binwidth_select = Slider(start=16,
end=160,
step=16,
value=80,
title='Bin number',
sizing_mode="stretch_both")
# RangeSlider control to select start and end of plotted delays
range_select = RangeSlider(start=-1,
end=999,
value=(-.2, 99),
step=.1,
title='Range (sec)',
sizing_mode="stretch_both")
# Switch from lines to hists
type_switch = RadioButtonGroup(labels=["Histogram", "Cumulated dist."],
active=0,
sizing_mode="stretch_both")
# Find the initially selected carrieres
plottype = type_switch.labels[type_switch.active]
src = {}
for output in ['Latencies', 'Delays', 'PSD']:
src[output] = make_dataset(flights,
initial_carriers,
range_start=range_select.value[0],
range_end=range_select.value[1],
bin_width=binwidth_select.value,
output=output,
plottype=plottype)
callback = partial(update,
output='Delays',
type_switch=type_switch,
flights=flights,
src=src,
selections=selections,
range_select=range_select,
binwidth_select=binwidth_select)
callbacklat = partial(update,
output='Latencies',
type_switch=type_switch,
flights=flights,
src=src,
range_select=range_select,
selections=selections,
binwidth_select=binwidth_select)
callbackpsd = partial(update,
output='PSD',
type_switch=type_switch,
flights=flights,
src=src,
range_select=range_select,
selections=selections,
binwidth_select=binwidth_select)
callbackneedsread = partial(needsreadupdate, refresh_button=refresh_button)
callbackread = partial(readupdate,
src=src,
selections=selections,
range_select=range_select,
type_switch=type_switch,
binwidth_select=binwidth_select,
pastdays_select=pastdays_select,
bufferdays_select=bufferdays_select,
refresh_button=refresh_button)
[
s.on_change('active', callback, callbacklat, callbackpsd)
for s in selections
]
type_switch.on_change('active', callback, callbacklat, callbackpsd)
binwidth_select.on_change('value', callback, callbacklat, callbackpsd)
range_select.on_change('value', callback, callbacklat, callbackpsd)
pastdays_select.on_change('value', callbackneedsread)
bufferdays_select.on_change('value', callbackneedsread)
refresh_button.on_click(callbackread)
p = {}
for output in ['PSD', 'Latencies', 'Delays']:
p[output] = make_plot(src[output], output=output)
# Create a row layout
graphs = [p[k] for k in p]
controls = [
type_switch, binwidth_select, range_select, refresh_button,
pastdays_select, bufferdays_select, *selections[:maxnstation]
]
graphslayout = column(children=graphs, sizing_mode="stretch_both")
controlslayout = column(
children=controls,
sizing_mode='fixed', #stretch_width',
width=400,
)
layout = row(children=[graphslayout, controlslayout],
sizing_mode='stretch_both')
# Make a tab with the layout
return Panel(child=layout, title='Channels')
with xr.open_dataset(db_path) as db:
path = get_full_path(image_select.value)
fitting_results = (['time'], fitting_results)
cross_correlation_results = (['time',
'distance'], cross_correlation_results)
# TODO: Needs to be associated with an ROI
db.loc[{
'path': path
}].assign(cross_correlation_results=cross_correlation_results)
db.loc[{'path': path}].assign(fitting_results=fitting_results)
os.remove(db_path)
db.to_netcdf(db_path, mode='w')
run_roi_button = Button(label='Run ROI', button_type='primary')
run_roi_button.disabled = True
run_roi_button.on_click(run_flics_on_roi)
run_flics_button = Button(label='Run FLICS', button_type='primary')
message_paragraph = Paragraph(text='')
analysis_status_paragraph = Paragraph(text='')
def get_roi_params(index: int) -> list:
values = roi_source.data
return [
values['x'][index],
values['y'][index],
values['width'][index],
values['height'][index],
if rssi < statistics['min']:
statistics['min'] = rssi
elif rssi > statistics['max']:
statistics['max'] = rssi
statistics['sum'] = statistics['sum'] + rssi
label2.text = "min=%s, max=%s, avg=%.3f" % (
statistics['min'], statistics['max'],
statistics['sum'] / saving_num)
if saving_num == conf.SAVED_DATA_NUMBER:
saving = False
label1.text = label1.text + " finished! " + str(
len(statistics['data']))
label2.text = label2.text + ", median=" + str(
np.median(statistics['data']))
write_raw_data("end saving")
show_statistics()
os.system('say "completed"')
# update plot
def update_plot(client_data):
doc.add_next_tick_callback(partial(update, client_data=client_data))
if len(conf.BEACONS) > 1:
button.disabled = True
button.on_click(save_data)
curdoc().add_root(column([row([button])], width=150))
def TabModels():
"""available_modelscales = ['cells', 'microcircuit', 'network']
"""
def get_select_menu(menu_type, menu_list):
if menu_type == "modelscales":
title = "Modeling Scale Options"
elif menu_type == "models":
title = "Choose a model name"
elif menu_type == "responses":
title = "Choose a response (file)"
return Select(title=title, value=menu_list[0][0], options=menu_list)
def get_menu_modelscales():
#NOTE: available_modelscale & scale_and_models are global variables
menu = [("None", "None")]
for modelscale in available_modelscales:
# tag the modelscale as first element in the value = modellist
modellist = ' '.join([modelscale] + scale_and_models[modelscale])
menu.append(
(modellist, modelscale)) # tuple (string of models, scale)
return menu
def get_menu_models(modellist):
#NOTE: models_with_filenames is a global variable
menu = [("None", "Below are available models")]
if modellist[1] == "No_Models": #modellist[0]=modelname
menu[0] = (modellist[1], modellist[1].replace("_", " ")
) #tuple (scale, string of models)
else:
for modelname in modellist[1:]:
# tag modelscale & modelname as 1st-two elements in the value
itsvalue = ' '.join([modellist[0], modelname])
menu.append(
(itsvalue, modelname)) # tuple (string of models, scale)
return menu
def update_models_list(attr, old, new):
if new == "No_Models":
menu_list = [''.join(list(new))] # ["No Models"]
else:
menu_list = new.split()
models_select.options = get_menu_models(menu_list)
runmodel.disabled = True
#print new
#print modelscales_select.value
#print menu_list
#print menu_list[0]
def update_global_model(attr, old, new):
menu_list = new.split()
modelscale = menu_list[0] # update global modelscale
modelname = menu_list[1] # update glocal modelname
#print modelscale, modelname
sys.path.append(pwd) # uncomment only when using executiveViz
chosenmodel = ExecutiveControl.choose_model(modelscale=str(modelscale),
modelname=str(modelname))
modeltitle.text = chosenmodel.name
modeldescr.text = chosenmodel.description
modelregions.text = "Potential stimulation sites: " + str(
chosenmodel.regions)
runmodel.disabled = False
def update_stimulation_parameters_input_status(attr, old, new):
if new == "no":
stim_type_input.disabled = True
stim_list_input.disabled = True
stim_loc_input.disabled = True
else:
stim_type_input.disabled = False
stim_list_input.disabled = False
stim_loc_input.disabled = False
def clicked():
print "clicked"
def simulate():
print "running"
#if modelscales_select.value == "No_Models":
#print modelscales_select.value
#else:
#print modelscales_select.value
print pwd
sys.path.append(pwd) # uncomment only when using executiveViz
ec = ExecutiveControl()
modelscale = models_select.value.split()[0]
modelname = models_select.value.split()[1]
chosenmodel = ec.choose_model(modelscale=modelscale,
modelname=modelname)
parameters = ast.literal_eval(runtime_input.value)
print parameters
print stimulation.value
if stimulation.value == "yes":
stimparameters = ast.literal_eval(stim_type_input.value)
stimparameters.update(
{"stimlist": ast.literal_eval(stim_list_input.value)})
ec.launch_model(parameters=parameters,
onmodel=chosenmodel,
stimparameters=stimparameters,
stimloc=stim_loc_input.value)
#with Profiler() as prof, ResourceProfiler() as rprof:
# ec.launch_model ( parameters=parameters, onmodel=chosenmodel,
# stimparameters=stimparameters, stimloc=stim_loc_input.value )
else:
ec.launch_model(parameters=parameters, onmodel=chosenmodel)
#with Profiler() as prof, ResourceProfiler() as rprof:
# ec.launch_model( parameters=parameters, onmodel=chosenmodel )
#myplot = visualize([prof, rprof])
ec.save_response()
print "done running"
#viz_source.data['diagnostic'][0] = prof
#viz_source.data['diagnostic'][1] = rprof
#viz_source.data['diagnostic'] = [prof, rprof]
#viz_source.data['diagnostic'][0].results[0] = prof.results[0]
#myplot.data['diagplots'][0] = visualize([prof, rprof])
#return visualize([prof, rprof])
#
### +++++++++++++++++++GENERATE DATA FOR THE OPTIONS MENU++++++++++++++++++
# available_modelscales -- list
# scale_and_models -- dictionary with list as key value
# models_with_filenames -- dictionary with list as key value
# responses_with_filepaths -- dictionary with string as key value
# Generate Model Info
#os.chdir("..") # line required for calling ~/managers/bokehtest.py
#available_modelscales = fm.available_modelscales()
#os.chdir(rootwd) # for running it from ~/managers
available_modelscales = ExecutiveControl.list_modelscales()
scale_and_models = {}
for modelscale in available_modelscales: # get list of models in each scale
try:
#modelslist = fm.modelscale_inventory(model_scale=modelscale)
modelslist = ExecutiveControl.list_models(modelscale=modelscale)
except:
modelslist = ["No_Models"]
scale_and_models.update({modelscale: modelslist})
#os.chdir(pwd) # for running it from ~/managers
#print scale_and_models
### ++++++++++++++++++++END GENERATE DATA FOR THE OPTIONS++++++++++++++++++
#
modelscale = None
modelname = None
chosenmodel = None
#
menu = get_menu_modelscales()
modelscales_select = get_select_menu("modelscales", menu)
#
dummy_model_menu = [('None', "First select a model scale")]
models_select = get_select_menu("models", dummy_model_menu)
#
runtime_input = TextInput(
value="{'dt': 0.1, 'celsius': 30, 'tstop': 10, 'v_init': 65}",
title="Runtime Parameters:")
#print runtime_input.value
#print type(runtime_input.value)
#
stimulation_menu = [("No", "no"), None, ("Yes", "yes")]
stimulation = Dropdown(label="Stimulation Yes/No",
button_type="warning",
menu=stimulation_menu)
stim_type_input = TextInput(
value="{'type': ['current', 'IClamp']}",
title="Stimulation Parameters (Stimulation Type):")
stim_list_input = TextInput(
value="[{'amp': 0.5, 'dur': 10.0, 'delay': 5.0}, "
" {'amp': 1.0, 'dur': 20.0, 'delay': 15.0}]",
title="Stimulation Parameters (Stimuli):")
stim_loc_input = TextInput(value='soma', title="Stimulation location:")
# disable stimulation by DEFAULT
stim_type_input.disabled = True
stim_list_input.disabled = True
stim_loc_input.disabled = True
#
runmodel = Button(label="Run Simulation", button_type="success")
runmodel.disabled = True
#
modeltitle = Div(text="""No Model has been selected yet.""",
width=290,
height=40)
modeldescr = Paragraph(text="""There is no Model Description.""",
width=290,
height=200)
modelregions = Div(
text="""Main Locations within the model for stimulation""",
width=290,
height=50)
# disable the model texts by DEFAULT
modeltitle.disabled = True
modeldescr.disabled = True
modelregions.disabled = True
def viz():
return visualize(viz_source.data['diagnostic'])
# Put controls in a single element
viz_source = ColumnDataSource(
data={'diagnostic': [Profiler(), ResourceProfiler()]})
myplot = viz()
#diagplot = visualize( viz_source.data['diagnostic'] )
#myplot = ColumnDataSource(data={'diagplots': [diagplot]})
#myplot = ColumnDataSource(data={'diagplots': [visualize([Profiler(), ResourceProfiler()])]})
# INTERACTION
modelscales_select.on_change("value", update_models_list)
models_select.on_change("value", update_global_model)
#responses_select.on_change("value", update_plot)
stimulation.on_change("value", update_stimulation_parameters_input_status)
runmodel.on_click(simulate)
# Create a row layout
mylayout = row(
WidgetBox(modelscales_select, models_select, runtime_input,
stimulation, stim_type_input, stim_list_input,
stim_loc_input, runmodel),
WidgetBox(modeltitle, modeldescr, modelregions),
#row(viz_source.data['diagnostic'][0].visualize()))
#row(myplot.data['diagplots'][0]))
row(myplot))
# Make a tab with the layout
tab = Panel(child=mylayout, title='Choose Model')
return tab
def calculate_datapoints(self, graphId: int, button: Button,
metadata: Metadata):
# Thread(target=lambda: UnlockedDocumentProxy(button.document).add_next_tick_callback()).start()
self.threadCorelate(graphId, button, metadata)
button.label = 'Find Similarities'
button.disabled = False
def uploadFile(self, file_source, button: Button):
button.label = "Upload"
button.disabled = False
def disableButton(self, event, button: Button):
button.label = "Uploading"
button.disabled = True
UnlockedDocumentProxy(button.document)\
.add_next_tick_callback(partial(self.uploadFile, file_source=self.file_source, button=button))
if not run_thread.pause:
run_thread.pause = True
print("Simulation paused")
pause_button.label = "Resume simulation"
else:
run_thread.pause = False
print("Simulation resumed")
pause_button.label = "Pause simulation"
start_button = Button(label="Start simulation")
start_button.on_click(run_sim)
pause_button = Button(label="Pause simulation")
pause_button.on_click(pause_sim)
pause_button.disabled = True
stop_button = Button(label="Stop simulation")
stop_button.on_click(stop_sim)
stop_button.disabled = True
generations_input = TextInput(value="1000", title="Number of generations:")
population_input = TextInput(value="1000", title="Population size:")
doc.add_root(
row(
widgetbox(population_input,
generations_input,
start_button,
pause_button,
stop_button,
y_axis_location="left",
y_axis_label="Density",
toolbar_location=None,
)
DensitySource = ColumnDataSource({
"x": np.array(range(a, a + n + 1)),
"normalized": np.zeros(n + 1, dtype="int")
})
DensityPanel.vbar(x="x", top="normalized", width=0.2, source=DensitySource)
DensityPanel.min_border, WalkPanel.min_border = 5, 5
DensityPanel.xaxis.visible = False
DensityPanel.yaxis.visible = True
start_button = Button(label="Go", button_type="success", width=100)
stop_button = Button(label="Stop", button_type="success", width=100)
stop_button.disabled = True
print("!!!!!!!!!")
a_field = Spinner(high=10.0,
low=1.0,
step=1.0,
value=a,
title="White Balls",
width=100)
b_field = Spinner(high=10.0,
low=1.0,
step=1.0,
value=b,
title="Black Balls",
width=100)
