Command Profile in TVB

This is a simple demo showing for to interract with TVB in the command profile.

More examples can be found here: https://github.com/the-virtual-brain/tvb-framework/tree/master/tvb/interfaces/command/demos

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from tvb.interfaces.command.lab import *
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list_projects()

Create a new project to test with

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import uuid
proj = new_project("sandbox" + str(uuid.uuid4()))
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list_projects()

If you have the web UI open at the same time, you'll notice there's now a new project named "sandbox_project"

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list_datatypes(proj.id)

Nothing! Let's import a connectivity

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import os
import tvb_data
p = os.path.join(os.path.dirname(tvb_data.__file__), 'connectivity/connectivity_66.zip')
import_op = import_conn_zip(proj.id, p)

import_op = wait_to_finish(import_op)
import_op
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list_operation_results(import_op.id)
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conectivity_gid = get_operation_results(import_op.id)[0].gid

Now let's grab that connectivity from the database. IMPORTANT: Make sure to adjust the DT gid below to match the value in the id column above and run a simulation with it.

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simulator_model = SimulatorAdapterModel()
# ConnectivityIndex gid from the column above
simulator_model.connectivity = conectivity_gid
simulator_model.simulation_length = 100
sim_op = fire_simulation(proj.id, simulator_model)
sim_op = wait_to_finish(sim_op)
sim_op

We should wait for the simulation to finish, and afterwards, TimeSeries should also be part of this project.

Refresh the Web GUI to see the status of your operation.

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list_operation_results(sim_op.id)
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time_series_region_index_id = get_operation_results(sim_op.id)[1].id
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%matplotlib inline
import matplotlib.pyplot as plt

# Use TimeSeriesRegionIndex id
ts  = load_dt(time_series_region_index_id)
for reg in range(66):
    plt.plot(ts.data[:, 0, reg, 0])
plt.show()

You can re-evaluate this cell multiple times while it's running to see how the results gradually show up as the simulation finishes.

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