bmtk.tests.simulator.bionet package
Submodules
bmtk.tests.simulator.bionet.bionet_virtual_files module
-
class
bmtk.tests.simulator.bionet.bionet_virtual_files.
EdgeRow
[source]
Bases: object
-
with_dynamics_params
-
class
bmtk.tests.simulator.bionet.bionet_virtual_files.
EdgesFile
(target_nodes, source_nodes)[source]
Bases: object
-
edges_itr
(target_gid)[source]
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load
(edges_file, edge_types_file)[source]
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source_network
Name of network containing the source gids
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target_network
Name of network containing the target gids
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class
bmtk.tests.simulator.bionet.bionet_virtual_files.
NodeRow
[source]
Bases: object
-
with_dynamics_params
-
class
bmtk.tests.simulator.bionet.bionet_virtual_files.
NodesFile
(N)[source]
Bases: object
-
get_node
(gid, cache=False)[source]
-
gids
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load
(nodes_file, node_types_file)[source]
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name
name of network containing these nodes
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next
()[source]
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node_types_table
-
version
bmtk.tests.simulator.bionet.conftest module
bmtk.tests.simulator.bionet.set_cell_params module
-
bmtk.tests.simulator.bionet.set_cell_params.
Biophys1
(cell_prop)[source]
Set parameters for cells from the Allen Cell Types database
Prior to setting parameters will replace the axon with the stub
-
bmtk.tests.simulator.bionet.set_cell_params.
IntFire1
(cell_prop)[source]
Set parameters for the IntFire1 cell models.
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bmtk.tests.simulator.bionet.set_cell_params.
fix_axon
(hobj)[source]
Replace reconstructed axon with a stub
Parameters: |
- hobj: instance of a Biophysical template
NEURON’s cell object
|
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bmtk.tests.simulator.bionet.set_cell_params.
set_params_peri
(hobj, params_file_name)[source]
Set biophysical parameters for the cell
Parameters: |
- hobj: instance of a Biophysical template
NEURON’s cell object
- params_file_name: string
name of json file containing biophysical parameters for cell’s model which determine spiking behavior
|
bmtk.tests.simulator.bionet.set_syn_params module
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bmtk.tests.simulator.bionet.set_syn_params.
exp2syn
(syn_params, xs, secs)[source]
Create a list of exp2syn synapses
Parameters: |
- syn_params: dict
parameters of a synapse
- xs: float
normalized distance along the section
- secs: hoc object
target section
|
Returns: |
- syns: synapse objects
|
bmtk.tests.simulator.bionet.set_weights module
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bmtk.tests.simulator.bionet.set_weights.
gaussianLL
(tar_prop, src_prop, con_prop)[source]
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bmtk.tests.simulator.bionet.set_weights.
wmax
(tar_prop, src_prop, con_prop)[source]
bmtk.tests.simulator.bionet.test_biograph module
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bmtk.tests.simulator.bionet.test_biograph.
test_add_edges
()[source]
-
bmtk.tests.simulator.bionet.test_biograph.
test_add_nodes
()[source]
bmtk.tests.simulator.bionet.test_gids module
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bmtk.tests.simulator.bionet.test_gids.
test_gid_pool
()[source]
bmtk.tests.simulator.bionet.test_nrn module
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bmtk.tests.simulator.bionet.test_nrn.
test_cell_model
()[source]
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bmtk.tests.simulator.bionet.test_nrn.
test_cell_model_decorator
()[source]
-
bmtk.tests.simulator.bionet.test_nrn.
test_load_py_modules
()[source]
-
bmtk.tests.simulator.bionet.test_nrn.
test_synapse_model
()[source]
-
bmtk.tests.simulator.bionet.test_nrn.
test_synapse_model_decorator
()[source]
-
bmtk.tests.simulator.bionet.test_nrn.
test_weight
()[source]
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bmtk.tests.simulator.bionet.test_nrn.
test_weight_decorator
()[source]
bmtk.tests.simulator.bionet.test_virtualcell module
-
class
bmtk.tests.simulator.bionet.test_virtualcell.
MockNode
[source]
Bases: object
-
node_id
= 0
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class
bmtk.tests.simulator.bionet.test_virtualcell.
MockSpikes
(spike_times)[source]
Bases: object
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get_times
(node_id)[source]
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bmtk.tests.simulator.bionet.test_virtualcell.
test_spiketrain
(spike_times)[source]
-
bmtk.tests.simulator.bionet.test_virtualcell.
test_spiketrains_negative
(spike_times)[source]
Module contents