snudda.neurons.neuron_morphology

class snudda.neurons.neuron_morphology.NeuronMorphology(name=None, position=<Mock name='mock.zeros()' id='140674829498192'>, rotation=None, swc_filename=None, param_filename=None, param_data=None, mech_filename=None, modulation=None, neuron_path=None, morphology_id=None, parameter_id=None, modulation_id=None, parameter_key=None, morphology_key=None, modulation_key=None, verbose=False, load_morphology=True, hoc=None, colour=None, use_cache=True, pickle_version=-1, logfile=None, virtual_neuron=False, axon_stump_id_flag=False, snudda_data=None)

Neuron morphology object. Also see NeuronPrototype class which handles multiple morphology variations.

cache_exist(cache_file=None)

Checks if cache_file exists

clone(load_morphology=None, position=<Mock name='mock.zeros()' id='140674829498192'>, rotation=None, morphology_id=None, parameter_id=None, modulation_id=None, parameter_key=None, morphology_key=None, modulation_key=None)

Creates a clone copy of a neuron.

Parameters

• load_morphology (bool) – Load morphology into clone?

• position (float,float,float) – x,y,z coordinate of clone

• rotation (rotation matrix) – Rotation matrix for clone

• morphology_id – Morphology ID for the clone

• parameter_id – Parameter ID for the clone

• modulation_id – Neuromodulation parameter ID for the clone

• parameter_key (str) – Parameter Key for clone

• morphology_key (str) – Morphology Key for clone

• modulation_key (str) – Modulation Key for clone

cluster_synapses(sec_id, sec_x, count, distance, rng)

Randomize sec_x for cluster of ‘count’ synapses with centre placed at ‘sec_id’, ‘sec_x’ spread over ‘distance’ (but constrained to current section extent).

Parameters

• sec_id – Section id of cluster centre

• sec_x – Section x of cluster centre

• count – Number of synapses in cluster

• distance – Maximal spread of cluster along dendrite

• rng – Numpy random stream

Returns

Section x for cluster synapse coords : Coordinates for synapse (in meters) soma_dist : Distance to soma (in meters)

Return type

cluster_sec_x

compartment_length(comp_type='dend')

Calculates compartment length comp_type (“axon” or “dend”)

dendrite_input_locations(synapse_density, rng, num_locations=None, cluster_size=None, cluster_spread=2e-05)

Randomises input locations on dendrites.

Parameters

• synapse_density – Synapse density as a function f(d), d=distance from soma

• rng – Numpy random stream

• num_locations – Number of input locations (this is average number returned, results vary)

• cluster_size (int) – Number of synapse clusters to place (None = no clusters, all placed independently)

dendrite_input_locations_helper(synapse_density, rng, num_locations, cluster_size=1, cluster_spread=2e-05)

Helper function. Places num_location clusters, each containing cluster_size synapses. Density is relative, scaled.

Parameters

• synapse_density – Synapse density as a function f(d), d = distance on dendrite from soma

• rng – Numpy random stream

• num_locations (int) – Number of locations

• cluster_size (int) – Size of synapse clusters

find_radius()

Find finds maximum axon and dendrite radius of neuron.

load_cache(cache_file=None)

Loads morphology from cache_file.

load_neuron_morphology()

Loads neuron morphology from SWC file or from cache file.

load_swc(swc_file=None)

Loads morphology from swc_file

place(rotation=None, position=None)

Placing a neuron and rotating it. Will give a warning if it was previously rotated.

Parameters

• rotation – 3D rotation matrix

• position – x,y,z position for neuron

plot_neuron(axis=None, plot_axon=True, plot_dendrite=True, line_style='-', alpha=1.0, plot_origo=None, plot_scale=1.0, axon_colour=None, dend_colour=None, soma_colour=None, show_plot=True)

Plots neuron.

Parameters

• axis –

• plot_axon –

• plot_dendrite –

• line_style –

• alpha –

• plot_origo –

• plot_scale –

• axon_colour –

• dend_colour –

• soma_colour –

• show_plot –

static rand_rotation_matrix(deflection=1.0, rand_nums=None)

Creates a random rotation matrix.

deflection: the magnitude of the rotation. For 0, no rotation; for 1, competely random rotation. Small deflection => small perturbation. rand_nums: 3 random numbers in the range [0, 1]. If None, they will be auto-generated.

save_cache(cache_file=None)

Saves cache_file with morphology

set_axon_voxel_radial_density(density, max_axon_radius)

Sets axon radial density

Parameters

• density – Axon density f(r), r = radius from soma

• max_axon_radius – Axon density is calculated within a sphere of radius max_axon_radius

set_axon_voxel_xyz_density(density, axon_density_bounds_xyz)

Sets axon density

Parameters

• density – Axon density f(x,y,z), x,y,z = SWC coordinates in relative to soma

• axon_density_bounds_xyz – Bounding box for the axon density in x,y,z

write_log(text, is_error=False)

Write text to log file. Prints on screen if self.verbose or is_error