snudda.place.region_mesh

class snudda.place.region_mesh.RegionMesh(filename, d_view=None, role='master', use_cache=True, pickle_version=-1, raytrace_borders=True, d_min=1.5e-05, bin_width=0.0001, logfile_name=None, log_file=None, random_seed=112, verbose=False)

Handles neuron placement within a 3D mesh.

Constructor.

Parameters

• filename (str) – Path to wavefront mesh file

• d_view – ipyparallel direct view object

• role (str) – Role, ie. “master” or “worker”

• use_cache (bool) – The meshes voxel representation is cached, use the cache?

• pickle_version (int) – Which version of pickle to use? (-1 latest)

• raytrace_borders (bool) – Raytrace positions in border regions? Slower, but more accurate.

• d_min (float) – Closest distance between soma

• bin_width (float) – Mesh size

• logfile_name (str) – Path to logfile

• log_file – File pointer to log file

• random_seed (int) – Random seed value

• verbose (bool) – Flag to be verbose?

cache_exist()

Check if cache for 3D mesh exists. Returns True or False.

check_inside(coords)

Check if coordinates are inside 3D mesh.

define_density(neuron_type, density_function)

Defines density for neuron type.

Parameters

• neuron_type (str) – Neuron type

• density_function (str) – density_function is either None, or a function of pos = [x,y,z] (in SI units)

get_subset(centre, radius=None, num_neurons=None, shape='cube', return_idx_flag=False)

Returns subset of positions, either within a radius, or the closest num_neurons neurons.

Parameters

• centre (float,float,float) – Centre of space

• radius (float) – Radius if sphere, half-side if cube

• num_neurons (int) – Number of neurons (if None, all within radius are returned)

• shape (str) – “sphere” or “cube”

• return_idx_flag (bool) – Return the indexes instead of coordinates (default False)

inner_voxel_volume()

Volume of all inner voxels.

load_cache()

Loading 3D mesh cache.

load_mesh(filename)

Load 3D mesh.

mark_borders()

Mark border voxels in 3D mesh.

plot_neurons(plot_idx=None, pdf_name=None)

Plot neurons.

Parameters

• plot_idx (list) – Neuron ID to plot

• pdf_name (str) – Name of file to save figure to (default None)

plot_struct(pdf_name=None)

Plot structure.

Parameters

pdf_name (str) – Save file name (default None)

pre_compute()

Helper function, precomputes values for raytracing.

ray_casting(point)

Ray-casting, to determine if a point is inside or outside of mesh.

save_cache()

Save 3D mesh cache.

setup_parallel(d_view=None)

Setup workers for parallel execution.

setup_place_neurons(d_min=None)

Initialises variables for neuron placement.

Parameters

d_min (float) – Minimal distance between neuron somas, in SI units (meters)

setup_voxel_filter()

Setup voxel filter for 3D mesh.

setup_voxel_list()

Setup voxel list, these are voxels that needs to be checked for neurons close by.

test_plot()

Test plot

test_plot_cached()

Test plot cached.

update_padding_mask()

Updates padding mask. We add neurons outside our region of interest, to avoid artificially inflating neuron density at the edges (which would happen without the padding region).

update_random_pool()

Refills the random pool with new random numbers.

verify_d_min()

Verify that d_min constraint is met.

verify_inside(num_points=1000)

Verify the check-inside method against the ray-casting method to make sure they give same results.

write_log(text, flush=True, is_error=False)

Writes to log file. Use setup_log first. Text is only written to screen if self.verbose=True, or is_error = True, or force_print = True.

test (str) : Text to write flush (bool) : Should all writes be flushed to disk directly? is_error (bool) : Is this an error, always written. force_print (bool) : Force printing, even if self.verbose=False.