# -*- coding: utf-8 -*-
"""
Created on Wed April 03 14:27:26 2019
Description: Functions for calculating cell distances to electrode. Distance is
calculated similar to space.distance, but distance is now between
a cell position and a point for an electrode rather than between two cell positions
Edits:
10-01-18: Created electrode_distance function
@author: John Fleming, john.fleming@ucdconnect.ie
"""
# There must be some Python package out there that provides most of this stuff.
# Distance computations are provided by scipy.spatial, but scipy is a fairly heavy dependency.
try:
reduce
except NameError:
from functools import reduce
import numpy
import math
from operator import and_
from pyNN.random import NumpyRNG
from pyNN import descriptions
import logging
logger = logging.getLogger("PyNN")
def distance_to_electrode(src_electrode, tgt_cell, mask=None):
"""
Return the Euclidian distance from a point source electrode to a cell.
`mask` allows only certain dimensions to be considered, e.g.::
* to ignore the z-dimension, use `mask=array([0,1])`
* to ignore y, `mask=array([0,2])`
* to just consider z-distance, `mask=array([2])`
'src_electrode' is the electrode positon in xyz co-ordinates.
'tgt_cell' is the cell that the distance will be calculated to.
"""
d = src_electrode - tgt_cell.position
if mask is not None:
d = d[mask]
return numpy.sqrt(numpy.dot(d, d))
def distances_to_electrode(src_electrode, tgt_pop, coordinate_mask=None):
"""
Return an array of the Euclidian distances from a point source
electrode to a population of cells.
`coordinate_mask` allows only certain dimensions to be considered, e.g.::
* to ignore the z-dimension, use `coordinate_mask=array([0,1])`
* to ignore y, `coordinate_mask=array([0,2])`
* to just consider z-distance, `coordinate_mask=array([2])`
'src_electrode' is the electrode positon in xyz co-ordinates.
'tgt_pop' is the population of cells that the distance will be calculated to.
"""
row_size,col_size = tgt_pop.positions.shape
cell_electrode_distances = numpy.zeros((col_size,1))
cell_electrode_distances.flatten()
for cell_id, tgt_cell in enumerate(tgt_pop):
cell_electrode_distances[cell_id] = distance_to_electrode(src_electrode,tgt_cell,mask=coordinate_mask)
return cell_electrode_distances
#return cell_electrode_distances.flatten()
def collateral_distances_to_electrode(src_electrode, tgt_pop, L, nseg):
"""
Return an nd-array of the Euclidian distances from a point source
electrode to a population of cells. Each row corresponds to a collateral
from the cortical population. Each column corresponds to the segments of the
collateral, with 0 being the furthest segment from the 2d plane the cells are
distributed in and 1 being in the plane.
'src_electrode' is the electrode positon in xyz co-ordinates.
'tgt_pop' is the population of cells that the distance will be calculated to.
'L' is the length of the cortical collateral
'nseg' is the number of segments in a collateral
'segment_electrode_distances' is the distance from the centre of each collateral
segment to the stimulating electrode. Each row corresponds to a collateral of a single
cortical cell. Each column corresponds to a segment of the collateral.
"""
row_size,col_size = tgt_pop.positions.shape
segment_electrode_distances = numpy.zeros((col_size,nseg))
segment_centres = numpy.arange(0, nseg+3-1)*(1/nseg)
segment_centres = segment_centres - (1/(2*nseg))
segment_centres[0] = 0
segment_centres[-1] = 1
segment_centres = segment_centres[1:len(segment_centres)-1]
z_coordinate = L*segment_centres - L/2
#print(z_coordinate)
for cell_id, tgt_cell in enumerate(tgt_pop):
for seg in numpy.arange(nseg):
tgt_cell.position = numpy.array([tgt_cell.position[0], tgt_cell.position[1], z_coordinate[seg]])
segment_electrode_distances[cell_id][seg] = distance_to_electrode(src_electrode,tgt_cell)
return segment_electrode_distances |