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313 lines
10 KiB
313 lines
10 KiB
2 years ago
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#!/usr/bin/python
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"""
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Basic test of initialization of multiple cells in the model, and running multiple cells at one time.
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Plots the resposnes to a series of current injections for most implemented baseic cell types in
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in cnmodel.
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Usage:
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python examples/toy_model.py (no arguments)
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"""
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from __future__ import print_function
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import sys
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from neuron import h
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import numpy as np
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import cnmodel.cells as cells
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from cnmodel.protocols import Protocol
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from cnmodel.util import custom_init
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from collections import OrderedDict
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import re
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import pyqtgraph.exporters
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from cnmodel.util import pyqtgraphPlotHelpers as PH
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from cnmodel.protocols import IVCurve
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try: # check for pyqtgraph install
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import pyqtgraph as pg
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except ImportError:
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raise ImportError("This model requires pyqtgraph")
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from cnmodel.util.stim import make_pulse
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def autorowcol(n):
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"""
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return a reasonable layout (cols, rows) for n plots on a page
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up to 16.
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Otherwise return floor(sqrt(n)) + 1 for both r and c.
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"""
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nmap = {
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1: (1, 1),
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2: (2, 1),
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3: (3, 1),
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4: (2, 2),
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5: (3, 2),
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6: (3, 2),
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7: (3, 3),
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8: (3, 3),
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9: (3, 3),
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10: (3, 4),
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11: (3, 4),
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12: (3, 4),
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13: (4, 4),
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14: (4, 4),
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15: (4, 4),
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16: (4, 4),
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}
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if n <= 16:
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return nmap[n][0], nmap[n][1]
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else:
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nx = np.floor(np.sqrt(n)) + 1
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return nx, nx
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def makeLayout(cols=1, rows=1, letters=True, margins=4, spacing=4, nmax=None):
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"""
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Create a multipanel plot, returning the various pyptgraph elements.
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The layout is always a rectangular grid with shape (cols, rows)
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if letters is true, then the plot is labeled "A, B, C..."
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margins sets the margins around the outside of the plot
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spacing sets the spacing between the elements of the grid
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"""
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import string
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letters = string.ascii_uppercase
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widget = pg.QtGui.QWidget()
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gridLayout = pg.QtGui.QGridLayout()
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widget.setLayout(gridLayout)
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gridLayout.setContentsMargins(margins, margins, margins, margins)
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gridLayout.setSpacing(spacing)
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plots = [[0 for x in range(cols)] for x in range(rows)]
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i = 0
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for c in range(cols):
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for r in range(rows):
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plots[r][c] = pg.PlotWidget()
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gridLayout.addWidget(plots[r][c], r, c)
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# labelUp(plots[r][c], 'T(s)', 'Y', title = letters[i])
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i += 1
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if i > 25:
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i = 0
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if nmax is not None and i >= nmax:
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break # that's all - leave out empty plots
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return (plots, widget, gridLayout)
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def getnextrowcol(plx, row, col, cols):
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col += 1
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if col >= cols:
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col = 0
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row += 1
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return (plx[row][col], row, col)
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class Toy(Protocol):
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"""
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Calls to encapsulate the model runs
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Run a set of cells with defined parameters to show excitability patterns.
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Note that cells from Rothman and Manis are run at 22C; others at various
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temperatures depending on how they were initially measured and defined.
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"""
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def __init__(self):
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super(Toy, self).__init__()
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def current_name(self, name, n):
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"""
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From the name of the current model, get the current injection information
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Parameters
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---------
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name : str (no default)
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name of the cell type
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n : int (no default)
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"""
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if len(self.celltypes[name][3]) > 2:
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injs = self.celltypes[name][3]
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injarr = np.linspace(injs[0], injs[1], injs[2], endpoint=True)
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return "%.3f" % injarr[n]
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else:
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return "%.3f" % self.celltypes[name][3][n]
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def getname(self, cell, ninj):
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name = self.make_name(cell)
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iname = self.current_name(name, ninj)
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nname = name + " " + iname
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return name, nname
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def make_name(self, cell):
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return cell + ", " + self.celltypes[cell][1] + ":"
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def run(self):
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sre = re.compile(
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"(?P<cell>\w+)(?:[, ]*)(?P<type>[\w-]*)(?:[, ]*)(?P<species>[\w-]*)"
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) # regex for keys in cell types
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self.celltypes = OrderedDict(
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[
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("Bushy, II", (cells.Bushy, "II", "guineapig", (-0.5, 0.5, 11), 22)),
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(
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"Bushy, II-I",
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(cells.Bushy, "II-I", "guineapig", (-0.5, 0.5, 11), 22),
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),
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(
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"DStellate, I-II",
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(cells.DStellate, "I-II", "guineapig", (-0.3, 0.3, 9), 22),
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),
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(
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"TStellate, I-c",
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(cells.TStellate, "I-c", "guineapig", (-0.15, 0.15, 9), 22),
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),
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(
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"TStellate, I-t",
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(cells.TStellate, "I-t", "guineapig", (-0.15, 0.15, 9), 22),
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),
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(
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"Octopus, II-o",
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(cells.Octopus, "II-o", "guineapig", (-2.5, 2.5, 11), 22),
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),
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("Bushy, II, Mouse", (cells.Bushy, "II", "mouse", (-1, 1.2, 13), 34)),
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(
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"TStellate, I-c, Mouse",
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(cells.TStellate, "I-c", "mouse", (-1, 1, 9), 34),
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),
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(
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"DStellate, I-II, Mouse",
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(cells.DStellate, "I-II", "mouse", (-0.5, 0.5, 9), 34),
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),
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(
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"Pyramidal, I, Rat",
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(cells.Pyramidal, "I", "rat", (-0.3, 0.4, 11), 34),
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),
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(
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"Cartwheel, I, Mouse",
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(cells.Cartwheel, "I", "mouse", (-0.5, 0.5, 9), 34),
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),
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(
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"Tuberculoventral, I, Mouse",
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(cells.Tuberculoventral, "I", "mouse", (-0.35, 1, 11), 34),
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),
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("SGC, bm, Mouse", (cells.SGC, "bm", "mouse", (-0.2, 0.6, 9), 34)),
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("SGC, a, Mouse", (cells.SGC, "a", "mouse", (-0.2, 0.6, 9), 34)),
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]
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)
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dt = 0.025
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h.dt = dt
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h.celsius = 22
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stim = {"NP": 1, "delay": 10, "dur": 100, "amp": 0.0, "dt": h.dt}
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tend = stim["delay"] + stim["dur"] + 20.0
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netcells = {}
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for c in list(self.celltypes.keys()):
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g = sre.match(c)
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cellname = g.group("cell")
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modelType = g.group("type")
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species = self.celltypes[c][2]
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if g.group("type") == "":
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netcells[c] = self.celltypes[c][0].create()
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else:
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netcells[c] = self.celltypes[c][0].create(
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modelType=modelType, species=species, debug=False
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)
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# dicts to hold data
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pl = OrderedDict([])
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pl2 = OrderedDict([])
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rvec = OrderedDict([])
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vec = OrderedDict([])
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istim = OrderedDict([])
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ncells = len(list(self.celltypes.keys()))
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#
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# build plotting area
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#
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app = pg.mkQApp()
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self.win = pg.GraphicsWindow()
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self.win.setBackground("w")
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self.win.resize(800, 600)
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cols, rows = autorowcol(ncells)
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row = 0
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col = 0
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labelStyle = {"color": "#000", "font-size": "9pt", "weight": "normal"}
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tickStyle = pg.QtGui.QFont("Arial", 9, pg.QtGui.QFont.Light)
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self.iv = IVCurve() # use standard IVCurve here...
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for n, name in enumerate(self.celltypes.keys()):
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nrn_cell = netcells[
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name
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] # get the Neuron object we are using for this cell class
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injcmds = list(self.celltypes[name][3]) # list of injections
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injcmds[2] = (injcmds[1] - injcmds[0]) / (
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float(injcmds[2] - 1)
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) # convert to pulse format for IVCurve
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temperature = self.celltypes[name][4]
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nrn_cell.set_temperature(float(temperature))
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ninjs = len(injcmds)
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print("cell: ", name)
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# print( 'injs: ', injcmds)
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pl[name] = self.win.addPlot(
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labels={"left": "V (mV)", "bottom": "Time (ms)"}
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)
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PH.nice_plot(pl[name])
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pl[name].setTitle(title=name, font=pg.QtGui.QFont("Arial", 10))
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col += 1
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if col >= cols:
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col = 0
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self.win.nextRow()
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row += 1
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self.iv.reset()
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self.iv.run(
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{"pulse": [injcmds]},
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nrn_cell,
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durs=(stim["delay"], stim["dur"], 20.0),
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sites=None,
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reppulse=None,
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temp=float(temperature),
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)
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for k in range(len(self.iv.voltage_traces)):
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pl[name].plot(
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self.iv.time_values,
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self.iv.voltage_traces[k],
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pen=pg.mkPen("k", width=0.75),
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)
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pl[name].setRange(xRange=(0.0, 130.0), yRange=(-160.0, 40.0))
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PH.noaxes(pl[name])
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PH.calbar(
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pl[list(self.celltypes.keys())[0]],
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calbar=[0, -120.0, 10.0, 20.0],
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unitNames={"x": "ms", "y": "mV"},
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)
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text = u"{0:2d}\u00b0C {1:.2f}-{2:.2f} nA".format(
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int(temperature),
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np.min(self.iv.current_cmd),
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np.max(self.iv.current_cmd),
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)
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ti = pg.TextItem(text, anchor=(1, 0))
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ti.setFont(pg.QtGui.QFont("Arial", 9))
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ti.setPos(120.0, -120.0)
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pl[name].addItem(ti)
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# get overall Rin, etc; need to initialize all cells
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nrn_cell.cell_initialize()
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for n, name in enumerate(self.celltypes.keys()):
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nrn_cell = netcells[name]
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nrn_cell.vm0 = nrn_cell.soma.v
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pars = nrn_cell.compute_rmrintau(auto_initialize=False)
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print(
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"{0:>14s} [{1:>24s}] *** Rin = {2:6.1f} M\ohm Tau = {3:6.1f} ms Vm = {4:6.1f} mV".format(
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nrn_cell.status["name"], name, pars["Rin"], pars["tau"], pars["v"]
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)
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)
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if __name__ == "__main__":
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t = Toy()
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t.run()
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if sys.flags.interactive == 0:
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pg.QtGui.QApplication.exec_()
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# exporter = pg.exporters.ImageExporter(t.win.scene())
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# exporter.export('~/Desktop/Model_Figure2.svg')
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