def plotRxDConcentration(speciesLabel,
regionLabel,
plane='xy',
figSize=(5, 10),
fontSize=10,
scalebar=False,
title=True,
showFig=True,
saveFig=True):
from .. import sim
# set font size
plt.rcParams.update({'font.size': fontSize})
species = sim.net.rxd['species'][speciesLabel]['hObj']
region = sim.net.rxd['regions'][regionLabel]['hObj']
plane2mean = {'xz': 1, 'xy': 2}
fig = plt.figure(figsize=figSize)
plt.imshow(species[region].states3d[:].mean(plane2mean[plane]).T,
interpolation='nearest',
origin='upper') # extent=k[extracellular].extent('xy')
ax = plt.gca()
if scalebar:
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
sb = ScaleBar(1e-6)
sb.location = 'lower left'
ax.add_artist(sb)
plt.colorbar(label='[' + species.name + '] (mM)')
plt.xlabel(plane[0] + ' location (um)')
plt.ylabel(plane[1] + ' location (um)')
if title:
plt.title('RxD: ' + species.name + ' concentration')
plt.tight_layout()
# show fig
if showFig: _showFigure()
# save figure
if saveFig:
if isinstance(saveFig, basestring):
filename = saveFig
else:
filename = sim.cfg.filename + '_rxd_concentration.png'
plt.savefig(filename)
return fig, {'data': species[region].states3d[:].mean(plane2mean[plane])}
def plotRxDConcentration(speciesLabel,
regionLabel,
plane='xy',
figSize=(5, 10),
clim=None,
fontSize=10,
scalebar=False,
title=True,
showFig=True,
saveFig=True,
**kwargs):
"""
Function to plot reaction-diffusion concentrations
Parameters
----------
speciesLabel : <type>
<Short description of speciesLabel>
**Default:** *required*
regionLabel : <type>
<Short description of regionLabel>
**Default:** *required*
plane : str
<Short description of plane>
**Default:** ``'xy'``
**Options:** ``<option>`` <description of option>
figSize : tuple
<Short description of figSize>
**Default:** ``(5, 10)``
**Options:** ``<option>`` <description of option>
fontSize : int
<Short description of fontSize>
**Default:** ``10``
**Options:** ``<option>`` <description of option>
scalebar : bool
<Short description of scalebar>
**Default:** ``False``
**Options:** ``<option>`` <description of option>
title : bool
<Short description of title>
**Default:** ``True``
**Options:** ``<option>`` <description of option>
showFig : bool
<Short description of showFig>
**Default:** ``True``
**Options:** ``<option>`` <description of option>
saveFig : bool
<Short description of saveFig>
**Default:** ``True``
**Options:** ``<option>`` <description of option>
"""
from .. import sim
print('Plotting RxD concentration ...')
# set font size
plt.rcParams.update({'font.size': fontSize})
species = sim.net.rxd['species'][speciesLabel]['hObj']
region = sim.net.rxd['regions'][regionLabel]['hObj']
plane2mean = {'xz': 1, 'xy': 2}
extent = []
extent.append(sim.net.rxd['regions'][regionLabel][plane[0] + 'lo'])
extent.append(sim.net.rxd['regions'][regionLabel][plane[0] + 'hi'])
extent.append(sim.net.rxd['regions'][regionLabel][plane[1] + 'lo'])
extent.append(sim.net.rxd['regions'][regionLabel][plane[1] + 'hi'])
vmin = None
vmax = None
if clim is not None:
vmin = clim[0]
vmax = clim[1]
fig = plt.figure(figsize=figSize)
plt.imshow(species[region].states3d[:].mean(plane2mean[plane]).T,
interpolation='nearest',
origin='upper',
extent=extent,
vmin=vmin,
vmax=vmax)
import numpy as np
print(' min:',
np.min(species[region].states3d[:].mean(plane2mean[plane]).T))
print(' max:',
np.max(species[region].states3d[:].mean(plane2mean[plane]).T))
ax = plt.gca()
if scalebar:
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
sb = ScaleBar(1e-6)
sb.location = 'lower left'
ax.add_artist(sb)
cb = plt.colorbar(label='[' + species.name + '] (mM)')
plt.xlabel(plane[0] + ' location (um)')
plt.ylabel(plane[1] + ' location (um)')
if saveFig == 'movie':
from neuron import h
cb.ax.set_title('Time = ' + str(round(h.t, 1)), fontsize=fontSize)
if title:
plt.title('RxD: ' + species.name + ' concentration')
plt.tight_layout()
# show fig
if showFig: _showFigure()
# save figure
if saveFig:
if isinstance(saveFig, basestring):
if saveFig == 'movie':
filename = sim.cfg.filename + '_rxd_concentration_movie_' + str(
round(h.t, 1)) + '.png'
else:
filename = saveFig
else:
filename = sim.cfg.filename + '_rxd_concentration.png'
plt.savefig(filename)
return fig, {'data': species[region].states3d[:].mean(plane2mean[plane])}
cax = divider.append_axes('bottom', size='5%', pad=0.1)
cbar = plt.colorbar(mapColor, cax=cax, orientation='horizontal')
xpos = np.linspace(vmin, vmax, 7)
xpos = np.around(xpos, decimals=1)
cbar.set_ticks(xpos)
cbar.ax.xaxis.tick_bottom()
cbar.ax.xaxis.set_label_position('bottom')
cbar.ax.set_xlabel('Composição de {} (% massa)'.format(el))
# ax.text(s=el, x=15, y=170, backgroundcolor='white')
ax.axhline(135, color='black', ls='--', lw=1.5)
if i == 0:
from matplotlib_scalebar.scalebar import ScaleBar
scalebar = ScaleBar(1e-6)
scalebar.location = 'lower right'
ax.add_artist(scalebar)
i += 1
I['C'] = comp['C'].values.reshape(400, -1)
ax = axes[i][0]
Si = np.mean(I['Si'][129:131, :], axis=0)
Mn = np.mean(I['Mn'][129:131, :], axis=0)
Cu = np.mean(I['Cu'][129:131, :], axis=0)
C = np.mean(I['C'][129:131, :], axis=0)
C[100:110] = 100.
x = np.linspace(0, 400., 400)
ax.plot(x, Si, lw=1.)
def plotRxDConcentration(speciesLabel, regionLabel, plane='xy', figSize=(5,10), fontSize=10, scalebar=False, title=True, showFig=True, saveFig=True):
"""
Function for/to <short description of `netpyne.analysis.rxd.plotRxDConcentration`>
Parameters
----------
speciesLabel : <type>
<Short description of speciesLabel>
**Default:** *required*
regionLabel : <type>
<Short description of regionLabel>
**Default:** *required*
plane : str
<Short description of plane>
**Default:** ``'xy'``
**Options:** ``<option>`` <description of option>
figSize : tuple
<Short description of figSize>
**Default:** ``(5, 10)``
**Options:** ``<option>`` <description of option>
fontSize : int
<Short description of fontSize>
**Default:** ``10``
**Options:** ``<option>`` <description of option>
scalebar : bool
<Short description of scalebar>
**Default:** ``False``
**Options:** ``<option>`` <description of option>
title : bool
<Short description of title>
**Default:** ``True``
**Options:** ``<option>`` <description of option>
showFig : bool
<Short description of showFig>
**Default:** ``True``
**Options:** ``<option>`` <description of option>
saveFig : bool
<Short description of saveFig>
**Default:** ``True``
**Options:** ``<option>`` <description of option>
"""
from .. import sim
# set font size
plt.rcParams.update({'font.size': fontSize})
species = sim.net.rxd['species'][speciesLabel]['hObj']
region = sim.net.rxd['regions'][regionLabel]['hObj']
plane2mean = {'xz': 1, 'xy': 2}
extent = []
extent.append(sim.net.rxd['regions'][regionLabel][plane[0] + 'lo'])
extent.append(sim.net.rxd['regions'][regionLabel][plane[0] + 'hi'])
extent.append(sim.net.rxd['regions'][regionLabel][plane[1] + 'lo'])
extent.append(sim.net.rxd['regions'][regionLabel][plane[1] + 'hi'])
fig = plt.figure(figsize=figSize)
plt.imshow(species[region].states3d[:].mean(plane2mean[plane]).T, interpolation='nearest', origin='upper', extent=extent)
ax = plt.gca()
if scalebar:
ax.xaxis.set_visible(False)
ax.yaxis.set_visible(False)
sb = ScaleBar(1e-6)
sb.location = 'lower left'
ax.add_artist(sb)
plt.colorbar(label='[' + species.name + '] (mM)')
plt.xlabel(plane[0] + ' location (um)')
plt.ylabel(plane[1] + ' location (um)')
if title:
plt.title('RxD: ' + species.name + ' concentration')
plt.tight_layout()
# show fig
if showFig: _showFigure()
# save figure
if saveFig:
if isinstance(saveFig, basestring):
filename = saveFig
else:
filename = sim.cfg.filename + '_rxd_concentration.png'
plt.savefig(filename)
return fig, {'data': species[region].states3d[:].mean(plane2mean[plane])}
