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])}