def plot(iter_info, min_max_concns):
axis = figure.add_subplot('',
111,
frameon=options.frameon,
projection='3d')
axis.view_init(azim=45, elev=35)
if not options.solute_name == "none":
solute_output = toolbox_results.SoluteOutput(iter_info.env_output,
name=options.solute_name)
cs = toolbox_idynomics.solute_contour_3d(
axis,
solute_output,
concn_range=min_max_concns[options.solute_name])
if options.color_bar:
matplotlib.pyplot.colorbar(cs)
toolbox_idynomics.color_cells_by_species(iter_info.agent_output,
species_color_dict)
toolbox_idynomics.plot_cells_3d(axis, iter_info.agent_output)
if options.titleon:
axis.set_title(r'Biofilm (%s g L$^{-1}$)' % (options.solute_name))
if options.frameon:
axis.set_xlabel('x')
axis.set_ylabel('y')
axis.set_zlabel('z')
save_num = str(iter_info.number)
save_num = (num_digits - len(save_num)) * '0' + save_num
figure.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
figure.save(
os.path.join(sim.figures_dir, save_name + '_' + save_num + '.png'))
def plot(iter_info, min_max_concns):
axis = figure.add_subplot('', 111,
frameon=options.frameon, projection='3d')
axis.view_init(azim=45, elev=35)
if not options.solute_name == "none":
solute_output = toolbox_results.SoluteOutput(
iter_info.env_output, name=options.solute_name)
cs = toolbox_idynomics.solute_contour_3d(axis, solute_output,
concn_range=min_max_concns[options.solute_name])
if options.color_bar:
matplotlib.pyplot.colorbar(cs)
toolbox_idynomics.color_cells_by_species(
iter_info.agent_output, species_color_dict)
toolbox_idynomics.plot_cells_3d(axis, iter_info.agent_output)
if options.titleon:
axis.set_title(r'Biofilm (%s g L$^{-1}$)'%(options.solute_name))
if options.frameon:
axis.set_xlabel('x')
axis.set_ylabel('y')
axis.set_zlabel('z')
save_num = str(iter_info.number)
save_num = (num_digits - len(save_num))*'0' + save_num
figure.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
figure.save(os.path.join(sim.figures_dir, save_name+'_'+save_num+'.png'))
arrayX = array[:, :, 0]
Y, Z = numpy.meshgrid(numpy.linspace(0, depth, solute_output.grid_nK),
numpy.linspace(0, height, solute_output.grid_nI))
cs = axis.contourf(arrayX, Y, Z, zdir='x', cmap='gray', offset=0,
zorder=-1, levels=levels)#, vmin=min_concn, vmax=max_concn)
arrayY = array[:, 0, :]
X, Z = numpy.meshgrid(numpy.linspace(0, width, solute_output.grid_nJ),
numpy.linspace(0, height, solute_output.grid_nI))
cs = axis.contourf(X, arrayY, Z, zdir='y', cmap='gray', offset=0,#depth,
zorder=-1, levels=levels)#, vmin=min_concn, vmax=max_concn)
#arrayZ = array[1][:][:]
arrayZ = numpy.zeros([17, 17])
X, Y = numpy.meshgrid(numpy.linspace(0, width, solute_output.grid_nJ),
numpy.linspace(0, depth, solute_output.grid_nK))
cs = axis.contourf(X, Y, arrayZ, zdir='z', cmap='gray', offset=0,
zorder=-1, levels=levels)#, vmin=min_concn, vmax=max_concn)
toolbox_idynomics.plot_cells_3d(axis, iter_info.agent_output)
axis.set_xlim([0, width])
axis.set_ylim([0, depth])
axis.set_zlim([0, height])
#axis.set_xlabel('x')
#axis.set_ylabel('y')
#axis.set_zlabel('z')
#toolbox_plotting.make_colorbar(axis, cs, side="left")
#figure.fig.colorbar(cs)
figure.save('blah.png')
