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')