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) toolbox_idynomics.color_cells_by_species(iter_info.agent_output, species_color_dict) toolbox_idynomics.plot_cells_2d(axis, iter_info.agent_output) if options.substratum: axis.fill_between([0, nJ*res], [0]*2, y2=[-res]*2, color='k', zorder=-1) figure.subplots_adjust(left=0.01, bottom=0.01, right=0.9, top=0.9) figure.inset_axes() if not options.solute_name == "none": #print min_max_concns[options.solute_name] solute_output = toolbox_results.SoluteOutput(iter_info.env_output, name=options.solute_name) cs = toolbox_idynomics.solute_contour(axis, solute_output, concn_range=min_max_concns[options.solute_name], interpolation='bicubic') if options.color_bar: toolbox_plotting.make_colorbar(axis, cs) 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') if options.timeon: axis.text(0.0, nI*res, 'Time: %d h'%(int(iter_info.time)), va='top', ha='left') axis.set_xlim(0, nJ * res) axis.set_ylim(-res, nI * res) save_num = str(iter_info.number) #save_num = str(counter) #counter += 1 save_num = (num_digits - len(save_num))*'0' + save_num save_path = os.path.join(sim.figures_dir, save_name+'_'+save_num+options.file_ext) figure.save(save_path, dpi=options.dpi)
def plot(iter_info): axis = figure.add_subplot('', 111, frameon=options.frameon) toolbox_idynomics.color_cells_by_species( iter_info.agent_output, species_color_dict) toolbox_idynomics.plot_cells_3d_curtains(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(r'y ($\mu$m') axis.set_ylabel(r'x ($\mu$m') 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) toolbox_idynomics.color_cells_by_species(iter_info.agent_output, species_color_dict) toolbox_idynomics.plot_cells_2d(axis, iter_info.agent_output) if options.substratum: axis.fill_between([0, nJ * res], [0] * 2, y2=[-res] * 2, color='k', zorder=-1) lb = 0.01 if options.frameon: lb = 0.06 figure.process_lines() figure.subplots_adjust(left=lb, bottom=lb, right=0.9, top=0.9) figure.inset_axes() if not options.solute_name == "none": #print min_max_concns[options.solute_name] solute_output = toolbox_results.SoluteOutput(iter_info.env_output, name=options.solute_name) cs = toolbox_idynomics.solute_contour( axis, solute_output, concn_range=min_max_concns[options.solute_name], interpolation='bicubic') if options.color_bar: toolbox_plotting.make_colorbar(axis, cs) if options.titleon: axis.set_title(r'Biofilm (%s g L$^{-1}$)' % (options.solute_name)) if options.frameon: axis.set_xlabel(r'x ($\mu$m)') axis.set_ylabel(r'y ($\mu$m)') if options.timeon: axis.text(0.1 * res, (nI + 0.1) * res, 'Time: %d h' % (int(iter_info.time)), va='bottom', ha='left', color='0.5') axis.set_xlim(0, nJ * res) axis.set_ylim(-res, nI * res) save_num = str(iter_info.number) #save_num = str(counter) #counter += 1 save_num = (num_digits - len(save_num)) * '0' + save_num save_path = os.path.join(sim.figures_dir, save_name + '_' + save_num + options.file_ext) figure.save(save_path, dpi=options.dpi)
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'))
sim = toolbox_idynomics.SimulationDirectory(options.results_dir) iter_info = sim.get_single_iterate(options.iter_num) save_name = 'biofilm_'+options.solute_name num_digits = len(str(sim.get_last_iterate_number())) colors = [(0, 0, 1), (0, 1, 0), (1, 0, 0), (0, 1, 1), (1, 1, 0), (1, 0, 1)] species_color_dict = {} script = 'Species name\t\tRGB color\n' for species_name in sim.get_species_names(): script += species_name+'\t\t'+str(colors[0])+'\n' species_color_dict[species_name] = colors[0] colors.pop(0) toolbox_idynomics.color_cells_by_species(iter_info.agent_output, species_color_dict) figure = toolbox_plotting.SlideFigure() axis = figure.add_subplot('', 111, frameon=False, projection='3d') axis.view_init(azim=45, elev=35) solute_output = toolbox_results.SoluteOutput(iter_info.env_output, name=options.solute_name) res = solute_output.grid_res width = solute_output.grid_nJ * res height = solute_output.grid_nI * res depth = solute_output.grid_nK * res extent = [0, width, 0, height] array = solute_output.concentration_array()