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()
