How to use the landlab.plot.channel_profile function in landlab

mg = fr.route_flow()
    # mg.calculate_gradient_across_cell_faces(mg.at_node['topographic__elevation'])
    #neighbor_slopes = mg.calculate_gradient_along_node_links(mg.at_node['topographic__elevation'])
    #mean_slope = np.mean(np.fabs(neighbor_slopes),axis=1)
    #max_slope = np.max(np.fabs(neighbor_slopes),axis=1)
    #mg,_,capacity_out = tl.erode(mg,dt,slopes_at_nodes='topographic__steepest_slope')
    #mg,_,capacity_out = tl.erode(mg,dt,slopes_at_nodes=max_slope)
    mg_copy = deepcopy(mg)
    mg, _ = tl.erode(mg, dt, stability_condition='loose')
    if i % 20 == 0:
        print('loop ', i)
        print('subdivisions of dt used: ', tl.iterations_in_dt)
        print('max_slope', np.amax(
            mg.at_node['topographic__steepest_slope'][mg.core_nodes]))
        pylab.figure("long_profiles")
        profile_IDs = prf.channel_nodes(mg, mg.at_node['topographic__steepest_slope'],
                                        mg.at_node['drainage_area'], mg.at_node['flow_receiver'])
        dists_upstr = prf.get_distances_upstream(mg, len(mg.at_node['topographic__steepest_slope']),
                                                 profile_IDs, mg.at_node['links_to_flow_receiver'])
        prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node[
                          'topographic__elevation'])
    # mg.update_boundary_nodes()
    #vid.add_frame(mg, 'topographic__elevation')


print('Completed the simulation. Plotting...')

time_off = time()

#Finalize and plot

elev = mg['node']['topographic__elevation']

#neighbor_slopes = mg.calculate_gradient_along_node_links(mg.at_node['topographic__elevation'])
    #mean_slope = np.mean(np.fabs(neighbor_slopes),axis=1)
    #max_slope = np.max(np.fabs(neighbor_slopes),axis=1)
    #mg,_,capacity_out = tl.erode(mg,dt,slopes_at_nodes='topographic__steepest_slope')
    #mg,_,capacity_out = tl.erode(mg,dt,slopes_at_nodes=max_slope)
    mg_copy = deepcopy(mg)
    mg, _ = tl.erode(mg, dt, stability_condition='loose')
    if i % 20 == 0:
        print('loop ', i)
        print('subdivisions of dt used: ', tl.iterations_in_dt)
        print('max_slope', np.amax(
            mg.at_node['topographic__steepest_slope'][mg.core_nodes]))
        pylab.figure("long_profiles")
        profile_IDs = prf.channel_nodes(mg, mg.at_node['topographic__steepest_slope'],
                                        mg.at_node['drainage_area'], mg.at_node['flow_receiver'])
        dists_upstr = prf.get_distances_upstream(mg, len(mg.at_node['topographic__steepest_slope']),
                                                 profile_IDs, mg.at_node['links_to_flow_receiver'])
        prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node[
                          'topographic__elevation'])
    # mg.update_boundary_nodes()
    #vid.add_frame(mg, 'topographic__elevation')


print('Completed the simulation. Plotting...')

time_off = time()

#Finalize and plot

elev = mg['node']['topographic__elevation']
#imshow.imshow_node_grid(mg, elev)

#mg,_,capacity_out = tl.erode(mg,dt,slopes_at_nodes='topographic__steepest_slope')
    #mg,_,capacity_out = tl.erode(mg,dt,slopes_at_nodes=max_slope)
    mg_copy = deepcopy(mg)
    mg, _ = sde.erode(mg, dt)
    # print sde.iterations_in_dt
    # print 'capacity ', np.amax(capacity_out[mg.core_nodes])
    # print 'rel sed ',
    # np.nanmax(sed_in[mg.core_nodes]/capacity_out[mg.core_nodes])
    if i % 100 == 0:
        print('loop ', i)
        print('max_slope', np.amax(
            mg.at_node['topographic__steepest_slope'][mg.core_nodes]))
        pylab.figure("long_profiles")
        profile_IDs = prf.channel_nodes(mg, mg.at_node['topographic__steepest_slope'],
                                        mg.at_node['drainage_area'], mg.at_node['flow__receiver_node'])
        dists_upstr = prf.get_distances_upstream(mg, len(mg.at_node['topographic__steepest_slope']),
                                                 profile_IDs, mg.at_node['flow__link_to_receiver_node'])
        prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node[
                          'topographic__elevation'])
    #vid.add_frame(mg, 'topographic__elevation')


print('Completed the simulation. Plotting...')

time_off = time()

#Finalize and plot

elev = mg['node']['topographic__elevation']
#imshow.imshow_node_grid(mg, elev)

print('Done.')

print("Short step!")
        dt = time_to_run - elapsed_time
    mg = fr.run_one_step()
    #print 'Area: ', numpy.max(mg.at_node['drainage_area'])
    #mg = fsp.erode(mg)
    mg,_,_ = sp.erode(mg, dt, K_if_used='K_values')

    #plot long profiles along channels
    if numpy.allclose(elapsed_time%out_tstep,0.) or numpy.allclose(elapsed_time%out_tstep,1.):
        pylab.figure("long_profiles")
        profile_IDs = prf.channel_nodes(mg, mg.at_node['topographic__steepest_slope'],
                        mg.at_node['drainage_area'], mg.at_node['flow__receiver_node'])
        dists_upstr = prf.get_distances_upstream(mg, len(mg.at_node['topographic__steepest_slope']),
                        profile_IDs, mg.at_node['flow__link_to_receiver_node'])

        prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node['topographic_elevation'])
        x_profiles.append(dists_upstr[:])
        z_profiles.append(mg.at_node['topographic_elevation'][profile_IDs])
        S_profiles.append(mg.at_node['steepest_slope'][profile_IDs])
        A_profiles.append(mg.at_node['drainage_area'][profile_IDs])
        prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node['topographic__elevation'])


    #add uplift
    mg.at_node['topographic__elevation'][mg.core_nodes] += 5.*uplift*dt

    elapsed_time += dt

#Finalize and plot
elev = mg['node']['topographic__elevation']
elev_r = mg.node_vector_to_raster(elev)

dt=10000.
out_tstep = 50000.
elapsed_time = 0. #total time in simulation
while elapsed_time < time_to_run:
    if elapsed_time+dt>time_to_run:
        print("Short step!")
        dt = time_to_run - elapsed_time
    mg = fr.run_one_step()
    #print 'Area: ', numpy.max(mg.at_node['drainage_area'])
    #mg = fsp.erode(mg)
    mg,_,_ = sp.erode(mg, dt, K_if_used='K_values')

    #plot long profiles along channels
    if numpy.allclose(elapsed_time%out_tstep,0.) or numpy.allclose(elapsed_time%out_tstep,1.):
        pylab.figure("long_profiles")
        profile_IDs = prf.channel_nodes(mg, mg.at_node['topographic__steepest_slope'],
                        mg.at_node['drainage_area'], mg.at_node['flow__receiver_node'])
        dists_upstr = prf.get_distances_upstream(mg, len(mg.at_node['topographic__steepest_slope']),
                        profile_IDs, mg.at_node['flow__link_to_receiver_node'])

        prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node['topographic_elevation'])
        x_profiles.append(dists_upstr[:])
        z_profiles.append(mg.at_node['topographic_elevation'][profile_IDs])
        S_profiles.append(mg.at_node['steepest_slope'][profile_IDs])
        A_profiles.append(mg.at_node['drainage_area'][profile_IDs])
        prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node['topographic__elevation'])


    #add uplift
    mg.at_node['topographic__elevation'][mg.core_nodes] += 5.*uplift*dt

    elapsed_time += dt

precip_perturb = PrecipitationDistribution(input_file=input_file_string, mean_storm=10., mean_interstorm=40., total_t=time_to_run)
    out_interval = 5000.
    last_trunc = time_to_run #we use this to trigger taking an output plot
    for (interval_duration, rainfall_rate) in precip_perturb.yield_storm_interstorm_duration_intensity():
        if rainfall_rate != 0.:
            mg.at_node['water__unit_flux_in'].fill(rainfall_rate)
            mg = fr.run_one_step() #the runoff_rate should pick up automatically
            #print 'Area: ', numpy.max(mg.at_node['drainage_area'])
            mg,_,_ = sp.erode(mg, interval_duration, Q_if_used='surface_water__discharge', K_if_used='K_values')

        #plot long profiles along channels
        this_trunc = precip_perturb.elapsed_time//out_interval
        if this_trunc != last_trunc: #a new loop round
            print('saving a plot at perturbed loop ', out_interval*this_trunc)
            pylab.figure("long_profiles")
            profile_IDs = prf.channel_nodes(mg, mg.at_node['topographic__steepest_slope'],
                            mg.at_node['drainage_area'], mg.at_node['flow__receiver_node'])
            dists_upstr = prf.get_distances_upstream(mg, len(mg.at_node['topographic__steepest_slope']),
                            profile_IDs, mg.at_node['flow__link_to_receiver_node'])
            prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node['topographic__elevation'])
            last_trunc=this_trunc
            x_profiles.append(dists_upstr[:])
            z_profiles.append(mg.at_node['topographic_elevation'][profile_IDs])
            S_profiles.append(mg.at_node['steepest_slope'][profile_IDs])
            A_profiles.append(mg.at_node['drainage_area'][profile_IDs])

        #add uplift
        mg.at_node['topographic__elevation'][mg.core_nodes] += 5.*uplift*interval_duration

#Finalize and plot
elev = mg['node']['topographic__elevation']
elev_r = mg.node_vector_to_raster(elev)

for i in range(nt):
    # print 'loop ', i
    mg.at_node["topographic__elevation"][mg.core_nodes] += uplift_per_step
    mg = fr.route_flow(grid=mg)
    if DL_or_TL == "TL":
        mg, _ = tle.erode(mg, dt)
    else:
        mg, _, _ = spe.erode(mg, dt=dt)
    if i % init_interval == 0:
        print("loop {0}".format(i))
        print(
            "max_slope",
            np.amax(mg.at_node["topographic__steepest_slope"][mg.core_nodes]),
        )
        pylab.figure("long_profiles_init")
        profile_IDs = prf.channel_nodes(
            mg,
            mg.at_node["topographic__steepest_slope"],
            mg.at_node["drainage_area"],
            mg.at_node["flow__receiver_node"],
        )
        dists_upstr = prf.get_distances_upstream(
            mg,
            len(mg.at_node["topographic__steepest_slope"]),
            profile_IDs,
            mg.at_node["flow__link_to_receiver_node"],
        )
        prf.plot_profiles(
            dists_upstr, profile_IDs, mg.at_node["topographic__elevation"]
        )

print("completed run to steady state...")

else:
        mg, _, _ = spe.erode(mg, dt=dt)
    if i % init_interval == 0:
        print("loop {0}".format(i))
        print(
            "max_slope",
            np.amax(mg.at_node["topographic__steepest_slope"][mg.core_nodes]),
        )
        pylab.figure("long_profiles_init")
        profile_IDs = prf.channel_nodes(
            mg,
            mg.at_node["topographic__steepest_slope"],
            mg.at_node["drainage_area"],
            mg.at_node["flow__receiver_node"],
        )
        dists_upstr = prf.get_distances_upstream(
            mg,
            len(mg.at_node["topographic__steepest_slope"]),
            profile_IDs,
            mg.at_node["flow__link_to_receiver_node"],
        )
        prf.plot_profiles(
            dists_upstr, profile_IDs, mg.at_node["topographic__elevation"]
        )

print("completed run to steady state...")
if show_figs_in_run:
    show()  # will cause a hang

# save a copy of the init conditions:
mg_init = deepcopy(mg)

fr = FlowRouter(mg)
sp = SPEroder(mg, input_file)
diffuse = PerronNLDiffuse(mg, input_file)
lin_diffuse = DiffusionComponent(grid=mg, input_stream=input_file)

#perform the loops:
for i in xrange(nt):
    #note the input arguments here are not totally standardized between modules
    #mg = diffuse.diffuse(mg, i*dt)
    mg = lin_diffuse.diffuse(mg, dt)
    mg = fr.route_flow(grid=mg)
    sp.erode(dt)
    
    ##plot long profiles along channels
    pylab.figure(6)
    profile_IDs = prf.channel_nodes(mg, mg.at_node['steepest_slope'],
            mg.at_node['drainage_area'], mg.at_node['upstream_ID_order'],
            mg.at_node['flow_receiver'])
    dists_upstr = prf.get_distances_upstream(mg, len(mg.at_node['steepest_slope']),
            profile_IDs, mg.at_node['links_to_flow_receiver'])
    prf.plot_profiles(dists_upstr, profile_IDs, mg.at_node['topographic_elevation'])

    print 'Completed loop ', i
 
print 'Completed the simulation. Plotting...'


#Finalize and plot
# Clear previous plots
pylab.figure(1)
pylab.close()
pylab.figure(1)

sde = SedDepEroder(mg, input_file)
# don't allow overwriting of these, just in case
try:
    x_profiles
except NameError:
    x_profiles = []
    z_profiles = []
    S_profiles = []
    A_profiles = []

# plot init conds
if make_output_plots:
    mg = fr.route_flow(grid=mg)
    pylab.figure("long_profile_anim")
    ylim([0, y_max])
    prf.analyze_channel_network_and_plot(mg)
    savefig("0profile_anim_init.png")
    close("long_profile_anim")

(profile_IDs, dists_upstr) = prf.analyze_channel_network_and_plot(mg)
start_node = [profile_IDs[0]]

time_on = time()
# perform the loops:
for i in range(nt):
    # print 'loop ', i
    mg.at_node["topographic__elevation"][mg.core_nodes] += uplift_per_step
    mg = fr.run_one_step()
    # mg.calc_grad_across_cell_faces(mg.at_node['topographic__elevation'])
    # neighbor_slopes = mg.calc_grad_along_node_links(mg.at_node['topographic__elevation'])
    # mean_slope = np.mean(np.fabs(neighbor_slopes),axis=1)
    # max_slope = np.max(np.fabs(neighbor_slopes),axis=1)