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bl_topogenr.py
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##~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~##
## ##
## This file forms part of the BayesLands surface processes modelling companion. ##
## ##
## For full license and copyright information, please refer to the LICENSE.md file ##
## located at the project root, or contact the authors. ##
## ##
##~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~##
#Main Contributer: Danial Azam Email: [email protected]
"""
This script is intended to generate the input and final-time topography used by the mcmc file.
"""
import os
import numpy as np
import random
import time
import math
import copy
import fnmatch
import shutil
import plotly
import collections
import argparse
import plotly.plotly as py
import matplotlib as mpl
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import cmocean as cmo
import plotly.graph_objs as go
from copy import deepcopy
from pylab import rcParams
from PIL import Image
from io import StringIO
from cycler import cycler
from matplotlib.patches import Polygon
from matplotlib.collections import PatchCollection
from scipy.spatial import cKDTree
from scipy import stats
from pyBadlands.model import Model as badlandsModel
from mpl_toolkits.axes_grid1 import make_axes_locatable
from mpl_toolkits.mplot3d import Axes3D
from scipy.stats import multivariate_normal
from plotly.graph_objs import *
from plotly.offline.offline import _plot_html
plotly.offline.init_notebook_mode()
parser=argparse.ArgumentParser(description='PTBayeslands modelling')
parser.add_argument('-p','--problem', help='Problem Number 1-crater-fast,2-crater,3-etopo-fast,4-etopo,5-null,6-mountain', required=True, dest="problem",type=int)
args = parser.parse_args()
problem = args.problem
def interpolateArray(coords=None, z=None, dz=None):
"""
Interpolate the irregular spaced dataset from badlands on a regular grid.
Parameters
----------
variable : coords
R.
variable: z
F.
variable: dz
F.
"""
x, y = np.hsplit(coords, 2)
dx = (x[1]-x[0])[0]
nx = int((x.max() - x.min())/dx+1)
ny = int((y.max() - y.min())/dx+1)
xi = np.linspace(x.min(), x.max(), nx)
yi = np.linspace(y.min(), y.max(), ny)
xi, yi = np.meshgrid(xi, yi)
xyi = np.dstack([xi.flatten(), yi.flatten()])[0]
XY = np.column_stack((x,y))
tree = cKDTree(XY)
distances, indices = tree.query(xyi, k=3)
if len(z[indices].shape) == 3:
z_vals = z[indices][:,:,0]
dz_vals = dz[indices][:,:,0]
else:
z_vals = z[indices]
dz_vals = dz[indices]
zi = np.average(z_vals,weights=(1./distances), axis=1)
dzi = np.average(dz_vals,weights=(1./distances), axis=1)
onIDs = np.where(distances[:,0] == 0)[0]
if len(onIDs) > 0:
zi[onIDs] = z[indices[onIDs,0]]
dzi[onIDs] = dz[indices[onIDs,0]]
zreg = np.reshape(zi,(ny,nx))
dzreg = np.reshape(dzi,(ny,nx))
return zreg,dzreg
def topoGenerator(directory, inputname, rain, erodibility, m, n, simtime, erdp_coords, final_noise):
"""
Parameters
----------
variable : directory
variable: inputname
variable: height
variable: zmin
variable: zmax
variable: height
variable: zData
variable: title
"""
sim_interval = np.arange(0, simtime+1, simtime/4)
model = badlandsModel()
model.load_xml(str(simtime), inputname, verbose = False, muted = True)
model.input.SPLero = erodibility
model.flow.erodibility.fill(erodibility)
model.force.rainVal[:] = rain
model.input.SPLm = m
model.input.SPLn = n
# bPts = model.recGrid.boundsPt
# print ('bPTs', bPts)
# ePts = model.recGrid.edgesPt
# print ('ePTs', ePts)
# print(model.disp)
# # model.force.disp[::bPts] = 0
# return
elev_vec = collections.OrderedDict()
erdp_vec = collections.OrderedDict()
erdp_pts_vec = collections.OrderedDict()
for x in range(len(sim_interval)):
simtime = sim_interval[x]
model.run_to_time(simtime, muted = True)
elev, erdp = interpolateArray(model.FVmesh.node_coords[:, :2], model.elevation, model.cumdiff)
erdp_pts = np.zeros((erdp_coords.shape[0]))
for count, val in enumerate(erdp_coords):
erdp_pts[count] = erdp[val[0], val[1]]
# Adding Noise
tausq_elev = elev.max()* (0.01) + 0.5
tausq_erdp = erdp.max()* (0.01) + 0.5
tausq_erdp_pts = erdp_pts.max()*(0.01) + 0.5
elev_noise = np.random.normal(0, np.sqrt(abs(tausq_elev)), elev.size)
elev_noise = np.reshape(elev_noise,(elev.shape[0],elev.shape[1]))
erdp_noise = np.random.normal(0, np.sqrt(abs(tausq_erdp)), erdp.size)
erdp_noise = np.reshape(erdp_noise,(erdp.shape[0],erdp.shape[1]))
erdp_pts_noise = np.random.normal(0, np.sqrt(abs(tausq_erdp_pts)), erdp_pts.size)
erdp_pts_noise = np.reshape(erdp_pts_noise,(erdp_pts.shape))
elev_=np.matrix(elev)
erdp_=np.matrix(erdp)
erdp_pts_ = np.matrix(erdp_pts)
if final_noise and simtime==sim_interval[-1]:
elev_mat=np.add(elev_, elev_noise)
erdp_mat=np.add(erdp_, erdp_noise)
erdp_pts_mat = np.add(erdp_pts_, erdp_pts_noise)
else:
elev_mat = elev_
erdp_mat = erdp_
erdp_pts_mat = erdp_pts_
elev_vec[simtime] = elev_mat
erdp_vec[simtime] = erdp_mat
erdp_pts_vec[simtime] = erdp_pts_mat
for k, v in elev_vec.items():
if k == sim_interval[0]:
np.savetxt('%s/data/initial_elev.txt' %directory, elev_vec[k],fmt='%.5f')
viewGrid(directory,'initial_elev', 'N/A', rain, erodibility, zData=elev_vec[k], title='Export Slope Grid')
elif k == sim_interval[-1]:
np.savetxt('%s/data/final_elev.txt' %directory, elev_vec[k],fmt='%.5f')
viewGrid(directory,'final_elev', 'N/A', rain, erodibility, zData=elev_vec[k], title='Export Slope Grid')
for k, v in erdp_vec.items():
# if k == sim_interval[0]:
# np.savetxt('%s/data/initial_erdp.txt' %directory, erdp_vec[k],fmt='%.5f')
# viewMap(directory,'initial_erdp', 'N/A', rain, erodibility, zData=erdp_vec[k], title='Export Slope Grid')
if k == sim_interval[-1]:
np.savetxt('%s/data/final_erdp.txt' %directory, erdp_vec[k],fmt='%.5f')
viewMap(directory,'final_erdp', 'N/A', rain, erodibility, zData=erdp_vec[k], title='Export Slope Grid')
erdp_pts_arr = np.zeros((sim_interval.size, erdp_pts_mat.size))
count = 0
for k, v in erdp_pts_vec.items():
erdp_pts_arr[count] = v
count +=1
# if k == sim_interval[0]:
# np.savetxt('%s/data/initial_erdp_pts.txt' %directory, erdp_pts_vec[k],fmt='%.5f')
# viewBar(directory,'initial_erdp_pts', 'N/A', rain, erodibility, xData = erdp_coords, yData=erdp_pts_mat, title='Export Slope Grid')
if k == sim_interval[-1]:
np.savetxt('%s/data/final_erdp_pts.txt' %directory,erdp_pts_arr,fmt='%.5f')
viewBar(directory,'final_erdp_pts', 'N/A', rain, erodibility, xData = erdp_coords ,yData=erdp_pts_arr[-1], title='Export Slope Grid')
return
def viewGrid(directory,sample_num, likl, rain, erod, width = 1000, height = 1000, zmin = None, zmax = None, zData = None, title='Export Grid'):
"""
Use Plotly library to visualise the grid in 3D.
Parameters
----------
variable : resolution
Required resolution for the model grid (in metres).
variable: width
Figure width.
variable: height
Figure height.
variable: zmin
Minimal elevation.
variable: zmax
Maximal elevation.
variable: height
Figure height.
variable: zData
Elevation data to plot.
variable: title
Title of the graph.
"""
if zmin == None:
zmin = zData.min()
if zmax == None:
zmax = zData.max()
axislabelsize = 20
data = Data([ Surface( x=zData.shape[0], y=zData.shape[1], z=zData, colorscale='YlGnBu', showscale = False ) ])
layout = Layout(
autosize=True,
width=width,
height=height,
scene=Scene(
zaxis=ZAxis(title = 'Elev.(m) ', range=[zmin,zmax], autorange=False, nticks=4, gridcolor='rgb(255, 255, 255)',
gridwidth=2, zerolinecolor='rgb(255, 255, 255)', zerolinewidth=2, showticklabels = True, titlefont=dict(size=axislabelsize),
tickfont=dict(size=14 ),),
xaxis=XAxis(title = 'X (km) ',nticks = 8, gridcolor='rgb(255, 255, 255)', gridwidth=2,zerolinecolor='rgb(255, 255, 255)',
zerolinewidth=2, showticklabels = True, titlefont=dict(size=axislabelsize), tickfont=dict(size=14 ),),
yaxis=YAxis(title = 'Y (km) ',nticks = 8, gridcolor='rgb(255, 255, 255)', gridwidth=2,zerolinecolor='rgb(255, 255, 255)',
zerolinewidth=2, showticklabels = True, titlefont=dict(size=axislabelsize), tickfont=dict(size=14 ),),
bgcolor="rgb(244, 244, 248)"
)
)
fig = Figure(data=data, layout=layout)
if directory == 'Examples/crater':
camera = dict(
up=dict(x=0, y=0, z=1),
center=dict(x=0.1, y=0.0, z=-0.15),
eye=dict(x=0.85, y=1.1, z=1.4)
)
elif directory == 'Examples/etopo':
camera = dict(
up=dict(x=0, y=0, z=1),
center=dict(x=-0.075, y=-0.075, z=-0.1),
eye=dict(x=1.25, y=-1.25, z=1.35)
)
else: #Default
camera = dict(
up=dict(x=0, y=0, z=1),
center=dict(x=0.0, y=0.0, z=0.0),
eye=dict(x=1.25, y=1.25, z=1.25)
)
fig['layout'].update(scene=dict(camera=camera))
graph = plotly.offline.plot(fig, auto_open=False, output_type='file', filename='%s/images/elev_grid_%s.html' %(directory,sample_num), validate=False)
return
def viewMap(directory,sample_num, likl, rain, erod, width = 600, height = 600, zmin = None, zmax = None, zData = None, title='Export Grid'):
"""
Use Plotly library to visualise the Erosion Deposition Heatmap.
Parameters
----------
variable : resolution
Required resolution for the model grid (in metres).
variable: width
Figure width.
variable: height
Figure height.
variable: zmin
Minimal elevation.
variable: zmax
Maximal elevation.
variable: height
Figure height.
variable: zData
Elevation data to plot.
variable: title
Title of the graph.
"""
if zmin == None:
zmin = zData.min()
if zmax == None:
zmax = zData.max()
trace = go.Heatmap(z=zData)
data=[trace]
layout = Layout(
title='',
autosize=True,
width=width,
height=height,
scene=Scene(
zaxis=ZAxis(range=[zmin, zmax],autorange=False,nticks=10,gridcolor='rgb(255, 255, 255)',gridwidth=2,zerolinecolor='rgb(255, 255, 255)',zerolinewidth=2),
xaxis=XAxis(nticks=10,gridcolor='rgb(255, 255, 255)',gridwidth=2,zerolinecolor='rgb(255, 255, 255)',zerolinewidth=2),
yaxis=YAxis(nticks=10,gridcolor='rgb(255, 255, 255)',gridwidth=2,zerolinecolor='rgb(255, 255, 255)',zerolinewidth=2),
bgcolor="rgb(244, 244, 248)"
)
)
fig = Figure(data=data, layout=layout)
graph = plotly.offline.plot(fig, auto_open=False, output_type='file', filename='%s/images/erdp_heatmap_%s.html' %(directory,sample_num), validate=False)
return
def viewBar(directory,sample_num, likl, rain, erod, width = 500, height = 500, xData = None, yData = None, title='Export Grid'):
"""
Use Plotly library to visualise the BarPlot of Erosion Deposition at certain coordinates.
Parameters
----------
variable : resolution
Required resolution for the model grid (in metres).
variable: width
Figure width.
variable: height
Figure height.
variable: zmin
Minimal elevation.
variable: zmax
Maximal elevation.
variable: height
Figure height.
variable: zData
Elevation data to plot.
variable: title
Title of the graph.
"""
xData = np.array_str(xData)
trace = go.Bar(x=xData, y = yData)
data=[trace]
layout = Layout(
title='',
autosize=True,
width=width,
height=height,
scene=Scene(
xaxis=XAxis(nticks=10,gridcolor='rgb(255, 255, 255)',gridwidth=2,zerolinecolor='rgb(255, 255, 255)',zerolinewidth=2),
yaxis=YAxis(nticks=10,gridcolor='rgb(255, 255, 255)',gridwidth=2,zerolinecolor='rgb(255, 255, 255)',zerolinewidth=2),
bgcolor="rgb(244, 244, 248)"
)
)
fig = Figure(data=data, layout=layout)
graph = plotly.offline.plot(fig, auto_open=False, output_type='file', filename='%s/images/erdppts_barcht_%s.html' %(directory, sample_num), validate=False)
return
def checkUplift(directory, u_filename, t_filename):
upl = np.loadtxt('%s%s.csv' %(directory,u_filename))
top = np.loadtxt('%s%s.csv' %(directory,t_filename))
upl = upl.reshape(upl.shape[0],1)
# print(upl.shape)
# print(top.shape)
comb = np.hstack((top, upl))
min_bound_x = comb[:,0].min()
max_bound_x = comb[:,0].max()
min_bound_y = comb[:,1].min()
max_bound_y = comb[:,1].max()
# print ('comb.shape', comb.shape)
# print ('comb[:,0:2]', comb[:,0:2])
# print ('max_b x', max_bound_x, 'min_b x', min_bound_x)
# print ('max_b y', max_bound_y, 'min_b y', min_bound_y)
for x in range(comb.shape[0]):
# print (comb[x,:])
row = comb[x,:]
ind_min_x = (row == min_bound_x)
ind_max_x = (row == max_bound_x)
ind_min_y = (row == min_bound_y)
ind_max_y = (row == max_bound_y)
# print (ind_min)
if (ind_min_x[0] == True or ind_max_x[0] == True) or (ind_min_y[1] == True or ind_max_y[1]==True):
# print('Im in the IF')
comb[x,3] = 0.0
# print (comb[x,:])
try:
if os.path.exists('%s%s.csv'% (directory, u_filename)):
os.remove('%s%s.csv'% (directory, u_filename))
except OSError:
pass
np.savetxt('%s%s.csv'% (directory, u_filename), comb[:,3])
return True
def main():
"""
"""
uplift_verified = False
# problem = input("Please choose a Badlands example to create an Initial and Final Topography for:\n 1) crater_fast\n 2) crater\n 3) etopo_fast\n 4) etopo\n 5) mountain\n 6) tasmania\n 7) australia\n")
directory = ""
erdp_coords_crater = np.array([[60,60],[52,67],[74,76],[62,45],[72,66],[85,73],[90,75],[44,86],[100,80],[88,69]])
erdp_coords_crater_fast = np.array([[60,60],[72,66],[85,73],[90,75],[44,86],[100,80],[88,69],[79,91],[96,77],[42,49]])
erdp_coords_etopo = np.array([[42,10],[39,8],[75,51],[59,13],[40,5],[6,20],[14,66],[4,40],[72,73],[46,64]])
erdp_coords_etopo_fast = np.array([[42,10],[39,8],[75,51],[59,13],[40,5],[6,20],[14,66],[4,40],[68,40],[72,44]])
erdp_coords_mountain = np.array([[5,5],[10,10],[20,20],[30,30],[40,40],[50,50],[25,25],[37,30],[44,27],[46,10]])
erdp_coords_tasmania = np.array([[260,320],[400,350],[270,180],[290,50],[500,120],[500,195],[44,200],[5,315],[450,50],[95,260]]) # need to hand pick given your problem
erdp_coords_australia = np.array([[260,320],[400,350],[270,180],[290,50],[500,120],[500,195],[44,200],[5,315],[450,50],[95,260]]) # need to hand pick given your problem
final_noise = True
if problem == 1:
tstart = time.clock()
directory = 'Examples/crater_fast'
topoGenerator(directory,'%s/crater.xml' %(directory), 1.5 , 5.e-5, 0.5, 1, 15000, erdp_coords_crater,final_noise)
print 'TopoGen for crater_fast completed in (s):',time.clock()-tstart
elif problem == 2:
tstart = time.clock()
directory = 'Examples/crater'
# topoGenerator(directory,'%s/crater.xml' %(directory), 1.5 , 5.e-5, 0.5, 1, 50000, erdp_coords_crater,final_noise)
#combination 1
# topoGenerator(directory,'%s/crater.xml' %(directory), 1.14 , 5.72e-5, 0.5, 1, 50000, erdp_coords_crater,final_noise)
#combination 2
topoGenerator(directory,'%s/crater.xml' %(directory), 1.98 , 4.36e-5, 0.5, 1, 50000, erdp_coords_crater,final_noise)
print 'TopoGen for crater completed in (s):',time.clock()-tstart
elif problem == 3:
tstart = time.clock()
directory = 'Examples/etopo_fast'
topoGenerator(directory,'%s/etopo.xml' %(directory), 1.5 , 5.e-6, 0.5, 1, 500000, erdp_coords_etopo,final_noise)
print 'TopoGen for etopo fast completed in (s):',time.clock()-tstart
elif problem == 4:
tstart = time.clock()
directory = 'Examples/etopo'
# topoGenerator(directory,'%s/etopo.xml' %(directory), 1.5 , 5.e-6, 0.5, 1, 1000000, erdp_coords_etopo,final_noise)
#combination 1
# topoGenerator(directory,'%s/etopo.xml' %(directory), 2.64 , 3.96e-6, 0.5, 1, 1000000, erdp_coords_etopo,final_noise)
#combination 2
topoGenerator(directory,'%s/etopo.xml' %(directory), 2.58 , 3.4e-6, 0.5, 1, 1000000, erdp_coords_etopo,final_noise)
print 'TopoGen for etopo completed in (s):',time.clock()-tstart
elif problem == 5:
tstart = time.clock()
directory = 'Examples/mountain'
uplift_verified = checkUplift(directory, '/data/uplift', '/data/nodes')
# uplift_verified = True
if uplift_verified:
topoGenerator(directory,'%s/mountain.xml' %(directory), 1.5 , 5.e-6, 0.5, 1, 1000000, erdp_coords_mountain,final_noise)
print 'TopoGen for mountain completed in (s):',time.clock()-tstart
elif problem == 6:
tstart = time.clock()
directory = 'Examples/tasmania'
topoGenerator(directory,'%s/tasmania.xml' %(directory), 1.5 , 5.e-6, 0.5, 1, 1000000, erdp_coords_tasmania,final_noise)
print 'TopoGen for tasmania completed in (s):',time.clock()-tstart
elif problem == 7:
tstart = time.clock()
directory = 'Examples/australia'
topoGenerator(directory,'%s/australia.xml' %(directory), 1.5 , 1.e-6, 0.5, 1, 10000000, erdp_coords_australia,final_noise)
print 'TopoGen for australia completed in (s):',time.clock()-tstart
if __name__ == "__main__": main()