465 lines
17 KiB
Python
465 lines
17 KiB
Python
"""
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@author: AJMR
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Plotting and animation script for NTC sediment tests
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April 17, 2023
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"""
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import os
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import pandas as pd
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import geopandas as gpd
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import netCDF4 as nc
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import math
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import numpy as np
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import matplotlib as mpl
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import matplotlib.pyplot as plt
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from scipy.interpolate import LinearNDInterpolator, interp1d
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import matplotlib.animation as animation
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import dfm_tools as dfmt
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# Geotiff
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import cartopy.crs as ccrs
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import contextily as ctx
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import pathlib as pl
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from shapely.geometry import Point, MultiPoint
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import alphashape
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import rioxarray
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import xarray as xr
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import cartopy.crs as ccrs
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import contextily as ctx
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from dfm_tools.regulargrid import scatter_to_regulargrid
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from pathlib import Path
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# Colormaps
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import cm_xml_to_matplotlib as cm
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#%% Read Model Log
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runLog = pd.read_excel('C:/Users/arey/files/Projects/Newtown/Model Log NTC.xlsx', 'ModelLog')
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dataPath = "FlowFM/dflowfm/output/FlowFM_map.nc"
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histPath = "FlowFM/dflowfm/output/FlowFM_his.nc"
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#%% Import Model results for static images
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# Define which models to import
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modelPlot = [144]
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d3dfm_DataArray = [None] * (max(modelPlot)+1)
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sedMass = [None] * (max(modelPlot)+1) # Available Mass of Sediment
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erodeSed = [None] * (max(modelPlot)+1) # Erosion and deposition
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initialBed = [None] * (max(modelPlot)+1) # Erosion and deposition
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modelCRS = [None] * (max(modelPlot)+1) # Model CRS
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sedConc = [None] * (max(modelPlot)+1) # Model CRS
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for i in modelPlot:
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file_nc_map = Path(runLog['Run Location'][i]) / dataPath
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# Open Map file as xarrray Dataset
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d3dfm_DataArray[i] = dfmt.open_partitioned_dataset(file_nc_map.as_posix())
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# Get Var info
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vars_pd = dfmt.get_ncvarproperties(d3dfm_DataArray[i])
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# Get last timestep
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tStep = d3dfm_DataArray[i].time[-1].values
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# Import sand sediment class
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sedMass[i] = d3dfm_DataArray[i].mesh2d_bodsed[-1, :, 2].compute()
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initialBed[i]= d3dfm_DataArray[i].mesh2d_s1[0, :] - d3dfm_DataArray[i].mesh2d_waterdepth[0, :]
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finalBed = d3dfm_DataArray[i].mesh2d_s1[-1, :] - d3dfm_DataArray[i].mesh2d_waterdepth[-1, :]
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erodeSed[i] = finalBed - initialBed[i]
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erodeSed[i] = erodeSed[i].compute()
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initialBed[i] = initialBed[i].compute()
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# Import concentration of sediment 2 at timestep 95 and layer 10
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sedConc[i] = d3dfm_DataArray[i].mesh2d_sedfrac_concentration[94, 2, :, 9].compute()
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modelCRS[i] = vars_pd['EPSG_code']['projected_coordinate_system']
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#%% Define axis limits
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axLim_Xmin = []
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axLim_Xmax = []
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axLim_Ymin = []
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axLim_Ymax = []
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# Set axis limits
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# Full domain
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axLim_Xmin.append(298500)
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axLim_Xmax.append(306800)
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axLim_Ymin.append(58500)
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axLim_Ymax.append(68000)
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# Zoom North River
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axLim_Xmin.append(303500)
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axLim_Xmax.append(305500)
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axLim_Ymin.append(66000)
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axLim_Ymax.append(68000)
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# Zoom Tribs
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axLim_Xmin.append(305500)
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axLim_Xmax.append(306800)
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axLim_Ymin.append(60000)
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axLim_Ymax.append(62500)
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# Zoom far trib
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axLim_Xmin.append(305800)
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axLim_Xmax.append(305900)
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axLim_Ymin.append(60150)
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axLim_Ymax.append(60400)
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#%% Plot using DFM functions
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for i in modelPlot:
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# Create figure
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fig, axesFig = plt.subplots(1, 4, figsize=(8, 2))
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axes = axesFig.flatten()
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# Loop through axis and plot with different limits
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for subIDX in range(0, 4):
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# # Plot Sediment Mass
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# smp = sedMass[i].ugrid.plot(ax=axes[subIDX], edgecolors='face', cmap='turbo',
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# vmin=0, vmax=2000, add_colorbar=False)
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# # Plot Erosion
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# smp = erodeSed[i].ugrid.plot(ax=axes[subIDX], edgecolors='face', cmap='coolwarm',
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# vmin=-1, vmax=1, add_colorbar=False)
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# Plot Bed
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smp = initialBed[i].ugrid.plot(ax=axes[subIDX], edgecolors='face', cmap='nipy_spectral',
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vmin=-25, vmax=0, add_colorbar=False)
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# Set axis labels
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axes[subIDX].set_xlabel('')
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axes[subIDX].set_ylabel('')
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axes[subIDX].set_title('')
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axes[subIDX].set_xticks([])
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axes[subIDX].set_yticks([])
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axes[subIDX].set_xlim(axLim_Xmin[subIDX], axLim_Xmax[subIDX])
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axes[subIDX].set_ylim(axLim_Ymin[subIDX], axLim_Ymax[subIDX])
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# Add basemap
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# ctx.add_basemap(ax=axes, source=ctx.providers.Esri.WorldImagery, crs=modelCRS[i], attribution=False)
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mapbox = 'https://api.mapbox.com/styles/v1/alexander0042/ckemxgtk51fgp19nybfmdcb1e/tiles/256/{z}/{x}/{y}@2x?access_token=pk.eyJ1IjoiYWxleGFuZGVyMDA0MiIsImEiOiJjazVmdG4zbncwMHY4M2VrcThwZGUzZDFhIn0.w6oDHoo1eCeRlSBpwzwVtw'
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ctx.add_basemap(axes[subIDX], source=mapbox, crs=modelCRS[i])
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# cbar = plt.colorbar(smp, ax=axesFig.ravel().tolist(), label='Sand Mass [kg/m2]')
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# cbar = plt.colorbar(smp, ax=axesFig.ravel().tolist(), label='Erosion/ deposition [m]')
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cbar = plt.colorbar(smp, ax=axesFig.ravel().tolist(), label='Initial Bed [mNAVD88]')
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plt.show()
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# fig.savefig('C:/Users/arey/files/Projects/Newtown/SedFigs2/SedMass_' + runLog['Run'][i] + '.png',
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# bbox_inches='tight', dpi=300)
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# fig.savefig('C:/Users/arey/files/Projects/Newtown/SedFigs2/ErodeDep_' + runLog['Run'][i] + '.png',
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# bbox_inches='tight', dpi=300)
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# fig.savefig('C:/Users/arey/files/Projects/Newtown/SedFigs2/InitialBed_' + runLog['Run'][i] + '.png',
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# bbox_inches='tight', dpi=300)
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#%% Plot using DFM functions
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#Cmap Path
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cmap_path = 'C:/Users/arey/Repo/MATLAB_Q/Downloads/KeyColormaps/'
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for i in modelPlot:
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fig, axes = plt.subplots(nrows=1, ncols=1, subplot_kw={'projection': ccrs.epsg(32118)}, figsize=(6, 6))
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fig.patch.set_facecolor('white')
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fig.tight_layout(pad=3.0)
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# Load cmaps
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cmap = 'AJMR_Sed5_RevE.xml'
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plotcmap = cm.make_cmap(cmap_path + cmap)
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pc = plot_netmapdata(ugrid_all[i].verts, values=modelMaxShear[i][0, :],
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ax=axes, linewidth=0.5, cmap=plotcmap)
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axes.set_xlim(305900, 306400)
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axes.set_ylim(61500, 62200)
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# axes.quiver(modelX[i], modelX[i], U[i], V[i], color='w', scale=1.00)
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mapbox = 'https://api.mapbox.com/styles/v1/alexander0042/ckemxgtk51fgp19nybfmdcb1e/tiles/256/{z}/{x}/{y}@2x?access_token=pk.eyJ1IjoiYWxleGFuZGVyMDA0MiIsImEiOiJjazVmdG4zbncwMHY4M2VrcThwZGUzZDFhIn0.w6oDHoo1eCeRlSBpwzwVtw'
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ctx.add_basemap(axes, source=mapbox, crs='EPSG:32118')
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extent = axes.get_extent()
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axes.set_xticks(np.linspace(extent[0], extent[1], 4))
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axes.set_yticks(np.linspace(extent[2], extent[3], 4))
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pc.set_clim([0, 0.145])
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cbarTicks = [0, 0.0378, 0.063, 0.0826, 0.11, 0.145]
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cbar = fig.colorbar(pc, ax=axes, shrink=0.95,
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ticks=cbarTicks)
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cbar.set_label('Total Max Shear Stress [N/m^2]')
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# Add label on colorbar
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cbar.ax.text(0.08, (cbarTicks[0]+cbarTicks[1])/2, 'CLAY', ha='center', va='center',
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rotation=90, fontweight='bold')
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cbar.ax.text(0.08, (cbarTicks[1]+cbarTicks[2])/2, 'FSILT', ha='center', va='center',
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rotation=90, fontweight='bold')
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cbar.ax.text(0.08, (cbarTicks[2]+cbarTicks[3])/2, 'MSILT', ha='center', va='center',
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rotation=90, fontweight='bold')
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cbar.ax.text(0.08, (cbarTicks[3]+cbarTicks[4])/2, 'CSILT', ha='center', va='center',
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rotation=90, fontweight='bold')
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cbar.ax.text(0.08, (cbarTicks[4]+cbarTicks[5])/2, 'FSAND', ha='center', va='center',
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rotation=90, fontweight='bold')
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plt.show()
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fig.savefig('C:/Users/arey/files/Projects/Newtown/SedFigs/Shear_Class_' + runLog['Run'][i] + '.png',
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bbox_inches='tight', dpi=300)
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#%% Import Model results for animations
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# modelPlot = [20, 22]
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# modelPlot = [18, 20, 21, 22]
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# modelPlot = [18, 21]
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modelPlot = [25, 26]
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modelSedConc = [None] * (max(modelPlot)+1)
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modelMaxShear_animate = [None] * (max(modelPlot)+1)
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ugrid_all = [None] * (max(modelPlot)+1)
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tSteps = [None] * (max(modelPlot)+1)
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for i in modelPlot:
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file_nc_map = Path(runLog['Run Location'][i]) / dataPath
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# Get Var info
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vars_pd, dims_pd = get_ncvardimlist(file_nc=file_nc_map.as_posix())
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# Import
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tSteps[i] = get_timesfromnc(file_nc=file_nc_map.as_posix(), varname='time')
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ugrid_all[i] = get_netdata(file_nc=file_nc_map.as_posix())
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modelSedConc[i] = get_ncmodeldata(file_nc=file_nc_map.as_posix(), varname='mesh2d_sedfrac_concentration',
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timestep='all', station=0, layer=0) #timestep='all' OR timestep=range(0, 30)
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modelMaxShear_animate[i] = get_ncmodeldata(file_nc=file_nc_map.as_posix(), varname='mesh2d_tausmax',
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timestep='all')
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# %% Import water levels from hist
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modelHistWL = [None] * (max(modelPlot)+1)
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modelHistTime = [None] * (max(modelPlot)+1)
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# tSteps = [None] * (max(modelPlot)+1)
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for i in modelPlot:
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file_nc_hist = Path(runLog['Run Location'][i]) / histPath
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vars_pd, dims_pd = get_ncvardimlist(file_nc=file_nc_hist.as_posix())
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# Get station names
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histStations = get_hisstationlist(file_nc=file_nc_hist.as_posix(), varname='waterlevel')
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# Import
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modelHistTime[i] = get_timesfromnc(file_nc=file_nc_hist.as_posix(), varname='time')
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modelHistWL[i] = get_ncmodeldata(file_nc=file_nc_hist.as_posix(), varname='waterlevel',
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timestep='all', station=1)
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#%% Sediment animations
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plt.rcParams['animation.ffmpeg_path'] = \
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'C:/Users/arey/Local/ffmpeg-2022-02-14-git-59c647bcf3-full_build/bin/ffmpeg.exe'
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mapbox = 'https://api.mapbox.com/styles/v1/alexander0042/ckex9vtri0o6619p55sl5qiyv/tiles/256/{z}/{x}/{y}@2x?access_token=pk.eyJ1IjoiYWxleGFuZGVyMDA0MiIsImEiOiJjazVmdG4zbncwMHY4M2VrcThwZGUzZDFhIn0.w6oDHoo1eCeRlSBpwzwVtw'
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x, y, arrow_length = 0.93, 0.95, 0.12
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# fontprops = fm.FontProperties(size=12)
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# Set model to plot
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# modelPlot = [20, 22]
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# modelPlot = [18, 20, 21, 22]
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modelPlot = [25, 26]
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cmap_path = 'C:/Users/arey/Repo/MATLAB_Q/Downloads/KeyColormaps/'
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for m in modelPlot:
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vmax = 0.75
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vmin = 0
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# vmax = 0.145
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# vmin = 0
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cbarTicks = [0, 0.0378, 0.063, 0.0826, 0.11, 0.145]
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cmapName = 'turbo'
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cmap = mpl.cm.turbo
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# cmapName = 'AJMR_Sed5_RevE.xml'
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# cmap = cm.make_cmap(cmap_path + cmapName)
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# Zoom limits
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# xLimits = [305900, 306500]
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# yLimits = [61400, 62200]
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# Wide Limits
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xLimits = [302719.4, 306934.2]
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yLimits = [60263.7, 64194.8]
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# Setup Video
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metadata = dict(title='NTC Sediment Animation', artist='Matplotlib',
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comment='AJMR June 28, 2022')
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writer = animation.FFMpegWriter(fps=2, metadata=metadata, codec='h264', bitrate=5000)
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fig, axes = plt.subplots(figsize=(6, 6))
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writer.setup(fig, '//srv-ott3/Projects/11934.201 Newtown Creek TPP – Privileged and Confidential/' +
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'06_Models/04_Delft3D/Figures/SedConc/HQ3_Wide_RevC_Long_Sed_Cond_'
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+ runLog['Run'][m] + '.mp4')
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mapbox = 'https://api.mapbox.com/styles/v1/alexander0042/ckemxgtk51fgp19nybfmdcb1e/tiles/256/{z}/{x}/{y}@2x?access_token=pk.eyJ1IjoiYWxleGFuZGVyMDA0MiIsImEiOiJjazVmdG4zbncwMHY4M2VrcThwZGUzZDFhIn0.w6oDHoo1eCeRlSBpwzwVtw'
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for i in np.arange(1, len(modelSedConc[m])-1, 1): #289
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# Clear axes for video
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axes.cla()
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# Create new figure for stills
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# fig, axes = plt.subplots(figsize=(6, 6))
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# Clear inset WL Plot
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# if i > 1:
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# axin1.cla()
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# Plot sediment
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pc = plot_netmapdata(ugrid_all[m].verts, values=modelSedConc[m][i, 0, :, 0],
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ax=axes, cmap=cmapName,
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antialiaseds=False)
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# Plot shear
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# pc = plot_netmapdata(ugrid_all[m].verts, values=modelMaxShear_animate[m][i,:],
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# ax=axes, cmap=cmap,
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# antialiaseds=False)
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# Set map limits
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axes.set_xlim(xLimits[0], xLimits[1])
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axes.set_ylim(yLimits[0], yLimits[1])
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# Add basemap
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ctx.add_basemap(axes, source=mapbox, crs='EPSG:32118')
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# Set map ticks
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axes.set_xticks(np.linspace(xLimits[0], xLimits[1], 4))
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axes.set_yticks(np.linspace(yLimits[0], yLimits[1], 4))
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# Color Limits
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pc.set_clim([vmin, vmax])
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# Add title
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axes.title.set_text('Bottom Sediment Concentration at: ' + tSteps[m][i].strftime("%Y/%m/%d %H:%M"))
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# axes.title.set_text('Total Max Shear Stress at: ' + str(tSteps[m][i]))
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# Add inset wl plot
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axin1 = axes.inset_axes([0.1, 0.1, 0.4, 0.15])
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axin1.plot(modelHistTime[m], modelHistWL[m])
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# Add current point
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# Find closest time
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abs_deltas_from_target_date = np.absolute(modelHistTime[m] - tSteps[m][i])
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axin1.scatter(modelHistTime[m][np.argmin(abs_deltas_from_target_date)], modelHistWL[m][np.argmin(abs_deltas_from_target_date)], 10, 'r')
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# axin1.set_xticks([modelHistTime[m][0], modelHistTime[m][len(modelHistTime[m])-1]])
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axin1.set_xticks([])
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axin1.set_yticks([])
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plt.setp(axin1.get_xticklabels(), backgroundcolor="white")
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plt.setp(axin1.get_yticklabels(), backgroundcolor="white")
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if i == 1: #i < 1000
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fig.subplots_adjust(right=0.8)
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norm = mpl.colors.Normalize(vmin=vmin, vmax=vmax)
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# Create colorbar axis
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# cax = plt.axes([0.82, 0.25, 0.04, 0.5])
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cax = plt.axes([0.85, 0.15, 0.04, 0.7])
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# Add colorbar with designated tick marks
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# cb1 = mpl.colorbar.ColorbarBase(cax, cmap=cmap,
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# norm=norm,
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# orientation='vertical',
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# ticks=cbarTicks)
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# Add colorbar without designated tick marks
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cb1 = mpl.colorbar.ColorbarBase(cax, cmap=cmap,
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norm=norm,
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orientation='vertical')
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# Colorbar lavel
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cb1.set_label('Sediment Concentration [$kg/m^3$]')
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# cb1.set_label('Total Max Shear Stress [N/m^2]')
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# Add label on colorbar
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# cb1.ax.text(0.08, (cbarTicks[0] + cbarTicks[1]) / 2, 'CLAY', ha='center', va='center',
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# rotation=90, fontweight='bold')
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# cb1.ax.text(0.08, (cbarTicks[1] + cbarTicks[2]) / 2, 'FSILT', ha='center', va='center',
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# rotation=90, fontweight='bold')
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||
# cb1.ax.text(0.08, (cbarTicks[2] + cbarTicks[3]) / 2, 'MSILT', ha='center', va='center',
|
||
# rotation=90, fontweight='bold')
|
||
# cb1.ax.text(0.08, (cbarTicks[3] + cbarTicks[4]) / 2, 'CSILT', ha='center', va='center',
|
||
# rotation=90, fontweight='bold')
|
||
# cb1.ax.text(0.08, (cbarTicks[4] + cbarTicks[5]) / 2, 'FSAND', ha='center', va='center',
|
||
# rotation=90, fontweight='bold')
|
||
|
||
|
||
# Change label font size for only the primary axis
|
||
for item in ([axes.xaxis.label, axes.yaxis.label] +
|
||
axes.get_xticklabels() + axes.get_yticklabels()):
|
||
item.set_fontsize(4)
|
||
|
||
|
||
# Save video frame
|
||
writer.grab_frame()
|
||
plt.show()
|
||
print(i)
|
||
|
||
# Save stills
|
||
fig.savefig('//srv-ott3/Projects/11934.201 Newtown Creek TPP – Privileged and Confidential/' +
|
||
'06_Models/04_Delft3D/Figures/SedConc/Wide_RevC_SedConc_' +
|
||
runLog['Run'][m] + '_Frame_' + str(i) + '.png',
|
||
bbox_inches='tight', dpi=300)
|
||
# fig.savefig('//srv-ott3/Projects/11934.201 Newtown Creek TPP – Privileged and Confidential/' +
|
||
# '06_Models/04_Delft3D/Figures/ShearStress/Wide_ShearStress_' +
|
||
# runLog['Run'][m] + '_Frame_' + str(i) + '.png',
|
||
# bbox_inches='tight', dpi=300)
|
||
|
||
# Save video
|
||
writer.finish()
|
||
|
||
|
||
|
||
#%% Save Sediment Geotiff
|
||
|
||
# Create mask within bounds
|
||
boundSelect = 2
|
||
croppedGridMask = (d3dfm_DataArray[i].mesh2d_face_x >= axLim_Xmin[boundSelect]) &\
|
||
(d3dfm_DataArray[i].mesh2d_face_x <= axLim_Xmax[boundSelect]) &\
|
||
(d3dfm_DataArray[i].mesh2d_face_y >= axLim_Ymin[boundSelect]) &\
|
||
(d3dfm_DataArray[i].mesh2d_face_y <= axLim_Ymax[boundSelect])
|
||
croppedGridMask = croppedGridMask.compute()
|
||
|
||
# Step through time steps
|
||
for sedTstep in range(105, 120):
|
||
# Rasterize sediment concentration within bounds
|
||
sedConcTif = dfmt.rasterize_ugrid(d3dfm_DataArray[i]['mesh2d_sedfrac_concentration'].isel(
|
||
time=sedTstep, mesh2d_nLayers=4, nSedSus=0).where(croppedGridMask, drop=True).to_dataset(),
|
||
resolution=2)
|
||
|
||
# Add CRS
|
||
sedConcTif.rio.write_crs("epsg:32118", inplace=True)
|
||
sedConcTif.rio.to_raster('C:/Users/arey/files/Projects/Newtown/SedFigs2/GeoTiff_RevB_'
|
||
+ 'Sed_Conc4_Time_' + str(sedTstep) + '.tif')
|