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Updated documentation, descriptions for v1.0 release.
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#!/usr/bin/env Python3
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import numpy as np
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import sys
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from AstroAtmosphere import *
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import matplotlib.pyplot as plt
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from netCDF4 import Dataset
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from pdb import set_trace
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from matplotlib import cm
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from scipy.interpolate import interp1d, interp2d
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from matplotlib.colors import LogNorm
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import json
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# Saves a variable, preferably a list or string to json text file.
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# Useful for long simulations, where you're making a plot
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def saveVariableToTXT(variable, filename):
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variableFile = open(filename, 'w')
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if type(variable) == np.ndarray:
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json.dump(variable.tolist(), variableFile)
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elif type(variable) in [list, str, float]:
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json.dump(variable, variableFile)
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else:
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print('Not a list, array or string. Check variable type.')
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variableFile.close()
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return
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# Load a variable from a json text file.
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def loadVariableFromTXT(filename):
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variableFile = open(filename, 'r')
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variable = json.load(variableFile)
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variableFile.close()
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return variable
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def calculateDistanceResolution(lat, lon):
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# Calculate local radius of the earth
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_A = 6378.137 # km
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_B = 6356.752 # km
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_phi = np.deg2rad(lat)
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_rc0 = (_A*_B)**2 / (_A**2 * np.cos(_phi)**2 + _B**2 * np.sin(_phi)**2)**(3/2)
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# Calculate circumference of the earth at constant latitude.
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latR = 2 * np.pi * np.cos(_phi) * _rc0
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distRes = latR/360 * lon
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return distRes
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def H_isotherm(T, lat):
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'''
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Calculates the reduced height of the atmosphere, assuming an isotherm distribution.
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'''
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_kb = 1.38064852e-23 # kg m2 s-2 K-1
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_m = 4.809651698e-26 # kg (weight per molecule of air, assuming dry air)
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_phi = np.deg2rad(lat)
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_c1 = 5.2790414e-3
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_c2 = 2.32718e-5
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_c3 = 1.262e-7
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_c4 = 7e-10
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_g0 = 9.780327 # m/s^2
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_g0_local = _g0 * (1 + _c1 * np.sin(_phi)**2 + _c2 * np.sin(_phi)**4 + _c3 * np.sin(_phi)**6 + _c4 * np.sin(_phi)**8)
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return (_kb*T) / (_m * _g0_local)
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def calculatePressure(Th, P0, h, lat):
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redH = H_isotherm(Th, lat)
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Ph = P0 * np.exp(-h/redH)
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return Ph
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plt.rc('font', family='serif')
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plt.rc('axes', labelsize='large')
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# Import the real data
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nc = Dataset('air.201806.nc', 'r')
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latitudes = np.asarray(nc.variables['lat'][:])
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longitudes = np.asarray(nc.variables['lon'][:])
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air_temp = nc.variables['air']
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air_press = np.asarray(nc.variables['level'])
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at = Observatory()
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# Parameters at Cerro Armazones
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T = air_temp[0,:,0,0][0] # k
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P = air_press[0] # Pa
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H = 0
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xc = 450 # ppm
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lat = 24.44768
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h = 0 # m
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l1 = 1.49 # micron
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l2 = 1.78 # micron
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rho = at.rho(p=P, T=T, RH=H, xc=xc)
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disp = dispersion(lat, h)
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disp.setReducedHeight(P, rho)
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air_dens = at.rho(p=air_press, T=air_temp[0,:,0,0], RH=np.asarray([0]*len(air_press)), xc=np.asarray([0]*len(air_press)))
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heights = disp.calcHeight(air_press, air_temp[0,:,0,0], RH=np.asarray([0]*len(air_press)), xc=np.asarray([0]*len(air_press)), P0=air_press[0]) / 1e3
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distance_lat = calculateDistanceResolution(latitudes[100], longitudes[100,:]) - calculateDistanceResolution(latitudes[100,0], longitudes[100,0])
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temp_selection_ground = air_temp[0,0,100,:]
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temp_selection_upper = air_temp[0,-1,100,:]
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print(distance_lat[1])
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#########################################################
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# Extrapolating using the U.S. Standard Atmosphere 1976.
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# The end point of the real data is used to shift the USSA data accordingly (linearly)
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h_ussa1976, _, _, _, air_temp_ussa1976, air_press_ussa1976,_,_,_,_ = np.genfromtxt('../US1976 Standard Atmosphere/si1py_modified.txt', unpack=True, skip_header=6)
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temp_ip = interp1d(h_ussa1976, air_temp_ussa1976)
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press_ip = interp1d(h_ussa1976, air_press_ussa1976)
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ussa1976_start = temp_ip(heights[-1])
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diff_temp_list = temp_selection_upper - ussa1976_start
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start_i = np.argmax(h_ussa1976 > heights[-1])
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ussa1976_temp_array = np.tile(air_temp_ussa1976[start_i:], (len(temp_selection_upper),1))
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ussa1976_temp_array = np.asarray([ussa1976_temp_array[i] + diff_temp_list[i] for i in range(len(diff_temp_list))]).T
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# Combining the (masked) arrays
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new_heights = np.append(heights, h_ussa1976[start_i:])
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tempData = np.append(air_temp[0,:,100,:], ussa1976_temp_array, axis=0)
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tempData_mask = np.append(air_temp[0,:,100,:].mask, np.zeros(ussa1976_temp_array.shape), axis=0)
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tempData = np.ma.masked_array(tempData, mask=tempData_mask)
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# Now the same for the pressure data
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# Combining the (masked) arrays
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start_i = np.argmax(h_ussa1976 > heights[-1])
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new_heights = np.append(heights, h_ussa1976[start_i:])
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pressData = []
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for i in range(len(temp_selection_upper)):
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calc_press_data = calculatePressure(Th=ussa1976_temp_array[:,i], P0=air_press[0], h=h_ussa1976[start_i:]*1000, lat=lat)
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pressData_i = np.append(air_press*100, calc_press_data*100, axis=0)
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pressData.append(pressData_i)
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pressData = np.asarray(pressData).T
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#########################################################
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# We'd now like to export a subset of the atmospheric data for a distance of ~200 km.
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# Let's use interpolation to create a uniform gridded dataset
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export_heights = np.linspace(0,new_heights.max(),400)
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export_dist = np.linspace(0,distance_lat[136]-distance_lat[130],1000)
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atmosphere_temp_func = interp2d(distance_lat[130:136]-distance_lat[130], new_heights, tempData[:,130:136], kind='linear')
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export_temp_atmosphere = atmosphere_temp_func(export_dist, export_heights)
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atmosphere_press_func = interp2d(distance_lat[130:136]-distance_lat[130], new_heights, pressData[:,130:136], kind='linear')
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export_press_atmosphere = atmosphere_press_func(export_dist, export_heights)
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# saveVariableToTXT(export_heights, 'export_heights.txt')
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# saveVariableToTXT(export_dist, 'export_dist.txt')
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# saveVariableToTXT(export_temp_atmosphere, 'export_temp_atmosphere.txt')
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# saveVariableToTXT(export_press_atmosphere, 'export_press_atmosphere.txt')
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# Plot the real data + extrapolated standard atmosphere.
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# fig = plt.figure()
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# ax = fig.add_subplot(211)
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# ax2 = fig.add_subplot(212)
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# im1 = ax.pcolormesh(export_dist, export_heights, export_temp_atmosphere, cmap=cm.coolwarm)
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# im2 = ax2.pcolormesh(export_dist, export_heights, export_press_atmosphere, cmap=cm.coolwarm, norm=LogNorm())
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# ax2.set_xlabel('Lateral distance (km)')
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# ax.set_ylabel('Height (km)')
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# ax2.set_ylabel('Height (km)')
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# cbar = fig.colorbar(im1, ax=ax, label='Temperature (K)')
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# lbls = cbar.get_ticks()
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# cbar.ax.invert_yaxis()
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# cbar.set_ticks(lbls[::-1])
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# cbar2 = fig.colorbar(im2, ax=ax2, label='Pressure (Pa)')
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# lbls = cbar2.get_ticks()
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# cbar2.ax.invert_yaxis()
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# cbar2.set_ticks(lbls[::-1])
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# plt.tight_layout()
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# plt.show(block=False)
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# set_trace()
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# # Plot the real data + extrapolated standard atmosphere.
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# fig = plt.figure()
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# ax = fig.add_subplot(211)
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# ax2 = fig.add_subplot(212)
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# im1 = ax.imshow(tempData[:,130:137], cmap=cm.coolwarm, interpolation= 'bicubic', aspect='auto', origin='lower')
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# # im1 = ax.pcolormesh(distance_lat[130:137], new_heights, tempData[:,130:137], cmap=cm.coolwarm)
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# im2 = ax2.pcolormesh(distance_lat, new_heights, pressData, cmap=cm.coolwarm, norm=LogNorm())
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# ax2.set_xlabel('Lateral distance (km)')
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# ax.set_ylabel('Height (km)')
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# ax2.set_ylabel('Height (km)')
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# cbar = fig.colorbar(im1, ax=ax, label='Temperature (K)')
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# lbls = cbar.get_ticks()
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# cbar.ax.invert_yaxis()
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# cbar.set_ticks(lbls[::-1])
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# cbar2 = fig.colorbar(im2, ax=ax2, label='Pressure (Pa)')
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# lbls = cbar2.get_ticks()
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# cbar2.ax.invert_yaxis()
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# cbar2.set_ticks(lbls[::-1])
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# plt.tight_layout()
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# plt.show(block=False)
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# Plot the real data and properties
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fig = plt.figure(figsize=(9,4))
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fig2 = plt.figure()
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ax1 = fig2.add_subplot(221)
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ax2 = fig2.add_subplot(222)
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ax3 = fig2.add_subplot(223)
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ax4 = fig.add_subplot(121)
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ax5 = fig2.add_subplot(224)
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ax6 = fig.add_subplot(122)
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ax1.grid(alpha=0.3)
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ax2.grid(alpha=0.3)
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ax3.grid(alpha=0.3)
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ax5.grid(alpha=0.3)
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ax1.plot(air_temp[0,:,0,0], heights)
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ax1.set_xlabel('Temperature (K)')
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ax1.set_ylabel('Height (km)')
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ax2.plot(air_press, heights)
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ax2.set_xlabel('Pressure (Pa)')
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ax2.set_ylabel('Height (km)')
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ax3.plot(air_dens, heights)
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ax3.set_xlabel('Density (g cm$^{-3}$)')
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ax3.set_ylabel('Height (km)')
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im = ax4.imshow(np.rot90(air_temp[0,0,:,:].T), aspect=1, cmap='jet')
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ax4.set_yticks([])
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ax4.set_xticks([])
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# fig.colorbar(im, ax=ax4, label='Temperature (K)')
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ax5.plot(distance_lat, temp_selection_ground, 'b-', label='ground')
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ax5.plot(distance_lat, temp_selection_upper, 'r-', label='upper atmosphere')
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ax5.legend()
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ax5.set_ylabel('Temperature (K)')
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ax5.set_xlabel('Distance (km)')
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im2 = ax6.imshow(air_temp[0,:,100,:], aspect='auto', origin='lower', interpolation='bilinear', extent=[0,distance_lat[-1],0,heights[-1] ], cmap='jet')
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ax6.set_xlabel('Distance (km)', fontsize=18)
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ax6.set_ylabel('Height (km)', fontsize=18)
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cbar = fig.colorbar(im2, ax=ax6)#, label='Temperature (K)')
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cbar.ax.tick_params(labelsize=16)
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cbar.set_label('Temperature (K)', size=18)
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lbls = cbar.get_ticks()
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cbar.ax.invert_yaxis()
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cbar.set_ticks(lbls[::-1])
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ax6.tick_params(axis ='both', direction='in', labelsize=16)
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plt.tight_layout()
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plt.show()
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