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Copy pathfract_macrosystemsPY_without_microclim.py
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fract_macrosystemsPY_without_microclim.py
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from time import time as what_time
from random import choice, gauss
import numpy as np
from numpy.random import *
from scipy.stats.mstats import *
from scipy.interpolate import interp1d
from numpy.random import uniform, seed, normal, binomial
from numpy import pi, min, max, percentile, radians, degrees
from numpy.fft import ifft2
import multiprocessing
from time import time
from scipy.interpolate import *
#from matplotlib.mlab import prctile as percent
from numpy import flipud
from math import exp, log, sin, cos, sqrt, acos, asin, atan, atan2
#from numpy import arctan as atan
#from numpy import arctan2 as atan2
#from numpy import arcsin as asin
#from numpy import arccos as acos
import pandas as pd ## added by LN
import math
seed() #99
h = 0. #input("elevational range? ") #10.
high = 1
#D = 3 #input("fractal dimension (between 2 and 3)? ") #1 # D = 3 - H, for 0 < H < 1
#cdef double H #= 3. - D
N = 100 #input("spatial extent? ") #128
MU= 0.
SD = 1.
J = 150 #input("day? ")
from time import time
## read in elev, slope, aspect, veget files
## LR2
#elev = pd.DataFrame(pd.read_csv('/Users/laurenneel/Desktop/Grass_RGB_DSM_Oct22/LR2/LR2_elevation'))
#elev = elev.iloc[8:]
#elev.reset_index(drop=True, inplace=True)
#
#slope = pd.DataFrame(pd.read_csv('/Users/laurenneel/Desktop/Grass_RGB_DSM_Oct22/LR2/LR2_slope'))
#slope=slope.iloc[8:]
#slope.reset_index(drop=True, inplace=True)
#
#aspect = pd.DataFrame(pd.read_csv('/Users/laurenneel/Desktop/Grass_RGB_DSM_Oct22/LR2/LR2_aspect'))
#aspect = aspect.iloc[8:]
#aspect.reset_index(drop=True, inplace=True)
#
#
#veget = pd.DataFrame(pd.read_csv('/Users/laurenneel/Desktop/Grass_RGB_DSM_Oct22/LR2/LR2_VARI'))
#veget=veget.iloc[8:]
#veget.reset_index(drop=True, inplace=True)
def read_it():
x=[]
while True:
line=finput.readline()
if not line: break
x.append(line.split())
finput.close()
return(x)
#i=0
def char2int(y):
i=0
while i < len(y):
j = 0
while j < len(y[i]):
y[i][j] = float(y[i][j])
j = j + 1
i = i + 1
return y
path_txt_input_folder='/Users/laurenneel/Desktop/Grass_RGB_DSM_Oct22/LR2/'
finput = open(path_txt_input_folder + "LR2_elev_1m", "r")
ELEV = []
ELEV = read_it()
HEADER1 = ELEV[:8] #creates raster header
ELEV = ELEV[8:]
ELEV=char2int(ELEV)
elev = np.array(ELEV, dtype=float)
del ELEV
finput = open(path_txt_input_folder + "LR2_slope_1m", "r")
SLOPE = []
SLOPE= read_it()
HEADER2 = SLOPE[:8] #creates raster header
SLOPE = SLOPE[8:]
SLOPE = char2int(SLOPE)
slope = np.array(SLOPE, dtype=float)
del SLOPE
finput = open(path_txt_input_folder + "LR2_VARI_1m", "r")
VEG = []
VEG= read_it()
HEADER4 = VEG[:8] #creates raster header
VEG = VEG[8:]
VEG = char2int(VEG)
veget = np.array(VEG, dtype=float)
del VEG
finput = open(path_txt_input_folder + "LR2_aspect_1m", "r")
ASPECT = []
ASPECT= read_it()
HEADER4 = ASPECT[:8] #creates raster header
ASPECT = ASPECT[8:]
ASPECT = char2int(ASPECT)
aspect = np.array(ASPECT, dtype=float)
del ASPECT
#### modifying the shape of input drone files
elev = elev[elev != -9999]
shape = elev.shape[0]
if shape > (132 * 132):
shape = (132, 132)
elev = np.reshape(elev[:shape[0]*shape[1]], shape)
else:
elev = np.reshape(elev, (int(np.sqrt(shape)), int(np.sqrt(shape))))
#### aspect
aspect = aspect[aspect != -9999]
shape = aspect.shape[0]
if shape > (132 * 132):
shape = (132, 132)
aspect = np.reshape(elev[:shape[0]*shape[1]], shape)
else:
aspect = np.reshape(aspect, (int(np.sqrt(shape)), int(np.sqrt(shape))))
#### slope
slope = slope[slope != -9999]
shape = slope.shape[0]
if shape > (132 * 132):
shape = (132, 132)
slope = np.reshape(elev[:shape[0]*shape[1]], shape)
else:
slope = np.reshape(slope, (int(np.sqrt(shape)), int(np.sqrt(shape))))
#### veget
veget = veget[veget != -9999]
shape = veget.shape[0]
if shape > (132 * 132):
shape = (132, 132)
veget = np.reshape(elev[:shape[0]*shape[1]], shape)
else:
veget = np.reshape(veget, (int(np.sqrt(shape)), int(np.sqrt(shape))))
def do_sim():
SIGMA = 5.673 * 10**(-8) # Stephan-Boltmann constant
SOLAR = 1360. # Solar constant
#filename = raw_input("site? ")
#t = input("time of day? ")
climate_change = 0 #input("Climate change scenario? 0 = no, 1= yes: ")
if climate_change==1:
minTemps = np.array([-5., -5.2, -2.7, 1.3, 5.8, 11.5 , 16.2, 18.5, 17.3, 12.7, 6.6, -1.0, -5.0, -5.2]) +3.
maxTemps = np.array([14.4,15.2, 17.6, 21.4, 26.6, 31.2, 35.6, 36.0, 34.7, 31.2, 25.4, 18.8, 14.4, 15.2]) +3.
g=3.
climname = "change"
else:
minTemps = np.array([-5.,-5.2, -2.7, 1.3, 5.8, 11.5, 16.2, 18.5, 17.3, 12.7, 6.6, -1.0, -5.0, -5.2])
maxTemps = np.array([14.4,15.2, 17.6, 21.4, 26.6, 31.2, 35.6, 36.0, 34.7, 31.2, 25.4, 18.8, 14.4, 15.2])
g=0.
climname = "norm"
#write_to_file = raw_input("Write thermal map to: ")
# DATA
# Create air temperatures and soil temperatures
# from splined climate records
# Air temperature data from Zion NP, east entrance
days = np.array([-16, 15, 46, 75, 106, 136, 167, 197, 228, 259, 289, 320, 350, 381]) ## you need 14 numbers to get jan after and dec before the year you want
maxT = UnivariateSpline(days, maxTemps, k=3)
minT = UnivariateSpline(days, minTemps, k=3)
# Ground temperature data from splines of raw data from 24 days <0.5 C from average MIN & MAX for that day
hours = np.array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23.,24.])
janTemps = np.array([-7.01,-7.77,-7.89,-8.28,-8.72,-8.99,-9.32,-9.74,-8.6,-5.61,-1.41,2.74,6.3,8.37,8.65,6.85,3.44,0.28,-2.03,-3.38,-4.68,-5.22,-5.91,-6.82,-7.01]) + g
febTemps = np.array([-5.15,-6.06,-6.16,-6.59,-6.46,-7.39,-7.75,-7.71,-5.5,-1.36,3.6,7.96,11.43,13.52,13.71,12.09,8.77,4.29,1.23,-0.84,-1.93,-2.98,-3.64,-4.49,-5.11]) + g
marTemps = np.array([-1.24,-2.36,-2.52,-3.05,-2.81,-3.97,-4.31,-3.5,0.33,5.38,11.2,15.95,19.81,22.14,23.03,21.03,17.54,12.34,8,5.08,3.05,1.76,0.62,-0.76,-1.14]) + g
aprTemps = np.array([1.7,0.86,0.09,-0.33,-0.84,-1.12,-1.23,1.34,5.94,11.43,17.02,22.06,25.62,27.8,28.09,26.95,23.81,18.94,13.68,9.61,6.88,5.31,3.89,2.94,1.85]) + g
mayTemps = np.array([7.78,6.76,6.03,5.11,4.91,4.31,5.1,8.89,13.94,19.55,25.38,30.42,34.1,36.79,37,35.81,32.65,28.4,22.89,17.18,14.25,12.02,10.67,8.97,7.84]) + g
junTemps = np.array([11.87,10.92,10.14,9.26,8.96,8.49,9.92,13.89,19.07,24.5,30.68,35.81,39.59,42.44,42.66,41.56,38.49,34.26,28.76,22.88,19.22,16.69,14.81,12.9,12.08]) + g
julTemps = np.array([17.73,16.67,15.93,14.97,14.78,14.27,15.26,19.37,24.45,30.41,35.81,40.79,44.37,46.65,47.28,46.63,43.27,38.9,33.85,28.06,24.45,21.91,20.33,18.91,17.92]) + g
augTemps = np.array([16.17,15.02,14.3,14.42,13.15,12.65,13.28,16.21,21.04,26.26,32.55,37.76,41.68,43.98,44.6,43.14,40.12,35.4,29.63,24.99,21.99,19.85,18.38,17.11,15.59]) + g
sepTemps = np.array([9.99,9.23,8.59,7.83,7.53,7.07,6.87,8.59,12.79,18.13,23.99,29.24,33.2,36.07,36.17,34.71,31.08,26.37,20.91,17.34,14.67,13.43,12.11,11.29,10.11]) + g
octTemps = np.array( [1.92,1.03,0.67,0.16,-0.75,-0.73,-1.13,-0.97,2.13,6.87,12.26,17.56,21.76,24.31,25.28,23.18,19.49,14.15,10.33,7.82,6.02,4.76,3.68,2.3,1.99]) + g
novTemps = np.array( [-4.09,-3.99,-5.08,-5.51,-5.54,-6.28,-6.62,-7.01,-5.96,-1.85,2.78,7.13,11.2,13.47,13.88,12.1,8.58,4.35,1.83,0.2,-0.61,-1.98,-2.79,-3.79,-4.07]) + g
decTemps = np.array([-9.46,-9.49,-10.35,-10.75,-10.47,-11.46,-11.79,-12.02,-11.42,-8.67,-4.58,0.16,3.44,5.67,6.01,4.15,0.66,-2.1,-4.52,-5.83,-6.52,-7.66,-8.35,-9.23,-9.47]) + g
janSpline = UnivariateSpline(hours,janTemps,k=3)
febSpline = UnivariateSpline(hours,febTemps,k=3)
marSpline = UnivariateSpline(hours,marTemps,k=3)
aprSpline = UnivariateSpline(hours,aprTemps,k=3)
maySpline = UnivariateSpline(hours,mayTemps,k=3)
junSpline = UnivariateSpline(hours,junTemps,k=3)
julSpline = UnivariateSpline(hours,julTemps,k=3)
augSpline = UnivariateSpline(hours,augTemps,k=3)
sepSpline = UnivariateSpline(hours,sepTemps,k=3)
octSpline = UnivariateSpline(hours,octTemps,k=3)
novSpline = UnivariateSpline(hours,novTemps,k=3)
decSpline = UnivariateSpline(hours,decTemps,k=3)
def make_elevation(h, high, D, N, MU, SD):
seed(100) # just to get same fractal dimensions <-normally this changes
Arand = high
i0, j0 = 0., 0.
H = 3. - D
A = np.zeros((N,N),dtype = complex) #complex number plane
for i in range(N//2):
for j in range(N//2):
phase = 2. * pi * uniform(0,high)/Arand
if i != 0 or j != 0:
rad = pow(i*i + j*j,-(H + 1.)/2.) * normal(MU, SD)
else:
rad = 0.
A[i][j] = complex(rad * cos(phase), rad * sin(phase))
if i == 0.:
i0 = 0.
else:
i0 = N-i #i added int(N-i)
if j0 == 0.:
j0 = 0.
else:
j0 = N-j #i added int(N-i)
if A[int(i0)][int(j0)] == complex(rad * cos(phase), -rad*sin(phase)):
break
A[N//2][0]= complex(A[N//2][0].real, 0)
A[0][N//2]= complex(A[N//2][0].real, 0)
A[N//2][N//2]= complex(A[N//2][0].real, 0)
for i in range(1, int(N/2 -1)):
for j in range(1, int(N/2 -1)):
phase = 2.* pi* uniform(0,high)/Arand
rad = pow(i*i + j*j, -(H+1)/2.) * normal(MU,SD)
A[i][N-j] = complex(rad * cos(phase), rad * sin(phase))
A[N-i][j] = complex(rad * cos(phase), -rad * sin(phase))
X = ifft2(A).real
X= h * (X - min(X.real)) / (max(X.real) - min(X.real))
z = X.view(float)
return z
def make_temp_vegetation(h, high, D, N, MU, SD):
print(D)
H = 3. - D
temp_v = make_elevation(h, high, D, N, MU, SD)
return temp_v
def make_vegetation(temp_v, pcnt):
return np.array(temp_v > percentile(temp_v, 100.-pcnt))#, int)
# e is the center cell to a moving grid.
# Because we want to preserve the fractal nature of the surface,
# we must move as if over a tesselation.
#
# a b c
#
# d e f
#
# g h i
def calc_slope(elev_map, x, y, N):
if (0<x<N-1) and (0 < y < N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (x == 0) and (0 < y < N-1):
a = elev_map[y-1][N-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][N-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][N-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (x == 0) and (y == N-1):
a = elev_map[y-1][N-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][N-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[0][N-1]
h = elev_map[0][x]
i = elev_map[0][x+1]
if (x == 0) and (y == 0):
a = elev_map[N-1][N-1]
b = elev_map[N-1][x]
c = elev_map[N-1][x+1]
d = elev_map[y][N-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][N-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (x == N-1) and (0 < y < N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][0]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][0]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][0]
if (x == N-1) and (y == N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][0]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][0]
g = elev_map[0][x-1]
h = elev_map[0][x]
i = elev_map[0][0]
if (x == N-1) and (y == 0):
a = elev_map[N-1][x-1]
b = elev_map[N-1][x]
c = elev_map[N-1][0]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][0]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][0]
if (0 < x < N-1) and (y == 0):
a = elev_map[N-1][x-1]
b = elev_map[N-1][x]
c = elev_map[N-1][x+1]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (0 < x < N-1) and (y == N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[0][x-1]
h = elev_map[0][x]
i = elev_map[0][x+1]
x_cell_size, y_cell_size = 1,1
dzdx = ((c + 2*f + i) - (a + 2*d + g)) / (8 * x_cell_size)
dzdy = ((g + 2*h + i) - (a + 2*b + c)) / (8 * y_cell_size)
rise_run = sqrt(dzdx**2 +dzdy**2)
slope_degrees = atan(rise_run) * 57.29578
return slope_degrees
def calc_aspect(elev_map, x, y, N):
if (0<x<N-1) and (0 < y < N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (x == 0) and (0 < y < N-1):
a = elev_map[y-1][N-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][N-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][N-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (x == 0) and (y == N-1):
a = elev_map[y-1][N-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][N-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[0][N-1]
h = elev_map[0][x]
i = elev_map[0][x+1]
if (x == 0) and (y == 0):
a = elev_map[N-1][N-1]
b = elev_map[N-1][x]
c = elev_map[N-1][x+1]
d = elev_map[y][N-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][N-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (x == N-1) and (0 < y < N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][0]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][0]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][0]
if (x == N-1) and (y == N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][0]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][0]
g = elev_map[0][x-1]
h = elev_map[0][x]
i = elev_map[0][0]
if (x == N-1) and (y == 0):
a = elev_map[N-1][x-1]
b = elev_map[N-1][x]
c = elev_map[N-1][0]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][0]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][0]
if (0 < x < N-1) and (y == 0):
a = elev_map[N-1][x-1]
b = elev_map[N-1][x]
c = elev_map[N-1][x+1]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[y+1][x-1]
h = elev_map[y+1][x]
i = elev_map[y+1][x+1]
if (0 < x < N-1) and (y == N-1):
a = elev_map[y-1][x-1]
b = elev_map[y-1][x]
c = elev_map[y-1][x+1]
d = elev_map[y][x-1]
e = elev_map[y][x]
f = elev_map[y][x+1]
g = elev_map[0][x-1]
h = elev_map[0][x]
i = elev_map[0][x+1]
dzdx = ((c + 2*f + i) - (a + 2*d + g)) / 8
dzdy = ((g + 2*h + i) - (a + 2*b + c)) / 8
aspect = 57.29578 * atan2(dzdy, -dzdx)
if aspect < 0:
cell = 90.0 - aspect
elif aspect > 90.0:
cell = 360.0 - aspect + 90.0
else:
cell = 90.0 - aspect
return cell
def make_maps(h, high, N, MU, SD):
seed()
elev_range = 4. #uniform(0, h)
elev_fract = 2.2 #input("elev fract? ") #uniform(2,3)
veg_range = uniform(0,100) #float(input("veg %? ")) #uniform(0,100)
veg_fract = uniform(2,3) #float(input("veg fract? ")) #uniform(2,3)
#H_elev = 3. - elev_fract
#H_veg = 3. - veg_fract
print(elev_range, elev_fract, veg_range, veg_fract)
#X = make_elevation(h, high, D, H, N, MU, SD)
X = make_elevation(elev_range, high, elev_fract, N, MU, SD)
_slope = np.zeros((N,N),dtype = float) #[range(len(X)) for i in range(len(X[0]))]
_aspect = np.zeros((N,N),dtype = float) #[range(len(X)) for i in range(len(X[0]))]
for y in range(len(X)):
for x in range(len(X[y])):
_slope[y][x] = calc_slope(X, x, y, N)
_aspect[y][x] = calc_aspect(X, x, y, N)
S = _slope #possibly read-in slope here and
A = _aspect
tV = make_temp_vegetation(1., high, veg_fract, N, MU, SD) # h needs to be veg specific
V = make_vegetation(tV, veg_range)
return X, S, A, V, elev_range, elev_fract, veg_range, veg_fract
#get_topo_data(name,limit)
#print elev_header[4][1]
class T_e():
def __init__(self, emissivity = 0.95, phi = 34., longitude = 74., elev = 0., h = 0.07, d = 0.2, emmiss_animal = 0.95, sky = 0.7, r_soil = 0.3, emmiss_soil = 0.95, abs_animal_long = 0.97, abs_animal_short = 0.7, Ta_min0 = 20., Ta_min1 = 20., Ta_min2 = 20., Ta_max0 = 35., Ta_max1 = 35., Ta_max2 = 35., ampl = 15., wind = 0.1):
self.SIGMA = 5.673e-8
self.SOLAR = 1360.
self.emissivity = emissivity
self.phi = phi
self.longitude = longitude
self.elev = elev
self.h = h
self.d = d
self.emmiss_animal = emmiss_animal
self.char_dim = d
self.sky = sky
self.r_soil = r_soil
self.emmiss_soil = emmiss_soil
self.abs_animal_long = abs_animal_long
self.abs_animal_short = abs_animal_short
self.Ta_min0 = Ta_min0
self.Ta_min1 = Ta_min1
self.Ta_min2 = Ta_min2
self.Ta_max0 = Ta_max0
self.Ta_max1 = Ta_max1
self.Ta_max2 = Ta_max2
self.ampl = ampl
self.wind = wind
self.size = 10.
self.h_t = exp(log(self.size) * 0.36 + 0.72)
self.c_t = exp(log(0.42 + 0.44 * self.size))
self.Z=0.
self.TA= 0.
self.x_min, self.y_min = 0., 0.
self.x_max, self.y_max = 132., 132. #x_max = ncols, y_max = nrows #### CHANGED FROM SEARS 99. for each 8feb!
self.position = {'x':rand() * self.x_max, 'y': rand() * self.y_max}
self.thigh = 35.
self.tlow = 29.
self.topt = 32.
self.mu = 0.
self.kappa = 0.25
self.beta_alpha = 1.
self.beta_beta = 3.
self.d_max = 5.*(np.log10(self.size)+1.)
self.p1 = 0.5
self.p2 = 0.0
self.p3 = 0.0
self.decisions = 6
self.tb = 20.
self.te = 20.
self.orientation = vonmises(self.mu, self.kappa)
self.dist = 0.
self.ctmax = 39.
self.moved = 0
self.cost = 0
self.totenergy = 0.
self.dist = 0.
self.active = 0
self.t_target = 32.
self.db = 0.
self.de = 0.
self.energy_balance = 0.
self.moved = 0.
self.tot_dist_moved = 0.
self.total_activity = 0.
self.ate = 0.
def tprops(self): #thermal preoperties
self.h_t = exp(log(self.size) * 0.36 + 0.72)
self.c_t = exp(0.42 + 0.44 * log(self.size))
def greybody(self, K):
return self.emissivity * self.SIGMA * (K + 273)**4
## original MS fxn
#def zenith(self ,t, J): # phi = lattitde, delta = solar declination, t0 = solar noon
# self.Z = degrees(acos(sin(radians(self.phi)) * sin(radians(self.declination(J))) + cos(radians(self.phi)) * cos(radians(self.declination(J))) * cos(radians(15. * (t - self.noon(J))))))
# if self.Z <0.: #or self.Z is None: ##LN modified
# self.Z = 0.
# if self.Z >90: # or self.Z is None: ##LN modified
# self.Z = 90.
# return
def zenith(self ,t, J): # phi = lattitde, delta = solar declination, t0 = solar noon
self.Z = degrees(acos(sin(radians(self.phi)) * sin(radians(self.declination(J))) + cos(radians(self.phi)) * cos(radians(self.declination(J))) * cos(radians(15. * (t - self.noon(J))))))
if self.Z <0. or self.Z is None: ##LN modified
self.Z = 0.
if self.Z >90 or self.Z is None: ##LN modified
self.Z = 90.
return self.Z # adding return statement so it always returns a value preventing 'NoneType" error
def altitude(self, t, J):
return degrees(asin(sin(radians(self.phi)) * sin(radians(self.declination(J))) + cos(radians(self.phi)) * cos(radians(self.declination(J))) * cos(radians(15. * (t - self.noon(J))))))
def azimuth(self, t, J):
#return degrees(asin(-cos(radians(self.declination(J))) * sin(radians(15. * (t - self.noon(J))))/cos(radians(self.altitude(t,J)))))
self.zenith(t,J)
#print self.Z, self.phi
if t<self.noon(J):
#return 180.- degrees(acos(-(sin(radians(self.declination(J)))-cos(radians(self.zenith(t,J)))*sin(radians(self.phi)))/(cos(radians(self.phi))*sin(radians(self.zenith(t,J))))))
return 180.- degrees(acos(-(sin(radians(self.declination(J)))-cos(radians(self.Z))*sin(radians(self.phi)))/(cos(radians(self.phi))*sin(radians(self.Z)))))
else:
#return 180.+ degrees(acos(-(sin(radians(self.declination(J)))-cos(radians(self.zenith(t,J)))*sin(radians(self.phi)))/(cos(radians(self.phi))*sin(radians(self.zenith(t,J))))))
return 180.+ degrees(acos(-(sin(radians(self.declination(J)))-cos(radians(self.Z))*sin(radians(self.phi)))/(cos(radians(self.phi))*sin(radians(self.Z)))))
def t_adj(self, t, J):
return t -12. + self.noon(J)
def declination(self, J): # delta
return degrees(asin(0.39785* sin(radians(278.97 + 0.9856 * J + 1.9165 * sin(radians(356.6 + 0.9856 * J))))))
def LC(self):
return self.longitude % 15
def f(self, J):
return 279.575 + 0.9856 * J
def ET(self, J):
return (-104.7 * sin(radians(self.f(J))) + 596.2 * sin(radians(2 * self.f(J))) + 4.3 * sin(radians(3 * self.f(J))) - 12.7 * sin(radians(4 * self.f(J))) -429.3 * cos(radians(self.f(J)))- 2.0 * cos(radians(2 * self.f(J))) + 19.3 * cos(radians(3 * self. f(J))))/3600.
def noon(self ,J):
return 12 + self.LC() / 15. - self.ET(J)
def bardd2(self, J):
return 1 + 2 * 0.01675 * cos(2 * pi / 365 * J)
def sol_noatm(self, t, J, a_s, alpha_s):
if self.zenith(t,J)<90.:
s = self.SOLAR * self.bardd2(J) * cos(self.a_o_i(t, J, a_s, alpha_s))##*cos(self.a_o_i(t, J, a_s, alpha_s))#(radians(self.zenith(t, J)))#cos(radians(self.zenith(t, J)))#
if s >= 0: return s
else: return 0. ##LN added .
else: return 0. ##LN added .
def p_a(self):
return 101.3 * exp(-self.elev / 8200.)
def t_m(self, t, J):
#return self.sky**(self.p_a() / (101.3 * cos(radians(self.zenith(t, J)))))
return self.sky**(self.p_a() / (101.3 * cos(radians(self.Z))))
def sol_atm(self, t, J, a_s=0, alpha_s=0):
return self.sol_noatm(t, J, a_s, alpha_s) * self.t_m(t, J)
def sol_diffuse(self, t, J, a_s, alpha_s):
return self.sol_noatm(t, J, a_s, alpha_s) * 0.3 * (1 - self.t_m(t, J))
def h_g(self, t, J, a_s=0, alpha_s=0):
return self.sol_diffuse(t, J, a_s, alpha_s) + self.sol_atm(t, J, a_s=0, alpha_s=0)
def short_ground(self, t, J):
return self.h_g(t, J) * self.r_soil
def gamma_t(self, t):
return 0.44 - 0.46 * sin(t * pi / 12. + 0.9) + 0.11 * sin(2. * t * pi / 12. + 0.9)
def t_air(self, t, J):
if (t >= 0.) and (t <= 5.):
self.TA = maxT(J - 1) * self.gamma_t(self.t_adj(t, J)) + minT(J) * (1 - self.gamma_t(self.t_adj(t, J)))
return self.TA
if (t > 5.) and (t <= 14.):
self.TA = maxT(J) * self.gamma_t(self.t_adj(t, J)) + minT(J) * (1 - self.gamma_t(self.t_adj(t, J)))
return self.TA
if (t > 14.) and (t <= 24.):
self.TA = maxT(J) * self.gamma_t(self.t_adj(t, J)) + minT(J + 1) * (1 - self.gamma_t(self.t_adj(t, J)))
return self.TA
def t_ground(self, t, J, sun = 1.):
if 15 > J >= 0: # for days between jan 1 and jan 15
return sun * ((J - 0.)/(14. - -17.) * (janSpline(t)[0] - decSpline(t)[0]) + decSpline(t)[0]) + (1.-sun)*self.t_air(t,J)
if 46 > J >= 15: # for days between jan 15 and feb 15
return sun *((J - 15.)/(45. - 15.) * (febSpline(t)[0] - janSpline(t)[0]) + janSpline(t)[0])+ (1.-sun)*self.t_air(t,J)
if 75 > J >= 46:
return sun *((J - 46.)/(74. - 46.) * (marSpline(t)[0] - febSpline(t)[0]) + febSpline(t)[0]) + (1.-sun)*self.t_air(t,J)
if 106 > J >= 75:
return sun *((J - 75.)/(105. - 75.) * (aprSpline(t) - marSpline(t)) + marSpline(t)) + (1.-sun)*self.t_air(t,J)
if 136 > J >= 106:
return sun *((J - 106.)/(135. - 106.) * (maySpline(t) - aprSpline(t)) + aprSpline(t)) + (1.-sun)*self.t_air(t,J)
if 167 > J >= 136:
return sun *((J - 136.)/(166. - 136.) * (junSpline(t) - maySpline(t)) + maySpline(t)) + (1.-sun)*self.t_air(t,J)
if 197 > J >= 167:
return sun *((J - 167.)/(196. - 167.) * (julSpline(t) - junSpline(t)) + junSpline(t)) + (1.-sun)*self.t_air(t,J)
if 228 > J >= 197:
return sun *((J - 197.)/(227. - 197.) * (augSpline(t) - julSpline(t)) + julSpline(t)) + (1.-sun)*self.t_air(t,J)
if 259 > J >= 228:
return sun *((J - 228.)/(258. - 228.) * (sepSpline(t)[0] - augSpline(t)[0]) + augSpline(t)[0]) + (1.-sun)*self.t_air(t,J)
if 289 > J >= 259:
return sun *((J - 259.)/(288. - 259.) * (octSpline(t)[0] - sepSpline(t)[0]) + sepSpline(t)[0]) + (1.-sun)*self.t_air(t,J)
if 320 > J >= 289:
return sun *((J - 289.)/(319. - 289.) * (novSpline(t)[0] - octSpline(t)[0]) + octSpline(t)[0]) + (1.-sun)*self.t_air(t,J)
if 350 > J >= 320:
return sun *((J - 320.)/(349. - 320.) * (decSpline(t)[0] - novSpline(t)[0]) + novSpline(t)[0])+ (1.-sun)*self.t_air(t,J)
if 367 > J >= 350:
return sun *((J - 350.)/(380. - 350.) * (janSpline(t)[0] - decSpline(t)[0]) + decSpline(t)[0]) + (1.-sun)*self.t_air(t,J)
def long_atmos(self, t, J): #### UPDATE FOR MICROCLIM INPUT DATA...SUN Ta at 2m input!!
return 53.1e-14 * (self.t_air(t, J) + 273.)**6
def t_ave(self):
temp=[]
for i in range(24):
temp.append(self.t_air(i, J))
return np.mean(temp)
#def t_ground(self, t, sun):
# return sun*(self.t_ave() + self.ampl * sin((pi / 12.) * (t - 8.))) + (1.- sun) * self.t_air(t)
def long_ground(self, t, J, sun): #### UPDATE FOR MICROCLIM INPUT DATA... sun/shade GROUND input
#micro = pd.read_csv('/Users/laurenneel/Desktop/Grass_RGB_DSM_Oct22/microclim_input_era5/hourly_df_TC_2021.csv', usecols=["Tg_avg"])
#Tg_avg = micro.iloc[t, J, sun]["Tg_avg"]
#return self.emmiss_soil * self.SIGMA * (Tg_avg + 273)**4
#print(Tg_avg)
return self.emmiss_soil * self.SIGMA * (self.t_ground(t, J, sun) + 273)**4
def Ap_over_A(self, t,J,a_s, alpha_s):
Ap = 1.+ 4. * self.h * sin(self.a_o_i(t,J,a_s,alpha_s)) / (pi * self.d)
A= 4.+ 4. * self.h / self.d
return Ap / A
def R_abs(self, t, J, sun, a_s, alpha_s): #### UPDATE FOR MICROCLIM INPUT DATA..... needs to call the right ground and air temp
return sun * self.abs_animal_short * (self.Ap_over_A(t,J,a_s,alpha_s) * self.sol_atm(t, J, a_s, alpha_s) + 0.5 * self.sol_diffuse(t, J, a_s, alpha_s) + 0.5 * self.short_ground(t, J)) + 0.5 * self.abs_animal_long * (self.long_atmos(t, J) + self.long_ground(t, J, sun))
def Q_rad(self, t, J):
#return self.emmiss_animal * self.SIGMA * (self.t_air(t,J) + 273.)**4
return self.emmiss_animal * self.SIGMA * (self.TA + 273.)**4
def g_Ha(self, wind):
#return 1.4 * 0.135 * sqrt(self.wind / self.char_dim)
return 1.4 * 0.135 * sqrt(wind / self.char_dim)
def g_r(self, t, J, sun): #### input ground data in sun/shade here!!!
#return 4.* self.SIGMA * ((self.t_air(t,J) + 273.)**3) / 29.3
return 4.* self.SIGMA * ((self.TA + 273.)**3) / 29.3
def a_o_i(self, t, J, a_s, alpha_s): #angle of incidence...NEED INPUTS for a_s = slope, alpha_s = aspect with N=0 E=90
self.zenith(t,J)
if 0.<self.Z<=90.:
tmp=acos(cos(radians(a_s)) * cos(radians(self.altitude(t,J))) * cos(radians(self.azimuth(t, J) - alpha_s)) + sin(radians(a_s)) * sin(radians(self.altitude(t,J))))
#print tmp
if tmp<=pi/2:
return tmp
if tmp > pi/2.:
return pi/2.
else: return pi/2
else: return pi/2
def t_e(self, t, J, sun, a_s, alpha_s,veg): #UPDATE FOR MICROCLIM INPUT DATA .... t_ground should be replaced with Ta at 2cm... need to set it up for different sun/shade 2cm input
#_wind = 0. #note, this is to mimic convection shadow effect
if sun ==1 and veg == 0: #was or not and
sun = 1
else:
sun = 0.375
if veg == 1:
wind = 0.1
else:
wind = 2.0
return self.t_ground(t, J, sun) + (self.R_abs(t, J, sun, a_s, alpha_s) - self.Q_rad(t, J)) / (29.3 * (self.g_Ha(wind) + self.g_r(t, J, sun)))
def mass(self):
return ((self.h * 100.) * pi * (0.5 * self.d * 100.)**2.) / 1000.
def update_tb(self):
if self.tb <= self.te:
return self.tb + (1. - exp(-1. / self.h_t)) * (self.te - self.tb) #heating
if self.tb > self.te:
return self.tb + (1. - exp(-1. / self.c_t)) * (self.te - self.tb) #cooling
def mei(self, x):
#mass = 10.
max_con=-328.7+22.82*x-0.32*x**2
act_con= max_con * self.size /24.
asin_de= 85.34-0.5*x
de = (sin((3.14159/180)*asin_de))**2
return (act_con * 0.25*de/1000.*25600.)/60. #per minute
def smr(self):
act_scope = 1. + 4. * self.moved/self.d_max #* 0.5
return (act_scope*20.2*10**(0.038*self.tb-1.771)*self.size**0.82)/60.
def net(self,x, dist=10.):
return self.mei(x) - self.smr(x,dist)
def mei(self):
max_con=-328.7+22.82*self.tb-0.32*self.tb**2
act_con= max_con * self.size /24.
asin_de= 85.34-0.5*self.tb
de = (sin((3.14159/180)*asin_de))**2
return (act_con * 0.25*de/1000.*25600.)/60.
def net(self):
#E=mei(self.tb)- (dist/10.)*smr(self.tb,1)-(1.-dist/10.)*smr(self.tb,0)
return (self.moved/self.d_max)*self.smr()+(1.-self.dist/self.d_max)*self.smr()
#return self.mei() - self.smr()
#return E
def getDisp(self):
incre = vonmises(self.mu, self.kappa)
c = beta(self.beta_alpha, self.beta_beta) * self.d_max
a, b = c * sin(self.orientation + incre), c * cos(self.orientation + incre)
return a, b, c, incre
def move_reg(self, t, J, elev, slope, aspect, veget):
incre, x1, y1 = 0., self.position['x'], self.position['y'] #, 0.
#self.active = 1
lenx = len(elev[0])
leny = len(elev)
az=radians(self.azimuth(t, J))
al=radians(self.altitude(t, J))
#self.te = self.t_e(t,J, sun=horizon_master(az, elev[int(self.position['y'])][int(self.position['x'])], x=self.position['x'], y=self.position['y']), a_s=90.- slope[int(self.position['y'])][int(self.position['x'])], alpha_s=aspect[int(self.position['y'])][int(self.position['x'])], veg=veg) # at the moment this is just a holder from ast code
diff_tb = 50.
temp_c = 32.
while elev[int(y1)][int(x1)] == -9999 or slope[int(y1)][int(x1)] == -9999 or aspect[int(y1)][int(x1)] == -9999 or veget[int(y1)][int(x1)] == -9999:
a, b, c, incre = self.getDisp()
if self.thigh >= self.tb >= self.tlow:
if binomial(1, self.p1): # remain still
#self.active = 0 # x, y = x, y ...
self.moved = 0.
else: # move
for l in range(self.decisions): # needs to be one per second
a, b, c, incre = self.getDisp()
if (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
while (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
a, b, c, incre = self.getDisp()
x1 = self.position['x'] + a
y1 = self.position['y'] + b
az=radians(self.azimuth(t, J))
al=radians(self.altitude(t, J))
self.te = self.t_e(t,J, sun=horizon_master(az, elev[int(y1)][int(x1)], x=x1, y=y1), a_s=90.- slope[int(y1)][int(x1)], alpha_s=aspect[int(y1)][int(x1)], veg=veget[int(y1)][int(x1)])
up_tb = self.update_tb()
diff_tb_new = abs(self.t_target - up_tb)
if diff_tb_new <= diff_tb: # and c <= temp_c:
diff_tb = diff_tb_new
temp_c = c
temp_x1, temp_y1 = x1, y1
else:
pass
if l == (self.decisions -1):
self.position['x'], self.position['y'], c = temp_x1, temp_y1, temp_c
self.dist += temp_c
self.orientation += incre
self.moved = c
elif self.tb > self.thigh:
if self.tb > self.thigh > self.t_e(t,J, sun=horizon_master(az, elev[int(y1)][int(x1)], x=x1, y=y1), a_s=90.- slope[int(y1)][int(x1)], alpha_s=aspect[int(y1)][int(x1)], veg=veget[int(y1)][int(x1)]):
if binomial(1, self.p2):
self.active = 0 #remain still
self.moved = 0.
else: # move
for l in range(self.decisions): # needs to be one per second
a, b, c, incre = self.getDisp()
if (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
while (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
a, b, c, incre = self.getDisp()
x1 = self.position['x'] + a
y1 = self.position['y'] + b
az=radians(self.azimuth(t, J))
al=radians(self.altitude(t, J))
self.te = self.t_e(t,J, sun=horizon_master(az, elev[int(y1)][int(x1)], x=x1, y=y1), a_s=90.- slope[int(y1)][int(x1)], alpha_s=aspect[int(y1)][int(x1)], veg=veget[int(y1)][int(x1)])
up_tb = self.update_tb()
diff_tb_new = abs(self.t_target - up_tb)
if diff_tb_new <= diff_tb: # and c <= temp_c:
diff_tb = diff_tb_new
temp_c = c
temp_x1, temp_y1 = x1, y1
else:
pass
if l == (self.decisions -1):
self.position['x'], self.position['y'], c = temp_x1, temp_y1, temp_c
self.dist += temp_c
self.orientation += incre
self.moved = c
else: # move
for l in range(self.decisions): # needs to be one per second
a, b, c, incre = self.getDisp()
if (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
while (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
a, b, c, incre = self.getDisp()
x1 = self.position['x'] + a
y1 = self.position['y'] + b
az=radians(self.azimuth(t, J))
al=radians(self.altitude(t, J))
self.te = self.t_e(t,J, sun=horizon_master(az, elev[int(y1)][int(x1)], x=x1, y=y1), a_s=90.- slope[int(y1)][int(x1)], alpha_s=aspect[int(y1)][int(x1)], veg=veget[int(y1)][int(x1)])
up_tb = self.update_tb()
diff_tb_new = abs(self.t_target - up_tb)
if diff_tb_new <= diff_tb:# and c <= temp_c:
diff_tb = diff_tb_new
temp_c = c
temp_x1, temp_y1 = x1, y1
else:
pass
if l == (self.decisions -1):
self.position['x'], self.position['y'], c = temp_x1, temp_y1, temp_c
self.dist += temp_c
self.orientation += incre
self.moved = c
else: #self.tb < self.tlow:
if self.tb < self.tlow < self.t_e(t,J, sun=horizon_master(az, elev[int(y1)][int(x1)], x=x1, y=y1), a_s=90.- slope[y1][x1], alpha_s=aspect[int(y1)][int(x1)], veg=veget[int(y1)][int(x1)]):
if binomial(1, self.p3):
self.active = 0 #remain still
self.moved = 0.
else: # move
for l in range(self.decisions): # needs to be one per second
a, b, c, incre = self.getDisp()
if (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
while (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
a, b, c, incre = self.getDisp()
x1 = self.position['x'] + a
y1 = self.position['y'] + b
az=radians(self.azimuth(t, J))
al=radians(self.altitude(t, J))
self.te = self.t_e(t,J, sun=horizon_master(az, elev[int(y1)][int(x1)], x=x1, y=y1), a_s=90.- slope[int(y1)][int(x1)], alpha_s=aspect[int(y1)][int(x1)], veg=veget[int(y1)][int(x1)])
up_tb = self.update_tb()
diff_tb_new = abs(self.t_target - up_tb)
if diff_tb_new <= diff_tb: # and c <= temp_c:
diff_tb = diff_tb_new
temp_c = c
temp_x1, temp_y1 = x1, y1
else:
pass
if l == (self.decisions - 1):
self.position['x'], self.position['y'], c = temp_x1, temp_y1, temp_c
self.dist += temp_c
self.orientation += incre
self.moved = c
else:
for l in range(self.decisions): # needs to be one per second
a, b, c, incre = self.getDisp()
if (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
while (not (0.<=self.position['x']+a<=lenx-1)) or (not (0.<=self.position['y']+b<=leny-1)):
a, b, c, incre = self.getDisp()
x1 = self.position['x'] + a
y1 = self.position['y'] + b
az=radians(self.azimuth(t, J))
al=radians(self.altitude(t, J))
self.te = self.t_e(t,J, sun=horizon_master(az, elev[int(y1)][int(x1)], x=x1, y=y1), a_s=90.- slope[int(y1)][int(x1)], alpha_s=aspect[int(y1)][int(x1)], veg=veget[int(y1)][int(x1)])
up_tb = self.update_tb()
diff_tb_new = abs(self.t_target - up_tb)
if diff_tb_new <= diff_tb: # and c <= temp_c:
diff_tb = diff_tb_new
temp_c = c
temp_x1, temp_y1 = x1, y1
else:
pass
if l == (self.decisions - 1):
self.position['x'], self.position['y'], c = temp_x1, temp_y1, temp_c
self.dist += temp_c
self.orientation += incre
self.moved = c
### MAKE MAPS
#elev, slope, aspect, veget, e_range, e_fract, v_range, v_fract = make_maps(h, high, N, MU, SD) ###only need these first 4 variables -- assign
# Save Maps
#write_file = "maps/elev" + "_" + '{:.4}'.format(e_fract) + "_" + '{:.3}'.format(e_range)+ "_" + '{:.3}'.format(v_fract+3.) + "_" + '{:.3}'.format(v_range)+ ".asc"
#output=open(write_file, 'w')
#for i in range(N):
# for j in range(N):
# output.write(str(elev[i][j])), output.write(' ')
# output.write("\n")
#output.close()
#
#write_file = "maps/slope" + "_" +'{:.4}'.format(e_fract) + "_" + '{:.3}'.format(e_range)+ "_" + '{:.3}'.format(v_fract+3.) + "_" + '{:.3}'.format(v_range)+ ".asc"
#output=open(write_file, 'w')
#for i in range(N):
# for j in range(N):
# output.write(str(slope[i][j])), output.write(' ')
# output.write("\n")
#output.close()
#
#write_file = "maps/aspect" + "_" + '{:.4}'.format(e_fract) + "_" + '{:.3}'.format(e_range)+ "_" + '{:.3}'.format(v_fract+3.) + "_" + '{:.3}'.format(v_range)+ ".asc"
#output=open(write_file, 'w')
#for i in range(N):
# for j in range(N):
# output.write(str(aspect[i][j])), output.write(' ')
# output.write("\n")
#output.close()
#
#write_file = "maps/veg" + "_" + '{:.4}'.format(e_fract) + "_" + '{:.3}'.format(e_range)+ "_" + '{:.3}'.format(v_fract+3.) + "_" + '{:.3}'.format(v_range)+ ".asc"
#output=open(write_file, 'w')
#for i in range(N):