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My program is optimizing the charging and decharging of a home battery to minimize the cost of electricity at the end of the year. The electricity usage of homes is measured each 15 minutes, so I have 96 measurement point in 1 day. I want to optimilize the charging and decharging of the battery for 2 days, so that day 1 takes the usage of day 2 into account. I wrote the following code and it works.
from gekko import GEKKO
import numpy as np
import pandas as pd
import time
import math
# ------------------------ Import and read input data ------------------------
file = r'D:\Bedrijfseconomie\MP Thuisbatterijen\Spyder - Gekko\Data Sim 1.xlsx'
data = pd.read_excel(file, sheet_name='Input', na_values='NaN')
dataRead = pd.DataFrame(data, columns= ['Timestep','Verbruik woning (kWh)','Prijs afname (€/kWh)',
'Capaciteit batterij (kW)','Capaciteit batterij (kWh)',
'Rendement (%)','Verbruikersprofiel'])
timestep = dataRead['Timestep'].to_numpy()
usage_home = dataRead['Verbruik woning (kWh)'].to_numpy()
price = dataRead['Prijs afname (€/kWh)'].to_numpy()
cap_batt_kW = dataRead['Capaciteit batterij (kW)'].iloc[0]
cap_batt_kWh = dataRead['Capaciteit batterij (kWh)'].iloc[0]
efficiency = dataRead['Rendement (%)'].iloc[0]
usersprofile = dataRead['Verbruikersprofiel'].iloc[0]
# ---------------------------- Optimization model ----------------------------
# Initialise model
m = GEKKO()
# Global options
m.options.SOLVER = 1
# Constants
snelheid_laden = cap_batt_kW/4
T = len(timestep)
loss_charging = m.Const(value = (1-efficiency)/2)
max_cap_batt = m.Const(value = cap_batt_kWh)
min_cap_batt = m.Const(value = 0)
max_charge = m.Const(value = snelheid_laden) # max battery can charge in 15min
max_decharge = m.Const(value = -snelheid_laden) # max battery can decharge in 15min
# Parameters
dummy = np.array(np.ones([T]))
# Variables
e_batt = m.Array(m.Var, (T), lb = min_cap_batt, ub = max_cap_batt) # energy in battery
usage_net = m.Array(m.Var, (T)) # usage home & charge/decharge battery
price_paid = m.Array(m.Var, (T)) # price paid each 15min
charging = m.Array(m.Var, (T), lb = max_decharge, ub = max_charge) # amount charge/decharge each 15min
# Intermediates
e_batt[0] = m.Intermediate(charging[0])
for t in range(T):
e_batt[t] = m.Intermediate(m.sum([charging[i]*(1-loss_charging) for i in range(t)]))
usage_net = [m.Intermediate(usage_home[t] + charging[t]) for t in range(T)]
price_paid = [m.Intermediate(usage_net[t] * price[t] / 100) for t in range(T)]
total_price = m.Intermediate(m.sum([price_paid[t] for t in range(T)]))
# Equations (constraints)
m.Equation([min_cap_batt*dummy[t] <= e_batt[t] for t in range(T)])
m.Equation([max_cap_batt*dummy[t] >= e_batt[t] for t in range(T)])
m.Equation([max_charge*dummy[t] >= charging[t] for t in range(T)])
m.Equation([max_decharge*dummy[t] <= charging[t] for t in range(T)])
m.Equation([min_cap_batt*dummy[t] <= usage_net[t] for t in range(T)])
m.Equation([(-1*charging[t]) <= (1-loss_charging)*e_batt[t] for t in range(T)])
# Objective
m.Minimize(total_price)
# Solve problem
m.solve()
My code is running and it works but despite that it gives a Solution time of 10 seconds, the total time for it to run is around 8 minutes. Does anyone know a way I can speed it up?
There are a few ways to speed up the Gekko code:
Solve locally instead of on the public server. The option is m=GEKKO(remote=False). The public server can slow down with many jobs.
Use sum() instead of m.sum(). This can be faster for compiling the model. Otherwise, use m.integral(x) if you need the integral of x.
Many of the equations are repeated at each time horizon step. Gekko is more efficient using a single equation definition with IMODE=2 (for algebraic equation models) or IMODE=6 (for differential / algebraic equation models) and then it creates the equations over the time horizon. You may need to use m.vsum() instead of m.sum().
For additional diagnosis, try setting m.options.DIAGLEVEL=1 to get a detailed timing report of how long it takes to compile the model and perform each function, 1st derivative, and 2nd derivative calculation. It also gives a detailed view of the solver versus model time during the solution phase.
Update with Data File Testing
Thanks for sending the data file. The run directory shows that the model file is 58,682 lines long. It takes a while to compile a model that size. Here is the solution from the files you sent:
--------- APM Model Size ------------
Each time step contains
Objects : 193
Constants : 5
Variables : 20641
Intermediates: 578
Connections : 18721
Equations : 20259
Residuals : 19681
Number of state variables: 20641
Number of total equations: - 19873
Number of slack variables: - 1152
---------------------------------------
Degrees of freedom : -384
* Warning: DOF <= 0
----------------------------------------------
Steady State Optimization with APOPT Solver
----------------------------------------------
Iter Objective Convergence
0 3.37044E+01 5.00000E+00
1 2.81987E+01 1.00000E-10
2 2.81811E+01 5.22529E-12
3 2.81811E+01 2.10942E-15
4 2.81811E+01 2.10942E-15
Successful solution
---------------------------------------------------
Solver : APOPT (v1.0)
Solution time : 10.5119999999879 sec
Objective : 28.1811214884047
Successful solution
---------------------------------------------------
Here is a version that uses IMODE=6 instead. You define the variables and equations once and let Gekko handle the time discretization. It makes a much more efficient model because there is no unnecessary duplication of equations.
from gekko import GEKKO
import numpy as np
import pandas as pd
import time
import math
# ------------------------ Import and read input data ------------------------
file = r'Data Sim 1.xlsx'
data = pd.read_excel(file, sheet_name='Input', na_values='NaN')
dataRead = pd.DataFrame(data, columns= ['Timestep','Verbruik woning (kWh)','Prijs afname (€/kWh)',
'Capaciteit batterij (kW)','Capaciteit batterij (kWh)',
'Rendement (%)','Verbruikersprofiel'])
timestep = dataRead['Timestep'].to_numpy()
usage_home = dataRead['Verbruik woning (kWh)'].to_numpy()
price = dataRead['Prijs afname (€/kWh)'].to_numpy()
cap_batt_kW = dataRead['Capaciteit batterij (kW)'].iloc[0]
cap_batt_kWh = dataRead['Capaciteit batterij (kWh)'].iloc[0]
efficiency = dataRead['Rendement (%)'].iloc[0]
usersprofile = dataRead['Verbruikersprofiel'].iloc[0]
# ---------------------------- Optimization model ----------------------------
# Initialise model
m = GEKKO()
m.open_folder()
# Global options
m.options.SOLVER = 1
m.options.IMODE = 6
# Constants
snelheid_laden = cap_batt_kW/4
m.time = timestep
loss_charging = m.Const(value = (1-efficiency)/2)
max_cap_batt = m.Const(value = cap_batt_kWh)
min_cap_batt = m.Const(value = 0)
max_charge = m.Const(value = snelheid_laden) # max battery can charge in 15min
max_decharge = m.Const(value = -snelheid_laden) # max battery can decharge in 15min
# Parameters
usage_home = m.Param(usage_home)
price = m.Param(price)
# Variables
e_batt = m.Var(value=0, lb = min_cap_batt, ub = max_cap_batt) # energy in battery
price_paid = m.Var() # price paid each 15min
charging = m.Var(lb = max_decharge, ub = max_charge) # amount charge/decharge each 15min
usage_net = m.Var(lb=min_cap_batt)
# Equations
m.Equation(e_batt==m.integral(charging*(1-loss_charging)))
m.Equation(usage_net==usage_home + charging)
price_paid = m.Intermediate(usage_net * price / 100)
m.Equation(-charging <= (1-loss_charging)*e_batt)
# Objective
m.Minimize(price_paid)
# Solve problem
m.solve()
import matplotlib.pyplot as plt
plt.plot(m.time,e_batt.value,label='Battery Charge')
plt.plot(m.time,charging.value,label='Charging')
plt.plot(m.time,price_paid.value,label='Price')
plt.plot(m.time,usage_net.value,label='Net Usage')
plt.xlabel('Time'); plt.grid(); plt.legend(); plt.show()
The model is only 31 lines long (see gk0_model.apm) and it solves much faster (a couple seconds total).
--------- APM Model Size ------------
Each time step contains
Objects : 0
Constants : 5
Variables : 8
Intermediates: 1
Connections : 0
Equations : 6
Residuals : 5
Number of state variables: 1337
Number of total equations: - 955
Number of slack variables: - 191
---------------------------------------
Degrees of freedom : 191
----------------------------------------------
Dynamic Control with APOPT Solver
----------------------------------------------
Iter Objective Convergence
0 3.46205E+01 3.00000E-01
1 3.30649E+01 4.41141E-10
2 3.12774E+01 1.98558E-11
3 3.03148E+01 1.77636E-15
4 2.96824E+01 3.99680E-15
5 2.82700E+01 8.88178E-16
6 2.82039E+01 1.77636E-15
7 2.81334E+01 8.88178E-16
8 2.81085E+01 1.33227E-15
9 2.81039E+01 8.88178E-16
Iter Objective Convergence
10 2.81005E+01 8.88178E-16
11 2.80999E+01 1.77636E-15
12 2.80996E+01 8.88178E-16
13 2.80996E+01 8.88178E-16
14 2.80996E+01 8.88178E-16
Successful solution
---------------------------------------------------
Solver : APOPT (v1.0)
Solution time : 0.527499999996508 sec
Objective : 28.0995878585948
Successful solution
---------------------------------------------------
There is no long compile time. Also, the solver time is reduced from 10 sec to 0.5 sec. The objective function is nearly the same (28.18 versus 28.10).
Here is a complete version without the data file dependency (in case the data file isn't available in the future).
from gekko import GEKKO
import numpy as np
import pandas as pd
import time
import math
# ------------------------ Import and read input data ------------------------
timestep = np.arange(1,193)
usage_home = np.array([0.05,0.07,0.09,0.07,0.05,0.07,0.07,0.07,0.06,
0.05,0.07,0.07,0.09,0.07,0.06,0.07,0.07,
0.07,0.16,0.12,0.17,0.08,0.10,0.11,0.06,
0.06,0.06,0.06,0.06,0.07,0.07,0.07,0.08,
0.08,0.06,0.07,0.07,0.07,0.07,0.05,0.07,
0.07,0.07,0.07,0.21,0.08,0.07,0.08,0.27,
0.12,0.09,0.10,0.11,0.09,0.09,0.08,0.08,
0.12,0.15,0.08,0.10,0.08,0.10,0.09,0.10,
0.09,0.08,0.10,0.12,0.10,0.10,0.10,0.11,
0.10,0.10,0.11,0.13,0.21,0.12,0.10,0.10,
0.11,0.10,0.11,0.12,0.12,0.10,0.11,0.10,
0.10,0.10,0.11,0.10,0.10,0.09,0.08,0.12,
0.10,0.11,0.11,0.10,0.06,0.05,0.06,0.06,
0.06,0.07,0.06,0.06,0.05,0.06,0.05,0.06,
0.05,0.06,0.05,0.06,0.07,0.06,0.09,0.10,
0.10,0.22,0.08,0.06,0.05,0.06,0.08,0.08,
0.07,0.08,0.07,0.07,0.16,0.21,0.08,0.08,
0.09,0.09,0.10,0.09,0.09,0.08,0.12,0.24,
0.09,0.08,0.09,0.08,0.10,0.24,0.08,0.09,
0.09,0.08,0.08,0.07,0.06,0.05,0.06,0.07,
0.07,0.05,0.05,0.06,0.05,0.28,0.11,0.20,
0.10,0.09,0.28,0.10,0.15,0.09,0.10,0.18,
0.12,0.13,0.30,0.10,0.11,0.10,0.10,0.11,
0.10,0.21,0.10,0.10,0.12,0.10,0.08])
price = np.array([209.40,209.40,209.40,209.40,193.00,193.00,193.00,
193.00,182.75,182.75,182.75,182.75,161.60,161.60,
161.60,161.60,154.25,154.25,154.25,154.25,150.70,
150.70,150.70,150.70,150.85,150.85,150.85,150.85,
150.00,150.00,150.00,150.00,153.25,153.25,153.25,
153.25,153.25,153.25,153.25,153.25,151.35,151.35,
151.35,151.35,151.70,151.70,151.70,151.70,154.95,
154.95,154.95,154.95,150.20,150.20,150.20,150.20,
153.75,153.75,153.75,153.75,160.55,160.55,160.55,
160.55,179.90,179.90,179.90,179.90,202.00,202.00,
202.00,202.00,220.25,220.25,220.25,220.25,245.75,
245.75,245.75,245.75,222.90,222.90,222.90,222.90,
203.40,203.40,203.40,203.40,205.30,205.30,205.30,
205.30,192.80,192.80,192.80,192.80,177.00,177.00,
177.00,177.00,159.90,159.90,159.90,159.90,152.50,
152.50,152.50,152.50,143.95,143.95,143.95,143.95,
142.10,142.10,142.10,142.10,143.75,143.75,143.75,
143.75,170.80,170.80,170.80,170.80,210.35,210.35,
210.35,210.35,224.45,224.45,224.45,224.45,226.30,
226.30,226.30,226.30,227.85,227.85,227.85,227.85,
225.45,225.45,225.45,225.45,225.80,225.80,225.80,
225.80,224.50,224.50,224.50,224.50,220.30,220.30,
220.30,220.30,220.00,220.00,220.00,220.00,221.90,
221.90,221.90,221.90,230.25,230.25,230.25,230.25,
233.60,233.60,233.60,233.60,225.20,225.20,225.20,
225.20,179.85,179.85,179.85,179.85,171.85,171.85,
171.85,171.85,162.90,162.90,162.90,162.90,158.85,
158.85,158.85,158.85])
cap_batt_kW = 3.00
cap_batt_kWh = 5.00
efficiency = 0.95
usersprofile = 1
# ---------------------------- Optimization model ----------------------------
# Initialise model
m = GEKKO()
#m.open_folder()
# Global options
m.options.SOLVER = 1
m.options.IMODE = 6
# Constants
snelheid_laden = cap_batt_kW/4
m.time = timestep
loss_charging = m.Const(value = (1-efficiency)/2)
max_cap_batt = m.Const(value = cap_batt_kWh)
min_cap_batt = m.Const(value = 0)
max_charge = m.Const(value = snelheid_laden) # max battery can charge in 15min
max_decharge = m.Const(value = -snelheid_laden) # max battery can decharge in 15min
# Parameters
usage_home = m.Param(usage_home)
price = m.Param(price)
# Variables
e_batt = m.Var(value=0, lb = min_cap_batt, ub = max_cap_batt) # energy in battery
price_paid = m.Var() # price paid each 15min
charging = m.Var(lb = max_decharge, ub = max_charge) # amount charge/decharge each 15min
usage_net = m.Var(lb=min_cap_batt)
# Equations
m.Equation(e_batt==m.integral(charging*(1-loss_charging)))
m.Equation(usage_net==usage_home + charging)
price_paid = m.Intermediate(usage_net * price / 100)
m.Equation(-charging <= (1-loss_charging)*e_batt)
# Objective
m.Minimize(price_paid)
# Solve problem
m.solve()
import matplotlib.pyplot as plt
plt.plot(m.time,e_batt.value,label='Battery Charge')
plt.plot(m.time,charging.value,label='Charging')
plt.plot(m.time,price_paid.value,label='Price')
plt.plot(m.time,usage_net.value,label='Net Usage')
plt.xlabel('Time'); plt.grid(); plt.legend(); plt.show()
I have been spending FAR too much time trying to figure this out - so time to seek help. I am attempting to use lmfit to fit two lognormals (a and c) as well as the sum of these two lognormals (a+c) to a size distribution. Mode a centers around x=0.2, y=1, mode c centers around x=1.2, y=<<<1. There are numerous size distributions (>200) which are all slightly different and are passed in to the following code from an outside loop. For this example, I have provided a real life distribution and have not included the loop. Hopefully my code is sufficiently annotated to allow understanding of what I am trying to achieve.
I must be missing some fundamental understanding of lmfit (spoiler alert - I'm not great at Maths either) as I have 2 problems:
the fits (a, c and a+c) do not accurately represent the data. Note how the fit (red solid line) diverts away from the data (blue solid line). I assume this is something to do with the initial guess parameters. I have tried LOTS and have been unable to get a good fit.
re-running the model with "new" best fit values (results2, results3) doesn't appear to significantly improve the fit at all. Why?
Example result using provided x and y data:
Here is one-I-made-earlier showing the type of fit I am after (produced using the older mpfit module, using different data than provided below and using unique initial best guess parameters (not in a loop). Excuse the legend format, I had to remove certain information):
Any assistance is much appreciated. Here is the code with an example distribution:
from lmfit import models
import matplotlib.pyplot as plt
import numpy as np
# real life data example
y = np.array([1.000000, 0.754712, 0.610303, 0.527856, 0.412125, 0.329689, 0.255756, 0.184424, 0.136819,
0.102316, 0.078763, 0.060896, 0.047118, 0.020297, 0.007714, 0.010202, 0.008710, 0.005579,
0.004644, 0.004043, 0.002618, 0.001194, 0.001263, 0.001043, 0.000584, 0.000330, 0.000179,
0.000117, 0.000050, 0.000035, 0.000017, 0.000007])
x = np.array([0.124980, 0.130042, 0.135712, 0.141490, 0.147659, 0.154711, 0.162421, 0.170855, 0.180262,
0.191324, 0.203064, 0.215738, 0.232411, 0.261810, 0.320252, 0.360761, 0.448802, 0.482528,
0.525526, 0.581518, 0.658988, 0.870114, 1.001815, 1.238899, 1.341285, 1.535134, 1.691963,
1.973359, 2.285620, 2.572177, 2.900414, 3.342739])
# create the joint model using prefixes for each mode
model = (models.LognormalModel(prefix='p1_') +
models.LognormalModel(prefix='p2_'))
# add some best guesses for the model parameters
params = model.make_params(p1_center=0.1, p1_sigma=2, p1_amplitude=1,
p2_center=1, p2_sigma=2, p2_amplitude=0.000000000000001)
# bound those best guesses
# params['p1_amplitude'].min = 0.0
# params['p1_amplitude'].max = 1e5
# params['p1_sigma'].min = 1.01
# params['p1_sigma'].max = 5
# params['p1_center'].min = 0.01
# params['p1_center'].max = 1.0
#
# params['p2_amplitude'].min = 0.0
# params['p2_amplitude'].max = 1
# params['p2_sigma'].min = 1.01
# params['p2_sigma'].max = 10
# params['p2_center'].min = 1.0
# params['p2_center'].max = 3
# actually fit the model
result = model.fit(y, params, x=x)
# ====================================
# ================================
# re-run using the best-fit params derived above
params2 = model.make_params(p1_center=result.best_values['p1_center'], p1_sigma=result.best_values['p1_sigma'],
p1_amplitude=result.best_values['p1_amplitude'],
p2_center=result.best_values['p2_center'], p2_sigma=result.best_values['p2_sigma'],
p2_amplitude=result.best_values['p2_amplitude'], )
# re-fit the model
result2 = model.fit(y, params2, x=x)
# ================================
# re-run again using the best-fit params derived above
params3 = model.make_params(p1_center=result2.best_values['p1_center'], p1_sigma=result2.best_values['p1_sigma'],
p1_amplitude=result2.best_values['p1_amplitude'],
p2_center=result2.best_values['p2_center'], p2_sigma=result2.best_values['p2_sigma'],
p2_amplitude=result2.best_values['p2_amplitude'], )
# re-fit the model
result3 = model.fit(y, params3, x=x)
# ================================
# add individual fine and coarse modes using the revised fit parameters
model_a = models.LognormalModel()
params_a = model_a.make_params(center=result3.best_values['p1_center'], sigma=result3.best_values['p1_sigma'],
amplitude=result3.best_values['p1_amplitude'])
result_a = model_a.fit(y, params_a, x=x)
model_c = models.LognormalModel()
params_c = model_c.make_params(center=result3.best_values['p2_center'], sigma=result3.best_values['p2_sigma'],
amplitude=result3.best_values['p2_amplitude'])
result_c = model_c.fit(y, params_c, x=x)
# ====================================
plt.plot(x, y, 'b-', label='data')
plt.plot(x, result.best_fit, 'r-', label='best_fit_1')
plt.plot(x, result.init_fit, 'lightgrey', ls=':', label='ini_fit_1')
plt.plot(x, result2.best_fit, 'r--', label='best_fit_2')
plt.plot(x, result2.init_fit, 'lightgrey', ls='--', label='ini_fit_2')
plt.plot(x, result3.best_fit, 'r.-', label='best_fit_3')
plt.plot(x, result3.init_fit, 'lightgrey', ls='--', label='ini_fit_3')
plt.plot(x, result_a.best_fit, 'grey', ls=':', label='best_fit_a')
plt.plot(x, result_c.best_fit, 'grey', ls='--', label='best_fit_c')
plt.xscale("log")
plt.yscale("log")
plt.legend()
plt.show()
There are three main pieces of advice I can give:
initial values matter and should not be so far off as to make
portions of the model completely insensitive to the parameter
values. Your initial model is sort of off by several orders of
magnitude.
always look at the fit result. This is the primary
result -- the plot of the fit is a representation of the actual
numerical results. Not showing that you printed out the fit
report is a good indication that you did not look at the actual
result. Really, always look at the results.
if you are judging the quality of the fit based on a plot of
the data and model, use how you choose to plot the data to guide
how you fit the data. Specifically in your case, if you are
plotting on a log scale, then fit the log of the data to the log
of the model: fit in "log space".
Such a fit might look like this:
from lmfit import models, Model
from lmfit.lineshapes import lognormal
import matplotlib.pyplot as plt
import numpy as np
y = np.array([1.000000, 0.754712, 0.610303, 0.527856, 0.412125, 0.329689, 0.255756, 0.184424, 0.136819,
0.102316, 0.078763, 0.060896, 0.047118, 0.020297, 0.007714, 0.010202, 0.008710, 0.005579,
0.004644, 0.004043, 0.002618, 0.001194, 0.001263, 0.001043, 0.000584, 0.000330, 0.000179,
0.000117, 0.000050, 0.000035, 0.000017, 0.000007])
x = np.array([0.124980, 0.130042, 0.135712, 0.141490, 0.147659, 0.154711, 0.162421, 0.170855, 0.180262,
0.191324, 0.203064, 0.215738, 0.232411, 0.261810, 0.320252, 0.360761, 0.448802, 0.482528,
0.525526, 0.581518, 0.658988, 0.870114, 1.001815, 1.238899, 1.341285, 1.535134, 1.691963,
1.973359, 2.285620, 2.572177, 2.900414, 3.342739])
# use a model that is the log of the sum of two log-normal functions
# note to be careful about log(x) for x < 0.
def log_lognormal(x, amp1, cen1, sig1, amp2, cen2, sig2):
comp1 = lognormal(x, amp1, cen1, sig1)
comp2 = lognormal(x, amp2, cen2, sig2)
total = comp1 + comp2
total[np.where(total<1.e-99)] = 1.e-99
return np.log(comp1+comp2)
model = Model(log_lognormal)
params = model.make_params(amp1=5.0, cen1=-4, sig1=1,
amp2=0.1, cen2=-1, sig2=1)
# part of making sure that the lognormals are strictly positive
params['amp1'].min = 0
params['amp2'].min = 0
result = model.fit(np.log(y), params, x=x)
print(result.fit_report()) # <-- HERE IS WHERE THE RESULTS ARE!!
# also, make a plot of data and fit
plt.plot(x, y, 'b-', label='data')
plt.plot(x, np.exp(result.best_fit), 'r-', label='best_fit')
plt.plot(x, np.exp(result.init_fit), 'grey', label='ini_fit')
plt.xscale("log")
plt.yscale("log")
plt.legend()
plt.show()
This will print out
[[Model]]
Model(log_lognormal)
[[Fit Statistics]]
# fitting method = leastsq
# function evals = 211
# data points = 32
# variables = 6
chi-square = 0.91190970
reduced chi-square = 0.03507345
Akaike info crit = -101.854407
Bayesian info crit = -93.0599914
[[Variables]]
amp1: 21.3565856 +/- 193.951379 (908.16%) (init = 5)
cen1: -4.40637490 +/- 3.81299642 (86.53%) (init = -4)
sig1: 0.77286862 +/- 0.55925566 (72.36%) (init = 1)
amp2: 0.00401804 +/- 7.5833e-04 (18.87%) (init = 0.1)
cen2: -0.74055538 +/- 0.13043827 (17.61%) (init = -1)
sig2: 0.64346873 +/- 0.04102122 (6.38%) (init = 1)
[[Correlations]] (unreported correlations are < 0.100)
C(amp1, cen1) = -0.999
C(cen1, sig1) = -0.999
C(amp1, sig1) = 0.997
C(cen2, sig2) = -0.964
C(amp2, cen2) = -0.940
C(amp2, sig2) = 0.849
C(sig1, amp2) = -0.758
C(cen1, amp2) = 0.740
C(amp1, amp2) = -0.726
C(sig1, cen2) = 0.687
C(cen1, cen2) = -0.669
C(amp1, cen2) = 0.655
C(sig1, sig2) = -0.598
C(cen1, sig2) = 0.581
C(amp1, sig2) = -0.567
and generate a plot like
I have been tasked with making plots of winds at various levels of the atmosphere to support aviation. While I have been able to make some nice plots using GFS model data (see code below), I'm really having to make a rough approximation of height using pressure coordinates available from the GFS. I'm using winds at 300 hPA, 700 hPA, and 925 hPA to make an approximation of the winds at 30,000 ft, 9000 ft, and 3000 ft. My question is really for those out there who are metpy gurus...is there a way that I can interpolate these winds to a height surface? It sure would be nice to get the actual winds at these height levels! Thanks for any light anyone can share on this subject!
import cartopy.crs as ccrs
import cartopy.feature as cfeature
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
import numpy as np
from netCDF4 import num2date
from datetime import datetime, timedelta
from siphon.catalog import TDSCatalog
from siphon.ncss import NCSS
from PIL import Image
from matplotlib import cm
# For the vertical levels we want to grab with our queries
# Levels need to be in Pa not hPa
Levels = [30000,70000,92500]
# Time deltas for days
Deltas = [1,2,3]
#Deltas = [1]
# Levels in hPa for the file names
LevelDict = {30000:'300', 70000:'700', 92500:'925'}
# The path to where our banners are stored
impath = 'C:\\Users\\shell\\Documents\\Python Scripts\\Banners\\'
# Final images saved here
imoutpath = 'C:\\Users\\shell\\Documents\\Python Scripts\\TVImages\\'
# Quick function for finding out which variable is the time variable in the
# netCDF files
def find_time_var(var, time_basename='time'):
for coord_name in var.coordinates.split():
if coord_name.startswith(time_basename):
return coord_name
raise ValueError('No time variable found for ' + var.name)
# Function to grab data at different levels from Siphon
def grabData(level):
query.var = set()
query.variables('u-component_of_wind_isobaric', 'v-component_of_wind_isobaric')
query.vertical_level(level)
data = ncss.get_data(query)
u_wind_var = data.variables['u-component_of_wind_isobaric']
v_wind_var = data.variables['v-component_of_wind_isobaric']
time_var = data.variables[find_time_var(u_wind_var)]
lat_var = data.variables['lat']
lon_var = data.variables['lon']
return u_wind_var, v_wind_var, time_var, lat_var, lon_var
# Construct a TDSCatalog instance pointing to the gfs dataset
best_gfs = TDSCatalog('http://thredds-jetstream.unidata.ucar.edu/thredds/catalog/grib/'
'NCEP/GFS/Global_0p5deg/catalog.xml')
# Pull out the dataset you want to use and look at the access URLs
best_ds = list(best_gfs.datasets.values())[1]
#print(best_ds.access_urls)
# Create NCSS object to access the NetcdfSubset
ncss = NCSS(best_ds.access_urls['NetcdfSubset'])
print(best_ds.access_urls['NetcdfSubset'])
# Looping through the forecast times
for delta in Deltas:
# Create lat/lon box and the time(s) for location you want to get data for
now = datetime.utcnow()
fcst = now + timedelta(days = delta)
timestamp = datetime.strftime(fcst, '%A')
query = ncss.query()
query.lonlat_box(north=78, south=45, east=-90, west=-220).time(fcst)
query.accept('netcdf4')
# Now looping through the levels to create our plots
for level in Levels:
u_wind_var, v_wind_var, time_var, lat_var, lon_var = grabData(level)
# Get actual data values and remove any size 1 dimensions
lat = lat_var[:].squeeze()
lon = lon_var[:].squeeze()
u_wind = u_wind_var[:].squeeze()
v_wind = v_wind_var[:].squeeze()
#converting to knots
u_windkt= u_wind*1.94384
v_windkt= v_wind*1.94384
wspd = np.sqrt(np.power(u_windkt,2)+np.power(v_windkt,2))
# Convert number of hours since the reference time into an actual date
time = num2date(time_var[:].squeeze(), time_var.units)
print (time)
# Combine 1D latitude and longitudes into a 2D grid of locations
lon_2d, lat_2d = np.meshgrid(lon, lat)
# Create new figure
#fig = plt.figure(figsize = (18,12))
fig = plt.figure()
fig.set_size_inches(26.67,15)
datacrs = ccrs.PlateCarree()
plotcrs = ccrs.LambertConformal(central_longitude=-150,
central_latitude=55,
standard_parallels=(30, 60))
# Add the map and set the extent
ax = plt.axes(projection=plotcrs)
ext = ax.set_extent([-195., -115., 50., 72.],datacrs)
ext2 = ax.set_aspect('auto')
ax.background_patch.set_fill(False)
# Add state boundaries to plot
ax.add_feature(cfeature.STATES, edgecolor='black', linewidth=2)
# Add geopolitical boundaries for map reference
ax.add_feature(cfeature.COASTLINE.with_scale('50m'))
ax.add_feature(cfeature.OCEAN.with_scale('50m'))
ax.add_feature(cfeature.LAND.with_scale('50m'),facecolor = '#cc9666', linewidth = 4)
if level == 30000:
spdrng_sped = np.arange(30, 190, 2)
windlvl = 'Jet_Stream'
elif level == 70000:
spdrng_sped = np.arange(20, 100, 1)
windlvl = '9000_Winds_Aloft'
elif level == 92500:
spdrng_sped = np.arange(20, 80, 1)
windlvl = '3000_Winds_Aloft'
else:
pass
top = cm.get_cmap('Greens')
middle = cm.get_cmap('YlOrRd')
bottom = cm.get_cmap('BuPu_r')
newcolors = np.vstack((top(np.linspace(0, 1, 128)),
middle(np.linspace(0, 1, 128))))
newcolors2 = np.vstack((newcolors,bottom(np.linspace(0,1,128))))
cmap = ListedColormap(newcolors2)
cf = ax.contourf(lon_2d, lat_2d, wspd, spdrng_sped, cmap=cmap,
transform=datacrs, extend = 'max', alpha=0.75)
cbar = plt.colorbar(cf, orientation='horizontal', pad=0, aspect=50,
drawedges = 'true')
cbar.ax.tick_params(labelsize=16)
wslice = slice(1, None, 4)
ax.quiver(lon_2d[wslice, wslice], lat_2d[wslice, wslice],
u_windkt[wslice, wslice], v_windkt[wslice, wslice], width=0.0015,
headlength=4, headwidth=3, angles='xy', color='black', transform = datacrs)
plt.savefig(imoutpath+'TV_UpperAir'+LevelDict[level]+'_'+timestamp+'.png',bbox_inches= 'tight')
# Now we use Pillow to overlay the banner with the appropriate day
background = Image.open(imoutpath+'TV_UpperAir'+LevelDict[level]+'_'+timestamp+'.png')
im = Image.open(impath+'Banner_'+windlvl+'_'+timestamp+'.png')
# resize the image
size = background.size
im = im.resize(size,Image.ANTIALIAS)
background.paste(im, (17, 8), im)
background.save(imoutpath+'TV_UpperAir'+LevelDict[level]+'_'+timestamp+'.png','PNG')
Thanks for the question! My approach here is for each separate column to interpolate the pressure coordinate of GFS-output Geopotential Height onto your provided altitudes to estimate the pressure of each height level for each column. Then I can use that pressure to interpolate the GFS-output u, v onto. The GFS-output GPH and winds have very slightly different pressure coordinates, which is why I interpolated twice. I performed the interpolation using MetPy's interpolate.log_interpolate_1d which performs a linear interpolation on the log of the inputs. Here is the code I used!
from datetime import datetime
import numpy as np
import metpy.calc as mpcalc
from metpy.units import units
from metpy.interpolate import log_interpolate_1d
from siphon.catalog import TDSCatalog
gfs_url = 'https://tds.scigw.unidata.ucar.edu/thredds/catalog/grib/NCEP/GFS/Global_0p5deg/catalog.xml'
cat = TDSCatalog(gfs_url)
now = datetime.utcnow()
# A shortcut to NCSS
ncss = cat.datasets['Best GFS Half Degree Forecast Time Series'].subset()
query = ncss.query()
query.var = set()
query.variables('u-component_of_wind_isobaric', 'v-component_of_wind_isobaric', 'Geopotential_height_isobaric')
query.lonlat_box(north=78, south=45, east=-90, west=-220)
query.time(now)
query.accept('netcdf4')
data = ncss.get_data(query)
# Reading in the u(isobaric), v(isobaric), isobaric vars and the GPH(isobaric6) and isobaric6 vars
# These are two slightly different vertical pressure coordinates.
# We will also assign units here, and this can allow us to go ahead and convert to knots
lat = units.Quantity(data.variables['lat'][:].squeeze(), units('degrees'))
lon = units.Quantity(data.variables['lon'][:].squeeze(), units('degrees'))
iso_wind = units.Quantity(data.variables['isobaric'][:].squeeze(), units('Pa'))
iso_gph = units.Quantity(data.variables['isobaric6'][:].squeeze(), units('Pa'))
u = units.Quantity(data.variables['u-component_of_wind_isobaric'][:].squeeze(), units('m/s')).to(units('knots'))
v = units.Quantity(data.variables['v-component_of_wind_isobaric'][:].squeeze(), units('m/s')).to(units('knots'))
gph = units.Quantity(data.variables['Geopotential_height_isobaric'][:].squeeze(), units('gpm'))
# Here we will select our altitudes to interpolate onto and convert them to geopotential meters
altitudes = ([30000., 9000., 3000.] * units('ft')).to(units('gpm'))
# Now we will interpolate the pressure coordinate for model output geopotential height to
# estimate the pressure level for our given altitudes at each grid point
pressures_of_alts = np.zeros((len(altitudes), len(lat), len(lon)))
for ilat in range(len(lat)):
for ilon in range(len(lon)):
pressures_of_alts[:, ilat, ilon] = log_interpolate_1d(altitudes,
gph[:, ilat, ilon],
iso_gph)
pressures_of_alts = pressures_of_alts * units('Pa')
# Similarly, we will use our interpolated pressures to interpolate
# our u and v winds across their given pressure coordinates.
# This will provide u, v at each of our interpolated pressure
# levels corresponding to our provided initial altitudes
u_at_levs = np.zeros((len(altitudes), len(lat), len(lon)))
v_at_levs = np.zeros((len(altitudes), len(lat), len(lon)))
for ilat in range(len(lat)):
for ilon in range(len(lon)):
u_at_levs[:, ilat, ilon], v_at_levs[:, ilat, ilon] = log_interpolate_1d(pressures_of_alts[:, ilat, ilon],
iso_wind,
u[:, ilat, ilon],
v[:, ilat, ilon])
u_at_levs = u_at_levs * units('knots')
v_at_levs = v_at_levs * units('knots')
# We can use mpcalc to calculate a wind speed array from these
wspd = mpcalc.wind_speed(u_at_levs, v_at_levs)
I was able to take my output from this and coerce it into your plotting code (with some unit stripping.)
Your 300-hPa GFS winds
My "30000-ft" GFS winds
Here is what my interpolated pressure fields at each estimated height level look like.
Hope this helps!
I am not sure if this is what you are looking for (I am very new to Metpy), but I have been using the metpy height_to_pressure_std(altitude) function. It puts it in units of hPa which then I convert to Pascals and then a unitless value to use in the Siphon vertical_level(float) function.
I don't think you can use metpy functions to convert height to pressure or vice versus in the upper atmosphere. There errors are too when using the Standard Atmosphere to convert say pressure to feet.
I feel I must be missing something obvious, in struggling to get a positive control for logistic regression going in tensorflow probability.
I've modified the example for logistic regression here, and created a positive control features and labels data. I struggle to achieve accuracy over 60%, however this is an easy problem for a 'vanilla' Keras model (accuracy 100%). What am I missing? I tried different layers, activations, etc.. With this method of setting up the model, is posterior updating actually being performed? Do I need to specify an interceptor object? Many thanks..
### Added positive control
nSamples = 80
features1 = np.float32(np.hstack((np.reshape(np.ones(40), (40, 1)),
np.reshape(np.random.randn(nSamples), (40, 2)))))
features2 = np.float32(np.hstack((np.reshape(np.zeros(40), (40, 1)),
np.reshape(np.random.randn(nSamples), (40, 2)))))
features = np.vstack((features1, features2))
labels = np.concatenate((np.zeros(40), np.ones(40)))
featuresInt, labelsInt = build_input_pipeline(features, labels, 10)
###
#w_true, b_true, features, labels = toy_logistic_data(FLAGS.num_examples, 2)
#featuresInt, labelsInt = build_input_pipeline(features, labels, FLAGS.batch_size)
with tf.name_scope("logistic_regression", values=[featuresInt]):
layer = tfp.layers.DenseFlipout(
units=1,
activation=None,
kernel_posterior_fn=tfp.layers.default_mean_field_normal_fn(),
bias_posterior_fn=tfp.layers.default_mean_field_normal_fn())
logits = layer(featuresInt)
labels_distribution = tfd.Bernoulli(logits=logits)
neg_log_likelihood = -tf.reduce_mean(labels_distribution.log_prob(labelsInt))
kl = sum(layer.losses)
elbo_loss = neg_log_likelihood + kl
predictions = tf.cast(logits > 0, dtype=tf.int32)
accuracy, accuracy_update_op = tf.metrics.accuracy(
labels=labelsInt, predictions=predictions)
with tf.name_scope("train"):
optimizer = tf.train.AdamOptimizer(learning_rate=FLAGS.learning_rate)
train_op = optimizer.minimize(elbo_loss)
init_op = tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer())
with tf.Session() as sess:
sess.run(init_op)
# Fit the model to data.
for step in range(FLAGS.max_steps):
_ = sess.run([train_op, accuracy_update_op])
if step % 100 == 0:
loss_value, accuracy_value = sess.run([elbo_loss, accuracy])
print("Step: {:>3d} Loss: {:.3f} Accuracy: {:.3f}".format(
step, loss_value, accuracy_value))
### Check with basic Keras
kerasModel = tf.keras.models.Sequential([
tf.keras.layers.Dense(1)])
optimizer = tf.train.AdamOptimizer(5e-2)
kerasModel.compile(optimizer = optimizer, loss = 'binary_crossentropy',
metrics = ['accuracy'])
kerasModel.fit(features, labels, epochs = 50) #100% accuracy
Compared to the github example, you forgot to divide by the number of examples when defining the KL divergence:
kl = sum(layer.losses) / FLAGS.num_examples
When I change this to your code, I quickly get to an accuracy of 99.9% on your toy data.
Additionaly, the output layer of your Keras model actually expects a sigmoid activation for this problem (binary classification):
kerasModel = tf.keras.models.Sequential([
tf.keras.layers.Dense(1, activation='sigmoid')])
It's a toy problem, but you will notice that the model gets to 100% accuracy faster with a sigmoid activation.
Here's my code. I keep getting that error, no matter if I use inside_sig_r or inside_sig_r2. If I take out the last line I don't get this error. Thanks for any help.
import numpy as np
from scipy import integrate, interpolate
from math import sqrt,pi,cos,sin,exp
rho = 2.78e11 * .3
delta = 1.68
def M(r):
return ((4*pi)/3)*(r**3)*rho
def R(M):
return (( 3 * M) / (4 * pi * rho)) ** (.3333)
def W(x):
return 3.*(sin(x) - x*cos(x))/(x**3.)
data = np.loadtxt("//Users//Slemons//Downloads//pk2.dat", float)
k_data = (10**data[:,0])
Pk_data = (10**data[:,1])
Pk = interpolate.interp1d(k_data,Pk_data,kind='cubic')
Masses = np.arange(1e10,1e16,1e10)
r_from_M = np.array(map(R,Masses),float)
print r_from_M[0]
def inside_sig_r(k,r):
return ((W(k*r)**2.) * Pk(k) * (k**2.)) / (2. * (pi ** 2.))
def inside_sig_r2(z,r):
k = (1.+z)/(1.-z)
return inside_sig_r(k,r) *2./(1.-z)**2.
sigma_r = lambda k : sqrt(integrate.quad(inside_sig_r,.4,np.inf,args=(k)))
sigr = np.array(map(sigma_r,Masses),float)
It is not really a standalone code, since I can't see your data in '//Users//Slemons//Downloads//pk2.dat'. However, the error is quite specific - the data produced by inside_sig_r(2) are above or below the range you supplied (0.4, np.inf). You should either change the range or make sure that the functions return values inside this range.