I am running a public code downloaded from GitHub, but I have a problem when it gets to the end and it has to plot the results using LaTeX. I get the following error:
FileNotFoundError: [Errno 2] No such file or directory: 'latex': 'latex'.
I have Anaconda installed with Python 3.6. I have installed LaTeX on my Mac using MacTex-2018 distribution pkg. Analyzing the code I have seen that the problem is in the main when it plots the results. It uses a utility called plotting which is imported at the beginning of the code. I have tried changing the plotting.py file and I have managed to run the code with success, showing the final plots. The key is deleting from the plotting.py code the part that is used to say to matplotlib to use LaTeX in the plots. I will now post all the codes so that you can better understand my problem.
Here is the main code:
"""
@author: Maziar Raissi
"""
import sys
sys.path.insert(0, '../../Utilities/')
import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import scipy.io
from scipy.interpolate import griddata
from pyDOE import lhs
from plotting import newfig, savefig
from mpl_toolkits.mplot3d import Axes3D
import time
import matplotlib.gridspec as gridspec
from mpl_toolkits.axes_grid1 import make_axes_locatable
np.random.seed(1234)
tf.set_random_seed(1234)
class PhysicsInformedNN:
# Initialize the class
def __init__(self, X_u, u, X_f, layers, lb, ub, nu):
self.lb = lb
self.ub = ub
self.x_u = X_u[:,0:1]
self.t_u = X_u[:,1:2]
self.x_f = X_f[:,0:1]
self.t_f = X_f[:,1:2]
self.u = u
self.layers = layers
self.nu = nu
# Initialize NNs
self.weights, self.biases = self.initialize_NN(layers)
# tf placeholders and graph
self.sess = tf.Session(config=tf.ConfigProto(allow_soft_placement=True,
log_device_placement=True))
self.x_u_tf = tf.placeholder(tf.float32, shape=[None, self.x_u.shape[1]])
self.t_u_tf = tf.placeholder(tf.float32, shape=[None, self.t_u.shape[1]])
self.u_tf = tf.placeholder(tf.float32, shape=[None, self.u.shape[1]])
self.x_f_tf = tf.placeholder(tf.float32, shape=[None, self.x_f.shape[1]])
self.t_f_tf = tf.placeholder(tf.float32, shape=[None, self.t_f.shape[1]])
self.u_pred = self.net_u(self.x_u_tf, self.t_u_tf)
self.f_pred = self.net_f(self.x_f_tf, self.t_f_tf)
self.loss = tf.reduce_mean(tf.square(self.u_tf - self.u_pred)) + \
tf.reduce_mean(tf.square(self.f_pred))
self.optimizer = tf.contrib.opt.ScipyOptimizerInterface(self.loss,
method = 'L-BFGS-B',
options = {'maxiter': 50000,
'maxfun': 50000,
'maxcor': 50,
'maxls': 50,
'ftol' : 1.0 * np.finfo(float).eps})
init = tf.global_variables_initializer()
self.sess.run(init)
def initialize_NN(self, layers):
weights = []
biases = []
num_layers = len(layers)
for l in range(0,num_layers-1):
W = self.xavier_init(size=[layers[l], layers[l+1]])
b = tf.Variable(tf.zeros([1,layers[l+1]], dtype=tf.float32), dtype=tf.float32)
weights.append(W)
biases.append(b)
return weights, biases
def xavier_init(self, size):
in_dim = size[0]
out_dim = size[1]
xavier_stddev = np.sqrt(2/(in_dim + out_dim))
return tf.Variable(tf.truncated_normal([in_dim, out_dim], stddev=xavier_stddev), dtype=tf.float32)
def neural_net(self, X, weights, biases):
num_layers = len(weights) + 1
H = 2.0*(X - self.lb)/(self.ub - self.lb) - 1.0
for l in range(0,num_layers-2):
W = weights[l]
b = biases[l]
H = tf.tanh(tf.add(tf.matmul(H, W), b))
W = weights[-1]
b = biases[-1]
Y = tf.add(tf.matmul(H, W), b)
return Y
def net_u(self, x, t):
u = self.neural_net(tf.concat([x,t],1), self.weights, self.biases)
return u
def net_f(self, x,t):
u = self.net_u(x,t)
u_t = tf.gradients(u, t)[0]
u_x = tf.gradients(u, x)[0]
u_xx = tf.gradients(u_x, x)[0]
f = u_t + u*u_x - self.nu*u_xx
return f
def callback(self, loss):
print('Loss:', loss)
def train(self):
tf_dict = {self.x_u_tf: self.x_u, self.t_u_tf: self.t_u, self.u_tf: self.u,
self.x_f_tf: self.x_f, self.t_f_tf: self.t_f}
self.optimizer.minimize(self.sess,
feed_dict = tf_dict,
fetches = [self.loss],
loss_callback = self.callback)
def predict(self, X_star):
u_star = self.sess.run(self.u_pred, {self.x_u_tf: X_star[:,0:1], self.t_u_tf: X_star[:,1:2]})
f_star = self.sess.run(self.f_pred, {self.x_f_tf: X_star[:,0:1], self.t_f_tf: X_star[:,1:2]})
return u_star, f_star
if __name__ == "__main__":
nu = 0.01/np.pi
noise = 0.0
N_u = 100
N_f = 10000
layers = [2, 20, 20, 20, 20, 20, 20, 20, 20, 1]
data = scipy.io.loadmat('../Data/burgers_shock.mat')
t = data['t'].flatten()[:,None]
x = data['x'].flatten()[:,None]
Exact = np.real(data['usol']).T
X, T = np.meshgrid(x,t)
X_star = np.hstack((X.flatten()[:,None], T.flatten()[:,None]))
u_star = Exact.flatten()[:,None]
# Doman bounds
lb = X_star.min(0)
ub = X_star.max(0)
xx1 = np.hstack((X[0:1,:].T, T[0:1,:].T))
uu1 = Exact[0:1,:].T
xx2 = np.hstack((X[:,0:1], T[:,0:1]))
uu2 = Exact[:,0:1]
xx3 = np.hstack((X[:,-1:], T[:,-1:]))
uu3 = Exact[:,-1:]
X_u_train = np.vstack([xx1, xx2, xx3])
X_f_train = lb + (ub-lb)*lhs(2, N_f)
X_f_train = np.vstack((X_f_train, X_u_train))
u_train = np.vstack([uu1, uu2, uu3])
idx = np.random.choice(X_u_train.shape[0], N_u, replace=False)
X_u_train = X_u_train[idx, :]
u_train = u_train[idx,:]
model = PhysicsInformedNN(X_u_train, u_train, X_f_train, layers, lb, ub, nu)
start_time = time.time()
model.train()
elapsed = time.time() - start_time
print('Training time: %.4f' % (elapsed))
u_pred, f_pred = model.predict(X_star)
error_u = np.linalg.norm(u_star-u_pred,2)/np.linalg.norm(u_star,2)
print('Error u: %e' % (error_u))
U_pred = griddata(X_star, u_pred.flatten(), (X, T), method='cubic')
Error = np.abs(Exact - U_pred)
######################################################################
############################# Plotting ###############################
######################################################################
fig, ax = newfig(1.0, 1.1)
ax.axis('off')
####### Row 0: u(t,x) ##################
gs0 = gridspec.GridSpec(1, 2)
gs0.update(top=1-0.06, bottom=1-1/3, left=0.15, right=0.85, wspace=0)
ax = plt.subplot(gs0[:, :])
h = ax.imshow(U_pred.T, interpolation='nearest', cmap='rainbow',
extent=[t.min(), t.max(), x.min(), x.max()],
origin='lower', aspect='auto')
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.05)
fig.colorbar(h, cax=cax)
ax.plot(X_u_train[:,1], X_u_train[:,0], 'kx', label = 'Data (%d points)' % (u_train.shape[0]), markersize = 4, clip_on = False)
line = np.linspace(x.min(), x.max(), 2)[:,None]
ax.plot(t[25]*np.ones((2,1)), line, 'w-', linewidth = 1)
ax.plot(t[50]*np.ones((2,1)), line, 'w-', linewidth = 1)
ax.plot(t[75]*np.ones((2,1)), line, 'w-', linewidth = 1)
ax.set_xlabel('$t$')
ax.set_ylabel('$x$')
ax.legend(frameon=False, loc = 'best')
ax.set_title('$u(t,x)$', fontsize = 10)
####### Row 1: u(t,x) slices ##################
gs1 = gridspec.GridSpec(1, 3)
gs1.update(top=1-1/3, bottom=0, left=0.1, right=0.9, wspace=0.5)
ax = plt.subplot(gs1[0, 0])
ax.plot(x,Exact[25,:], 'b-', linewidth = 2, label = 'Exact')
ax.plot(x,U_pred[25,:], 'r--', linewidth = 2, label = 'Prediction')
ax.set_xlabel('$x$')
ax.set_ylabel('$u(t,x)$')
ax.set_title('$t = 0.25$', fontsize = 10)
ax.axis('square')
ax.set_xlim([-1.1,1.1])
ax.set_ylim([-1.1,1.1])
ax = plt.subplot(gs1[0, 1])
ax.plot(x,Exact[50,:], 'b-', linewidth = 2, label = 'Exact')
ax.plot(x,U_pred[50,:], 'r--', linewidth = 2, label = 'Prediction')
ax.set_xlabel('$x$')
ax.set_ylabel('$u(t,x)$')
ax.axis('square')
ax.set_xlim([-1.1,1.1])
ax.set_ylim([-1.1,1.1])
ax.set_title('$t = 0.50$', fontsize = 10)
ax.legend(loc='upper center', bbox_to_anchor=(0.5, -0.35), ncol=5, frameon=False)
ax = plt.subplot(gs1[0, 2])
ax.plot(x,Exact[75,:], 'b-', linewidth = 2, label = 'Exact')
ax.plot(x,U_pred[75,:], 'r--', linewidth = 2, label = 'Prediction')
ax.set_xlabel('$x$')
ax.set_ylabel('$u(t,x)$')
ax.axis('square')
ax.set_xlim([-1.1,1.1])
ax.set_ylim([-1.1,1.1])
ax.set_title('$t = 0.75$', fontsize = 10)
savefig('./figures/Burgers')
Here is the plotting.py code:
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 9 20:11:57 2017
@author: mraissi
"""
import numpy as np
import matplotlib as mpl
#mpl.use('pgf')
def figsize(scale, nplots = 1):
fig_width_pt = 390.0 # Get this from LaTeX using \the\textwidth
inches_per_pt = 1.0/72.27 # Convert pt to inch
golden_mean = (np.sqrt(5.0)-1.0)/2.0 # Aesthetic ratio (you could change this)
fig_width = fig_width_pt*inches_per_pt*scale # width in inches
fig_height = nplots*fig_width*golden_mean # height in inches
fig_size = [fig_width,fig_height]
return fig_size
pgf_with_latex = { # setup matplotlib to use latex for output
"pgf.texsystem": "pdflatex", # change this if using xetex or lautex
"text.usetex": True, # use LaTeX to write all text
"font.family": "serif",
"font.serif": [], # blank entries should cause plots to inherit fonts from the document
"font.sans-serif": [],
"font.monospace": [],
"axes.labelsize": 10, # LaTeX default is 10pt font.
"font.size": 10,
"legend.fontsize": 8, # Make the legend/label fonts a little smaller
"xtick.labelsize": 8,
"ytick.labelsize": 8,
"figure.figsize": figsize(1.0), # default fig size of 0.9 textwidth
"pgf.preamble": [
r"\usepackage[utf8x]{inputenc}", # use utf8 fonts becasue your computer can handle it :)
r"\usepackage[T1]{fontenc}", # plots will be generated using this preamble
]
}
mpl.rcParams.update(pgf_with_latex)
import matplotlib.pyplot as plt
# I make my own newfig and savefig functions
def newfig(width, nplots = 1):
fig = plt.figure(figsize=figsize(width, nplots))
ax = fig.add_subplot(111)
return fig, ax
def savefig(filename, crop = True):
if crop == True:
# plt.savefig('{}.pgf'.format(filename), bbox_inches='tight', pad_inches=0)
plt.savefig('{}.pdf'.format(filename), bbox_inches='tight', pad_inches=0)
plt.savefig('{}.eps'.format(filename), bbox_inches='tight', pad_inches=0)
else:
# plt.savefig('{}.pgf'.format(filename))
plt.savefig('{}.pdf'.format(filename))
plt.savefig('{}.eps'.format(filename))
## Simple plot
#fig, ax = newfig(1.0)
#
#def ema(y, a):
# s = []
# s.append(y[0])
# for t in range(1, len(y)):
# s.append(a * y[t] + (1-a) * s[t-1])
# return np.array(s)
#
#y = [0]*200
#y.extend([20]*(1000-len(y)))
#s = ema(y, 0.01)
#
#ax.plot(s)
#ax.set_xlabel('X Label')
#ax.set_ylabel('EMA')
#
#savefig('ema')
If I change the plotting code removing the part that start with pgf_with_latex then everything works right.
Here is the code that I have to delete:
pgf_with_latex = { # setup matplotlib to use latex for output
"pgf.texsystem": "pdflatex", # change this if using xetex or lautex
"text.usetex": True, # use LaTeX to write all text
"font.family": "serif",
"font.serif": [], # blank entries should cause plots to inherit fonts from the document
"font.sans-serif": [],
"font.monospace": [],
"axes.labelsize": 10, # LaTeX default is 10pt font.
"font.size": 10,
"legend.fontsize": 8, # Make the legend/label fonts a little smaller
"xtick.labelsize": 8,
"ytick.labelsize": 8,
"figure.figsize": figsize(1.0), # default fig size of 0.9 textwidth
"pgf.preamble": [
r"\usepackage[utf8x]{inputenc}", # use utf8 fonts becasue your computer can handle it :)
r"\usepackage[T1]{fontenc}", # plots will be generated using this preamble
]
}
mpl.rcParams.update(pgf_with_latex)
I would like to use my code without deleting this part. What should I do to make LaTeX work?
Best Answer
First check the latex on your system by doing the following :
if you got empty output then install these packages :