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I have this function implemented in Cython:
def count_kmers_cython(str string, list alphabet, int kmin, int kmax):
"""
Count occurrence of kmers in a given string.
"""
counter = {}
cdef int i
cdef int j
cdef int N = len(string)
limits = range(kmin, kmax + 1)
for i in range(0, N - kmax + 1):
for j in limits:
kmer = string[i:i+j]
counter[kmer] = counter.get(kmer, 0) + 1
return counter
Can I do better with cython? Or Can I have any away to improve it?
I am new to cython, that is my first attempt.
I will use this to count kmers in DNA with alphabet restrict to 'ACGT'. The length of the general input string is the average bacterial genomes (130 kb to over 14 Mb, where each 1 kb = 1000 bp).
The size of the kmers will be 3 < kmer < 16.
I wish to know if I could go further and maybe use cython in this function to:
def compute_kmer_stats(kmer_list, counts, len_genome, max_e):
"""
This function computes the z_score to find under/over represented kmers
according to a cut off e-value.
Inputs:
kmer_list - a list of kmers
counts - a dictionary-type with k-mers as keys and counts as values.
len_genome - the total length of the sequence(s).
max_e - cut off e-values to report under/over represented kmers.
Outputs:
results - a list of lists as [k-mer, observed count, expected count, z-score, e-value]
"""
print(colored('Starting to compute the kmer statistics...\n',
'red',
attrs=['bold']))
results = []
# number of tests, used to convert p-value to e-value.
n = len(list(kmer_list))
for kmer in kmer_list:
k = len(kmer)
prefix, sufix, center = counts[kmer[:-1]], counts[kmer[1:]], counts[kmer[1:-1]]
# avoid zero division error
if center == 0:
expected = 0
else:
expected = (prefix * sufix) // center
observed = counts[kmer]
sigma = math.sqrt(expected * (1 - expected / (len_genome - k + 1)))
# avoid zero division error
if sigma == 0.0:
z_score = 0.0
else:
z_score = ((observed - expected) / sigma)
# pvalue for all kmers/palindromes under represented
p_value_under = (math.erfc(-z_score / math.sqrt(2)) / 2)
# pvalue for all kmers/palindromes over represented
p_value_over = (math.erfc(z_score / math.sqrt(2)) / 2)
# evalue for all kmers/palindromes under represented
e_value_under = (n * p_value_under)
# evalue for all kmers/palindromes over represented
e_value_over = (n * p_value_over)
if e_value_under <= max_e:
results.append([kmer, observed, expected, z_score, p_value_under, e_value_under])
elif e_value_over <= max_e:
results.append([kmer, observed, expected, z_score, p_value_over, e_value_over])
return results
OBS - Thank you CodeSurgeon by the help. I know there are other tools to count kmer efficiently but I am learning Python so I am trying to write my own functions and code.
Consider a set of 3D points:
| y/z | -1 | 0 | 1 |
|:---:|:------:|:------:|:------:|
| 5 | 19.898 | 19.905 | 19.913 |
| 0 | 19.898 | 19.92 | 19.935 |
| -3 | 19.883 | 19.883 | 19.92 |
| -4 | 19.86 | 19.898 | 19.898 |
where the rows are yis, columns are zis and the content are xis.
I want to fit a plane of
Ax + By + Cz + D = 0
into these points in a way the total distance of:
E = ∑ (|Axi + Byi + Czi + D| / √(A^2 + B^2 + C^2))
to be minimized. Consider that I want to have the absolute deviation |...| not the variance as used in conventional regression methods. Also please consider that the dimension of the actual data frame is much bigger, so it will be great if the solution is computationally efficient too.
I would appreciate if you could help me with this issue. Thanks in advance.
Reference: equations from here.
This stand-alone Python program should do what you want for the fitting. I do not know how to call it from Calc, or pass data and results back and forth between Calc and Python.
Ax + By + Cz + D = 0
rearranges to
Ax + By + D = -Cz
which rearranges to
(Ax + By + D) / -C = z
That is a 3D surface equation of the form "z = f(x,y)", easily fit with scipy's curve_fit as shown here:
import numpy, scipy, scipy.optimize
import matplotlib
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm # to colormap 3D surfaces from blue to red
import matplotlib.pyplot as plt
graphWidth = 800 # units are pixels
graphHeight = 600 # units are pixels
# 3D contour plot lines
numberOfContourLines = 16
def SurfacePlot(func, data, fittedParameters):
f = plt.figure(figsize=(graphWidth/100.0, graphHeight/100.0), dpi=100)
matplotlib.pyplot.grid(True)
axes = Axes3D(f)
x_data = data[0]
y_data = data[1]
z_data = data[2]
xModel = numpy.linspace(min(x_data), max(x_data), 20)
yModel = numpy.linspace(min(y_data), max(y_data), 20)
X, Y = numpy.meshgrid(xModel, yModel)
Z = func(numpy.array([X, Y]), *fittedParameters)
axes.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.coolwarm, linewidth=1, antialiased=True)
axes.scatter(x_data, y_data, z_data) # show data along with plotted surface
axes.set_title('Surface Plot (click-drag with mouse)') # add a title for surface plot
axes.set_xlabel('X Data') # X axis data label
axes.set_ylabel('Y Data') # Y axis data label
axes.set_zlabel('Z Data') # Z axis data label
plt.show()
plt.close('all') # clean up after using pyplot or else thaere can be memory and process problems
def ContourPlot(func, data, fittedParameters):
f = plt.figure(figsize=(graphWidth/100.0, graphHeight/100.0), dpi=100)
axes = f.add_subplot(111)
x_data = data[0]
y_data = data[1]
z_data = data[2]
xModel = numpy.linspace(min(x_data), max(x_data), 20)
yModel = numpy.linspace(min(y_data), max(y_data), 20)
X, Y = numpy.meshgrid(xModel, yModel)
Z = func(numpy.array([X, Y]), *fittedParameters)
axes.plot(x_data, y_data, 'o')
axes.set_title('Contour Plot') # add a title for contour plot
axes.set_xlabel('X Data') # X axis data label
axes.set_ylabel('Y Data') # Y axis data label
CS = matplotlib.pyplot.contour(X, Y, Z, numberOfContourLines, colors='k')
matplotlib.pyplot.clabel(CS, inline=1, fontsize=10) # labels for contours
plt.show()
plt.close('all') # clean up after using pyplot or else thaere can be memory and process problems
def ScatterPlot(data):
f = plt.figure(figsize=(graphWidth/100.0, graphHeight/100.0), dpi=100)
matplotlib.pyplot.grid(True)
axes = Axes3D(f)
x_data = data[0]
y_data = data[1]
z_data = data[2]
axes.scatter(x_data, y_data, z_data)
axes.set_title('Scatter Plot (click-drag with mouse)')
axes.set_xlabel('X Data')
axes.set_ylabel('Y Data')
axes.set_zlabel('Z Data')
plt.show()
plt.close('all') # clean up after using pyplot or else thaere can be memory and process problems
def func(data, A, B, C, D):
x = data[0]
y = data[1]
return (A*x + B*y + D) / -C
if __name__ == "__main__":
xData = numpy.array([1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0])
yData = numpy.array([11.0, 12.1, 13.0, 14.1, 15.0, 16.1, 17.0, 18.1, 90.0])
zData = numpy.array([1.1, 2.2, 3.3, 4.4, 5.5, 6.6, 7.7, 8.0, 9.9])
data = [xData, yData, zData]
initialParameters = [1.0, 1.0, 1.0, 1.0] # these are the same as scipy default values in this example
# here a non-linear surface fit is made with scipy's curve_fit()
fittedParameters, pcov = scipy.optimize.curve_fit(func, [xData, yData], zData, p0 = initialParameters)
ScatterPlot(data)
SurfacePlot(func, data, fittedParameters)
ContourPlot(func, data, fittedParameters)
print('fitted prameters', fittedParameters)
modelPredictions = func(data, *fittedParameters)
absError = modelPredictions - zData
SE = numpy.square(absError) # squared errors
MSE = numpy.mean(SE) # mean squared errors
RMSE = numpy.sqrt(MSE) # Root Mean Squared Error, RMSE
Rsquared = 1.0 - (numpy.var(absError) / numpy.var(zData))
print('RMSE:', RMSE)
print('R-squared:', Rsquared)
I'm just starting out learning Q-learning, and I've been okay with using the tabular method to get some decent results. One game I found quite fun to use Q-learning was with Blackjack, which seemed like a perfect MDP type problem.
I've been wanting to extend this to using a neural network as a function approximator, but I'm not having any luck at all. The approach is to calculate the expected value for every action in a given state and then pick the best one with a small chance of picking something random (epsilon greedy). Nothing converges, it learns silly Q-values, and it can't even figure out how to play when the only card in the deck is 5.
I am genuinely stuck, after spending hours on this and tuning hyper parameters and everything else I can think of. I feel like I must have made a fundamental error with Q-learning that I can't see. My code is below:
import gym
from gym import spaces
from gym.utils import seeding
import numpy as np
import random
import pandas as pd
import sklearn
import math
import itertools
import tensorflow as tf
from matplotlib import pyplot as plt
############################ START BLACKJACK CLASS ############################
class Blackjack(gym.Env):
"""Simple Blackjack environment"""
def __init__(self, natural=False):
self.action_space = spaces.Discrete(2)
self._seed()
# Start the first game
self.prevState = self.reset()
def _seed(self, seed=None):
self.np_random, seed = seeding.np_random(seed)
return seed
# Returns a tuple of the form (str, int) where str is "H" or "S" depending on if its a
# Soft or Hard hand and int is the sum total of the cards in hand
# Example output: ("H", 15)
def getTotal(cards):
running_total = 0
softs = 0
for c in cards:
running_total += c
if c == 11:
softs += 1
if running_total > 21 and softs > 0:
softs -= 1
running_total -= 10
return "H" if softs == 0 else "S", running_total
def drawCard():
# Draw a random card from the deck with replacement. 11 is ACE
# I've set it to always draw a 5. In theory this should be very easy to learn and
# The only possible states, and their correct Q values should be:
# Q[10_5, stand] = -1 Q[10_5, hit] = 0
# Q[15_5, stand] = -1 Q[15_5, hit] = 0
# Q[20_5, stand] = 0 Q[20_5, hit] = -1
# The network can't even learn this!
return 5
return random.choice([5,6])
return random.choice([2,3,4,5,6,7,8,9,10,10,10,10,11])
def isBlackjack(cards):
return sum(cards) == 21 and len(cards) == 2
def getState(self):
# Defines the state of the current game
pstate, ptotal = Blackjack.getTotal(self.player)
dstate, dtotal = Blackjack.getTotal(self.dealer)
return "{}_{}".format("BJ" if Blackjack.isBlackjack(self.player) else pstate+str(ptotal), dtotal)
def reset(self):
# Resets the game - Dealer is dealt 1 card, player is dealt 2 cards
# The player and dealer are represented by an array of numbers, which are the cards they were
# dealt in order
self.soft = "H"
self.dealer = [Blackjack.drawCard()]
self.player = [Blackjack.drawCard() for _ in range(2)]
pstate, ptotal = Blackjack.getTotal(self.player)
dstate, dtotal = Blackjack.getTotal(self.dealer)
# Returns the current state of the game
return self.getState()
def step(self, action):
assert self.action_space.contains(action)
# Action should be 0 or 1.
# If standing, the dealer will draw all cards until they are >= 17. This will end the episode
# If hitting, a new card will be added to the player, if over 21, reward is -1 and episode ends
# Stand
if action == 0:
pstate, ptotal = Blackjack.getTotal(self.player)
dstate, dtotal = Blackjack.getTotal(self.dealer)
while dtotal < 17:
self.dealer.append(Blackjack.drawCard())
dstate, dtotal = Blackjack.getTotal(self.dealer)
# if player won with blackjack
if Blackjack.isBlackjack(self.player) and not Blackjack.isBlackjack(self.dealer):
rw = 1.5
# if dealer bust or if the player has a higher number than dealer
elif dtotal > 21 or (dtotal <= 21 and ptotal > dtotal and ptotal <= 21):
rw = 1
# if theres a draw
elif dtotal == ptotal:
rw = 0
# player loses in all other situations
else:
rw = -1
state = self.getState()
# Returns (current_state, reward, boolean_true_if_episode_ended, empty_dict)
return state, rw, True, {}
# Hit
else:
# Player draws another card
self.player.append(Blackjack.drawCard())
# Calc new total for player
pstate, ptotal = Blackjack.getTotal(self.player)
state = self.getState()
# Player went bust and episode is over
if ptotal > 21:
return state, -1, True, {}
# Player is still in the game, but no observed reward yet
else:
return state, 0, False, {}
############################ END BLACKJACK CLASS ############################
# Converts a player or dealers hand into an array of 10 cards
# that keep track of how many of each card are held. The card is identified
# through its index:
# Index: 0 1 2 3 4 5 6 7 9 10
# Card: 2 3 4 5 6 7 8 9 T A
def cardsToX(cards):
ans = [0] * 12
for c in cards:
ans[c] += 1
ans = ans[2:12]
return ans
# Easy way to convert Q values into weighted decision probabilities via softmax.
# This is useful if we probablistically choose actions based on their values rather
# than always choosing the max.
# eg Q[s,0] = -1
# Q[s,1] = -2
# softmax([-1,-2]) = [0.731, 0.269] --> 73% chance of standing, 27% chance of hitting
def softmax(x):
"""Compute softmax values for each sets of scores in x."""
e_x = np.exp(x - np.max(x))
return e_x / e_x.sum()
plt.ion()
# Define number of Neurons per layer
K = 20 # Layer 1
L = 10 # Layer 2
M = 5 # Layer 2
N_IN = 20 # 10 unique cards for player, and 10 for dealer = 20 total inputs
N_OUT = 2
SDEV = 0.000001
# Input / Output place holders
X = tf.placeholder(tf.float32, [None, N_IN])
X = tf.reshape(X, [-1, N_IN])
# This will be the observed reward + decay_factor * max(Q[s+1, 0], Q[s+1, 1]).
# This should be an estimate of the 'correct' Q-value with the ony caveat being that
# the Q-value of the next state is a biased estimate of the true value.
Q_TARGET = tf.placeholder(tf.float32, [None, N_OUT])
# LAYER 1
W1 = tf.Variable(tf.random_normal([N_IN, K], stddev = SDEV))
B1 = tf.Variable(tf.random_normal([K], stddev = SDEV))
# LAYER 2
W2 = tf.Variable(tf.random_normal([K, L], stddev = SDEV))
B2 = tf.Variable(tf.random_normal([L], stddev = SDEV))
# LAYER 3
W3 = tf.Variable(tf.random_normal([L, M], stddev = SDEV))
B3 = tf.Variable(tf.random_normal([M], stddev = SDEV))
# LAYER 4
W4 = tf.Variable(tf.random_normal([M, N_OUT], stddev = SDEV))
B4 = tf.Variable(tf.random_normal([N_OUT], stddev = SDEV))
H1 = tf.nn.relu(tf.matmul(X, W1) + B1)
H2 = tf.nn.relu(tf.matmul(H1, W2) + B2)
H3 = tf.nn.relu(tf.matmul(H2, W3) + B3)
# The predicted Q value, as determined by our network (function approximator)
# outputs expected reward for standing and hitting in the form [stand, hit] given the
# current game state
Q_PREDICT = (tf.matmul(H3, W4) + B4)
# Is this correct? The Q_TARGET should be a combination of the real reward and the discounted
# future rewards of the future state as predicted by the network. Q_TARGET - Q_PREDICT should be
# the error in prediction, which we want to minimise. Does this loss function work to help the network
# converge to the true Q values with sufficient training?
loss_func = tf.reduce_sum(tf.square(Q_TARGET - Q_PREDICT))
# This are some placeholder values to enable manually set decayed learning rates. For now, use
# the same learning rate all the time.
LR_START = 0.001
#LR_END = 0.000002
#LR_DECAY = 0.999
# Optimizer
LEARNING_RATE = tf.Variable(LR_START, trainable=False)
optimizer = tf.train.GradientDescentOptimizer(LEARNING_RATE)#(LEARNING_RATE)
train_step = optimizer.minimize(loss_func)
init = tf.global_variables_initializer()
sess = tf.Session()
sess.run(init)
# Initialise the game environment
game = Blackjack()
# Number of episodes (games) to play
num_eps = 10000000
# probability of picking a random action. This decays over time
epsilon = 0.1
# discount factor. For blackjack, future rewards are equally important as immediate rewards.
discount = 1.0
all_rewards = [] # Holds all observed rewards. The rolling mean of rewards should improve as the network learns
all_Qs = [] # Holds all predicted Q values. Useful as a sanity check once the network is trained
all_losses = [] # Holds all the (Q_TARGET - Q_PREDICTED) values. The rolling mean of this should decrease
hands = [] # Holds a summary of all hands played. (game_state, Q[stand], Q[hit], action_taken)
# boolean switch to use the highest action value instead of a stochastic decision via softmax on Q-values
use_argmax = True
# Begin generating episodes
for ep in range(num_eps):
game.reset()
# Keep looping until the episode is not over
while True:
# x is the array of 20 numbers. The player cards, and the dealer cards.
x = cardsToX(game.player) + cardsToX(game.dealer)
# Q1 refers to the predicted Q-values before any action was taken
Q1 = sess.run(Q_PREDICT, feed_dict = {X : np.reshape( np.array(x), (-1, N_IN) )})
all_Qs.append(Q1)
if use_argmax:
# action is selected to be the one with the highest Q-value
act = np.argmax(Q1)
else:
# action is a weighted selection based on predicted Q_values
act = np.random.choice(range(N_OUT), p = softmax(Q1)[0])
if random.random() < epsilon:
# action is selected randomly
act = random.randint(0, N_OUT-1)
# Get game state before action is taken
game_state = game.getState()
# Take action! Observe new state, reward, and if the game is over
game_state_new, reward, done, _ = game.step(act)
hands.append( (game_state, Q1[0][0], Q1[0][1], act, reward) )
# Store the new state vector to feed into our network.
# x2 corresponds to the x vector observed in state s+1
x2 = cardsToX(game.player) + cardsToX(game.dealer)
# Q2 refers to the predicted Q-values in the new s+1 state. This is used for the 'SARSA' update.
Q2 = sess.run(Q_PREDICT,feed_dict = {X : np.reshape( np.array(x2), (-1, N_IN) )})
# Store the maximum Q-value in this new state. This should be the expected reward from this new state
maxQ2 = np.max(Q2)
# targetQ is the same as our predicted one initially. The index of the action we took will be
# updated to be [observed reward] + [discount_factor] * max(Q[s+1])
targetQ = np.copy(Q1)
# If the game is done, then there is no future state
if done:
targetQ[0,act] = reward
all_rewards.append(reward)
else:
targetQ[0,act] = reward + discount * maxQ2
# Perform one gradient descent update, filling the placeholder value for Q_TARGET with targetQ.
# The returned loss is the difference between the predicted Q-values and the targetQ we just calculated
loss, _, _ = sess.run([loss_func, Q_PREDICT, train_step],
feed_dict = {X : np.reshape( np.array(x), (-1, N_IN) ),
Q_TARGET : targetQ}
)
all_losses.append(loss)
# Every 1000 episodes, show how the q-values moved after the gradient descent update
if ep % 1000 == 0 and ep > 0:
Q_NEW = sess.run(Q_PREDICT, feed_dict = {X : np.reshape( np.array(x), (-1, N_IN) ),
Q_TARGET : targetQ})
#print(game_state, targetQ[0], Q1[0], (Q_NEW-Q1)[0], loss, ep, epsilon, act)
rolling_window = 1000
rolling_mean = np.mean( all_rewards[-rolling_window:] )
rolling_loss = np.mean( all_losses[-rolling_window:] )
print("Rolling mean reward: {:<10.4f}, Rolling loss: {:<10.4f}".format(rolling_mean, rolling_loss))
if done:
# Reduce chance of random action as we train the model.
epsilon = 2/((ep/500) + 10)
epsilon = max(0.02, epsilon)
# rolling mean of rewards should increase over time!
if ep % 1000 == 0 and ep > 0:
pass# Show the rolling mean of all losses. This should decrease over time!
#plt.plot(pd.rolling_mean(pd.Series(all_losses), 5000))
#plt.pause(0.02)
#plt.show()
break
print(cardsToX(game.player))
print(game.dealer)
Any ideas? I'm stuck :(
I'm trying to train a convolutional autoencoder to encode and decode a piano roll representation of monophonic midi clips. I reduced the note range to 3 octaves, divide songs into 100 time step pieces (where 1 time step = 1/100th of a second), and train the net in batches of 3 pieces.
I'm using Adagrad as my optimizer, and MSE as my loss function. The loss is huge, and I see no decrease in average loss even after hundreds of training examples are fed in.
Here's my code:
"""
Most absolutely simple assumptions:
- not changing the key of any of the files
- not changing the tempo of any of the files
- take blocks of 36 by 100
- divide up all songs by this amount, cutting off any excess from the
end, train
"""
from __future__ import print_function
import cPickle as pickle
import numpy as np
import torch
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from reverse_pianoroll import piano_roll_to_pretty_midi as pr2pm
N = 1000
# load a NxMxC dataset
# N: Number of clips
# M: Piano roll size, the number of midi notes that could possibly be 'on'
# C: Clip length, in 100ths of a second
dataset = pickle.load(open('mh-midi-data.pickle', 'rb'))
######## take a subset of the data for training ######
# based on the mean and standard deviation of non zero entries in the data, I've
# found that the most populous, and thus best range of notes to take is from
# 48 to 84 (C2 - C5); this is 3 octaves, which is much less than the original
# 10 and a half. Additionally, we're going to take a subsample of 1000 because
# i'm training on my macbook and the network is pretty simple
######################################################
dataset = dataset[:, :, 48:84, :]
dataset = dataset[:N]
######################################################
midi_dim, clip_len = dataset.shape[2:]
class Autoencoder(nn.Module):
def __init__(self, **kwargs):
super(Autoencoder, self).__init__(**kwargs)
# input is 3 x 1 x 36 x 100
self.conv1 = nn.Conv2d(in_channels=1, out_channels=14, kernel_size=(midi_dim, 2))
# now transformed to 3 x 14 x 1 x 99
self.conv2 = nn.Conv2d(in_channels=14, out_channels=77, kernel_size=(1, 4))
# now transformed to 3 x 77 x 1 x 96
input_size = 3*77*1*96
self.fc1 = nn.Linear(input_size, input_size/2)
self.fc2 = nn.Linear(input_size/2, input_size/4)
self.fc3 = nn.Linear(input_size/4, input_size/2)
self.fc4 = nn.Linear(input_size/2, input_size)
self.tconv2 = nn.ConvTranspose2d(in_channels=77, out_channels=14, kernel_size=(1, 4))
self.tconv1 = nn.ConvTranspose2d(in_channels=14, out_channels=1, kernel_size=(midi_dim, 2))
self.sigmoid = nn.Sigmoid()
return
def forward(self, x):
# print("1: {}".format(x.size()))
x = F.relu(self.conv1(x))
# print("2: {}".format(x.size()))
x = F.relu(self.conv2(x))
# print("3: {}".format(x.size()))
x = x.view(-1, np.prod(x.size()[:]))
# print("4: {}".format(x.size()))
x = F.relu(self.fc1(x))
# print("5: {}".format(x.size()))
h = F.relu(self.fc2(x))
# print("6: {}".format(h.size()))
d = F.relu(self.fc3(h))
# print("7: {}".format(d.size()))
d = F.relu(self.fc4(d))
# print("8: {}".format(d.size()))
d = d.view(3, 77, 1, 96)
# print("9: {}".format(d.size()))
d = F.relu(self.tconv2(d))
# print("10: {}".format(d.size()))
d = self.tconv1(d)
d = self.sigmoid(d)
# print("11: {}".format(d.size()))
return d
net = Autoencoder()
loss_fn = nn.MSELoss()
# optimizer = optim.SGD(net.parameters(), lr=1e-3, momentum=0.9)
optimizer = optim.Adagrad(net.parameters(), lr=1e-3)
batch_count = 0
avg_loss = 0.0
print_every = 3
print("Beginning Training")
for epoch in xrange(2):
# for i, clip in enumerate(dataset):
for i in xrange(len(dataset)/3):
batch = dataset[(3*i):(3*i + 3), :, :]
# get the input, wrap it in a Variable
inpt = Variable(torch.from_numpy(batch).type(torch.FloatTensor))
# zero the parameter gradients
optimizer.zero_grad()
# forward + backward + optimize
outpt = net(inpt)
loss = loss_fn(outpt, inpt)
loss.backward()
optimizer.step()
# print stats out
avg_loss += loss.data[0]
if batch_count % print_every == print_every - 1:
print('epoch: %d, batch_count: %d, loss: %.3f'%(
epoch + 1, batch_count + 1, avg_loss / print_every))
avg_loss = 0.0
batch_count += 1
print('Finished Training')
I'm really a beginner with this stuff, so any advice would be greatly appreciated.
Double check that you normalize your inpt to be in the range of 0 to 1. For instance, if you are working with images you could just divide inpt variable by 255.
I have written a code for adding the numbers from two different text files. For a very big data 2-3 GB, I get the MemoryError. So, I am writing a new code using some functions to avoid loading the whole data into memory.
This code opens an input file 'd.txt' an reads the numbers after some lines from a bigger data as following:
SCALAR
ND 3
ST 0
TS 1000
1.0
1.0
1.0
SCALAR
ND 3
ST 0
TS 2000
3.3
3.4
3.5
SCALAR
ND 3
ST 0
TS 3000
1.7
1.8
1.9
and adds to the number have read from a smaller text file 'e.txt' as following:
SCALAR
ND 3
ST 0
TS 0
10.0
10.0
10.0
The result is written in a text file 'output.txt' like this:
SCALAR
ND 3
ST 0
TS 1000
11.0
11.0
11.0
SCALAR
ND 3
ST 0
TS 2000
13.3
13.4
13.5
SCALAR
ND 3
ST 0
TS 3000
11.7
11.8
11.9
The code which I prepared:
def add_list_same(list1, list2):
"""
list2 has the same size as list1
"""
c = [a+b for a, b in zip(list1, list2)]
print(c)
return c
def list_numbers_after_ts(n, f):
result = []
for line in f:
if line.startswith('TS'):
for node in range(n):
result.append(float(next(f)))
return result
def writing_TS(f1):
TS = []
ND = []
for line1 in f1:
if line1.startswith('ND'):
ND = float(line1.split()[-1])
if line1.startswith('TS'):
x = float(line1.split()[-1])
TS.append(x)
return TS, ND
with open('d.txt') as depth_dat_file, \
open('e.txt') as elev_file, \
open('output.txt', 'w') as out:
m = writing_TS(depth_dat_file)
print('number of TS', m[1])
for j in range(0,int(m[1])-1):
i = m[1]*j
out.write('SCALAR\nND {0:2f}\nST 0\nTS {0:2f}\n'.format(m[1], m[0][j]))
list1 = list_numbers_after_ts(int(m[1]), depth_dat_file)
list2 = list_numbers_after_ts(int(m[1]), elev_file)
Eh = add_list_same(list1, list2)
out.writelines(["%.2f\n" % item for item in Eh])
the output.txt is like this:
SCALAR
ND 3.000000
ST 0
TS 3.000000
SCALAR
ND 3.000000
ST 0
TS 3.000000
SCALAR
ND 3.000000
ST 0
TS 3.000000
The addition of lists does not work, besides I checked separately the functions, they work. I don't find the error. I changed it a lot, but it does not work. Any suggustion? I really appreciate any help you can provide!
You can use grouper to read files by fixed count of lines. Next code should works if order of lines in groups is unchanged.
from itertools import zip_longest
#Split by group iterator
#See http://stackoverflow.com/questions/434287/what-is-the-most-pythonic-way-to-iterate-over-a-list-in-chunks
def grouper(iterable, n, padvalue=None):
return zip_longest(*[iter(iterable)]*n, fillvalue=padvalue)
add_numbers = []
with open("e.txt") as f:
# Read data by 7 lines
for lines in grouper(f, 7):
# Suppress first SCALAR line
for line in lines[1:]:
# add last number in every line to array (6 elements)
add_numbers.append(float(line.split()[-1].strip()))
#template for every group
template = 'SCALAR\nND {:.2f}\nST {:.2f}\nTS {:.2f}\n{:.2f}\n{:.2f}\n{:.2f}\n'
with open("d.txt") as f, open('output.txt', 'w') as out:
# As before
for lines in grouper(f, 7):
data_numbers = []
for line in lines[1:]:
data_numbers.append(float(line.split()[-1].strip()))
# in result_numbers sum elements of two arrays by pair (6 elements)
result_numbers = [x + y for x, y in zip(data_numbers, add_numbers)]
# * unpack result_numbers as 6 arguments of function format
out.write(template.format(*result_numbers))
I had to change some small things in the code and now it works but just for small input files, because many variables are loaded into memory. Can you please tell me how can I work with yield.
from itertools import zip_longest
def grouper(iterable, n, padvalue=None):
return zip_longest(*[iter(iterable)]*n, fillvalue=padvalue)
def writing_ND(f1):
for line1 in f1:
if line1.startswith('ND'):
ND = float(line1.split()[-1])
return ND
def writing_TS(f):
for line2 in f:
if line2.startswith('TS'):
x = float(line2.split()[-1])
TS.append(x)
return TS
TS = []
ND = []
x = 0.0
n = 0
add_numbers = []
with open("e.txt") as f, open("d.txt") as f1,\
open('output.txt', 'w') as out:
ND = writing_ND(f)
TS = writing_TS(f1)
n = int(ND)+4
f.seek(0)
for lines in grouper(f, int(n)):
for item in lines[4:]:
add_numbers.append(float(item))
i = 0
for l in grouper(f1, n):
data_numbers = []
for line in l[4:]:
data_numbers.append(float(line.split()[-1].strip()))
result_numbers = [x + y for x, y in zip(data_numbers, add_numbers)]
del data_numbers
out.write('SCALAR\nND %d\nST 0\nTS %0.2f\n' % (ND, TS[i]))
i += 1
for item in result_numbers:
out.write('%s\n' % item)