Dumping numpy arrays into neural network - csv

I am trying to solve the titanic machine learning challenge from kaggle using a neural network. I removed most of the irrelevant data and converted the useful data into a 2D numpy array while the survival is converted into a 1D numpy array. For some reason it throws an error saying dimension 0 in both shape must be equal, I've been trying to solve it for quite a while and I hope that you guys can help out.
TensorFlowNumpy.py
import tensorflow as tf
def numpy2tensor(numpy):
sess = tf.Session()
with sess.as_default():
return tf.constant(numpy)
def tensor2numpy(tensor):
sess = tf.Session()
with sess.as_default():
return tensor.eval()
Dataset.py
import pandas
import numpy as np
dataset = pandas.read_csv('train.csv')
dataset2= dataset.drop(['PassengerId','Survived','Name','Ticket','Fare','Cabin','Embarked'],axis=1)
dataset3= dataset2.fillna(0)
survive = pandas.read_csv('train.csv')
survival = np.float32(survive.Survived)
dataset4 = np.float32(dataset3)
MainCode.py
import tensorflow as tf
import numpy
from dataset import dataset4,survival
from sklearn.model_selection import train_test_split
from TensorFlowNumpy import numpy2tensor
train_x,test_x,train_y,test_y = train_test_split(dataset4,survival,test_size
= 0.2)
tensor_train_x = numpy2tensor(train_x)
tensor_train_y = numpy2tensor(train_y)
tensor_test_x = numpy2tensor(test_x)
tensor_test_y = numpy2tensor(test_y)
n_nodes_hl1 = 10
n_nodes_hl2 = 10
n_classes = 2
x = tf.placeholder(tf.float32)
y = tf.placeholder(tf.float32)
def neural_network_model(data):
hidden_1_layer = {'weights':tf.Variable(tf.random_normal([5,
n_nodes_hl1])),
'biases':tf.Variable(tf.random_normal([n_nodes_hl1]))}
hidden_2_layer = {'weights':tf.Variable(tf.random_normal([n_nodes_hl1,
n_nodes_hl2])),
'biases':tf.Variable(tf.random_normal([n_nodes_hl2]))}
output_layer = {'weights':tf.Variable(tf.random_normal([n_nodes_hl2,
n_classes])),
'biases':tf.Variable(tf.random_normal([n_classes]))}
l1 = tf.add(tf.matmul(data,hidden_1_layer['weights']),
hidden_1_layer['biases'])
l1 = tf.nn.relu(l1)
l2 = tf.add(tf.matmul(l1,hidden_2_layer['weights']),
hidden_2_layer['biases'])
l2 = tf.nn.relu(l2)
output = tf.matmul(l2,output_layer['weights']) + output_layer['biases']
return output
def train_neural_network(x):
prediction = neural_network_model(x)
cost =
tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(logits=prediction,
labels=tensor_train_y))
optimizer1 = tf.train.GradientDescentOptimizer(0.001).minimize(cost)
hm_epochs = 100
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
for epoch in range(hm_epochs):
epoch_loss = 0
_, c = sess.run([optimizer1, cost], feed_dict={x:tensor_train_x,
y:tensor_train_y})
epoch_loss += c
print('Epoch', epoch+1, 'completed out
of',hm_epochs,'loss:',epoch_loss)
correct = tf.equal(tf.argmax(prediction, 1), tf.argmax(y, 1))
accuracy = tf.reduce_mean(tf.cast(correct, 'float'))
print('Accuracy:',accuracy.eval({x:test_x, y:test_y}))
train_neural_network(tensor_train_x)

I have faced this error several times, problem is obviously in our code. I didn't look through your code thoroughly as i am leaving for the day, but i smell that your dependent variable/ output variable shape is [1,712] which should be [712,1] so some where in the code try to fix it. Basically what it meant is you are having one row with 712 columns but it should be 712 rows with 1 column(output). Please mark this as answer if it helps. Ping me tomorrow if problem still exists. I will take a look at it.

Related

How to plot a 2 dimensional density / heatmap in plotnine?

I am trying to recreate the following graph in plotnine. It's asking me for more details but I don't want to distract from the example. I think it's pretty obvious what I'm trying to do. I have been given a function by a colleague. I'm not interested in rewriting the function. I want to take sm and use plotnine to plot it instead of matplotlib. I plot lots of dataframes with plotnine but I'm not sure how to use it in this case. I have tried on my own to figure it out and I keep getting lost. I hope that for someone more experienced I am overlooking something simple.
import matplotlib.pyplot as plt
def getSuccess(y,x):
return((y*(-x))*.5+.5)
steps = 100
stepSize = 1/steps
sm = []
for y in range(steps*2+1):
sm.append([getSuccess((y-steps)*stepSize,(x-steps)*stepSize) for x in range(steps*2+1)])
plt.imshow(sm)
plt.ylim(-1, 1)
plt.colorbar()
plt.yticks([0,steps,steps*2],[str(y) for y in [-1.0,0.0,1.0]])
plt.xticks([0,steps,steps*2],[str(x) for x in [-1.0,0.0,1.0]])
plt.show()
You could try geom_raster.
I have taken your synthetic data sm and converted to a dataframe as plotnine will need this.
import pandas as pd
import numpy as np
from plotnine import *
df = pd.DataFrame(sm).melt()
df.rename(columns={'variable':'x','value':'density'}, inplace=True)
df.insert(1,'y',df.index % 201)
p = (ggplot(df, aes('x','y'))
+ geom_raster(aes(fill='density'), interpolate=True)
+ labs(x=None,y=None)
+ scale_x_continuous(expand=(0,0), breaks=[0,100,200], labels=[-1,0,1])
+ scale_y_continuous(expand=(0,0), breaks=[0,100,200], labels=[-1,0,1])
+ theme_matplotlib()
+ theme(
text = element_text(family="Calibri", size=9),
legend_title = element_blank(),
axis_ticks = element_blank(),
legend_key_height = 29.6,
legend_key_width = 6,
)
)
p.save(filename='C:\\Users\\BRB\\geom_raster.png', height=10, width=10, units = 'cm', dpi=400)
This result is:

How to feed an LSTM/GRU model multiple independent Time Series?

In Order to explain it simply: I have 53 Oil Producing wells measurements, each well has been measured each day for 6 years, we recorded multiple variables (Pressure, water production, gas production...etc), and our main component(The one we want to study and forecast) is the Oil production rate. How can I Use all the data to train my model of LSTM/GRU knowing that the Oil wells are independent and that the measurments have been done in the same time for each one?
The knowledge that "the measurments have been done in the same time for each [well]" is not necessary if you want to assume that the wells are independent. (Why do you think that that knowledge is useful?)
So if the wells are considered independent, treat them as individual samples. Split them into a training set, validation set, and test set, as usual. Train a usual LSTM or GRU on the training set.
By the way, you might want to use the attention mechanism instead of recurrent networks. It is easier to train and usually yields comparable results.
Even convolutional networks might be good enough. See methods like WaveNet if you suspect long-range correlations.
These well measurements sound like specific and independent events. I work in the finance sector. We always look at different stocks, and each stocks specific time neries using LSTM, but not 10 stocks mashed up together. Here's some code to analyze a specific stock. Modify the code to suit your needs.
from pandas_datareader import data as wb
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.pylab import rcParams
from sklearn.preprocessing import MinMaxScaler
start = '2019-06-30'
end = '2020-06-30'
tickers = ['GOOG']
thelen = len(tickers)
price_data = []
for ticker in tickers:
prices = wb.DataReader(ticker, start = start, end = end, data_source='yahoo')[['Open','Adj Close']]
price_data.append(prices.assign(ticker=ticker)[['ticker', 'Open', 'Adj Close']])
#names = np.reshape(price_data, (len(price_data), 1))
df = pd.concat(price_data)
df.reset_index(inplace=True)
for col in df.columns:
print(col)
#used for setting the output figure size
rcParams['figure.figsize'] = 20,10
#to normalize the given input data
scaler = MinMaxScaler(feature_range=(0, 1))
#to read input data set (place the file name inside ' ') as shown below
df['Adj Close'].plot()
plt.legend(loc=2)
plt.xlabel('Date')
plt.ylabel('Price')
plt.show()
ntrain = 80
df_train = df.head(int(len(df)*(ntrain/100)))
ntest = -80
df_test = df.tail(int(len(df)*(ntest/100)))
#importing the packages
from sklearn.preprocessing import MinMaxScaler
from keras.models import Sequential
from keras.layers import Dense, Dropout, LSTM
#dataframe creation
seriesdata = df.sort_index(ascending=True, axis=0)
new_seriesdata = pd.DataFrame(index=range(0,len(df)),columns=['Date','Adj Close'])
length_of_data=len(seriesdata)
for i in range(0,length_of_data):
new_seriesdata['Date'][i] = seriesdata['Date'][i]
new_seriesdata['Adj Close'][i] = seriesdata['Adj Close'][i]
#setting the index again
new_seriesdata.index = new_seriesdata.Date
new_seriesdata.drop('Date', axis=1, inplace=True)
#creating train and test sets this comprises the entire data’s present in the dataset
myseriesdataset = new_seriesdata.values
totrain = myseriesdataset[0:255,:]
tovalid = myseriesdataset[255:,:]
#converting dataset into x_train and y_train
scalerdata = MinMaxScaler(feature_range=(0, 1))
scale_data = scalerdata.fit_transform(myseriesdataset)
x_totrain, y_totrain = [], []
length_of_totrain=len(totrain)
for i in range(60,length_of_totrain):
x_totrain.append(scale_data[i-60:i,0])
y_totrain.append(scale_data[i,0])
x_totrain, y_totrain = np.array(x_totrain), np.array(y_totrain)
x_totrain = np.reshape(x_totrain, (x_totrain.shape[0],x_totrain.shape[1],1))
#LSTM neural network
lstm_model = Sequential()
lstm_model.add(LSTM(units=50, return_sequences=True, input_shape=(x_totrain.shape[1],1)))
lstm_model.add(LSTM(units=50))
lstm_model.add(Dense(1))
lstm_model.compile(loss='mean_squared_error', optimizer='adadelta')
lstm_model.fit(x_totrain, y_totrain, epochs=10, batch_size=1, verbose=2)
#predicting next data stock price
myinputs = new_seriesdata[len(new_seriesdata) - (len(tovalid)+1) - 60:].values
myinputs = myinputs.reshape(-1,1)
myinputs = scalerdata.transform(myinputs)
tostore_test_result = []
for i in range(60,myinputs.shape[0]):
tostore_test_result.append(myinputs[i-60:i,0])
tostore_test_result = np.array(tostore_test_result)
tostore_test_result = np.reshape(tostore_test_result,(tostore_test_result.shape[0],tostore_test_result.shape[1],1))
myclosing_priceresult = lstm_model.predict(tostore_test_result)
myclosing_priceresult = scalerdata.inverse_transform(myclosing_priceresult)
totrain = df_train
tovalid = df_test
#predicting next data stock price
myinputs = new_seriesdata[len(new_seriesdata) - (len(tovalid)+1) - 60:].values
# Printing the next day’s predicted stock price.
print(len(tostore_test_result));
print(myclosing_priceresult);
Final result:
1
[[1396.532]]

Train Caffe CNN to output multidimensional features

I'd like to build a feature extractor using Caffe's CNNs and I already have a large sample of input features and desired output features.
Now I need to train some convolutional layers to learn how to transform the input features into the output.
My question is: How can I achieve this on Caffe?
As a minimal example, suppose I wanted to train a CNN that inverts the values of a 2D array.
For example, if my input is
[[0,1,0],
[1,1,1],
[0,1,0]]
the CNN should output
[[1,0,1],
[0,0,0],
[1,0,1]].
For
[[0,0,0],
[0,1,0],
[0,0,0]]
the output should be
[[1,1,1],
[1,0,1],
[1,1,1]]
and so on.
Of course this is just a minimal example to share, the actual problem is nearly impossible to tackle without the use of multiple convolutions.
I was able to create this code for this problem. I used the Euclidean Loss at the end, but unfortunately the CNN is not learning anything.
ROOT_DIR = '/home'
from os.path import join
import numpy as np
import h5py
from itertools import product
import caffe
from caffe import layers
from caffe.proto import caffe_pb2
#%% GENERATE DATA
data_in = np.array([np.array(seq).reshape(1,3,3) for seq in product([0,1], repeat=9)])
data_out = np.array([-1*array+1 for array in data_in])
with open(join(ROOT_DIR, 'data.txt'), 'w') as ftxt:
with h5py.File(join(ROOT_DIR, 'data.hdf5'), 'w') as fhdf5:
fhdf5['data'] = data_in.astype(np.float32)
fhdf5['label'] = data_out.astype(np.float32)
ftxt.write(join(ROOT_DIR, 'data.hdf5'))
#%%DEFINE NET
net = caffe.NetSpec()
net.data, net.label = layers.HDF5Data(batch_size=64, source=join(ROOT_DIR, 'data.txt'), ntop=2)
net.conv1 = layers.Convolution(net.data, kernel_size=1, num_output=128)
net.relu1 = layers.ReLU(net.conv1, in_place=True)
net.conv2 = layers.Convolution(net.relu1, kernel_size=1, num_output=1)
net.relu2 = layers.ReLU(net.conv2, in_place=True)
net.loss = layers.EuclideanLoss(net.relu2, net.label)
net.to_proto()
with open(join(ROOT_DIR, 'invert_net.prototxt'), 'w') as f:
f.write(str(net.to_proto()))
#%% DEFINE SOLVER
solver = caffe_pb2.SolverParameter()
solver.train_net = join(ROOT_DIR, 'invert_net.prototxt')
solver.max_iter = 10000
solver.base_lr = 0.01
solver.lr_policy = 'fixed'
with open(join(ROOT_DIR, 'solver.prototxt'), 'w') as f:
f.write(str(solver))
#%% TRAIN NET
caffe.set_mode_cpu()
solver = caffe.SGDSolver(join(ROOT_DIR, 'solver.prototxt'))
solver.solve()

Getting polynomial regression to overfit with TensorFlow

The Sklearn documentation contains an example of a polynomial regression which beautifully illustrates the idea of overfitting (link).
The third plot shows a 15th order polynomial that overfits the simulated data. I replicated this model in TensorFlow, but I cannot get it to overfit.
Even when tuning the learning rate and the numbers of learning epochs, I cannot get the model to overfit. What am I missing?
import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
def true_fun(X):
return np.cos(1.5 * np.pi * X)
# Generate dataset
n_samples = 30
np.random.seed(0)
x_train = np.sort(np.random.rand(n_samples)) # Draw from uniform distribution
y_train = true_fun(x_train) + np.random.randn(n_samples) * 0.1
x_test = np.linspace(0, 1, 100)
y_true = true_fun(x_test)
# Helper function
def run_dir(base_dir, dirname='run'):
"Number log directories incrementally"
import os
import re
pattern = re.compile(dirname+'_(\d+)')
try:
previous_runs = os.listdir(base_dir)
except FileNotFoundError:
previous_runs = []
run_number = 0
for name in previous_runs:
match = pattern.search(name)
if match:
number = int(match.group(1))
if number > run_number:
run_number = number
run_number += 1
logdir = os.path.join(base_dir, dirname + '_%02d' % run_number)
return(logdir)
# Define the polynomial model
def model(X, w):
"""Polynomial model
param X: data
param y: coeficients in the polynomial regression
returns: Polynomial function Y(X, w)
"""
terms = []
for i in range(int(w.shape[0])):
term = tf.multiply(w[i], tf.pow(X, i))
terms.append(term)
return(tf.add_n(terms))
# Create the computation graph
order = 15
tf.reset_default_graph()
X = tf.placeholder("float")
Y = tf.placeholder("float")
w = tf.Variable([0.]*order, name="parameters")
lambda_reg = tf.placeholder('float', shape=[])
learning_rate_ph = tf.placeholder('float', shape=[])
y_model = model(X, w)
loss = tf.div(tf.reduce_mean(tf.square(Y-y_model)), 2) # Square error
loss_rg = tf.multiply(lambda_reg, tf.reduce_sum(tf.square(w))) # L2 pentalty
loss_total = tf.add(loss, loss_rg)
loss_hist1 = tf.summary.scalar('loss', loss)
loss_hist2 = tf.summary.scalar('loss_rg', loss_rg)
loss_hist3 = tf.summary.scalar('loss_total', loss_total)
summary = tf.summary.merge([loss_hist1, loss_hist2, loss_hist3])
train_op = tf.train.GradientDescentOptimizer(learning_rate_ph).minimize(loss_total)
init = tf.global_variables_initializer()
def train(sess, x_train, y_train, lambda_val=0, epochs=2000, learning_rate=0.01):
feed_dict={X: x_train, Y: y_train, lambda_reg: lambda_val, learning_rate_ph: learning_rate}
logdir = run_dir("logs/polynomial_regression2/")
writer = tf.summary.FileWriter(logdir)
sess.run(init)
for epoch in range(epochs):
_, summary_str = sess.run([train_op, summary], feed_dict=feed_dict)
writer.add_summary(summary_str, global_step=epoch)
final_cost, final_cost_rg, w_learned = sess.run([loss, loss_rg, w], feed_dict=feed_dict)
return final_cost, final_cost_rg, w_learned
def plot_test(w_learned, x_test, x_train, y_train):
y_learned = calculate_y(x_test, w_learned)
plt.scatter(x_train, y_train)
plt.plot(x_test, y_true, label="true function")
plt.plot(x_test, y_learned,'r', label="learned function")
#plt.title('$\lambda = {:03.2f}$'.format(lambda_values[i]))
plt.ylabel('y')
plt.xlabel('x')
plt.legend()
plt.show()
def calculate_y(x, w):
y = 0
for i in range(w.shape[0]):
y += w[i] * np.power(x, i)
return y
sess = tf.Session()
final_cost, final_cost_rg, w_learned = train(sess, x_train, y_train, lambda_val=0,
learning_rate=0.3, epochs=2000)
sess.close()
plot_test(w_learned, x_test, x_train, y_train)
I have same problem about this. When I do polynomial regression, I also can't overfit the data by using GD in Tensorflow.
Then I compare the coefficients(weights) of the model by using sklearn LinearRegression, I found when the polynomial degree is larger the coefficient of high order is very smaller(i.e. 1e-4), and the low order is relative large(i.e. 0.1).
That's mean when you using GD algorithm for searching the best value of weights, the high order coefficient become extreme sensitive about the value change, and the low order coefficient is not.
And I guess the best coefficient(overfit with data) of low order term is large, and of high order term is tiny. When you set large learning rate, it's impossible to find the right answer, and when you set tiny learning rate, you need lots of iterations.
It's obvious when you using GD algorithm with small data set to make overfit.

Can I export a tensorflow summary to CSV?

Is there a way to extract scalar summaries to CSV (preferably from within tensorboard) from tfevents files?
Example code
The following code generates tfevent files in a summary_dir within the same directory. Suppose you let it run and you find something interesting. You want to get the raw data for further investigation. How would you do that?
#!/usr/bin/env python
"""A very simple MNIST classifier."""
import argparse
import sys
from tensorflow.examples.tutorials.mnist import input_data
import tensorflow as tf
ce_with_logits = tf.nn.softmax_cross_entropy_with_logits
FLAGS = None
def inference(x):
"""
Build the inference graph.
Parameters
----------
x : placeholder
Returns
-------
Output tensor with the computed logits.
"""
W = tf.Variable(tf.zeros([784, 10]))
b = tf.Variable(tf.zeros([10]))
y = tf.matmul(x, W) + b
return y
def loss(logits, labels):
"""
Calculate the loss from the logits and the labels.
Parameters
----------
logits : Logits tensor, float - [batch_size, NUM_CLASSES].
labels : Labels tensor, int32 - [batch_size]
"""
cross_entropy = tf.reduce_mean(ce_with_logits(labels=labels,
logits=logits))
return cross_entropy
def training(loss, learning_rate=0.5):
"""
Set up the training Ops.
Parameters
----------
loss : Loss tensor, from loss().
learning_rate : The learning rate to use for gradient descent.
Returns
-------
train_op: The Op for training.
"""
optimizer = tf.train.GradientDescentOptimizer(learning_rate)
train_step = optimizer.minimize(loss)
return train_step
def main(_):
# Import data
mnist = input_data.read_data_sets(FLAGS.data_dir, one_hot=True)
# Create the model
x = tf.placeholder(tf.float32, [None, 784])
y = inference(x)
# Define loss and optimizer
y_ = tf.placeholder(tf.float32, [None, 10])
loss_ = loss(logits=y, labels=y_)
train_step = training(loss_)
# Test trained model
correct_prediction = tf.equal(tf.argmax(y, 1), tf.argmax(y_, 1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
with tf.name_scope('accuracy'):
tf.summary.scalar('accuracy', accuracy)
merged = tf.summary.merge_all()
sess = tf.InteractiveSession()
train_writer = tf.summary.FileWriter('summary_dir/train', sess.graph)
test_writer = tf.summary.FileWriter('summary_dir/test', sess.graph)
tf.global_variables_initializer().run()
for train_step_i in range(100000):
if train_step_i % 100 == 0:
summary, acc = sess.run([merged, accuracy],
feed_dict={x: mnist.test.images,
y_: mnist.test.labels})
test_writer.add_summary(summary, train_step_i)
summary, acc = sess.run([merged, accuracy],
feed_dict={x: mnist.train.images,
y_: mnist.train.labels})
train_writer.add_summary(summary, train_step_i)
batch_xs, batch_ys = mnist.train.next_batch(100)
sess.run(train_step, feed_dict={x: batch_xs, y_: batch_ys})
print(sess.run(accuracy, feed_dict={x: mnist.test.images,
y_: mnist.test.labels}))
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('--data_dir',
type=str,
default='/tmp/tensorflow/mnist/input_data',
help='Directory for storing input data')
FLAGS, unparsed = parser.parse_known_args()
tf.app.run(main=main, argv=[sys.argv[0]] + unparsed)
While the answer here is as requested within tensorboard it only allows to download a csv for a single run of a single tag.
If you have for example 10 tags and 20 runs (what is not at all much) you would need to do the above step 200 times (that alone will probably take you more than a hour).
If now you for some reason would like to actually do something with the data for all runs for a single tag you would need to write some weird CSV accumulation script or copy everything by hand (what will probably cost you more than a day).
Therefore I would like to add a solution that extracts a CSV file for every tag with all runs contained. Column headers are the run path names and row indices are the run step numbers.
import os
import numpy as np
import pandas as pd
from collections import defaultdict
from tensorboard.backend.event_processing.event_accumulator import EventAccumulator
def tabulate_events(dpath):
summary_iterators = [EventAccumulator(os.path.join(dpath, dname)).Reload() for dname in os.listdir(dpath)]
tags = summary_iterators[0].Tags()['scalars']
for it in summary_iterators:
assert it.Tags()['scalars'] == tags
out = defaultdict(list)
steps = []
for tag in tags:
steps = [e.step for e in summary_iterators[0].Scalars(tag)]
for events in zip(*[acc.Scalars(tag) for acc in summary_iterators]):
assert len(set(e.step for e in events)) == 1
out[tag].append([e.value for e in events])
return out, steps
def to_csv(dpath):
dirs = os.listdir(dpath)
d, steps = tabulate_events(dpath)
tags, values = zip(*d.items())
np_values = np.array(values)
for index, tag in enumerate(tags):
df = pd.DataFrame(np_values[index], index=steps, columns=dirs)
df.to_csv(get_file_path(dpath, tag))
def get_file_path(dpath, tag):
file_name = tag.replace("/", "_") + '.csv'
folder_path = os.path.join(dpath, 'csv')
if not os.path.exists(folder_path):
os.makedirs(folder_path)
return os.path.join(folder_path, file_name)
if __name__ == '__main__':
path = "path_to_your_summaries"
to_csv(path)
My solution builds upon: https://stackoverflow.com/a/48774926/2230045
EDIT:
I created a more sophisticated version and released it on GitHub: https://github.com/Spenhouet/tensorboard-aggregator
This version aggregates multiple tensorboard runs and is able to save the aggregates to a new tensorboard summary or as a .csv file.
Just check the "Data download links" option on the upper-left in TensorBoard, and then click on the "CSV" button that will appear under your scalar summary.
Here is my solution which bases on the previous solutions but can scale up.
import os
import numpy as np
import pandas as pd
from collections import defaultdict
from tensorboard.backend.event_processing.event_accumulator import EventAccumulator
def tabulate_events(dpath):
final_out = {}
for dname in os.listdir(dpath):
print(f"Converting run {dname}",end="")
ea = EventAccumulator(os.path.join(dpath, dname)).Reload()
tags = ea.Tags()['scalars']
out = {}
for tag in tags:
tag_values=[]
wall_time=[]
steps=[]
for event in ea.Scalars(tag):
tag_values.append(event.value)
wall_time.append(event.wall_time)
steps.append(event.step)
out[tag]=pd.DataFrame(data=dict(zip(steps,np.array([tag_values,wall_time]).transpose())), columns=steps,index=['value','wall_time'])
if len(tags)>0:
df= pd.concat(out.values(),keys=out.keys())
df.to_csv(f'{dname}.csv')
print("- Done")
else:
print('- Not scalers to write')
final_out[dname] = df
return final_out
if __name__ == '__main__':
path = "youre/path/here"
steps = tabulate_events(path)
pd.concat(steps.values(),keys=steps.keys()).to_csv('all_result.csv')
Very minimal example:
import pandas as pd
from tensorboard.backend.event_processing.event_accumulator import EventAccumulator
log_dir = "lightning_logs/version_1"
event_accumulator = EventAccumulator(log_dir)
event_accumulator.Reload()
events = event_accumulator.Scalars("train_loss")
x = [x.step for x in events]
y = [x.value for x in events]
df = pd.DataFrame({"step": x, "train_loss": y})
df.to_csv("train_loss.csv")
print(df)
step train_loss
0 0 700.491516
1 1 163.593246
2 2 146.365448
3 3 153.830215
...
Plotting loss vs epochs example:
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from tensorboard.backend.event_processing.event_accumulator import EventAccumulator
log_dir = "lightning_logs/version_1"
y_key = "val_loss"
event_accumulator = EventAccumulator(log_dir)
event_accumulator.Reload()
steps = {x.step for x in event_accumulator.Scalars("epoch")}
x = list(range(len(steps)))
y = [x.value for x in event_accumulator.Scalars(y_key) if x.step in steps]
df = pd.DataFrame({"epoch": x, y_key: y})
df.to_csv(f"{y_key}.csv")
fig, ax = plt.subplots()
sns.lineplot(data=df, x="epoch", y=y_key)
fig.savefig("plot.png", dpi=300)
Just to add to #Spen
in case you want to export the data when you have varying numbers of steps.
This will make one large csv file.
Might need to change around the keys for it to work for you.
import os
import numpy as np
import pandas as pd
from collections import defaultdict
from tensorboard.backend.event_processing.event_accumulator import EventAccumulator
import glob
import pandas as pd
listOutput = (glob.glob("*/"))
listDF = []
for tb_output_folder in listOutput:
print(tb_output_folder)
x = EventAccumulator(path=tb_output_folder)
x.Reload()
x.FirstEventTimestamp()
keys = ['loss', 'mean_absolute_error', 'val_loss', 'val_mean_absolute_error']
listValues = {}
steps = [e.step for e in x.Scalars(keys[0])]
wall_time = [e.wall_time for e in x.Scalars(keys[0])]
index = [e.index for e in x.Scalars(keys[0])]
count = [e.count for e in x.Scalars(keys[0])]
n_steps = len(steps)
listRun = [tb_output_folder] * n_steps
printOutDict = {}
data = np.zeros((n_steps, len(keys)))
for i in range(len(keys)):
data[:,i] = [e.value for e in x.Scalars(keys[i])]
printOutDict = {keys[0]: data[:,0], keys[1]: data[:,1],keys[2]: data[:,2],keys[3]: data[:,3]}
printOutDict['Name'] = listRun
DF = pd.DataFrame(data=printOutDict)
listDF.append(DF)
df = pd.concat(listDF)
df.to_csv('Output.csv')