I am trying to port this python code to Go but there is no beta() in math package. Where can i find beta and other functions required for this?
from numpy import *
from scipy.stats import beta
class BetaBandit(object):
def __init__(self, num_options=2, prior=(1.0,1.0)):
self.trials = zeros(shape=(num_options,), dtype=int)
self.successes = zeros(shape=(num_options,), dtype=int)
self.num_options = num_options
self.prior = prior
def add_result(self, trial_id, success):
self.trials[trial_id] = self.trials[trial_id] + 1
if (success):
self.successes[trial_id] = self.successes[trial_id] + 1
def get_recommendation(self):
sampled_theta = []
for i in range(self.num_options):
#Construct beta distribution for posterior
dist = beta(self.prior[0]+self.successes[i],
self.prior[1]+self.trials[i]-self.successes[i])
#Draw sample from beta distribution
sampled_theta += [ dist.rvs() ]
# Return the index of the sample with the largest value
return sampled_theta.index( max(sampled_theta) )
If you are talking about numpy.random.beta, the Beta distribution which is a special case of the Dirichlet distribution, and is related to the Gamma distribution, you can check the project gostat.
It has a beta.go source code which implements that function.
Related
I create a yaml file that update some parameters and uses a standard IMU sensor message, sensor_msgs/Imu. The code is here
#!/usr/bin/python3
import numpy as np
from node_registry.decorators import rosnode, register
from geometry_msgs.msg import Quaternion
from sensor_msgs.msg import Imu
from test_ros_common.coordinate_converter import rpy2quaternion, quaternion2rpy
_pub_topic = "imu"
_sub_topic = "imu_postprocess"
_qos = 1
#rosnode.parameter("period", 0.025)
#rosnode.publisher(Imu, _pub_topic, _qos)
#rosnode
def node_name():
return "test_imu_inverse"
#rosnode.inject
def yaw_deg():
return 0
#rosnode.timer(rosnode.period)
def timer_cb():
imu = Imu()
quaternion = rpy2quaternion([np.deg2rad(rosnode.yaw_deg), 0, 0])
imu.imu.orientation = Quaternion(
w=quaternion[0], x=quaternion[1], y=quaternion[2], z=quaternion[3]
)
rosnode.get_publisher(_pub_topic).publish(imu)
rosnode.logger.info(f"Input yaw: {rosnode.yaw_deg}")
rosnode.yaw_deg += 1
rosnode.yaw_deg %= 180
#rosnode.subscribe(Imu, _sub_topic, _qos)
def subscrbe_cb(msg):
orientation = imu.orientation
yaw_rad = quaternion2rpy(
[orientation.w, orientation.x, orientation.y, orientation.z]
)[0][0]
rosnode.logger.info(f"Output yaw: {np.rad2deg(yaw_rad)}")
register()
My question is the correct implementation of IMU standard messages. In this two parts of the code . First here
imu.imu.orientation = Quaternion(
w=quaternion[0], x=quaternion[1], y=quaternion[2], z=quaternion[3]
Is this correct or should be
imu.orientation = Quaternion(
w=quaternion[0], x=quaternion[1], y=quaternion[2], z=quaternion[3]
And also here
def subscrbe_cb(msg):
orientation = imu.orientation
yaw_rad = quaternion2rpy(
[orientation.w, orientation.x, orientation.y, orientation.z]?
Thanks
I am trying to do a simple custom training loop.
For some reason, the train_step() function gets ignored and a normal training loop is carried. I noticed when the word "Hello" is not printed when I run the script on my MacBook Pro with M1 chip. My old MacBook Pro (AMD) works perfectly and the code also worked perfectly on Google Colab.
The tensor flow version is 2.0.0 and Keras is 2.3.1. Thanks in advance for your help.
My Code is:
import numpy as np
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import Model
# tf.config.run_functions_eagerly(True)
class CustomModel(Model):
# #tf.function
def train_step(self, data):
# Unpack the data. Its structure depends on your model and
# on what you pass to `fit()`.
x, y = data
print('Hello')
with tf.GradientTape() as tape:
y_pred = self(x, training=True) # Forward pass
# Compute the loss value
# (the loss function is configured in `compile()`)
loss = self.compiled_loss(y, y_pred, regularization_losses=self.losses)
# Compute gradients
trainable_vars = self.trainable_variables
gradients = tape.gradient(loss, trainable_vars)
# Update weights
self.optimizer.apply_gradients(zip(gradients, trainable_vars))
# Update metrics (includes the metric that tracks the loss)
self.compiled_metrics.update_state(y, y_pred)
# Return a dict mapping metric names to current value
return {m.name: m.result() for m in self.metrics}
# Construct and compile an instance of CustomModel
inputs = keras.Input(shape=(32,))
outputs = keras.layers.Dense(1)(inputs)
model = CustomModel(inputs, outputs)
model.compile(optimizer="adam", loss="mse", metrics=["mae"])
# Just use `fit` as usual
x = np.random.random((1000, 32))
y = np.random.random((1000, 1))
model.fit(x, y, epochs=3)
Hello is not printed:
Hello is printed during training:
I would like to use a RobustScaler for preprocessing data. In sklearn it can be found in
sklearn.preprocessing.RobustScaler
. However, I am using pyspark, so I tried to import it with:
from pyspark.ml.feature import RobustScaler
However, I receive the following error:
ImportError: cannot import name 'RobustScaler' from 'pyspark.ml.feature'
As pault pointed out, RobustScaler is implemented only in pyspark 3. I am trying to implement it as:
class PySpark_RobustScaler(Pipeline):
def __init__(self):
pass
def fit(self, df):
return self
def transform(self, df):
self._df = df
for col_name in self._df.columns:
q1, q2, q3 = self._df.approxQuantile(col_name, [0.25, 0.5, 0.75], 0.00)
self._df = self._df.withColumn(col_name, 2.0*(sf.col(col_name)-q2)/(q3-q1))
return self._df
arr = np.array(
[[ 1., -2., 2.],
[ -2., 1., 3.],
[ 4., 1., -2.]]
)
rdd1 = sc.parallelize(arr)
rdd2 = rdd1.map(lambda x: [int(i) for i in x])
df_sprk = rdd2.toDF(["A", "B", "C"])
df_pd = pd.DataFrame(arr, columns=list('ABC'))
PySpark_RobustScaler().fit(df_sprk).transform(df_sprk).show()
print(RobustScaler().fit(df_pd).transform(df_pd))
However I have found that to obtain the same result of sklearn I have to multiply the result by 2. Furthermore, I am worried that if a column has many values close to zero, the interquartile range q3-q1 could become too small and let the result diverge, creating null values.
Does anyone have any suggestions on how to improve it?
This feature has been released in recent pyspark versions.
I am trying to load my own dataset and I use a custom Dataloader that reads in images and labels and converts them to PyTorch Tensors. However when the Dataloader is instantiated it returns strings x "image" and y "labels" but not the real values or tensors when read (iter)
print(self.train_loader) # shows a Tensor object
tic = time.time()
with tqdm(total=self.num_train) as pbar:
for i, (x, y) in enumerate(self.train_loader): # x and y are returned as string (where it fails)
if self.use_gpu:
x, y = x.cuda(), y.cuda()
x, y = Variable(x), Variable(y)
This is how dataloader.py looks like:
from __future__ import print_function, division #ds
import numpy as np
from utils import plot_images
import os #ds
import pandas as pd #ds
from skimage import io, transform #ds
import torch
from torchvision import datasets
from torch.utils.data import Dataset, DataLoader #ds
from torchvision import transforms
from torchvision import utils #ds
from torch.utils.data.sampler import SubsetRandomSampler
class CDataset(Dataset):
def __init__(self, csv_file, root_dir, transform=None):
"""
Args:
csv_file (string): Path to the csv file with annotations.
root_dir (string): Directory with all the images.
transform (callable, optional): Optional transform to be applied
on a sample.
"""
self.frame = pd.read_csv(csv_file)
self.root_dir = root_dir
self.transform = transform
def __len__(self):
return len(self.frame)
def __getitem__(self, idx):
img_name = os.path.join(self.root_dir,
self.frame.iloc[idx, 0]+'.jpg')
image = io.imread(img_name)
# image = image.transpose((2, 0, 1))
labels = np.array(self.frame.iloc[idx, 1])#.as_matrix() #ds
#landmarks = landmarks.astype('float').reshape(-1, 2)
#print(image.shape)
#print(img_name,labels)
sample = {'image': image, 'labels': labels}
if self.transform:
sample = self.transform(sample)
return sample
class ToTensor(object):
"""Convert ndarrays in sample to Tensors."""
def __call__(self, sample):
image, labels = sample['image'], sample['labels']
#print(image)
#print(labels)
# swap color axis because
# numpy image: H x W x C
# torch image: C X H X W
image = image.transpose((2, 0, 1))
#print(image.shape)
#print((torch.from_numpy(image)))
#print((torch.from_numpy(labels)))
return {'image': torch.from_numpy(image),
'labels': torch.from_numpy(labels)}
def get_train_valid_loader(data_dir,
batch_size,
random_seed,
#valid_size=0.1, #ds
#shuffle=True,
show_sample=False,
num_workers=4,
pin_memory=False):
"""
Utility function for loading and returning train and valid
multi-process iterators over the MNIST dataset. A sample
9x9 grid of the images can be optionally displayed.
If using CUDA, num_workers should be set to 1 and pin_memory to True.
Args
----
- data_dir: path directory to the dataset.
- batch_size: how many samples per batch to load.
- random_seed: fix seed for reproducibility.
- #ds valid_size: percentage split of the training set used for
the validation set. Should be a float in the range [0, 1].
In the paper, this number is set to 0.1.
- shuffle: whether to shuffle the train/validation indices.
- show_sample: plot 9x9 sample grid of the dataset.
- num_workers: number of subprocesses to use when loading the dataset.
- pin_memory: whether to copy tensors into CUDA pinned memory. Set it to
True if using GPU.
Returns
-------
- train_loader: training set iterator.
- valid_loader: validation set iterator.
"""
#ds
#error_msg = "[!] valid_size should be in the range [0, 1]."
#assert ((valid_size >= 0) and (valid_size <= 1)), error_msg
#ds
# define transforms
#normalize = transforms.Normalize((0.1307,), (0.3081,))
trans = transforms.Compose([
ToTensor(), #normalize,
])
# load train dataset
#train_dataset = datasets.MNIST(
# data_dir, train=True, download=True, transform=trans
#)
train_dataset = CDataset(csv_file='/home/Desktop/6June17/util/train.csv',
root_dir='/home/caffe/data/images/',transform=trans)
# load validation dataset
#valid_dataset = datasets.MNIST( #ds
# data_dir, train=True, download=True, transform=trans #ds
#)
valid_dataset = CDataset(csv_file='/home/Desktop/6June17/util/eval.csv',
root_dir='/home/caffe/data/images/',transform=trans)
num_train = len(train_dataset)
train_indices = list(range(num_train))
#ds split = int(np.floor(valid_size * num_train))
num_valid = len(valid_dataset) #ds
valid_indices = list(range(num_valid)) #ds
#if shuffle:
# np.random.seed(random_seed)
# np.random.shuffle(indices)
#ds train_idx, valid_idx = indices[split:], indices[:split]
train_idx = train_indices #ds
valid_idx = valid_indices #ds
train_sampler = SubsetRandomSampler(train_idx)
valid_sampler = SubsetRandomSampler(valid_idx)
train_loader = torch.utils.data.DataLoader(
train_dataset, batch_size=batch_size, sampler=train_sampler,
num_workers=num_workers, pin_memory=pin_memory,
)
print(train_loader)
valid_loader = torch.utils.data.DataLoader(
valid_dataset, batch_size=batch_size, sampler=valid_sampler,
num_workers=num_workers, pin_memory=pin_memory,
)
# visualize some images
if show_sample:
sample_loader = torch.utils.data.DataLoader(
dataset, batch_size=9, #shuffle=shuffle,
num_workers=num_workers, pin_memory=pin_memory
)
data_iter = iter(sample_loader)
images, labels = data_iter.next()
X = images.numpy()
X = np.transpose(X, [0, 2, 3, 1])
plot_images(X, labels)
return (train_loader, valid_loader)
def get_test_loader(data_dir,
batch_size,
num_workers=4,
pin_memory=False):
"""
Utility function for loading and returning a multi-process
test iterator over the MNIST dataset.
If using CUDA, num_workers should be set to 1 and pin_memory to True.
Args
----
- data_dir: path directory to the dataset.
- batch_size: how many samples per batch to load.
- num_workers: number of subprocesses to use when loading the dataset.
- pin_memory: whether to copy tensors into CUDA pinned memory. Set it to
True if using GPU.
Returns
-------
- data_loader: test set iterator.
"""
# define transforms
#normalize = transforms.Normalize((0.1307,), (0.3081,))
trans = transforms.Compose([
ToTensor(), #normalize,
])
# load dataset
#dataset = datasets.MNIST(
# data_dir, train=False, download=True, transform=trans
#)
test_dataset = CDataset(csv_file='/home/Desktop/6June17/util/test.csv',
root_dir='/home/caffe/data/images/',transform=trans)
test_loader = torch.utils.data.DataLoader(
test_dataset, batch_size=batch_size, shuffle=False,
num_workers=num_workers, pin_memory=pin_memory,
)
return test_loader
#for i_batch, sample_batched in enumerate(dataloader):
# print(i_batch, sample_batched['image'].size(),
# sample_batched['landmarks'].size())
# # observe 4th batch and stop.
# if i_batch == 3:
# plt.figure()
# show_landmarks_batch(sample_batched)
# plt.axis('off')
# plt.ioff()
# plt.show()
# break
A minimal working sample will be difficult to post here but basically I am trying to modify this project http://torch.ch/blog/2015/09/21/rmva.html which works smoothly with MNIST. I am just trying to run it with my own dataset with the custom dataloader.py I use above.
It instantiates a Dataloader like this:
in trainer.py:
if config.is_train:
self.train_loader = data_loader[0]
self.valid_loader = data_loader[1]
self.num_train = len(self.train_loader.sampler.indices)
self.num_valid = len(self.valid_loader.sampler.indices)
-> run from main.py:
if config.is_train:
data_loader = get_train_valid_loader(
config.data_dir, config.batch_size,
config.random_seed, #config.valid_size,
#config.shuffle,
config.show_sample, **kwargs
)
You are not properly using python's enumerate(). (x, y) are currently assigned the 2 keys of your batch dictionary i.e. the strings "image" and "labels". This should solve your problem:
for i, batch in enumerate(self.train_loader):
x, y = batch["image"], batch["labels"]
# ...
pymc.__version__ = '3.0'
theano.__version__ = '0.6.0.dev-RELEASE'
I'm trying to use PyMC3 with a complex likelihood function:
First question: Is this possible?
Here's my attempt using Thomas Wiecki's post as a guide:
import numpy as np
import theano as th
import pymc as pm
import scipy as sp
# Actual data I'm trying to fit
x = np.array([52.08, 58.44, 60.0, 65.0, 65.10, 66.0, 70.0, 87.5, 110.0, 126.0])
y = np.array([0.522, 0.659, 0.462, 0.720, 0.609, 0.696, 0.667, 0.870, 0.889, 0.919])
yerr = np.array([0.104, 0.071, 0.138, 0.035, 0.102, 0.096, 0.136, 0.031, 0.024, 0.035])
th.config.compute_test_value = 'off'
a = th.tensor.dscalar('a')
with pm.Model() as model:
# Priors
alpha = pm.Normal('alpha', mu=0.3, sd=5)
sig_alpha = pm.Normal('sig_alpha', mu=0.03, sd=5)
t_double = pm.Normal('t_double', mu=4, sd=20)
t_delay = pm.Normal('t_delay', mu=21, sd=20)
nu = pm.Uniform('nu', lower=0, upper=20)
# Some functions needed for calculation of the y estimator
def T(eqd):
doses = np.array([52.08, 58.44, 60.0, 65.0, 65.10,
66.0, 70.0, 87.5, 110.0, 126.0])
tmt_times = np.array([29,29,43,29,36,48,22,11,7,8])
return np.interp(eqd, doses, tmt_times)
def TCP(a):
time = T(x)
BCP = pm.exp(-1E7*pm.exp(-alpha*x*1.2 + 0.69315/t_delay(time-t_double)))
return pm.prod(BCP)
def normpdf(a, alpha, sig_alpha):
return 1./(sig_alpha*pm.sqrt(2.*np.pi))*pm.exp(-pm.sqr(a-alpha)/(2*pm.sqr(sig_alpha)))
def normcdf(a, alpha, sig_alpha):
return 1./2.*(1+pm.erf((a-alpha)/(sig_alpha*pm.sqrt(2))))
def integrand(a):
return normpdf(a,alpha,sig_alpha)/(1.-normcdf(0,alpha,sig_alpha))*TCP(a)
func = th.function([a,alpha,sig_alpha,t_double,t_delay], integrand(a))
y_est = sp.integrate.quad(func(a, alpha, sig_alpha,t_double,t_delay), 0, np.inf)[0]
likelihood = pm.T('TCP', mu=y_est, nu=nu, observed=y_tcp)
start = pm.find_MAP()
step = pm.NUTS(state=start)
trace = pm.sample(2000, step, start=start, progressbar=True)
which produces the following message regarding the expression for y_est:
TypeError: ('Bad input argument to theano function with name ":42" at index 0(0-based)', 'Expected an array-like object, but found a Variable: maybe you are trying to call a function on a (possibly shared) variable instead of a numeric array?')
I've overcome various other hurdles to get this far, and this is where I'm stuck. So, provided the answer to my first question is 'yes', then am I on the right track? Any guidance would be helpful!
N.B. Here is a similar question I found, and another.
Disclaimer: I'm very new at this. My only previous experience is successfully reproducing the linear regression example in Thomas' post. I've also successfully run the Theano test suite, so I know it works.
Yes, its possible to make something with a complex or arbitrary likelihood. Though that doesn't seem like what you're doing here. It looks like you have a complex transformation of one variable into another, the integration step.
Your particular exception is that integrate.quad is expecting a numpy array, not a pymc Variable. If you want to do quad within pymc, you'll have to make a custom theano Op (with derivative) for it.