Tensorflow while loop : dealing with lists - python-2.7

import tensorflow as tf
array = tf.Variable(tf.random_normal([10]))
i = tf.constant(0)
l = []
def cond(i,l):
return i < 10
def body(i,l):
temp = tf.gather(array,i)
l.append(temp)
return i+1,l
index,list_vals = tf.while_loop(cond, body, [i,l])
I want to process a tensor array in the similar way as described in the above code. In the body of the while loop I want to process the array by element by element basis to apply some function. For demonstration, I have given a small code snippet. However, it is giving an error message as follows.
ValueError: Number of inputs and outputs of body must match loop_vars: 1, 2
Any help in resolving this is appreciated.
Thanks

Citing the documentation:
loop_vars is a (possibly nested) tuple, namedtuple or list
of tensors that is passed to both cond and body
You cannot pass regular python array as a tensor. What you can do, is:
i = tf.constant(0)
l = tf.Variable([])
def body(i, l):
temp = tf.gather(array,i)
l = tf.concat([l, [temp]], 0)
return i+1, l
index, list_vals = tf.while_loop(cond, body, [i, l],
shape_invariants=[i.get_shape(),
tf.TensorShape([None])])
The shape invariants are there, because normally tf.while_loop expects the shapes of tensors inside while loop won't change.
sess = tf.Session()
sess.run(tf.global_variables_initializer())
sess.run(list_vals)
Out: array([-0.38367489, -1.76104736, 0.26266089, -2.74720812, 1.48196387,
-0.23357525, -1.07429159, -1.79547787, -0.74316853, 0.15982138],
dtype=float32)

TF offers a TensorArray to deal with such cases. From the doc,
Class wrapping dynamic-sized, per-time-step, write-once Tensor arrays.
This class is meant to be used with dynamic iteration primitives such as while_loop and map_fn. It supports gradient back-propagation via special "flow" control flow dependencies.
Here is an example,
import tensorflow as tf
array = tf.Variable(tf.random_normal([10]))
step = tf.constant(0)
output = tf.TensorArray(dtype=tf.float32, size=0, dynamic_size=True)
def cond(step, output):
return step < 10
def body(step, output):
output = output.write(step, tf.gather(array, step))
return step + 1, output
_, final_output = tf.while_loop(cond, body, loop_vars=[step, output])
final_output = final_output.stack()
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
print(sess.run(final_output))

Related

Official ZeroOut gradient example error: AttributeError: 'list' object has no attribute 'eval'

I followed the official tutorial of the tensorflow website: https://www.tensorflow.org/extend/adding_an_op
There is also described how to call the gradient of the example ZeroOut in the tutorial that I want to try in this short code snippet underneath.
I have found the code here: https://github.com/MatteoRagni/tf.ZeroOut.gpu
import numpy as np
import tensorflow as tf
from tensorflow.python.framework import ops
from tensorflow.python.ops import array_ops
from tensorflow.python.ops import sparse_ops
zero_out_module = tf.load_op_library('./libzeroout.so')
#ops.RegisterGradient("ZeroOut")
def _zero_out_grad(op, grad):
to_zero = op.inputs[0]
shape = array_ops.shape(to_zero)
index = array_ops.zeros_like(shape)
first_grad = array_ops.reshape(grad, [-1])[0]
to_zero_grad = sparse_ops.sparse_to_dense([index], shape, first_grad, 0)
return [to_zero_grad] # List of one Tensor, since we have one input
t_in = tf.placeholder(tf.int32, [None,None])
ret = zero_out_module.zero_out(t_in)
grad = tf.gradients(ys=tf.reduce_sum(ret), xs=t_in)
with tf.Session(''):
feed_dict = {t_in: [[1, 2], [3, 4]]}
print "ret val: ", ret.eval(feed_dict=feed_dict)
print "grad: ", grad
print "grad: ", grad.eval(feed_dict=feed_dict)
I got this error ...
AttributeError: 'list' object has no attribute 'eval'
... but I can do ret.eval().
Why I cant call grad.eval()? I want to see these values inside the grad tensor. How to debug gradient?
Answer to old question
The implementation
def _zero_out_grad(op, *grads):
topdiff = grads[0]
bottom = op.inputs[0]
shape = array_ops.shape(bottom)
index = array_ops.zeros_like(shape)
first_grad = array_ops.reshape(topdiff, [-1])[0]
to_zero_grad = sparse_ops.sparse_to_dense([index], shape, first_grad, 0)
return to_zero_grad
works quite nicely here. Are you sure "#ops.RegisterGradient("ZeroOut")" is executed before the tf.Session()?
Usually the
zero_out_module = tf.load_op_library('./libzeroout.so')
#ops.RegisterGradient("ZeroOut")
def _zero_out_grad(op, grad):
# ...
is placed in a different file and just imported. A full working example even with the recent TensorFlow version is here.
Answer to completely changed question
Your gradient function returns a list and a Python list has no 'eval()'. Try either:
grad = tf.gradients(ys=tf.reduce_sum(ret), xs=t_in)[0]
Or follow best practice and use
grad = tf.gradients(ys=tf.reduce_sum(ret), xs=t_in)
with tf.Session() as sess:
sess.run(grad, feed_dict=feed_dict)
Please do not change your entire question

Counting matrix pairs using a threshold

I have a folder with hundreds of txt files I need to analyse for similarity. Below is an example of a script I use to run similarity analysis. In the end I get an array or a matrix I can plot etc.
I would like to see how many pairs there are with cos_similarity > 0.5 (or any other threshold I decide to use), removing cos_similarity == 1 when I compare the same files, of course.
Secondly, I need a list of these pairs based on file names.
So the output for the example below would look like:
1
and
["doc1", "doc4"]
Will really appreciate your help as I feel a bit lost not knowing which direction to go.
This is an example of my script to get the matrix:
doc1 = "Amazon's promise of next-day deliveries could be investigated amid customer complaints that it is failing to meet that pledge."
doc2 = "The BBC has been inundated with comments from Amazon Prime customers. Most reported problems with deliveries."
doc3 = "An Amazon spokesman told the BBC the ASA had confirmed to it there was no investigation at this time."
doc4 = "Amazon's promise of next-day deliveries could be investigated amid customer complaints..."
documents = [doc1, doc2, doc3, doc4]
# In my real script I iterate through a folder (path) with txt files like this:
#def read_text(path):
# documents = []
# for filename in glob.iglob(path+'*.txt'):
# _file = open(filename, 'r')
# text = _file.read()
# documents.append(text)
# return documents
import nltk, string, numpy
nltk.download('punkt') # first-time use only
stemmer = nltk.stem.porter.PorterStemmer()
def StemTokens(tokens):
return [stemmer.stem(token) for token in tokens]
remove_punct_dict = dict((ord(punct), None) for punct in string.punctuation)
def StemNormalize(text):
return StemTokens(nltk.word_tokenize(text.lower().translate(remove_punct_dict)))
nltk.download('wordnet') # first-time use only
lemmer = nltk.stem.WordNetLemmatizer()
def LemTokens(tokens):
return [lemmer.lemmatize(token) for token in tokens]
remove_punct_dict = dict((ord(punct), None) for punct in string.punctuation)
def LemNormalize(text):
return LemTokens(nltk.word_tokenize(text.lower().translate(remove_punct_dict)))
from sklearn.feature_extraction.text import CountVectorizer
LemVectorizer = CountVectorizer(tokenizer=LemNormalize, stop_words='english')
LemVectorizer.fit_transform(documents)
tf_matrix = LemVectorizer.transform(documents).toarray()
from sklearn.feature_extraction.text import TfidfTransformer
tfidfTran = TfidfTransformer(norm="l2")
tfidfTran.fit(tf_matrix)
tfidf_matrix = tfidfTran.transform(tf_matrix)
cos_similarity_matrix = (tfidf_matrix * tfidf_matrix.T).toarray()
from sklearn.feature_extraction.text import TfidfVectorizer
TfidfVec = TfidfVectorizer(tokenizer=LemNormalize, stop_words='english')
def cos_similarity(textlist):
tfidf = TfidfVec.fit_transform(textlist)
return (tfidf * tfidf.T).toarray()
cos_similarity(documents)
Out:
array([[ 1. , 0.1459739 , 0.03613371, 0.76357693],
[ 0.1459739 , 1. , 0.11459266, 0.19117117],
[ 0.03613371, 0.11459266, 1. , 0.04732164],
[ 0.76357693, 0.19117117, 0.04732164, 1. ]])
As I understood your question, you want to create a function that reads the output numpy array and a certain value (threshold) in order to return two things:
how many docs are bigger than or equal the given threshold
the names of these docs.
So, here I've made the following function which takes three arguments:
the output numpy array from cos_similarity() function.
list of document names.
a certain number (threshold).
And here it's:
def get_docs(arr, docs_names, threshold):
output_tuples = []
for row in range(len(arr)):
lst = [row+1+idx for idx, num in \
enumerate(arr[row, row+1:]) if num >= threshold]
for item in lst:
output_tuples.append( (docs_names[row], docs_names[item]) )
return len(output_tuples), output_tuples
Let's see it in action:
>>> docs_names = ["doc1", "doc2", "doc3", "doc4"]
>>> arr = cos_similarity(documents)
>>> arr
array([[ 1. , 0.1459739 , 0.03613371, 0.76357693],
[ 0.1459739 , 1. , 0.11459266, 0.19117117],
[ 0.03613371, 0.11459266, 1. , 0.04732164],
[ 0.76357693, 0.19117117, 0.04732164, 1. ]])
>>> threshold = 0.5
>>> get_docs(arr, docs_names, threshold)
(1, [('doc1', 'doc4')])
>>> get_docs(arr, docs_names, 1)
(0, [])
>>> get_docs(lst, docs_names, 0.13)
(3, [('doc1', 'doc2'), ('doc1', 'doc4'), ('doc2', 'doc4')])
Let's see how this function works:
first, I iterate over every row of the numpy array.
Second, I iterate over every item in the row whose index is bigger than the row's index. So, we are iterating in a traingular shape like so:
and that's because each pair of documents is mentioned twice in the whole array. We can see that the two values arr[0][1] and arr[1][0] are the same. You also should notice that the diagonal items arn't included because we knew for sure that they are 1 as evey document is very similar to itself :).
Finally, we get the items whose values are bigger than or equal the given threshold, and return their indices. These indices are used later to get the documents names.

Convert a concrete model in an abstract one

I am just starting with Pyomo and I have a big problem.
I want to run an Abstract Model without using the terminal. I can do it with a concrete model but I have serious problems to do it in with the abstract one.
I just want to use F5 and run the code.
This ismy program:
import pyomo
from pyomo.environ import *
#
# Model
#
model = AbstractModel()
#Set: Indices
model.Unit = Set()
model.Block = Set()
model.DemBlock = Set()
#Parameters
model.EnergyBid = Param(model.Unit, model.Block)
model.PriceBid = Param(model.Unit, model.Block)
model.EnergyDem = Param(model.DemBlock)
model.PriceDem = Param(model.DemBlock)
model.Pmin = Param(model.Unit)
model.Pmax = Param(model.Unit)
#Variables definition
model.PD = Var(model.DemBlock, within=NonNegativeReals)
model.PG = Var(model.Unit,model.Block, within=NonNegativeReals)
#Binary variable
model.U = Var(model.Unit, within = Binary)
#Objective
def SocialWellfare(model):
SocialWellfare = sum([model.PriceDem[i]*model.PD[i] for i in model.DemBlock]) - sum([model.PriceBid[j,k]*model.PG[j,k] for j in model.Unit for k in model.Block ])
return SocialWellfare
model.SocialWellfare = Objective(rule=SocialWellfare, sense=maximize)
#Constraints
#Max and min Power generated
def PDmax_constraint(model,p):
return ((model.PD[p] - model.EnergyDem[p])) <= 0
model.PDmax = Constraint(model.DemBlock, rule=PDmax_constraint)
def PGmax_constraint(model,n,m):
return ((model.PG[n,m] - model.EnergyBid[n,m])) <= 0
model.PGmax = Constraint(model.Unit, model.Block,rule = PGmax_constraint)
def Power_constraintDW(model,i):
return ((sum(model.PG[i,k] for k in model.Block))-(model.Pmin[i] * model.U[i]) ) >= 0
model.LimDemandDw = Constraint(model.Unit, rule=Power_constraintDW)
def Power_constraintUP(model,i):
return ((sum(model.PG[i,k] for k in model.Block) - (model.Pmax[i])*model.U[i])) <= 0
model.LimDemandaUp = Constraint(model.Unit, rule=Power_constraintUP)
def PowerBalance_constraint(model):
return (sum(model.PD[i] for i in model.DemBlock) - sum(model.PG[j,k] for j in model.Unit for k in model.Block)) == 0
model.PowBalance = Constraint(rule = PowerBalance_constraint)
model.pprint()
instance = model.create('datos_transporte.dat')
## Create the ipopt solver plugin using the ASL interface
solver = 'ipopt'
solver_io = 'nl'
opt = SolverFactory(solver,solver_io=solver_io)
results = opt.solve(instance)
results.write()
Any help with the last part??
Thanks anyway,
I think your example is actually working. Starting in Pyomo 4.1, the solution returned from the solver is stored directly into the instance that was solved, and is not returned in the solver results object. This change was made because generating the representation of the solution in the results object was rather expensive and was not easily parsed by people. Working with the model instance directly is more natural.
It is unfortunate that the results object reports the number of solutions: 0, although this is technically correct: the results object holds no solutions ... but the Solver section should indicate that a solution was returned and stored into the model instance.
If you want to see the result returned by the solver, you can print out the current status of the model using:
instance.display()
after the call to solve(). That will report the current Var values that were returned from the solver. You will want to pay attention to the stale column:
False indicates the value is not "stale" ... that is, it was either set by the user (before the call to solve()), or it was returned from the solver (after the call to solve()).
True indicates the solver did not return a value for that variable. This is usually because the variable was not referenced by the objective or any enabled constraints, so Pyomo never sent the variable to the solver.
[Note: display() serves a slightly different role than pprint(): pprint() outputs the model structure, whereas display() outputs the model state. So, for example, where pprint() will output the constraint expressions, display() will output the numerical value of the expression (using the current variable/param values).]
Edited to expand the discussion of display() & pprint()

How to sort python lists due to certain criteria

I would like to sort a list or an array using python to achive the following:
Say my initial list is:
example_list = ["retg_1_gertg","fsvs_1_vs","vrtv_2_srtv","srtv_2_bzt","wft_3_btb","tvsrt_3_rtbbrz"]
I would like to get all the elements that have 1 behind the first underscore together in one list and the ones that have 2 together in one list and so on. So the result should be:
sorted_list = [["retg_1_gertg","fsvs_1_vs"],["vrtv_2_srtv","srtv_2_bzt"],["wft_3_btb","tvsrt_3_rtbbrz"]]
My code:
import numpy as np
import string
example_list = ["retg_1_gertg","fsvs_1_vs","vrtv_2_srtv","srtv_2_bzt","wft_3_btb","tvsrt_3_rtbbrz"]
def sort_list(imagelist):
# get number of wafers
waferlist = []
for image in imagelist:
wafer_id = string.split(image,"_")[1]
waferlist.append(wafer_id)
waferlist = set(waferlist)
waferlist = list(waferlist)
number_of_wafers = len(waferlist)
# create list
sorted_list = []
for i in range(number_of_wafers):
sorted_list.append([])
for i in range(number_of_wafers):
wafer_id = waferlist[i]
for image in imagelist:
if string.split(image,"_")[1] == wafer_id:
sorted_list[i].append(image)
return sorted_list
sorted_list = sort_list(example_list)
works but it is really awkward and it involves many for loops that slow down everything if the lists are large.
Is there any more elegant way using numpy or anything?
Help is appreciated. Thanks.
I'm not sure how much more elegant this solution is; it is a bit more efficient. You could first sort the list and then go through and filter into final set of sorted lists:
example_list = ["retg_1_gertg","fsvs_1_vs","vrtv_2_srtv","srtv_2_bzt","wft_3_btb","tvsrt_3_rtbbrz"]
sorted_list = sorted(example_list, key=lambda x: x[x.index('_')+1])
result = [[]]
current_num = sorted_list[0][sorted_list[0].index('_')+1]
index = 0
for i in example_list:
if current_num != i[i.index('_')+1]:
current_num = i[i.index('_')+1]
index += 1
result.append([])
result[index].append(i)
print result
If you can make assumptions about the values after the first underscore character, you could clean it up a bit (for example, if you knew that they would always be sequential numbers starting at 1).

Construct a matrix in openCV based on a given matrix

I am writing some code using the OpenCV library in Python. In the process, I need to construct a matrix based on another matrix given. Now my code looks like the following:
for x in range(0, width):
for y in range(0, height):
if I_mat[x][y]>=0 and I_mat[x][y]<=c_low:
w_mat[x][y] = float(I_mat[x][y])/c_low
elif I_mat[x][y]>c_low and I_mat[x][y]<c_high:
w_mat[x][y] = 1
else:
w_mat[x][y] = float((255-I_mat[x][y]))/float((255-c_high))
where, I_mat is the input matrix and w_mat is the matrix I am going to construct. Since the input matrix is quite large, this algorithm is quite slow. I wonder if there are any other methods to construct w_mat more efficiently. Thank a lot!
(It is not necessary to show the solution in Python.)
edit:you might want to use numba
import numpy as np
import timeit
from numba import void,jit
c_low = .3
c_high = .6
def func(val):
if val>=0 and val<=c_low:
return float(val)/c_low
elif val>c_low and val<c_high:
return 1.
else:
return (255.-val)/(255.-c_high)
def npvectorize():
global w_mat
vfunc = np.vectorize(func)
w_mat = vfunc(I_mat)
def orig():
for x in range(I_mat.shape[0]):
for y in range(I_mat.shape[1]):
if I_mat[x][y]>=0 and I_mat[x][y]<=c_low:
w_mat[x][y] = float(I_mat[x][y])/c_low
elif I_mat[x][y]>c_low and I_mat[x][y]<c_high:
w_mat[x][y] = 1
else:
w_mat[x][y] = float((255-I_mat[x][y]))/float((255-c_high))
I_mat = np.array(np.random.random((1000,1000)), dtype = np.float)
w_mat = np.empty_like(I_mat)
fast = jit(void(),nopython=True)(orig)
print timeit.Timer(fast).timeit(1)
print timeit.Timer(npvectorize).timeit(1)
print timeit.Timer(orig).timeit(1)
output:
0.0352660446331
0.472590475098
4.78634474265