Operands Could not be Broadcast with Shapes (19,)(0,) -- KNN - numpy

I am working on how to use KNN to predict a rating for a movie. I use a video and a book to teach myself how to go about it
I tried to run the code I found in the book but it gave me error message. I googled the error message so as to understand it and fix my problem but I don't think I know how to adapt the solutions to my problem.
import numpy as np
import pandas as pd
r_cols = ['user_id', 'movie_id', 'rating']
ratings = pd.read_csv('C:/Users/dell/Downloads/DataScience/DataScience-Python3/ml-100k/u.data', sep='\t', engine='python', names=r_cols, usecols=range(3)) # please enter your file path here. The file is u.data
print(ratings.head())
movieProperties = ratings.groupby('movie_id').agg({'rating': [np.size, np.mean]})
print(movieProperties.head())
movieNumRatings = pd.DataFrame(movieProperties['rating']['size'])
movieNormalizedNumRatings = movieNumRatings.apply(lambda x: (x - np.min(x)) / (np.max(x) - np.min(x)))
print(movieNormalizedNumRatings.head())
movieDict = {}
with open('C:/Users/dell/Downloads/DataScience/DataScience-Python3/ml-100k/u.item') as f: # The file is u.item
temp = ''
for line in f:
fields = line.rstrip('\n').split('|')
movieID = int(fields[0])
name = fields[1]
genres = fields[5:25]
genres = map(int, genres)
movieDict[movieID] = (name, genres, movieNormalizedNumRatings.loc[movieID].get('size'), movieProperties.loc[movieID].rating.get('mean'))
print(movieDict[1])
from scipy import spatial
def ComputeDistance(a, b):
genresA = np.array(list(a[1]))
genresB = np.array(list(b[1]))
genreDistance = spatial.distance.cosine(genresA, genresB)
popularityA = np.array(a[2])
popularityB = np.array(b[2])
popularityDistance = abs(popularityA - popularityB)
return genreDistance + popularityDistance
print(ComputeDistance(movieDict[2], movieDict[4]))
import operator
def getNeighbors(movieID, K):
distances = []
for movie in movieDict:
if (movie != movieID):
dist = ComputeDistance(movieDict[movieID], movieDict[movie])
distances.append((movie, dist))
distances.sort(key=operator.itemgetter(1))
neighbors = []
for x in range(K):
neighbors.append(distance[x][0])
return neighbors
K = 10
avgRating = 0
neighbors = getNeighbors(1, K)
I got this error message from PowerShell:
Traceback(most recent call last):
neighbors = getNeighbors(1, K)
dist = ComputeDistance(movieDict[movieID], movieDict[movie])
genreDistance = spatial.distance.cosine(genresA, genresB)
return correlation(u, v, w=w, centered=False)
uv = np.average(u*v, weights=w)
ValueError: operands could not be broadcast together with shape (19,)(0,)
I got this error message when I tried to debug the problem from ipython terminal:
c:\programdata\anaconda3\lib\site-packages\scipy\spatial\distance.py(695)correlation()
693 u = u - umu
694 v = v - vmu
---> 695 uv = np.average(u*v, weights=w)
696 uu = np.average(np.square(u), weights=w)
697 vv = np.average(np.square(v), weights=w)
**Note**: The code ran fine and produced results up until *print(Cprint(ComputeDistance(movieDict[2], movieDict[4]))*
My guess is the problem is with this part of the code:
import operator
def getNeighbors(movieID, K):
distances = []
for movie in movieDict:
if (movie != movieID):
dist = ComputeDistance(movieDict[movieID], movieDict[movie])
distances.append((movie, dist))
distances.sort(key=operator.itemgetter(1))
neighbors = []
for x in range(K):
neighbors.append(distance[x][0])
return neighbors
K = 10
avgRating = 0
neighbors = getNeighbors(1, K)
The code can be found in this link: https://hendra-herviawan.github.io/Movie-Recommendation-based-on-KNN-K-Nearest-Neighbors.html

The error of "operands could not be broadcast together with shape (x,)(y,)" usually raises when you are trying to perform an operation between two arrays that must have the same shape but they don't. In your case you are trying to take an weighted average between two arrays u and v. The arrays u and v don't have the length.
I saw that you parsing a movies list by splitting the lines with the "|" character and then storing these results in a dictionary. Probably this file or its division with "|" are returning different results.
The error log shows that the second array doesn't have any element, this could be generated by an empty line on the movies files.

Related

AttributeError: 'list' object has no attribute 'reshape'. for big frames

this is my code. and i don't know what is the problem. the my goal is read more number frames and then convert them to array and finally split them to train and test data.
def read_frames(PATH, num1, num2,seq_len,count,num):
directory = os.listdir(PATH)
for i in range(num1,num2):
source_folder = PATH + '/' +'{}'.format(directory[i])
print("appending the images is started for:", directory[i])
for item in sorted(os.listdir(source_folder), key = len):
img = Image.open(os.path.join(source_folder, item))
frames.append(item)
x.append(np.asarray(img))
count+=1
if count == seq_len:
break
this is a function that read the frames from the path and convert them to array. seq_len is the number of frames.i read the frames in 3 parts. 2 parts using the function that mentioned and other part is:
seq_len = 1624
frames = []
x = []
y = []
w=[]
count = 0
num = 0
PATH = ""
directory = os.listdir(PATH)
print("#.................reading and appending the frames for PART1 are started...........#","\n")
for i in range(0, len(directory)):
source_folder = "PATH/{}".format(directory[i])
print(num)
# print(source_folder)
print("appending the images is started for:", directory[i])
for item in sorted(os.listdir(source_folder), key = len):
# print(item)
# print(count)
img = Image.open(os.path.join(source_folder, item))
frames.append(item)
x.append(np.asarray(img))
count+=1
if count == seq_len:
break
the total number of frames that reading from 3 parts are 333060.
when running this cell:
w = np.array(x)
print('w_shape: ', np.array(w, dtype='uint8').shape)
i expected that the output be (333060,224,224,3) but it is not. and i face this error.
ValueError: setting an array element with a sequence.
when the number of frames are not more this error doesn't happening and when the number of frames are more i face with that error. i using this frames for my pre-trained cnn + lstm network.
please help me to solve that.

can i use OR-tools for TSP with partial distance matrix (for a huge set of nodes)?

i'm trying to solve tsp with OR-tools for a problem of something like 80,000 nodes, the problem is, I need a huge distance matrix that takes to much memory ,so its infeasible and i don't get a solution.
so:
is there an option to work with partial distance matrix in or-tools?
if not is there a way to improve my code?
is there another external solver that can work for this task in python?
import math
from collections import namedtuple
import random
import time
from collections import namedtuple
from sklearn.metrics.pairwise import euclidean_distances
import numpy as np
import numba
from scipy.spatial import distance_matrix
from sklearn.metrics.pairwise import euclidean_distances
from math import sqrt
Point = namedtuple("Point", ['x', 'y'])
def solve_it(input_data):
# Modify this code to run your optimization algorithm
global POINTS
# parse the input
lines = input_data.split('\n')
nodeCount = int(lines[0])
points = []
for i in range(1, nodeCount+1):
line = lines[i]
parts = line.split()
points.append(Point(float(parts[0]), float(parts[1])))
#2.routing with or tools
def dist_matrix(nodeCount,points):
data=[]
for k in range(len(points)):
data.append([int(points[k].x),int(points[k].y)])
D=euclidean_distances(data, data)
return D
def create_data_model(D):
"""Stores the data for the problem."""
data = {}
data['distance_matrix'] = D # yapf: disable
data['num_vehicles'] = 1
data['depot'] = 0
return data
def print_solution(manager, routing, solution):
index = routing.Start(0)
plan_output = []#Route for vehicle 0:\n'
route_distance = 0
while not routing.IsEnd(index):
plan_output.append(manager.IndexToNode(index))
index = solution.Value(routing.NextVar(index))
return plan_output
def or_main(nodeCount,points):
from ortools.constraint_solver import routing_enums_pb2
from ortools.constraint_solver import pywrapcp
"""Entry point of the program."""
# Instantiate the data problem.
global sol
D=dist_matrix(nodeCount,points)
data = create_data_model(D)
# Create the routing index manager.
manager = pywrapcp.RoutingIndexManager(len(data['distance_matrix']),
data['num_vehicles'], data['depot'])
# Create Routing Model.
routing = pywrapcp.RoutingModel(manager)
def distance_callback(from_index, to_index):
"""Returns the distance between the two nodes."""
# Convert from routing variable Index to distance matrix NodeIndex.
from_node = manager.IndexToNode(from_index)
to_node = manager.IndexToNode(to_index)
return data['distance_matrix'][from_node][to_node]
transit_callback_index = routing.RegisterTransitCallback(distance_callback)
# Define cost of each arc.
routing.SetArcCostEvaluatorOfAllVehicles(transit_callback_index)
# Setting first solution heuristic.
search_parameters = pywrapcp.DefaultRoutingSearchParameters()
search_parameters.local_search_metaheuristic = (
routing_enums_pb2.LocalSearchMetaheuristic.GUIDED_LOCAL_SEARCH)
k = 100
if nodeCount <= 100:
k = 30
elif 100 <= nodeCount <= 1000:
k = 300
elif nodeCount > 1000:
k = 17000
search_parameters.time_limit.seconds =k
search_parameters.log_search = True
# Solve the problem.
solution = routing.SolveWithParameters(search_parameters)
# #print solution on console.
if solution:
sol=print_solution(manager, routing, solution)
return sol
######################################################################
solution=or_main(nodeCount,points)
# calculate the length of the tour
obj = length(points[solution[-1]], points[solution[0]])
for index in range(0, nodeCount-1):
obj += length(points[solution[index]], points[solution[index+1]])
# prepare the solution in the specified output format
output_data = '%.2f' % obj + ' ' + str(0) + '\n'
output_data += ' '.join(map(str, solution))
return output_data
if __name__ == '__main__':
import sys
if len(sys.argv) > 1:
file_location = sys.argv[1].strip()
with open(file_location, 'r') as input_data_file:
input_data = input_data_file.read()
#print(solve_it(input_data))
else:
print('This test requires an input file. Please select one from the data directory. (i.e. python solver.py ./data/tsp_51_1)')

How to calculate cosine similarity given sparse matrix data in TensorFlow?

I'm supposed to change part of a python script on the GitHub website. This code is an attention-based similarity measure, but I want to turn it to cosine similarity.
The respective code is in the layers.py file (inside the call method).
Attention-Based:
def __call__(self, inputs):
x = inputs
# dropout
if self.sparse_inputs:
x = sparse_dropout(x, 1-self.dropout, self.num_features_nonzero)
else:
x = tf.nn.dropout(x, 1-self.dropout)
# graph learning
h = dot(x, self.vars['weights'], sparse=self.sparse_inputs)
N = self.num_nodes
edge_v = tf.abs(tf.gather(h,self.edge[0]) - tf.gather(h,self.edge[1]))
edge_v = tf.squeeze(self.act(dot(edge_v, self.vars['a'])))
sgraph = tf.SparseTensor(indices=tf.transpose(self.edge), values=edge_v, dense_shape=[N, N])
sgraph = tf.sparse_softmax(sgraph)
return h, sgraph
I edited the above code to what I believe are my requirements (cosine similarity). However, when I run the following code, like so:
def __call__(self, inputs):
x = inputs
# dropout
if self.sparse_inputs:
x = sparse_dropout(x, 1-self.dropout, self.num_features_nonzero)
else:
x = tf.nn.dropout(x, 1-self.dropout)
# graph learning
h = dot(x, self.vars['weights'], sparse=self.sparse_inputs)
N = self.num_nodes
h_norm = tf.nn.l2_normalize(h)
edge_v = tf.matmul(h_norm, tf.transpose(h_norm))
h_norm_1 = tf.norm(h_norm)
edge_v /= h_norm_1 * h_norm_1
edge_v = dot(edge_v, self.vars['a']) # It causes an error when I add this line
zero = tf.constant(0, dtype=tf.float32)
where = tf.not_equal(edge_v, zero)
indices = tf.where(where)
values = tf.gather_nd(edge_v, indices)
sgraph = tf.SparseTensor(indices, values, dense_shape= [N,N])
return h, sgraph
The script shows some runtime errors:
Screenshot of error message
I suspect the error here is related to line 226:
edge_v = dot(edge_v, self.vars['a']) # It causes an error when I add this line
Any admonition on how to accomplish this successfully?
Link of the script on GitHub:
https://github.com/jiangboahu/GLCN-tf
Note: I don't want to use built-in functions, because I think they are not precise to do this job.
ETA: It appears that there are some answers around but they seem to tackle different problems, as far, as I understood them.
Thanks a bunch in advance
What's the dot? Have you imported the method?
It should either be:
edge_v = tf.keras.backend.dot(edge_v, self.vars['a'])
or
edge_v = tf.tensordot(edge_v, self.vars['a'])

dask how to define a custom (time fold) function that operates in parallel and returns a dataframe with a different shape

I am trying to implement a time fold function to be 'map'ed to various partitions of a dask dataframe which in turn changes the shape of the dataframe in question (or alternatively produces a new dataframe with the altered shape). This is how far I have gotten. The result 'res' returned on compute is a list of 3 delayed objects. When I try to compute each of them in a loop (last tow lines of code) this results in a "TypeError: 'DataFrame' object is not callable" After going through the examples for map_partitions, I also tried altering the input DF (inplace) in the function with no return value which causes a similar TypeError with NoneType. What am I missing?
Also, looking at the visualization (attached) I feel like there is a need for reducing the individually computed (folded) partitions into a single DF. How do I do this?
#! /usr/bin/env python
# Start dask scheduler and workers
# dask-scheduler &
# dask-worker --nthreads 1 --nprocs 6 --memory-limit 3GB localhost:8786 --local-directory /dev/shm &
from dask.distributed import Client
from dask.delayed import delayed
import pandas as pd
import numpy as np
import dask.dataframe as dd
import math
foldbucketsecs=30
periodicitysecs=15
secsinday=24 * 60 * 60
chunksizesecs=60 # 1 minute
numts = 5
start = 1525132800 # 01/05
end = 1525132800 + (3 * 60) # 3 minute
c = Client('127.0.0.1:8786')
def fold(df, start, bucket):
return df
def reduce_folds(df):
return df
def load(epoch):
idx = []
for ts in range(0, chunksizesecs, periodicitysecs):
idx.append(epoch + ts)
d = np.random.rand(chunksizesecs/periodicitysecs, numts)
ts = []
for i in range(0, numts):
tsname = "ts_%s" % (i)
ts.append(tsname)
gts.append(tsname)
res = pd.DataFrame(index=idx, data=d, columns=ts, dtype=np.float64)
res.index = pd.to_datetime(arg=res.index, unit='s')
return res
gts = []
load(start)
cols = len(gts)
idx1 = pd.DatetimeIndex(start=start, freq=('%sS' % periodicitysecs), end=start+periodicitysecs, dtype='datetime64[s]')
meta = pd.DataFrame(index=idx1[:0], data=[], columns=gts, dtype=np.float64)
dfs = [delayed(load)(fn) for fn in range(start, end, chunksizesecs)]
from_delayed = dd.from_delayed(dfs, meta, 'sorted')
nfolds = int(math.ceil((end - start)/foldbucketsecs))
cprime = nfolds * cols
gtsnew = []
for i in range(0, cprime):
gtsnew.append("ts_%s,fold=%s" % (i%cols, i/cols))
idx2 = pd.DatetimeIndex(start=start, freq=('%sS' % periodicitysecs), end=start+foldbucketsecs, dtype='datetime64[s]')
meta = pd.DataFrame(index=idx2[:0], data=[], columns=gtsnew, dtype=np.float64)
folded_df = from_delayed.map_partitions(delayed(fold)(from_delayed, start, foldbucketsecs), meta=meta)
result = c.submit(reduce_folds, folded_df)
c.gather(result).visualize(filename='/usr/share/nginx/html/svg/df4.svg')
res = c.gather(result).compute()
for f in res:
f.compute()
Never mind! It was my fault, instead of wrapping my function in delayed I simply passed it to the map_partitions call like so and it worked.
folded_df = from_delayed.map_partitions(fold, start, foldbucketsecs, nfolds, meta=meta)

Odd-size numpy arrays send/receive

I would like to gather numpy array contents from all processors to one. In case all arrays are of the same size, it works. However I don't see a natural way of doing the same task for arrays of proc-dependent size. Please consider the following code:
from mpi4py import MPI
import numpy
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
if rank >= size/2:
nb_elts = 5
else:
nb_elts = 2
# create data
lst = []
for i in xrange(nb_elts):
lst.append(rank*3+i)
array_lst = numpy.array(lst, dtype=int)
# communicate array
result = []
if rank == 0:
result = array_lst
for p in xrange(1, size):
received = numpy.empty(nb_elts, dtype=numpy.int)
comm.Recv(received, p, tag=13)
result = numpy.concatenate([result, received])
else:
comm.Send(array_lst, 0, tag=13)
My problem is at the "received" allocation. How can I know what is the size to be allocated? Do I have to first send/receive each array size?
Based on a suggestion below, I'll go with
data_array = numpy.ones(rank + 3, dtype=int)
data_array *= rank + 5
print '[{}] data: {} ({})'.format(rank, data_array, type(data_array))
# make all processors aware of data array sizes
all_sizes = {rank: data_array.size}
gathered_all_sizes = comm_py.allgather(all_sizes)
for d in gathered_all_sizes:
all_sizes.update(d)
# prepare Gatherv as described by #francis
nbsum = 0
sendcounts = []
displacements = []
for p in xrange(size):
n = all_sizes[p]
displacements.append(nbsum)
sendcounts.append(n)
nbsum += n
if rank==0:
result = numpy.empty(nbsum, dtype=numpy.int)
else:
result = None
comm_py.Gatherv(data_array,[result, tuple(sendcounts), tuple(displacements), MPI.INT64_T], root=0)
print '[{}] gathered data: {}'.format(rank, result)
In the code you pasted, both Send() and Recv() sends nb_elts elements. The problem is that nb_elts is not the same for every processes... Hence, the number of item received does not match the number of elements that were sent and the program complains:
mpi4py.MPI.Exception: MPI_ERR_TRUNCATE: message truncated
To prevent that, the root process must compute the number of items that the other processes have sent. Hence, in the loop for p in xrange(1, size), nb_elts must be computed according to p, not rank.
The following code based on yours has been corrected. I would add that the natural way to perform this gathering operation is to use Gatherv(). See http://materials.jeremybejarano.com/MPIwithPython/collectiveCom.html and the documentation of mpi4py for instance. I added the corresponding sample code. The only tricky point is that numpy.int is 64bit long. Hence, the Gatherv() uses the MPI type MPI_DOUBLE.
from mpi4py import MPI
import numpy
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
if rank >= size/2:
nb_elts = 5
else:
nb_elts = 2
# create data
lst = []
for i in xrange(nb_elts):
lst.append(rank*3+i)
array_lst = numpy.array(lst, dtype=int)
# communicate array
result = []
if rank == 0:
result = array_lst
for p in xrange(1, size):
if p >= size/2:
nb_elts = 5
else:
nb_elts = 2
received = numpy.empty(nb_elts, dtype=numpy.int)
comm.Recv(received, p, tag=13)
result = numpy.concatenate([result, received])
else:
comm.Send(array_lst, 0, tag=13)
if rank==0:
print "Send Recv, result= "+str(result)
#How to use Gatherv:
nbsum=0
sendcounts=[]
displacements=[]
for p in xrange(0,size):
displacements.append(nbsum)
if p >= size/2:
nbsum+= 5
sendcounts.append(5)
else:
nbsum+= 2
sendcounts.append(2)
if rank==0:
print "nbsum "+str(nbsum)
print "sendcounts "+str(tuple(sendcounts))
print "displacements "+str(tuple(displacements))
print "rank "+str(rank)+" array_lst "+str(array_lst)
print "numpy.int "+str(numpy.dtype(numpy.int))+" "+str(numpy.dtype(numpy.int).itemsize)+" "+str(numpy.dtype(numpy.int).name)
if rank==0:
result2=numpy.empty(nbsum, dtype=numpy.int)
else:
result2=None
comm.Gatherv(array_lst,[result2,tuple(sendcounts),tuple(displacements),MPI.DOUBLE],root=0)
if rank==0:
print "Gatherv, result2= "+str(result2)