# Questions tagged [numpy-ndarray]

221 questions

-2

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0

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14

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### Efficient way to calculate matrix cell distance from arbitrary coordinate in numpy

I am looking for an efficient numpy solution to the following problem:
I have a N by N numpy matrix. Given an arbitrary i,j coordinate (can be decimal) of the matrix and an arbitrary range, I need to calculate the value of each cell of the matrix divided by its euclidian distance to the coordinate w...

1

votes

3

answer

92

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### Subtracting minimum of row from the row

I know that
a - a.min(axis=0)
will subtract the minimum of each column from every element in the column. I want to subtract the minimum in each row from every element in the row. I know that
a.min(axis=1)
specifies the minimum within a row, but how do I tell the subtraction to go by rows instead...

1

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4

answer

76

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### Increasing the speed of finding an index of an item in list

I'm trying to speed up a program I've written, and after importing cProfile, I see that one function takes up a massive bit of computation time.
It's this, which finds an numpy.ndarray in a list:
def locate(arr, l ):
for i in range(len(l)):
if np.all(l[i] == arr):
return i
return -1
As the list can'...

1

votes

2

answer

150

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### Python numpy array negative indexing

I'm a bit confused about the indexing of numpy. Assume the following example:
>>> import numpy as np
>>> x = np.arange(10)
>>> x.shape = (2,5)
>>> x
array([[0, 1, 2, 3, 4],
[5, 6, 7, 8, 9]])
>>> x[0:-1]
array([[0, 1, 2, 3, 4]])
>>> x[1:-1]
array([], shape=(0, 5), dtype=int64)
>>> x[1:]
array([[5, 6,...

1

votes

2

answer

39

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### Numpy optimized reshape : 2D array to 3D

I was wondering if there is a more pythonic/efficient way of reshaping my 2d-array into a 3d-array ? Here is the following working code :
import numpy as np
#
# Declaring the dimensions
n_ddl = 2
N = 3
n_H = n_ddl*N
#
# Typical 2D array to reshape
x_tilde_2d = np.array([[111,112,121,122,131,132],[21...

1

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1

answer

39

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### Check if two 3D numpy arrays contain overlapping 2D arrays

I have two very large numpy arrays, which are both 3D. I need to find an efficient way to check if they are overlapping, because turning them both into sets first takes too long. I tried to use another solution I found here for this same problem but for 2D arrays, but I didn't manage to make it work...

1

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3

answer

39

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### How can I multiply more than 3 vectors at once in NumPy

I'm looking for a vectorised way to multiply more than 3 vectors in NumPy.
As an example,
X = np.array([1,2,3])
Y = np.array([4,5,6])
Z = np.array([7,8,9])
Multiply([X,Y,Z])
would produce as an output
np.array([28, 80, 162])
The vectors I want to multiply need not to be defined separately as I did a...

1

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2

answer

54

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### how to change a dimension of array in python?

I am a newbie in python. I have a question about the dimension of array.
I have (10,192,192,1) array which type is (class 'numpy.ndarray').
I would like to divid this array to 10 separated array like 10 * (1,192,192,1). but I always got (192,192,1) array when I separate.
How can I get separated arra...

1

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0

answer

37

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### “ 'numpy.ndarray' object is not callable” error occurs when I get dictionary keys into a list

My dictionay items are as follows,
dict_items([(3.0, 0), (2.0, 23), (1.0, 30), (4.0, 41)])
I need to access these dictionary values in terms of the key's index.In order to do that, I used index=list(positions.keys()).pop(0)
It renders an error as follows.
TypeError: 'numpy.ndarray' object is not cal...

1

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0

answer

21

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### Searching a smaller array in a larger array and returning the indices of larger array

I am working on Feature Selection. I got the selected features but instead of manually searching each time which features are selected, is there any built-in method in python that compare the first row (smaller array) of selected features to the first row of full features(larger array) and return th...

1

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0

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27

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### numpy slicing screws image colors (werid)

I have an RGB image as an ndarray
print(img.shape)
>>> (64, 64, 3)
I want to store a bunch of images into another ndarray:
batch = np.empty((64, 64, 3, 2))
batch[...,0] = img
Now if I do
plt.imshow(img)
everything is looks fine. But if I do
plt.imshow(batch[...,0])
the colors are messed up! It looks...

1

votes

0

answer

33

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### Size of objects in Numpy Array: Sympy Points example

Here is attached some code in which it is attempted to instantiate a Numpy Array of Sympy Points given their coordinates.
from sympy.geometry import Point
import numpy as np
coordinates = np.array([2,0, 1,-1, 0,0, -2,3, -3,-2, 0.01,-0.01]).reshape(6,2)
v1 = np.empty((coordinates.shape[0],),dtype=np...

1

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1

answer

38

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### What affects tensorlayer.prepro.threading_data's return type?

I've been trying to use tensorlayer.prepro.threading_data, but I'm getting a different return type for different inputs. Sometimes it returns an ndarray and sometimes it returns a list. The documentation doesn't specify what's the reason for the different return types.
Can anyone shed some light on...

1

votes

1

answer

834

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### ValueError: could not convert string to float: 'lisans' in Python

I am trying to calculate the silhouette index of the output of k-prototypes algorithm to cluster mixed featured dataset. I am getting ValueError: could not convert string to float: 'lisans' as an error, even if my code works fine when I only execute k-prototypes algorithm. My input is an excel file,...

1

votes

0

answer

64

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### How to define the sampling rate in a 3D numpy array for a multi frame TIFF file?

I have a multi frame TIF file which is a recording of neuronal fluorescence intensity changes over time.
The TIF file has 80 x 60 pixels and 2000 frames.
I would like to analyse the frequency of the fluorescence intensity changes for each pixel and for that I would need to define the sampling rate o...

1

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1

answer

167

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### NumPy saving an object with arrays of different shape but same leading dimension

I experienced some unexpected behavior of np.save().
Assume, you want to save two numpy arrays into one .npy file (as an object). As long both arrays have the same shape this works without any problem, but when the leading dimension is the same an error occurs.
The problem is caused by np.asanyarray...

1

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0

answer

54

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### Rotate a float ndarray without changing the values

I'd like to rotate a numpy array like this
[[0. 0.... 0.771... 0. 0.162 0. ...]
[0.987 0.... 0.074 0. 0... 0. ...]
[...]]
I'm using scipy.ndimage.rotate.
Here is my code:
matrix = read_mat_file(file_name).reshape((shape[0],shape[1]))
matrix_rot = scipy.ndimage.rotate(matrix, angle=60, reshap...

1

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0

answer

25

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### Numpy, same value inputs get different dot product

I want to get the dot product of matrix X and Adjugate(X) in Python, Numpy, I tried both methods found from here. The adjugate from both method give same answer but when I perform dot product, different answers were given. Here is the code:
#first method
def CM(A):
row, col = A.shape
minor = np.zero...

1

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2

answer

80

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### How to merge 2 numpy ndarray on a ndarray using values of a column?

I have 2 ndarray:
a = np.array([[1,2], [5,0], [6,4]])
b = np.array([[1,10],[6,30], [5,20]])
I wish merge them in a array as this:
[[ 1 2 10]
[ 5 0 20]
[ 6 4 30]]
Someone knows a not iterative mode to merge 2 array by values of column 0?
I've found only this way:
import numpy as np
a = np.array([[...

1

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1

answer

120

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### Multi-dimensional indexing of 4d numpy array

I have two 3d volumes stacked in a 4d array with dimensions 2x5x5x5.
If I want to get the values of some/all voxel for a single 3d volume, I can use three vectors and get the following:
x_new_mesh, y_new_mesh, z_new_mesh = np.meshgrid(np.arange(m),
np.arange(n),
np.arange(p))
x_new = x_new_mesh.fl...

1

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0

answer

126

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### boost::python linking error (undefined reference to numpy::empty and numpy::detail::get_float_dtype<64>()) when using templates

I'm experiencing difficulties working with boost::python and boost::python::numpy, with python 2.7, boost 1.67.0, and Eigen3.3. My compiler is g++ (Ubuntu 5.4.0-6ubuntu1~16.04.10) 5.4.0.
I'm trying to convert Eigen::Matrix types to python ndarray and back (vector_list.hpp):
#ifndef VECTOR_PYLIST_HH...

1

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0

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140

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### How to convert image in TensorProto in Java

I have written python client for converting my image in TensorProto which I am sending in the predict request. However, I have a need of writing similar client in Java.
Below is my python code:
def run():
host= 'localhost'
port= '9000'
request = tensorflow__serving_dot_apis_dot_predict__pb2.Predict...

1

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0

answer

49

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### overwriting “|” operator to concatenate numpy arrays

I am wondering how to overload/overwrite the | operator to concatenate (two-dimensional) numpy arrays along the second axis, so that
u = np.array([[7], [8], [9]])
v = np.array([[1, 2], [3, 4], [5, 6]])
w = u | v
produces the same result as
u = np.array([[7], [8], [9]])
v = np.array([[1, 2], [3, 4],...

1

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0

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50

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### integral over a cone

Is there a fast way (standard or via some library) to compute integrals over cones in python?
I.e. I have an array A containing some values and I want to compute and integral over an index cone specified by numbers in array sliceNums. I can do it directly:
n = 10; m=100 # jus...

1

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1

answer

61

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### How to apply an index-dependent function to a numpy ndarray?

So numpy ndarrays are quite handy in that you can just type in f(A) for any one-dimensional function f and any ndarray A and it will apply f element-wise. It is also, I was told, a very efficient way of applying a function to a ndarray and avoiding for loops. Avoid for loops, is what I have been tol...

1

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0

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23

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### Profiling TensorFlow Code to improve efficiency

I’m new to tensorflow. I takes images and returns a preference score for each image, using a pre-trained siamese cnn model. I would like to figure out what parts of my code are expensive. Is there a way to do that with tensorflow or tensorboard? Or does anyone see what parts of my code could b...

1

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1

answer

45

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### Error when trying to round values in an ndarray

I am working on a memory-based collaborative filtering algorithm. I am building a matrix that I want to write into CSV file that contains three columns: users, app and ratings.
fid = fopen('pred_ratings.csv','wt');
for i=1:user_num
for j=1:item_num
if R(j,i) == 1
entry = Y(j,i);
else
entry = round(P...

1

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0

answer

43

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### .wav file to numpay array

I am new to python language, i have around 100 of .wav file sample which i want to read from my pc and convert them into numpy-array and gave output of my files. but i can not achieve that until now. So i need help
i am following this but i got to know that i just giving irrelevant output because it...

1

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1

answer

35

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### Plotting 2darray with matplotlib

a = np.arange(1,10).reshape((3,3))
plt.plot(a[0],a[1:])
Why am I getting: ValueError: x and y must have same first dimension error?

1

votes

1

answer

579

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### How to convert Tensor to ndarray (tensor with adversarial images inside)

NOTE: I already have tried solutions from different SO questions with no success, details follow.
I'm studying cleverhans Pyhton tutorials, focusing on this code (keras model case).
I have a base keras knowledge but I've just started with Tensorflow (total newbie).
I'm trying to visualize the advers...

1

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0

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60

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### Why does numpy.ndarray's data address change?

I recently ran this in a jupyter notebook (cell), because I wanted to verify memory-address behavior of a numpy array when slicing. The slicing is left out, though, to create a minimal failing example.
import numpy as np
x = np.zeros(10)
x.data.__repr__(), x.data, x.data.__repr__()
I was surprised t...

1

votes

2

answer

36

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### How to get the exacte value of an np.array?

I have just calculated a probability as an np.array:
Proba = [[7.4687206e-10]]
but when I compute the complement of this probability, I got:
Comp = 1- Proba = [[1.]]
The expected value is Comp = [[0.99999999925]]
Can any one please, clarify why np.arrays do not give the exact values, and what should...

1

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1

answer

48

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### Masking a multidimensional NumPy array

I want to mask a multidimensional array, say the 4D array A of shape N x N x N x N, where I have a different mask (a, b, and c) for the last three dimension. So a, b, and c are vectors with values True and False of length N. Trying to mask A as A[:,a,b,c] yields an exception (what does this try to d...

1

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0

answer

42

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### Peak finding in a 3D noise-free scalar field using Python

I have found multiple questions about peak finding in the forum. However, questions and solutions are almost exclusively only treating the 1D case and usually assume noisy data.
I have a 3D field with essentially no noise. I would like to find (i) all the peaks in the field above a certain threshold...

1

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1

answer

41

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### getting square and cube of numpy and appending it

I have a numpy array like below :-
array([[2],
[3],
[4],
[5]])
I want to square and cube each element and then append it in numpy.
and i want the output like below
array([[2, 4, 8],
[3, 9, 27],
[4, 16, 64],
[5, 25, 125]])

1

votes

0

answer

73

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### Converting a vti file to a numpy array

I have a 3D geometry (vessels) in vit format which I do not have any information about, but I just visualize it with paraview. I do not know how to read and then convert this vti file to a 3D numpy array in python. Does anyone know how can I do this conversion?

1

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0

answer

11

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### Numpy Array Value Error, looking for specific element in Array

I have loaded an Image of the Array shape (1024, 1152, 3).
Then reshaping it into 2D:
x, y, z = img.shape
img_2d = img.reshape(x*y,z)
The second row contains values of the RGB System (e.g. print(img_2d[70000,:]) gives the Output [171 135 115].
I now want to assign each RGB Color Code to one integer...

1

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2

answer

34

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### applying array of function to array of elements by position

Assume the following:
def x2(x):
res=x*x
return res
def tx(x):
res=2*x
return res
def x3(x):
res=x*x*x
return res
x=np.array([1,2,3])
f=np.array([x2,tx,x3])
Im trying to return an array that is array([x2(1),tx(2),x3(3)]) without using a for loop.
Is this possible in python?

1

votes

1

answer

31

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### Numpy: adding n-dimensional vector to m-dimensional vector to get (n, m) matrix

Suppose I have the array [1,2,3,4,5].
I want to 'add' the array [2,4,6,8] to it so I get
[[3,5,7,9],
[4,6,8,10],
[5,7,9,11],
[6,8,10,12],
[7,9,11,13]]
(or its transpose).
There is probably a function for this but I can't seem to find it because I'm not sure what to search for.

1

votes

0

answer

57

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### how to animate png images using matplotlib with animation.FuncAnimation

I would like to animate an image loaded in python.
To load an image, I wrote
myrondarray = plt.imread(myimage.png)
myrwndarray = myrondarray.copy()
So myrwndarray is a RGBA array (x,y,4)
I wrote an update function to update myrwndarray, but I'm unable to use with animation.FuncAnimation because it...