NumPy is the fundamental package for scientific computing with the programming language Python.

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Calculating the distance squared between all vertex-pairs of a number of 2D polygons

I have implemented my code using Cython. It is the current bottleneck in my computations. There are two non-numpy functions involved: calculate_2D_dist_squared ...
2
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0answers
43 views

Speed up a function using NumPy

I have a function written in Python 2.7 that I call several times in a program. This function is rather slow, and I'd like to rewrite it in NumPy. However, I don't know how to do it. I basically have ...
3
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0answers
33 views

Find binary sequence in NumPy binary array

As part of creating a software defined receiver and decoder, I want to find sync pulses in weather satellite data. The data is first digitized to a 0-1 array. The code below is working. The ...
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0answers
30 views

How to improve this piece of python code to run it faster

Here is the code. ...
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2answers
58 views

Extracting maximum values from each of the subsets of an array

Problem description: I have a numpy array cps from which I want to extract the maximum value in each of the subsets of the array (a subset is defined as non-zero ...
3
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1answer
55 views

Python implementation of multidimensional power spectral density with Welch method

I have done my best to write Welch method implementation for python for multidimensional time series and still in the case of one dimensional time series I am getting inconsistent response compared to ...
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1answer
42 views

Bernoulli trials using a condition in a vectorized operation

I was wondering how to vectorize the following code instead of using the for-loop and still be able to check for a condition. ...
5
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1answer
57 views

Optimizing a loop for catalogue manipulation

I have a catalogue of 56000 objects and I want to replace some columns with new values for instance replace NaN with -99 and ...
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1answer
36 views

List of lists of arrays, zipping, modifying in place

I came back to some old code today and freaked out. I was like "How does this even work, and if it works it can't do what I intended." I ran a few quick tests and confirmed it did actually do what ...
3
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1answer
50 views

Averaging a list of intersecting rectangles

I have a list of rectangles as tuples (x, y, w, h). I need to find which ones intersect and if they do, average all the intersecting rectangles into a new rectangle. I also track the resultant ...
5
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1answer
73 views

Monte Carlo estimation of the Hypergeometric Function

I am trying to implement the algorithm described in the paper Statistical Test for the Comparison of Samples from Mutational Spectra (Adams & Skopek, 1986) DOI: 10.1016/0022-2836(87)90669-3: $$p ...
3
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1answer
95 views

K-Mean with Numpy

I have implemented the K-Mean clustering Algorithm in Numpy: ...
5
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1answer
135 views

Groupby in NumPy

To avoid the XY problem, here is an example of what I need. Given the sorted integer input array [1 1 1 2 2 3], I would like to produce the following slices, ...
4
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1answer
39 views

Stable partition in Numpy

In essence, I need to do a stable partition: All elements of the 1D np.array a that are present in ...
3
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1answer
66 views

Where is the bottleneck in my Cython code?

The profile tells me it took ~15s to run, but without telling me more. ...
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1answer
75 views

Neighbours from point connections

I am working with a mesh of triangles (in 3D, although I doubt it makes a difference). The mesh is given as list of lists, each list containing the indices of the three vertices of a triangle in said ...
3
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0answers
45 views

Parallelizing some model fitting code using multiprocessing

I'm trying to refactor some code for fitting parametric models that are defined symbolically using Theano. My goal is for all models to expose a common interface so that, as far as possible, they can ...
2
votes
1answer
63 views

How can I make this implementation of Euler's method more efficient?

I have an implementation of an Euler method for solving N-many 1st order coupled differential equations, but I feel that I did not write it as efficiently as I could, due to lack of programming ...
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22 views

Function that transforms input file based on a numpy poly1d function

I have written a function that gets a function as input (acquired from numpy.poly1d). The function has access to the GUI variables ...
3
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2answers
88 views

Optimization/speed up of reduction function

I'm working on an implementation of Rainbow tables as part of a project. I understand the main principles behind it had have a working solution. Unfortunately the reduction function portion of my ...
8
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1answer
138 views

Interpolate then maximize

I need to optimize $$ \max_{a',\ m'} f(a, m, e, m', a') $$ I have approximated \$f\$ with a grid \$F\$ — it has shape \$(nA, nM, nE, nM, nA)\$. Now, I want to interpolate over the last two ...
3
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2answers
77 views

Calculating mesh centers runs very slowly

I have a piece of code that is used to calculate the cell centers in a rectangular mesh. The mesh size is pretty large (650 columns by 1150 rows). The code runs very slowly. I was wondering if I could ...
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1answer
47 views

Hints to make Sukoku solver more Pythonic (II)

I tried to implement as many changes suggested as possible as well as expanding the code base according to the suggested link. The original question can be found here. It does solve Sudokus gives ...
5
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1answer
393 views

Hints to make Sudoku solver more Pythonic

As you will see, I am not very familiar with Python and NumPy but want to learn it. The following code is a very basic Sudoku solver which works fine for simple examples. Although it runs, I still ...
4
votes
1answer
146 views

Fixed point iteration and cobweb plot

I'm using Python to find fixed points of a given function and then draw a cobweb plot to visualize it. Thanks to this question, I have the core of the code written and can accomplish the task, but I ...
3
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2answers
175 views

Connect 4 game for AI agents

This Connect 4 game will be used for implementing game-playing AI. Sample players are supplied. One takes user input, and the other plays randomly. Right now it's set for a human player to play ...
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1answer
320 views

Efficient numpy cosine distance calculation

I want to calculate the nearest cosine neighbors of a vector using the rows of a matrix, and have been testing the performance of a few Python functions for doing this. ...
4
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1answer
157 views

Flood fill algorithm

I am implementing a flood fill algorithm using Python and NumPy. I have written the following fill function which works fine: ...
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1answer
128 views

Calculating the distance between one point, and many others

In my program, I have entities that I call "blobs", because they have a blobby shape. Blobs are polygons. If I have two blobs, then their information array would look like: ...
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2answers
135 views

Calculating if a point is within a polygon, or outside of it

Here is the function (along with its support functions): ...
5
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1answer
141 views

Calculating “element-wise” the angles between two lists of vectors

Let's say you have two lists of vectors: v1s = [a, b, c] v2s = [d, e, f] I am interested in generating the following ...
5
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2answers
75 views

Taking wind data and simulating future wind profiles

I am new to programming, and am using Python to take wind data and simulate future wind profiles. The code as written takes a while to execute and I was hoping someone could suggest ways to make my ...
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0answers
58 views

Cythonized version of FDCT (fast discrete cosine transform) function, ported from Java

This is my Cython code for an FDCT function (invoked here): ...
3
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1answer
103 views

Point in a polygon algorithm

I am implementing a Point in polygon algorithm. Inputs: M, N: size of the matrix poly: a ...
3
votes
1answer
66 views

Fast loop to create an array of values

I have a code that creates a 3D array of values from a minimum to a maximum in X and Z with constant Y. Right now I make it in normal Python, and then I transform it in a ...
2
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1answer
50 views

Plotting many images at once in matplotlib

I am using numpy and matplotlib to do a statistical simulation. The simulation itself is pretty fast thanks to numPy vectorizatio, however the plotting is slow since I still use a ...
8
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2answers
498 views

Possible optimizations for calculating squared euclidean distance

I need to do a few hundred million euclidean distance calculations every day in a Python project. Here is what I started out with: ...
5
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2answers
812 views

K-means clustering in Python

The following code uses scikit-learn to carry out K-means clustering where \$K = 4\$, on an example related to wine marketing from the book DataSmart. That book uses excel but I wanted to learn Python ...
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0answers
89 views

implementation of a new algorithm for sklearn

In the python library sklearn is implemented the algorithm for SparsePCA. I have written the code for a another version of this algorithm that is much faster in some situations. I have not enough ...
5
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1answer
532 views

Sieve of Eratosthenes - Standard and Optimized implementation

I am a Java developer who is taking Python for the first time. I'm sure this is not at all elegant since I am thinking more in C syntax. ...
4
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1answer
53 views

Calculating minima values for each column of given data

Can anyone help make this perform faster? ...
0
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1answer
135 views

My Python code (for creation of MxM matrix) is much slower than my Matlab version

I have written the same code in Python (NumPy) and in Matlab, and I tried to use the same structure for both language and follow the same procedure. Now my problem is that when I run my code in Python ...
4
votes
1answer
66 views

Performing a special multiplication on two square matrices

I have a function called mult2 that takes in two square NumPy matrices and returns a matrix that is the result of a special multiplication: ...
6
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1answer
77 views

Average of positive and negative part of numpy matrix

I’ve got a matrix of data and I want to take the average of the positive and negative parts of the values. Is there a more Pythonic way of doing it? ...
5
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1answer
51 views

Determining the least-accurately known physical constants

So, I thought I'd do this using scipy.constants: ...
3
votes
1answer
54 views

Building a dict/list of lists

I have code which is matching features within regions. The first thing it does it matches features from one region to an entire database of region features. I have a mapping from query feature index ...
12
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1answer
137 views

Temperature Interpolation

I want to interpolate temperature in correlation with height. I have temperature data from stations with coordinates and height in this format: ...
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1answer
342 views

Parse Bloomberg Excel/CSV with Pandas DataFrame

I retrieved Bloomberg data using the Excel API. In the typical fashion, the first row contains tickers in every fourth column, and the second row has the labels Date, PX_LAST, [Empty Column], Date, ...
6
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1answer
162 views

Calculating Euclidean norm for each vector in a sparse matrix

Below is a naive algorithm to find nearest neighbours for a point in some n-dimensional space. ...
2
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0answers
152 views

numpy array as quasi-hash table

Motivation: I have a large number of large read-only dicts with large string keys mapped to tuples of two floats. They are taking up a large amount of heap space. Proposed solution: a 3xn numpy ...