NumPy is the fundamental package for scientific computing with the programming language Python.
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Calculating the correlation coefficient between two arrays
I have two given arrays: x and y. I want to calculate the correlation coefficient between two arrays as follows:
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48 views
Confidence score calculation
I was looking for a way to calculate a score 'x' for each pair of elements in two separate arrays. The goal of the code is to return an output array containing the score for each entry in the input ...
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1answer
72 views
Look up parameters based on a numpy array of input values
Aim: Write a function that looks up empirical parameters A, B and C for a solar radiation ...
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1answer
113 views
Harmonic analysis of time series applied to arrays
I've developed some code in Python to apply a harmonic analysis of timeseries (for satellite imagery data). It's based on this, but then I would like to optimize the performance. So instead of a ...
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2answers
45 views
Scoring system of a pool of dice
I want to do some Monte Carlo simulations on a system based on a pool of dice. For each trial, a number of dies are rolled, and the winner is the highest value, getting as many points as dice are over ...
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1answer
115 views
Intersection between arrays
I'm a Python beginner (more used to code in R) and I'd like to optimize a function.
2 arrays ares filled by integers from 0 to 100. A number can't appear twice in a row and they're stored in an ...
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1answer
31 views
Printer Color Templates
I'm new to Python and I just wrote my first program with OOP. The program works just fine and gives me what I want. Is the code clear? Can you review the style or anything else?
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1answer
35 views
Improving excution time for list and sampling in Python
Here is my code for generating edge list based on Price model algorithm. I think there have two points to reduce execution time:
use proper data type
use faster random sampling
Originally, I used ...
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1answer
67 views
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1answer
79 views
Generate sample coordinates inside a Polygon
I have a Polygon named as poly. I attempted to randomly select 5 coordinate points that lies inside the polygon.
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49 views
Fastest computation of N likelihoods on normal distributions
In the context of a Gibbs sampler, I profiled my code and my major bottleneck is the following:
I need to compute the likelihood of N points assuming they have been drawn from N normal distributions ...
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2answers
125 views
Sieve of Erathosthenes speedup
While reading HackerNews, I learned about a data set of the first 50 million primes. This would be a lot, but his website has disclaimer:
n this directory I have the first fifty million primes in ...
3
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1answer
60 views
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 ...
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1answer
94 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 ...
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50 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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2answers
97 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 ...
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1answer
98 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
62 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.
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1answer
67 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
42 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
57 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 ...
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2answers
104 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 ...
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1answer
190 views
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224 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, ...
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1answer
43 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
79 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
91 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 ...
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95 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
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1answer
78 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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37 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 ...
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2answers
93 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 ...
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1answer
139 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 ...
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2answers
80 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
51 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 ...
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1answer
426 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 ...
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1answer
339 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 ...
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2answers
416 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
623 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.
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1answer
284 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
278 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
194 views
Calculating if a point is within a polygon, or outside of it
Here is the function (along with its support functions):
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1answer
233 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
78 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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Cythonized version of FDCT (fast discrete cosine transform) function, ported from Java
This is my Cython code for an FDCT function (invoked here):
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1answer
121 views
Point in a polygon algorithm
I am implementing a Point in polygon algorithm.
Inputs:
M, N: size of the matrix
poly: a ...
3
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1answer
85 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 ...
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1answer
68 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 ...
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2answers
665 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:
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6
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2answers
2k 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
94 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 ...
