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

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4
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2answers
58 views

Export data from Python to spreadsheet

I have written the following code to export to data to a spreadsheet with this result: Please let me know how to improve it. ...
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1answer
34 views

Mean of combined sublists with different lengths

I have a seemingly simple issue. Consider this list: a = [[12.0, 5.0, 63.0], [0.1, 2.0, 7.1, 3.0, 2.3, 5.0, 8.4]] I want to find the mean (using ...
5
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0answers
64 views

Computing intersections of a Polyline and a line

I wrote a script to compute / interpolate the nodes of a Polyline at a given latitude, input_lat. It works for my purpose but I am wondering if there is a better, ...
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1answer
55 views

Sum over selected numpy.ndarray column and write to a file

I am trying to write the sum of selected NumPy array column and write to a file. The following code snippet is working fine: ...
6
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2answers
103 views

Crop black border of image using NumPy

Objective: Crop the image so only the number stays in the image Problem: Slow Performance I have code that crops an image. The image pixels are 0 or 255. There are no values between. The ...
2
votes
2answers
80 views

Plot heat map from csv file using numpy and matplotlib

There's a csv file with format: x0, y0, v00 x0, y1, v01 ... x1, y0 v10 ... And what I want to do is to plot a heat map, in which at location (x, y) the value v ...
3
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1answer
52 views

Scoreboard with score evolution plots using classes

I've very recently started using OOP paradigms for the code in my work (academic research). As an exercise I tried coding this quick scoreboard. I'm not interested in improving the 'display' part, I ...
4
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0answers
100 views

Optimizing the calculation of complex exponential numbers using OpenMP

I am trying to create a function that can either beat numexpr or perform comparably for the vectorized mathematical operation ...
3
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2answers
93 views

Assembling edges of a graph

I'm making a neural network that comprises five populations of feature-selective neurons and one population of non-selective neurons. Each neuron in this network receives connections from c * f * ...
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2answers
111 views

Histogram of a string

I'm teaching myself Python and when a friend posted this sentence Only the fool would take trouble to verify that his sentence was composed of ten a's, three b's, four c's, four d's, forty-six e'...
5
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1answer
120 views

Koch snowflake in Python with numpy and pygame

I've drawn a Koch snowflake with Python 3. I'm new to the Python world and would appreciate all feedback on how to make the code more Pythonic as I'm not used to these idioms, styles and modules. All ...
3
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1answer
52 views

Normalizing data over a distribution

I have a list X containg the data performed by different users N so the the number of the ...
5
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1answer
128 views

k-means clustering algorithm implementation

Here is my personal implementation of the clustering k-means algorithm. ...
2
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1answer
108 views

Check if a numpy array contains numerical data

This function serves me as a testing-utility to check if the result is really numeric and sometimes as input-validation if there are a lot of operations before I would find out (with an Exception) if ...
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1answer
56 views

Finding cointegrated pair with minimal t-score

The function findMinimal() receives a tuple from a list which contains 171 tuples, each of them go into the function one by one and, for each tuple, it searches the ...
3
votes
1answer
44 views

Slicing a big NumPy array

I have a function that takes a four-dimensional NumPy array M and, for each value i of its second index, takes all of M without the i-th "column", evaluates the product over all other columns, and ...
3
votes
1answer
85 views

Checking convergence of 2-layer neural network in python

I am working with the following code: ...
2
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0answers
29 views

Picking seats in a matrix

I'm trying to write a Python class that creates a matrix of zeros, then uses a random number generator to pick 'seats' on the matrix. It changes the zero in that seat to a one, until the matrix is all ...
2
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1answer
50 views

Performance optimization when switching from nested to flat representation (genetic algorithm)

The code below is the core of a Genetic Algorithm (NSGA-II to be precise, without crowding-distance calculation), but I've taken out all the GA-specific parts and made a generic example. I think I've ...
2
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1answer
73 views

Project Euler problem #11 - Largest product in a grid

I have recently solved the following Project Euler problem: In the 20×20 grid below, four numbers along a diagonal line have been marked in red [here bold]. ...
1
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1answer
17 views

Organizing a Python list of lists as function of number of occurances

I am having a Python list of lists, that I get as an output of python-igraph (membership to clusters). The integers represent an association of a vertex to a ...
5
votes
1answer
143 views

Python Octree Implementation

I'm working with 3D point clouds stored in Numpy arrays. I'd succesfully used the scipy's KDTree implementation for task like k-neighbors search and outlier filtering. However I wanted to try the ...
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0answers
56 views

Snell's law using Zoeppritz equation by matrices

I have created the following code to calculate Snell's law angles, based on Zoeppritz equations on complex plane. The code works, seems it is returning valid values, but after all the code just looks ...
2
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2answers
143 views

Simulation of 2D elastic balls

Following this SO post and this Wikipedia article, I wrote a Python script to simulate physics of 2D elastic balls. I define the physical behaviour of each ball in the ...
0
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1answer
61 views

Computing logits for a vector and for all vectors in a set

I've had to write two different functions (shown below), but I want to combine the two functions into one. Is there a way to do this? softmax_a_set() takes a list ...
2
votes
1answer
50 views

Quickly find percentile with high precision

I need to find the percentile where a list of values is higher than a threshold. I am doing this in the context of optimization, so it important that the answer is precise. I am also trying to ...
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0answers
63 views

Memory efficient alternative passing mostly static variables w/ 1 dynamic variable to an external function (COM) instead of a for loop in Python

Massive data problem, 7/8 variables are repeated 1000 times in a for loop, sending 8 input vectors * 50,000 values per loop for each function call. Only 1 input ...
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1answer
61 views

Finding the percentile corresponding to a threshold

I need to find which percentile of a group of numbers is over a threshold value. Is there a way that this can be speed up? My implementation is much too slow for the intended application. In case this ...
3
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2answers
48 views

In matrix of sub-matrices, select diagonal indices of off-diagonal submatrices

Let's say I have a square matrix of size (n*m) x (n*m) that is composed of n x n sub-matrices, with each submatrix being a square of size m x m. I want to select the diagonal indices of the off-...
2
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1answer
38 views

Measuring the distance between NumPy matrixes

This takes two sets of five random points stored as a NumPy matrix, and then calculates the NumPy matrix between a point of the first set and a point of the second set. While the code works, I feel it'...
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3answers
159 views

Fast Python spring network solver

I wanted a very simple spring system written in Python. The system would be defined as a simple network of knots, linked by links...
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3answers
373 views

Recursively Save Python Dictionaries to HDF5 Files Using h5py

I have a bunch of custom classes for which I've implemented a method of saving files in HDF5 format using the h5py module. A bit of background: I've accomplished ...
9
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1answer
232 views

Simple Phase Locked Loop

Here is a simple Phase Locked Loop, which is a circuit used in radio communications for synchronisation between transmitter and receiver. The loop works by calculating the (phase) difference between ...
2
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1answer
58 views

Sampling with weighted probabilities

In an exam question I need to output some numbers self.random_nums with a certain probability self.probabilities: I have ...
3
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3answers
86 views

Creating and manipulating FITS files

I wrote a program that manipulated data from VLA observations and created FITS files to be used in creating spectral energy distributions of high redshift radio galaxies. I really tried to be as ...
2
votes
2answers
265 views

Efficiently index rows of numpy array by exclusion

I need a function that takes a numpy array and a row number as inputs and returns the array (or copy of the array) excluding the given row. I want to do this as efficiently as possible. ...
4
votes
1answer
99 views

Skip list in Python

I've made an attempt at writing a skip list in Python. I'm using NumPy to generate geometric random variables, but since that's a bit of a heavy dependency to drag around I could easily implement that ...
3
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1answer
61 views

Comparing pixels against RGB value in NumPy

Assume I created an image in NumPy: image = imread(...) And the image is RGB: ...
5
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2answers
108 views

Attempting to run multiple simulations of the Gillespie algorithm for a set of stochastic chemical reactions in less than 10 minutes

I have written Python code that generates a plot. In the code below, when I set maxtime = 0.1, the program takes ~50s and when I set ...
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1answer
54 views

Write binary save file in Python

I'm fixed on the save file format. There are only three types of data: long (NumPy int32 array, independent of platform) ...
5
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2answers
122 views

Jacobian product

Do you have in mind a way to compute the following sum $$R_{i,j,k} = \sum_{l=0}^{2} J_{i,j,l+3k} v_{i,j,l}$$ obviously in a vectorised fashion? This may sound like an equivalent of: ...
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0answers
24 views

Spatial parametric scaling in agent-based model

I’m running a simple agent-based disease spread model on a 2D lattice, where disease transmission in a population depends on each individual’s chance of avoiding infection at every time step, which ...
4
votes
2answers
130 views

Backtracing Sudoku solver

I have made a backtracking Sudoku solver in Python but it's working quite slow. Originally, It had been working on 4 by 4 grids, which worked fine. But now, trying to solve 9 by 9 grids takes a very ...
8
votes
2answers
61 views

Iterate list to map entries in Python

I have two files, namely: File1: CL1 AA XX YY ZZ SS \n CL2 3_b AA File2: AA string1 AA string2 3_b string3 My ...
10
votes
2answers
108 views

A 3-D vector class built on top of numpy.array

I wanted a convenient class to easy access the parameters inside. I am using a lot of math in my game; that's why a wanted to access them through x, ...
7
votes
1answer
113 views

Optimizing a python script with large arrays

I have a python script that I'd like to speed up. I'm hoping some of the gurus here can offer some advice. The script reads in some data from file: 2 arrays with lat/lon vals, 3 arrays with image ...
6
votes
1answer
195 views

Combining two clock tick vectors with NumPy

I have two long (7683200 length) 1D arrays corresponding to two clock cycles, that I wish to combine into single 1D array. The clock_ticks_fine cycles between 0-255,...
14
votes
3answers
423 views

Orbital Trajectory simulator

I have written a simple program to do trajectory simulation in the Earth-Moon system, it still has a long way to go I am working on making it more class oriented and am looking into implementing a ...
5
votes
1answer
285 views

A matplotlib scatter function inside a for loop

This function is working exactly as I want, only, it's taking too long. For speed ups, I've tried to do as much as I can before the main for loop by declaring ...
0
votes
1answer
109 views

Benchmark using floating point math

I wrote some code in Python, to benchmark mathematical operations. It does not do anything in particular besides just calculating a lot of floating point numbers. To clarify: I need 128-bits ...