NumPy is the fundamental package for scientific computing with the programming language Python.
2
votes
1answer
32 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 ...
3
votes
0answers
76 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
votes
2answers
89 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 * ...
6
votes
1answer
70 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 ...
5
votes
1answer
88 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
votes
1answer
49 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
votes
1answer
93 views
k-means clustering algorithm implementation
Here is my personal implementation of the clustering k-means algorithm.
...
2
votes
1answer
69 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 ...
1
vote
1answer
48 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
38 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
76 views
2
votes
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
votes
1answer
49 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
votes
1answer
71 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
vote
1answer
16 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
104 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 ...
1
vote
0answers
50 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
votes
2answers
120 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
votes
1answer
57 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
41 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 ...
0
votes
0answers
59 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 ...
1
vote
1answer
51 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 ...
2
votes
1answer
29 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 ...
2
votes
1answer
37 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 ...
11
votes
3answers
154 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 ...
1
vote
3answers
257 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
votes
1answer
179 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
votes
1answer
56 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
votes
3answers
80 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
212 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
94 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
votes
1answer
52 views
Comparing pixels against RGB value in NumPy
Assume I created an image in NumPy:
image = imread(...)
And the image is RGB:
...
5
votes
2answers
106 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 ...
1
vote
1answer
47 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
votes
2answers
120 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:
...
1
vote
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
125 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
60 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
104 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
105 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
190 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 ...
14
votes
3answers
386 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
200 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
105 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 ...
6
votes
3answers
96 views
Python differential analysis of heat loss across a pipe
I made a differential equation solver to forecast heat loss through a pipe with heat loss coefficient contours. It does what I want it to do but I had to use global variables to change the outputs of ...
2
votes
1answer
213 views
Cross validation of gradient boosting machines
I am fairly new to Python. I implemented a short cross-validation tool for gradient boosting methods.
...
3
votes
1answer
367 views
“back substitution” method for solving linear system
I'm using numpy to write the "back substitution" method for solving linear system where "A" is a nonsingular upper triangular matrix.
...
1
vote
1answer
95 views
Latent Dirichlet Allocation in Python
I've recently finished writing a "simple-as-possible" LDA code in Python.
The theory from which I've developed my code can be found in the book Computer Vision by Simon Prince, free (courtesy of ...
4
votes
1answer
196 views
Applying a formula to 2D numpy arrays row-wise
The user has two 2D input arrays A and B, and a given matrix S. He wants to apply a
...
2
votes
1answer
43 views
Extracting an arbitrary element from each row of a np.array
I have a large numpy array of shape (n,m). I need to extract one element from each row, and I have another array of shape (n,) that gives the column index of the element I need. The following code ...
