NumPy is the fundamental package for scientific computing with the programming language Python.
3
votes
1answer
49 views
Jacobian product
Do you have in mind a way to compute the following sum?
$$R_{i,j,k} = \sum_{l=0}^{2} J_{i,j,l+3k} v_{i,j,l}$$
This is obviously vectorised. This may sound like an equivalent of:
...
1
vote
0answers
14 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
96 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
54 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 ...
8
votes
2answers
78 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, ...
6
votes
1answer
87 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
173 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 ...
13
votes
3answers
261 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 ...
4
votes
1answer
49 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
85 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
80 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
47 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
73 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
58 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 ...
2
votes
1answer
70 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
33 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 ...
3
votes
0answers
255 views
ID3 Decision Tree in python
I've been working my way through Pedro Domingos' machine learning course videos (although the course is not currently active). His first homework assignment starts with coding up a decision tree ...
1
vote
3answers
45 views
Convert scalar arguments to arrays, and check that lengths are equal
I've got a Python function that takes two arguments, lat and lon. These arguments can be either scalar values (...
6
votes
1answer
97 views
Fastest possible Cython for Black-Scholes algorithm
I started with a pure python implementation, and have been trying to get the performance as close to native C as possible using numpy, numexpr, and cython. Here is the the numpy version that I ...
5
votes
1answer
48 views
Slicing time spans into calendar months
I have apparently correct code that still runs for weeks on my data (tens of millions of rows). I show the entire code for reference (and maybe other gains to be made), but the key operation is in the ...
2
votes
1answer
49 views
Create symmetrical matrix from list of values
I need to make a matrix (in the form of a numpy array) by taking a list of
parameters of length N and returning an array of dimensions N+1 x N+1 where the off-diagonals are symmetric and each triangle ...
4
votes
3answers
184 views
Kadane's Algorithm for 2D array with known boundaries
I asked this question first on StackOverflow but I didn't get an answer and was advised to try here too. So here we go.
I have implemented Kadane's algorithm for a 2D array in Python 2 with known ...
4
votes
5answers
55 views
Create matrices of a certain format
I need to create matrices that follow a specific format: the matrix is a square NxN matrix and the off-diagonals all have the same value (param) and the diagonals ...
11
votes
1answer
311 views
Balanced Random Assignment in Python
It has been a very long time since I've used Python.
What I'm looking for: I would like to create a 6-by-6 random matrix where each component is either 1 or 2, so that there are 18 ones and 18 twos.
...
12
votes
1answer
113 views
Racetrack plotter
My Racetrack is just that. A Racetrack. You can't race it (yet) because I had trouble with collision detection, but I wanted to share it anyway.
It creates a base polygon by using ...
2
votes
1answer
40 views
3
votes
0answers
48 views
2D disease problem modeling [closed]
I'm modeling a disease problem where each individual in a 2D landscape has a transmissibility described by a (radial basis) kernel function. My goal is to convolve the kernel with the population ...
3
votes
2answers
92 views
Duplicate the previous input if zero or not a number
I have the following code which duplicates the previous input if any entry is less than zero or NaN, except the first row of a matrix.
Is there any other efficient way to do this without using ...
6
votes
3answers
162 views
Numerical Python code to generate artificial data from a time series process
I'm writing code to generate artificial data from a bivariate time series process, i.e. a vector autoregression. This is my first foray into numerical Python, and it seemed like a good place to start.
...
8
votes
1answer
155 views
A big “Game of Life”
Our quest: Create a big simulation for Conway's Game of Life, and record the entire simulation history.
Current Approach: Cython is used for an iterate method. The ...
2
votes
1answer
38 views
Similar manipulations on several numpy arrays
I have n numpy arrays which all contain time series data for t periods. It is not an option to instead have one ...
10
votes
2answers
145 views
Numerics for a game theory calculation using expected utility
I am trying to replicate Bruce B. de Mesquita's (BDM) results on political game theory for prediction. Based on where actors stand on issues, their capabilities, salience, BDM's method attempts to ...
3
votes
1answer
192 views
Imputing values with non-negative matrix factorization
X is a DataFrame w/ about 90% missing values and around 10% actual values. My goal is to use nmf in a successive imputation loop to predict the actual values I have ...
4
votes
1answer
227 views
Order a list of tuples or a NumPy array in a specific format
I have a list of tuples or a NumPy array (it can be either of them as the variable comes as a list and will end up being a NumPy array) and I want to order them in a specific way (that I am not able ...
5
votes
1answer
145 views
Comparing FFTs to deduplicate IVR recordings
I've got a Python script that traverses two file trees, checking all .wav files for duplication.
I'm still an undergrad, and have never worked with audio before. I'm not entirely sure this is going ...
2
votes
2answers
392 views
Converting a 1D Array of Strings to a 2D Array in Python
I was solving this question on a site that gives you a 1d array called grid
...
1
vote
1answer
71 views
3
votes
1answer
87 views
Reimplementing numpy.genfromtxt in Fortran for Python
I've found that the function genfromtxt from numpy in Python is very slow.
Therefore I decided to wrap a subroutine with f2py to read my data. The data is a ...
4
votes
3answers
216 views
Rating tennis players in a database, taking days to run
I have this project in data analysis for creating a ranking of tennis players. Currently, it takes more than 6 days to run on my computer.
Can you review the code and see where's the problem?
...
7
votes
1answer
69 views
Weighted phase Laplacian formula
We have the following equation (weighted phase Laplacian):
\$c_{i,j} = U(i,j)\Delta^{^x}_{i,j} - U(i-l, j)\Delta^{x}_{i-1,j} + V(i,j)\Delta^{y}_{i,j} - V(i,j-1)\Delta^{y}_{i,j-1}\$
Where
\$U(i,j) = ...
2
votes
1answer
204 views
Plotting non continuous functions and a real scatter example with Bokeh
I've written a python 3 code using Bokeh. With this code you can learn howto to plot math functions and a scatter plot with regression linear functions in a webpage. The target is how to plot ...
5
votes
1answer
66 views
Creating a flood from a seed point in an array
I have created a python script that takes a 2D NumPy array of elevation values and given a seed value and an elevation it will grow a flood from that seed point. It does this by checking all adjacent ...
11
votes
1answer
986 views
Sending a C++ array to Python/NumPy and back
I am going to send a C++ array to a Python function as NumPy array and get back another NumPy array. After consulting with NumPy documentation and some other threads and tweaking the code, the code is ...
3
votes
2answers
65 views
Calculating doubling times from data points
In the code below, noisy data points with unique errors are created. From this, an exponential function is fitted to the data points, and then doubling times (10 unit windows) are calculated.
I'm ...
5
votes
1answer
95 views
Python factory method with easy registry
My aim is to define a set of classes, each providing methods for comparing a particular type of file. My idea is to use some kind of factory method to instantiate the class based upon a string, which ...
2
votes
2answers
104 views
Computation of population patterns in simple agent-based model
I've modeled the population changes for a group of agents that inhabit a 2D lattice (with wrapped boundaries) made up of M x M number of grids. At each time step:
...
8
votes
2answers
211 views
Approximate (250 over 100) permutation best fitting certain criteria
Given a list of 250 words of 4 letters each, what is the fastest way, in Python, to find a subsample of 100 words (drawn without replacement) so that the distribution of letters across the whole ...
5
votes
2answers
253 views
Efficient element-wise function computation in Python
I have the following optimization problem:
Given two np.arrays X,Y and a function K I ...
3
votes
1answer
179 views
NumPy array filter optimisation
I've got a filter that I'd like to work out how to optimise. The most basic implementation, using loops is like the following:
...
6
votes
1answer
132 views
Statistics about gaps in DNA sequences
Noobie to Numba here, I'm trying to get faster code from existing function but the result is not faster. 10 times faster would be heaven, but I know nothing about optimization.
This is code about ...
