NumPy is the fundamental package for scientific computing with the programming language Python.
-1
votes
1answer
48 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 ...
1
vote
1answer
27 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 ...
-1
votes
0answers
46 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
36 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
19 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
24 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 ...
7
votes
2answers
84 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
74 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
86 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
49 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
69 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
77 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.
...
3
votes
1answer
66 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
34 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
94 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
39 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
114 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
18 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
108 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
56 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 ...
9
votes
2answers
94 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
94 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
182 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
318 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
87 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
97 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
91 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
115 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
185 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
65 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
113 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
37 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
2k 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
56 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
120 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
54 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
57 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
235 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 ...
5
votes
5answers
59 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
331 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
123 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
45 views
3
votes
0answers
51 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
94 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
176 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
168 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
173 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
257 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
282 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 ...
