Questions tagged [scipy]

SciPy is an open source library of algorithms and mathematical tools for the Python programming language.

5
votes
2answers
102 views

Simulation of spring-loaded inverted pendulum

I've finally committed to moving to Python 3 from MATLAB. I'm currently porting my MATLAB code, and I'm sure I'm missing a lot of common best-practices. For reference, I'm simulating a spring-loaded ...
11
votes
1answer
1k views

Factorio analysis: data munging

This project is... a little ridiculous. It's working, but it's a complete mess. Data about Factorio's game economy are pulled from the wiki via the MediaWiki API, scrubbed, preprocessed, and thrown ...
1
vote
0answers
32 views

Scipy basinhopping custom step update and constrained looping

I am searching for the global minimum of a certain function and trying to use its gradient (here same as Jacobin) to guide the step counter. However, my x is fix ...
2
votes
0answers
186 views

Local maxima 3D array python

I'm trying to find the local maxima in a 3D numpy array, but I can't seem to find an easy way to do that using numpy, scipy, or anything else. For now I implemented it using ...
6
votes
1answer
68 views

Monte Carlo errors estimation routine

I would value your opinion on the following piece of code. I am rather new to both Python and Monte Carlo analysis, so I was wondering whether the routine makes sense to more experienced and ...
2
votes
0answers
27 views

Solve multi-dimentional optimization problem using basinhopping

I am searching for an optimization solution, which is a 8d vector representing 4 complex elements, where each element is within the complex circle with maximal radius 1.2. The objective function is: ...
6
votes
0answers
46 views

Reading sparse matrix from binary file

I have binary files containing sparse matrices. Their format is: number of rows int length of a row int column index int value float Reading ...
0
votes
0answers
15 views

Create an interpolant based on data in a csv

I have a csv file with many columns (e.g. A,B,C,D,...
4
votes
1answer
337 views

Fast distance calculation for Starcraft2 bot

I am coding a bot for Starcraft 2, in which many distances have to be calculated every frame. Here is the part of the library that is being used and I want to improve: https://github.com/Dentosal/...
1
vote
0answers
42 views

Applying a filter to a large array with elements that are not regularly spaced

I need to apply a Gaussian filter to a 2D numpy array where the distance between adjacent array elements depends on the row of the array. (Specifically, the data are evenly spaced in latitude and ...
2
votes
1answer
215 views

Convert list of dictionaries to iterable list

Due to another module coupled to my function, I can only receive the input to my part in the form of a JSON object structured roughly like this: ...
3
votes
1answer
61 views

Simple natural language classifier

This program estimates the likelihood for a string to belong to a certain natural language by computing the cosine similarity between an input string's and several natural languages' letter frequency, ...
5
votes
1answer
682 views

Spearman correlations between Numpy array and every Pandas DataFrame row

I want to efficiently calculate Spearman correlations between a Numpy array and every Pandas DataFrame row: ...
2
votes
1answer
42 views

Implement metaclass for Maximumlikelihood estimator

For the purpose of defining a lot of Maximum Likelihood estimators, I think I need a metaclass. At the moment I have to copy/paste a lot of code for every new class definition and just substitute the ...
2
votes
1answer
43 views

Grade of Service Probability Function Python

Consider the following typical probability scenario: I defined this function to handle that scenario, I'm curious if Python has a more efficient method to handle this, or if this is the best way: <...
7
votes
1answer
218 views

2d linear Partial Differential Equation Solver using finite differences

This is code that solves partial differential equations on a rectangular domain using partial differences. fd_solve takes an equation, a partially filled in output, ...
0
votes
1answer
98 views

Ensuring performance of sketching/streaming algorithm (countSketch)

I have implemented what is know as a countSketch in python (page 17: https://arxiv.org/pdf/1411.4357.pdf) but my implementation is currently lacking in performance. The algorithm is to compute the ...
8
votes
2answers
325 views

Calculate electric field of a charged annulus

This script calculates the shape of the electric field on a 2D grid perpendicular to a uniformly charged annulus using SciPy's dblquad (tutorial, documentation). I'...
2
votes
0answers
4k views

Fuzzy c Means in Python

This is my implementation of Fuzzy c-Means in Python. In the main section of the code, I compared the time it takes with the sklearn implementation of kMeans. ...
5
votes
1answer
174 views

Probability of event using Central Limit Theorem + plotting results

I've been doing a Udemy course called: "Statistics for Data Science" and I decided to solve one of the homework with Python to kill two birds with one rocket #elon. The task was: The team of ...
5
votes
1answer
387 views

kNN with Python

I'm writing a k nearest neighbors implementation to solve multiclass classification. ...
3
votes
0answers
327 views

Compute distance matrix using DTW acceptable for scipy.cluster.hierarchy

I am new to both data science and python. I have a dataset of the time-dependent samples, which I want to run agglomerative hierarchical clustering on them. I have found that Dynamic Time Warping (DTW)...
11
votes
1answer
3k views

Farthest point algorithm in Python

I am learning Python and I tried to do a program to find K points from a set of N points, farthest as much as possible (I'm not ...
4
votes
0answers
399 views

Find the closest parametric values corresponding to a BSpline's control points

On a curve generated by scipy.interpolate.BSpline I want to find the closest parameters relative to each control point, so that the given parametric range is ...
3
votes
0answers
208 views

Applying Scikit-Learn Linear Kernel with a generator for low memory pressure

matrix = # a sparse matrix of TFIDF vectors - 28458x3218988 My aim was to create a similarity matrix comparing all documents to all documents using ...
5
votes
0answers
3k views

Calculate relationship between 2 categorical variables in a pandas Dataset with chi square test

I'm working on a Machine Learning project and I'm in Data Exploration step, and my dataset has both categorical and continuous attributes. I decided to compute a chi square test between 2 categorical ...
2
votes
1answer
182 views

Multidimensional matrix exponentiation

Is there a more efficient way of exponentiating a multidimensional matrix? This is how I am currently doing it: ...
2
votes
0answers
43 views

MCMC Metropolis Hastings for German Tank Puzzle

I have implemented the following MCMC algorithm for the german tank puzzle found here I just want to make sure everything is legit and that I am not getting the right answer by chance. ...
8
votes
0answers
151 views

Root finding and integration

I am trying to implement the modified Next Reaction Method with time varying propensities as mentioned in sections IV and V of this paper. At one step in the process this expression must be evaluated: ...
8
votes
1answer
775 views

Fitting multiple piecewise functions to data and return functions and derivatives as Fortran code

Background For a future workshop I'll have to fit arbitrary functions (independent variable is height z) to data from multiple sources (output of different ...
2
votes
0answers
355 views

Single-pass clustering algorithm for sparse matrices

I have written single pass clustering algo for reading sparse matrices passed from scikit tfidfvectoriser but the speed is king of average for medium size matrix. How can I scale for large size ...
3
votes
1answer
203 views

Cython code for adaptive binning

Here is my Cython code used for adaptive binning. The calcAdaptiveBinnedRateMap function is called from another Python script. The script is compiled using Cython ...
7
votes
1answer
197 views

Raster processing for climate change model

I am working on a project on how climate change may affect the development of spruce budworm larvae throughout each year (historical and projected) using different climate change models and emission ...
6
votes
0answers
2k views

Calculating T-Test within Large Pandas Dataframes

The below code runs a t-statistic within a large dataframe (rnadf) based on masked values from another dataframe (cnvdf_maked). ...
2
votes
1answer
2k views

Polynomial curve-fitting over a large 3D data set

I have a list of 4 images, called listfile.list, which looks like this: image1 image2 image3 image4 Each image has 10 frames containing a 2000 x 2000 array of ...
6
votes
2answers
340 views

Runge-Kutta 4th order using Python numexpr.evaluate()

I am implementing an ODE solver, where the user provides rates and coefficients as a string. ODE solver has to work with vectors. The best implementation I got so far is the following: ...
3
votes
2answers
569 views

Crank-Nicolson. Advection - Diffusion

I am writing an advection-diffusion solver in Python. I am quite experienced in MATLAB and, therefore, the code implementation looks very close to possible implementation in MATLAB. I implemented the ...
4
votes
2answers
144 views

Temporal kernel filtering on video frames coming in a loop

I have a video which I read in a loop frame by frame. For every frame, I want to do temporal kernel filtering, the coefficients of which come from the input variable model (a dictionary). The temporal ...
8
votes
2answers
691 views

Epidemic simulation

The purpose of this code is to simulate epidemics across a population. There are 625 (pop) individuals at random locations. The epidemic parameters are infectious period (inf_period), trans (...
4
votes
1answer
3k views

Compute Gini Coefficient

Recently, I was given a math assignment to calculate Gini Indexes for a table of percent distributions of aggregate income. The table takes the form of: ...
4
votes
1answer
349 views

Python script to store nd array into images

I am trying to write a generic Python script that do the following types of tasks: Load .npy file (the .npy file is of shape (m_samples, channels, row, column), which corresponds to ...
0
votes
1answer
3k views

Cosine similarity computation

I have a matrix of ~4.5 million vector [4.5mil, 300] and I want to calculate the distance between a vector of length 300 against all the entries in the matrix. I got some great performance time ...
4
votes
1answer
41 views

Accessing an unreturned list within a function in Python without disturbing Scipy [closed]

Here is the code I'm working on. I'm trying to find the optimum alpha value to get the minimum MAE/MAD. With scipy.optimize, it works quite well. However, when <...
1
vote
1answer
83 views

Counts instances for each category for many Matlab files

This is for machine learning. I have 5 matlab files: AWA, REM, S1, S2, SWS. Each one has 2 arrays: x and y. ...
4
votes
1answer
216 views

Surface Density Profile

I am trying to compute the surface density profile, given the spherical density profile in 3D for different parameters in order to interpolate and have it as a function of them to use later on for ...
4
votes
1answer
3k views

Conditional removal of columns in sparse matrix

I have a large dataset (78k instances x 490k features) that is loaded as a scipy.sparse.csr_matrix format. From this dataset I want to filter certain features (i.e. ...
8
votes
2answers
136 views

20+ functions for generating different waveforms

I added a guard clause to the functions in scipy.signal.windows, but the way they are currently written means the same 11 lines are now repeated in every function. ...
2
votes
1answer
83 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'...
6
votes
3answers
225 views

Energy curve plotter

I am not much experienced in Python, just write some small script. All my codes are procedural. They work fine, and I always check them with pep8. One of them is: ...
8
votes
3answers
539 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 ...