Questions tagged [scipy]

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

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Calculate correlation of genes stored in dataframe rows

This script is to calculate the Spearman correlation of genes that are stored in rows of a pandas dataframe. The original df has around 2000 row names. With my current code, this requires 2000*2000 ...
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5 votes
1 answer
35 views

Rainbow Trails Video Effect

This is an effect to augment juggling videos: The goal of this effect is to add a rainbow trail to a video using a tracked set of points. Link to source video Link to source data Link to complete ...
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2 votes
1 answer
252 views

Applying Minimum Image Convention in Python

I am computing pairwise Euclidean distances for 3-D vectors representing particle positions in a periodic system. The minimum image convention is applied for each periodic boundary such that a ...
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3 votes
0 answers
220 views

Speed up interpolation in Python

I am trying to plot heatmap with three variables x, y and z, each with vector length of 932826. The time taken with the function below is 28 seconds, with a bin size of 10 on each x and y. I have been ...
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5 votes
1 answer
123 views

compare between two labels /objects -dominance rules

I have a function dominates() that seems to be the bottleneck of my algorithm (after profiling it). the function is as follows: ...
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  • 51
1 vote
0 answers
15 views

LP constraint problem with scipy

For this graph and its vertex cover I try to compare the LP solution with the optimal and the rounded solution. ...
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1 vote
1 answer
206 views

Reduce one for loop to decrease time complexity

I'm using NumPy to find out langrage polynomial interpolation. I'm using 2 for loop to find out langrage polynomial, but I want to reduce 2nd for loop so that my code time complexity can be less. Can ...
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1 vote
0 answers
100 views

Numerical Double Integration using numba and scipy

Please see the following code. I am using it to calculate the double integration. Please help me to improve the code. ...
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1 vote
1 answer
94 views

What would be the computationally faster way to implement this 2D numerical integration?

I am interested in doing a 2D numerical integration. Right now I am using the scipy.integrate.dblquad but it is very slow. Please see the code below. My need is to ...
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1 vote
0 answers
144 views

Custom Model intended to be used for Curve Fitting. Vectorization vs For Loop and jit numba capabilities

I am new to community and please pardon me if I didn't provide information as intended. This code is supposed to be creating a custom model which will be used with ...
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1 vote
0 answers
42 views

Python Implementation of Canopy Structural Dynamic Model using scipy.optimize.least_squares

I am using the least_squares() function from the scipy.optimize module to calibrate a Canopy structural dynamic model (CSDM). The calibrated model is then used to predict leaf area index (lai) based ...
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  • 11
3 votes
1 answer
190 views

Optical dispersion calculation from spectrograms with Python

First, I'd like to provide a little explanation on what my code is supposed to do. It is part of a middle-sized project. I restructured the code to work on its own, and also added little comments to ...
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3 votes
1 answer
99 views

Many parameter curve-fitting

In my project I have to make curve-fitting with a lots of parameters, so scipy curve_fit struggles to find the answer. For example: \$\ c_0 + c_1 \cdot cos (b_0 + b_1\cdot x + b_2\cdot x^2+ b_3\cdot ...
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4 votes
1 answer
353 views

Counting Bouncy Numbers: Project Euler #113

Problem statement: Working from left-to-right if no digit is exceeded by the digit to its left it is called an increasing number; for example, 134468. Similarly if no digit is exceeded by ...
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5 votes
2 answers
88 views

A/B testing using chi-square to calculate the significance in an elegant way

The definition of ABtest Goal: For input data, each pair row is a group such as 0 and 1, 2 and 3. I want to test whether each group is significant using chi-square. If result is significant and ...
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  • 161
3 votes
0 answers
362 views

Double pendulum real time plot

Double Pendulum I made a little application that embeds a matplotlib dynamic plot into tkinter that enables control through the ...
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5 votes
2 answers
621 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 ...
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12 votes
1 answer
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 ...
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1 vote
0 answers
71 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 ...
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3 votes
0 answers
1k 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 ...
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6 votes
1 answer
134 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 ...
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2 votes
0 answers
37 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: ...
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6 votes
0 answers
208 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 ...
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  • 161
4 votes
1 answer
358 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/...
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  • 769
1 vote
0 answers
189 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 ...
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  • 111
2 votes
1 answer
301 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: ...
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3 votes
1 answer
79 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, ...
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  • 33
5 votes
1 answer
2k 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: ...
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2 votes
1 answer
76 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 ...
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  • 842
2 votes
1 answer
77 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: <...
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  • 247
7 votes
1 answer
508 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, ...
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  • 3,512
2 votes
1 answer
152 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 ...
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  • 21
7 votes
2 answers
530 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'...
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  • 401
1 vote
0 answers
7k 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. ...
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  • 195
5 votes
1 answer
299 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 ...
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4 votes
1 answer
461 views

kNN with Python

I'm writing a k nearest neighbors implementation to solve multiclass classification. ...
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  • 866
3 votes
0 answers
535 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)...
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13 votes
1 answer
10k 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 ...
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  • 265
4 votes
0 answers
661 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 ...
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  • 383
3 votes
0 answers
404 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 ...
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4 votes
0 answers
4k 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 ...
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2 votes
1 answer
212 views

Multidimensional matrix exponentiation

Is there a more efficient way of exponentiating a multidimensional matrix? This is how I am currently doing it: ...
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  • 81
2 votes
0 answers
50 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. ...
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8 votes
1 answer
179 views

Root finding and integration [closed]

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: ...
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9 votes
1 answer
1k 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 ...
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  • 143
2 votes
0 answers
589 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 ...
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  • 131
3 votes
1 answer
240 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 ...
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  • 31
7 votes
1 answer
240 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 ...
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6 votes
0 answers
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). ...
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2 votes
1 answer
6k 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 ...
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