# Questions tagged [scipy]

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

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1 vote
56 views

### 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 ...
• 129
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 ...
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 ...
• 21
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 ...
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: ...
• 51
1 vote
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. ...
• 1,827
1 vote
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 ...
1 vote
100 views

1 vote
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 ...
1 vote
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 ...
1 vote
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 ...
• 11
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 ...
• 285
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 ...
• 285
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 ...
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 ...
• 161
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 ...
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 ...
• 153
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 ...
• 47.9k
1 vote
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 ...
• 241
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 ...
• 31
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 ...
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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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 ...
• 161
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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1 vote
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 ...
• 111
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: ...
• 123
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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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: ...
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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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: <...
• 247
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, ...
• 3,512
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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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'...
• 401
1 vote
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. ...
• 195
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 ...
461 views

### kNN with Python

I'm writing a k nearest neighbors implementation to solve multiclass classification. ...
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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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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 ...
• 265
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 ...
• 383
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 ...
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 ...
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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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. ...
• 121
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: ...
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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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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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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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 ...