Questions tagged [scipy]

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

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23 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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1answer
29 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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0answers
40 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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0answers
35 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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1answer
118 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 ...
3
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1answer
67 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 ...
4
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1answer
156 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 ...
5
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2answers
68 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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175 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 ...
5
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2answers
284 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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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 ...
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0answers
55 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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0answers
675 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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1answer
82 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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0answers
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: ...
6
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0answers
104 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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1answer
348 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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0answers
88 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
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1answer
280 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
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1answer
75 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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1answer
1k 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
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1answer
63 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
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1answer
50 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
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1answer
371 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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1answer
113 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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2answers
405 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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0answers
6k 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
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1answer
252 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 ...
4
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1answer
423 views

kNN with Python

I'm writing a k nearest neighbors implementation to solve multiclass classification. ...
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0answers
453 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)...
12
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1answer
5k 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
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0answers
519 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
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0answers
313 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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0answers
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 ...
2
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1answer
201 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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0answers
47 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
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1answer
176 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: ...
8
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1answer
968 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
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0answers
439 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
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1answer
223 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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1answer
231 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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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
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1answer
4k 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 ...
5
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2answers
375 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
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2answers
669 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
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2answers
161 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
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2answers
947 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
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1answer
4k 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
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1answer
602 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
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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 ...