# Questions tagged [scipy]

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

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0answers
36 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 ...
2answers
134 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 ...
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 ...
0answers
40 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 ...
0answers
297 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 ...
1answer
70 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 ...
0answers
32 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: ...
0answers
55 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 ...
0answers
17 views

### Create an interpolant based on data in a csv

I have a csv file with many columns (e.g. A,B,C,D,...
1answer
341 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/...
0answers
46 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 ...
1answer
233 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: ...
1answer
62 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, ...
1answer
806 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: ...
1answer
49 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 ...
1answer
44 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: <...
1answer
235 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, ...
1answer
104 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 ...
2answers
341 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'...
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. ...
1answer
178 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 ...
1answer
396 views

### kNN with Python

I'm writing a k nearest neighbors implementation to solve multiclass classification. ...
0answers
355 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)...
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 ...
0answers
424 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 ...
0answers
237 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 ...
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 ...
1answer
191 views

### Multidimensional matrix exponentiation

Is there a more efficient way of exponentiating a multidimensional matrix? This is how I am currently doing it: ...
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. ...
1answer
174 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: ...
1answer
817 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 ...
0answers
367 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 ...
1answer
205 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 ...
1answer
198 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 ...
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). ...
1answer
3k 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 ...
2answers
346 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: ...
2answers
589 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 ...
2answers
146 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 ...
2answers
695 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 (...
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: ...
1answer
370 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 ...
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 ...
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 <...
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. ...
1answer
218 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 ...
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. ...
2answers
140 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. ...
1answer
91 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'...
3answers
228 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: ...