Questions tagged [vectorization]

Vectorization refers to a programming paradigm where functions operate on whole arrays in one go. Use this tag if your code contains vectorized operations

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Vectorizing a working custom similarity function further using numpy

I am new to python, and even more new to vectorization. I have attempted to vectorize a custom similarity function that should return a matrix of pairwise similarities between each row in an input ...
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3answers
1k views

My blit function for my own graphics library

Here is a blit function for a graphics library I made. I've built a small graphics library that uses an palette-indexed spritesheet to hold all of the game's sprites. The blit function copies parts of ...
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87 views

Computing the angle between two vectors (vectorized) for small angles and with few copies

I am implementing a function that computes the angle between two vectors when given two n-dimensional arrays and an axis along which to operate. I want to do this with as few copies as possible, and ...
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1answer
40 views

Correcting coordinates of an image with polynomial root in python

I want to optimize this for loop for correcting coordinates of an image, it takes too long which is not suited for my system. I have done some profiling, the numpy roots is taking most of the time (...
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74 views

Faster Tridiagonal Matrix Multiplication

I have a function that I've been trying to make faster that computes \$XA + B\$, where \$A \in \mathbb{R}^{n \times n}\$ is a tridiagonal matrix, and \$X, B \in \mathbb{R}^{m \times n}\$. In the code, ...
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1answer
49 views

Snake from the viewpoint of the snake

I wrote a little game of snake that where you can see the field in which the snake moves fixed and you can also see the "viewpoint" of the snake, which is basically calculating the positions ...
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1answer
40 views

optimize binary classification method for speed

I have the following code for determining TP, TN, FP and FN values for binary classification given two sparse vectors as input (using the sparse library): ...
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0answers
62 views

Speed-up anomaly detection for pandas dataframes with vectorized operations

Motivation: I very often face a task where I need to check that dataframe's values are correct or not. Based on it I can create another dataframe with True/False values which are based on the first ...
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77 views

Vectorized numpy co-occurrence matrix generation

Update The implementation did not consider multiple occurrences of a same word, and self word occurrences. For instance when stride=2 and the word at the position is ...
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0answers
121 views

Implement vectorization instead of nested loops on dataframe

I have a dataset ('sample_data.csv') of the form below: ...
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1answer
75 views

Can this numpy code be vectorized?

I've written the following function to produce n realizations of a CIR process for a given set of parameters: ...
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0answers
122 views

C# Generic high performance vectorized math operations

I'm writing a library which simplifies the usage of intrinsics in C#. It's a generic library which supports all numeric types. The goal of this library is to perform these operations at the highest ...
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1answer
106 views

Vectorized crosstabulation in Python for two arrays with two categories each

I have two Python lists, label and presence. I want to do cross-tabulation and get the count for each block out of four, such as ...
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2answers
178 views

N-Body Optimization

I've created a serial C++ code for gravitational N-Body calculation. Because I expect to have upwards of 8-71 sparse bodies (ie, where Barnes-Hut is not necessarily practical) and running for long ...
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0answers
41 views

Vectorize a function that, once per row, updates multiple rows in data.table

Requirements I have a table of the different diagnoses a patient has received, with the date the diagnosis was first recorded. It so happens that in medicine, diagnoses are recorded as codes from a ...
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0answers
33 views

Vectorization of Mersenne Twister? [closed]

Ahoy friends. Right now i'm selling a huge amount of HDDs and usually i used DBAN or nwipe to perform this actions. Unfortunately the PRNG Mersenne Twister is quite slow, so i get a throughput of ...
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1answer
95 views

Efficiently shift elements right by one in an __mm256 vector [closed]

The code below correctly shifts v256f_stats by one and puts the results into v256f_x3. This is then used to get the delta ...
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0answers
94 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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1answer
410 views

AVX Vectorized Multi-threaded Mandelbrot Renderer

I wrote a Mandelbrot renderer in C++ that uses AVX intrinsics to calculate 8 pixels per thread in parallel. It can compute 1080p frames with 256 max iterations in about 40 milliseconds on a 2 core 4 ...
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1answer
108 views

Vectorizing equations for fsolve

I have a system of 49 equations and 49 unknowns (\$x_{1},...,x_{49}\$). All equations have the following form. \$x_{s}\sum_{r=1}^{R}\sum_{t=1}^{T}a_{s,t}b_{rs,t}=\sum_{r=1}^{R}\sum_{t=1}^{T}a_{r,t}...
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1answer
109 views

Vectorization, 7-bit encoding

I was curious how vectorization works and how to write suck code. To start simple I choose 7-bit encoding as my test suspect. I'm not expecting improved throughput in any way. My implementation works ...
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0answers
222 views

How to make my groupby and transpose operations efficient?

I have a DataFrame of size 3,745,802 rows and 30 columns. I would like to perform certain groupby and ...
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0answers
99 views

condensed nearest centroid classifier in numpy

This is my attempt to write a numpy-optimized version of a nearest centroid classifier to classify some images from the MNIST data set of handwritten digits. I am ...
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2answers
810 views

PyTorch Vectorized Implementation for Thresholding and Computing Jaccard Index

I have been trying to optimize a code snippet which finds the optimal threshold value in a n_patch * 256 * 256 probability map to get the highest Jaccard index ...
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1answer
646 views

C# System.Numerics.Vector<T> Clamp

The software that I develop uses large floating-point arrays up to the maximum size that can be allocated in C#. I have a large number of algorithms such as convolutions and filters that get executed ...
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2answers
683 views

Converting Array of `Float32` (`float`) to Array of `UINT8` (`unsigned char`) Using AVX2 [closed]

Given input array of Float32 (float) with numElements how could one efficiently convert it ...
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1answer
318 views

Converting Array of `UINT8` (`unsigned char`) to Array of `Float32` (`float`) Using AVX2

Given input array of UINT8 (unsigned char) with numElements how could one efficiently ...
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0answers
62 views

Optimising multiplication of matrix rows with matrix slice/page

I've recently vectorized most of the code for an optimization problem but this one still eludes me. As the procedure and not the actual values are important here, I have replaced the original matrices ...
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1answer
284 views

Vectorized N-Dimensional Random Walk in Cartesian Coordinates

I have written a random-walk routine that I hope to build upon in the future. Before doing so, I was hoping to get some critique. I believe the implementation is correct. I noticed that many other ...
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1answer
106 views

Vectorizing matrix operation instead of for loop in circular matrices

I have a vector \$X_k\$ and a matrix \$Y_{k,j}\$, where \$k \in \{1,\dots,K\}\$ and \$j \in \{1, \dots, J\}\$. They are circular, meaning that $$\eqalign{X_{k+K} &= X_k \\ Y_{k+K,j} &= Y_{k,j} ...
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1answer
234 views

Optimizations of C Code - Bilateral Filter

I'm working on a nice approximation for the Bilateral Filter. I have a working code which runs pretty fast yet still I think much can be improved. The code (C Code,...
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1answer
76 views

Generic pixel class to seamlessly alpha-blend and convert between different pixel structure layouts

Does what it says in the title. I just finished this and wanted to share with someone. Looking for possible optimizations, bugs (most of it is tested to work) or any constructive criticism. ...
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1answer
3k views

Find first threshold crossing in numpy array

Given the following artificially generated data: ...
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2answers
382 views

Vectorizing a complex nested for loop in R (running models on different subsets of a data set, subsetting the data differently for each loop)

This is my first time posting so hopefully I manage to get my question across in a clear and concise manner. I'm not sure this is the right place but someone on StackOverflow suggested I ask here. I ...
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1answer
65 views

Determining whether a list of pathways and its genes are all included in another list

I am evaluating if a list of pathways and its genes has pathways included in another pathways. So the way I thought about it is to create a function that does just a single comparison. ...
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1answer
84 views

Find the minimum value that data could have had before it was rounded

I have this function in R: ...
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1answer
70 views

1D data classification

This R code separates the values in rData. They are classified according to the class in rClass. To do that, ...
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2answers
7k views

Compute a numerical derivative

Since I could not get numpy.gradient() to compute a derivative successfully, I wrote a script to compute it manually. Running the script below will output a plot of ...
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0answers
186 views

Merging bin-data via a bin count threshold

When performing a chi-squared test, one takes the square of the differences of the expected counts per bin and observed counts per bin, and divides these per-bin differences by the expected counts per ...
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1answer
80 views

vectorize 2D gradient with spatially varying bins

The following code takes in some values ssh and solves the equations for the geostrophic motion (slide 8 here). The main part of the code is the computation of the ...
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1answer
654 views

Normalise list of N dimensional numpy arrays

I have a list of N dimensional NumPy arrays. num_vecs = 10 dims = 2 vecs = np.random.normal(size=(num_vecs, dims)) I want to normalize them, so the magnitude/...
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2answers
2k views

Remove outliers from a point cloud

This function accepts a cloud of points, and returns those points that are within delta distance of the average (mean) position. ...
6
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3answers
2k views

Converting Array of Floats to UINT8 (`char`) or UINT16 (`unsigned short`) Using SSE4

The problem is given image in 32 Bit Floating Point Format (float) how to convert it to UINT8 (char) or UNIT16 (...
1
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1answer
81 views

Extracting data from meshgrid output

I am trying to extract data from meshgrid output where zCs is 1000 x 1000 matrix of z values which is produced from meshgrid of s using bin2mat. s is a struct which has x, y, z data. res is 1000. ...
3
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1answer
60 views

Function that fills a time series row-by-row by using the values in the row before

Summary: performance issue with for-loop, vectorization possible? I am processing a time series of securities price data, stored in a pandas dataframe df_buy_sell. ...
7
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1answer
874 views

Implementation of linear regression in Python

I wrote an implementation for multivariate linear regression in Python, for data in this link: http://www-bcf.usc.edu/~gareth/ISL/Advertising.csv My main focus is to avoid loops as much as possible ...
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2answers
1k views

Vectorized and Multi Threaded Image Convolution

I created code for Image Convolution. The code is in my Image Convolution GitHub Repository. It includes the case for arbitrary Image Convolution and for Separable Kernel Convolution. The code is a ...
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1answer
251 views

Calculate the closest point to many hyperbolic paraboloids

In this question I asked for a way to compute the closest projected point to a hyperbolic paraboloid using python. Using the iterative approximation answer, I'm able to use the code below to ...
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2answers
91 views

Efficient calculation of bond overlap

For a small library dealing with molecules, I have to calculate a so called connectivity table for the chemical bonds. I assume that there is a bond between atom i and atom j, if the distance between ...
6
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1answer
108 views

Calculating parking and charging statistics for a car-sharing service

I am looking for help in designing my code more efficiently and also in keeping the slope of my personal learning curve steep: For a research project I have per car data from two different car ...