Questions tagged [vectorization]
Use this tag if your code contains vectorized operations - where functions operate on whole arrays in one go. If it doesn't, but you want it to, then you should make those changes (perhaps with help from elsewhere) before presenting code for review.
101
questions
2
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1
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Agent based Dengue transmission simulation
I'm trying to implement the dynamics of Dengue transmission between mosquitoes and humans. I decided create two classes, one for the human population and another for the mosquitoes. Both are based on ...
- 65
4
votes
1
answer
175
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Vectorized 16-bit addition in Standard C
The idea is to add a given 16-bit number N to each element of an array of 16-bit integers of arbitrary length, taking advantage of 64-bit integer types and instructions to perform the additions 4 at a ...
- 823
1
vote
2
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141
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Replace personal names and addresses with company ones
The problem:
I am given a data frame. Somewhere in that dataframe there is 3*N
number of columns that I need to modify based on a condition. The
columns of interest look like this:
names_1
address_1
...
- 129
4
votes
1
answer
387
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Implementation of Iterative Closest Point in C++
Here, is my implementation of Iterative Closest Point algorithm in C++. The code is written using the Eigen library. I have tried to implement an efficient coding methodology best to my knowledge ...
1
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1
answer
63
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Make unique id based on text data column with similarity scoring
I have the following dataframe:
...
- 111
0
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0
answers
66
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Three-dimensional DCT implementation for GPU computation in Matlab
This is a follow-up question for Three-dimensional DCT spatial frequency components illustration and Parallel 3D Discrete Cosine Transformation Implementation in Matlab. I am trying to perform three-...
- 3,996
1
vote
1
answer
487
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Exponentially-weighted moving mean and standard deviation of an irregularly-spaced weighted time series
The following numpy/python function computes exponentially-weighted moving mean and standard deviation of an irregularly-spaced weighted time series. I want to make it faster by getting rid of the ...
- 123
0
votes
2
answers
50
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Tips to Finetuning to increase the GFLOPS of a SIMD kernel
Given an Image I with dimensions as {rows, columns}, for every pixel in the image, the following needs to be computed -
...
- 101
3
votes
1
answer
145
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Matlab vs C: Tensorproduct or Vec-trick (multiple times)
I am searching for a more efficient way to calculate the so called vec-trick used in Tensor algebra, see Wikipedia.
Introduction:
Suppose you have a matrix vector multiplication, where a matrix C ...
- 133
2
votes
0
answers
77
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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 ...
- 121
11
votes
3
answers
2k
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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 ...
- 113
1
vote
0
answers
140
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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 ...
- 1,051
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1
answer
54
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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 (...
1
vote
0
answers
128
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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, ...
- 101
3
votes
1
answer
146
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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 ...
4
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1
answer
50
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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):
...
- 155
3
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0
answers
202
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Implement vectorization instead of nested loops on dataframe
I have a dataset ('sample_data.csv') of the form below:
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- 31
4
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1
answer
92
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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:
...
- 183
6
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0
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392
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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 ...
4
votes
1
answer
149
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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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10
votes
2
answers
370
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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 ...
- 173
2
votes
0
answers
43
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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 ...
- 201
1
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0
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53
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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 ...
- 11
0
votes
1
answer
405
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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 ...
- 191
1
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0
answers
161
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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 ...
- 31
11
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1
answer
584
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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 ...
- 211
2
votes
1
answer
183
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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}...
2
votes
1
answer
155
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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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6
votes
1
answer
294
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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 ...
- 237
1
vote
0
answers
198
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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 ...
- 127
4
votes
2
answers
1k
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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 ...
- 73
4
votes
1
answer
1k
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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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2
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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 ...
- 582
0
votes
1
answer
890
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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 ...
- 582
3
votes
0
answers
65
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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 ...
- 131
1
vote
1
answer
476
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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 ...
user182606
3
votes
1
answer
224
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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} ...
- 197
4
votes
1
answer
314
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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,...
- 582
3
votes
1
answer
90
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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.
...
- 223
2
votes
1
answer
6k
views
Find first threshold crossing in numpy array
Given the following artificially generated data:
...
- 1,527
4
votes
2
answers
579
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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 ...
- 41
3
votes
1
answer
68
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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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- 273
1
vote
1
answer
118
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Find the minimum value that data could have had before it was rounded
I have this function in R:
...
- 21
0
votes
1
answer
78
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1D data classification
This R code separates the values in rData. They are classified according to the class in rClass.
To do that, ...
- 41
6
votes
2
answers
8k
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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 ...
user127168
3
votes
0
answers
294
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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 ...
user127168
1
vote
1
answer
91
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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 ...
- 255
1
vote
1
answer
959
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/...
- 1,527
6
votes
2
answers
3k
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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.
...
- 475
7
votes
3
answers
3k
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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 (...
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