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.
103 questions
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Find the minimum value that data could have had before it was rounded
I have this function in R:
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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, ...
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2
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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 ...
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314
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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 ...
CommunityBot
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Implementation of MATLAB's `im2col`
The function im2col in MATLAB is very useful to vectorize Patch based Image Processing algorithms. The problem is the function isn't optimized and doesn't use C ...
CommunityBot
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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/...
- 1,535
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133
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Vectorizing a polar coordinate conversion loop in a fingerprint-matching process
I am working on a fingerprint matching technique and it takes a lot of computation time to obtain the result. I am trying to implement the matching process given in A Minutia Matching Algorithm in ...
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3
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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 (...
CommunityBot
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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 ...
CommunityBot
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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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113
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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.
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- 2,067
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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. ...
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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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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 ...
- 944
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164
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Increase performance in an R function using a vectorized approach
Goal
Write an R function to generate probabilities modeled by the following equation (IRT; 2 Parameter Logistic Model):
Data
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479
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Vectorizing a pixel-averaging operation in Numpy
I am reading from a file containing some segments (irregular parcels of the image) and trying to average the entire segment to have one pixel value. This is the code I use:
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- 75.1k
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1
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Find signal's maximum peak in window
I have a 9-dimensional signal (as a csv from this Gist) that looks like this:
A signal peaks every 30 steps. I want to get the maximum values of the peaks in that ...
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1
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Generate a random discrete signal
I currently have this code to generate a discrete signal with random amplitudes, but a fixed frequency:
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Extract the largest value for each day from a matrix
I have a matrix in which the right-most elements are repeated YYYYMMDD dates in descending order, for example:
...
CommunityBot
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Vectorizing Two Sample Kolmogorov-Smirnov test
I'm implementing the Two-sample Kolmogorov-Smirnov test in MATLAB. I must admit I know very little of formal statistics and was simply trying to implement the description in wikipedia's page.
Right ...
- 2,067
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1
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140
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Horizontally concatenating the entries of two matrices, and padding with NaNs
I have two matrices a and b that have, on each line, some values (null or not) and then a bunch of zeros at the end.
I want to ...
- 2,067
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3
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351
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Improving Matlab function within big simulation
I have a very big Matlab simulation project in my hands, which I wanted to optimize, since I'm running it many times to tune parameters and the like.
Using Matlab's ...
CommunityBot
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Matlab Computer Vision
The code below takes a video as input (a drop onto a fabric surface) and I want it to return the area of the drop.
Currently the code works, but I'm no Matlab expert, and wrote it entirely through ...
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Pattern recognition and machine learning - Bernoulli mixture model
I have been reading the book Pattern Recognition and Machine Learning (Bishop) for a while, and recently I came across this figure, which was created using Bernoulli mixture model on the MNIST dataset:...
CommunityBot
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135
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Biometric matching score calculator
I'm working on a biometric matching system and I would like to have few suggestions regarding vectorizing the following code:
...
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127
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Merging two square matrices
I would like to optimize a snippet of code, which uses a multiple nested if statements. I am looking for a formula to make it as a combination of multiple arrays ...
CommunityBot
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Evaluating a series of Legendre polynomials
The following function represents the electrostatic potential, in spherical coordinates, due to a ring of charge \$q=1\$ and radius \$R=1\$, placed in the plane \$x\$-\$y\$:
$$\phi(r,\theta) = \sum_{...
- 144k
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Speeding up loop-rich Matlab function to calculate temperature distribution
I would like to speed up this function as much as possible in Matlab.
This is part of a bigger simulation project, and as it is one of the most called functions within the simulation, this is crucial.
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CommunityBot
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156
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Catalogue manipulation
I have a catalogue of 56000 objects and I want to replace some columns with new values for instance replace NaN with -99 and <...
- 34.9k
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2
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573
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Jacobian product
Do you have in mind a way to compute the following sum
$$R_{i,j,k} = \sum_{l=0}^{2} J_{i,j,l+3k} v_{i,j,l}$$
obviously in a vectorised fashion? This may sound like an equivalent of:
...
- 9,613
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8k
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Remove duplicates in list of lists where an item in each list is ignored when determining duplicity
I have lines_list_copy of the form:
[['a1', 'b1', 'c1', 'd1', 'e1'], ['a2', 'b2', 'c2', 'd2', 'e2'], ... ]
I needed to ...
- 203
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Vectorization for temperature simulation
I'm new to Matlab and I would like to know tips in order to reduce the processing time of such program. The scheme of the actual code is very similar to typical C++ code and I would like to vectorize ...
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Weighted dice with n faces
Here you find some code that returns the value of a multivariate Bernoulli density function - for a dice with n faces, where each face has its weight (weight must be positive reals, not necessarily ...
- 241
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638
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Operating multiple columns of one pandas DataFrame using data from another
I have a DataFrame of data from a survey that was repeated over several years, asking people about their income and how much money they had in savings. For simplicity, let's pretend it looks like this:...
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Updating an inventory with R using apply functions
I have created an inventory that works via QR codes. Briefly: the QR code codes for an email with the book/student checking it out. The email is downloaded into R using the gmailR package (code not ...
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166
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Efficient element-wise function computation in Python
I have the following optimization problem:
Given two np.arrays X,Y and a function K I ...
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880
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Optimization of multiple arrays for filtering
My app will be running on an iPad with A7. I pass in 3 JSON arrays and right now do some simple filtering, in the future the operation will be much more complicated. I realize the ...
- 25.3k
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Vectorized numpy version of arange with multiple start stop
Given a single start and stop, numpy.arange is a good solution for building a NumPy array of evenly spaced values. However, given an array of start and an array of ...
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Optimize matlab triple for loop
I have a large matrix samples, I want to make another matrix sampleProb which is the same size, but modified as below:
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1
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1k
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NumPy eliminate double loop [closed]
How can I vectorize this code snippet and eliminate this double loop? Even with "only" 1001 elements in a this takes almost 30s.
...
- 34.9k
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Merging overlapping/intersecting string vectors
I am trying to merge overlapping/intersecting sets given as a list of string vectors below in R (my actual data set has thousands of such sets). The overlap/intersection is based on the ...
- 226
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124
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Modeling and plotting neuron responses
I want to assign the row of a matrix the return value of a function, but the only way I can figure out how to do this is with a for-loop. I'm assuming this is bad ...
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Generate random unit vectors around circle
I'm trying to generate a bunch of uniformly distributed unit vectors around the unit circle. Here's my code, which is working, but unfortunately I have a for-loop. How do I get rid of this for-loop?
<...
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1
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Run length encoding of vectors in MATLAB: looped version and vectorized version
A project I'm working on requires something akin to run length encoding on a vector in matlab. The data is in the form of a numeric vector, and the output is in the form of two vectors, ...
CommunityBot
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1
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Using Gibbs sampling to segment an image
I have been reading some NumPy guides but can't seem to figure it out. My TA told me I should be able to speed up my code by using a NumPy array instead of a for ...
- 144k
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Fast counting of interactions between groups given users interactions and groups assignments
Given:
An array c that contains the group assignment of every user (c[i]=4 indicates that user i belongs to group 4)
A matrix ...
- 235
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149
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Vector comparison inside for-loop
The following code finds no-rain periods in a time series that were preceded by rain over a threshold (e.g. 10mm in 2 days [k=48]).
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Extracting maximum values from each of the subsets of an array
Problem description:
I have a numpy array cps from which I want to extract the maximum value in each of the
subsets of the array (a subset is defined as non-zero ...
- 227
3
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2
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91
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Determining the value of a position on an array based on its nearest datapoint known value
I was wondering what would be the efficient way to determine the value of a position on an array based on its nearest datapoint known value in Python?
Problem description:
There are datapoints ...
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