Carson Purnell

Last seen: 5 days ago | Active since 2022

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randomAffine3d is not properly random
the transformations are highly biased, and don't cover the unit sphere with any angle coverage. Image shows 4 compass points ran...

18 days ago | 3 answers | 2

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answers

Answered
making a label/category atlas of overlapping component images
Self-answer after topic ping: Binarization and component analysis are distractions. If every pixel/voxel needs one and only one...

1 year ago | 0

| accepted

Submitted

randv - random vectors, with constraint axis
Generate random vectors on a unit sphere/circle/etc, and random vectors from a given axis based on cone-like constraints.

1 year ago | 1 download |

Question

Octree implementation: how to quickly search through tree?
I need to do hundreds/thousands of searches comparing ~1e4 points against ~1e6-1e7 points in 3d. It's terribly slow. I currently...

1 year ago | 1 answer | 0

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answer

Answered
Why is MATLABs knnsearch with KDTreeSearcher approx. 300 times slower than my own naive kd-tree implementation?
It isn't slower, you're just calling the function overhead 1000 times in a way that also bypasses all optimizations. instead of...

1 year ago | 0

Question

Generating a distribution of points relative to closed surface (alphshape)
Is it possible to generate a set of points in a random distribution relative to a known surface? As in, a beta distribution upon...

1 year ago | 1 answer | 0

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answer

Question

optimizing: fastest way to detect if ANY points are within distance N of points?
I'm creating a volume from a very large number of points, created by accumulating a large number of point cloud objects in a box...

2 years ago | 2 answers | 0

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answers

Question

Inlined code segment slower than internal function pass - why?
I'm trying to speed up prototype code and have found a strange instance of speed increase when replacing standard inlined code i...

2 years ago | 1 answer | 0

1

answer

Question

Fastest selection of a coordinate in 3d array that fulfills a condition?
I have a relatively simple problem: I need to generate random coordinates of an array, but they must fulfill a condition. I thou...

2 years ago | 2 answers | 0

2

answers

Answered
Thinning 3d object borders to pixel thickness
I couldn't find any existing implementation of a 3d ridge detector using hessian matrices, but I found a much simpler solution t...

2 years ago | 0

| accepted

Question

Thinning 3d object borders to pixel thickness
I am attempting to perform an operation in 3d similar to skeletonization, but instead of producing pixel-width lines I want to p...

2 years ago | 1 answer | 0

1

answer

Question

Skeletonize 3d cylinders
I'm having trouble figuring out a reliable way to draw lines marking the midpoints of mostly hollow cylinders in a 3d volume. De...

2 years ago | 1 answer | 1

1

answer

Question

making a label/category atlas of overlapping component images
I'm trying to create an atlas image from several different images that record occupancy of objects in a 3d space. Object type A ...

2 years ago | 2 answers | 0

2

answers

Question

Efficient way to read variable column number data from a mixed-format text file?
I'm trying to read in specific data from .cif files, which have an unfortunate text format. A relevant section is below: the sec...

2 years ago | 2 answers | 0

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answers

Submitted

helper_pdb2vol - PDB files to atom coord list and volume
Generates a density volume from a PDB, and provides intermediate list of atom coordinates. Dramatically faster than pdbread.

2 years ago | 1 download |

Answered
pdbread function doesn't read individual models
Well I ended up needed to make my own pdb reader function for my purpose (generating density maps). Here's the function if anyon...

2 years ago | 0

| accepted

Answered
getting a radial vector relative to a 3d shape of unknown orientation
I ended up having to write my own function to determine the major axis. https://www.mathworks.com/matlabcentral/fileexchange/113...

2 years ago | 0

| accepted

Answered
Merge 2 columns with strings
given column 1==A and column 2==B, this stacks those columns without sorting. %example arrays A = {'a',1;'b',2}; B = {'c',11;'...

2 years ago | 0

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Answered
How can the major axis of a 3d object be determined?
Seems like no matlab code has this functionality built in, so I ended up doing it myself. Demo code, assuming you already have a...

2 years ago | 0

| accepted

Submitted

shapeaxis - compute the axis/orientation of 3d shapes
Provides a vector describing the major axis of any 3d shape represented by a grayscale 3d array.

2 years ago | 1 download |

Solved

Times 2 - START HERE
Try out this test problem first. Given the variable x as your input, multiply it by two and put the result in y. Examples:...

2 years ago

Question

Indexing a range of a 3d matrix incredibly slow?
I have a function that does several different operations between a source and destination matrix (each 3d), generally inserting ...

2 years ago | 1 answer | 0

1

answer

Question

How can the major axis of a 3d object be determined?
I have some rodlike objects in 3d, below is an example. Is there a way to find its longitudinal axis? I'm trying to generate a b...

2 years ago | 2 answers | 0

2

answers

Answered
How to extract different (256,256) images from a (512,512) image and calculate the average of them?
Just loop through the step sizes and accumulate a sum, then divide by the count. imsiz = 512; im = rand(imsiz); step = 16; s...

2 years ago | 1

| accepted

Question

getting a radial vector relative to a 3d shape of unknown orientation
I'm trying to generate a random 'bundle' of shapes in 3d space. The shapes are long, rodlike, and approximately cylindrical, i'm...

2 years ago | 1 answer | 0

1

answer

Question

pdbread function doesn't read individual models
The matlab pdbread function (and a similar function from a toolbox with the same codebase) appears to never correctly execute th...

2 years ago | 2 answers | 0

2

answers

Question

How can a curved surface be generated with a thickness and density?
I've got a weird problem here. I'm trying to generate a weird feature in 3d, a cell membrane EM density. Is there some way to ge...

2 years ago | 2 answers | 0

2

answers

Answered
How to fill a 3d volume with non-overlapping structures?
To answer my own question, I went with #1. it ended up being very efficient, combined with a refactoring of the function I was u...

2 years ago | 0

| accepted

Question

How to fill a 3d volume with non-overlapping structures?
I have a problem that I haven't seem any general solution for in other answers. I need to randomly place arbitrary, irregular sh...

2 years ago | 1 answer | 1

1

answer

Carson Purnell

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