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catsim

A structural similarity index for binary or categorical images that works in 2D or 3D.

https://github.com/gzt/catsim

Science Score: 23.0%

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    Low similarity (17.5%) to scientific vocabulary

Keywords

binary-data binary-image-classification binary-image-processing categorical-data categorical-images classification image-processing r
Last synced: 6 months ago · JSON representation

Repository

A structural similarity index for binary or categorical images that works in 2D or 3D.

Basic Info
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
binary-data binary-image-classification binary-image-processing categorical-data categorical-images classification image-processing r
Created about 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Support

README.Rmd 

---
output: github_document
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```



[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
  [![Coverage status](https://codecov.io/gh/gzt/catsim/branch/master/graph/badge.svg)](https://app.codecov.io/github/gzt/catsim?branch=master)
  [![R build status](https://github.com/gzt/catsim/workflows/R-CMD-check/badge.svg)](https://github.com/gzt/catsim/actions)
  

# `catsim`: a Categorical Image Similarity Index

The goal of `catsim` is to provide a similarity measure for binary or categorical images in either 2D or 3D
similar to the [MS-SSIM index](https://en.wikipedia.org/wiki/Structural_similarity) for color images. 
Suppose you have a ground truth segmentation of some image
that has been segmented into regions - perhaps a brain scan with different types of tissues or a map 
with different types of terrain - and a segmentation produced by some classification method.
Comparing the two pixel-by pixel (or voxel-by-voxel) might work well, but a method that captures 
structural similarities might work better for your purposes. MS-SSIM is an image comparison metric
that tries to match the assessment of the human visual system by considering structural similarities
across multiple scales. CatSIM applies a similar logic in the case of 2-D and 3-D binary and multicategory
images, such as might be found in image segmentation or classification problems.


## Installation

You can install the released version of catsim from [CRAN](https://CRAN.R-project.org) with:

```r
install.packages("catsim")
#### or the dev version with:
#devtools::install_github("gzt/catsim")
```

## Usage

If you have two images, `x` and `y`, the simplest method of comparing them is:

```{r displayimage}
library(catsim)
set.seed(20200505)
x <- besag
y <- x
y[10:20,10:20] <- 1
catsim(x, y, levels = 3)
```

By default, this performs 5 levels of downsampling and uses Cohen's kappa as the local 
similarity metric on `11 x 11` windows for a 2-dimensional image and `5 x 5 x 5`
windows for a 3-D image. Those can be adjusted using the `levels`, `method`, and `window`
arguments. 


Please note that the `catsim` project is released with a [Contributor Code of Conduct](https://gzt.github.io/catsim/CODE_OF_CONDUCT.html).
By contributing to this project, you agree to abide by its terms.

Owner

  • Name: g z thompson
  • Login: gzt
  • Kind: user
  • Location: Bloomington, IN

Data Scientist and Statistician. Interests: clustering, multivariate statistics, unsupervised learning, semisupervised learning. R, some C

GitHub Events

Total
Last Year

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 263
  • Total Committers: 9
  • Avg Commits per committer: 29.222
  • Development Distribution Score (DDS): 0.087
Past Year
  • Commits: 7
  • Committers: 1
  • Avg Commits per committer: 7.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
gzt g****n@g****m 240
gzt g****t@i****u 16
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
runner r****r@M****l 1
Committer Domains (Top 20 + Academic)
iastate.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 336 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: catsim

Binary and Categorical Image Similarity Index

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 336 Last month
Rankings
Forks count: 21.9%
Stargazers count: 24.2%
Average: 29.7%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Downloads: 37.1%
Maintainers (1)
gzthompson@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • Rcpp * imports
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
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