wire

R package wire

https://github.com/yuhangtom/wire

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
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DOI references
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Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary

Last synced: 11 months ago · JSON representation ·

Repository

R package wire

Basic Info

Host: GitHub
Owner: YuhangTom
License: other
Language: R
Default Branch: main
Homepage: https://yuhangtom.github.io/wire/
Size: 44.7 MB

Statistics

Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Created almost 3 years ago · Last pushed about 2 years ago

Metadata Files

Readme License Citation

README.Rmd

---
output: github_document
editor_options: 
  chunk_output_type: console
---



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

set.seed(0)
```


# wire 



[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](https://github.com/YuhangTom/wire/commits/main)
[![CRAN
status](https://www.r-pkg.org/badges/version/wire.png)](https://CRAN.R-project.org/package=wire)
[![Codecov test coverage](https://codecov.io/gh/YuhangTom/wire/branch/main/graph/badge.svg)](https://app.codecov.io/gh/YuhangTom/wire?branch=main)
[![R-CMD-check](https://github.com/YuhangTom/wire/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/YuhangTom/wire/actions/workflows/R-CMD-check.yaml)


The goal of `wire` is to provide a systematic reproducible automatic algorithm to analyze the similarity between wire cut scans.


# Installation


You can install the development version of wire from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("YuhangTom/wire")
```


# Usage


## Data


The original scans for the wire cuts are stored in `x3p` format of width around 2300 and height around 1800,
under a resolution $0.645 \mu m \times 0.645 \mu m$,
with each file being at least 15 MB,
which is much larger compared to the file limit of 5 MB for a `R` package.
Therefore,
we subsampled the original scans by a factor of 10,
and saved them as `x3p_subsamples` in the package.
The data can be used by:

```{r data}
library(wire)

x3p_subsamples
```


## Inner polygon


To remove the edge effect,
we extract the inner part of the scan,
which can be achieved by:

```{r insidepoly}
x3p <- x3p_subsamples[[1]]
insidepoly_df <- x3p_insidepoly_df(x3p, mask_col = "#FF0000", concavity = 1.5, b = 1, ifplot = TRUE)

attr(insidepoly_df, "x3p_plot")
attr(insidepoly_df, "number_of_missing_immediate_neighbors_plot")
attr(insidepoly_df, "standard_deviation_of_non_missing_immediate_neighbors_plot")
attr(insidepoly_df, "number_of_missing_immediate_neighbors_boxplot")
```


## Remove trend


To remove the overall trend on the inner surface,
we can use:

```{r rmtrend}
x3p_inner_nomiss_res <- df_rmtrend_x3p(insidepoly_df)
x3p_inner_nomiss_res
```


## Imputation


We can impute the missing values inside the surface by:

```{r impute}
x3p_inner_impute <- x3p_impute(x3p_inner_nomiss_res, ifout = TRUE, ifsave = FALSE, dir_name = NULL, ifplot = TRUE)
attr(x3p_inner_impute, "x3p_impute_0_plot")
attr(x3p_inner_impute, "x3p_impute_1_plot")
attr(x3p_inner_impute, "x3p_impute_n_plot")
```


## Rotation


We can rotate the surface to the correct angle by:

```{r rotate}
x3p_bin_rotate <- x3p_vertical(x3p_inner_impute, min_score_cut = 5, ifplot = TRUE)

attr(x3p_bin_rotate, "nfline_red_plot")
attr(x3p_bin_rotate, "MLE_loess_red_plot")
attr(x3p_bin_rotate, "nfline_blue_plot")
attr(x3p_bin_rotate, "MLE_loess_blue_plot")
```


## Signal extraction


To extract signals from the rotated surface,
two methods are provided,
implemented by
`wire::x3p_raw_sig_df`
and
`wire::x3p_shift_sig_df`,
respectively:

```{r signal}
raw_sig_df <- x3p_raw_sig_df(x3p_bin_rotate, ifplot = TRUE)
attr(raw_sig_df, "sig_df_plot")

shift_sig_df <- x3p_shift_sig_df(x3p_bin_rotate, ifplot = TRUE)
attr(shift_sig_df, "x3p_before_shift_plot")
attr(shift_sig_df, "x3p_after_shift_plot")
attr(shift_sig_df, "fn_align_plot")
attr(shift_sig_df, "MSE_plot")
attr(shift_sig_df, "sig_df_plot")
```

The signals and hooks can be further smoothed and removed by:

```{r ccsignals}
raw_ccsig_df <- df_ccsig(raw_sig_df, ifplot = TRUE)
attr(raw_ccsig_df, "sig_df_plot")
```



## Signal alignment


Extracted signals can be aligned,
and the cross-correlation can be computed:

```{r align}
aligned <- vec_align_sigs_list(raw_sig_df$sig, shift_sig_df$sig, ifplot = TRUE)
attr(aligned, "sig_align_plot")
```

Owner

Name: Yuhang (Tom) Lin
Login: YuhangTom
Kind: user
Location: Ames, IA
Company: Iowa State University

Website: https://yuhangtom.github.io/
Repositories: 1
Profile: https://github.com/YuhangTom

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "wire" in publications use:'
type: software
license: MIT
title: 'wire: Tools for Analyzing Similarity Between Wires'
version: 0.0.0.9000
abstract: This `wire` package allows everyone to conduct reproducible automatic analysis
  to compare different wire scans in 'x3p' format. A conclusion for similarity or
  dissimilarity can be easily drawn based on the resulting cross-correlation.
authors:
- family-names: Lin
  given-names: Yuhang
  email: yhlin@iastate.edu
  orcid: https://orcid.org/0000-0002-3600-9889
- family-names: Hofmann
  given-names: Heike
  email: hofmann@iastate.edu
  orcid: https://orcid.org/0000-0001-6216-5183
preferred-citation:
  type: manual
  title: Tools for Analyzing Similarity Between Wires
  authors:
  - family-names: Lin
    given-names: Yuhang
    email: yhlin@iastate.edu
    orcid: https://orcid.org/0000-0002-3600-9889
  - family-names: Hofmann
    given-names: Heike
    email: hofmann@iastate.edu
    orcid: https://orcid.org/0000-0001-6216-5183
  year: '2023'
  url: https://github.com/YuhangTom/wire
repository-code: https://github.com/YuhangTom/wire
url: https://yuhangtom.github.io/wire/
contact:
- family-names: Lin
  given-names: Yuhang
  email: yhlin@iastate.edu
  orcid: https://orcid.org/0000-0002-3600-9889
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    orcid: https://orcid.org/0000-0001-8049-7069
  year: '2024'
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    email: james.hester@rstudio.com
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  institution:
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    address: Vienna, Austria
  year: '2024'
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  repository: https://CRAN.R-project.org/package=tidyr
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    given-names: Hadley
    email: hadley@posit.co
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    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
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  repository: https://CRAN.R-project.org/package=magick
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    given-names: Hadley
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    orcid: https://orcid.org/0000-0002-5147-4711
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  - family-names: Barthelme
    given-names: Simon
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  authors:
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    given-names: Duncan
    email: murdoch.duncan@gmail.com
  - family-names: Adler
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    email: dadler@dyncall.org
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  abstract: 'htmltools: Tools for HTML'
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  url: https://rstudio.github.io/htmltools/
  repository: https://CRAN.R-project.org/package=htmltools
  authors:
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Sievert
    given-names: Carson
    email: carson@posit.co
    orcid: https://orcid.org/0000-0002-4958-2844
  - family-names: Schloerke
    given-names: Barret
    email: barret@posit.co
    orcid: https://orcid.org/0000-0001-9986-114X
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Xie
    given-names: Yihui
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  - family-names: Allen
    given-names: Jeff
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  - family-names: Bache
    given-names: Stefan Milton
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  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
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  authors:
  - family-names: Hofmann
    given-names: Heike
    email: hofmann@iastate.edu
    orcid: https://orcid.org/0000-0001-6216-5183
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    given-names: Susan
    email: susan.vanderplas@unl.edu
    orcid: https://orcid.org/0000-0001-6216-5183
  - family-names: Ju
    given-names: Will
    email: wju@iastate.edu
  - family-names: Krishnan
    given-names: Ganesh
    email: ganeshk@iastate.edu
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  version: '>= 0.2.0.9000'
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  abstract: 'x3ptools: Tools for Working with 3D Surface Measurements'
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  url: https://heike.github.io/x3ptools/
  repository: https://CRAN.R-project.org/package=x3ptools
  authors:
  - family-names: Hofmann
    given-names: Heike
    email: hofmann@iastate.edu
    orcid: https://orcid.org/0000-0001-6216-5183
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    given-names: Susan
    email: srvander@iastate.edu
    orcid: https://orcid.org/0000-0002-3803-0972
  - family-names: Lin
    given-names: Yuhang
    email: yhlin@iastate.edu
    orcid: https://orcid.org/0000-0002-3600-9889
  - family-names: Krishnan
    given-names: Ganesh
    email: ganeshk@iastate.edu
  - family-names: Hare
    given-names: Eric
    email: eric@oaiti.org
    orcid: https://orcid.org/0000-0002-4277-3146
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  abstract: 'concaveman: A Very Fast 2D Concave Hull Algorithm'
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  url: https://joelgombin.github.io/concaveman/
  repository: https://CRAN.R-project.org/package=concaveman
  authors:
  - family-names: Gombin
    given-names: Joël
    email: joel.gombin@gmail.com
  - family-names: Vaidyanathan
    given-names: Ramnath
  - family-names: Agafonkin
    given-names: Vladimir
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    Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32)
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  url: http://www.rforge.net/Cairo/
  repository: https://CRAN.R-project.org/package=Cairo
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    email: erich.neuwirth@univie.ac.at
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  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 2.10'

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