Merge branch 'main' into fix/x3p_rotate

heike · Mar 5, 2024 · ce9f822 · ce9f822
2 parents 0b49857 + 33d1952
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: x3ptools
 Type: Package
 Title: Tools for Working with 3D Surface Measurements
-Version: 0.0.4
+Version: 0.0.4.9000
 Date: 2024-01-21
 Authors@R: c(
     person("Heike", "Hofmann", role = c("aut", "cre", "cph"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -45,6 +45,7 @@ export(x3p_mask_quantile)
 export(x3p_modify_xml)
 export(x3p_read)
 export(x3p_read_dat)
+export(x3p_read_folder)
 export(x3p_read_plux)
 export(x3p_rotate)
 export(x3p_sample)
@@ -67,6 +68,7 @@ importFrom(assertthat,assert_that)
 importFrom(digest,digest)
 importFrom(dplyr,add_tally)
 importFrom(dplyr,arrange)
+importFrom(dplyr,as_tibble)
 importFrom(dplyr,between)
 importFrom(dplyr,desc)
 importFrom(dplyr,filter)

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,10 @@
 
 # x3ptools 0.0.4.9000
 
+## minor functionality
+
+* `x3p_read_folder` allows an import of multiple x3p files (recursively) into a single data frame (in tibble format) with a list variable of x3p objects.
+
 
 # x3ptools 0.0.4
 

diff --git a/R/x3p_read_folder.R b/R/x3p_read_folder.R
@@ -0,0 +1,22 @@
+#' Read all x3p files in a folder
+#' 
+#' This function is provided with a path to a folder, it will search recursively for all x3p files within the folder, read the x3p files, and return the results as part of a tibble dataset.
+#' @param path character string to a folder
+#' @return tibble with two variables: source contains the file path to the x3p file, and x3p is a list variable of x3p objects.
+#' @export
+#' @importFrom dplyr as_tibble
+#' @examples
+#' # example code
+#' path <- dirname(system.file("csafe-logo.x3p", package="x3ptools"))
+#' x3p_read_folder(path) # show all x3p files installed with x3ptools
+x3p_read_folder <- function(path) {
+  files <- dir(path, pattern = ".x3p$", ignore.case = TRUE, recursive = TRUE, full.names = TRUE, include.dirs = TRUE)  
+  if (length(files) == 0) {
+    warning(sprintf("No x3p files found at '%s'", path))
+    return(dplyr::as_tibble(data.frame("source" = NULL, "x3p" = NULL)))
+  }
+  read_x3p_try <- function(...) try(x3ptools::x3p_read(...))
+  scans <- lapply(files, FUN = read_x3p_try)
+
+  dplyr::as_tibble(data.frame(source = files, x3p = I(scans), stringsAsFactors = F))
+}
diff --git a/README.Rmd b/README.Rmd
@@ -228,3 +228,7 @@ x3p_image(logoplus, size=c(741, 419)/2, zoom=0.5, multiply = 30, file="man/figur
 ```{r, echo=FALSE}
 knitr::include_graphics("man/figures/logo-lines.png")
 ```
+
+### Acknowledgement
+
+This work was partially funded by the Center for Statistics and Applications in Forensic Evidence (CSAFE) through Cooperative Agreements 70NANB15H176 and 70NANB20H019 between NIST and Iowa State University, which includes activities carried out at Carnegie Mellon University, Duke University, University of California Irvine, University of Virginia, West Virginia University, University of Pennsylvania, Swarthmore College and University of Nebraska, Lincoln.
diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@ status](https://www.r-pkg.org/badges/version/x3ptools)](https://CRAN.R-project.o
 downloads](https://cranlogs.r-pkg.org/badges/last-month/x3ptools?color=blue)](https://r-pkg.org/pkg/x3ptools)
 [![Lifecycle:
 stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2024--03--02-yellowgreen.svg)](https://github.com/heike/x3ptools/commits/main)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--03--04-yellowgreen.svg)](https://github.com/heike/x3ptools/commits/main)
 [![Codecov test
 coverage](https://codecov.io/gh/heike/x3ptools/graph/badge.svg?token=80NyJNOg5b)](https://app.codecov.io/gh/heike/x3ptools)
 [![R-CMD-check](https://github.com/heike/x3ptools/workflows/R-CMD-check/badge.svg)](https://github.com/heike/x3ptools/actions)
@@ -178,6 +178,11 @@ visualize these raster images, e.g. using `ggplot2`:
 
 ``` r
 library(ggplot2)
+```
+
+    ## Warning: package 'ggplot2' was built under R version 4.3.2
+
+``` r
 library(magrittr)
 
 logo_df %>% ggplot(aes( x= x, y=y, fill= value)) +
@@ -332,3 +337,13 @@ x3p_image(logoplus, size=c(741, 419)/2, zoom=0.5, multiply = 30, file="man/figur
 ```
 
 <img src="man/figures/logo-lines.png" width="370" />
+
+### Acknowledgement
+
+This work was partially funded by the Center for Statistics and
+Applications in Forensic Evidence (CSAFE) through Cooperative Agreements
+70NANB15H176 and 70NANB20H019 between NIST and Iowa State University,
+which includes activities carried out at Carnegie Mellon University,
+Duke University, University of California Irvine, University of
+Virginia, West Virginia University, University of Pennsylvania,
+Swarthmore College and University of Nebraska, Lincoln.
diff --git a/man/x3p_read_folder.Rd b/man/x3p_read_folder.Rd
diff --git a/tests/testthat/test_read_x3p_folder.R b/tests/testthat/test_read_x3p_folder.R
@@ -0,0 +1,14 @@
+context("x3p_read_folder")
+
+
+test_that("x3p_read_folder works as expected", {
+
+  # Test nonexistent file path
+  expect_warning(x3p_read_folder(file.path("does", "not", "exist")))
+
+  # Test files installed with x3ptools
+  path <- dirname(system.file("csafe-logo.x3p", package="x3ptools"))
+  res <- x3p_read_folder(path) # show all x3p files installed with x3ptools
+  expect_equal(names(res), c("source", "x3p"))
+  expect_equal(class(res$x3p[[1]]), "x3p")
+})