zip: Zip and unzip raw .tif images for ZooImage and embed metadata

In SciViews/zooimage: Analysis of Numerical Plankton Images

Zip and unzip raw .tif images for ZooImage and embed metadata

Description

Perform simple zip/unzip operations on images. Corresponding metadata from .zim files are embedded as zip comments.

Usage

zipImg(imagefile, zimfile = NULL, check.zim = TRUE, replace = FALSE,
    delete.source = FALSE)
zipImgAll(path = ".", images = NULL, check.zim = TRUE, replace = FALSE,
    delete.source = FALSE)
unzipImg(zipfile, replace = FALSE, delete.source = FALSE)
unzipImgAll(path = ".", zipfiles = NULL, replace = FALSE,
    delete.source = FALSE)

Arguments

imagefile	file path of the .tif image to compress.
zimfile	file path of the corresponding .zim file (calculated automatically if NULL, by default).
check.zim	do we verify the .zim file before zipping data?
replace	do we replace existing .zip files?
delete.source	should the original .tif file be deleted (the .zim file is never deleted)?
path	directory where .tif images to be zipped are located.
images	a list of .tif images to zip. If NULL, the list of all .tif images present in path is computed.
zipfile	a zipfile to unzip.
zipfiles	a list of zipfiles to unzip. If NULL, a list of all .zip files found is path is calculated.

Value

All these functions are designed to be run in batch mode. Problems are reported as warnings, and the function always returns TRUE or FALSE, depending if the process succeeds or fails. The xxxAll() functions are convenient wrapper around batch() to process several items in a row. Take care that, despite the functions possibly use internal R code to zip or unzip files, they still need the zip and unzip programs for injecting and extracting .zim files metadata in the .zip archive!

Author(s)

Philippe Grosjean <[e-mail]>

See Also

zipNoteAdd, zipNoteGet

Examples

## Create a fake example of two .tif images and their associated .zim files
testdir <- file.path(tempdir(), "ziptest")
dir.create(testdir)
file.copy(system.file("examples", "BIO.2000-05-05.p72.zid",
    package = "zooimage"), testdir)
curdir <-setwd(testdir)
unzip("BIO.2000-05-05.p72.zid", junkpaths = TRUE)
## Keep only first 3 image plus the .zim file
unlink("BIO.2000-05-05.p72.zid")
unlink("BIO.2000-05-05.p72_dat1.RData")
unlink(dir(pattern = "[.]jpg$")[-(1:3)])
## Rename .jpg images, pretending they are .tif images
jpgFiles <- dir(pattern = "[.]jpg$")
tifFiles <- sub("[.]jpg$", ".tif", jpgFiles)
file.rename(jpgFiles, tifFiles)
## Recreate the .zim file
zimData <- readLines("BIO.2000-05-05.p72+A_dat1.zim", n = 32)
zimFile <- "BIO.2000-05-05.p72+A_.zim"
writeLines(zimData, zimFile)
unlink("BIO.2000-05-05.p72+A_dat1.zim")
## Here is what we got...
dir()

## Zip first image...
(zipImg(tifFiles[1]))
## It is added in the _raw subdirectory
dir()
zipDir <- file.path(".", "_raw")
dir(zipDir)

## Now, zip all images in batch and delete sources
(zipImgAll(".", delete.source = TRUE))
dir() # .zim files are never deleted!
(zipFiles <- dir(zipDir, full.names = TRUE)) # All three are there
## Force delete of the .zim file
unlink(zimFile)

## Unzip first zip file...
#####(unzipImg(zipFiles[1]))
## The image and .zim file are recreated
dir()
## Check extracted .zim file
#####all(readLines(zimFile) == zimData)

## Unzip all images...
(unzipImgAll(zipDir, replace = TRUE, delete.source = TRUE))
## All original files are there...
dir()
## and the _raw subdir is now empty
dir(zipDir)

## Reset and clean up
setwd(curdir)
unlink(testdir, recursive = TRUE)
rm(testdir, curdir, jpgFiles, tifFiles, zimFile, zimData, zipDir, zipFiles)

SciViews/zooimage documentation built on March 4, 2023, 4:03 a.m.