zidb: Manage .zidb files (ZooImage Databases)
In SciViews/zooimage: Analysis of Numerical Plankton Images

zidb	R Documentation

Manage .zidb files (ZooImage Databases)

Description

Compress, uncompress .zidb files that contain data for a sample. Starting from ZooImage 3, the new format uses filehash tables for better performances. Conversion from and to the old .zid format (a zip archive indeed) is supported for compatibility with old datasets. Display content of a .zidb file is a simple way (both data/metadata and vignettes)

Usage

zidbMake(zidir, zidbfile = paste0(sub("[/\\]+$", "", zidir), ".zidb"), zisfile =
    file.path(dirname(zidir), "Description.zis"), type = "ZI5", smptime = "",
    check = FALSE, check.vignettes = FALSE, replace = FALSE, delete.source = replace)
zidbMakeAll(path = ".", samples, zisfiles = file.path(dirname(samples),
    "Description.zis"), type = "ZI5", check = FALSE,
    check.vignettes = FALSE, replace = FALSE, delete.source = replace)

zidToZidb(zidfile, zisfile = file.path(dirname(zidfile),
    "Description.zis"), replace = FALSE, delete.source = replace)
zidToZidbAll(path = ".", zidfiles, zisfiles = file.path(dirname(zidfiles),
    "Description.zis"), replace = FALSE, delete.source = replace)
zidbToZid(zidbfile, zisfile = file.path(dirname(zidbfile),
    "Description.zis"), replace = FALSE, delete.source = replace)
zidbToZidAll(path = ".", zidbfiles, zisfiles = file.path(dirname(zidbfiles),
    "Description.zis"), replace = FALSE, delete.source = replace)

zidbLink(zidbfile)
zidbDatRead(zidbfile)
zidbSampleRead(zidbfile)
zidbSummary(zidbfile, n = 3)

zidbPlotNew(main = "ZooImage collage", ...)
zidbDrawVignette(rawimg, type, item, nx = 5, ny = 5, vmar = 0.01)
zidbPlotPage(zidbfile, page = 1, title = NULL, type = "guess", method = NULL,
class = NULL)

Arguments

`zidir`	a directory containing data to put in a .zidb files.
`zidbfile`	the path of the .zidb file.
`zidbfiles`	the path of a series of .zidb files.
`zidfile`	the path of a .zid file.
`zidfiles`	the path of a series of .zid files.
`zisfile`	the path of the .zis file that contains description of this sample.
`zisfiles`	the path of a series of .zis files that contain description of the processed samples.
`type`	the ZI file format, currently only 'ZI5' type is supported. For `zidbDrawVignette()` and `zidbPlotPage()`, it is the type of vignette image. Currently, it can be either "jpg", or "png". If not provided, or if `type = "guess"` it will be guessed by the function.
`smptime`	the time the sample was collected. This value will replace a `<<<TIME>>>` placeholder in the metadata. You can also use `<<<SMP>>>` and `<<<DATE>>>` placeholders in corresponding metadata and they will be replaced by values computed from the sample name.
`check`	do we check the files in this directory before/after compression?
`check.vignettes`	do we check if the future .zidb file contains all vignettes? This is `FALSE` by default because they may not exist yet. This is the case when they are generated on the fly, like in the new version 5.5 processes.
`replace`	do we replace existing files?
`delete.source`	do we delete source files after compression?
`n`	the number of line of the data to print. If `n <= 0` no data is printed (only metadata).
`path`	look for files in this path.
`samples`	a list of 'samples', i.e., subdirectories to process.
`main`	the title of the new plot.
`...`	further arguments passed to the `plot()` function.
`rawimg`	the raw content of a vignette, as stored in a .zidb file.
`item`	the item number to draw (enumeration from left to right and from top to bottom).
`nx`	the number of vignettes in a column.
`ny`	the number of vignettes in a row.
`vmar`	the relative size of vignette margins.
`page`	the page to display (each page contains 25 vignettes).
`title`	the title of the page.
`method`	the name of the validation method to use to extract validation data.
`class`	a character vector with one or more classes for the validation data that we want to keep.