zidb {zooimage}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.

Author(s)

Philippe Grosjean <Philippe.Grosjean@umons.ac.be>

See Also

zidCompress

Examples

##TODO...

[Package zooimage version 5.5.2 Index]