import: Function to import data from the FlowCAM

In SciViews/zooimage: Analysis of Numerical Plankton Images

Function to import data from the FlowCAM

Description

These functions read data and metadata from FlowCAM runs and import them into ZooImage objects.

Usage

readFlowCAMctx(ctx, stop.it = TRUE)
readFlowCAMlst(lst, skip = 2, read.ctx = TRUE)
importFlowCAM(lst, rgb.vigs = FALSE,  type = "ZI3", replace = FALSE)

Arguments

ctx	the path to a .ctx FlowCAM file.
stop.it	should the process stop in case of an error? Set this to FALSE when you run in batch mode and want the error to be repported back to the calling code.
lst	the path to a .lst FlowCAM file.
skip	the number of lines to skip in the .lst table before reading the data. This is usally two lines.
read.ctx	should we also read the .ctx file with readFlowCAMctx()?
rgb.vigs	do we build color vignettes that mix OD, visual and mask in the three RGB channels? By default, not (FALSE)
type	the type of .zidb file to create. Currently, only supports type = "ZI3" (defaulf value).
replace	a boolean indicating if an existing .zidb file should be replaced by a new one.

Details

The Visual Spreadsheet software provided with the FlowCAM is constantly changing specifications from version to version. This is mainly tested with VS 1.5.14 and 3.2.3.

Value

A zidb object with the converted data, metadata and images.

Author(s)

Philippe Grosjean <[e-mail]>

See Also

selectObject

Examples

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