colorZapper

Extract colour from user defined areas.

remotes::install_github("mpio-be/colorZapper")

require(colorZapper)
# path to image directory
dir = system.file(package = "colorZapper", "sample")
# open/create a colorZapper file
cz_file = tempfile(fileext = '.sqlite')
CZopen(path = cz_file)
# associate files with the opened file
CZaddFiles(dir)

Interactively define points or polygons

# define 1 point per image
CZdefine(points = 1)

# check status
CZshowStatus()

# over-write points defined for Falco_peregrinus (id = 2)
CZdefine(points = 1, what  = 2)
CZshowStatus()
# define points using marks
# 2 points per mark = 4 points per image
# 'what' is set so only particular images are going to be loaded
CZdefine(points = 1, marks = c("wing", "tail") , what = 4)
CZshowStatus()

#define polygons: 1 polygon per mark
# see help(locator) for info on how to draw on an R graphic. 
CZdefine(polygons = 1, marks = c("wing", "tail"), what = 3 )

Extract RGB values from Regions of Interest

CZextractROI()

# fetch data
d = CZdata(what = 'ROI')

Extract RGB values from the entire image (batch mode).

CZextractALL()
d = CZdata(what = 'ALL')

Points to remember:

• CZ works better outside Rstudio so just run it from a plain R console.
• Data are saved to a database file on your disk so you can stop and resume your work any time.