fullplot.imageJ: Convert pixels to coordinates within a quadrat.
In forestgeo/ctfs: Tools for the Analysis of Forest Dynamics

Description Usage Arguments Details Arguments details Examples

Reads quadrat maps created by imageJ, converting the digitized pixel to coordinates within a quadrat (local coordinates).

fullplot.imageJ(path = "", outfile = "plotLxLy.txt", delim = ",",
  include.subdir = T, corners = c("p1", "p2", "p3", "p4"),
  colrange = c(0, 49), rowrange = c(0, 24), prefix = "Map_",
  suffix = ".txt", subquadsuffix = c("_1", "_2", "_3", "_4"),
  gridsize = c(10, 10), debug = NULL)

`path`	The complete path name where the map files to be converted are found.
`outfile`	Filename for output.
`include.subdir`	whether the subfolders are to be searched for map files also
`corners`	specify the tags used for the map corners used for calibration. They must be named in a clockwise direction starting with the lower left corner. These tags must be the same in each and every map file.
`colrange`	specifies the range of the columns, found as the first two digits of the quadrat name
`rowrange`	specifies the range of the rows, found in the last two digits of the quadrat name
`prefix`	the prefix used for all the map files before the quadrat name
`suffix`	the extension used for the map files. The imageJ default is ".txt".
`gridsize`	Size of each individual map.
`debug`	Logical. If TRUE, call browser to debug.
`subquadratsuffix`	Suffixes used to indicate what section of the map the subquadrat refers to. They should be named clockwise from the lower left. It can be used for map files that are smaller than 20x20m (i.e. 10x10m).

The input imageJ files must be named in a very specific way: all should have the same prefix and the quadrat names should have 4 digits. If there are subquadrats, the names should end with the same consistent suffixes. Only those files with this specific naming convention are read and converted. Updated Aug 2014 to handle files with no trees (just 4 corner labels).

outfile This file will be saved in the folder specified by the path. If outfile = NULL, the results will not be written to a file.

## Not run: 
mapfolder = '/maps/rabi/'
coords =
  fullplot.imageJ(
    path = mapfolder,
    include.subdir = T,
    gridsize = c(10, 10),
    outfile = 'location.txt',
    corners = c('p2', 'p1', 'p4', 'p3'),
    prefix = 'Map_',
    colrange = c(0, 49),
    rowrange = c(0, 24),
    subquadsuffix = c('_1', '_2', '_3', '_4')
  )
head(coords)
dim(coords)
range(coords$lx)
range(coords$ly)

## End(Not run)