CTFS Tutorials

• Tutorials: Top Level
• Server Use
• Growth changes
• Mortality changes
• Mortality vs. dbh
• Population Changes
• Biomass
• Growth vs. DBH
• ImageJ
• Plot maps
• Topography

Source file: http://ctfs.si.edu/ctfsdev/CTFSRPackageNew/files/tutorials/imageJTutorial

ImageJ

This tutorial demonstrates use of an R program designed to read all quadrat maps created by imageJ, converting the digitized pixel to coordinates within a quadrat (local coordinates). The commands shown here lead step by step through the process. The input imageJ files must be named in a very specific way, and there must be 4 separate files for each quadrat, in the case of 10x10 m sections of a single 20x20 m quadrat.

This tutorial is also available for download as a pdf from https://ctfs.arnarb.harvard.edu/Public/CTFSRPackage/tutorials/imageJTutorial/imageJ.pdf.

1. Directory and file naming

All files must be stored in one folder, and that overarching folder can be given any name. You need to give the entire path of this folder as a parameter to the function. The map files may all be saved in one folder, divided into column subfolders, or even into quadrat sub-subfolders. In a laptop running Unix, for example, the maps may be in the folder ’/home/condit/data/other_plots/rabi’. On a Windows system, the entire path would be something like ’c:/data/other_plots’ etc. A Mac uses :: instead of slashes. In the following examples, I assign this folder to a variable called mapfolder. You will have to name mapfolder to the name appropriate for your computer.

We suggest you save the files using the folder structure detailed below, which makes it easy to find a particular map or quadrat. It is not absolutely necessary to use this structure, but you do need to use the following file naming convention: 1. you have to use the same prefix for all the resulting quadrat files 2. they should all use the same delimiter (comma- or tab-delimited) 3. the quadrat names have to have 4 digits (i.e. pad with zeros for single digit columns or rows) 4. the subquadrat suffixes should be named consistently (i.e. the first suffix refers to the lower left subquadrat, second suffix to the upper left subquadrat, third suffix to the upper right subquadrat, and the fourth to the lower right subquadrat)

Within mapfolder, we suggest you make one folder for each column of data. These folders can be named ’Column##’, for example ’Column01’, ’Column02’, etc. Within every one of the Column folders, there can be one subfolder per quadrat, and each can be named Quadrat_##, for example Quadrat_0101, Quadrat_2309, etc. Within those quadrat subfolders, there should be four imageJ files named Map_####_#.txt, for example Map_0101_1.txt, corresponding to the maps of the four subquadrats. The first number (usually 4 digits) is the quadrat number, matching the number for the Quadrat folder it is in. The second number may be a 1, 2, 3, or 4, indicating which of the 4 subsections of the map is included in the file.

mapfolder

• Column01
  • Quadrat_0101
    • Map_0101_1.txt
    • Map_0101_2.txt
    • Map_0101_3.txt
    • Map_0101_4.txt
  • Quadrat_0102
  • Quadrat_0103
  • Quadrat_0104
  • Quadrat_0105
    • Map_0105_1.txt
    • Map_0105_2.txt
    • Map_0105_3.txt
    • Map_0105_4.txt
  • etc
• Column02
  • Quadrat_0201
    • Map_0201_1.txt
    • Map_0201_2.txt
    • Map_0201_3.txt
    • Map_0201_4.txt
  • Quadrat_0202
  • Quadrat_0203
  • Quadrat_0204
  • Quadrat_0205
  • etc
• etc

2. Executing

Download and Source the CTFS R Package following instructions at the home page.

The conversion program is called fullplot.imageJ. As a test, run it first with just one folder by setting the path to that folder. The other arguments are:

• Colrange specifies the range of the columns and rowrange the range of the rows, as per the first two digits and last two digits respectively, of our quadrat naming convention
• Gridsize is the size of each individual map.
• When include.subdir=F, only the folder specified in the path parameter is searched for map files. If include.subdir=T, all subfolders under the folder specified in the path parameter are searched also.
• Four arguments name map corners; they must match the labels in the imageJ output for the four corners of each map. They must be identical for every map, else the program cannot work. It does not matter where these four rows appear in the file; they can be any rows and in any order.
• The corner labels are caps-insensitive, so the labels p1 and P1 will be considered identical.
• The prefix used to name the map files should be consistent. It can be Map_ or just plain q, for example.
• The subquadrat suffixes should be consistent, and named clockwise from the lower left subquadrat.
• Setting outfile=NULL means the data will NOT be written to a file, only returned as the R object named coords.col02.

In the example below, I set a variable mapfolder to the name of the directory where one of the column folders are found. You will have to set this to the folder on your computer.

If that works, then execute from the rabi folder. Every column will be read and converted. The program will read all files within the Quadrat subfolders.

All the values should be between 0 and 20. If this works, you can repeat, this time saving the results to a text file. The file will be saved into the folder specified in the path. The four columns of this file can then be uploaded into the tempLocations table in the database via a simple SQL script.

3. Sweaving

These are the commands used to create the HTML help page; they are not involved with imageJ.