Segmentation and Fitting

To run the LandTrendr segmentation and fitting procedure using outputs from the jdbcode/LandsatLinkr (LLR) library you need to modify two files included in the code library. One is a segmentation parameter file and the other is a batch file. Before you can run anything, however, you need to have completed the "Composite imagery" step of LLR. See the LLR user guide section on composite outputs to familiarize yourself with the files and directories that you'll be needing to define in the batchfile.

When running the LLR composite imagery step you defined a folder where the composite images are place. In this folder are subfolders for each spectral index that was composited. Currently it will include "tca", "tcb", "tcg", "tcw" (tasseled cap brightness, greenness, wetness, and angle). You will define the full path to these directories when you fill out the batchfile.

You need to create a folder for LandTrendr outputs, you can put this where you like - I usually put it at the same level as the composite image folders mentioned just a couple lines up. I call it "lt_outputs" or "landtrendr".

Keep this folder open so you can copy two files into it. These files will come from the code library. Copy the "segmentation_parameters.txt" file found in the "parameter_files" directory - paste it in the folder you just made. Now open the "run_files" directory in the code library and copy the "run_llr_lt_seg_and_fit_batchfile.pro" into the folder you just made.

Open the copied/pasted "segmentation_parameters" in a text editor (Notepad++ is a good). You need to edit the "run_name" and "base_index" parameters. The "run_name" is a unique identifier that will be added to the output filenames - just a descriptor to help keep your outputs organized - ie is this for a specific project you are working on. The "base_index" parameter tells the segmentation and fitting procedures what the spectral index it is that you are running so it know how to interpret spectral trend direction. It is really important that it is defined strictly as either: brightness, greenness, wetness, or tcangle - whichever you happen to be running. The other parameters affect the segmentation algorithms and can be set as you like, though the defaults are generally appropriate. For more information see Robert Kennedy's paper describing the method or his instructions on github. Save the file.

The last step is to edit the batchfile. Open the copied/pasted "run_llr_lt_seg_and_fit_batchfile.pro" file in IDL. There are 6 parameters.

• llr_composite_dir: provide the full path to the llr composite image index directory you want to run LandTrendr on. It should be the same index you just defined in the "segmentation_parameters" file. Example: "K:\test\composite\tca" - make sure the "" character is at the end of the path.
• lt_output_dir: full path to the LandTrendr outputs directory you just made and copied the "segmentation_parameters" and "run_llr_lt_seg_and_fit_batchfile.pro" files to. Example: "K:\test\composite\landtrendr" - make sure the "" character is at the end of the path.
• seg_params_txt: full path to the "segmentation_parameters" file you just edited. Make sure that the in "base_index" parameter you set in it corresponds to the "llr_composite_dir" path you just set. Example: "K:\test\composite\landtrendr\tca_segmentation_parameters.txt"
• mask_image: full path to a region of interest file that defines what pixel LandTrendr should be run on. It should be a .bsq raster file that contains only values 1 and 0. 1 for pixels to run LandTrendr on and 0 to ignore. This file can be the same file you provided to the LLR compositing function. However, you may need to convert it to a .bsq file - gdal can be helpful here, I will add a function to the LLR library as well. Example:"K:\test\composite\useareafile.bsq"
• eval: a logical parameter for setting whether to run LandTrendr in evaluation mode (run every 3rd pixel and interpolate the rest) or full. 0 for full, 1 for evaluation.
• resume: a logical parameter for resuming a LandTrendr run that has crashed because of a power or data transfer interruption. If this situation occurs, set resume to 1 and the process should continue where it was just before being interrupted. Leave set a 0 otherwise.

When you have finished editing the batchfile, save it and in the IDL command prompt type the @ symbol followed by the full path to the "run_llr_lt_seg_and_fit_batchfile.pro" file you just edited enclosed in quotes and hit enter. Example: @"K:\test\composite\landtrendr\tca_run_llr_lt_seg_and_fit_batchfile.pro"

IDL should be cranking away and a progress bar should be reporting its status. Files should be generated in a spectral index subfolder of the LandTrendr outputs folder you defined. You need to repeat the above steps for all spectral indices you want processed with LandTrendr. I use the same LandTrendr folder and just make new copies of the "segmentation_parameters.txt" and "run_llr_lt_seg_and_fit_batchfile.pro" files with unique spectral indices appended to the file names.