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Basic GDAL/OGR/PKTOOLS Commands

Basic GDAL Commands

 ssh -X YaleID@omega.hpc.yale.edu

Get the geo Software

 cp -r /lustre/scratch/client/fas/sbsc/ga254/software/*  $HOME

Copy the .bashrc to set software links

 cp /lustre/scratch/client/fas/sbsc/ga254/software/.bashrc $HOME
 source $HOME/.bashrc

Data Directory: /lustre/scratch/client/fas/geodata/aw524/data/

Change the directory, and explore the files.

ls /lustre/scratch/client/fas/geodata/aw524/data/
gdalinfo /lustre/scratch/client/fas/geodata/aw524/data/worldclim/bio_9.bil

Reply to the following questions:
What is the pixel size?
How do you get min and max pixel values?

Calculate minimum and maximum values for all the images:

for file in  /lustre/scratch/client/fas/geodata/aw524/data/worldclim/bio_*.bil ; do 
gdalinfo  -mm  $file # write a bash command to get only min/max values
done


Exercise:
Use one of the gdal commands and try to clip all the images using a square box:
xmin : -81
xmax : -63
ymin : -19
ymax : 12

  1. Open gedit and save the the script with the extension .sh
   gedit cropscript.sh
  1. Create a working directory in your home
  2. Identify the gdal command going to the gdal Internet site.
  3. Identify the option of the command to make the clip using the given coordinates .
  4. Do a test with one image and open it by openev.
  5. Create a loop for all the images.


Use all the previous examples stored in this wiki.
All the commands have already been explained - you just need to combine them.
Your script should be able to be run the script by bash cropscript.sh.

mkdir ~/cropimage
 
for file in  /lustre/scratch/client/fas/geodata/aw524/data/worldclim/bio_*.bil ; do
filename=$(basename $file) 
gdal_translate   -projwin  -81 12 -63 -19 $file   ~/cropimage/crop$filename  
done

Basic PKTOOLS Commands

Perform a composite (getting the mean) between two images.

Create a composite
 pkcomposite  -of GTiff   -co COMPRESS=LZW -co ZLEVEL=9 -ulx -81 -uly 12 -lrx -63 -lry -19 \
 -cr mean -i /lustre/scratch/client/fas/geodata/aw524/data/worldclim/bio_1.bil \
 -i /lustre/scratch/client/fas/geodata/aw524/data/worldclim/bio_2.bil  -o mean.tif

Check the nodata value in the image and set it in the pkcomposite. Re-run

Set up a mask
 pksetmask -i mean.tif  -m mean.tif  -msknodata 150 -nodata 0 -p '<' -o mean150.tif

You can find more example here or the in offcial pktools page

wiki/gdalbasic_yale.txt · Last modified: 2017/12/05 22:53 (external edit)