Overview

This is a temporary workflow until the JRSO has the opportunity to integrate image reduction in the Correlation Downloader application.

To use images in the Correlator 4 application, you need to:

1. Retrieve the correct images from the LIMS via LORE;
2. Place the images in a specifically named R directory;
3. Run the provided R script to reduce and rename the images;
4. Place the reduced images in the correlation data directory from where the Correlator app will import them.

Your Desktop directory

You can organize your worksspace workspace as you like. However, the image reduction process requires that the file path in the provided R script match your directory. Your will also manage quite a bit of data so keeping things orderly helps. Here is a recommended structure for the overall process.

• Desktop

  • Data from LIMS for Correlator (the folder Correlator will remember to look at for data updates)

    • Site U###1 (has files for each hole and datatype for a site, and a folder for each hole with reduced images)
      • Hole A data type 1 file
      • Hole A data type 2 file
      • ...
      • Hole B data type 1 file
      • Hole B data type 2 file
      • ...
      • Hole A image folder
      • Hole B image folder
      • ....
    • Site U###2
      • .....
    • Peter's play data (a subdirectory with legacy data to exercise)

  • Image reduction for Correlator

    • ImageResample_input (has hole folders with large images downloaded via LORE)
      
      • SiteHole A folder with images
      • SiteHole B folder with images
      • ...
    • ImageResample_output (has hole folders with reduced and renames images for Correlator)
      
      • SiteHole A folder with images
      • SiteHole B folder with images
      • ...
    • ImageResample.R (the script that reads from input folder and writes to output folder)
  • Correlation plots (your plots of the correlation results using whatever tool you like, e.g., Kaleidagraph)
    
    • Site U###1
      • your plots
    • Site U###2
      • your plots
    • ...

Retrieve images from LORE

• Go to the LORE page at
  • http://web.iodp.tamu.edu/LORE/  (shore)
  • http://web.ship.iodp.tamu.edu/LORE/ (ship) 
• Select the Images > Core Section (LSIMG) > Standard report
• Select the hole for which you want to reduce the section half images
• Click View data, then click Batch download linked files
• When prompted, click Cropped image (JPG link)
• Click the Chose a link button.
  • A zip file with all the images will be written to whatever download folder your workstation has configured.

Place images in the R directory

On your Desktop, find or create a folder named Image reduction for Correlator. Inside this folder:

• ImageResample_input
  • This is where you put a folder for each hole with images.
• ImageResample_output
  • This is where the script will place the reduced images.
• ImageResample.R
  • This is the script that should be in that folder.

ImageResample_input:

• create a subfolder with the hole name, as in 'U1476A'
• place all images downloaded for that hole in the folder, as in:
  • img_redux_input/U1476A/(all image files for Hole U1476A)
• Note: you can keep the hole folders or delete them when you are done with a hole. Just make sure only one is not commented out in the script.

Run the R script

Double-click the img_redux script to open it.

First time you use the script:

• If you name your top directories differently from what is shown in the previous section, you may need to adjust the file paths in the script.
  • Ask your friendly IT technician if you struggle with directory paths.
  • Once this is set correctly, it should not bother you for the remainder of the project.

Each time you run another batch of images, you need to add or edit a line in the script (see section '1.3. Set the test'):

• Typically, a test means running all image files of a hole, but it could also be any subset of images. Thus, you typically want:
  •  test="U1476A"
  • Note quotation marks!
  • The test name must exactly match a subfolder name in the img_redux_input folder (or the script will create it).
• You can overwrite the hole name for each test, or you can add test lines: the last one that is not commented out will be executed, i.e.:
  • #test="U1476A"     #Will be skipped
  • #test="U1476B"     #Will be skipped
  • test="U1476C"      #Will be executed

Run the script:

• Save the changes to the script (recommended).
• Select all and press command-return (or click the RUN button in RStudio).
• Get coffee and a cookie while the program will:
  • Loop through the test (hole) input directory to load and process one image at a time.
  • Crop the images by 200 pixels on each side (can be changed to any number of pixels in the script).
  • Scale the images to 25% (targeting ~200 kb per image, can be set at any percentage in the script).
  • Rename the image files to a simpler section half ID.
  • Write the reduced file to the img_redux_output folder. 
• You should find the reduced images in the img_redux_output folder.
  • Images should each be in the order of ~200 kb, which is the maximum that Correlator can display.
  • The output file size is based on the latest camera resolution and the reduction parameters set in the script. If you are working with older images that had half (one quarter) of that resolution, the parameters might have to be adjusted in the script.

Move the reduced images into the Correlator site folder

As recommended elsewhere, you should have a data folder for each site in your top folder from where Correlator is importing data, something like:

• .../StratigraphicCorrelation
  • IMG_REDUX
    • img_redux (script)
    • img_redux_input (folder)
    • img_redux_output (folder)
  • Site U1476
    • data_type-hole files from Correlation Downloader
    • image folder for each hole, moved here from the img_redux_output folder
  • Site U1477
    • etc.

Now move your test (hole) folder from the img_redux_output folder into the site data folder.