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

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

Assuming that you have a 'StratigraphicCorrelation' folder at the top of your workstation directory, create a subfolder 'IMG_REDUX' as in :

• /Users/daq/Documents/StratigraphicCorrelation/IMG_REDUX

The IMG_REDUX folder should have the script and must have the following two subfolder in it:

• img_redux_input
• img_redux_output

In the input folder:

• 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.Modify

First time you use the script to run the batch of images you want to reduce.:

• If you name your top directories differently than from what is shown in the previous section, you may need to adjust the folder namesfile 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.
  Add

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 green RUN arrow.
• 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 The reduced images should be 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 resulting 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 the (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_input
    • img_redux_output
  • Site U1476
    • data_type-hole files from Correlation Downloader
    • hole folders with images from IMG_REDUX
  • Site U1477
    • etc.

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