Gigapixel Viewer Instructions

Software to Install

• Windows: PuTTY

• MacOS / Linux : None

Instructions 

1. Select of the images from here and download it to you computer.

2. Next, rename the image you've downloaded to cs1951t_2020_YOUR_NAME.tif

3. If you are on:

   • MacOS / Linux: 

     • Open the terminal on your computer and navigate to the directory where you've downloaded the image.

     • Next, type: scp cs1951t_2020_YOUR_NAME.tif  YOUR_CCV_USERNAME@ssh.ccv.brown.edu:~/

     • This command will copy the image you've downloaded to your home directory on OSCAR.

     • Note that you will asked to enter your CCV password

   • Windows:

     • Open cmd and type: pscp -scp C:\PATH\TO\YOUR\DOWNLOAD\cs1951t_2020_YOUR_NAME.tif   YOUR_CCV_USERNAME@ssh.ccv.brown.edu:~/

4. If you are on:

   • MacOS / Linux:

     • Type: ssh YOUR_CCV_USERNAME@ssh.ccv.brown.edu in your terminal 

     • This will allow you to log into your CCV account 

   • Windows:

     • Open PuTTY 

     • Click on Session and in the Host Name field type: ssh.ccv.brown.edu

     • Next, click the Open button. 

     • Then, a new window will open and you will be asked to type your CCV username and password

5. Now, type ls to list the files in your home directory; you should see the filename of file you downloaded 

6. Now, type module load gigapixelviewer . This command will load the gigapixel viewer and its tools. 

7. Next, you will need to convert cs1951t_2020_YOUR_NAME.tif to a format supported by the gigapixel viewer. This can be done by using the convert command. More concretely, run: convertData cs1951t_2020_YOUR_NAME.tif cs1951t_2020_YOUR_NAME_out.tif

8. Then, copy your file to ~/data/cs1951t/gigapixel_imgs/ using the command: 

   • cp cs1951t_2020_YOUR_NAME_out.tif ~/data/cs1951t/gigapixel_imgs/

Previous Tutorial 

The examples (on the page this page is linked from) would be great to have converted to be viewable in the Gigapixel Viewer in the Yurt.  Below is part of a recipe to do so.  It is from the ccv cluster (ssh.ccv.brown.edu).  You can apply on their website for an exploratory account.

Gigapixel Data Conversion

Images have to be converted to be viewable with the Gigapixel viewer.

• 1. go to /users/cavedemo/demos/geoviewer/convertDataForGeoviewer/ as cavedemo user

  2. run convertData INPUTIMAGE.tif OUTPUTIMAGE.tif

  3. then add the image to the data-file which should be displayed as a new line. The entry should have a PTIF in front and 1 1 at the end, e.g. PTIF OUTPUTIMAGE.tif 1 1

More info from Benjamin Knorlein regarding making this kind of data viewable in the yurt:

1. The convertData script is also in the gigapixelviewer module and can be run from the commandline with 'convertData' after loading the module.

2. The configFile which is currently loaded for the button on the Demo-Tab is /tmp/yurt-data/geoviewerData/demo.prj. However, these are only copies on the local disk while the original resides in /users/cavedemo/data/model-tmp/geoviewerData/demo.prj. I would advise to only change the original and then to copy it to the tmp-folders. If the original is not changed after the next reboot the changes will be lost.

3. The files which are in /users/cavedemo/data/model-tmp are automatically copied to all /tmp folders of the nodes using the script /users/cavedemo/bin/copy_data_to_tmp. The script is executed after a reboot of the system to sync the folders model-tmp folder to the tmp-folders of the nodes. But you should be able to execute it if you want to update files once they are in the model-tmp.