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Probability Map Viewer in single image analysis mode

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Chris Churas edited this page Jul 18, 2018 · 16 revisions

This page provides a tutorial on running Probability Map Viewer in single image analysis mode which just performs probability map generation on a single tiled image using Image Magick convert utility to threshold the image.

Requirements to run this tutorial

  • Centos 6+, Ubuntu 12+, and most other linux distributions should work
  • Java 8+ (jdk to build)
  • Image Magick command line programs (namely convert)
  • Internet connection
  • Web browser. This tutorial was tested on Chrome 52 on Centos 7.2.
  • Wget

OR

One can launch via AWS CloudFormation by following instructions here:

Launch Probability Map Viewer via AWS CloudFormation

Step 1) Download Probability Map Viewer

Instructions can be found here

Step 2) Tile image

This step downloads example.png and tiles it using ImageMagick's convert command

wget https://github.com/CRBS/probabilitymapviewer/wiki/images/example.png
# If no wget or on Mac os try:
# curl -L https://github.com/CRBS/probabilitymapviewer/wiki/images/example.png 
mkdir tiles
convert example.png -crop 128x128 -set filename:tile "r%[fx:page.y/128]_c%[fx:page.x/128]" +repage +adjoin "tiles/0-%[filename:tile].png"

Step 4) Download threshold script

wget https://github.com/CRBS/probabilitymapviewer/wiki/data/myprobmapgenerator.sh
chmod a+x myprobmapgenerator.sh

Step 4) Launch Probability Map Viewer

java -jar probabilitymapviewer-3.0.0-jar-with-dependencies.jar --inputimage ./tiles --disableanalyzingtile --imageheight 4000 --imagewidth 5500 --cores 1 --custom Threshold,red,./myprobmapgenerator.sh,52%

Things to note about above command:

  • --imageheight and --imagewidth are set to the size of this example image. For larger images set accordingly.

  • --disableanalyzingtile turns off a feature in Probability Map Viewer that displays a lighter color overlay tile for the tiles that are currently being processed. Reason for this is some browsers (firefox) seem to cache this tile and never show the real probability map.

  • --cores sets the number or probability map generator jobs that can run concurrently. This lets a user throttle the load on the server for more intensive processing such as CHM.

  • --custom flag lets caller add probability map generator scripts. See Probability Map Viewer Custom Flag for more information.

Step 5) View Probability Map Viewer in browser

Launch browser and go to: http://localhost:8080 which should bring a page that looks like the following:

initial page

Click on the layer icon (3 squares pancaked together in upper left corner) which can be seen in the image above.

Select the Base image radio button to display the tiled image as seen below:

image shown

Image should now be visible as seen below:

image shown

Step 7) Display threshold probability map generation

Click on layer icon again and click the checkbox for the newly added layer Threshold this should add the overlay as seen below:

overlay added

The solid colored overlays are those to be analyzed. After 10 or so seconds the solid colored overlays will be replaced with probability maps as seen below:

some probability maps

Feel free to left click and drag the mouse to move around the image. As the image is panning the Probability Map Viewer will generate probability maps for the tiles displayed.

To shutdown Probability Map Viewer click the red power icon in the browser or in the window the Probability Map Viewer jar was invoked hit Ctrl c

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