Peroxi Tracker

Build & Pack

• Mouse double-click BuildJar.ant
• Select menu > Run > Run

Debug

• Launch Eclipse with PeroDriver as main class

Run as Hadoop task

• upload Peroxitracker.jar and Peroxitracker_lib to

$ ssh <Hadoop-NameNode>

• load MapReducer job with external libraries, with argument -libjars dir/A.jar,dir/B.jar,dir/C.jar
• Syntax: hadoop jar -libjars <HDFS_Input_Dir> <HDFS_Output_Dir>

$ hadoop jar Peroxitracker.jar -libjars Peroxitracker_lib/ij.jar input output

Done

• Pipeline HDFS file system to ImageJ, through InputStream objects

ToDo: Break X11 requirements by rewriting code

• IJ.run() requires X11 environment, not feasible for Azure environment
• See Well.java contrastEnhance() function.
• Refer - http://imagejdocu.tudor.lu/doku.php?id=faq:technical:how_do_i_run_imagej_without_a_graphics_environment_headless
• Tried headless.jar patch from http://sourceforge.net/projects/imageja/files/headless/experimental/
• Unfortunately it's not okay due to invalid signature.
• Error code

  No X11 DISPLAY variable was set, but this program performed an operation which requires it.
	at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159)
	at java.awt.MenuComponent.<init>(MenuComponent.java:145)
	at java.awt.MenuItem.<init>(MenuItem.java:174)
	at java.awt.MenuItem.<init>(MenuItem.java:158)
	at java.awt.Menu.<init>(Menu.java:132)
	at java.awt.Menu.<init>(Menu.java:112)
	at ij.Menus.getMenu(Menus.java:690)
	at ij.Menus.getMenu(Menus.java:680)
	at ij.Menus.addMenuBar(Menus.java:105)
	at ij.IJ.init(IJ.java:325)
	at ij.IJ.run(IJ.java:252)
	at ij.IJ.run(IJ.java:316)
	at peroJava.Well.contrastEnhance(Well.java:24)

Cell counting starts...
warning: your version of GraphicsMagick limits images to 8 bits per pixel
error: regionprops: first input argument must be a NxM matrix
error: called from:
error:   /usr/share/octave/packages/image-1.0.14/regionprops.m at line 100, column 5
error:   /home/cloudera/AzureBlob/MATLAB/cell_object_identification.m at line 68, column 4
error:   /home/cloudera/AzureBlob/MATLAB/Peroxitracker.m at line 37, column 30