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Bug 411 - Stitching from known tile configuration file does not work
Stitching from known tile configuration file does not work
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-03-06 18:33 CST by Sietse Braakman
Modified: 2012-03-06 18:57 CST
1 user (show)

See Also:

Attachments
Settings in dialog box (65.23 KB, image/png)
2012-03-06 18:33 CST, Sietse Braakman

Description Sietse Braakman 2012-03-06 18:33:11 CST 
I used the Grid/Collection plug-in to stitch greyscale .tif files together using a predefined set of translation points from another stitch (which was successful).
I selected the folder with my images, selected max intensity fusion, did not touch the three parameter and did not select any of the three check boxes. I then clicked go and got the following error:
----
java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:637)
Caused by: java.lang.NullPointerException
	at plugin.Stitching_Grid.getLayoutFromFile(Stitching_Grid.java:721)
	at plugin.Stitching_Grid.run(Stitching_Grid.java:336)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	... 8 more
----


The TileConfiguration.registred-file
----
# Define the number of dimensions we are working on
dim = 2

# Define the image coordinates
2_120125010.tif; ; (0.0, 0.0)
2_12012502.tif; ; (-363.9996, -2998.9973)
2_12012503.tif; ; (-365.9996, -2671.9973)
2_12012504.tif; ; (-368.9996, -2292.9973)
2_12012505.tif; ; (-301.99963, -1908.9977)
2_12012506.tif; ; (-228.99971, -1532.9982)
2_12012507.tif; ; (-231.99977, -1145.9987)
2_12012508.tif; ; (-173.99983, -733.9991)
2_12012509.tif; ; (-81.999916, -354.99954)
----

Thanks for your help! Best regards,

Sietse Braakman


Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_15
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_15-b03-219
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 14.1-b02-90
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

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Comment 1 Sietse Braakman 2012-03-06 18:33:55 CST 
Created attachment 57
Settings in dialog box
Comment 2 Stephan Preibisch 2012-03-06 18:48:10 CST 
It is not a "real" bug, it means that he could not find the tileconfiguration file. I added a message telling the user exactly this. 

Please just check that the tileconfiguration.registered.txt that you want to use as input exists (and points to the right files that you want to stitch)
Comment 3 Stephan Preibisch 2012-03-06 18:57:21 CST 
I see the little mistake in the attachment, the ".txt" is missing in "tileconfiguration.registered.txt" ...