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Bug 593 - TrakEM2 mipmap generate replciates images fetched via http
TrakEM2 mipmap generate replciates images fetched via http
Status: NEW
Product: Fiji
Classification: Unclassified
Component: TrakEM2
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-04-23 09:23 CDT by Eric Perlman
Modified: 2013-04-23 14:21 CDT
4 users (show)

See Also:

Attachments
Simple project with two tiles (14.91 KB, text/xml)
2013-04-23 09:26 CDT, Eric Perlman

Description Eric Perlman 2013-04-23 09:23:52 CDT 
We often generate TrakEM2 projects where each of the patches are retrieved via http rather than the local file system.  At some point in the past few months, this functionality is now broken in a very weird way:  the image contents end replicated accross multiple patches.

Basically, if a project conains 10 patches, the first five will be a replica of the first patch, and the next five will be a replica of the second.

To reproduce:
- Patches must have a remote file path (file_path="http://...")
- n_mipmap_threads >= 2
- Patches must be "slow" to load (~ >= 1M)

I will attach a sample project file when I figure out how to do that. ;-)

I suspect the problem lies with ij.io.Opener.openURL() being called from multiple mipmap threads, but I haven't ruled out the TrakEM2 mipmap generation code either.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.8.3
  java.version => 1.6.0_45
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_45-b06-451-11M4406
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.45-b01-451
  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: CHECK_TURNED_OFF

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 Eric Perlman 2013-04-23 09:26:02 CDT 
Created attachment 97
Simple project with two tiles

This project shows the most simple case where I am able to "confuse" the mipmap generation.  On both my Mac and Linux machine, these two patches will appear to be the same image
Comment 2 Albert Cardona 2013-04-23 09:35:16 CDT 
Eric,
indeed nothing has changed on the TrakEM2 side. This means the way ImageJ opens the file from an URL has changed, and likely has become not Thread-safe anymore.

Having looked at the ij.io.Opener.openURL, nothing there looks unsafe, neither has changed recently that I know of. The one potential issue is with the HandleExtraFileTypes, which I have read in the list has changed recently. Johannes, Curtis, do you know about potential non Thread-safe changes to HandleExtraFileTypes that could explain this issue?
Comment 3 Johannes Schindelin 2013-04-23 11:34:58 CDT 
Albert, maybe you can come up with unit tests displaying the issue?
Comment 4 Albert Cardona 2013-04-23 14:18:30 CDT 
Eric,
which images are you using? MRC, TIFF, ... ?
Comment 5 Eric Perlman 2013-04-23 14:21:13 CDT 
Uncompressed 8-bit TIFF

See the example project if needed -- I copied the source images to an external server.