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Bug 444 - Stitching Plugin Problem
Stitching Plugin Problem
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P2 major
Assigned To: Stephan Preibisch
Depends on:
Blocks:
 
Reported: 2012-06-26 11:06 CDT by Sebastian Rhode
Modified: 2014-06-16 13:34 CDT
2 users (show)

See Also:

Description Sebastian Rhode 2012-06-26 11:06:51 CDT
Hi,

i tried to stitch a data set. The data are saves as 418 tiles(22x18), 20 z-planes each inside a directory. All together the data 1.5GB in size. The stiching seems to work ok, until it comes to Fuse&Display... at the very end
The system is Windows7, 64bit, 8GB RAM. Fiji (is up-to-date) allocated 6GB of it. To even save memory I activated the virtual stack option for the stitching plugin.

The output says something about memory problems. 

Here is the error message:

java.lang.reflect.InvocationTargetException
	at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
	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 ij.IJ.run(IJ.java:251)
	at ij.macro.Functions.doRun(Functions.java:579)
	at ij.macro.Functions.doFunction(Functions.java:82)
	at ij.macro.Interpreter.doStatement(Interpreter.java:216)
	at ij.macro.Interpreter.doStatements(Interpreter.java:204)
	at ij.macro.Interpreter.run(Interpreter.java:103)
	at ij.macro.Interpreter.run(Interpreter.java:73)
	at CLI.Refresh_Macros.runScript(Refresh_Macros.java:56)
	at CLI.Refresh_Macros.runScript(Refresh_Macros.java:46)
	at common.RefreshScripts.run(RefreshScripts.java:284)
	at CLI.Refresh_Macros.run(Refresh_Macros.java:37)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	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 ij.IJ.run(IJ.java:251)
	at ij.IJ.run(IJ.java:229)
	at ij.macro.Functions.doRun(Functions.java:581)
	at ij.macro.Functions.doFunction(Functions.java:82)
	at ij.macro.Interpreter.doStatement(Interpreter.java:216)
	at ij.macro.Interpreter.doStatements(Interpreter.java:204)
	at ij.macro.Interpreter.run(Interpreter.java:103)
	at ij.macro.Interpreter.run(Interpreter.java:73)
	at ij.macro.MacroRunner.run(MacroRunner.java:130)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.OutOfMemoryError: Java heap space
	at ij.process.FloatProcessor.<init>(FloatProcessor.java:37)
	at mpicbg.imglib.container.imageplus.FloatImagePlus.<init>(FloatImagePlus.java:77)
	at mpicbg.imglib.container.imageplus.ImagePlusContainerFactory.createFloatInstance(ImagePlusContainerFactory.java:99)
	at mpicbg.imglib.type.numeric.real.FloatType.createSuitableDirectAccessContainer(FloatType.java:82)
	at mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:68)
	at mpicbg.imglib.container.DirectAccessContainerFactory.createContainer(DirectAccessContainerFactory.java:54)
	at mpicbg.imglib.image.Image.<init>(Image.java:112)
	at mpicbg.imglib.image.Image.<init>(Image.java:135)
	at mpicbg.imglib.image.ImageFactory.createImage(ImageFactory.java:68)
	at mpicbg.imglib.image.ImagePlusAdapter.convertToFloat(ImagePlusAdapter.java:216)
	at mpicbg.imglib.image.ImagePlusAdapter.convertFloat(ImagePlusAdapter.java:204)
	at mpicbg.imglib.image.display.imagej.ImageJFunctions.convertFloat(ImageJFunctions.java:153)
	at mpicbg.stitching.fusion.Fusion.fuse(Fusion.java:119)
	at plugin.Stitching_Grid.run(Stitching_Grid.java:527)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at sun.reflect.GeneratedMethodAccessor8.invoke(Unknown Source)
	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 ij.IJ.run(IJ.java:251)
	at ij.macro.Functions.doRun(Functions.java:579)
	at ij.macro.Functions.doFunction(Functions.java:82)
	at ij.macro.Interpreter.doStatement(Interpreter.java:216)
	at ij.macro.Interpreter.doStatements(Interpreter.java:204)
	at ij.macro.Interpreter.run(Interpreter.java:103)
	at ij.macro.Interpreter.run(Interpreter.java:73)
	at CLI.Refresh_Macros.runScript(Refresh_Macros.java:56)
	at CLI.Refresh_Macros.runScript(Refresh_Macros.java:46)
	at common.RefreshScripts.run(RefreshScripts.java:284)
Comment 1 Stephan Preibisch 2012-06-26 15:33:24 CDT
Hi,  did you try to not display but save the result to disc?
Comment 2 Sebastian Rhode 2012-06-27 12:33:50 CDT
Hi,

well I just tried this and so far it looks (it runs for 4h now) OK, but I noticed something strange. The output images are all called:

img_t1_z01_c1
...
img_t1_z35_c1

Besides there is no extension, my image data only has 20 z-planes ...?

Sebi
Comment 3 Sebastian Rhode 2012-06-27 14:47:00 CDT
Hi Stefan,

Stitching finished the process without a memory problem when I used the save option. But the result looks really strange. The data were 22x19 Tile, 1 Channel, 1 timepoint and 20 z-planes (dz=0.5micron).

The results (I imported all the saves tiles) looks like 22x24 Tile, 1 Channel, 1 timepoint and 37 z-planes. Some of them only contain "nonsense" and even all zeros. Any idea how to improve this?

Sebi
Comment 4 Curtis Rueden 2014-01-08 12:23:40 CST
Sebastian: Is this bug still an issue with an up-to-date Fiji? And is this problem distinct from Bug #496 (http://fiji.sc/bugzilla/﷒0﷓)?
Comment 5 Curtis Rueden 2014-06-16 13:34:23 CDT
No news is good news!