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Bug 923 - # -*- coding: iso-8859-15 -*- not working
# -*- coding: iso-8859-15 -*- not working
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-29 10:21 CDT by Leon
Modified: 2014-09-02 08:35 CDT
3 users (show)

See Also:
Description Leon 2014-08-29 10:21:54 CDT 
In jython scripts
 # -*- coding: iso-8859-15 -*- 
in the first line generates this error message :

org.python.antlr.ParseException: encoding declaration in Unicode string
	at org.python.core.ParserFacade.prepBufReader(ParserFacade.java:275)
	at org.python.core.ParserFacade.parseExpressionOrModule(ParserFacade.java:119)
	at org.python.util.PythonInterpreter.compile(PythonInterpreter.java:259)
	at org.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:695)

org.python.antlr.ParseException: org.python.antlr.ParseException: encoding declaration in Unicode string

	at org.python.core.PyException.fillInStackTrace(PyException.java:70)
	at java.lang.Throwable.<init>(Throwable.java:181)
	at java.lang.Exception.<init>(Exception.java:29)
	at java.lang.RuntimeException.<init>(RuntimeException.java:32)
	at org.python.core.PyException.<init>(PyException.java:46)
	at org.python.core.PyException.<init>(PyException.java:43)
	at org.python.core.Py.JavaError(Py.java:495)
	at org.python.core.ParserFacade.parseExpressionOrModule(ParserFacade.java:124)
	at org.python.util.PythonInterpreter.compile(PythonInterpreter.java:259)
	at org.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:695)
Caused by: org.python.antlr.ParseException: encoding declaration in Unicode string
	at org.python.core.ParserFacade.prepBufReader(ParserFacade.java:275)
	at org.python.core.ParserFacade.parseExpressionOrModule(ParserFacade.java:119)
	... 12 more

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-10M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Users/leon/Desktop/Fiji 15-44-09.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140827202801)
Fiji: http://fiji.sc/update/ (last check:20140829105108)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20140828215710)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20140829032636)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606172449)
LOCI: http://sites.imagej.net/LOCI/ (last check:20140401205514)

Files not up-to-date:
  3dd1594c (MODIFIED) 20140825141652 Contents/Info.plist
  6371c533 (LOCAL_ONLY) 20140715155020 plugins/MicrobeJ_.jar
  7db97d4f (LOCAL_ONLY) 20140828161903 plugins/New_test.py
  46489f0a (LOCAL_ONLY) 20140701135356 plugins/morphology/0_readme.txt
  ddbcea63 (LOCAL_ONLY) 20100913095428 plugins/morphology/AnnularClosing.ijm
  f070b583 (LOCAL_ONLY) 20100913095434 plugins/morphology/AnnularDilation.ijm
  b737a487 (LOCAL_ONLY) 20081019152450 plugins/morphology/BinaryDilateTest.ijm
  a7a43fad (LOCAL_ONLY) 20081019152918 plugins/morphology/BinaryErodeTest.ijm
  5dee5f51 (LOCAL_ONLY) 20060525101716 plugins/morphology/BinaryFilterReconstruct.ijm
  3b7d4dcf (LOCAL_ONLY) 20070712112240 plugins/morphology/BinaryLabelMacro.ijm
  b556d6c5 (LOCAL_ONLY) 20060525101718 plugins/morphology/BinaryPrune.ijm
  80fa5684 (LOCAL_ONLY) 20060525101718 plugins/morphology/Boundary4.ijm
  9a6fa507 (LOCAL_ONLY) 20060525101718 plugins/morphology/Boundary8_.ijm
  19d1d593 (LOCAL_ONLY) 20140218125448 plugins/morphology/Catalogue_Particles.ijm
  76b601ed (LOCAL_ONLY) 20090511083446 plugins/morphology/CloseByReconstructionTopHat.ijm
  9085414c (LOCAL_ONLY) 20130625111326 plugins/morphology/CloseByReconstruction_.ijm
  f3b1ba06 (LOCAL_ONLY) 20060525101718 plugins/morphology/ConvexHull1.ijm
  041b1595 (LOCAL_ONLY) 20060525101718 plugins/morphology/ConvexHull2.ijm
  d683ccd9 (LOCAL_ONLY) 20060525101718 plugins/morphology/ConvexHull3.ijm
  1cd0182f (LOCAL_ONLY) 20060525101718 plugins/morphology/Corners.ijm
  bc7ba05a (LOCAL_ONLY) 20081019163010 plugins/morphology/Delete_ZeroArea.ijm
  5829dba5 (LOCAL_ONLY) 20060525101718 plugins/morphology/Diagonal8to4.ijm
  75883a06 (LOCAL_ONLY) 20060525101718 plugins/morphology/Domes_stack.ijm
  31be1598 (LOCAL_ONLY) 20111208091210 plugins/morphology/DrawBoundingBox.ijm
  afcd1cfd (LOCAL_ONLY) 20111208091158 plugins/morphology/DrawBoundingCircle.ijm
  64e2f805 (LOCAL_ONLY) 20111208091142 plugins/morphology/DrawConvexHulls.ijm
  2527830b (LOCAL_ONLY) 20111208091226 plugins/morphology/DrawFeret&Breadth.ijm
  49911676 (LOCAL_ONLY) 20111208091236 plugins/morphology/DrawMinR&MaxR.ijm
  69e9b48e (LOCAL_ONLY) 20111208100126 plugins/morphology/DrawROIs.ijm
  8ae9fde6 (LOCAL_ONLY) 20100805124116 plugins/morphology/EDM_16bits.ijm
  6ad262c7 (LOCAL_ONLY) 20081019170232 plugins/morphology/Euler.ijm
  c9b603a1 (LOCAL_ONLY) 20090511083446 plugins/morphology/Extended_Maxima.ijm
  6c2c686e (LOCAL_ONLY) 20090511083446 plugins/morphology/Extended_Minima.ijm
  ad76520b (LOCAL_ONLY) 20130625143654 plugins/morphology/FillHolesReconstruct.ijm
  c6ca60fc (LOCAL_ONLY) 20130726145852 plugins/morphology/Fill_Border_Holes.ijm
  3c489a8f (LOCAL_ONLY) 20130726145642 plugins/morphology/Fill_Greyscale_Holes.ijm
  b4ddda4a (LOCAL_ONLY) 20101001143722 plugins/morphology/GreyBlackTopHatByReconstruction_.ijm
  8e6943da (LOCAL_ONLY) 20130625145618 plugins/morphology/GreyWhiteTopHatByReconstruction_.ijm
  1236438f (LOCAL_ONLY) 20090504142458 plugins/morphology/GreyscaleCentreFilter.ijm
  b50acb45 (LOCAL_ONLY) 20100920132950 plugins/morphology/GreyscaleKillBorders.ijm
  374fe065 (LOCAL_ONLY) 20090503182436 plugins/morphology/GreyscaleProperAutomedian.ijm
  44b959d8 (LOCAL_ONLY) 20090504122820 plugins/morphology/GreyscaleProperClose.ijm
  28b87cfe (LOCAL_ONLY) 20090504123000 plugins/morphology/GreyscaleProperOpen.ijm
  dfe7f5f5 (LOCAL_ONLY) 20100908144402 plugins/morphology/GreyscaleTopHat.ijm
  d0e5d8c4 (LOCAL_ONLY) 20100908144826 plugins/morphology/GreyscaleWell.ijm
  3cd35a92 (LOCAL_ONLY) 20060525101718 plugins/morphology/H-break.ijm
  05b76254 (LOCAL_ONLY) 20130625143022 plugins/morphology/HMaxima_Transform.ijm
  adf1eb0c (LOCAL_ONLY) 20130625143036 plugins/morphology/HMinima_Transform.ijm
  fa1c3e58 (LOCAL_ONLY) 20080605122624 plugins/morphology/Hole_Counter.ijm
  75f4f8b6 (LOCAL_ONLY) 20090527171616 plugins/morphology/HomotopicMarking.ijm
  8ad902a5 (LOCAL_ONLY) 20060525101718 plugins/morphology/Hysteresis.ijm
  baafcbde (LOCAL_ONLY) 20090513103656 plugins/morphology/Impose_Minimum.ijm
  b9b7d39e (LOCAL_ONLY) 20060525101718 plugins/morphology/Influence_Zones.ijm
  96e69ed4 (LOCAL_ONLY) 20060525101718 plugins/morphology/KeepLargestParticle.ijm
  131aab9f (LOCAL_ONLY) 20080521222500 plugins/morphology/KeepLargestParticlePixels_.ijm
  70a7143b (LOCAL_ONLY) 20080605144602 plugins/morphology/KeepParticlesInRange.ijm
  2d155dbb (LOCAL_ONLY) 20090519121520 plugins/morphology/LocalMaxima.ijm
  d52787b3 (LOCAL_ONLY) 20090519122406 plugins/morphology/LocalMinMax.ijm
  f3d08c4b (LOCAL_ONLY) 20090519121444 plugins/morphology/LocalMinima.ijm
  114b6aec (LOCAL_ONLY) 20060525101718 plugins/morphology/MCentroids.ijm
  7ccd76f0 (LOCAL_ONLY) 20101007145910 plugins/morphology/MinimaDynamic.ijm
  34cc741d (LOCAL_ONLY) 20060525101718 plugins/morphology/Morphological2Derivative1.ijm
  92704459 (LOCAL_ONLY) 20060525101718 plugins/morphology/Morphological2Derivative2.ijm
  4be76166 (LOCAL_ONLY) 20060525101718 plugins/morphology/Morphological2Derivative3.ijm
  682d48d2 (LOCAL_ONLY) 20130625145130 plugins/morphology/MorphologicalContrastTopHat.ijm
  4d2abfd9 (LOCAL_ONLY) 20100906132436 plugins/morphology/MorphologicalExternalGradient.ijm
  287862a5 (LOCAL_ONLY) 20100908173708 plugins/morphology/MorphologicalGradient3.ijm
  523a8a07 (LOCAL_ONLY) 20100906132436 plugins/morphology/MorphologicalGradientBeucher.ijm
  0e4759d2 (LOCAL_ONLY) 20100906132436 plugins/morphology/MorphologicalInternalGradient.ijm
  dbb5c1f9 (LOCAL_ONLY) 20060525101718 plugins/morphology/MorphologicalSharpGradient.ijm
  6e58fbd9 (LOCAL_ONLY) 20060525101718 plugins/morphology/MorphologicalSmoothing1.ijm
  a4a99a42 (LOCAL_ONLY) 20060525101718 plugins/morphology/MorphologicalSmoothing2.ijm
  26413055 (LOCAL_ONLY) 20140205080622 plugins/morphology/Morphological_Clustering.ijm
  bc8fe76e (LOCAL_ONLY) 20140205080622 plugins/morphology/Morphological_PCA.ijm
  deae6c03 (LOCAL_ONLY) 20101005101848 plugins/morphology/Morphological_SelfDualCentre.ijm
  47747892 (LOCAL_ONLY) 20130624092626 plugins/morphology/Morphological_contrast.ijm
  652c41d6 (LOCAL_ONLY) 20130624102506 plugins/morphology/Morphological_contrast_thr.ijm
  4bd9650e (LOCAL_ONLY) 20100908144252 plugins/morphology/MultiscaleGradient.ijm
  85c14c19 (LOCAL_ONLY) 20131007085502 plugins/morphology/NumberParticles8_.ijm
  673ae8e9 (LOCAL_ONLY) 20090511083446 plugins/morphology/OpenByReconstructionTopHat.ijm
  30cd493e (LOCAL_ONLY) 20130625144140 plugins/morphology/OpenByReconstruction_.ijm
  0839e90a (LOCAL_ONLY) 20080521221818 plugins/morphology/Parameter_Matrix.ijm
  c31bb024 (LOCAL_ONLY) 20080529224340 plugins/morphology/ParticleHoleArea.ijm
  aa63665d (LOCAL_ONLY) 20080529224456 plugins/morphology/ParticleHoleNumber.ijm
  bdd6e002 (LOCAL_ONLY) 20080529224152 plugins/morphology/Particle_Data_Map.ijm
  95f9dcd4 (LOCAL_ONLY) 20140410095854 plugins/morphology/Particles8ToCalibratedUnits.ijm
  17fab527 (LOCAL_ONLY) 20120123135452 plugins/morphology/Plot_BivariateGraphs.ijm
  e0364cbb (LOCAL_ONLY) 20080606114752 plugins/morphology/Plot_Histograms.ijm
  9180e82d (LOCAL_ONLY) 20060525101718 plugins/morphology/Prune1.ijm
  18becd17 (LOCAL_ONLY) 20060525101718 plugins/morphology/PruneAll.ijm
  2e176098 (LOCAL_ONLY) 20090511083446 plugins/morphology/RegionalMinMax.ijm
  5d319663 (LOCAL_ONLY) 20090511083446 plugins/morphology/Regional_Maxima.ijm
  74f1ae7b (LOCAL_ONLY) 20101001113926 plugins/morphology/Regional_Minima.ijm
  4d95ab38 (LOCAL_ONLY) 20100922235812 plugins/morphology/SelfComplementaryTopHat.ijm
  157ee2f2 (LOCAL_ONLY) 20121122092014 plugins/morphology/SelfDualReconstruction_.ijm
  b5f9d524 (LOCAL_ONLY) 20060525101718 plugins/morphology/Skeleton1.ijm
  aa82d5c2 (LOCAL_ONLY) 20060525101718 plugins/morphology/Skeleton2.ijm
  b51a4a36 (LOCAL_ONLY) 20060525101718 plugins/morphology/Skeleton3.ijm
  81e4ccdf (LOCAL_ONLY) 20090511121302 plugins/morphology/Skeleton4.ijm
  e7a5c0a4 (LOCAL_ONLY) 20100922212400 plugins/morphology/SkeletonFiltering.ijm
  5f6d1134 (LOCAL_ONLY) 20080521215352 plugins/morphology/Summarize_Results.ijm
  e504aa9b (LOCAL_ONLY) 20080603111018 plugins/morphology/Thin_Results_Table.ijm
  a39e72ba (LOCAL_ONLY) 20100621090218 plugins/morphology/UnbiasedCounting.ijm
  b1a45583 (LOCAL_ONLY) 20080605121016 plugins/morphology/UnbiasedParticleArea.ijm
  ca945167 (LOCAL_ONLY) 20090330080642 plugins/morphology/Viscous_Geodesic_Reconstruction.ijm
  83cb8345 (LOCAL_ONLY) 20140723154636 plugins/morphology/morphology_collection.jar
Comment 1 Mark Hiner 2014-08-29 11:10:25 CDT 
This may be a jython issue.. for example, see: http://python.6.x6.nabble.com/How-do-I-set-PythonInterpreter-encoding-to-UTF-8-before-using-it-It-is-ascii-by-default-td4998432.html

From what I understand, since the script is encoded as a UTF-16 String in Java and then passed to the jython interpreter, you will necessarily get the syntax error you're seeing.

Perhaps there's a way to set encoding programmatically?
Comment 2 Johannes Schindelin 2014-09-02 08:35:35 CDT 
The script editor -- from its very beginning -- only supported UTF-8 encoded source code.

If earlier versions of the script editor did not complain loudly about different encodings, that is most likely the bug.