[ImageJ-bugs] [Bug 903] New: Stack Tools convert composite to interleaved

bugzilla at fiji.sc bugzilla at fiji.sc
Fri Aug 15 12:35:05 CDT 2014 

http://fiji.sc/bugzilla/show_bug.cgi?id=903

            Bug ID: 903
           Summary: Stack Tools convert composite to interleaved
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: glenmac at uw.edu
                CC: glenmac at uw.edu

If I apply Image>Stacks>Tools, Slice Keeper or Slice Remover, to a
multi-channel 16-bit Composite stack, the resulting stack is converted to a
simple 16-bit grayscale stack and interleaves the channels.

Don't recall this happening in the past.  also occurs with a MacBookPro.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.4
  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-b14-462-11M4609
  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: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140814090445)
Fiji: http://fiji.sc/update/ (last check:20140813115223)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20140603230506)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140811053030)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606082449)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723075558)
PTBIOP: http://biop.epfl.ch/Fiji-Update/ (last check:20140730023856)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140812082844)
SCIFIO-dev: http://sites.imagej.net/SCIFIO/ (last check:20140801104207)
Stowers: http://research.stowers.org/imagejplugins/updates/ (last
check:20140805084656)
Bio-Formats daily builds: http://sites.imagej.net/Bio-Formats/ (last
check:20140813182633)

Files not up-to-date:
  07f4044a (LOCAL_ONLY) 20140612110153 macros/CLAHE stack.ijm
  9d962521 (LOCAL_ONLY) 20120618120603 macros/PIMP_2f-3ivariant.ijm
  b69e6838 (LOCAL_ONLY) 20120622105927 macros/PIMP_2g.ijm
  eb509ed0 (LOCAL_ONLY) 20120717095350 macros/PIMP_2gbgsubtraction.ijm
  e56187b3 (LOCAL_ONLY) 20120710174431 macros/PIMP_2gtests.ijm
  41baa729 (LOCAL_ONLY) 20120717105146 macros/PIMP_2h.ijm
  c46ef207 (LOCAL_ONLY) 20120717110725 macros/PIMP_2i.ijm
  22596c68 (LOCAL_ONLY) 20120615161654
macros/PIMP_finalGHMarrays2e3DguassThold.ijm
  7fb3cc04 (LOCAL_ONLY) 20120615161647
macros/PIMP_finalGHMarrays2e3Dguassian.ijm
  87255328 (LOCAL_ONLY) 20140206150200 macros/delete2slices.ijm
  74f75823 (LOCAL_ONLY) 20120719100435 macros/toolsets/3DClusterAnalysis.ijm
  0fe955a3 (LOCAL_ONLY) 20120305144333 macros/toolsets/Andrew Macro4b.ijm
  6cc0aae2 (LOCAL_ONLY) 20110901171448 macros/toolsets/Arminda timelapse macro
3.8b.ijm
  f4074bbb (LOCAL_ONLY) 20120702084321 macros/toolsets/BPCounting3g.ijm
  8e86396d (LOCAL_ONLY) 20131018145317 macros/toolsets/FWHM.ijm
  2fe75fec (LOCAL_ONLY) 20131107171559 macros/toolsets/FWHM3.ijm
  c68a09eb (LOCAL_ONLY) 20120911102147 macros/toolsets/Fill ROI Macro.ijm
  ead280e3 (LOCAL_ONLY) 20120808153016 macros/toolsets/GTTR Segmentation3.ijm
  d198e5e7 (LOCAL_ONLY) 20100916121922
macros/toolsets/Import_Channel_Order3.8a.txt
  696ba2a6 (LOCAL_ONLY) 20131002104159
macros/toolsets/Import_Montage_Stacks3.8a.txt
  72ff0312 (LOCAL_ONLY) 20140814161438 macros/toolsets/Make_Composite.ijm
  17d1aba0 (LOCAL_ONLY) 20140404113537 macros/toolsets/Merge HuPro
Quadrants_3b.ijm
  01179b26 (LOCAL_ONLY) 20120913130241 macros/toolsets/Multiply.ijm
  4651471a (LOCAL_ONLY) 20121116153429 macros/toolsets/PIMP_3_Batch.ijm
  0c5c4a4c (LOCAL_ONLY) 20121116153510 macros/toolsets/PIMP_3_Single file.ijm
  4b5104ee (LOCAL_ONLY) 20120627100227 macros/toolsets/Placenta macro3.ijm
  24c3ebb4 (LOCAL_ONLY) 20131218123203 macros/toolsets/Scan macro.ijm
  5cf51025 (LOCAL_ONLY) 20140625172146 macros/toolsets/Stereology_grid2_4.ijm
  d45b5703 (LOCAL_ONLY) 20140625172158 macros/toolsets/Stereology_grid2_5.ijm
  232bca5e (LOCAL_ONLY) 20120910121056 macros/toolsets/Temporal Time
Encoder.ijm
  3d17a094 (LOCAL_ONLY) 20140115144252 macros/toolsets/Utricle_RGB_merge2_2.ijm
  618286ae (LOCAL_ONLY) 20121115152953 macros/toolsets/batchStackreg.ijm
  d53a8d48 (LOCAL_ONLY) 20120730154750 macros/toolsets/drift3b.ijm
  6cedb193 (LOCAL_ONLY) 20120730162148 macros/toolsets/drift3c.ijm
  fc424882 (LOCAL_ONLY) 20120305133512 macros/toolsets/macro development/Andrew
Macro4a.ijm
  0b91930b (LOCAL_ONLY) 20111007164331 macros/toolsets/macro
development/Arminda 3.98test.ijm
  07f111f8 (LOCAL_ONLY) 20120620161839 macros/toolsets/macro
development/FWHM.ijm
  607b8de2 (LOCAL_ONLY) 20110928161804 macros/toolsets/macro development/Import
Channel Order3.98.ijm
  891da2e3 (LOCAL_ONLY) 20110831161129 macros/toolsets/macro
development/Import_Channel_Order3.8atlapse.txt
  c1e7d84a (LOCAL_ONLY) 20110831163521 macros/toolsets/macro
development/Import_Channel_Order3.8btlapse.txt
  3fedd17e (LOCAL_ONLY) 20110901165057 macros/toolsets/macro
development/Import_Channel_Order3.8btlapse.txt.ijm
  6ddde9e7 (LOCAL_ONLY) 20110124183506 macros/toolsets/macro
development/Import_Channel_Order3.8f.txt
  76c91a2c (LOCAL_ONLY) 20120529122545 macros/toolsets/macro
development/PIMP_final.ijm
  45be256a (LOCAL_ONLY) 20120601113233 macros/toolsets/macro
development/PIMP_finalGHMarrays2b.ijm
  de11be1e (LOCAL_ONLY) 20120403145549 macros/toolsets/macro development/Scale
CellVizio Tiff stack.ijm
  ee6d3193 (LOCAL_ONLY) 20120221135146 macros/toolsets/macro
development/testscale.ijm
  83d10173 (LOCAL_ONLY) 20120712161724 macros/toolsets/plot coordinates.ijm
  d1a3a016 (LOCAL_ONLY) 20120712161713 macros/toolsets/plotresults.ijm
  73c35d52 (LOCAL_ONLY) 20121002143805 macros/toolsets/testbatchopen.ijm
  c1dcbd92 (LOCAL_ONLY) 20121008113151 macros/toolsets/transition stacks.ijm
  5a8a6e22 (LOCAL_ONLY) 20120821154843 macros/toolsets/waterjet2.ijm
  301245dd (LOCAL_ONLY) 20120822090138 macros/toolsets/waterjet2deltaf.ijm
  81fecfd4 (LOCAL_ONLY) 20120822172438 macros/toolsets/waterjet3.ijm
  d054d71f (LOCAL_ONLY) 20120717163446 macros/use copyand restore ROI.ijm
  bd7bc5d1 (LOCAL_ONLY) 20140604192402 plugins/ActionBar/Shared
Bars/BIOP_MultiManualSelect.ijm
  c271b415 (LOCAL_ONLY) 20140604192403 plugins/ActionBar/Shared
Bars/BIOP_PSF_Quality.ijm
  08afb731 (LOCAL_ONLY) 20140411093521 plugins/ActionBar/Shared
Bars/BIOP_VSI_Reader.ijm
  4edb1d6f (LOCAL_ONLY) 20140604192404 plugins/ActionBar/Shared
Bars/Common_Tools.ijm
  db280c9c (LOCAL_ONLY) 20140404162924 plugins/ActionBar/Shared
Bars/JaCoP_Tools.ijm
  c0f5f8c9 (LOCAL_ONLY) 20140618131422 plugins/BoneJ_.jar
  849a4e62 (LOCAL_ONLY) 20140227163214 plugins/ExtendedDepthField.txt
  d35ea3fc (LOCAL_ONLY) 20140709121718 plugins/New_.py
  6b8a0ed5 (LOCAL_ONLY) 20140411093001 plugins/action_bar201d.jar
  b2afde18 (LOCAL_ONLY) 20140115161834 plugins/cell_counter.jar
  71331805 (LOCAL_ONLY) 20140225164744 plugins/jacop_.jar
  9f4f8151 (LOCAL_ONLY) 20140724124554 plugins/jars/jython-2.5.2.jar

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