⚠

NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.

The Fiji project now uses GitHub Issues for issue tracking.

Please file all new issues there.

Bug 1156 - Merge channels with variables does not work any more
Merge channels with variables does not work any more
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: ImageJ1
unspecified
PC Windows
: P4 normal
Assigned To: Wayne Rasband
Depends on:
Blocks:
 
Reported: 2015-09-07 09:32 CDT by Leduc
Modified: 2015-09-11 12:08 CDT
2 users (show)

See Also:
Description Leduc 2015-09-07 09:32:23 CDT 
Hi,

Since the Fiji update of around August 2015, I have a problem with the Merge Channels command. It work fine when we put directly the names of the images to mergeHowver, it does not work anymore when we use the command in a macro and apply it to variables which contain the name of the images to merge. Please apply the simple macro below to a multi-color image which is not splitted.

Thank you in advance.

Cecile


//open a multi-color image without splitting the colors
title = getTitle();
run("Split Channels");

title_3="C3"+"-"+title;
title_2="C2"+"-"+title;
title_1="C1"+"-"+title;

run("Merge Channels...", "c1=[title_1] c2=[title_2] c3=[title_3] create keep ignore");

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\cleduc\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\cleduc\Desktop\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150903164407)
Fiji: http://update.fiji.sc/ (last check:20150904213156)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20130527145228 jars/jpedalSTD.jar
  464d39e0 (LOCAL_ONLY) 20060404164208 luts/000-gray.lut
  de36ff28 (LOCAL_ONLY) 20060404164206 luts/001-fire.lut
  68488b96 (LOCAL_ONLY) 20060404164206 luts/002-spectrum.lut
  753d5be7 (LOCAL_ONLY) 20060404164206 luts/003-ice.lut
  057404f8 (LOCAL_ONLY) 20060404164206 luts/004-phase.lut
  865df0ca (LOCAL_ONLY) 20060404164208 luts/005-random.lut
  c20786a9 (LOCAL_ONLY) 20060404164208 luts/16_equal.lut
  453e0717 (LOCAL_ONLY) 20060404164208 luts/16_ramps.lut
  4efec500 (LOCAL_ONLY) 20060404164208 luts/20_colors.lut
  9a3e32d3 (LOCAL_ONLY) 20060404164206 luts/32_colors.lut
  920b4fad (LOCAL_ONLY) 20060404164208 luts/6_reserved_colors.lut
  e8bd301d (LOCAL_ONLY) 20060404164206 luts/amber.lut
  23c249cc (LOCAL_ONLY) 20060404164206 luts/auxctq.lut
  fe53a379 (LOCAL_ONLY) 20060404164208 luts/blue_orange.lut
  724a437a (LOCAL_ONLY) 20060404164208 luts/brain.lut
  ad633626 (LOCAL_ONLY) 20060404164206 luts/cells.lut
  5e4825e8 (LOCAL_ONLY) 20060404164208 luts/cequal.lut
  9d336be2 (LOCAL_ONLY) 20060404164208 luts/cmy-cyan.lut
  773e51b4 (LOCAL_ONLY) 20060404164206 luts/cmy-magneta.lut
  97fddd80 (LOCAL_ONLY) 20060404164206 luts/cmy-yellow.lut
  939c8598 (LOCAL_ONLY) 20060404164206 luts/cmy.lut
  fa84d3d9 (LOCAL_ONLY) 20060404164208 luts/cold.lut
  67ce3b32 (LOCAL_ONLY) 20060404164206 luts/cti_ras.lut
  62852456 (LOCAL_ONLY) 20060404164206 luts/gem-16.lut
  a65bd7d6 (LOCAL_ONLY) 20060404164206 luts/gem-256.lut
  ad9e6ccd (LOCAL_ONLY) 20060404164208 luts/gold.lut
  8156b017 (LOCAL_ONLY) 20060404164208 luts/gyr_centre.lut
  5ca44893 (LOCAL_ONLY) 20060404164206 luts/heart.lut
  252ed9c2 (LOCAL_ONLY) 20060404164208 luts/hue.lut
  cdffdafc (LOCAL_ONLY) 20060404164206 luts/hue_ramps_08.lut
  7adf5fcd (LOCAL_ONLY) 20060404164206 luts/hue_ramps_16.lut
  f1f2fbd5 (LOCAL_ONLY) 20060404164208 luts/iman.lut
  79d85a69 (LOCAL_ONLY) 20060404164208 luts/invert_gray.lut
  44c6e3da (LOCAL_ONLY) 20060404164206 luts/isocontour.lut
  563a43c9 (LOCAL_ONLY) 20060404201958 luts/log_down.lut
  5473b9bc (LOCAL_ONLY) 20060404202034 luts/log_up.lut
  cbf7b6ba (LOCAL_ONLY) 20060404164208 luts/mixed.lut
  0d397123 (LOCAL_ONLY) 20060404202450 luts/neon-blue.lut
  2a87351a (LOCAL_ONLY) 20060404202516 luts/neon-green.lut
  f975e858 (LOCAL_ONLY) 20060404202600 luts/neon-magenta.lut
  defedcc1 (LOCAL_ONLY) 20060404202412 luts/neon-red.lut
  61b36d81 (LOCAL_ONLY) 20060404164208 luts/pastel.lut
  17ad8064 (LOCAL_ONLY) 20060404164206 luts/rgb-blue.lut
  647c7f8e (LOCAL_ONLY) 20060404164208 luts/rgb-green.lut
  f631b42a (LOCAL_ONLY) 20060404164208 luts/rgb-red.lut
  bf3b4af2 (LOCAL_ONLY) 20060404164206 luts/siemens.lut
  a01c35f1 (LOCAL_ONLY) 20060404164206 luts/split_blackblue_redwhite.lut
  c87ce743 (LOCAL_ONLY) 20060404164206 luts/split_blackwhite_ge.lut
  1bc23627 (LOCAL_ONLY) 20060404164206 luts/split_blackwhite_warmmetal.lut
  35106b60 (LOCAL_ONLY) 20060404164206 luts/split_bluered_warmmetal.lut
  a3859546 (LOCAL_ONLY) 20060404164208 luts/system_lut.lut
  5ff3037c (LOCAL_ONLY) 20141105162951 luts/test-cyan2.lut
  54ffd32b (LOCAL_ONLY) 20060404164206 luts/thal_16.lut
  b5dcc043 (LOCAL_ONLY) 20060404164208 luts/thal_256.lut
  d90432e1 (LOCAL_ONLY) 20060404164206 luts/topography.lut
  980982d2 (LOCAL_ONLY) 20060404164208 luts/vivid.lut
  2dd9e5c9 (LOCAL_ONLY) 20060404164206 luts/warhol.lut
  b2960775 (LOCAL_ONLY) 20110110113844 macros/Analyze_Hypothenuse_V1_1.ijm
  9546c829 (LOCAL_ONLY) 20140319122107 macros/Averaging_images.ijm
  8c5b2ec6 (LOCAL_ONLY) 20140203095456 macros/BatchAnalyseFA.ijm
  ac19ce23 (LOCAL_ONLY) 20140724113108 macros/BatchAnalyseFA_chiara.ijm
  31dee744 (LOCAL_ONLY) 20140203095501 macros/BatchAnalyseFA_one_sample.ijm
  f7ef05e4 (LOCAL_ONLY) 20140205160216 macros/BatchAnalyseFAnew.ijm
  880f12ab (LOCAL_ONLY) 20140825143952 macros/BatchAnalyseFAnew_F.ijm
  8f73f315 (LOCAL_ONLY) 20140828202906 macros/BatchAnalyseFAnew_Franck.ijm
  830ef494 (LOCAL_ONLY) 20140828142513 macros/BatchAnalyseFAnew_chiara.ijm
  300e73cf (LOCAL_ONLY) 20140724190447 macros/BatchAnalyseFAnew_chiara2.ijm
  ab7356fa (LOCAL_ONLY) 20140910160918 macros/BatchAnalyseFAnew_chiara4.ijm
  94a0b498 (LOCAL_ONLY) 20140919194659 macros/BatchAnalyseFAnew_chiara_fluo.ijm
  12834c3f (LOCAL_ONLY) 20150706114748 macros/Batch_cecile_siDHC.ijm
  3635cb84 (LOCAL_ONLY) 20150224135944 macros/Batch_cecile_siDHC_3channel.ijm
  7861bad4 (LOCAL_ONLY) 20150224140728 macros/Batch_cecile_siDHC_3channel_patrons.ijm
  aab01132 (LOCAL_ONLY) 20140402131951 macros/Batch_cecile_siDHC_freehand.ijm
  a1de7832 (LOCAL_ONLY) 20150518145532 macros/Batch_cecile_siDHC_patrons.ijm
  d472ce9e (LOCAL_ONLY) 20141006181724 macros/Batch_cecile_siKHC.ijm
  fd5dff1d (LOCAL_ONLY) 20150224182801 macros/Batch_cecile_vim_si_single cell.ijm
  291c9a6e 20150203165409 macros/CellRef_dC?mo_V2_1.ijm
  3e2cfee3 20140922200624 macros/CellRef_dC?mo_Vim-tub-_rond.ijm
  f0309fb3 20140922200439 macros/CellRef_dC?mo_Vim-tub-_test.ijm
  153cc702 20140922171601 macros/CellRef_dC?mo_Vim-tub.ijm
  f4743fae 20140922173325 macros/CellRef_dC?mo_Vim-tub_test.ijm
  0eb36e33 20140922172358 macros/CellRef_dC?mo_Vim.ijm
  63d3909e 20140922181532 macros/CellRef_dC?mo_Vim_test.ijm
  291c9a6e (LOCAL_ONLY) 20150203165409 macros/CellRef_dÇmo_V2_1.ijm
  3e2cfee3 (LOCAL_ONLY) 20140922200624 macros/CellRef_dÇmo_Vim-tub-_rond.ijm
  f0309fb3 (LOCAL_ONLY) 20140922200439 macros/CellRef_dÇmo_Vim-tub-_test.ijm
  153cc702 (LOCAL_ONLY) 20140922171601 macros/CellRef_dÇmo_Vim-tub.ijm
  f4743fae (LOCAL_ONLY) 20140922173325 macros/CellRef_dÇmo_Vim-tub_test.ijm
  0eb36e33 (LOCAL_ONLY) 20140922172358 macros/CellRef_dÇmo_Vim.ijm
  63d3909e (LOCAL_ONLY) 20140922181532 macros/CellRef_dÇmo_Vim_test.ijm
  985c53e8 (LOCAL_ONLY) 20150204131910 macros/CellRef_demo_Vim-tub_general.ijm
  07b13330 (LOCAL_ONLY) 20150204104923 macros/CellRef_demo_Vim-tub_general2.ijm
  b0d4bf5b (LOCAL_ONLY) 20150407210854 macros/CellRef_demo_Vim-tub_general3.ijm
  b708f50d (LOCAL_ONLY) 20140205092034 macros/Macro_Julien2.ijm
  37ea8b35 (LOCAL_ONLY) 20141105181139 macros/Temporal-Color_Code_flora.ijm
  30564178 (LOCAL_ONLY) 20150413192930 macros/analyse_protrusion.ijm
  0702dfb1 (LOCAL_ONLY) 20150520183010 macros/analyse_protrusion_3channels.ijm
  3cfa15b8 (LOCAL_ONLY) 20150506172420 macros/analyse_protrusion_4channels.ijm
  e88cae22 (LOCAL_ONLY) 20140411135442 macros/batch_Julien2.ijm
  052a8813 (LOCAL_ONLY) 20140416120627 macros/batch_Julien_acetyl.ijm
  fc01be8b (LOCAL_ONLY) 20140416120556 macros/batch_Julien_acetyl2.ijm
  0a48f157 (LOCAL_ONLY) 20140416121000 macros/batch_Julien_acetyl3.ijm
  f5be66c4 (LOCAL_ONLY) 20140923113852 macros/built-stack.ijm
  9291a290 (LOCAL_ONLY) 20150206172535 macros/division vim tub.ijm
  f5d2ab90 (LOCAL_ONLY) 20140506184723 macros/nprot.2014.024-S3.txt
  ac1e33ac (LOCAL_ONLY) 20141105135119 macros/projection_rainbow_flora.ijm
  b4ea133a (LOCAL_ONLY) 20140506184503 plugins/Macros/fibtool.txt
  34c9a395 (LOCAL_ONLY) 20150618173233 plugins/Mosaic_ToolSuite.jar
  3589dfdf (LOCAL_ONLY) 20100430080852 plugins/MultiStackReg1.45_.jar
  c32c3597 (LOCAL_ONLY) 20080521101406 plugins/MultiStackReg_.jar
  946ffba8 (LOCAL_ONLY) 20140616131337 plugins/MultipleKymograph_.class
  54d2cdf2 (LOCAL_ONLY) 20120608145248 plugins/MultipleOverlay_.class
  68fa4608 (LOCAL_ONLY) 20141008112622 plugins/Radial_Profile.class
  f1342766 (LOCAL_ONLY) 20141008112706 plugins/Radial_Profile_Angle_Ext.jar
  77bb5c2d (LOCAL_ONLY) 20130617173322 plugins/SpeckleLib.jar
  442cfeb6 (LOCAL_ONLY) 20140417175805 plugins/Speckle_TrackerJ.class
  bf8660d2 (LOCAL_ONLY) 20120608145250 plugins/StackDifference_.class
  4977336f (LOCAL_ONLY) 20140922205343 plugins/TransformationMatrices.txt
  e94c393a (LOCAL_ONLY) 20141105155557 plugins/Utilities/Color_Chooser.class
  d3721d57 (LOCAL_ONLY) 20120608145254 plugins/WalkingAverage_.class
  c6ab184a (LOCAL_ONLY) 20110426095720 plugins/draw_speckles/Draw_Speckles.class
  cbb448a8 (LOCAL_ONLY) 20110426095720 plugins/intensity_plots/Speckle_Intensity_Trajectories.class
Comment 1 Leduc 2015-09-08 04:08:33 CDT 
The error is:

There must ba a
Comment 2 Leduc 2015-09-08 04:10:18 CDT 
The error is:

There must be at least one source image or stack.
Comment 3 Wayne Rasband 2015-09-11 12:08:33 CDT 
The Split Channels command, with RGB images, produces files with names like title+" (red)", etc. You can get it to produce images with names like "C1-"+title, etc. by converting RGB images to composite color, as in the following example.

  run("Clown (14K)");
  if (!is("composite"))
     run("Make Composite");
  title = getTitle();
  run("Split Channels");
  t1 = "C1-"+title;
  t2 = "C2-"+title;
  t3 = "C3-"+title;
  run("Merge Channels...", "c1=&t1 c2=&t2 c3=&t3 create keep ignore");