⚠

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 1071 - LIF importer output windows not in order
LIF importer output windows not in order
Status: RESOLVED MOVED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-05-15 17:11 CDT by vbindoka
Modified: 2015-05-20 12:50 CDT
2 users (show)

See Also:
Description vbindoka 2015-05-15 17:11:55 CDT 
I am trying to open all series from tiling/stitching expt in a Leica LIF file. In bioformats, I select 'open all series' and 'select range' option, then pick one channel, #3, in all series. [arduous task] The extracted names are not the series name/number seen in preview GUI, but are all identical, the name of the LIF, and thus impossible to see the series order via titles.
IF there are more than 20 or so series, the order of fiji windows no longer matches the preview GUI order and there is no way to tell when the windows are no longer in sync with collection order.
I need to process the tiles in collection order so they can be re-stitched. My macros work for small LIF runs, but yield scrambles if there are many tiles.  
If the series import window order in fiji would remain in the order in the setup GUI, all is well. 
If the tile import windows used the series name vs the LIF name for tiled data, I would also be in good shape. --Every window has the name; LIFname - TileScan_001 [54 of them in present case!]. The FIJI taskbar WINDOWS pulldown is hopeless to select a particular series as well. [all the same name, no index number]
The TileScan LIF files use a  _s## format in their own tif export output; this is different vs regular LIF data. Perhaps this is a reason for the hiccups, or perhaps this is a WIndows7 thing. BUT I suspect there is more to this than just mixed file order since too many of the windows seem to lack data clearly present within LASAF software that generated it. I see too many black windows PLUS windows out of capture order.
Source files are big, but can upload LIF, if desired.

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: E:\DEC201~1/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\DEC201~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150501134914)
Fiji: http://fiji.sc/update/ (last check:20150509174919)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20150512235927)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606102449)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20150327072750)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214064119)
IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20150323044329)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723095558)
MIST: http://sites.imagej.net/NIST-ISG-MIST/ (last check:20150416125920)
OpenSPIM: http://openspim.org/update/ (last check:20150512090259)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221090506)
Micro-Manager-dev: http://sites.imagej.net/Micro-Manager-dev/ (last check:20150501012722)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20141222042830 jars/jpedalSTD.jar
  3b282216 (LOCAL_ONLY) 20150430163144 mm/win32/OlympusIX3Control/OlympusIX3Control.old.exe
  956e4529 (LOCAL_ONLY) 20150430163144 mm/win64/OlympusIX3Control/OlympusIX3Control.old.exe
  6d337b7a (LOCAL_ONLY) 20140730142734 plugins/Accurate_Gaussian_Blur.class
  6e9d50db (LOCAL_ONLY) 20140320051924 plugins/Adjustable_Watershed.class
  12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class
  0c575fd1 (LOCAL_ONLY) 20141209160514 plugins/BioVoxxel_Plugins.jar
  52ff6766 (LOCAL_ONLY) 20150115075008 plugins/Create_Template.jar
  55de57f2 (LOCAL_ONLY) 20050408121420 plugins/DecCredits$1.class
  66a64476 (LOCAL_ONLY) 20050408121420 plugins/DecCredits.class
  fd4ce3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionFFT.class
  b0398adb (LOCAL_ONLY) 20141028073350 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  8866a3cd (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionSolution.class
  ce989b93 (LOCAL_ONLY) 20050408103628 plugins/DeconvolutionWavelets.class
  13072662 (LOCAL_ONLY) 20050408121420 plugins/Deconvolution_.class
  11326750 (LOCAL_ONLY) 20050408103628 plugins/FFT1D.class
  18f23277 (LOCAL_ONLY) 20050408103628 plugins/FourierSpace.class
  44693e65 (LOCAL_ONLY) 20150325121214 plugins/Frac_Lac.jar
  348da731 (LOCAL_ONLY) 20141126044659 plugins/GHT_.jar
  15a0aac2 (LOCAL_ONLY) 20050408150536 plugins/GibsonPSF.class
  52861b7c (LOCAL_ONLY) 20050408150244 plugins/GibsonPSFF.class
  f481dc68 (LOCAL_ONLY) 20120817074900 plugins/Hybrid_2D_Filters.class
  6b2de3e5 (LOCAL_ONLY) 20120817084143 plugins/Hybrid_3D_Filters.class
  e9cb6eb7 (LOCAL_ONLY) 20150115083713 plugins/Image_CorrelationJ_1o.class
  d6bc39b9 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins.jar
  04b38ca7 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins2.jar
  71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class
  44f1acfa (LOCAL_ONLY) 20121128135145 plugins/Mexican_Hat_Filter.class
  53c5c1ad (LOCAL_ONLY) 20141103073745 plugins/NL_Means_.jar
  4ed208ff (LOCAL_ONLY) 20140929064046 plugins/NanoTrackJ_.jar
  21927175 (LOCAL_ONLY) 20140808090713 plugins/PIV_.jar
  b3b13b1f (LOCAL_ONLY) 20050408150244 plugins/PSFCredits$1.class
  cb99705d (LOCAL_ONLY) 20050408150244 plugins/PSFCredits.class
  de90b917 (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG$1.class
  e33950eb (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG.class
  9f2412ff (LOCAL_ONLY) 20141028082626 plugins/PSF_Generator.jar
  5a3abd78 (LOCAL_ONLY) 20050408150536 plugins/PSF_Gibson_.class
  65b190f7 (LOCAL_ONLY) 20121002063426 plugins/PSF_Simple_.class
  0c89ccf5 (LOCAL_ONLY) 20140507100709 plugins/PoissonNMF_.jar
  12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar
  33ca5f87 (LOCAL_ONLY) 20141215122204 plugins/Thunder_STORM.jar
  69b16199 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4.class
  f0990b22 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4Filter.class
  27901023 (LOCAL_ONLY) 20050408152652 plugins/Wavelet_Deconvolution_.class
  71331805 (LOCAL_ONLY) 20140314082430 plugins/jacop_.jar
  9bbfb280 (LOCAL_ONLY) 20140225135257 plugins/octane2_.jar
Comment 1 Mark Hiner 2015-05-20 12:50:31 CDT 
Thank you very much for taking the time to report this issue.

In general, the Bio-Formats team maintains a separate bug tracking process.
Instructions can be found here:

https://www.openmicroscopy.org/site/support/bio-formats5.1/about/bug-reporting.html

>--Every window has the name; LIFname - TileScan_001 [54 of them in present case!]

It does look like this is a general issue with the Bio-Formats importer bypassing the default ImageJ naming scheme. The "Window" menu should at least preserve the order things were opened.. but if they all have the same name that probably isn't helpful.

>Perhaps this is a reason for the hiccups, or perhaps this is a WIndows7 thing.

For what it's worth, I can confirm the window naming is an issue on OSX as well.

Anyway, I encourage you to send the Bio-Formats team a mail. Hopefully this will be resolved in a future Bio-Formats release.

Best,
Mark