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Bug 800 - FIJI 1.49b - problem with open/ drag-drop option
FIJI 1.49b - problem with open/ drag-drop option
Status: ASSIGNED
Product: ImageJ
Classification: Unclassified
Component: SCIFIO
unspecified
PC Windows
: P4 normal
Assigned To: Curtis Rueden
Depends on:
Blocks:
 
Reported: 2014-06-19 09:37 CDT by h.sasnowosielska
Modified: 2015-04-06 15:49 CDT
4 users (show)

See Also:

Attachments
I attach two images: before and after binarysation. The problem with OPEN vs DRAG/DROP option was with binary image (16.79 KB, image/tiff)
2014-06-19 09:43 CDT, h.sasnowosielska
ct slice (513.26 KB, application/dicom)
2014-07-07 04:40 CDT, Ilan Tal

Description h.sasnowosielska 2014-06-19 09:37:19 CDT 
I generated binary images ( tiff format) using ImageJ 1.48e. When I tried to open them in FIJI 1.49b with "standard" File>Open procedure it did not read the images properly (the location of black and white pixels was perturbed and their values were changed from 0-1 to 254-255). Strangely, when I opened the same images by dragging them from the file folder and dropping them to FIJI window they opened correctly.

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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Hania\Desktop\FIJI-W~1\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Hania\Desktop\FIJI-W~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140618215931)
Fiji: http://fiji.sc/update/ (last check:20140618220039)

Files not up-to-date:
  7ecaf631 (OBSOLETE_UNINSTALLED) 20140313092833 jars/jruby-complete-1.7.11.jar
  24d47d70 (OBSOLETE_UNINSTALLED) 20140313092833 jars/junit-4.8.1.jar
  fd2869f6 (LOCAL_ONLY) 20140619153401 macros/1906_RepFactorSegment-def.ijm
  8e7f9574 (LOCAL_ONLY) 20140617161108 macros/PCNA_calc.ijm
  907588c7 (LOCAL_ONLY) 20140618112535 macros/RepFactorSegment-def.ijm
  75095a77 (LOCAL_ONLY) 20140617143609 macros/RepFactorSegment.ijm
  37955112 (LOCAL_ONLY) 20140507171407 plugins/FRAP_Analysis.class
  7709e1f1 (LOCAL_ONLY) 20121031134702 plugins/FRAP_profiler/FRAP_Profiler.class
  6d88799a (OBSOLETE_UNINSTALLED) 20140313092829 plugins/Script_Editor-2.0.0-SNAPSHOT.jar
Comment 1 h.sasnowosielska 2014-06-19 09:43:20 CDT 
Created attachment 166
I attach two images: before and after binarysation. The problem with OPEN vs DRAG/DROP option was with binary image
Comment 2 Curtis Rueden 2014-06-20 23:48:03 CDT 
Thanks for reporting this problem. It is a bug in the SCIFIO library, which is now enabled by default in Fiji. You can avoid the issue by disabling SCIFIO: Edit > Options > ImageJ2 and unchecking the "Use SCIFIO when opening files" option.

The problem also occurs with Bio-Formats (i.e.: File > Import > Bio-Formats).

In the meantime, we will investigate how best to address the issue. I am guessing it is relating to the fact that there is an inverting LUT (the inverted values of 0-1 are 254-255).
Comment 3 Curtis Rueden 2014-06-23 15:30:27 CDT 
Assigning this bug to myself. I'll try to tackle it before the end of the week.
Comment 4 Ilan Tal 2014-07-07 04:38:32 CDT 
Hi Curtis,
I discovered that the drag and drop doesn't work for essentially any image I have. I'll attach a single slice of a CT series as an example. I can open the whole series with my Read from CD plugin so I'm sure the data is OK.
Since I can remember it has always been possible to drag and drop to the Fiji status bar and now this is broken as well. No error is given, just no image opens up.
For completeness I tried a File -> Open and get some errors:
(Fiji Is Just) ImageJ 2.0.0-rc-8/1.49c; Java 1.6.0_24 [32-bit]; Linux 3.13.0-30-generic; 9MB of 1176MB (<1%)
 
java.lang.NullPointerException
	at io.scif.formats.DICOMFormat$Parser.addFileToList(DICOMFormat.java:1649)
	at io.scif.formats.DICOMFormat$Parser.scanDirectory(DICOMFormat.java:1574)
	at io.scif.formats.DICOMFormat$Parser.makeFileList(DICOMFormat.java:1485)
	at io.scif.formats.DICOMFormat$Parser.typedParse(DICOMFormat.java:1432)
	at io.scif.formats.DICOMFormat$Parser.typedParse(DICOMFormat.java:1106)
	at io.scif.AbstractParser.parse(AbstractParser.java:252)
	at io.scif.AbstractParser.parse(AbstractParser.java:335)
	at io.scif.AbstractParser.parse(AbstractParser.java:52)
	at io.scif.AbstractReader.setSource(AbstractReader.java:270)
	at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
	at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
	at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
	at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
	at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
	at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
	at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:420)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:153)
	at ij.IJ.runPlugIn(IJ.java)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)

My Read from CD calls IJ.opener and that opens the series nicely. Just the drag and drop, which always used to work is apparently broken. The CT slice is called osseux0000.dcm.
Never a dull moment with the new software...

Regards,
Ilan
Comment 5 Ilan Tal 2014-07-07 04:40:22 CDT 
Created attachment 173
ct slice