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 876 - Null pointer Exception Reading DICOM format
Null pointer Exception Reading DICOM format
Status: NEW
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-08-04 10:20 CDT by Richard Tyson
Modified: 2014-08-04 10:25 CDT
1 user (show)

See Also:


Attachments
MRI image. DICOM format. 512x512. 16-bit (526.47 KB, image/DICOM)
2014-08-04 10:24 CDT, Richard Tyson

Description Richard Tyson 2014-08-04 10:20:51 CDT
Open a DICOM formated image

File->Open...

I had an MRI on 07/2014, and can open the images in this version. They open fine
in standard imageJ 1.48U.  I can upload an example, when I find out how.

Exception:
(Fiji Is Just) ImageJ 2.0.0-rc-9/1.49d; Java 1.6.0_65 [64-bit]; Mac OS X 10.7.5; 12MB of 3369MB (<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:421)
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:154)
	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:695)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.7.5
  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: CHECK_TURNED_OFF

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:20140802165300)
Fiji: http://fiji.sc/update/ (last check:20140730200634)

Files not up-to-date:
  ebcd76fa (MODIFIED) 20140613122205 Contents/Info.plist
  522879f2 (LOCAL_ONLY) 20120511154629 plugins/Intensity_Correlation_Analysis.class
  c33d5648 (LOCAL_ONLY) 20050928181804 plugins/MI_.class
  3589dfdf (LOCAL_ONLY) 20121214124358 plugins/MultiStackReg1.45_.jar
  617c3507 (LOCAL_ONLY) 20130723155349 plugins/QuickTime_Plugins.jar
  7785f532 (LOCAL_ONLY) 20140523155107 plugins/QuimP_11b.jar
  3c9ea4b7 (LOCAL_ONLY) 20120511155147 plugins/Ratio_Plus.class
  8e2e865e (LOCAL_ONLY) 20050928181804 plugins/Register_ROI.class
  38965c33 (LOCAL_ONLY) 20050928181804 plugins/Register_ROI_MI.class
  6970afac (LOCAL_ONLY) 20050927183506 plugins/Register_ROI_MI_Edges.class
  15089289 (LOCAL_ONLY) 20120425153958 plugins/Tracker_Plugins.jar
  86901120 (LOCAL_ONLY) 20050928181902 plugins/bij.jar
  f1ac6ce6 (LOCAL_ONLY) 20120416121230 plugins/lineagetracker_1.1.3.jar
  d3260180 (LOCAL_ONLY) 20110303194101 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20110303194101 scripts/Record_Window.py
Comment 1 Richard Tyson 2014-08-04 10:24:17 CDT
Created attachment 190
MRI image. DICOM format. 512x512. 16-bit
Comment 2 Richard Tyson 2014-08-04 10:25:49 CDT
*cannot open the images