[ImageJ-bugs] [Bug 1078] New: Exception when trying to run Cookbook > Deconvolution > Diffraction PSF 3D

bugzilla at fiji.sc bugzilla at fiji.sc
Fri May 29 06:38:58 CDT 2015 

http://fiji.sc/bugzilla/show_bug.cgi?id=1078

            Bug ID: 1078
           Summary: Exception when trying to run Cookbook > Deconvolution
                    > Diffraction PSF 3D
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: graemeball at googlemail.com
                CC: graemeball at googlemail.com

Exception when trying to run Cookbook > Deconvolution > Diffraction PSF 3D

In case the stack trace is not attached automatically from the console, here it
is:

javax.xml.transform.TransformerException: java.io.FileNotFoundException:
file:/var/folders/kz/js9r4l5159n2x4jzrvkz72dh000cc9/T/java1008253920954071734/pom.xml
(No such file or directory)
    at
org.apache.xalan.transformer.TransformerIdentityImpl.createResultContentHandler(TransformerIdentityImpl.java:245)
    at
org.apache.xalan.transformer.TransformerIdentityImpl.transform(TransformerIdentityImpl.java:278)
    at
org.scijava.plugins.scripting.java.JavaEngine.fakePOM(JavaEngine.java:744)
    at
org.scijava.plugins.scripting.java.JavaEngine.writeTemporaryProject(JavaEngine.java:631)
    at
org.scijava.plugins.scripting.java.JavaEngine.getMavenProject(JavaEngine.java:532)
    at
org.scijava.plugins.scripting.java.JavaEngine.access$600(JavaEngine.java:95)
    at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:410)
    at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:372)
    at
org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:198)
    at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
    at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
    at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
    at java.lang.Thread.run(Thread.java:695)
Caused by: java.io.FileNotFoundException:
file:/var/folders/kz/js9r4l5159n2x4jzrvkz72dh000cc9/T/java1008253920954071734/pom.xml
(No such file or directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:84)
    at
org.apache.xalan.transformer.TransformerIdentityImpl.createResultContentHandler(TransformerIdentityImpl.java:235)
    ... 20 more
---------
java.io.FileNotFoundException:
file:/var/folders/kz/js9r4l5159n2x4jzrvkz72dh000cc9/T/java1008253920954071734/pom.xml
(No such file or directory)
    at java.io.FileOutputStream.open(Native Method)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:194)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:84)
    at
org.apache.xalan.transformer.TransformerIdentityImpl.createResultContentHandler(TransformerIdentityImpl.java:235)
    at
org.apache.xalan.transformer.TransformerIdentityImpl.transform(TransformerIdentityImpl.java:278)
    at
org.scijava.plugins.scripting.java.JavaEngine.fakePOM(JavaEngine.java:744)
    at
org.scijava.plugins.scripting.java.JavaEngine.writeTemporaryProject(JavaEngine.java:631)
    at
org.scijava.plugins.scripting.java.JavaEngine.getMavenProject(JavaEngine.java:532)
    at
org.scijava.plugins.scripting.java.JavaEngine.access$600(JavaEngine.java:95)
    at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:410)
    at
org.scijava.plugins.scripting.java.JavaEngine$Builder.<init>(JavaEngine.java:372)
    at
org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:198)
    at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
    at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
    at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
    at
org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:181)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
    at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
    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 => 10.9.5
  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: REMIND_LATER

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:20150501194914)
Fiji: http://fiji.sc/update/ (last check:20150509234919)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20150513055927)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150302220629)
MOSAIC ToolSuite:
http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last
check:20150227190151)

Files not up-to-date:
  4aa5c2f5 (MODIFIED) 20150424135216 Contents/Info.plist
  14b8544b (MODIFIED) 20150512145526 jars/imagej-updater-0.7.4.jar
  4ccabde3 (MODIFIED) 20150526192326 jars/imagej-updater-0.7.5.jar
  1ad3be0d (LOCAL_ONLY) 20150109125307 jars/jpedalSTD.jar
  e7f9b16f (LOCAL_ONLY) 20150317134408 macros/BatchMacro.ijm
  726548fe (LOCAL_ONLY) 20150429005317 macros/Plot_Multicolor4.3.txt
  404c9259 (LOCAL_ONLY) 20150526173649 plugins/ICTN_.jar
  6f7ce779 (LOCAL_ONLY) 20150429005205 plugins/Macros/Plot_Multicolor4.3.txt
  ec17890b (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/JHotDraw.jar
  91ece67d (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/JWlz.jar
  36cb5c0a (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/TableLayout.jar
  c3a86bd0 (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/assumeng.jar
  7c4005e7 (LOCAL_ONLY) 20050801102630
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis-wsdl4j.jar
  364315a9 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis.jar
  3370a633 (LOCAL_ONLY) 20070427143948
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/axis2-saaj.jar
  0af1624e (LOCAL_ONLY) 20140714161754
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/backport-util-concurrent.jar
  07f50124 (LOCAL_ONLY) 20150427193612
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz-javadoc.jar
  ab21bcc1 (LOCAL_ONLY) 20150427193542
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz-sources.jar
  63fdcaa4 (LOCAL_ONLY) 20150427193618
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/blitz.jar
  189f61fa (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/bufr.jar
  94e35e33 (LOCAL_ONLY) 20150427193306
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common-javadoc.jar
  3646964f (LOCAL_ONLY) 20150427193302
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common-sources.jar
  c0f30819 (LOCAL_ONLY) 20150427193306
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/common.jar
  940245e0 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-codec.jar
  64d8a654 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-collections.jar
  86ab9004 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-digester.jar
  9e9eb622 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-discovery.jar
  d59d3e4c (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-io.jar
  f6139801 (LOCAL_ONLY) 20100225002342
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-lang.jar
  fa9b8239 (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-logging.jar
  60a83b54 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/commons-validator.jar
  abf211c5 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ehcache-core.jar
  e33cecc2 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/grib.jar
  2cd0d04c (LOCAL_ONLY) 20141125101518
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/guava.jar
  85c28658 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/hibernate-jpa-2.0-api.jar
  0c6e277e (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpclient.jar
  9f61e37d (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpcore.jar
  d216e98a (LOCAL_ONLY) 20141210140056
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/httpmime.jar
  1911c9e1 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-glacier2.jar
  b1d709fb (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-grid.jar
  c49b8fa2 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice-storm.jar
  53aa5393 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ice.jar
  84b54b46 (LOCAL_ONLY) 20150218193626
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ij.jar
  6ce638fb (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ini4j.jar
  f1b65457 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/java-getopt.jar
  c827227f (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/java-image-scaling.jar
  e72f9b2b (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jaxrpc.jar
  07f15e96 (LOCAL_ONLY) 20140724163642
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jcommon.jar
  c4eeeb8f (LOCAL_ONLY) 20140731133446
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jfreechart.jar
  5defc8da (LOCAL_ONLY) 20150320195720
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jhdf5.jar
  df7a0b63 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/jna.jar
  4c09d41c (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/joda-time.jar
  4a754817 (LOCAL_ONLY) 20140929140200
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/kryo.jar
  b47bd885 (LOCAL_ONLY) 20150427193148
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/lwf-stubs.jar
  ab8ff4ee (LOCAL_ONLY) 20150218193636
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/metadata-extractor.jar
  16b765c2 (LOCAL_ONLY) 20140929140200
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/minlog.jar
  c74b45b0 (LOCAL_ONLY) 20150427193258
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql-javadoc.jar
  0436d2f4 (LOCAL_ONLY) 20150427193246
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql-sources.jar
  6267f51d (LOCAL_ONLY) 20150427193258
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/model-psql.jar
  66de339f (LOCAL_ONLY) 20140905201058
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/native-lib-loader.jar
  a51a31db (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/netcdf.jar
  aff28c0e (LOCAL_ONLY) 20140929140200
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/objenesis.jar
  18382f06 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/ome-java.jar
  7af6ddeb (LOCAL_ONLY) 20140123090208
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/perf4j.jar
  b3056152 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/platform.jar
  4ef2cfd3 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/poi.jar
  eedc0cd9 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/serializer.jar
  5085d943 (LOCAL_ONLY) 20140321125832
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/slf4j-api.jar
  228d9879 (LOCAL_ONLY) 20150427193144
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/specification.jar
  ba32bfdf (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/swingx.jar
  c8694e76 (LOCAL_ONLY) 20140123090126
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xalan.jar
  93f166fd (LOCAL_ONLY) 20150218193636
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xercesImpl.jar
  a5c15945 (LOCAL_ONLY) 20150218193636
plugins/OMERO.insight-ij-5.1.1-ice35-b43/libs/xmpcore.jar
  d428b86d (LOCAL_ONLY) 20150427194034
plugins/OMERO.insight-ij-5.1.1-ice35-b43/omero_ij.jar
  0e8ddb6d (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/arpack-combo.jar
  1a08e201 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/csparsej.jar
  924b8d62 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/jplasma.jar
  fca468e8 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/jtransforms.jar
  14ccf036 (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/licenses/parallelcolt.LICENSE.txt
  c6c2bb4d (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/licenses/parallelfftj.LICENSE.txt
  89cb5823 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/netlib-java.jar
  25802519 (LOCAL_ONLY) 20130914180736 plugins/ParallelFFTJ/optimization.jar
  3a6c661d (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/parallel_fftj-1.4.jar
  87fc836e (LOCAL_ONLY) 20130914180736
plugins/ParallelFFTJ/parallelcolt-0.9.4.jar
  c58cb4bf 20150525222659 plugins/SIMcheck-0.9.9-SNAPSHOT-javadoc.jar
  bd5d5c61 20150525222659 plugins/SIMcheck-0.9.9-SNAPSHOT-sources.jar
  514d26dc (LOCAL_ONLY) 20150527125150 plugins/SIMcheck_-0.9.9.jar
  f57ea4b0 20150525222659 plugins/SIMcheck_0.9.9-SNAPSHOT.jar
  034d1e63 (LOCAL_ONLY) 20150422123024 plugins/Temporal_plugins-1.0.0.jar

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