Multiview Reconstruction: NullPointerException

[Lorenz Maier]

Hi everyone,

I just tried to use fresh download of Fiji (continuous release branch)  
for registering a small set of images.
Trying to detect the interest points for registration with the  
specification set to “interactive” gives me a NullPointerException.
Any ideas?

java.lang.NullPointerException
                 at  
net.imagej.legacy.translate.AbstractDisplayCreator.getDataset(AbstractDisplayCreator.java:76)
                 at  
net.imagej.legacy.translate.GrayDisplayCreator.grayCase(GrayDisplayCreator.java:159)
                 at  
net.imagej.legacy.translate.GrayDisplayCreator.makeDisplay(GrayDisplayCreator.java:129)
                 at  
net.imagej.legacy.translate.AbstractDisplayCreator.createDisplay(AbstractDisplayCreator.java:63)
                 at  
net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:100)
                 at  
net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:84)
                 at  
net.imagej.legacy.LegacyImageMap.registerLegacyImage(LegacyImageMap.java:271)
                 at  
net.imagej.legacy.DefaultLegacyHooks.registerImage(DefaultLegacyHooks.java:177)
                 at ij.gui.ImageWindow.show(ImageWindow.java)
                 at ij.gui.ImageWindow.<init>(ImageWindow.java:138)
                 at ij.gui.StackWindow.<init>(StackWindow.java:28)
                 at ij.gui.StackWindow.<init>(StackWindow.java:24)
                 at ij.ImagePlus.show(ImagePlus.java:388)
                 at ij.ImagePlus.show(ImagePlus.java:363)
                 at  
spim.fiji.plugin.interestpointdetection.DifferenceOfGaussian.setInteractiveValues(DifferenceOfGaussian.java:257)
                 at  
spim.fiji.plugin.interestpointdetection.DifferenceOf.queryParameters(DifferenceOf.java:206)
                 at  
spim.fiji.plugin.Interest_Point_Detection.run(Interest_Point_Detection.java:127)
                 at ij.IJ.runUserPlugIn(IJ.java:202)
                 at ij.IJ.runPlugIn(IJ.java:166)
                 at ij.Executer.runCommand(Executer.java:131)
                 at ij.Executer.run(Executer.java:64)
                 at java.lang.Thread.run(Thread.java:662)

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:\USERPR~1\Fiji.app/java/win64/jdk1.6.0_24//jre
   imagej.dir => C:\USERPR~1\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150226203217)
Fiji: http://fiji.sc/update/ (last check:20150226203401)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20141208085245)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221160506)
ClearVolume: http://sites.imagej.net/ClearVolume/ (last check:20150225131557)
HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214134119)
NucleusJ: http://sites.imagej.net/PouletAxel/ (last check:20141101103602)


Best regards,
Lorenz

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Lorenz,

> Trying to detect the interest points for registration with the
> specification set to “interactive” gives me a NullPointerException.

This ImageJ2 bug[1] only occurs when "Edit > Options > ImageJ2 > Enable
ImageJ2 data structures" is checked.

A fix is pending and will be uploaded soon. But in the meantime, disabling
that option avoids the issue.

Regards,
Curtis

[1] http://fiji.sc/bugzilla/show_bug.cgi?id=1010

On Sat, Feb 28, 2015 at 4:35 AM, Lorenz Maier <
[hidden email]> wrote:

> Hi everyone,
>
> I just tried to use fresh download of Fiji (continuous release branch) for
> registering a small set of images.
> Trying to detect the interest points for registration with the
> specification set to “interactive” gives me a NullPointerException.
> Any ideas?
>
> java.lang.NullPointerException
>                 at net.imagej.legacy.translate.AbstractDisplayCreator.
> getDataset(AbstractDisplayCreator.java:76)
>                 at net.imagej.legacy.translate.
> GrayDisplayCreator.grayCase(GrayDisplayCreator.java:159)
>                 at net.imagej.legacy.translate.GrayDisplayCreator.
> makeDisplay(GrayDisplayCreator.java:129)
>                 at net.imagej.legacy.translate.AbstractDisplayCreator.
> createDisplay(AbstractDisplayCreator.java:63)
>                 at net.imagej.legacy.translate.DefaultImageTranslator.
> createDisplay(DefaultImageTranslator.java:100)
>                 at net.imagej.legacy.translate.DefaultImageTranslator.
> createDisplay(DefaultImageTranslator.java:84)
>                 at net.imagej.legacy.LegacyImageMap.registerLegacyImage(
> LegacyImageMap.java:271)
>                 at net.imagej.legacy.DefaultLegacyHooks.registerImage(
> DefaultLegacyHooks.java:177)
>                 at ij.gui.ImageWindow.show(ImageWindow.java)
>                 at ij.gui.ImageWindow.<init>(ImageWindow.java:138)
>                 at ij.gui.StackWindow.<init>(StackWindow.java:28)
>                 at ij.gui.StackWindow.<init>(StackWindow.java:24)
>                 at ij.ImagePlus.show(ImagePlus.java:388)
>                 at ij.ImagePlus.show(ImagePlus.java:363)
>                 at spim.fiji.plugin.interestpointdetection.
> DifferenceOfGaussian.setInteractiveValues(DifferenceOfGaussian.java:257)
>                 at spim.fiji.plugin.interestpointdetection.
> DifferenceOf.queryParameters(DifferenceOf.java:206)
>                 at spim.fiji.plugin.Interest_Point_Detection.run(Interest_
> Point_Detection.java:127)
>                 at ij.IJ.runUserPlugIn(IJ.java:202)
>                 at ij.IJ.runPlugIn(IJ.java:166)
>                 at ij.Executer.runCommand(Executer.java:131)
>                 at ij.Executer.run(Executer.java:64)
>                 at java.lang.Thread.run(Thread.java:662)
>
> 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:\USERPR~1\Fiji.app/java/win64/jdk1.6.0_24//jre
>   imagej.dir => C:\USERPR~1\Fiji.app
>
> Information about the version of each plugin:
>
> Activated update sites:
> ImageJ: http://update.imagej.net/ (last check:20150226203217)
> Fiji: http://fiji.sc/update/ (last check:20150226203401)
> 3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last
> check:20141208085245)
> BigDataViewer: http://sites.imagej.net/Pietzsch/ (last
> check:20141221160506)
> ClearVolume: http://sites.imagej.net/ClearVolume/ (last
> check:20150225131557)
> HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214134119)
> NucleusJ: http://sites.imagej.net/PouletAxel/ (last check:20141101103602)
>
>
> Best regards,
> Lorenz
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Lorenz Maier]

Thanks Curtis!

Could you please CC me there? Or do you know a rough timespan when the fix will be included?

Best,
- Lorenz [mobile]

> On 28 Feb 2015, at 15:31, Curtis Rueden <[hidden email]> wrote:
>
> Hi Lorenz,
>
>> Trying to detect the interest points for registration with the
>> specification set to “interactive” gives me a NullPointerException.
>
> This ImageJ2 bug[1] only occurs when "Edit > Options > ImageJ2 > Enable
> ImageJ2 data structures" is checked.
>
> A fix is pending and will be uploaded soon. But in the meantime, disabling
> that option avoids the issue.
>
> Regards,
> Curtis
>
> [1] http://fiji.sc/bugzilla/show_bug.cgi?id=1010
>
> On Sat, Feb 28, 2015 at 4:35 AM, Lorenz Maier <
> [hidden email]> wrote:
>
>> Hi everyone,
>>
>> I just tried to use fresh download of Fiji (continuous release branch) for
>> registering a small set of images.
>> Trying to detect the interest points for registration with the
>> specification set to “interactive” gives me a NullPointerException.
>> Any ideas?
>>
>> java.lang.NullPointerException
>>               at net.imagej.legacy.translate.AbstractDisplayCreator.
>> getDataset(AbstractDisplayCreator.java:76)
>>               at net.imagej.legacy.translate.
>> GrayDisplayCreator.grayCase(GrayDisplayCreator.java:159)
>>               at net.imagej.legacy.translate.GrayDisplayCreator.
>> makeDisplay(GrayDisplayCreator.java:129)
>>               at net.imagej.legacy.translate.AbstractDisplayCreator.
>> createDisplay(AbstractDisplayCreator.java:63)
>>               at net.imagej.legacy.translate.DefaultImageTranslator.
>> createDisplay(DefaultImageTranslator.java:100)
>>               at net.imagej.legacy.translate.DefaultImageTranslator.
>> createDisplay(DefaultImageTranslator.java:84)
>>               at net.imagej.legacy.LegacyImageMap.registerLegacyImage(
>> LegacyImageMap.java:271)
>>               at net.imagej.legacy.DefaultLegacyHooks.registerImage(
>> DefaultLegacyHooks.java:177)
>>               at ij.gui.ImageWindow.show(ImageWindow.java)
>>               at ij.gui.ImageWindow.<init>(ImageWindow.java:138)
>>               at ij.gui.StackWindow.<init>(StackWindow.java:28)
>>               at ij.gui.StackWindow.<init>(StackWindow.java:24)
>>               at ij.ImagePlus.show(ImagePlus.java:388)
>>               at ij.ImagePlus.show(ImagePlus.java:363)
>>               at spim.fiji.plugin.interestpointdetection.
>> DifferenceOfGaussian.setInteractiveValues(DifferenceOfGaussian.java:257)
>>               at spim.fiji.plugin.interestpointdetection.
>> DifferenceOf.queryParameters(DifferenceOf.java:206)
>>               at spim.fiji.plugin.Interest_Point_Detection.run(Interest_
>> Point_Detection.java:127)
>>               at ij.IJ.runUserPlugIn(IJ.java:202)
>>               at ij.IJ.runPlugIn(IJ.java:166)
>>               at ij.Executer.runCommand(Executer.java:131)
>>               at ij.Executer.run(Executer.java:64)
>>               at java.lang.Thread.run(Thread.java:662)
>>
>> 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:\USERPR~1\Fiji.app/java/win64/jdk1.6.0_24//jre
>> imagej.dir => C:\USERPR~1\Fiji.app
>>
>> Information about the version of each plugin:
>>
>> Activated update sites:
>> ImageJ: http://update.imagej.net/ (last check:20150226203217)
>> Fiji: http://fiji.sc/update/ (last check:20150226203401)
>> 3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last
>> check:20141208085245)
>> BigDataViewer: http://sites.imagej.net/Pietzsch/ (last
>> check:20141221160506)
>> ClearVolume: http://sites.imagej.net/ClearVolume/ (last
>> check:20150225131557)
>> HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214134119)
>> NucleusJ: http://sites.imagej.net/PouletAxel/ (last check:20141101103602)
>>
>>
>> Best regards,
>> Lorenz
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Lorenz,

> do you know a rough timespan when the fix will be included?

The fix has been uploaded now; run Help > Update... to receive it.

> Could you please CC me there?

In the future, if you ever want to CC yourself on a Bugzilla issue, you
would need to create an account and then add yourself to the CC (IIRC,
Bugzilla only lets you CC registered users/emails).

Regards,
Curtis

On Sat, Feb 28, 2015 at 9:05 AM, Lorenz Maier <
[hidden email]> wrote:

> Thanks Curtis!
>
> Could you please CC me there? Or do you know a rough timespan when the fix
> will be included?
>
> Best,
> - Lorenz [mobile]
>
>
>
> > On 28 Feb 2015, at 15:31, Curtis Rueden <[hidden email]> wrote:
> >
> > Hi Lorenz,
> >
> >> Trying to detect the interest points for registration with the
> >> specification set to “interactive” gives me a NullPointerException.
> >
> > This ImageJ2 bug[1] only occurs when "Edit > Options > ImageJ2 > Enable
> > ImageJ2 data structures" is checked.
> >
> > A fix is pending and will be uploaded soon. But in the meantime,
> disabling
> > that option avoids the issue.
> >
> > Regards,
> > Curtis
> >
> > [1] http://fiji.sc/bugzilla/show_bug.cgi?id=1010
> >
> > On Sat, Feb 28, 2015 at 4:35 AM, Lorenz Maier <
> > [hidden email]> wrote:
> >
> >> Hi everyone,
> >>
> >> I just tried to use fresh download of Fiji (continuous release branch)
> for
> >> registering a small set of images.
> >> Trying to detect the interest points for registration with the
> >> specification set to “interactive” gives me a NullPointerException.
> >> Any ideas?
> >>
> >> java.lang.NullPointerException
> >>               at net.imagej.legacy.translate.AbstractDisplayCreator.
> >> getDataset(AbstractDisplayCreator.java:76)
> >>               at net.imagej.legacy.translate.
> >> GrayDisplayCreator.grayCase(GrayDisplayCreator.java:159)
> >>               at net.imagej.legacy.translate.GrayDisplayCreator.
> >> makeDisplay(GrayDisplayCreator.java:129)
> >>               at net.imagej.legacy.translate.AbstractDisplayCreator.
> >> createDisplay(AbstractDisplayCreator.java:63)
> >>               at net.imagej.legacy.translate.DefaultImageTranslator.
> >> createDisplay(DefaultImageTranslator.java:100)
> >>               at net.imagej.legacy.translate.DefaultImageTranslator.
> >> createDisplay(DefaultImageTranslator.java:84)
> >>               at net.imagej.legacy.LegacyImageMap.registerLegacyImage(
> >> LegacyImageMap.java:271)
> >>               at net.imagej.legacy.DefaultLegacyHooks.registerImage(
> >> DefaultLegacyHooks.java:177)
> >>               at ij.gui.ImageWindow.show(ImageWindow.java)
> >>               at ij.gui.ImageWindow.<init>(ImageWindow.java:138)
> >>               at ij.gui.StackWindow.<init>(StackWindow.java:28)
> >>               at ij.gui.StackWindow.<init>(StackWindow.java:24)
> >>               at ij.ImagePlus.show(ImagePlus.java:388)
> >>               at ij.ImagePlus.show(ImagePlus.java:363)
> >>               at spim.fiji.plugin.interestpointdetection.
> >> DifferenceOfGaussian.setInteractiveValues(DifferenceOfGaussian.java:257)
> >>               at spim.fiji.plugin.interestpointdetection.
> >> DifferenceOf.queryParameters(DifferenceOf.java:206)
> >>               at spim.fiji.plugin.Interest_Point_Detection.run(Interest_
> >> Point_Detection.java:127)
> >>               at ij.IJ.runUserPlugIn(IJ.java:202)
> >>               at ij.IJ.runPlugIn(IJ.java:166)
> >>               at ij.Executer.runCommand(Executer.java:131)
> >>               at ij.Executer.run(Executer.java:64)
> >>               at java.lang.Thread.run(Thread.java:662)
> >>
> >> 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:\USERPR~1\Fiji.app/java/win64/jdk1.6.0_24//jre
> >> imagej.dir => C:\USERPR~1\Fiji.app
> >>
> >> Information about the version of each plugin:
> >>
> >> Activated update sites:
> >> ImageJ: http://update.imagej.net/ (last check:20150226203217)
> >> Fiji: http://fiji.sc/update/ (last check:20150226203401)
> >> 3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last
> >> check:20141208085245)
> >> BigDataViewer: http://sites.imagej.net/Pietzsch/ (last
> >> check:20141221160506)
> >> ClearVolume: http://sites.imagej.net/ClearVolume/ (last
> >> check:20150225131557)
> >> HDF5: http://sites.imagej.net/Ronneber/ (last check:20150214134119)
> >> NucleusJ: http://sites.imagej.net/PouletAxel/ (last
> check:20141101103602)
> >>
> >>
> >> Best regards,
> >> Lorenz
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html