NoSuchFieldError between BlockMatching and TrakEM2

[Eva_Fiorinelli]

Dear all,

I'm using the block matching plugin of Stephan Saalfeld in Java.
When I execute the command :

IJ.run(Brain, "Extract Block Matching Correspondences", "source_image=IMG1.dcm target_image=Brain layer_scale=1 search_radius=50 block_radius=50 resolution=24 minimal_pmcc_r=0.10 maximal_curvature_ratio=1000 maximal_second_best_r/best_r=1 use_local_smoothness_filter approximate_local_transformation=Affine local_region_sigma=65 maximal_local_displacement=12 export");

I obtain this error :

java.lang.NoSuchFieldError: m00
        at mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:76)
        at mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:22)
        at mpicbg.models.AbstractModel.filter(AbstractModel.java:181)
        at mpicbg.models.AbstractModel.filter(AbstractModel.java:239)
        at mpicbg.models.AbstractModel.localSmoothnessFilter(AbstractModel.java:677)
        at mpicbg.ij.plugin.BlockMatching_ExtractPoinRoi.run(BlockMatching_ExtractPoinRoi.java:152)
        at ij.IJ.runUserPlugIn(IJ.java:199)
        at ij.IJ.runPlugIn(IJ.java:163)
        at ij.Executer.runCommand(Executer.java:132)
        at ij.Executer.run(Executer.java:65)
        at ij.IJ.run(IJ.java:279)
        at ij.IJ.run(IJ.java:334)
        at strokeDetection.model.ArterialMatching.match(ArterialMatching.java:110)
        at strokeDetection.model.ArterialMatching.<init>(ArterialMatching.java:24)
        at strokeDetection.Main.main(Main.java:25)

The documentation says that the NoSuchField error is :

Thrown if an application tries to access or modify a specified field of an object, and that object no longer has that field.
Normally, this error is caught by the compiler; this error can only occur at run time if the definition of a class has incompatibly changed.

So I think I have the bad version for one of the dependencies but I don't find which one.
In Fiji/jars there are mpicbg-1.0.1.jar and mpicbg-trakem2-1.2.2.
In Fiji/plugins I use TrakEM2_-1.0b-SNAPSHOT.jar and  blockmatching_-2.1.1.

Does anyone know what versions of blockmatching and TrakEM2 I need ?

Thank you,

Eva

[Saalfeld, Stephan]

Hi Eva,

you can find the most recent snapshots of all involved jar files at the
ImageJ maven repository:

http://maven.imagej.net/index.html#nexus-search;gav~sc.fiji~TrakEM2_~~~~kw,versionexpand

jars/mpicbg-1.0.1
jars/mpicbg-trakem-1.2.2
plugins/blockmatching_2.1.1
plugins/mpicbg_-1.0.1
plugins/TrakEM2_-1.0f

should work.  I.e. TrakEM2_ is outdated.

Cheers,
Stephan

On Tue, 2015-07-14 at 07:16 -0700, Eva_Fiorinelli wrote:

> Dear all,
>
> I'm using the block matching plugin of Stephan Saalfeld in Java.
> When I execute the command :
>
> IJ.run(Brain, "Extract Block Matching Correspondences",
> "source_image=IMG1.dcm target_image=Brain layer_scale=1 search_radius=50
> block_radius=50 resolution=24 minimal_pmcc_r=0.10
> maximal_curvature_ratio=1000 maximal_second_best_r/best_r=1
> use_local_smoothness_filter approximate_local_transformation=Affine
> local_region_sigma=65 maximal_local_displacement=12 export");
>
> I obtain this error :
>
> java.lang.NoSuchFieldError: m00
> at mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:76)
> at mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:22)
> at mpicbg.models.AbstractModel.filter(AbstractModel.java:181)
> at mpicbg.models.AbstractModel.filter(AbstractModel.java:239)
> at
> mpicbg.models.AbstractModel.localSmoothnessFilter(AbstractModel.java:677)
> at
> mpicbg.ij.plugin.BlockMatching_ExtractPoinRoi.run(BlockMatching_ExtractPoinRoi.java:152)
> at ij.IJ.runUserPlugIn(IJ.java:199)
> at ij.IJ.runPlugIn(IJ.java:163)
> at ij.Executer.runCommand(Executer.java:132)
> at ij.Executer.run(Executer.java:65)
> at ij.IJ.run(IJ.java:279)
> at ij.IJ.run(IJ.java:334)
> at strokeDetection.model.ArterialMatching.match(ArterialMatching.java:110)
> at strokeDetection.model.ArterialMatching.<init>(ArterialMatching.java:24)
> at strokeDetection.Main.main(Main.java:25)
>
> The  documentation
> <http://docs.oracle.com/javase/7/docs/api/java/lang/NoSuchFieldError.html>  
> says that the NoSuchField error is :
>
> Thrown if an application tries to access or modify a specified field of an
> object, and that object no longer has that field.
> Normally, this error is caught by the compiler; this error can only occur at
> run time if the definition of a class has incompatibly changed.
>
> So I think I have the bad version for one of the dependencies but I don't
> find which one.
> In Fiji/jars there are mpicbg-1.0.1.jar and mpicbg-trakem2-1.2.2.
> In Fiji/plugins I use TrakEM2_-1.0b-SNAPSHOT.jar and  blockmatching_-2.1.1.
>
> Does anyone know what versions of blockmatching and TrakEM2 I need ?
>
> Thank you,
>
> Eva
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/NoSuchFieldError-between-BlockMatching-and-TrakEM2-tp5013555.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[ctrueden]

Hi Eva, Stephan, everyone,

> TrakEM2_ is outdated.

In general, it should not be possible to receive NoSuchFieldError or
similar "jar skew" problems with a fully up-to-date version of all ImageJ
and Fiji components. If that happens, it is a bug.

Eva: is your Fiji fully up to date? [1]

Stephan: Do new versions of any TrakEM2 components need to be uploaded to
the Fiji update site? If so, which?

Regards,
Curtis

[1]
http://imagej.net/FAQ#How_can_I_verify_that_my_ImageJ_is_really_100.25_up_to_date.3F

On Wed, Jul 15, 2015 at 8:43 AM, Saalfeld, Stephan <
[hidden email]> wrote:

> Hi Eva,
>
> you can find the most recent snapshots of all involved jar files at the
> ImageJ maven repository:
>
>
> http://maven.imagej.net/index.html#nexus-search;gav~sc.fiji~TrakEM2_~~~~kw,versionexpand
>
> jars/mpicbg-1.0.1
> jars/mpicbg-trakem-1.2.2
> plugins/blockmatching_2.1.1
> plugins/mpicbg_-1.0.1
> plugins/TrakEM2_-1.0f
>
> should work.  I.e. TrakEM2_ is outdated.
>
> Cheers,
> Stephan
>
> On Tue, 2015-07-14 at 07:16 -0700, Eva_Fiorinelli wrote:
> > Dear all,
> >
> > I'm using the block matching plugin of Stephan Saalfeld in Java.
> > When I execute the command :
> >
> > IJ.run(Brain, "Extract Block Matching Correspondences",
> > "source_image=IMG1.dcm target_image=Brain layer_scale=1 search_radius=50
> > block_radius=50 resolution=24 minimal_pmcc_r=0.10
> > maximal_curvature_ratio=1000 maximal_second_best_r/best_r=1
> > use_local_smoothness_filter approximate_local_transformation=Affine
> > local_region_sigma=65 maximal_local_displacement=12 export");
> >
> > I obtain this error :
> >
> > java.lang.NoSuchFieldError: m00
> >       at
> mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:76)
> >       at
> mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:22)
> >       at mpicbg.models.AbstractModel.filter(AbstractModel.java:181)
> >       at mpicbg.models.AbstractModel.filter(AbstractModel.java:239)
> >       at
> > mpicbg.models.AbstractModel.localSmoothnessFilter(AbstractModel.java:677)
> >       at
> >
> mpicbg.ij.plugin.BlockMatching_ExtractPoinRoi.run(BlockMatching_ExtractPoinRoi.java:152)
> >       at ij.IJ.runUserPlugIn(IJ.java:199)
> >       at ij.IJ.runPlugIn(IJ.java:163)
> >       at ij.Executer.runCommand(Executer.java:132)
> >       at ij.Executer.run(Executer.java:65)
> >       at ij.IJ.run(IJ.java:279)
> >       at ij.IJ.run(IJ.java:334)
> >       at
> strokeDetection.model.ArterialMatching.match(ArterialMatching.java:110)
> >       at
> strokeDetection.model.ArterialMatching.<init>(ArterialMatching.java:24)
> >       at strokeDetection.Main.main(Main.java:25)
> >
> > The  documentation
> > <
> http://docs.oracle.com/javase/7/docs/api/java/lang/NoSuchFieldError.html>
> > says that the NoSuchField error is :
> >
> > Thrown if an application tries to access or modify a specified field of
> an
> > object, and that object no longer has that field.
> > Normally, this error is caught by the compiler; this error can only
> occur at
> > run time if the definition of a class has incompatibly changed.
> >
> > So I think I have the bad version for one of the dependencies but I don't
> > find which one.
> > In Fiji/jars there are mpicbg-1.0.1.jar and mpicbg-trakem2-1.2.2.
> > In Fiji/plugins I use TrakEM2_-1.0b-SNAPSHOT.jar and
> blockmatching_-2.1.1.
> >
> > Does anyone know what versions of blockmatching and TrakEM2 I need ?
> >
> > Thank you,
> >
> > Eva
> >
> >
> >
> > --
> > View this message in context:
> http://imagej.1557.x6.nabble.com/NoSuchFieldError-between-BlockMatching-and-TrakEM2-tp5013555.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > 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 again Eva,

I just noticed you said you are calling the plugin "from Java."

> Does anyone know what versions of blockmatching and TrakEM2 I need ?

The answer here is to use pom-fiji to manage the Bill of Materials [1], so
that you inherit compatible versions.

Use Maven [2] (or Maven-compatible tool such as Gradle), and extend or
import pom-fiji. Happy to go into more detail if needed; just ask.

Regards,
Curtis

[1] http://imagej.net/BOM
[2] http://imagej.net/Maven

On Wed, Jul 15, 2015 at 1:26 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Eva, Stephan, everyone,
>
> > TrakEM2_ is outdated.
>
> In general, it should not be possible to receive NoSuchFieldError or
> similar "jar skew" problems with a fully up-to-date version of all ImageJ
> and Fiji components. If that happens, it is a bug.
>
> Eva: is your Fiji fully up to date? [1]
>
> Stephan: Do new versions of any TrakEM2 components need to be uploaded to
> the Fiji update site? If so, which?
>
> Regards,
> Curtis
>
> [1]
> http://imagej.net/FAQ#How_can_I_verify_that_my_ImageJ_is_really_100.25_up_to_date.3F
>
> On Wed, Jul 15, 2015 at 8:43 AM, Saalfeld, Stephan <
> [hidden email]> wrote:
>
>> Hi Eva,
>>
>> you can find the most recent snapshots of all involved jar files at the
>> ImageJ maven repository:
>>
>>
>> http://maven.imagej.net/index.html#nexus-search;gav~sc.fiji~TrakEM2_~~~~kw,versionexpand
>>
>> jars/mpicbg-1.0.1
>> jars/mpicbg-trakem-1.2.2
>> plugins/blockmatching_2.1.1
>> plugins/mpicbg_-1.0.1
>> plugins/TrakEM2_-1.0f
>>
>> should work.  I.e. TrakEM2_ is outdated.
>>
>> Cheers,
>> Stephan
>>
>> On Tue, 2015-07-14 at 07:16 -0700, Eva_Fiorinelli wrote:
>> > Dear all,
>> >
>> > I'm using the block matching plugin of Stephan Saalfeld in Java.
>> > When I execute the command :
>> >
>> > IJ.run(Brain, "Extract Block Matching Correspondences",
>> > "source_image=IMG1.dcm target_image=Brain layer_scale=1 search_radius=50
>> > block_radius=50 resolution=24 minimal_pmcc_r=0.10
>> > maximal_curvature_ratio=1000 maximal_second_best_r/best_r=1
>> > use_local_smoothness_filter approximate_local_transformation=Affine
>> > local_region_sigma=65 maximal_local_displacement=12 export");
>> >
>> > I obtain this error :
>> >
>> > java.lang.NoSuchFieldError: m00
>> >       at
>> mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:76)
>> >       at
>> mpicbg.trakem2.transform.AffineModel2D.copy(AffineModel2D.java:22)
>> >       at mpicbg.models.AbstractModel.filter(AbstractModel.java:181)
>> >       at mpicbg.models.AbstractModel.filter(AbstractModel.java:239)
>> >       at
>> >
>> mpicbg.models.AbstractModel.localSmoothnessFilter(AbstractModel.java:677)
>> >       at
>> >
>> mpicbg.ij.plugin.BlockMatching_ExtractPoinRoi.run(BlockMatching_ExtractPoinRoi.java:152)
>> >       at ij.IJ.runUserPlugIn(IJ.java:199)
>> >       at ij.IJ.runPlugIn(IJ.java:163)
>> >       at ij.Executer.runCommand(Executer.java:132)
>> >       at ij.Executer.run(Executer.java:65)
>> >       at ij.IJ.run(IJ.java:279)
>> >       at ij.IJ.run(IJ.java:334)
>> >       at
>> strokeDetection.model.ArterialMatching.match(ArterialMatching.java:110)
>> >       at
>> strokeDetection.model.ArterialMatching.<init>(ArterialMatching.java:24)
>> >       at strokeDetection.Main.main(Main.java:25)
>> >
>> > The  documentation
>> > <
>> http://docs.oracle.com/javase/7/docs/api/java/lang/NoSuchFieldError.html>
>> > says that the NoSuchField error is :
>> >
>> > Thrown if an application tries to access or modify a specified field of
>> an
>> > object, and that object no longer has that field.
>> > Normally, this error is caught by the compiler; this error can only
>> occur at
>> > run time if the definition of a class has incompatibly changed.
>> >
>> > So I think I have the bad version for one of the dependencies but I
>> don't
>> > find which one.
>> > In Fiji/jars there are mpicbg-1.0.1.jar and mpicbg-trakem2-1.2.2.
>> > In Fiji/plugins I use TrakEM2_-1.0b-SNAPSHOT.jar and
>> blockmatching_-2.1.1.
>> >
>> > Does anyone know what versions of blockmatching and TrakEM2 I need ?
>> >
>> > Thank you,
>> >
>> > Eva
>> >
>> >
>> >
>> > --
>> > View this message in context:
>> http://imagej.1557.x6.nabble.com/NoSuchFieldError-between-BlockMatching-and-TrakEM2-tp5013555.html
>> > Sent from the ImageJ mailing list archive at Nabble.com.
>> >
>> > --
>> > 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

[Eva_Fiorinelli]

Hi all,

Despite my Fiji seems to be fully up to date, the last version of TrakEM2_ that I can see in the Fiji updater is TrakEM2_-1.0b-SNAPSHOT from Archipelago and it was released April 9th 2014.

As you said Curtis, I mavenized my Eclipse project, I used pom-fiji 12.1.0 as parent in my POM.xml and ij 1.49v as dependency. I use the repository http://maven.imagej.net/content/groups/public.
I added the plugins Volume_Viewer, blockmatching and TrakEM2 as dependencies in the POM file (compile scope).

It seems to work well, for example I can build a Volume Viewer object in my code. My problem is that I want to not display the windows so I would like to call these plugins in a macro with batch mode :

setBatchMode(true);
options = getArgument;

run("Extract Block Matching Correspondences", options+" layer_scale=1 search_radius=50 block_radius=50 resolution=24 minimal_pmcc_r=0.10 maximal_curvature_ratio=1000 maximal_second_best_r/best_r=1 use_local_smoothness_filter approximate_local_transformation=Affine local_region_sigma=65 maximal_local_displacement=12 maximal_local_displacement=3 export");

setBatchMode(false);

To execute this macro with runMacroFile in the project, I placed it in the src/main/resources directory of Maven. I obtain this error :

Unrecognized command: "Volume Viewer"
Unrecognized command: "Extract Block Matching Correspondences"

I have the same error with IJ.run(imp, "Volume Viewer", ""); directly in my Java class.

I don't know if Maven doesn't read plugins.config files or it comes from my Eclipse configuration.

[EDIT]

I found these discussions here and here, I'm trying to define -Dplugins.dir correctly.

-Dplugins.dir=C:\Users\fiorinelli\.m2\repository\sc\fiji\Volume_Viewer\2.01.1

is able to find the plugin but

-Dij1.plugin.dirs=C:\Users\fiorinelli\.m2\repository\sc\fiji\Volume_Viewer\2.01.1;C:\Users\fiorinelli\.m2\repository\sc\fiji\TrakEM2_\1.0f;C:\Users\fiorinelli\.m2\repository\sc\fiji\mpicbg-trakem2\1.2.2;C:\Users\fiorinelli\.m2\repository\sc\fiji\blockmatching_\2.1.1

doesn't find anything.

My temporary solution is to copy the jars I need from .m2\repository\... folder to the same folder and define -Dplugins.dir=<this directory>

[/EDIT]

Thank you very much for your help,

Eva