These are chat archives for fiji/fiji

30th
Nov 2018
Josh Moore
@joshmoore
Nov 30 2018 07:17
Morning folks. Definitely haven't solved blocks-vs-planes at this point. This has mostly been driven by the fact that we’re getting data submissions for BDV and KLB to the IDR, so having a reader was necessary step one. That combined with pyramidal tiffs ended up taking up much of the past year since discussions in Dresden. So if all goes well, we get back to the deeper (ha!) issue in 2019. Happy to go into more detail here or next week at I2K.
Ellen T Arena
@etarena
Nov 30 2018 21:09
@axtimwalde @StephanPreibisch SPIM_Registration fails to build against mpicbg 1.3.0:
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/BeadRegistration.java:[653,41] set(double,double,double,double,double,double,double,double,double,double,double,double) has private access in mpicbg.models.RigidModel3D
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/FixedModel.java:[34,8] mpicbg.pointdescriptor.model.FixedModel is not abstract and does not override abstract method reset() in mpicbg.models.Model
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantRigidModel2D.java:[54,8] mpicbg.pointdescriptor.model.TranslationInvariantRigidModel2D is not abstract and does not override abstract method reset() in mpicbg.models.Model
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/spim/io/IOFunctions.java:[1039,54] set(double,double,double,double,double,double,double,double,double,double,double,double) has private access in mpicbg.models.RigidModel3D
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantFixedModel.java:[34,8] mpicbg.pointdescriptor.model.TranslationInvariantFixedModel is not abstract and does not override abstract method reset() in mpicbg.models.Model
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantSimilarityModel3D.java:[44,8] mpicbg.pointdescriptor.model.TranslationInvariantSimilarityModel3D is not abstract and does not override abstract method reset() in mpicbg.models.Model
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantAffineModel3D.java:[57,8] mpicbg.pointdescriptor.model.TranslationInvariantAffineModel3D is not abstract and does not override abstract method reset() in mpicbg.models.Model
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantRigidModel3D.java:[47,8] mpicbg.pointdescriptor.model.TranslationInvariantRigidModel3D is not abstract and does not override abstract method reset() in mpicbg.models.Model
[ERROR] /Users/ellenarena/code/fiji/SPIM_Registration/src/main/java/mpicbg/util/TransformUtils.java:[194,22] set(double,double,double,double,double,double,double,double,double,double,double,double) has private access in mpicbg.models.RigidModel3D
any chance this could be fixed before I2K? @ctrueden wants to release a new Fiji beforehand - if possible.
Thank you!!! :smile:
Ellen T Arena
@etarena
Nov 30 2018 21:19
Too - sorry... but TrakEM2 also fails:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.7.0:compile (default-compile) on project TrakEM2_: Compilation failure: Compilation failure: 
[ERROR] /Users/ellenarena/code/fiji/fiji/melting-pot/sc.fiji/TrakEM2_/src/main/java/lenscorrection/PolynomialModel2D.java:[34,8] lenscorrection.PolynomialModel2D is not abstract and does not override abstract method reset() in mpicbg.models.Model
[ERROR] /Users/ellenarena/code/fiji/fiji/melting-pot/sc.fiji/TrakEM2_/src/main/java/mpicbg/trakem2/align/GenericAffineTile2D.java:[41,73] no suitable method found for set(java.awt.geom.AffineTransform)
[ERROR]     method mpicbg.models.InterpolatedModel.set(mpicbg.models.InterpolatedModel) is not applicable
[ERROR]       (argument mismatch; java.awt.geom.AffineTransform cannot be converted to mpicbg.models.InterpolatedModel)
[ERROR]     method mpicbg.models.InterpolatedAffineModel2D.set(mpicbg.models.InterpolatedAffineModel2D) is not applicable
[ERROR]       (argument mismatch; java.awt.geom.AffineTransform cannot be converted to mpicbg.models.InterpolatedAffineModel2D)
[ERROR] /Users/ellenarena/code/fiji/fiji/melting-pot/sc.fiji/TrakEM2_/src/main/java/bunwarpj/trakem2/transform/CubicBSplineTransform.java:[37,8] bunwarpj.trakem2.transform.CubicBSplineTransform is not abstract and does not override abstract method reset() in mpicbg.models.Model
Ellen T Arena
@etarena
Nov 30 2018 21:28
And BigWarp (@bogovicj ) fails as well (again, related issue):
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.7.0:compile (default-compile) on project bigwarp_fiji: Compilation failure
[ERROR] /Users/ellenarena/code/fiji/fiji/melting-pot/sc.fiji/bigwarp_fiji/src/main/java/bdv/viewer/animate/SimilarityModel3D.java:[30,8] bdv.viewer.animate.SimilarityModel3D is not abstract and does not override abstract method reset() in mpicbg.models.Model
Curtis Rueden
@ctrueden
Nov 30 2018 22:56
@etarena It occurs to me that the most expedient way forward is to downgrade mpicbg to 1.2.0 in pom-scijava.
Ellen T Arena
@etarena
Nov 30 2018 22:56
that's a quick/easy solution for the time-being...
Igor Pisarev
@igorpisarev
Nov 30 2018 22:58

@etarena I am the culprit for those errors, as one of my recent PRs introduced these changes: axtimwalde/mpicbg#42
Most of the above errors are due to a new abstract method reset(), which (as appears now) was not necessary as we ended up using the model classes directly for this functionality. Sorry for overlooking this -- I will file another PR to make the method non-abstract so that it doesn't break the public interface.

Regarding the very first error set(double,...) has private access in mpicbg.models.RigidModel3D, the same PR by me has changed this method to private because it is unsafe (one could easily supply an affine model which would violate the rigid property). Instead, there are now the following methods in RigidModel3D: set(TranslationModel3D) and set(RigidModel3D). I think this makes sense, so in order to achieve the desired functionality please consider using one of these methods.

Ellen T Arena
@etarena
Nov 30 2018 22:59
thanks for the response @igorpisarev ! :smile:
Curtis Rueden
@ctrueden
Nov 30 2018 23:00
@igorpisarev I suggest keeping the old set method but deprecate it.
Otherwise, you break downstream code as described above.
And the pom should have been set to 2.0.0-SNAPSHOT because it breaks API.
Igor Pisarev
@igorpisarev
Nov 30 2018 23:04
@ctrueden I agree that it would have been a smoother way to handle it. I'll submit a PR with backwards compatibility fixes.
Ellen T Arena
@etarena
Nov 30 2018 23:05
:thumbsup: @igorpisarev thank you !!!
Curtis Rueden
@ctrueden
Nov 30 2018 23:09
Thanks!
Philipp Hanslovsky
@hanslovsky
Nov 30 2018 23:27
I will be out of office beginning coming Monday, Dec 3. I will be back in office Monday, Dec 17.