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Philipp Kopp
May 10, 2018, 2:23:06 PM5/10/18
to scalismo-faces
Hi all!
I am trying to follow the steps described in the readme of the basel-face-pipeline repository. I downloaded the reference meshes and 2IDs of bu3dfe and installed sbt.
In "Step 0: Data pre-processing & Folder Structure Creation" I get the following output/error:
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0
[info] Loading project definition from [path]\basel-face-pipeline\project
[info] Loading settings from build.sbt ...
[info] Set current project to basel-face-pipeline (in build file:/[path]/basel-face-pipeline/)
[warn] Multiple main classes detected. Run 'show discoveredMainClasses' to see the list
[info] Running preprocessing.ConvertBu3DRawData
found 2 ids....
F0001_NE00WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_NE00WH_F3D.bmp
F0001_NE00WH_RAW converting landmarks
F0001_NE00WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_NE00WH_F3D.bmp
F0001_NE00WH_F3D converting landmarks
F0001_SA04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SA04WH_F3D.bmp
F0001_SA04WH_RAW converting landmarks
F0001_SA04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SA04WH_F3D.bmp
F0001_SA04WH_F3D converting landmarks
F0001_SU04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SU04WH_F3D.bmp
F0001_SU04WH_RAW converting landmarks
F0001_SU04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SU04WH_F3D.bmp
F0001_SU04WH_F3D converting landmarks
F0001_DI04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_DI04WH_F3D.bmp
F0001_DI04WH_RAW converting landmarks
F0001_DI04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_DI04WH_F3D.bmp
F0001_DI04WH_F3D converting landmarks
F0001_FE04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_FE04WH_F3D.bmp
F0001_FE04WH_RAW converting landmarks
F0001_FE04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_FE04WH_F3D.bmp
F0001_FE04WH_F3D converting landmarks
F0001_HA04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_HA04WH_F3D.bmp
F0001_HA04WH_RAW converting landmarks
F0001_HA04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_HA04WH_F3D.bmp
F0001_HA04WH_F3D converting landmarks
F0001_AN04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_AN04WH_F3D.bmp
F0001_AN04WH_RAW converting landmarks
F0001_AN04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_AN04WH_F3D.bmp
F0001_AN04WH_F3D converting landmarks
F0001_NE00WH_F3D calculating alignment
[error] (run-main-0) java.util.InputMismatchException
[error] java.util.InputMismatchException
[error] at java.util.Scanner.throwFor(Unknown Source)
[error] at java.util.Scanner.next(Unknown Source)
[error] at java.util.Scanner.nextFloat(Unknown Source)
[error] at scalismo.faces.io.ply.StringReader$FloatStringReader$$anonfun$read$3.apply$mcFI$sp(Readers.scala:135)
[error] at scalismo.faces.io.ply.StringReader$FloatStringReader$$anonfun$read$3.apply(Readers.scala:135)
[error] at scalismo.faces.io.ply.StringReader$FloatStringReader$$anonfun$read$3.apply(Readers.scala:135)
[error] at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
[error] at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
[error] at scala.collection.immutable.Range.foreach(Range.scala:160)
[error] at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
[error] at scala.collection.AbstractTraversable.map(Traversable.scala:104)
[error] at scalismo.faces.io.ply.StringReader$FloatStringReader$.read(Readers.scala:135)
[error] at scalismo.faces.io.ply.FixedLengthSequenceReader.read(Readers.scala:56)
[error] at scalismo.faces.io.ply.FixedLengthSequenceReader.read(Readers.scala:48)
[error] at scalismo.faces.io.ply.PlyPropertyReader.read(PlyMeshReader.scala:278)
[error] at scalismo.faces.io.ply.PlyElementReader$$anonfun$read$2$$anonfun$apply$mcVI$sp$2.apply(PlyMeshReader.scala:264)
[error] at scalismo.faces.io.ply.PlyElementReader$$anonfun$read$2$$anonfun$apply$mcVI$sp$2.apply(PlyMeshReader.scala:264)
[error] at scala.collection.immutable.List.foreach(List.scala:381)
[error] at scalismo.faces.io.ply.PlyElementReader$$anonfun$read$2.apply$mcVI$sp(PlyMeshReader.scala:264)
[error] at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:160)
[error] at scalismo.faces.io.ply.PlyElementReader.read(PlyMeshReader.scala:263)
[error] at scalismo.faces.io.ply.PlyReader$$anonfun$readData$1.apply(PlyReader.scala:71)
[error] at scalismo.faces.io.ply.PlyReader$$anonfun$readData$1.apply(PlyReader.scala:70)
[error] at scala.collection.immutable.List.map(List.scala:273)
[error] at scalismo.faces.io.ply.PlyReader$.readData(PlyReader.scala:70)
[error] at scalismo.faces.io.ply.PlyReader$.read(PlyReader.scala:62)
[error] at scalismo.faces.io.ply.PLYMesh$$anonfun$readTriangleMesh3D$1.apply(PLYMesh.scala:102)
[error] at scalismo.faces.io.ply.PLYMesh$$anonfun$readTriangleMesh3D$1.apply(PLYMesh.scala:100)
[error] at scala.util.Try$.apply(Try.scala:192)
[error] at scalismo.faces.io.ply.PLYMesh$.readTriangleMesh3D(PLYMesh.scala:100)
[error] at scalismo.faces.io.MeshIO$$anonfun$read$4.apply(MeshIO.scala:47)
[error] at scalismo.faces.io.MeshIO$$anonfun$read$4.apply(MeshIO.scala:47)
[error] at scala.util.Try.orElse(Try.scala:84)
[error] at scalismo.faces.io.MeshIO$.read(MeshIO.scala:46)
[error] at ch.unibas.cs.gravis.facepipeline.BU3DDataProvider$$anon$1.loadColoredMesh(BU3DDataProvider.scala:212)
[error] at ch.unibas.cs.gravis.facepipeline.BU3DDataProvider$$anon$1.loadColoredMesh(BU3DDataProvider.scala:208)
[error] at preprocessing.ConvertBu3DRawData$$anonfun$preprocessMaximalExpressions$2.apply(ConvertBu3DRawData.scala:132)
[error] at preprocessing.ConvertBu3DRawData$$anonfun$preprocessMaximalExpressions$2.apply(ConvertBu3DRawData.scala:125)
[error] at scala.collection.immutable.List.foreach(List.scala:381)
[error] at preprocessing.ConvertBu3DRawData.preprocessMaximalExpressions(ConvertBu3DRawData.scala:125)
[error] at preprocessing.ConvertBu3DRawData$$anonfun$run$1.apply(ConvertBu3DRawData.scala:61)
[error] at preprocessing.ConvertBu3DRawData$$anonfun$run$1.apply(ConvertBu3DRawData.scala:60)
[error] at scala.collection.Iterator$class.foreach(Iterator.scala:893)
[error] at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
[error] at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
[error] at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
[error] at preprocessing.ConvertBu3DRawData.run(ConvertBu3DRawData.scala:60)
[error] at preprocessing.ConvertBu3DRawData$.main(ConvertBu3DRawData.scala:46)
[error] at preprocessing.ConvertBu3DRawData.main(ConvertBu3DRawData.scala)
[error] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[error] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
[error] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
[error] at java.lang.reflect.Method.invoke(Unknown Source)
[error] at sbt.Run.invokeMain(Run.scala:93)
[error] at sbt.Run.run0(Run.scala:87)
[error] at sbt.Run.execute$1(Run.scala:65)
[error] at sbt.Run.$anonfun$run$4(Run.scala:77)
[error] at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
[error] at sbt.util.InterfaceUtil$$anon$1.get(InterfaceUtil.scala:10)
[error] at sbt.TrapExit$App.run(TrapExit.scala:252)
[error] at java.lang.Thread.run(Unknown Source)
[error] java.lang.RuntimeException: Nonzero exit code: 1
[error] at sbt.Run$.executeTrapExit(Run.scala:124)
[error] at sbt.Run.run(Run.scala:77)
[error] at sbt.Defaults$.$anonfun$bgRunMainTask$6(Defaults.scala:1150)
[error] at sbt.Defaults$.$anonfun$bgRunMainTask$6$adapted(Defaults.scala:1145)
[error] at sbt.internal.BackgroundThreadPool.$anonfun$run$1(DefaultBackgroundJobService.scala:366)
[error] at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
[error] at scala.util.Try$.apply(Try.scala:209)
[error] at sbt.internal.BackgroundThreadPool$BackgroundRunnable.run(DefaultBackgroundJobService.scala:289)
[error] at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
[error] at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
[error] at java.lang.Thread.run(Unknown Source)
[error] (Compile / runMain) Nonzero exit code: 1
[error] Total time: 111 s, completed 10.05.2018 15:32:02
Any idea what might cause this error? It seems like it has problems reading F0001_NE00WH_F3D. I opened the file in meshlab and everything looks fine. I also replaced it with a freshly saved version from meshlab. But that didn't solve the issue.
Any help would be appreciated! Thank you very much.
Any help would be appreciated! Thank you very much.
Best
Philipp
Andreas Forster
May 12, 2018, 5:33:33 AM5/12/18
to Philipp Kopp, scalismo-faces
Dear Philipp,
It looks like you found one problem of our PLY reader. I guess you are using Windows? Could you please send us your rough system specifications?
Unfortunately, this is a problem with the PLY reader of scalismo-faces we have on non-Linux systems. We already tried to fix most problems but still, there are few left. We are working on this issue. I have tried to update the full pipeline to use the newest version of scalismo-faces. The newest branch updateScalismoFaces should compile. However, I could not test the pipeline with data. So I can not guarantee that it will run through or produce the same results as the original pipeline. It is on our list to provide as soon as possible a fix for those problems. You are welcome to test this branch if you have time and report any issues you encounter.
Sorry for not having better news for you. I will let you know when I had time to further dig into that problem.
Best regards
Andreas
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*****************************************
Dr. Andreas Morel-Forster
Departement Mathematik und Informatik
Spiegelgasse 1
CH-4051 Basel
PHONE: +41 61 207 05 52
Departement Mathematik und Informatik
Spiegelgasse 1
CH-4051 Basel
PHONE: +41 61 207 05 52
Philipp Kopp
May 13, 2018, 5:32:28 AM5/13/18
to scalismo-faces
Hi Adreas,
Thank you for your help!
Yes I am using windows 10 version 1709 64 bit. sbt 1.1.4 and Scala 2.11.8
I switched to the branch updateScalismoFaces and ran the same script, but encountered a different error:
found 2 ids....
F0001_NE00WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_NE00WH_F3D.bmp
F0001_NE00WH_RAW already converted landmarks
F0001_NE00WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_NE00WH_F3D.bmp
F0001_NE00WH_F3D already converted landmarks
F0001_SA04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SA04WH_F3D.bmp
F0001_SA04WH_RAW already converted landmarks
F0001_SA04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SA04WH_F3D.bmp
F0001_SA04WH_F3D already converted landmarks
F0001_SU04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SU04WH_F3D.bmp
F0001_SU04WH_RAW already converted landmarks
F0001_SU04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_SU04WH_F3D.bmp
F0001_SU04WH_F3D already converted landmarks
F0001_DI04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_DI04WH_F3D.bmp
F0001_DI04WH_RAW already converted landmarks
F0001_DI04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_DI04WH_F3D.bmp
F0001_DI04WH_F3D already converted landmarks
F0001_FE04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_FE04WH_F3D.bmp
F0001_FE04WH_RAW already converted landmarks
F0001_FE04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_FE04WH_F3D.bmp
F0001_FE04WH_F3D already converted landmarks
F0001_HA04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_HA04WH_F3D.bmp
F0001_HA04WH_RAW already converted landmarks
F0001_HA04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_HA04WH_F3D.bmp
F0001_HA04WH_F3D already converted landmarks
F0001_AN04WH_RAW converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_AN04WH_F3D.bmp
F0001_AN04WH_RAW already converted landmarks
F0001_AN04WH_F3D converting mesh
pipeline-data\data\bu3dfe\original\F0001\F0001_AN04WH_F3D.bmp
F0001_AN04WH_F3D already converted landmarks
F0001_NE00WH_F3D calculating alignment
[error] (run-main-0) java.lang.IndexOutOfBoundsException: 2
[error] java.lang.IndexOutOfBoundsException: 2
[error] at scala.collection.LinearSeqOptimized$class.apply(LinearSeqOptimized.scala:65)
[error] at scala.collection.immutable.List.apply(List.scala:84)
[error] at scalismo.faces.io.ply.PlyMeshReader$$anonfun$getTriangles$1.apply(PlyMeshReader.scala:76)
[error] at scalismo.faces.io.ply.PlyMeshReader$$anonfun$getTriangles$1.apply(PlyMeshReader.scala:76)
[error] at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
[error] at scala.collection.Iterator$class.foreach(Iterator.scala:893)
[error] at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
[error] at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
[error] at scala.collection.immutable.VectorBuilder.$plus$plus$eq(Vector.scala:732)
[error] at scala.collection.immutable.VectorBuilder.$plus$plus$eq(Vector.scala:708)
[error] at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
[error] at scala.collection.AbstractIterator.to(Iterator.scala:1336)
[error] at scala.collection.TraversableOnce$class.toIndexedSeq(TraversableOnce.scala:300)
[error] at scala.collection.AbstractIterator.toIndexedSeq(Iterator.scala:1336)
[error] at scalismo.faces.io.ply.PlyMeshReader$.getTriangles(PlyMeshReader.scala:76)
[error] at scalismo.faces.io.ply.PLYMesh$$anonfun$readTriangleMesh3D$1.apply(PLYMesh.scala:108)
[error] Total time: 151 s, completed 13.05.2018 11:16:49
I will try to run the pipeline on linux then. Thanks for your help!
Philipp
Andreas Forster
May 16, 2018, 3:35:04 AM5/16/18
to Philipp Kopp, scalismo-faces
Dear Philipp,
I made a bugfix release of scalismo-faces, the version v0.9.1. I updated the dependency on the branch updateScalismoFaces you are already using. So updating the project and rebuilding should now hopefully let you import the data from the BU3D database. I checked the import step of the data on a Windows machine and it worked there.
Thank you for reporting the error and I hope you can now continue using our pipeline without having further issues.
Best regards
Andreas
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Philipp Kopp
May 17, 2018, 5:34:17 PM5/17/18
to scalismo-faces
Hi Andreas,
Thank you very much! I could successfully convert the Bu3D data on the updateScalismoFaces branch with your fix.
In "Step 1: Building the Neutral Prior Model" I encountered some memory problems. But running sbt with the -J-Xmx flag, as you suggest in the readme, did not help. Got the error messages
[error] Not a valid command: J-Xmx40g
[error] Not a valid project ID: J-Xmx40g
[error] Expected ':'
[error] Not a valid key: J-Xmx40g
[error] J-Xmx40g
I could solve the issue by adding the following two lines to build.sbt:
javaOptions += "-Xmx10G"
fork := true
Just mentioning this in case you want to update the readme. I also have to run sbt with runMain instead of run-main.
Didn't have any issues with Step 2 and 3.
Step 4 doesn't throw an error, but doesn't do the registration either. In https://github.com/unibas-gravis/basel-face-pipeline/blob/master/src/main/scala/registration/Registration.scala#L206 the second loadLandmarks function is never a success in my case.
It tries to load landmarks from for example \data\incoming\landmarks\F0001_SU04WH_RAW_basel.tlm But I only have F0001_SU04WH_RAW.tlms in that folder, created by step 0. I also tried to give the loadLandmarks function Original as DataFlag instead of the default Basel. It did find the files then, but crashed with following message:
[info] 23:02:58.197 [main] INFO registration.Registration - Successfully loaded reference and model
[info] 23:02:58.252 [main] INFO registration.Registration - Performing registration for id BU3DID(F0015,WH)
[error] Exception in thread "main" java.lang.Exception: Empty set of landmarks provided
[error] at scalismo.registration.LandmarkRegistration$.computeRigidNDTransformParams(LandmarkRegistration.scala:233)
[error] at scalismo.registration.LandmarkRegistration$.rigidSimilarity3DCommon(LandmarkRegistration.scala:57)
[error] at scalismo.registration.LandmarkRegistration$.similarity3DLandmarkRegistration(LandmarkRegistration.scala:148)
[error] at registration.Registration$$anonfun$run$1$$anonfun$apply$2.apply(Registration.scala:223)
[error] at registration.Registration$$anonfun$run$1$$anonfun$apply$2.apply(Registration.scala:214)
[error] at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733)
[error] at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
[error] at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
[error] at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732)
[error] at registration.Registration$$anonfun$run$1.apply(Registration.scala:214)
[error] at registration.Registration$$anonfun$run$1.apply(Registration.scala:197)
[error] at scala.collection.immutable.List.foreach(List.scala:381)
[error] at registration.Registration.run(Registration.scala:197)
[error] at registration.Registration$.main(Registration.scala:257)
[error] at registration.Registration.main(Registration.scala)
Not sure what could be the problem here.. Hope you have an idea.
Thanks again for your quick reply and fix!
kind regards,
Philipp
Andreas Forster
May 24, 2018, 7:23:03 AM5/24/18
to Philipp Kopp, scalismo-faces
Hi Philipp,
The filename is generated at the following position:
I can not see why you should get a filename ending in "*.tlm" this must be a bug hidden somewhere. In our framework, there exists only "*.tlms" files, but never a file without the 's'.
I will look into that problem hopefully next week.
Best regards,
Andreas
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Philipp Kopp
May 24, 2018, 11:34:00 AM5/24/18
to scalismo-faces
Hi Andreas,
I'm sorry, I was a bit unspecific and the missing s was a typo. The problem is that the function tries to open F0001_SU04WH_RAW_basel.tlms (so with a 's' , didn't copy that properly, sorry!) with '_basel', but I only have the file without '_basel'. (That filename was correct in the previous post.)
I also found the function you were referring to, but that function is not used with the default dataflag, which is '_basel'. https://github.com/unibas-gravis/basel-face-pipeline/blob/updateScalismoFaces/src/main/scala/preprocessing/ConvertBu3DRawData.scala#L111
So at least in the ConvertBu3DRawData.scala script there isn't a function call that would create this _basel.tlms landmarkfile. Am I correct in my assumption that this conversion script should create these files?
I also checked the path length and it's a lot shorter than 260, but as the s isn't the problem, we can rule that out.
Sorry for causing the confusion! Any ideas about this dataFlag mismatch?
kind regards, Philipp
I also found the function you were referring to, but that function is not used with the default dataflag, which is '_basel'. https://github.com/unibas-gravis/basel-face-pipeline/blob/updateScalismoFaces/src/main/scala/preprocessing/ConvertBu3DRawData.scala#L111
So at least in the ConvertBu3DRawData.scala script there isn't a function call that would create this _basel.tlms landmarkfile. Am I correct in my assumption that this conversion script should create these files?
I also checked the path length and it's a lot shorter than 260, but as the s isn't the problem, we can rule that out.
Sorry for causing the confusion! Any ideas about this dataFlag mismatch?
kind regards, Philipp
Andreas Forster
May 24, 2018, 2:39:38 PM5/24/18
to Philipp Kopp, scalismo-faces
Hi Philipp,
Sorry for my former too quick answer. While I spotted the missing 's' I overlooked the important part that you are missing the *_basel.tlms files. Those files are not generated by the pipeline, as you spotted in the code, but they are provided as additional data from our side. The files are part of the pipeline-data you can download. You can find the download on the Basel Face Model 2017 site:
You should read the license and need to accept it on top of the page. Then further down there is a section "Additional Data" where you can find a link to download those files in a zip folder together with some more data. If you downloaded them in the beginning, maybe you deleted them after having some problems you reported, and we resolved earlier because they reside in the directories of the pipeline where also the output is generated.
Hope this answer may help you with your problem.
Best regards,
Andreas
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Philipp Kopp
May 28, 2018, 10:13:56 AM5/28/18
to scalismo-faces
Hi Andreas,
Thanks a lot! Yeah I had downloaded the data, but accidentally deleted those files as they were in the same folder as the ones generated by the conversion script. The registration runs now!
Thank you for your help!
Kind regards,
Philipp
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