Added implicits for parallel loops, Scala version adjusted, organizat…

…ion corrected, file import cleanup (#3)
unibas-gravis · Apr 28, 2022 · 25736d6 · 25736d6
1 parent b8fb462
commit 25736d6
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Showing 41 changed files with 71 additions and 102 deletions.
diff --git a/build.sbt b/build.sbt
@@ -1,12 +1,12 @@
 import sbt.Resolver
 
-organization := "anonymous"
+organization := "ch.unibas.cs.gravis"
 
 name := "GiNGR"
 
 version := "0.1"
 
-scalaVersion := "2.12.8"
+scalaVersion := "2.13.8"
 
 scalacOptions := Seq("-unchecked", "-deprecation", "-encoding", "utf8")
 

diff --git a/src/main/scala/api/GeneralRegistrationState.scala b/src/main/scala/api/GeneralRegistrationState.scala
@@ -19,7 +19,7 @@ package api
 
 import breeze.linalg.{DenseMatrix, DenseVector}
 import scalismo.common.PointId
-import scalismo.geometry.{_3D, EuclideanVector, Landmark, Point}
+import scalismo.geometry.{EuclideanVector, Landmark, Point, _3D}
 import scalismo.mesh.TriangleMesh
 import scalismo.statisticalmodel.{MultivariateNormalDistribution, PointDistributionModel}
 import scalismo.transformations._

diff --git a/src/main/scala/api/GingrAlgorithm.scala b/src/main/scala/api/GingrAlgorithm.scala
@@ -17,17 +17,17 @@
 
 package api
 
-import api.sampling.{AcceptAll, Evaluator, Generator}
 import api.sampling.evaluators.EvaluatorWrapper
-import api.sampling.loggers.{BestAndCurrentSampleLogger, EmptyAcceptRejectLogger, EmptyChainStateLogger}
 import api.sampling.generators.{GeneratorWrapperDeterministic, GeneratorWrapperStochastic}
+import api.sampling.loggers.{BestAndCurrentSampleLogger, EmptyAcceptRejectLogger, EmptyChainStateLogger}
+import api.sampling.{AcceptAll, Evaluator, Generator}
 import scalismo.common.PointId
-import scalismo.geometry.{_3D, Point}
+import scalismo.geometry.{Point, _3D}
 import scalismo.mesh.TriangleMesh
 import scalismo.registration.LandmarkRegistration
 import scalismo.sampling.algorithms.MetropolisHastings
-import scalismo.sampling.loggers.{AcceptRejectLogger, ChainStateLogger, ChainStateLoggerContainer}
 import scalismo.sampling.loggers.ChainStateLogger.implicits._
+import scalismo.sampling.loggers.{AcceptRejectLogger, ChainStateLogger, ChainStateLoggerContainer}
 import scalismo.sampling.proposals.MixtureProposal
 import scalismo.sampling.proposals.MixtureProposal.implicits._
 import scalismo.sampling.{ProposalGenerator, TransitionProbability}

diff --git a/src/main/scala/api/ModelFittingParameters.scala b/src/main/scala/api/ModelFittingParameters.scala
@@ -18,10 +18,10 @@
 package api
 
 import breeze.linalg.DenseVector
-import scalismo.geometry.{_3D, EuclideanVector, Point}
+import scalismo.geometry.{EuclideanVector, Point, _3D}
 import scalismo.mesh.TriangleMesh
 import scalismo.statisticalmodel.PointDistributionModel
-import scalismo.transformations.{Rotation, Scaling, Scaling3D, Translation, TranslationAfterRotation, TranslationAfterScalingAfterRotation}
+import scalismo.transformations._
 
 case class ScaleParameter(s: Double) {
   def parameters: DenseVector[Double] = DenseVector(s)

diff --git a/src/main/scala/api/RegistrationState.scala b/src/main/scala/api/RegistrationState.scala
@@ -17,11 +17,10 @@
 
 package api
 
-import breeze.linalg.DenseVector
-import scalismo.geometry.{_3D, EuclideanVector, EuclideanVector3D, Landmark, Point}
+import scalismo.geometry.{EuclideanVector, Landmark, _3D}
 import scalismo.mesh.TriangleMesh
 import scalismo.statisticalmodel.PointDistributionModel
-import scalismo.transformations.{Rotation, RotationSpace3D, Translation, TranslationAfterRotation}
+import scalismo.transformations.Rotation
 
 trait RegistrationState[T] {
   def model(): PointDistributionModel[_3D, TriangleMesh] // Prior statistical mesh model

diff --git a/src/main/scala/api/gpmm/GPMMHelper.scala b/src/main/scala/api/gpmm/GPMMHelper.scala
@@ -17,16 +17,14 @@
 
 package api.gpmm
 
-import breeze.linalg.{diag, sum, trace, DenseMatrix}
+import breeze.linalg.sum
 import scalismo.common.DiscreteField.ScalarMeshField
-import scalismo.common.interpolation.{NearestNeighborInterpolator, TriangleMeshInterpolator3D}
-import scalismo.common.{DiscreteDomain, PointId, PointSet, ScalarMeshField, UnstructuredPoints, UnstructuredPointsDomain}
-import scalismo.geometry.{_1D, _2D, _3D, EuclideanVector, NDSpace}
+import scalismo.common._
+import scalismo.common.interpolation.NearestNeighborInterpolator
+import scalismo.geometry.{EuclideanVector, _1D, _2D, _3D}
 import scalismo.kernels.{DiagonalKernel, GaussianKernel, MatrixValuedPDKernel}
 import scalismo.mesh.TriangleMesh
-import scalismo.numerics.PivotedCholesky
-import scalismo.numerics.PivotedCholesky.NumberOfEigenfunctions
-import scalismo.statisticalmodel.{DiscreteLowRankGaussianProcess, GaussianProcess, LowRankGaussianProcess, PointDistributionModel}
+import scalismo.statisticalmodel.{GaussianProcess, LowRankGaussianProcess, PointDistributionModel}
 
 trait GPMM[D, DDomain[D] <: DiscreteDomain[D]] {
   def construct(reference: DDomain[D], kernel: MatrixValuedPDKernel[D], relativeTolerance: Double = 0.01): PointDistributionModel[D, DDomain]
@@ -133,12 +131,10 @@ case class GPMMTriangleMesh3D(reference: TriangleMesh[_3D], relativeTolerance: D
     val refPoints = reference.pointSet
     val psHelper = PointSetHelper[_3D, TriangleMesh](reference)
     val maxDist = psHelper.maximumPointDistance(refPoints)
-//    val minDist = psHelper.minimumPointDistance(refPoints)
     GaussianMixture(
       Seq(
         GaussianKernelParameters(maxDist / 4.0, maxDist / 8.0),
         GaussianKernelParameters(maxDist / 8.0, maxDist / 16.0)
-//        GaussianKernelParameters(maxDist/16.0, maxDist/32.0),
       ))
   }
 

diff --git a/src/main/scala/api/gpmm/KernelHelper.scala b/src/main/scala/api/gpmm/KernelHelper.scala
@@ -17,9 +17,9 @@
 
 package api.gpmm
 
-import breeze.linalg.{sum, DenseMatrix, DenseVector}
+import breeze.linalg.DenseMatrix
 import scalismo.common.EuclideanSpace
-import scalismo.geometry.{_3D, Point}
+import scalismo.geometry.{Point, _3D}
 import scalismo.kernels.{DiagonalKernel, MatrixValuedPDKernel, PDKernel}
 import scalismo.mesh.TriangleMesh
 

diff --git a/src/main/scala/api/gpmm/MatrixHelper.scala b/src/main/scala/api/gpmm/MatrixHelper.scala
@@ -17,7 +17,7 @@
 
 package api.gpmm
 
-import breeze.linalg.{diag, svd, DenseMatrix}
+import breeze.linalg.{DenseMatrix, diag, svd}
 
 object MatrixHelper {
   def pinv(m: DenseMatrix[Double], precision: Double = 0.00001): DenseMatrix[Double] = {

diff --git a/src/main/scala/api/helper/PosteriorHelper.scala b/src/main/scala/api/helper/PosteriorHelper.scala
@@ -21,7 +21,7 @@ import breeze.linalg.{DenseMatrix, DenseVector, trace}
 import scalismo.common.DiscreteField.ScalarMeshField
 import scalismo.common.ScalarMeshField
 import scalismo.geometry._3D
-import scalismo.mesh.{TriangleMesh, TriangleMesh3D}
+import scalismo.mesh.TriangleMesh
 
 object PosteriorHelper {
   private val sampleDim = 3

diff --git a/src/main/scala/api/registration/config/CPD.scala b/src/main/scala/api/registration/config/CPD.scala
@@ -17,17 +17,16 @@
 
 package api.registration.config
 
-import java.io.File
-
 import api.registration.utils.PointSequenceConverter
-import api.GingrAlgorithm
-import api.{CorrespondencePairs, GeneralRegistrationState, GingrConfig, GingrRegistrationState}
-import breeze.linalg.{sum, tile, Axis, DenseMatrix, DenseVector}
-import scalismo.common.{DiscreteField, DiscreteField3D, PointId, UnstructuredPointsDomain}
+import api._
+import breeze.linalg.{Axis, DenseMatrix, DenseVector, sum, tile}
+import scalismo.common.PointId
 import scalismo.geometry.Point.Point3DVectorizer
-import scalismo.geometry.{_3D, EuclideanVector, Point}
+import scalismo.geometry.{Point, _3D}
 import scalismo.statisticalmodel.MultivariateNormalDistribution
 
+import scala.collection.parallel.CollectionConverters.ImmutableSeqIsParallelizable
+
 object CPDCorrespondence {
   val vectorizer: Point.Point3DVectorizer.type = Point3DVectorizer
 

diff --git a/src/main/scala/api/registration/config/ICP.scala b/src/main/scala/api/registration/config/ICP.scala
@@ -17,13 +17,10 @@
 
 package api.registration.config
 
-import java.io.File
-
-import api.registration.utils.NonRigidClosestPointRegistrator.ClosestPointTriangleMesh3D
 import api._
+import api.registration.utils.NonRigidClosestPointRegistrator.ClosestPointTriangleMesh3D
 import breeze.linalg.{DenseMatrix, DenseVector}
-import scalismo.common.{DiscreteField, DiscreteField3D, PointId, UnstructuredPointsDomain}
-import scalismo.geometry.{_3D, EuclideanVector}
+import scalismo.common.PointId
 import scalismo.statisticalmodel.MultivariateNormalDistribution
 
 object ICPCorrespondence {

diff --git a/src/main/scala/api/registration/config/Template.scala b/src/main/scala/api/registration/config/Template.scala
@@ -17,7 +17,7 @@
 
 package api.registration.config
 
-import api.{CorrespondencePairs, GeneralRegistrationState, GingrAlgorithm, GingrConfig, GingrRegistrationState}
+import api._
 import breeze.linalg.{DenseMatrix, DenseVector}
 import scalismo.common.PointId
 import scalismo.statisticalmodel.MultivariateNormalDistribution

diff --git a/src/main/scala/api/registration/utils/ClosestPointRegistrator.scala b/src/main/scala/api/registration/utils/ClosestPointRegistrator.scala
@@ -17,8 +17,8 @@
 
 package api.registration.utils
 
-import scalismo.common.{DiscreteDomain, PointId, UnstructuredPoints, UnstructuredPointsDomain}
-import scalismo.geometry.{_1D, _2D, _3D, EuclideanVector, Point}
+import scalismo.common.{DiscreteDomain, PointId, UnstructuredPointsDomain}
+import scalismo.geometry._
 import scalismo.mesh.TriangleMesh
 
 trait ClosestPointRegistrator[D, DDomain[D] <: DiscreteDomain[D]] {

diff --git a/src/main/scala/api/registration/utils/GPMMHelper.scala b/src/main/scala/api/registration/utils/GPMMHelper.scala
@@ -17,16 +17,12 @@
 
 package api.registration.utils
 
-import java.io.File
-
+import scalismo.common.UnstructuredPoints
 import scalismo.common.interpolation.TriangleMeshInterpolator3D
-import scalismo.common.{EuclideanSpace, Field, UnstructuredPoints}
-import scalismo.geometry.{EuclideanVector, Point, _3D}
-import scalismo.io.MeshIO
+import scalismo.geometry.{EuclideanVector, _3D}
 import scalismo.kernels.{DiagonalKernel, GaussianKernel}
 import scalismo.mesh.TriangleMesh
 import scalismo.statisticalmodel.{GaussianProcess, LowRankGaussianProcess, PointDistributionModel}
-import scalismo.ui.api.ScalismoUI
 
 object GPMMHelper {
   // Todo: use implicit to build any kind of model based on the pointSet
@@ -73,4 +69,4 @@ object GPMMHelper {
 //  val gpmm = GPMMHelper.automaticGPMMfromTemplate(template)
 //    val ui = ScalismoUI()
 //    ui.show(gpmm, "model")
-//}
+//}
diff --git a/src/main/scala/api/registration/utils/PointSequenceConverter.scala b/src/main/scala/api/registration/utils/PointSequenceConverter.scala
@@ -22,6 +22,8 @@ import scalismo.common.{PointId, Vectorizer}
 import scalismo.geometry.Point.{Point1DVectorizer, Point2DVectorizer, Point3DVectorizer}
 import scalismo.geometry._
 
+import scala.collection.parallel.CollectionConverters.ImmutableSeqIsParallelizable
+
 trait PointSequenceConverter[D] {
   def toPointSequence(m: DenseMatrix[Double])(implicit vectorizer: Vectorizer[Point[D]]): Seq[Point[D]]
   def toPointSequence(v: DenseVector[Double])(implicit vectorizer: Vectorizer[Point[D]]): Seq[Point[D]]

diff --git a/src/main/scala/api/registration/utils/TransformationHelper.scala b/src/main/scala/api/registration/utils/TransformationHelper.scala
@@ -18,7 +18,7 @@
 package api.registration.utils
 
 import breeze.linalg.DenseMatrix
-import scalismo.geometry.{_2D, _3D, Point, SquareMatrix}
+import scalismo.geometry.{Point, SquareMatrix, _2D, _3D}
 import scalismo.registration.LandmarkRegistration
 import scalismo.transformations._
 

diff --git a/src/main/scala/api/sampling/Evaluator.scala b/src/main/scala/api/sampling/Evaluator.scala
@@ -18,7 +18,7 @@
 package api.sampling
 
 import api.GingrRegistrationState
-import api.sampling.evaluators.{AcceptAllEvaluator, EvaluationMode, IndependentPointDistanceEvaluator, ModelEvaluator, ModelToTargetEvaluation}
+import api.sampling.evaluators._
 import scalismo.sampling.DistributionEvaluator
 import scalismo.sampling.evaluators.ProductEvaluator
 

diff --git a/src/main/scala/api/sampling/Generator.scala b/src/main/scala/api/sampling/Generator.scala
@@ -18,11 +18,11 @@
 package api.sampling
 
 import api.GingrRegistrationState
-import api.sampling.generators.{GaussianAxisRotationProposal, GaussianAxisTranslationProposal, PitchAxis, RandomShapeUpdateProposal, RollAxis, YawAxis}
-import scalismo.sampling.{ProposalGenerator, TransitionProbability}
+import api.sampling.generators._
 import scalismo.sampling.proposals.MixtureProposal
-import scalismo.utils.Random
 import scalismo.sampling.proposals.MixtureProposal.implicits._
+import scalismo.sampling.{ProposalGenerator, TransitionProbability}
+import scalismo.utils.Random
 
 class Generator[State <: GingrRegistrationState[State]](implicit rnd: Random) {
 

diff --git a/src/main/scala/api/sampling/evaluators/IndependentPointDistanceEvaluator.scala b/src/main/scala/api/sampling/evaluators/IndependentPointDistanceEvaluator.scala
@@ -19,9 +19,9 @@ package api.sampling.evaluators
 
 import api.GingrRegistrationState
 import breeze.stats.distributions.ContinuousDistr
-import scalismo.common.{DomainWarp, PointId}
-import scalismo.geometry.{_3D, Point}
-import scalismo.mesh.{TriangleMesh, TriangleMesh3D}
+import scalismo.common.PointId
+import scalismo.geometry.{Point, _3D}
+import scalismo.mesh.TriangleMesh3D
 import scalismo.sampling.DistributionEvaluator
 
 trait EvaluationMode

diff --git a/src/main/scala/api/sampling/evaluators/ModelEvaluator.scala b/src/main/scala/api/sampling/evaluators/ModelEvaluator.scala
@@ -18,7 +18,7 @@
 package api.sampling.evaluators
 
 import api.GingrRegistrationState
-import breeze.linalg.{diag, DenseVector}
+import breeze.linalg.{DenseVector, diag}
 import scalismo.sampling.DistributionEvaluator
 import scalismo.statisticalmodel.MultivariateNormalDistribution
 

diff --git a/src/main/scala/api/sampling/generators/GeneratorWrapperDeterministic.scala b/src/main/scala/api/sampling/generators/GeneratorWrapperDeterministic.scala
@@ -18,7 +18,6 @@
 package api.sampling.generators
 
 import api.GingrRegistrationState
-import scalismo.sampling.{ProposalGenerator, TransitionProbability}
 import scalismo.utils.Random
 
 case class GeneratorWrapperDeterministic[State <: GingrRegistrationState[State]](update: (State, Boolean) => State, generatedBy: String = "Deterministic")(implicit rnd: Random)

diff --git a/src/main/scala/api/sampling/generators/GeneratorWrapperStochastic.scala b/src/main/scala/api/sampling/generators/GeneratorWrapperStochastic.scala
@@ -20,7 +20,6 @@ package api.sampling.generators
 import api.GingrRegistrationState
 import scalismo.geometry._3D
 import scalismo.mesh.TriangleMesh
-import scalismo.sampling.{ProposalGenerator, TransitionProbability}
 import scalismo.statisticalmodel.PointDistributionModel
 import scalismo.utils.{Memoize, Random}
 

diff --git a/src/main/scala/api/sampling/generators/RandomPoseUpdateProposal.scala b/src/main/scala/api/sampling/generators/RandomPoseUpdateProposal.scala
@@ -18,7 +18,6 @@
 package api.sampling.generators
 
 import api.{EulerRotation, GingrRegistrationState}
-import scalismo.sampling.{ProposalGenerator, TransitionProbability}
 
 sealed trait RotationAxis
 

diff --git a/src/main/scala/api/sampling/generators/RandomShapeUpdateProposal.scala b/src/main/scala/api/sampling/generators/RandomShapeUpdateProposal.scala
@@ -18,7 +18,6 @@
 package api.sampling.generators
 
 import api.{GingrRegistrationState, ShapeParameters}
-import scalismo.sampling.{ProposalGenerator, TransitionProbability}
 import scalismo.utils.Random
 
 case class RandomShapeUpdateProposal[State <: GingrRegistrationState[State]](stdev: Double, generatedBy: String = "RandomShapeUpdateProposal")(implicit random: Random)

diff --git a/src/main/scala/api/sampling/loggers/EmptyChainStateLogger.scala b/src/main/scala/api/sampling/loggers/EmptyChainStateLogger.scala
@@ -18,8 +18,8 @@
 package api.sampling.loggers
 
 import api.GingrRegistrationState
-import scalismo.sampling.{DistributionEvaluator, ProposalGenerator}
 import scalismo.sampling.loggers.{AcceptRejectLogger, ChainStateLogger}
+import scalismo.sampling.{DistributionEvaluator, ProposalGenerator}
 
 case class EmptyChainStateLogger[State <: GingrRegistrationState[State]]() extends ChainStateLogger[State] {
   override def logState(sample: State): Unit = {}

diff --git a/src/main/scala/api/sampling/loggers/JSONStateLogger.scala b/src/main/scala/api/sampling/loggers/JSONStateLogger.scala
@@ -17,23 +17,18 @@
 
 package api.sampling.loggers
 
-import api.{EulerAngles, EulerRotation, GeneralRegistrationState, GingrRegistrationState, ModelFittingParameters, PoseParameters, ScaleParameter, ShapeParameters}
-import spray.json.DefaultJsonProtocol.jsonFormat10
-import spray.json.RootJsonFormat
-import spray.json.DefaultJsonProtocol._
-import spray.json._
-import scalismo.sampling.{DistributionEvaluator, ProposalGenerator}
+import api._
+import api.sampling.Evaluator
+import breeze.linalg.DenseVector
+import scalismo.geometry.{EuclideanVector, Point}
 import scalismo.sampling.loggers.AcceptRejectLogger
+import scalismo.sampling.{DistributionEvaluator, ProposalGenerator}
+import spray.json.DefaultJsonProtocol._
+import spray.json.{RootJsonFormat, _}
 
-import java.io.{BufferedWriter, File, FileOutputStream, IOException, OutputStreamWriter}
+import java.io._
 import java.text.SimpleDateFormat
 import java.util.Calendar
-import api.sampling.Evaluator
-import breeze.linalg.DenseVector
-import scalismo.geometry.{EuclideanVector, Point, _3D}
-import scalismo.mesh.TriangleMesh
-import scalismo.statisticalmodel.PointDistributionModel
-
 import scala.collection.SortedSet
 import scala.collection.mutable.ListBuffer
 import scala.io.Source

diff --git a/src/main/scala/apps/DemoDatasetLoader.scala b/src/main/scala/apps/DemoDatasetLoader.scala
@@ -17,16 +17,16 @@
 
 package apps
 
-import apps.gpmm.{GaussDotKernel, GaussKernel, GaussMirrorKernel, GaussMixKernel, InvLapDotKernel, InvLapKernel, SimpleTriangleModels3D, WhichKernel}
-import java.io.File
-
+import apps.gpmm._
 import scalismo.common.interpolation.TriangleMeshInterpolator3D
-import scalismo.geometry.{_3D, Landmark, Point}
+import scalismo.geometry.{Landmark, Point, _3D}
 import scalismo.io.{LandmarkIO, MeshIO, StatisticalModelIO}
 import scalismo.mesh.TriangleMesh
 import scalismo.statisticalmodel.PointDistributionModel
 import scalismo.transformations.{TranslationAfterRotation, TranslationAfterRotationSpace3D}
 
+import java.io.File
+
 trait DataSetLoader {
   def name: String
   def path: File

diff --git a/src/main/scala/apps/registration/DemoCPD.scala b/src/main/scala/apps/registration/DemoCPD.scala
@@ -17,12 +17,10 @@
 
 package apps.registration
 
-import java.io.File
-
-import api.{NoTransforms, RigidTransforms}
+import api.NoTransforms
 import apps.DemoDatasetLoader
-import scalismo.geometry.{EuclideanVector, Point}
-import scalismo.transformations.{Rotation, Translation, TranslationAfterRotation}
+
+import java.io.File
 
 object DemoCPD extends App {
   scalismo.initialize()