Feature/cleanup action (#8)

feat: github action + scalafmt update + dummy test
unibas-gravis · Mar 11, 2024 · 54c2ae7 · 54c2ae7
1 parent f25acb3
commit 54c2ae7
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,29 @@
+name: Scala CI
+
+on:
+  push:
+    branches: [ main, release* ]
+  pull_request:
+    branches: [ main, release* ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: 11
+      - name: Run tests
+        run:  |
+          sudo apt-get update
+          sudo apt-get install -y libopengl0  
+          sbt -Djava.awt.headless=true +compile test
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Formatting
+        run: sbt scalafmtSbtCheck scalafmtCheck test:scalafmtCheck
diff --git a/.scalafmt.conf b/.scalafmt.conf
@@ -1,5 +1,13 @@
-version = "3.5.3"
-maxColumn = 120
-align = true
-align.preset = more
+version=3.8.0
+project.git = true
 runner.dialect = scala3
+align.openParenCallSite = true
+align.openParenDefnSite = true
+maxColumn = 120
+continuationIndent.defnSite = 2
+assumeStandardLibraryStripMargin = true
+danglingParentheses.preset = true
+rewrite.rules = [SortImports, SortModifiers]
+docstrings.style = Asterisk
+
+onTestFailure = "To fix this, run: sbt scalafmtAll"
diff --git a/build.sbt b/build.sbt
@@ -1,5 +1,3 @@
-ThisBuild / version := "0.1-SNAPSHOT"
-
 ThisBuild / scalaVersion := "3.3.1"
 
 lazy val root = (project in file("."))
@@ -37,6 +35,7 @@ lazy val root = (project in file("."))
     },
     javacOptions ++= Seq("-source", "1.8", "-target", "1.8"),
     libraryDependencies ++= Seq(
+      "org.scalatest" %% "scalatest" % "3.2.18" % "test",
       "ch.unibas.cs.gravis" %% "scalismo" % "1.0.0",
       "io.spray" %% "spray-json" % "1.3.6",
     ),

diff --git a/src/main/scala/gingr/api/CorrespondencePairs.scala b/src/main/scala/gingr/api/CorrespondencePairs.scala
@@ -18,7 +18,7 @@
 package gingr.api
 
 import scalismo.common.PointId
-import scalismo.geometry.{Point, _3D}
+import scalismo.geometry.{_3D, Point}
 
 case class CorrespondencePairs(pairs: IndexedSeq[(PointId, Point[_3D])])
 

diff --git a/src/main/scala/gingr/api/GeneralRegistrationState.scala b/src/main/scala/gingr/api/GeneralRegistrationState.scala
@@ -20,30 +20,30 @@ package gingr.api
 import breeze.linalg.{DenseMatrix, DenseVector}
 import gingr.api.FittingStatuses.FittingStatus
 import scalismo.common.PointId
-import scalismo.geometry.{EuclideanVector, Landmark, Point, _3D}
+import scalismo.geometry.{_3D, EuclideanVector, Landmark, Point}
 import scalismo.mesh.TriangleMesh
 import scalismo.statisticalmodel.{MultivariateNormalDistribution, PointDistributionModel}
 import scalismo.transformations._
 
 case class GeneralRegistrationState(
-    override val model: PointDistributionModel[_3D, TriangleMesh],
-    override val modelParameters: ModelFittingParameters,
-    override val modelLandmarks: Option[Seq[Landmark[_3D]]] = None,
-    override val target: TriangleMesh[_3D],
-    override val targetLandmarks: Option[Seq[Landmark[_3D]]] = None,
-    override val fit: TriangleMesh[_3D],
-    override val sigma2: Double = 1.0,
-    override val globalTransformation: GlobalTranformationType = RigidTransforms,
-    override val stepLength: Double = 1.0,
-    override val generatedBy: String = "",
-    override val iteration: Int = 0,
-    override val status: FittingStatus = FittingStatuses.None
+  override val model: PointDistributionModel[_3D, TriangleMesh],
+  override val modelParameters: ModelFittingParameters,
+  override val modelLandmarks: Option[Seq[Landmark[_3D]]] = None,
+  override val target: TriangleMesh[_3D],
+  override val targetLandmarks: Option[Seq[Landmark[_3D]]] = None,
+  override val fit: TriangleMesh[_3D],
+  override val sigma2: Double = 1.0,
+  override val globalTransformation: GlobalTranformationType = RigidTransforms,
+  override val stepLength: Double = 1.0,
+  override val generatedBy: String = "",
+  override val iteration: Int = 0,
+  override val status: FittingStatus = FittingStatuses.None
 ) extends RegistrationState[GeneralRegistrationState] {
 
   lazy val landmarkCorrespondences: IndexedSeq[(PointId, Point[_3D], MultivariateNormalDistribution)] = {
     if (modelLandmarks.nonEmpty && targetLandmarks.nonEmpty) {
-      val m             = modelLandmarks.get
-      val t             = targetLandmarks.get
+      val m = modelLandmarks.get
+      val t = targetLandmarks.get
       val commonLmNames = m.map(_.id) intersect t.map(_.id)
       commonLmNames.map { name =>
         val mPoint = m.find(_.id == name).get
@@ -61,15 +61,16 @@ case class GeneralRegistrationState(
     }
   }
 
-  /** Updates the current state with the new fit.
-    *
-    * @param next
-    *   The newly calculated shape / fit.
-    */
+  /**
+   * Updates the current state with the new fit.
+   *
+   * @param next
+   *   The newly calculated shape / fit.
+   */
   override def updateFit(next: TriangleMesh[_3D]): GeneralRegistrationState = this.copy(fit = next)
-  override def updateIteration(): GeneralRegistrationState                  = this.copy(iteration = this.iteration + 1)
-  override def clearIteration(): GeneralRegistrationState                   = this.copy(iteration = 0)
-  override def updateStatus(next: FittingStatus): GeneralRegistrationState  = this.copy(status = next)
+  override def updateIteration(): GeneralRegistrationState = this.copy(iteration = this.iteration + 1)
+  override def clearIteration(): GeneralRegistrationState = this.copy(iteration = 0)
+  override def updateStatus(next: FittingStatus): GeneralRegistrationState = this.copy(status = next)
 
   override private[api] def updateTranslation(next: EuclideanVector[_3D]): GeneralRegistrationState = {
     this.copy(modelParameters = this.modelParameters.copy(pose = this.modelParameters.pose.copy(translation = next)))
@@ -80,7 +81,7 @@ case class GeneralRegistrationState(
   }
 
   override private[api] def updateRotation(next: Rotation[_3D]): GeneralRegistrationState = {
-    val angles   = RotationSpace3D.rotMatrixToEulerAngles(next.rotationMatrix)
+    val angles = RotationSpace3D.rotMatrixToEulerAngles(next.rotationMatrix)
     val newEuler = EulerRotation(EulerAngles(angles._1, angles._2, angles._3), next.center)
     this.copy(modelParameters = this.modelParameters.copy(pose = this.modelParameters.pose.copy(rotation = newEuler)))
   }
@@ -115,29 +116,29 @@ case class GeneralRegistrationState(
 
 object GeneralRegistrationState {
   def apply(
-      model: PointDistributionModel[_3D, TriangleMesh],
-      target: TriangleMesh[_3D],
-      modelTranform: Option[TranslationAfterRotation[_3D]]
+    model: PointDistributionModel[_3D, TriangleMesh],
+    target: TriangleMesh[_3D],
+    modelTranform: Option[TranslationAfterRotation[_3D]]
   ): GeneralRegistrationState = {
     apply(model, target, RigidTransforms, modelTranform)
   }
 
   def apply(
-      model: PointDistributionModel[_3D, TriangleMesh],
-      target: TriangleMesh[_3D],
-      transform: GlobalTranformationType,
-      modelTranform: Option[TranslationAfterRotation[_3D]]
+    model: PointDistributionModel[_3D, TriangleMesh],
+    target: TriangleMesh[_3D],
+    transform: GlobalTranformationType,
+    modelTranform: Option[TranslationAfterRotation[_3D]]
   ): GeneralRegistrationState = {
     apply(model, Seq(), target, Seq(), transform, modelTranform)
   }
 
   def apply(
-      model: PointDistributionModel[_3D, TriangleMesh],
-      modelLandmarks: Seq[Landmark[_3D]],
-      target: TriangleMesh[_3D],
-      targetLandmarks: Seq[Landmark[_3D]],
-      transform: GlobalTranformationType,
-      modelTranform: Option[TranslationAfterRotation[_3D]]
+    model: PointDistributionModel[_3D, TriangleMesh],
+    modelLandmarks: Seq[Landmark[_3D]],
+    target: TriangleMesh[_3D],
+    targetLandmarks: Seq[Landmark[_3D]],
+    transform: GlobalTranformationType,
+    modelTranform: Option[TranslationAfterRotation[_3D]]
   ): GeneralRegistrationState = {
     val (t, r) = if (modelTranform.isDefined) {
       val initialAngles = RotationSpace3D.rotMatrixToEulerAngles(modelTranform.get.rotation.rotationMatrix)
@@ -178,11 +179,11 @@ object GeneralRegistrationState {
   }
 
   def apply(
-      model: PointDistributionModel[_3D, TriangleMesh],
-      modelLandmarks: Seq[Landmark[_3D]],
-      target: TriangleMesh[_3D],
-      targetLandmarks: Seq[Landmark[_3D]],
-      modelTranform: Option[TranslationAfterRotation[_3D]]
+    model: PointDistributionModel[_3D, TriangleMesh],
+    modelLandmarks: Seq[Landmark[_3D]],
+    target: TriangleMesh[_3D],
+    targetLandmarks: Seq[Landmark[_3D]],
+    modelTranform: Option[TranslationAfterRotation[_3D]]
   ): GeneralRegistrationState = {
     apply(model, modelLandmarks, target, targetLandmarks, RigidTransforms, modelTranform)
   }

diff --git a/src/main/scala/gingr/api/GingrAlgorithm.scala b/src/main/scala/gingr/api/GingrAlgorithm.scala
@@ -22,7 +22,7 @@ import gingr.api.sampling.generators.{GeneratorWrapperDeterministic, GeneratorWr
 import gingr.api.sampling.loggers.BestAndCurrentSampleLogger
 import gingr.api.sampling.{AcceptAll, Evaluator, Generator}
 import scalismo.common.PointId
-import scalismo.geometry.{Point, _3D}
+import scalismo.geometry.{_3D, Point}
 import scalismo.mesh.TriangleMesh
 import scalismo.registration.LandmarkRegistration
 import scalismo.sampling.algorithms.MetropolisHastings
@@ -43,8 +43,8 @@ import scalismo.utils.{Memoize, Random}
 import scala.util.Try
 
 case class ProbabilisticSettings[State <: GingrRegistrationState[State]](
-    evaluators: Evaluator[State],
-    randomMixture: Double = 0.5
+  evaluators: Evaluator[State],
+  randomMixture: Double = 0.5
 ) {
   require(randomMixture >= 0.0 && randomMixture <= 1.0)
 }
@@ -65,26 +65,26 @@ trait GingrRegistrationState[State] {
 trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConfig] {
   val getCorrespondence: State => CorrespondencePairs
   val getUncertainty: (PointId, State) => MultivariateNormalDistribution
-  private val cashedPosterior        = Memoize(computePosterior, 10)
+  private val cashedPosterior = Memoize(computePosterior, 10)
   private val retryCounterInitialize = 10
-  private var retryCounter           = 10
+  private var retryCounter = 10
 
   def name: String
 
   def initializeState(general: GeneralRegistrationState, config: config): State
 
   def estimateRigidTransform(
-      current: TriangleMesh[_3D],
-      update: IndexedSeq[(PointId, Point[_3D])]
+    current: TriangleMesh[_3D],
+    update: IndexedSeq[(PointId, Point[_3D])]
   ): TranslationAfterScalingAfterRotation[_3D] = {
     val pairs = update.map(f => (current.pointSet.point(f._1), f._2))
-    val t     = LandmarkRegistration.rigid3DLandmarkRegistration(pairs, Point(0, 0, 0))
+    val t = LandmarkRegistration.rigid3DLandmarkRegistration(pairs, Point(0, 0, 0))
     TranslationAfterScalingAfterRotation(t.translation, Scaling(1.0), t.rotation)
   }
 
   def estimateSimilarityTransform(
-      current: TriangleMesh[_3D],
-      update: IndexedSeq[(PointId, Point[_3D])]
+    current: TriangleMesh[_3D],
+    update: IndexedSeq[(PointId, Point[_3D])]
   ): TranslationAfterScalingAfterRotation[_3D] = {
     val pairs = update.map(f => (current.pointSet.point(f._1), f._2))
     LandmarkRegistration.similarity3DLandmarkRegistration(pairs, Point(0, 0, 0))
@@ -94,34 +94,35 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
     model.instance(state.modelParameters.shape.parameters).transform(state.modelParameters.similarityTransform)
   }
 
-  /** Runs the actual registration with the provided configuration through the passed parameters.
-    *
-    * @param initialState
-    *   State from which the registration is started.
-    * @param callBackLogger
-    *   Logger to provide call back functionality to user after each iteration
-    * @param acceptRejectLogger
-    *   Logger to use for advanced file logging
-    * @param probabilisticSettings
-    *   Evaluator to be used if probabilistic registration is set
-    * @param generators
-    *   Pass in external generators to use
-    * @param rnd
-    *   Implicit random number generator.
-    * @return
-    *   Returns the best sample of the chain given the evaluator..
-    */
+  /**
+   * Runs the actual registration with the provided configuration through the passed parameters.
+   *
+   * @param initialState
+   *   State from which the registration is started.
+   * @param callBackLogger
+   *   Logger to provide call back functionality to user after each iteration
+   * @param acceptRejectLogger
+   *   Logger to use for advanced file logging
+   * @param probabilisticSettings
+   *   Evaluator to be used if probabilistic registration is set
+   * @param generators
+   *   Pass in external generators to use
+   * @param rnd
+   *   Implicit random number generator.
+   * @return
+   *   Returns the best sample of the chain given the evaluator..
+   */
   def run(
-      initialState: State,
-      acceptRejectLogger: Option[AcceptRejectLogger[State]],
-      callBackLogger: Option[ChainStateLogger[State]],
-      probabilisticSettings: Option[ProbabilisticSettings[State]],
-      generators: Option[ProposalGenerator[State] with TransitionProbability[State]] = None
+    initialState: State,
+    acceptRejectLogger: Option[AcceptRejectLogger[State]],
+    callBackLogger: Option[ChainStateLogger[State]],
+    probabilisticSettings: Option[ProbabilisticSettings[State]],
+    generators: Option[ProposalGenerator[State] with TransitionProbability[State]] = None
   )(implicit rnd: Random): State = {
-    val evaluator             = probabilisticSettings.getOrElse(ProbabilisticSettings(AcceptAll(), randomMixture = 0.0))
+    val evaluator = probabilisticSettings.getOrElse(ProbabilisticSettings(AcceptAll(), randomMixture = 0.0))
     val registrationEvaluator = EvaluatorWrapper(probabilisticSettings.nonEmpty, evaluator.evaluators)
     val registrationGenerator = generatorCombined(probabilisticSettings, generators)
-    val bestSampleLogger      = BestAndCurrentSampleLogger[State](registrationEvaluator)
+    val bestSampleLogger = BestAndCurrentSampleLogger[State](registrationEvaluator)
     val logs =
       if (callBackLogger.isDefined) ChainStateLoggerContainer(Seq(callBackLogger.get, bestSampleLogger))
       else bestSampleLogger
@@ -133,7 +134,7 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
       else mhChain.iterator(initialState).loggedWith(logs)
 
     var converged: Boolean = false
-    var error: Boolean     = false
+    var error: Boolean = false
     // we need to query if there is a next element, otherwise due to laziness the chain is not calculated
     var currentState: Option[GeneralRegistrationState] = None
     states
@@ -174,8 +175,8 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
   }
 
   def generatorCombined(
-      probabilisticSettings: Option[ProbabilisticSettings[State]],
-      mixing: Option[ProposalGenerator[State] with TransitionProbability[State]]
+    probabilisticSettings: Option[ProbabilisticSettings[State]],
+    mixing: Option[ProposalGenerator[State] with TransitionProbability[State]]
   )(implicit rnd: Random): ProposalGenerator[State] with TransitionProbability[State] = {
     probabilisticSettings match {
       case Some(setting) =>
@@ -207,7 +208,7 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
       }
     } else {
       retryCounter = math.min(retryCounterInitialize, retryCounter + 1)
-      val shapeproposal        = if (!probabilistic) posterior.get.mean else posterior.get.sample()
+      val shapeproposal = if (!probabilistic) posterior.get.mean else posterior.get.sample()
       val transformedModelInit = current.general.model.transform(current.general.modelParameters.rigidTransform)
 
       val newCoefficients = Try(
@@ -240,7 +241,7 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
             .updateRotation(newGlobalAlignment.rotation)
             .updateScaling(ScaleParameter(globalTransform.scaling.s))
             .updateShapeParameters(ShapeParameters(alpha.get))
-          val newState  = current.updateGeneral(general)
+          val newState = current.updateGeneral(general)
           val newSigma2 = updateSigma2(newState)
           newState.updateGeneral(newState.general.updateSigma2(newSigma2))
         } else {
@@ -257,8 +258,8 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
   }
 
   def estimateRigidTransform(
-      current: TriangleMesh[_3D],
-      update: TriangleMesh[_3D]
+    current: TriangleMesh[_3D],
+    update: TriangleMesh[_3D]
   ): TranslationAfterScalingAfterRotation[_3D] = {
     val t = LandmarkRegistration.rigid3DLandmarkRegistration(
       current.pointSet.points.toSeq.zip(update.pointSet.points.toSeq),
@@ -268,8 +269,8 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
   }
 
   def estimateSimilarityTransform(
-      current: TriangleMesh[_3D],
-      update: TriangleMesh[_3D]
+    current: TriangleMesh[_3D],
+    update: TriangleMesh[_3D]
   ): TranslationAfterScalingAfterRotation[_3D] = {
     LandmarkRegistration.similarity3DLandmarkRegistration(
       current.pointSet.points.toSeq.zip(update.pointSet.points.toSeq),
@@ -281,7 +282,7 @@ trait GingrAlgorithm[State <: GingrRegistrationState[State], config <: GingrConf
     val correspondences = getCorrespondence(current)
     val correspondencesWithUncertainty = correspondences.pairs.map { pair =>
       val (pid, point) = pair
-      val uncertainty  = getUncertainty(pid, current)
+      val uncertainty = getUncertainty(pid, current)
       (pid, point, uncertainty)
     }
     val observationsWithUncertainty = if (current.config.useLandmarkCorrespondence) {