updates to doc

src/main/scala/scalismo/statisticalmodel/DiscreteLowRankGaussianProcess.scala

@@ -360,18 +360,22 @@ class DiscreteLowRankGaussianProcess[D: NDSpace, DDomain[DD] <: DiscreteDomain[D
   }
 
   /**
-   * realigns the model on the provided part of the domain. By default aligns over the translation and approximately
-   * over rotation as well. The rotation will always be calculated around the center of the provided ids. Rotations are
-   * around the cardinal directions.
+   * realigns the model on the provided part of the domain. Aligns over the translation and, when using
+   * withExtendedBasis = true, over the extended basis (the default implicit [[RealignExtendedBasis]] adds rotation.
+   * This rotation will always be calculated around the center of the provided ids. Rotations are around the cardinal
+   * directions.).
    *
    * @param ids
    *   these define the parts of the domain that are aligned to. Depending on the withExtendedBasis parameter has a
-   *   minimum requirements (default basis extension in 3D should be used with >=4 provided ids)
+   *   minimum length requirements (default basis extension in 3D should be used with >=4 provided ids)
    * @param withExtendedBasis
-   *   True if the extended basis should be included. By default this uses a rotation extension. that means False makes
-   *   the realignment over translation exact.
+   *   True if the extended basis should be included. By default this uses a rotation extension. False makes the
+   *   realignment only over translation. Translational alignment can be done exactly.
    * @param diagonalize
-   *   True if a diagonal basis should be returned. False is cheaper for exclusively drawing samples.
+   *   True if a diagonal basis should be returned. In general, it is strongly recommended to use a diagonal basis. This
+   *   option can be set to false if the resulting model is only sampled from (for example [[sample]] or [[instance]]).
+   *   This makes the same coefficient lead to very similar shapes in the pre- and after realignment model (or exactly
+   *   the same shapes if withExtendedBasis = false).
    * @return
    *   The resulting [[DiscreteLowRankGaussianProcess]] aligned on the provided instances of [[PointId]]
    */

src/main/scala/scalismo/statisticalmodel/PointDistributionModel.scala

@@ -258,7 +258,8 @@ case class PointDistributionModel[D: NDSpace, DDomain[D] <: DiscreteDomain[D]](
   }
 
   /**
-   * realigns the [[DiscreteLowRankGaussianProcess]] and returns the resulting [[PointDistributionModel]]
+   * realigns the internal [[DiscreteLowRankGaussianProcess]] and returns the resulting [[PointDistributionModel]]. this
+   * calls [[DiscreteLowRankGaussianProcess.realign]].
    */
   def realign(ids: IndexedSeq[PointId], withExtendedBasis: Boolean = true, diagonalize: Boolean = true)(using
     vectorizer: Vectorizer[EuclideanVector[D]],

src/main/scala/scalismo/statisticalmodel/RealignExtendedBasis.scala

@@ -4,10 +4,6 @@ import breeze.linalg.DenseMatrix
 import scalismo.common.DiscreteDomain
 import scalismo.geometry.*
 
-/**
- * types the whole discrete low rank gp to make sure that it is applied to the appropriate models. The value type could
- * be left out if the user knows what to do.
- */
 trait RealignExtendedBasis[D, Value]:
 
   def useTranslation: Boolean