From cda9762b868cb58be3fed5c94cfbb7d0a2c9395e Mon Sep 17 00:00:00 2001
From: Jakub Kolman <kubokolman@gmail.com>
Date: Tue, 30 Nov 2021 15:03:53 +0100
Subject: [PATCH] [#38] refactor: adding documantation and deleting dead code
---
.../procrustes/ProcrustesAnalysis.java | 199 +++---------------
.../ProcrustesAnalysisFaceModel.java | 36 +---
.../utils/ProcrustesAnalysisUtils.java | 77 -------
.../analyst/feature/api/IPosition.java | 1 +
4 files changed, 44 insertions(+), 269 deletions(-)
diff --git a/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysis.java b/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysis.java
index 400b13e9..43280fe2 100644
--- a/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysis.java
+++ b/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysis.java
@@ -27,9 +27,6 @@ public class ProcrustesAnalysis {
private Point3d modelCentroid1;
private Point3d modelCentroid2;
- // based on some example models this is an approximate centroid of feature points
-// private Point3d centroid = new Point3d(0, 0, 0);
-
/**
* Constructor
*
@@ -48,12 +45,8 @@ public class ProcrustesAnalysis {
throw new ProcrustesAnalysisException("Lists of feature points do not have the same size");
}
-// this.orderedFeaturePointList1 = new ArrayList<>(model1.getFeaturePointsMap().values());
-// this.orderedFeaturePointList2 = new ArrayList<>(model2.getFeaturePointsMap().values());
-
- if (!featurePointTypesEquivalence(
- model1.getFeaturePointValues(),
- model2.getFeaturePointValues())) {
+ if (!ProcrustesAnalysisUtils.checkFeaturePointsType(
+ model1.getFeaturePointValues(), model2.getFeaturePointValues())) {
throw new ProcrustesAnalysisException("Lists of feature points do not have the same feature point types");
}
@@ -62,85 +55,42 @@ public class ProcrustesAnalysis {
this.modelCentroid1 = ProcrustesAnalysisUtils.findCentroidOfFeaturePoints(model1.getFeaturePointValues());
this.modelCentroid2 = ProcrustesAnalysisUtils.findCentroidOfFeaturePoints(model2.getFeaturePointValues());
-
- }
-
- public ProcrustesAnalysisFaceModel getFaceModel1() {
- return faceModel1;
- }
-
- public ProcrustesAnalysisFaceModel getFaceModel2() {
- return faceModel2;
}
+ /**
+ * Method called for analysis after creating initial data in constructor. This method causes superimposition
+ * and rotation of the faces.
+ */
public void analyze() {
- List<SimpleMatrix> transformation = new ArrayList<>();
-
this.superImpose();
this.rotate();
}
- private Point3d computeCentroidsDistance(Point3d centroid1, Point3d centroid2) {
- double x = (centroid1.x - centroid2.x);
- double y = (centroid1.y - centroid2.y);
- double z = (centroid1.z - centroid2.z);
-
- Point3d computedCentroid = new Point3d(x, y, z);
- return computedCentroid;
- }
-
/**
* Imposes two face models (lists of feature points and vertices) over each other
*/
private void superImpose() {
-
- // moves vertices of face models
-// moveModelToSameOrigin(this.faceModel2.getVertices(), this.faceModel2.getFeaturePointsMap());
-
- normalize(this.faceModel1, this.modelCentroid1);
- normalize(this.faceModel2, this.modelCentroid2);
-
-// moveVertices(this.modelCentroid1, featurePointModel1.getVertices());
-// moveModelToPoint(this.modelCentroid1, faceModel1.getVertices(), faceModel1.getFeaturePointsMap());
-// moveModelToPoint(this.modelCentroid1, faceModel2.getVertices(), faceModel2.getFeaturePointsMap());
- }
-
- private void normalize(ProcrustesAnalysisFaceModel faceModel, Point3d centroid) {
-// float size = ProcrustesAnalysisUtils.countSize(centroid, faceModel.getFeaturePointsMap());
- centerToOrigin(faceModel, centroid);
+ centerToOrigin(this.faceModel1, this.modelCentroid1);
+ centerToOrigin(this.faceModel2, this.modelCentroid2);
}
+ /**
+ * Centers given face model to origin that is given centroid.
+ * Moves all vertices and feature points by value of difference between vertex/feature point and centroid.
+ *
+ * @param faceModel
+ * @param centroid
+ */
private void centerToOrigin(ProcrustesAnalysisFaceModel faceModel, Point3d centroid) {
for (FeaturePoint fp: faceModel.getFeaturePointsMap().values()) {
fp.getPosition().x -= centroid.x;
fp.getPosition().y -= centroid.y;
fp.getPosition().z -= centroid.z;
}
- SimpleMatrix centeredVertices = new SimpleMatrix(
- faceModel.getVerticesMatrix().numRows(), faceModel.getVerticesMatrix().numCols());
- for (int i = 0; i < faceModel.getVerticesMatrix().numRows(); i++) {
- centeredVertices.set(i, 0, faceModel.getVerticesMatrix().get(i, 0) - centroid.x);
- centeredVertices.set(i, 1, faceModel.getVerticesMatrix().get(i, 1) - centroid.y);
- centeredVertices.set(i, 2, faceModel.getVerticesMatrix().get(i, 2) - centroid.z);
- }
- faceModel.setVerticesMatrix(centeredVertices);
- }
-
- private void moveModelToSameOrigin(List<MeshPoint> vertices, HashMap<Integer, FeaturePoint> featurePointsMap) {
- Point3d diff = computeCentroidsDistance(this.modelCentroid1, this.modelCentroid2);
- moveModelToPoint(diff, vertices, featurePointsMap);
- }
-
- private void moveModelToPoint(Point3d centroid, List<MeshPoint> vertices, HashMap<Integer, FeaturePoint> featurePointsMap) {
- moveVertices(centroid, vertices);
- moveFeaturePointsToVertices(centroid, featurePointsMap);
- }
-
- private void moveFeaturePointsToVertices(Point3d centroid, HashMap<Integer, FeaturePoint> featurePointsMap) {
- for (FeaturePoint fp : featurePointsMap.values()) {
- fp.getPosition().x = fp.getPosition().x + centroid.x;
- fp.getPosition().y = fp.getPosition().y + centroid.y;
- fp.getPosition().z = fp.getPosition().z + centroid.z;
+ for (MeshPoint v : faceModel.getVertices()) {
+ v.getPosition().x = v.getX() - centroid.x;
+ v.getPosition().y = v.getY() - centroid.y;
+ v.getPosition().z = v.getZ() - centroid.z;
}
}
@@ -148,11 +98,6 @@ public class ProcrustesAnalysis {
* By rotation of matrices solves orthogonal procrustes problem
*/
private void rotate() {
-
- // There is no reason trying to rotate less than 3 elements
- if (this.getFaceModel1().getFeaturePointsMap().size() < 3) {
- throw new ProcrustesAnalysisException("To do procrustes analysis models have to have at least 3 feature points");
- }
SimpleMatrix primaryMatrix = ProcrustesAnalysisUtils.createMatrixFromList(this.faceModel2.getFeaturePointValues());
SimpleMatrix transposedMatrix = ProcrustesAnalysisUtils.createMatrixFromList(
this.faceModel1.getFeaturePointValues()).transpose();
@@ -160,44 +105,23 @@ public class ProcrustesAnalysis {
SimpleMatrix svdMatrix = transposedMatrix.mult(primaryMatrix);
SimpleSVD<SimpleMatrix> singularValueDecomposition = svdMatrix.svd();
SimpleMatrix transposedU = singularValueDecomposition.getU().transpose();
- SimpleMatrix r = singularValueDecomposition.getV().mult(transposedU);
- primaryMatrix = primaryMatrix.mult(r);
+ SimpleMatrix rotationMatrix = singularValueDecomposition.getV().mult(transposedU);
+ primaryMatrix = primaryMatrix.mult(rotationMatrix);
this.faceModel2.setFeaturePointsMap(
ProcrustesAnalysisUtils.createFeaturePointMapFromMatrix(
primaryMatrix, this.faceModel2));
-// for (int i = 0; i < this.faceModel2.getFeaturePointTypeCorrespondence().size(); i++) {
-// FeaturePoint fp = new FeaturePoint(
-// primaryMatrix.get(i, 0),
-// primaryMatrix.get(i, 1),
-// primaryMatrix.get(i, 2),
-// this.faceModel2.getFeaturePointsMap().get(
-// this.faceModel2.getFeaturePointTypeCorrespondence().get(i)).getFeaturePointType()
-// );
-// this.faceModel2.getFeaturePointsMap().put(i, fp);
-// }
-
- rotateVertices(this.faceModel2.getVertices(), r);
-
-// SimpleMatrix rotatedVertices = this.faceModel2.getVerticesMatrix().mult(r);
-// createListFromMatrix(rotatedVertices, this.faceModel2);
+ rotateVertices(this.faceModel2.getVertices(), rotationMatrix);
}
- private void createListFromMatrix(SimpleMatrix rotatedVertices, ProcrustesAnalysisFaceModel faceModel) {
- if (faceModel.getVertices() != null) {
- for (int i = 0; i < rotatedVertices.numRows(); i++) {
- faceModel.getVertices().get(i).getPosition().x = rotatedVertices.get(i, 0);
- faceModel.getVertices().get(i).getPosition().y = rotatedVertices.get(i, 1);
- faceModel.getVertices().get(i).getPosition().z = rotatedVertices.get(i, 2);
- }
- }
- }
/**
- * Rotates every vertex of model by given matrix
+ * Rotates all vertices.
*
- * @param model
+ * For more details check out single vertex rotation {@link #rotateVertex}.
+ *
+ * @param vertices
* @param matrix
*/
// if rotated vertices are drawn immediately it is better to set them after rotating them all
@@ -210,7 +134,13 @@ public class ProcrustesAnalysis {
}
}
- public static void rotateVertex(MeshPoint v,SimpleMatrix matrix) {
+ /**
+ * Rotates vertex v by simulating matrix multiplication with given matrix
+ *
+ * @param v
+ * @param matrix
+ */
+ private static void rotateVertex(MeshPoint v, SimpleMatrix matrix) {
double x = ((v.getX() * matrix.get(0, 0))
+ (v.getY() * matrix.get(1, 0))
+ (v.getZ() * matrix.get(2, 0)));
@@ -225,67 +155,4 @@ public class ProcrustesAnalysis {
v.getPosition().z = z;
}
- /**
- * Calculates new vertices adjusted to the centroid by method {@see findCenteroidOfFeaturePoints},
- * so moved featurepoints would correspond with the same place on face as they did before.
- *
- * @param centroid
- * @param vertices
- * @return
- */
- private void moveVertices(Point3d centroid, List<MeshPoint> vertices) {
- if (vertices != null && centroid != null) {
-// List<MeshPoint> movedVertices = null;
- for (MeshPoint v : vertices) {
- v.getPosition().x = (v.getPosition().x + centroid.x);
- v.getPosition().y = (v.getPosition().y + centroid.y);
- v.getPosition().z = (v.getPosition().z + centroid.z);
- }
- } else {
- throw new ProcrustesAnalysisException("Could not compute vertices locations after moving the centroid from model to feature points");
- }
- }
-
- /**
- * Creates sorted feature point lists and compares them whether they have
- * the same feature point types.
- *
- * @param fpList1
- * @param fpList2
- * @return
- */
- private boolean featurePointTypesEquivalence(List<FeaturePoint> fpList1, List<FeaturePoint> fpList2) {
- return ProcrustesAnalysisUtils.checkFeaturePointsType(fpList1, fpList2);
- }
-
- /**
- * Calculate scaling ratio of how much the appropriate object corresponding
- * to the second feature point list has to be scale up or shrunk.
- * <p>
- * If returned ratioValue is greater 1 then it means that the second object
- * should be scaled up ratioValue times. If returned ratioValue is smaller 1
- * than the second object should be shrunk.
- *
- * @return ratioValue
- */
-// private double calculateScalingValue() {
-// double[] distancesOfList1 = ProcrustesAnalysisUtils.calculateMeanDistancesFromOrigin(
-// this.faceModel1.getFeaturePointValues());
-// double[] distancesOfList2 = ProcrustesAnalysisUtils.calculateMeanDistancesFromOrigin(
-// this.faceModel2.getFeaturePointValues());
-//
-// double[] ratioArray = new double[distancesOfList1.length];
-// double ratioValue = 0;
-//
-// for (int i = 0; i < distancesOfList1.length; i++) {
-// ratioArray[i] += distancesOfList1[i] / distancesOfList2[i];
-// }
-//
-// for (double ratio : ratioArray) {
-// ratioValue += ratio;
-// }
-//
-// return ratioValue / distancesOfList1.length;
-// }
-
}
diff --git a/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysisFaceModel.java b/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysisFaceModel.java
index d828f00f..35b5114b 100644
--- a/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysisFaceModel.java
+++ b/Comparison/src/main/java/cz/fidentis/analyst/procrustes/ProcrustesAnalysisFaceModel.java
@@ -26,7 +26,6 @@ public class ProcrustesAnalysisFaceModel {
private final HumanFace humanFace;
private HashMap<Integer, FeaturePoint> featurePointsMap; // sorted by feature point type
private List<MeshPoint> vertices;
- private SimpleMatrix verticesMatrix;
private MeshModel meshModel;
private final HashMap<Integer, Integer> featurePointTypeCorrespondence;
@@ -43,8 +42,6 @@ public class ProcrustesAnalysisFaceModel {
this.featurePointsMap = createFeaturePointMap(
ProcrustesAnalysisUtils.sortListByFeaturePointType(modifiableFeaturePointList));
this.featurePointTypeCorrespondence = createFeaturePointTypeCorrespondence(face.getFeaturePoints());
- this.verticesMatrix = ProcrustesAnalysisUtils.createMatrixFromList(modifiableVertices);
-// this.featurePointMatrix = ProcrustesAnalysisUtils.createMatrixFromList(modifiableFeaturePointList);
}
/**
@@ -74,28 +71,19 @@ public class ProcrustesAnalysisFaceModel {
return featurePointsMap;
}
+ public HashMap<Integer, Integer> getFeaturePointTypeCorrespondence() {
+ return featurePointTypeCorrespondence;
+ }
+
/**
- * sets vertices map and also sets feature point on human face for visualisation
+ * Creates feature point hash map for internal use in Procrustes Analysis.
+ *
+ * Map key is feature point type (Integer).
+ * Value is feature point itself.
*
- * @param verticesMatrix
+ * @param featurePointList
+ * @return
*/
- public void setVerticesMatrix(SimpleMatrix verticesMatrix) {
- this.verticesMatrix = verticesMatrix;
- changeVerticesValues(verticesMatrix);
- }
-
- public SimpleMatrix getVerticesMatrix() {
- return verticesMatrix;
- }
-
- private void changeVerticesValues(SimpleMatrix matrix) {
- for (int i = 0; i < vertices.size(); i++) {
- vertices.get(i).getPosition().x = (float) matrix.get(i, 0);
- vertices.get(i).getPosition().y = (float) matrix.get(i, 1);
- vertices.get(i).getPosition().z = (float) matrix.get(i, 2);
- }
- }
-
private HashMap<Integer, FeaturePoint> createFeaturePointMap(List<FeaturePoint> featurePointList) {
HashMap<Integer, FeaturePoint> map = new HashMap<>();
for (FeaturePoint fp: featurePointList) {
@@ -104,10 +92,6 @@ public class ProcrustesAnalysisFaceModel {
return map;
}
- public HashMap<Integer, Integer> getFeaturePointTypeCorrespondence() {
- return featurePointTypeCorrespondence;
- }
-
/**
* Creates corresponding key value pair of matrix row index and a feature point type value.
* It is used in {@link cz.fidentis.analyst.procrustes.utils.ProcrustesAnalysisUtils#createFeaturePointMapFromMatrix}
diff --git a/Comparison/src/main/java/cz/fidentis/analyst/procrustes/utils/ProcrustesAnalysisUtils.java b/Comparison/src/main/java/cz/fidentis/analyst/procrustes/utils/ProcrustesAnalysisUtils.java
index 78baf70d..7d278cc5 100644
--- a/Comparison/src/main/java/cz/fidentis/analyst/procrustes/utils/ProcrustesAnalysisUtils.java
+++ b/Comparison/src/main/java/cz/fidentis/analyst/procrustes/utils/ProcrustesAnalysisUtils.java
@@ -34,21 +34,6 @@ public class ProcrustesAnalysisUtils {
return featurePointList;
}
- /**
- * Creates hash map with a key feature point type and value feature point
- * @param featurePointList
- * @return
- */
- public static HashMap<Integer, FeaturePoint> generateFeaturePointHashMap(List<FeaturePoint> featurePointList) {
- HashMap<Integer, FeaturePoint> map = new HashMap<>();
- for (FeaturePoint fp : featurePointList) {
- if (fp.getFeaturePointType().getType() > 0) {
- map.put(fp.getFeaturePointType().getType(), fp);
- }
- }
- return map;
- }
-
/**
* Checks if two feature point lists have the same types of feature points.
* <p>
@@ -75,20 +60,6 @@ public class ProcrustesAnalysisUtils {
return true;
}
- /**
- * Creates array of distance values from feature point to origin (0,0,0).
- *
- * @param featurePointList
- * @return array of distances
- */
- public static double[] calculateMeanDistancesFromOrigin(List<FeaturePoint> featurePointList) {
- double[] distances = new double[featurePointList.size()];
- for (int i = 0; i < featurePointList.size(); i++) {
- distances[i] = calculatePointDistanceFromOrigin(featurePointList.get(i));
- }
- return distances;
- }
-
/**
* Finds centrioid from given feature point List
*
@@ -107,33 +78,6 @@ public class ProcrustesAnalysisUtils {
return new Point3d(x / featurePointList.size(), y / featurePointList.size(), z / featurePointList.size());
}
- /**
- * Calculates distance of one feature point from another
- *
- * @param fp1
- * @param fp2
- * @return distance
- */
- public static double calculateDistanceOfTwoPoints(FeaturePoint fp1, FeaturePoint fp2) {
- return Math.sqrt(
- (Math.pow(fp1.getX(), 2) - Math.pow(fp2.getX(), 2))
- + (Math.pow(fp1.getY(), 2) - Math.pow(fp2.getY(), 2))
- + (Math.pow(fp1.getZ(), 2) - Math.pow(fp2.getZ(), 2)));
- }
-
- /**
- * Calculates distance of single feature point from origin (0,0,0)
- *
- * @param fp
- * @return distance
- */
- public static double calculatePointDistanceFromOrigin(FeaturePoint fp) {
- return Math.sqrt(
- Math.pow(fp.getX(), 2)
- + Math.pow(fp.getY(), 2)
- + Math.pow(fp.getZ(), 2));
- }
-
/**
* Creates matrix from given feature point list
*
@@ -174,25 +118,4 @@ public class ProcrustesAnalysisUtils {
return map;
}
-
- public static float countSize(Point3d point, HashMap<Integer, FeaturePoint> featurePointsMap) {
- float size = 0;
- for (FeaturePoint fp: featurePointsMap.values()) {
- size += (fp.getX() - point.x) * (fp.getX() - point.x);
- size += (fp.getY() - point.y) * (fp.getY() - point.y);
- size += (fp.getZ() - point.z) * (fp.getZ() - point.z);
- }
- return ((float) Math.sqrt(size));
- }
-
-// public List<MeshPoint> CreateVerticesListFromMatrix (SimpleMatrix matrix) {
-// List<MeshPoint> verticesList = new ArrayList<>();
-// for (int i = 0; i < matrix.numRows(); i++) {
-// float x = (float) matrix.get(i, 0);
-// float y = (float) matrix.get(i, 1);
-// float z = (float) matrix.get(i, 2);
-// verticesList.add(new MeshPoint() {
-// })
-// }
-// }
}
diff --git a/MeshModel/src/main/java/cz/fidentis/analyst/feature/api/IPosition.java b/MeshModel/src/main/java/cz/fidentis/analyst/feature/api/IPosition.java
index 3b7d412f..f1aea467 100644
--- a/MeshModel/src/main/java/cz/fidentis/analyst/feature/api/IPosition.java
+++ b/MeshModel/src/main/java/cz/fidentis/analyst/feature/api/IPosition.java
@@ -8,6 +8,7 @@ package cz.fidentis.analyst.feature.api;
import javax.vecmath.Point3d;
/**
+ * Interface for working.
*
* @author Jakub Kolman
*/
--
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