forked from fschiffers/FlorianDarkField
/
DarkFieldTensorClass.java
261 lines (188 loc) · 7.85 KB
/
DarkFieldTensorClass.java
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
package edu.stanford.rsl.science.darkfield.FlorianDarkField;
import java.io.BufferedWriter;
import java.io.DataOutputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.util.ArrayList;
import edu.stanford.rsl.conrad.data.PointwiseIterator;
import edu.stanford.rsl.conrad.data.numeric.Grid2D;
import edu.stanford.rsl.conrad.data.numeric.Grid4D;
import edu.stanford.rsl.conrad.data.numeric.NumericPointwiseOperators;
import edu.stanford.rsl.conrad.geometry.shapes.simple.Point3D;
import edu.stanford.rsl.conrad.geometry.shapes.simple.PointND;
import edu.stanford.rsl.conrad.numerics.SimpleMatrix;
import edu.stanford.rsl.conrad.numerics.SimpleOperators;
import edu.stanford.rsl.conrad.numerics.SimpleVector;
import edu.stanford.rsl.science.darkfield.darkfieldgrid.DarkFieldPhantom;
import edu.stanford.rsl.science.darkfield.iterative.PointwiseCorrection;
public class DarkFieldTensorClass{
// Defines dimension of volume box
protected int imgSizeX;
protected int imgSizeY;
protected int imgSizeZ;
private ArrayList<DarkFieldEigenVector> fieldList;
/**
* @param imgSizeX
* @param imgSizeY
* @param imgSizeZ
* @param spacing_world
* @param origin_world
*/
public DarkFieldTensorClass(int imgSizeX, int imgSizeY,int imgSizeZ, double[] spacing_world, double[] origin_world){
this.imgSizeX = imgSizeX;
this.imgSizeY = imgSizeY;
this.imgSizeZ = imgSizeZ;
// contain the eigenvectors (4th column is always the respective eigenvalue)
DarkFieldEigenVector eigenVec1 = new DarkFieldEigenVector(imgSizeX, imgSizeY, imgSizeZ, spacing_world, origin_world);
DarkFieldEigenVector eigenVec2 = new DarkFieldEigenVector(imgSizeX, imgSizeY, imgSizeZ, spacing_world, origin_world);
DarkFieldEigenVector eigenVec3 = new DarkFieldEigenVector(imgSizeX, imgSizeY, imgSizeZ, spacing_world, origin_world);
fieldList = new ArrayList<DarkFieldEigenVector>(3);
fieldList.add(eigenVec1);
fieldList.add(eigenVec2);
fieldList.add(eigenVec3);
}
public void setData(int x, int y, int z, DarkFieldPCA myPCA){
SimpleMatrix eigenVectors = myPCA.getEigenVectors();
SimpleVector eigenValues = myPCA.getEigenValues();
for(int i = 0; i < fieldList.size(); i++){
SimpleVector eigenVec = eigenVectors.getCol(i);
double eigenVal = eigenValues.getElement(i);
eigenVec = eigenVec.multipliedBy(eigenVal);
fieldList.get(i).setVector(x, y, z, eigenVec);
}
// /**
// * Threshold that checks, if 3 component of eigenvalues is too small
// * If 3 component is too small, don't consider it as a fiber orientation
// * and ignore it
// */
// double th = 1E-10;
// SimpleVector fiberDir;
// if(myPCA.getEigenValues().getElement(2)<th){
// fiberDir = new SimpleVector(3);
// }else{
// fiberDir = myPCA.getEigenVectors().getCol(2).normalizedL2();
// fiberDir.multiplyBy(myPCA.getEigenValues().getElement(2));
// }
}
/**
* Helper class, containing 3 index points representing
* the x,y,z coordinates of a given mesh point
*/
class Index3D {
int x;
int y;
int z;
Index3D(int x, int y, int z){
this.x = x;
this.y = y;
this.z = z;
}
}
/**
* @param pathFiberVTK
*/
public void writeToVectorField(String pathFiberVTK){
ArrayList<Index3D> indexListe = new ArrayList<Index3D>();
for (int x = 0; x < imgSizeX; x++){
for (int y = 0; y < imgSizeY; y++){
for (int z = 0; z < imgSizeZ; z++){
// Get EigenVec of smallest eigenValue
SimpleVector direction = fieldList.get(2).getSimpleVectorAtIndex(x,y,z);
double length = direction.normL2();
if(length != 0){
Index3D curIndex = new Index3D(x, y, z);
indexListe.add(curIndex);
}
}
}
}
try{
FileOutputStream foStream = new FileOutputStream(pathFiberVTK);
BufferedWriter bufWriter = new BufferedWriter(new OutputStreamWriter(foStream));
bufWriter.write("# vtk DataFile Version 2.0");
bufWriter.write(System.getProperty( "line.separator" ));
bufWriter.write("Unstructured Grid Example");
bufWriter.write(System.getProperty( "line.separator" ));
bufWriter.write("ASCII");
bufWriter.write(System.getProperty( "line.separator" ));
bufWriter.write("DATASET UNSTRUCTURED_GRID");
bufWriter.write(System.getProperty( "line.separator" ));
// TODO Not sure why that
bufWriter.write("POINTS " + indexListe.size() +" float");
bufWriter.write(System.getProperty( "line.separator" ));
// First write positions
for(int poinIdx = 0; poinIdx < indexListe.size(); poinIdx++){
Index3D index3D = indexListe.get(poinIdx);
bufWriter.write(index3D.x +" " +index3D.y +" " +index3D.z);
bufWriter.write(System.getProperty( "line.separator" ));
}
bufWriter.write("CELLS " + indexListe.size() + " " +2*indexListe.size());
bufWriter.write(System.getProperty( "line.separator" ));
int indCells = 0;
for(int poinIdx = 0; poinIdx < indexListe.size(); poinIdx++){
bufWriter.write("1 " +indCells);
bufWriter.write(System.getProperty( "line.separator" ));
indCells = indCells + 1;
}
bufWriter.write("CELL_TYPES " + indexListe.size());
bufWriter.write(System.getProperty( "line.separator" ));
for(int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++){
bufWriter.write("1");
bufWriter.write(System.getProperty( "line.separator" ));
}
bufWriter.write("POINT_DATA " + indexListe.size());
bufWriter.write(System.getProperty( "line.separator" ));
bufWriter.write("SCALARS eigenValues float 3");
bufWriter.write(System.getProperty( "line.separator" ));
bufWriter.write("LOOKUP_TABLE default");
bufWriter.write(System.getProperty( "line.separator" ));
// Write scalars
for(int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++){
Index3D coordIdx = indexListe.get(pointIdx);
SimpleVector vec1 = fieldList.get(0).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
SimpleVector vec2 = fieldList.get(1).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
SimpleVector vec3 = fieldList.get(2).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
bufWriter.write(vec1.normL2() +" " + vec2.normL2() +" " + vec3.normL2());
bufWriter.write(System.getProperty( "line.separator" ));
}
bufWriter.write("SCALARS scalarDirection float 1");
bufWriter.write(System.getProperty( "line.separator" ));
bufWriter.write("LOOKUP_TABLE default");
bufWriter.write(System.getProperty( "line.separator" ));
// Write scalars
for(int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++){
Index3D coordIdx = indexListe.get(pointIdx);
SimpleVector curEigVec = fieldList.get(2).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
curEigVec = curEigVec.absoluted();
if(curEigVec.max() == curEigVec.getElement(0)){
bufWriter.write("0");
}
else if(curEigVec.max() == curEigVec.getElement(1)){
bufWriter.write("0.5");
}
else{
bufWriter.write("1");
}
bufWriter.write(System.getProperty( "line.separator" ));
}
for(int eigIdx = 0; eigIdx < 3; eigIdx++){
bufWriter.write("VECTORS eigenVector" +eigIdx +" float");
// Write scalars
for(int pointIdx = 0; pointIdx < indexListe.size(); pointIdx++){
Index3D coordIdx = indexListe.get(pointIdx);
SimpleVector curEigVec = fieldList.get(eigIdx).getSimpleVectorAtIndex(coordIdx.x, coordIdx.y, coordIdx.z);
bufWriter.write(System.getProperty( "line.separator" ));
bufWriter.write(curEigVec.getElement(0) + " " + curEigVec.getElement(1)+" "+"" +curEigVec.getElement(2));
}
bufWriter.write(System.getProperty( "line.separator" ));
}
bufWriter.flush();
foStream.close();
}
catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}