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
|
/*=========================================================================
Program: GDCM (Grassroots DICOM). A DICOM library
Copyright (c) 2006-2011 Mathieu Malaterre
All rights reserved.
See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
import vtk.*;
import gdcm.*;
import java.io.File;
import java.awt.Canvas;
/*
* Compilation:
* CLASSPATH=vtkgdcm.jar:/usr/share/java/vtk.jar javac MIPViewer.java
*
* Usage:
* LD_LIBRARY_PATH=/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/xawt:/usr/lib/jni:. CLASSPATH=/usr/share/java/vtk.jar:vtkgdcm.jar:gdcm.jar:. java MIPViewer BRAINX
*
*/
public class MIPViewer extends Canvas
{
static {
// VTK
System.loadLibrary("vtkCommonJava");
System.loadLibrary("vtkFilteringJava");
System.loadLibrary("vtkIOJava");
System.loadLibrary("vtkImagingJava");
System.loadLibrary("vtkGraphicsJava");
System.loadLibrary("vtkRenderingJava");
System.loadLibrary("vtkVolumeRenderingJava"); // vtkSmartVolumeMapper
System.loadLibrary("vtkWidgetsJava"); // vtkBoxWidget
// VTK-GDCM
System.loadLibrary("vtkgdcmJava");
}
static FilenamesType fns = new FilenamesType();
protected native int Lock();
protected native int UnLock();
public static void process(String path)
{
fns.add( path );
}
// Process only files under dir
public static void visitAllFiles(File dir)
{
if (dir.isDirectory())
{
String[] children = dir.list();
for (int i=0; i<children.length; i++)
{
visitAllFiles(new File(dir, children[i]));
}
}
else
{
process(dir.getPath());
}
}
public static void main(String[] args) throws Exception
{
String dirname = args[0];
if( !PosixEmulation.FileIsDirectory( dirname ) )
{
return;
}
File dir = new File(dirname);
visitAllFiles(dir);
IPPSorter ipp = new IPPSorter();
ipp.SetComputeZSpacing( true );
ipp.SetZSpacingTolerance( 1e-3 );
boolean b = ipp.Sort( fns );
if(!b)
{
throw new Exception("Could not scan");
}
double ippzspacing = ipp.GetZSpacing();
FilenamesType sorted = ipp.GetFilenames();
vtkStringArray files = new vtkStringArray();
long nfiles = sorted.size();
//for( String f : sorted )
for (int i = 0; i < nfiles; i++) {
String f = sorted.get(i);
files.InsertNextValue( f );
}
vtkGDCMImageReader reader = new vtkGDCMImageReader();
reader.SetFileNames( files );
reader.Update(); // get spacing value
double[] spacing = reader.GetOutput().GetSpacing();
vtkImageChangeInformation change = new vtkImageChangeInformation();
change.SetInputConnection( reader.GetOutputPort() );
change.SetOutputSpacing( spacing[0], spacing[1], ippzspacing );
// Create our volume and mapper
vtkVolume volume = new vtkVolume();
vtkSmartVolumeMapper mapper = new vtkSmartVolumeMapper();
vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
// Add a box widget if the clip option was selected
vtkBoxWidget box = new vtkBoxWidget();
box.SetInteractor(iren);
box.SetPlaceFactor(1.01);
box.SetInputConnection(change.GetOutputPort());
//box.SetDefaultRenderer(renderer);
box.InsideOutOn();
box.PlaceWidget();
//vtkBoxWidgetCallback callback = vtkBoxWidgetCallback::New();
//callback.SetMapper(mapper);
//box.AddObserver(vtkCommand::InteractionEvent, callback);
//callback.Delete();
// Lock();
// box.EnabledOn();
// UnLock();
box.GetSelectedFaceProperty().SetOpacity(0.0);
mapper.SetInputConnection( change.GetOutputPort() );
// Create our transfer function
vtkColorTransferFunction colorFun = new vtkColorTransferFunction();
vtkPiecewiseFunction opacityFun = new vtkPiecewiseFunction();
// Create the property and attach the transfer functions
vtkVolumeProperty property = new vtkVolumeProperty();
property.IndependentComponentsOn();
property.SetColor( colorFun );
property.SetScalarOpacity( opacityFun );
property.SetInterpolationTypeToLinear();
// connect up the volume to the property and the mapper
volume.SetProperty( property );
volume.SetMapper( mapper );
vtkMedicalImageProperties medprop = reader.GetMedicalImageProperties();
int n = medprop.GetNumberOfWindowLevelPresets();
double opacityWindow = 4096;
double opacityLevel = 2048;
// Override default with value from DICOM files:
for( int i = 0; i < n; ++i )
{
double wl[] = medprop.GetNthWindowLevelPreset(i);
//System.out.println( "W/L: " + wl[0] + " " + wl[1] );
opacityWindow = wl[0];
opacityLevel = wl[1];
}
colorFun.AddRGBSegment(0.0, 1.0, 1.0, 1.0, 255.0, 1.0, 1.0, 1.0 );
opacityFun.AddSegment( opacityLevel - 0.5*opacityWindow, 0.0,
opacityLevel + 0.5*opacityWindow, 1.0 );
mapper.SetBlendModeToMaximumIntensity();
// Create the RenderWindow, Renderer
vtkRenderer ren1 = new vtkRenderer();
vtkRenderWindow renWin = new vtkRenderWindow();
renWin.AddRenderer(ren1);
// Set the default window size
renWin.SetSize(600,600);
// Add the volume to the scene
ren1.AddVolume( volume );
ren1.ResetCamera();
iren.SetRenderWindow( renWin );
// interact with data
renWin.Render();
iren.Start();
}
}
|
