public void reconstructOffline(ImagePlus imagePlus) throws Exception {
ImagePlusDataSink sink = new ImagePlusDataSink();
configure();
init();
for (int i = 0; i < imagePlus.getStackSize(); i++) {
backproject(ImageUtil.wrapImageProcessor(imagePlus.getStack().getProcessor(i + 1)), i);
}
waitForResult();
if (Configuration.getGlobalConfiguration().getUseHounsfieldScaling()) applyHounsfieldScaling();
int[] size = projectionVolume.getSize();
System.out.println(size[0] + " " + size[1] + " " + size[2]);
for (int k = 0; k < projectionVolume.getSize()[2]; k++) {
FloatProcessor fl =
new FloatProcessor(projectionVolume.getSize()[0], projectionVolume.getSize()[1]);
for (int j = 0; j < projectionVolume.getSize()[1]; j++) {
for (int i = 0; i < projectionVolume.getSize()[0]; i++) {
fl.putPixelValue(i, j, projectionVolume.getAtIndex(i, j, k));
}
}
sink.process(projectionVolume.getSubGrid(k), k);
}
sink.close();
ImagePlus revan =
ImageUtil.wrapGrid3D(sink.getResult(), "Reconstruction of " + imagePlus.getTitle());
revan.setTitle(imagePlus.getTitle() + " reconstructed");
revan.show();
reset();
}
@Override
public void configure() throws Exception {
slope = UserUtil.queryDouble("Enter slope of correction transformatoin", slope);
// offset = UserUtil.queryDouble("Enter offset of correction transformation", offset);
measureHard = UserUtil.queryDouble("Measurement of hard material [HU]", measureHard);
measureSoft = UserUtil.queryDouble("Measurement of soft material [HU]", measureSoft);
projectionXShift = UserUtil.queryDouble("Enter projection x shift", projectionXShift);
projectionYShift = UserUtil.queryDouble("Enter projection y shift", projectionYShift);
lambda0 = VolumeAttenuationFactorCorrectionTool.getLambda0(measureHard, measureSoft);
lut = Configuration.getGlobalConfiguration().getBeamHardeningLookupTable();
ImagePlus[] images = ImageUtil.getAvailableImagePlusAsArray();
hardMaterial =
ImageUtil.wrapImagePlus(
(ImagePlus)
JOptionPane.showInputDialog(
null,
"Select projections with hard material: ",
"Select source",
JOptionPane.PLAIN_MESSAGE,
null,
images,
images[0]));
configured = true;
}
public OpenCLVolumeRenderer(ImagePlus image) {
super(
new byte[image.getWidth() * image.getHeight() * image.getStackSize() / image.getNFrames()],
image.getWidth(),
image.getHeight(),
image.getStackSize() / image.getNFrames(),
false);
transferFunc =
new float[] {
0.0f, 0.0f, 0.0f, 0.0f,
1.0f, 1.0f, 1.0f, 1.0f,
0.0f, 0.0f, 0.0f, 0.0f,
};
minmax = ImageUtil.minAndMaxOfImageProcessor(image);
minmax[1] *= 1.05;
if (image.getNFrames() == 1) multiFrameMode = false;
else multiFrameMode = true;
nFrames = image.getNFrames();
// Create the image array
clImages = new ArrayList<CLImage3d<IntBuffer>>(image.getNFrames());
// rewrite imagePlus container into nFrames single byte volumes
volumes = new byte[image.getNFrames()][volumeSize[2] * volumeSize[1] * volumeSize[0]];
for (int n = 0; n < image.getNFrames(); n++) {
for (int k = 0; k < volumeSize[2]; k++) {
ImageProcessor img = image.getStack().getProcessor((n * volumeSize[2]) + k + 1);
for (int i = 0; i < image.getWidth(); i++) {
for (int j = 0; j < image.getHeight(); j++) {
setVoxel(volumes[n], i, j, k, img.getPixelValue(i, j));
}
}
}
}
initialized = false;
// System.out.println("init");
frame.setTitle("Volume: " + image.getTitle());
}
public void run(String arg) {
boolean display = false;
File test = new File(arg);
display = !test.exists();
OpenDialog od = new OpenDialog("Open mkt file...", arg);
if (od != null) {
String file = od.getFileName();
if (file == null) return;
String directory = od.getDirectory();
directory = directory.replace('\\', '/'); // Windows safe
if (!directory.endsWith("/")) directory += "/";
arg = directory + file;
}
try {
FileProjectionSource fileSource = new MKTProjectionSource();
fileSource.initStream(arg);
ImagePlusDataSink sink = new ImagePlusDataSink();
Grid2D imp = fileSource.getNextProjection();
int i = 0;
while (imp != null) {
sink.process(imp, i);
i++;
imp = fileSource.getNextProjection();
}
sink.close();
setStack(ImageUtil.wrapGrid3D(sink.getResult(), "").getStack());
setTitle(new File(arg).getName());
fileSource.close();
if (display) show();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
