VTK crop CT image

Before this, the materials that need to be prepared are about:
1. The VTK version compiled by Java, please search Camke by yourself. There are many tutorials on compiling VTK. If possible, if the English is good, please go directly to the VTK official website to search, there is the original editing process. I personally use the 7.1.1 version of VTK.
2. dcm4che-core 5.12.0 dependency package.

Development environment jdk1.8 64 bit, eclipse.

1

Don't talk nonsense, just start the topic. The code is tested by myself, and the specified layer thickness can be cut.

import java.io.File;

import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Implementation;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.VR;
import org.dcm4che3.io.DicomEncodingOptions;
import org.dcm4che3.io.DicomOutputStream;
import org.dcm4che3.util.UIDUtils;

import vtk.vtkAlgorithmOutput;
import vtk.vtkDICOMImageReader;
import vtk.vtkImageData;
import vtk.vtkImageReslice;
import vtk.vtkMatrix4x4;
import vtk.vtkNativeLibrary;

/**

• Cutting Machine
• @author Jmx 2020-09-03

*/
public class NewMPRReslicer {

// 需要静态引用vtk的dll类库等,否则会出错: java.lang.UnsatisfiedLinkLOG.error: VTKInit()
static {
	if (!vtkNativeLibrary.LoadAllNativeLibraries()) {
		for (vtkNativeLibrary lib : vtkNativeLibrary.values()) {
			if (!lib.IsLoaded()) {
				System.err.println(lib.GetLibraryName() + " not loaded");
			}
		}
	}
	//只是隐藏了在VTK错误或警告出现时可能会弹出的任何调试信息。您还可以提供一个文件路径，以便将任何错误写入磁盘。
	vtkNativeLibrary.DisableOutputWindow(null);
}

/**
 * 切割横断位
 * seriesDIR 要切割的序列文件夹
 * outDir 输出的文件夹
 * thickness 要输出的层厚，不写默认就是dicom序列原始层厚
 */
public static void excute(String seriesDIR, String outDir, Double thickness) {
	//加载体数据
	vtkDICOMImageReader imageReader = new vtkDICOMImageReader();
	imageReader.SetDirectoryName(seriesDIR);
	imageReader.Update();
	vtkImageData imageData = imageReader.GetOutput();
	//加载体数据结束

	double bounds[] = imageData.GetBounds();//获取体数据的边界
	double spacing[] = imageData.GetSpacing();//图像的像素间距 
	int extent[] = imageData.GetExtent();//图像的宽高和图像数量
	double origin[] = imageData.GetOrigin();//图像的坐标原点

	// 找到中心点位置(贯穿点)
	double center[] = new double[3];
	center[0] = origin[0] + spacing[0] * 0.5 * (extent[0] + extent[1]);// x
	center[1] = origin[1] + spacing[1] * 0.5 * (extent[2] + extent[3]);// y
	center[2] = origin[2] + spacing[2] * 0.5 * (extent[4] + extent[5]);// z

	// 通过修改切面和贯穿点，可以得到需要的重建图层(冠状、矢状、横断、斜切等)
	int columneIndex = 2;//横断位
	double[] imageOrientationPatient = new double[] { 1, 0, 0, 0, 1, 0 };//
	vtkMatrix4x4 resliceAxes = new vtkMatrix4x4();
	// 此矩阵为横断面(方式1)
	//	double axialElements[] = { 
	//	1, 0, 0, 0, 
	//	0, 1, 0, 0, 
	//	0, 0, 1, 0, 
	//	0, 0, 0, 1
	//	};
	//	resliceAxes.DeepCopy(axialElements);
	//方式2
	resliceAxes.SetElement(0, 0, 1);
	resliceAxes.SetElement(0, 1, 0);
	resliceAxes.SetElement(0, 2, 0);

	resliceAxes.SetElement(1, 0, 0);
	resliceAxes.SetElement(1, 1, 1);
	resliceAxes.SetElement(1, 2, 0);

	resliceAxes.SetElement(2, 0, 0);
	resliceAxes.SetElement(2, 1, 0);
	resliceAxes.SetElement(2, 2, 1);

	if (null != thickness && thickness > 0) {
		spacing[2] = thickness;//以用户传的层厚为准
	}
	int instanceCount = 0;
	//通过层厚计算dicom输出的数量
	double count = (bounds[5] - bounds[4]) / spacing[2] + 1;
	if (count - (int) count != 0) {
		//说明除不尽
		instanceCount = (int) count + 1;
	} else {
		instanceCount = (int) count;
	}

	// 设置中心点
	resliceAxes.SetElement(0, 3, center[0]);
	resliceAxes.SetElement(1, 3, center[1]);
	resliceAxes.SetElement(2, 3, center[2]);
	// 图像重取filter(从体数据中)
	vtkImageReslice imageReslice = new vtkImageReslice();
	vtkAlgorithmOutput algorithmOutput = imageReader.GetOutputPort();
	imageReslice.SetInputConnection(algorithmOutput);
	imageReslice.SetOutputDimensionality(2);// 输出为2D数据
	imageReslice.SetResliceAxes(resliceAxes);
	imageReslice.SetOutputSpacing(spacing);
	//设置插值法
	imageReslice.SetInterpolationModeToLinear();// 双线性插值法
	// 此处从中心点预切割一幅,目的为获取各种参数
	imageReslice.Update();
	//=======================重建结束，准备输出图像======

	vtkImageData imageResliceData = imageReslice.GetOutput();
	extent = imageResliceData.GetExtent();
	spacing = imageResliceData.GetSpacing();
	origin = imageResliceData.GetOrigin();
	bounds = imageResliceData.GetBounds();//获取体数据的边界
	int volume_x = extent[1] + 1;
	int volume_y = extent[3] + 1;

	Attributes fmi = new Attributes(6);
	fmi.setBytes(Tag.FileMetaInformationVersion, VR.OB, new byte[] { 0, 1 });
	fmi.setString(Tag.MediaStorageSOPClassUID, VR.UI, "1.2.840.10008.5.1.4.1.1.128");//这里要动态获取dicom的值
	fmi.setString(Tag.MediaStorageSOPInstanceUID, VR.UI, UIDUtils.createUID("2.25"));
	fmi.setString(Tag.TransferSyntaxUID, VR.UI, "1.2.840.10008.1.2.1");
	fmi.setString(Tag.ImplementationClassUID, VR.UI, Implementation.getClassUID());
	fmi.setString(Tag.ImplementationVersionName, VR.SH, Implementation.getVersionName());

	Attributes data = new Attributes();
	//图像必要的一些tag
	String studuUID = UIDUtils.createUID("1.1");
	String seriesUID = UIDUtils.createUID("1.2");
	//0020 Group
	data.setString(Tag.StudyInstanceUID, VR.UI, studuUID);
	data.setString(Tag.SeriesInstanceUID, VR.UI, seriesUID);

	//0028 Group
	data.setString(Tag.SamplesPerPixel, VR.US, "1");
	data.setString(Tag.PhotometricInterpretation, VR.CS, "MONOCHROME2");
	data.setInt(Tag.Rows, VR.IS, volume_x);
	data.setInt(Tag.Columns, VR.IS, volume_y);
	data.setInt(Tag.BitsAllocated, VR.IS, 16);
	data.setInt(Tag.BitsStored, VR.IS, 16);
	data.setInt(Tag.HighBit, VR.IS, 15);
	data.setInt(Tag.PixelRepresentation, VR.IS, 0);

	data.setInt(Tag.Rows, VR.US, volume_y);//必要的Tag
	data.setInt(Tag.Columns, VR.US, volume_x);//必要的Tag
	data.setInt(Tag.NumberOfSlices, VR.US, instanceCount);
	data.setDouble(Tag.ImageOrientationPatient, VR.DS, imageOrientationPatient);

	data.setDouble(Tag.PixelSpacing, VR.DS, spacing[0], spacing[1]);
	data.setDouble(Tag.SliceThickness, VR.DS, spacing[2]);

	double[] imagePositionPatient = new double[3];
	imagePositionPatient[0] = origin[0];
	imagePositionPatient[1] = origin[1];

	new File(outDir).mkdirs();
	for (int i = 0; i < instanceCount; i++) {
		double sliceLocation = i * spacing[2];
		resliceAxes.SetElement(columneIndex, 3, sliceLocation);//设置第4个切面，来切要的体数据
		imageReslice.SetResliceAxes(resliceAxes);
		imageReslice.Update();
		vtkImageData vtkImageData = imageReslice.GetOutput();
		data.setString(Tag.SeriesDescription, VR.LO, "JMX SC AXIL");
		imagePositionPatient[2] = sliceLocation;
		data.setDouble(Tag.ImagePositionPatient, VR.DS, imagePositionPatient);
		data.setDouble(Tag.SliceLocation, VR.DS, sliceLocation);
		data.setInt(Tag.InstanceNumber, VR.IS, i + 1);
		byte[] dicomarray = new byte[volume_x * volume_y * 2];
		int dicomindex = 0;
		for (int y = 0; y < volume_y; y++) {
			for (int x = 0; x < volume_x; x++) {
				double pixelvalue = vtkImageData.GetScalarComponentAsDouble(x, volume_y - y - 1, 0, 0);
				int intvalue = (int) pixelvalue;
				int highByte = (intvalue & 0xFF00) >> 8;
				int lowByte = intvalue & 0xFF;
				// 低位
				dicomarray[dicomindex++] = (byte) lowByte;
				// 高位
				dicomarray[dicomindex++] = (byte) highByte;
			}
		}
		String outPath = outDir + File.separator + (i + 1) + ".dcm";
		createdicomfile(new File(outPath), dicomarray, fmi, data);
	}
}

public static void createdicomfile(File outdcmfile, byte[] buffer, Attributes fmi, Attributes data) {
	try (DicomOutputStream dicomoutstream = new DicomOutputStream(outdcmfile);) {

		dicomoutstream.setEncodingOptions(DicomEncodingOptions.DEFAULT);
		// 使用meta信息,去构建数据集;(meta中含有传输语法)
		dicomoutstream.writeDataset(fmi, data);
		// 写入图像数据部分
		dicomoutstream.writeHeader(Tag.PixelData, VR.OB, buffer.length);
		// offset为输入buffer本身的偏移量
		dicomoutstream.write(buffer, 0, buffer.length);
	} catch (Exception e) {
		e.printStackTrace();
	}
}

}