Modify Dicom file metadata using dcm4che in Java

How to modify Dicom file metadata using dcm4che.

Please follow our previous tutorials on dcm4che.

Read the Dicom header information using dcm4che in Java

Read Dicom file metadata using dcm4che in Java

Let's create a sample java class ModifyMetadata.java to modify the available metadata in the given Dicom file.

 public static void main(String[] args) {
        String inputDicomPath = "path/to/dicom/N2D_0001.dcm";
        String outputDicomPath = "output/path/to/dicom/N2D_0001.dcm";
        try {
            modifyMetadata(inputDicomPath, outputDicomPath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

 private static void modifyMetadata(String inputDicomPath, String outputDicomPath) throws IOException {
        File file = new File(inputDicomPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        if (attributes.contains(Tag.PatientID))
            attributes.setString(Tag.PatientID, VR.LO, "L500400");
        if (attributes.contains(Tag.PatientName))
            attributes.setString(Tag.PatientName, VR.PN, "Test name");
        DicomOutputStream dos = new DicomOutputStream(new File(outputDicomPath));
        attributes.writeTo(dos);
        dis.close();
        dos.close();
    }

Here we are using the dcm4che standard library classes. Please follow our previous tutorial to set up dcm4che jar files. We have created modifyMetadata() method which accepts two arguments one for input Dicom image path and another is output Dicom image path where we are writing the file after modification.

DicomInputStream will read the file. We are reading all the available data set to get the attributes and try to modify the patient ID and the patient name.

After modification, DicomOutputStream will write the modified attributes to the output path. If we open the image and see, the name and patient id are changed. We can modify any available metadata similar to the above example. For Tag and VR follow the Dicom tag library

The overall code implementation looks as below

package dicom.dcm4che;

import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.VR;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.io.DicomOutputStream;

import java.io.File;
import java.io.IOException;

public class ModifyMetadata {

    public static void main(String[] args) {
        String inputDicomPath = "path/to/dicom/N2D_0001.dcm";
        String outputDicomPath = "output/path/to/dicom/N2D_0001.dcm";
        try {
            modifyMetadata(inputDicomPath, outputDicomPath);
        } catch (IOException e) {
            System.out.println("Error due to: "+e.getMessage());
        }
    }

    private static void modifyMetadata(String inputDicomPath, String outputDicomPath) throws IOException {
        File file = new File(inputDicomPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        if (attributes.contains(Tag.PatientID))
            attributes.setString(Tag.PatientID, VR.LO, "L500400");
        if (attributes.contains(Tag.PatientName))
            attributes.setString(Tag.PatientName, VR.PN, "Test name");
        DicomOutputStream dos = new DicomOutputStream(new File(outputDicomPath));
        attributes.writeTo(dos);
        dis.close();
        dos.close();
    }
}

Read More

Update the Dicom image metadata using Java

In this tutorial, we are going to learn how we can update the Dicom image metadata for the Dicom file.

We are using the SimpleITK library for this. SimpleITK library is very handy while working on medical image manipulation, processing, and analysis. Please follow our previous tutorial before starting this tutorial.

Simple Itk Installation for Java Application.

Read the Dicom Image metadata using Java

Let's create a sample java class ModifyMetaData.java. Create a main method that runs the update metadata code.

public static void main(String[] args) {
        String dcmImagePath = "input_dicom_image_path/N2D_0001.dcm";
        String metaDataKeyToUpdate = "0010|0020"; // Patient Id
        String metaDataValueToUpdate = "02L3000";
        String outputDcmPath = "output_dicom_image_path/output.dcm";
        try {
            ImageFileReader imageFileReader = getDcmImageFileReader(dcmImagePath);
            Image image = imageFileReader.execute(); // Read image
            updateMetaData(image, metaDataKeyToUpdate, metaDataValueToUpdate);
            writeImage(image, outputDcmPath);
        } catch (Exception e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

Here, we are defining the input Dicom image path, metadata key to update. The metadata tag must be in the format of 0010|0020. Metadata value to update and the output Dicom image path to save the update Dicom image.

First, we are reading the Dicom image then we are updating the image with the tag value for the tag. Here we are using the patient Id tag to update. Please visit the Dicom library for the universal Dicom tag and its description.

Let's implement the method used in the main method.

private static ImageFileReader getDcmImageFileReader(String imagePath) {
        ImageFileReader imageFileReader = new ImageFileReader();
        imageFileReader.setImageIO("GDCMImageIO");
        imageFileReader.setFileName(imagePath);
        return imageFileReader;
    }

This method reads the Dicom image using the SimpleItk library.

private static void updateMetaData(Image image, String metaDataKey, String metaDataValue) {
        image.setMetaData(metaDataKey, metaDataValue);
    }

Here, we are simply updating the patient id provided with the value

private static void writeImage(Image image, String outputImagePath) {
        SimpleITK.writeImage(image, outputImagePath);
    }

Here, we are writing the updated Dicom image to the output file path. If we verify the file then the Dicom image, the Patient Id value is changed.

The overall code implementation looks as below:

package simpleitk;

import org.itk.simple.Image;
import org.itk.simple.ImageFileReader;
import org.itk.simple.SimpleITK;

public class ModifyMetaData {

    public static void main(String[] args) {
        String dcmImagePath = "input_dicom_image_path/N2D_0001.dcm";
        String metaDataKeyToUpdate = "0010|0020"; // Patient Id
        String metaDataValueToUpdate = "02L3000";
        String outputDcmPath = "output_dicom_image_path/output.dcm";
        try {
            ImageFileReader imageFileReader = getDcmImageFileReader(dcmImagePath);
            Image image = imageFileReader.execute(); // Read image
            updateMetaData(image, metaDataKeyToUpdate, metaDataValueToUpdate);
            writeImage(image, outputDcmPath);
        } catch (Exception e) {
            System.out.println("Error due to: " + e.getMessage());
        }
    }

    private static ImageFileReader getDcmImageFileReader(String imagePath) {
        ImageFileReader imageFileReader = new ImageFileReader();
        imageFileReader.setImageIO("GDCMImageIO");
        imageFileReader.setFileName(imagePath);
        return imageFileReader;
    }

    private static void updateMetaData(Image image, String metaDataKey, String metaDataValue) {
        image.setMetaData(metaDataKey, metaDataValue);
    }

    private static void writeImage(Image image, String outputImagePath) {
        SimpleITK.writeImage(image, outputImagePath);
    }
}

Read More