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();
    }
}

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Read Dicom file meatadata using dcm4che in Java

How to read Dicom file metadata using dcm4che in Java.

dcm4che is a collection of open-source applications and utilities for the healthcare enterprise application for processing, manipulating, and analysis of medical images.

Please follow the tutorial for setting the dcm4che in our java application.

Let's create a java class DicomMetadataReader.java to read the available metadata in the given Dicom file.

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

private static void readMetadata(String dicomFilePath) throws IOException {
        File file = new File(dicomFilePath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String tagValue = attributes.getString(tag);
            System.out.println("Tag Address: " + tagAddress + " Value: " + tagValue);
        }
        dis.close();
    }

Here, we are using standard classes from the dcm4che core library jar file. DicomInputStream will read the file. We are reading the available dataset of the file and getting tags. After that, we are looping through the available tags and get the tag address and corresponding tag value.

The sample Output:

Total tag found in dicom file: 54
Tag Address: (0008,0008) Value: DERIVED
Tag Address: (0008,0016) Value: 1.2.840.10008.5.1.4.1.1.4
Tag Address: (0008,0018) Value: 1.2.826.0.1.3680043.2.1143.1590429688519720198888333603882344634
Tag Address: (0008,0020) Value: 20130717
Tag Address: (0008,0021) Value: 20130717
Tag Address: (0008,0022) Value: 20130717
Tag Address: (0008,0023) Value: 20130717
Tag Address: (0008,0030) Value: 141500
Tag Address: (0008,0031) Value: 142035.93000
Tag Address: (0008,0032) Value: 132518
Tag Address: (0008,0033) Value: 142035.93
Tag Address: (0008,0050) Value: null
Tag Address: (0008,0060) Value: MR
Tag Address: (0008,0070) Value: BIOLAB
Tag Address: (0008,0080) Value: null
Tag Address: (0008,0090) Value: null
Tag Address: (0008,1030) Value: Hanke_Stadler^0024_transrep
Tag Address: (0008,103E) Value: anat-T1w
Tag Address: (0008,1090) Value: nifti2dicom
Tag Address: (0010,0010) Value: Jane_Doe
Tag Address: (0010,0020) Value: 02
Tag Address: (0010,0030) Value: 19660101
Tag Address: (0010,0040) Value: F
Tag Address: (0010,1000) Value: null
Tag Address: (0010,1010) Value: 42
Tag Address: (0010,1030) Value: 75
Tag Address: (0010,21C0) Value: 4
Tag Address: (0018,0050) Value: 0.666666686534882
Tag Address: (0018,0088) Value: 0.666666686534882
Tag Address: (0018,1020) Value: 0.4.11
Tag Address: (0018,1030) Value: anat-T1w
Tag Address: (0020,000D) Value: 1.2.826.0.1.3680043.2.1143.2592092611698916978113112155415165916
Tag Address: (0020,000E) Value: 1.2.826.0.1.3680043.2.1143.515404396022363061013111326823367652
Tag Address: (0020,0010) Value: 433724515
Tag Address: (0020,0011) Value: 401
Tag Address: (0020,0012) Value: 1
Tag Address: (0020,0013) Value: 1
Tag Address: (0020,0020) Value: L
Tag Address: (0020,0032) Value: -91.4495864331908
Tag Address: (0020,0037) Value: 0.999032176441525
Tag Address: (0020,0052) Value: 1.2.826.0.1.3680043.2.1143.6856184167807409206647724161920598374
Tag Address: (0028,0002) Value: 1
Tag Address: (0028,0004) Value: MONOCHROME2
Tag Address: (0028,0010) Value: 384
Tag Address: (0028,0011) Value: 274
Tag Address: (0028,0030) Value: 0.666666686534882
Tag Address: (0028,0100) Value: 16
Tag Address: (0028,0101) Value: 16
Tag Address: (0028,0102) Value: 15
Tag Address: (0028,0103) Value: 1
Tag Address: (0028,1052) Value: 0
Tag Address: (0028,1053) Value: 1
Tag Address: (0028,1054) Value: US
Tag Address: (7FE0,0010) Value: 0

Please follow the Dicom standard library for tag and its description.

The overall code implementation looks as below:

package dicom.dcm4che;

import org.dcm4che3.data.Attributes;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.util.TagUtils;

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

public class DicomMetadataReader {

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

    private static void readMetadata(String dicomFilePath) throws IOException {
        File file = new File(dicomFilePath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String tagValue = attributes.getString(tag);
            System.out.println("Tag Address: " + tagAddress + " Value: " + tagValue);
        }
        dis.close();
    }
}

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Read the Dicom header information using dcm4che in Java

In this tutorial, we are going to learn how to get the Dicom file header information using dcm4che.

DICOM (Digital Imaging and Communications in Medicine) is the ubiquitous standard in the radiology and cardiology imaging industry for the exchange and management of images and image-related information.

For Dicom standard information please visit Dicom Library.

Before start writing code we need to use a couple of jar files. Download all the Dicom library files from the bundle. This bundle contains a lot of jar files we will use only the desired one.

Extract the downloaded file, go to the lib folder and grab two jar files. dcm4che-core-5.25.1.jar and another is slf4j-api-1.7.32.jar, the verison might be different at the time of implementation.

Now, create a folder called libs inside the project directory and add the jar file and load it from the IDE.

Loading Jar file in Maven Project:

<dependency>
          <groupId>com.dcm4che</groupId>
          <artifactId>dcm4che</artifactId>
          <version>20220117</version>
          <scope>system</scope>
          <systemPath>${basedir}/libs/dcm4che-core-5.25.1.jar</systemPath>
      </dependency>

<dependency>
          <groupId>com.slf4j</groupId>
          <artifactId>slf4j</artifactId>
          <version>20220217</version>
          <scope>system</scope>
          <systemPath>${basedir}/libs/slf4j-api-1.7.32.jar</systemPath>
      </dependency>

Note: use the downloaded jar file name.

Loading Jar in Gradle Project:

Add the following inside dependencies in build.gradle file.

dependencies {
//other dependencies
 
compile fileTree(dir: 'libs', include: '*.jar')
}

Let's create the java class ReadHeaderInfo.java to read the header information

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

private static void readHeader(String inputPath) throws IOException {
        File file = new File(inputPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in the given dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String vr = attributes.getVR(tag).toString();
            System.out.println("Tag Address: " + tagAddress + " VR: " + vr);
        }
    }

Basically, we are using the Dicom-core classes from the jar file to read the file information. We are providing the sample Dicom file and reading the Tag Address and VR available in that file. 

DicomInputStream is used to read the file. dis.readDataset() read all the tags available in that file and finally, we are getting Tag Address and VR and outputting the values.

Output:

Total tag found in the given dicom file: 54
Tag Address: (0008,0008) VR: CS
Tag Address: (0008,0016) VR: UI
Tag Address: (0008,0018) VR: UI
Tag Address: (0008,0020) VR: DA
Tag Address: (0008,0021) VR: DA
Tag Address: (0008,0022) VR: DA
Tag Address: (0008,0023) VR: DA
Tag Address: (0008,0030) VR: TM
Tag Address: (0008,0031) VR: TM
Tag Address: (0008,0032) VR: TM
Tag Address: (0008,0033) VR: TM
Tag Address: (0008,0050) VR: SH
Tag Address: (0008,0060) VR: CS
Tag Address: (0008,0070) VR: LO
Tag Address: (0008,0080) VR: LO
Tag Address: (0008,0090) VR: PN
Tag Address: (0008,1030) VR: LO
Tag Address: (0008,103E) VR: LO
Tag Address: (0008,1090) VR: LO
Tag Address: (0010,0010) VR: PN
Tag Address: (0010,0020) VR: LO
Tag Address: (0010,0030) VR: DA
Tag Address: (0010,0040) VR: CS
Tag Address: (0010,1000) VR: LO
Tag Address: (0010,1010) VR: AS
Tag Address: (0010,1030) VR: DS
Tag Address: (0010,21C0) VR: US
Tag Address: (0018,0050) VR: DS
Tag Address: (0018,0088) VR: DS
Tag Address: (0018,1020) VR: LO
Tag Address: (0018,1030) VR: LO
Tag Address: (0020,000D) VR: UI
Tag Address: (0020,000E) VR: UI
Tag Address: (0020,0010) VR: SH
Tag Address: (0020,0011) VR: IS
Tag Address: (0020,0012) VR: IS
Tag Address: (0020,0013) VR: IS
Tag Address: (0020,0020) VR: CS
Tag Address: (0020,0032) VR: DS
Tag Address: (0020,0037) VR: DS
Tag Address: (0020,0052) VR: UI
Tag Address: (0028,0002) VR: US
Tag Address: (0028,0004) VR: CS
Tag Address: (0028,0010) VR: US
Tag Address: (0028,0011) VR: US
Tag Address: (0028,0030) VR: DS
Tag Address: (0028,0100) VR: US
Tag Address: (0028,0101) VR: US
Tag Address: (0028,0102) VR: US
Tag Address: (0028,0103) VR: US
Tag Address: (0028,1052) VR: DS
Tag Address: (0028,1053) VR: DS
Tag Address: (0028,1054) VR: LO
Tag Address: (7FE0,0010) VR: OW

Extracting the header information is important to visualize the Dicom file information.

The overall code implementation looks as below:

package dicom.dcm4che;

import org.dcm4che3.data.Attributes;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.util.TagUtils;

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

public class ReadHeaderInfo {

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

    private static void readHeader(String inputPath) throws IOException {
        File file = new File(inputPath);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes attributes = dis.readDataset();
        int[] tags = attributes.tags();
        System.out.println("Total tag found in the given dicom file: "+tags.length);
        for (int tag: tags) {
            String tagAddress = TagUtils.toString(tag);
            String vr = attributes.getVR(tag).toString();
            System.out.println("Tag Address: " + tagAddress + " VR: " + vr);
        }
        dis.close();
    }

}

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