How to read the content of a DICOM file in Java?

Question

A DICOM file contains a series of CAT scan images. Is there an implementation of a DICOM library in Java that can read the files and extract the images stored in them? I would like to store those images into a BufferedImage data type.

Answer 1

Java Example: (reads patients ID from metadata)

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

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

public class Main {
    public static void main(String[] args) throws IOException {
        File file = new File(...);
        DicomInputStream dis = new DicomInputStream(file);
        Attributes dcmObj = dis.readDataset(-1, -1);
        String someVar = dcmObj.getString(Tag.PatientID);
        System.out.println(someVar);
    }
}

Maven:

  <repositories>
      <repository>
        <id>www.dcm4che.org</id>
        <name>dcm4che Repository</name>
        <url>http://www.dcm4che.org/maven2</url>
    </repository>
</repositories>
  
<dependencies>
  <dependency>
    <groupId>org.dcm4che</groupId>
    <artifactId>dcm4che-imageio</artifactId>
    <version>3.3.7</version>
  </dependency>
  <dependency>
    <groupId>org.dcm4che</groupId>
    <artifactId>dcm4che-imageio-rle</artifactId>
    <version>3.3.7</version>
    <scope>runtime</scope>
  </dependency>
  <dependency>
    <groupId>com.sun.media</groupId>
    <artifactId>jai_imageio</artifactId>
    <version>1.2-pre-dr-b04</version>
    <scope>runtime</scope>
  </dependency>
  <dependency>
    <groupId>org.dcm4che.tool</groupId>
    <artifactId>dcm4che-tool-common</artifactId>
    <version>3.3.7</version>
    <scope>compile</scope>
  </dependency>
<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-log4j12 -->
<dependency>
    <groupId>org.slf4j</groupId>
    <artifactId>slf4j-log4j12</artifactId>
    <version>2.0.0</version>
    <scope>test</scope>
</dependency>
</dependencies>

Answer 2

In Java:

One of the best article for DICOM read in JAVA follow this link

https://saravanansubramanian.com/dicomtutorials/#dicom-programming-tutorials-using-java

One more thing you need extra software to extract the image without this software you can't read the image and content .

jai-1_1_2_01-lib-windows-i586-jdk.exe

jai_imageio-1_0_01-lib-windows-i586-jre.exe

Because DICOM images are so highly resolution.

You also need JDK32 bit.

In Web Project:Configured the Jre Path instated of JDK path.

Answer 3

I wrote some time ago some code that permmitted me to read ".dcm" files and export them into an array of BufferedImage data type.

I used the library dcm4che that you can find here: http://www.dcm4che.org/

In the code I wrote I used those classes:

import org.dcm4che3.imageio.plugins.dcm.*;
import org.dcm4che3.data.Tag;
import org.dcm4che3.io.DicomOutputStream;

Firstly I used a method to read the DICOM file and get its pixel data into a raster:

static BufferedImage createBufferedImgdFromDICOMfile(File dicomFile) {
   Raster raster = null ;
   System.out.println("Input: " + dicomFile.getName());

   //Open the DICOM file and get its pixel data
   try {
       Iterator iter = ImageIO.getImageReadersByFormatName("DICOM");
       ImageReader reader = (ImageReader) iter.next();
       DicomImageReadParam param = (DicomImageReadParam) reader.getDefaultReadParam();
       ImageInputStream iis = ImageIO.createImageInputStream(dicomFile);
       reader.setInput(iis, false);
       //Returns a new Raster (rectangular array of pixels) containing the raw pixel data from the image stream
       raster = reader.readRaster(0, param);
       if (raster == null)
              System.out.println("Error: couldn't read Dicom image!");
       iis.close();
   }
    catch(Exception e) {
        System.out.println("Error: couldn't read dicom image! "+ e.getMessage());
        e.printStackTrace();
    }
   return get16bitBuffImage(raster);
}

Then I used this method to get the pixels from the raster previusly created from the DICOM file and put them in a BufferImage with a black an white ColorModel:

public static BufferedImage get16bitBuffImage(Raster raster) {
    short[] pixels = ((DataBufferUShort) raster.getDataBuffer()).getData();
    ColorModel colorModel = new ComponentColorModel(
        ColorSpace.getInstance(ColorSpace.CS_GRAY),
        new int[]{16},
        false,
        false,
        Transparency.OPAQUE,
        DataBuffer.TYPE_USHORT);
     DataBufferUShort db = new DataBufferUShort(pixels, pixels.length);
     WritableRaster outRaster = Raster.createInterleavedRaster(
        db,
        raster.getWidth(),
        raster.getHeight(),
        raster.getWidth(),
        1,
        new int[1],
        null);
     return new BufferedImage(colorModel, outRaster, false, null);
}

If you want to export the BufferImage to a JPEG file you can use this method:

private static void outputJpegImage(BufferedImage outputImage, String outputPath) {
   try {
   File outputJpegFile = new File(outputPath);
   OutputStream output = new BufferedOutputStream(new FileOutputStream(outputJpegFile));
   JPEGImageEncoder encoder = JPEGCodec.createJPEGEncoder(output);
   encoder.encode(outputImage);
   output.close();
    } catch (IOException e) {
        System.out.println("Error: couldn't write jpeg image! "+ e.getMessage());
        e.printStackTrace();
    }
   System.out.println("Output: " + outputPath);
}

Answer 4

You can use dcm4che-3.3.X. This new rewrite of the fabulous framework comes with jai-imageio library fully integrated and you don't need to download and configure it anymore.

Reading meta-information of a Dicom file is a mater of creating a org.dcm4che3.io.DicomInputStream from dicom file and parsing the stream with a class that implements org.dcm4che3.io.DicomInputHandler interface. You have to implements this methods:

void readValue(DicomInputStream dis, Attributes attrs) throws IOException;
void readValue(DicomInputStream dis, Sequence seq) throws IOException;
void readValue(DicomInputStream dis, Fragments frags) throws IOException;
void startDataset(DicomInputStream dis) throws IOException;
void endDataset(DicomInputStream dis) throws IOException;

startDataset and endDataset methods are launched when the stream is open/closed. The read methods are invoked when attributes, sequence or fragments are found. You can see a complete sample implementation in dcm4che/dcm4che-tool/dcm4che-tool-dcmdump.

To read dicom image into a java.awt.image.BufferedImage you need to get an javax.imageio.stream.ImageInputStream from a dicom file this way javax.imageio.ImageIO.createImageInputStream(dicomFile) where dicomFile is a java.io.File.

If you are wondering how this simple code works, this is because of dcm4che-imageio plugin.

Once again you can see a complete example implementation in dcm4che/dcm4che-tool/dcm4che-tool-dcm2jpg.

Obviously, you need a properly configured maven pom.xml with all dependencies you need, at least:

<dependencies>
  <dependency>
    <groupId>org.dcm4che</groupId>
    <artifactId>dcm4che-imageio</artifactId>
    <version>3.3.7</version>
  </dependency>
  <dependency>
    <groupId>org.dcm4che</groupId>
    <artifactId>dcm4che-imageio-rle</artifactId>
    <version>3.3.7</version>
    <scope>runtime</scope>
  </dependency>
  <dependency>
    <groupId>com.sun.media</groupId>
    <artifactId>jai_imageio</artifactId>
    <version>1.2-pre-dr-b04</version>
    <scope>runtime</scope>
  </dependency>
  <dependency>
    <groupId>org.dcm4che.tool</groupId>
    <artifactId>dcm4che-tool-common</artifactId>
    <version>3.3.7</version>
    <scope>compile</scope>
  </dependency>
  <dependency>
    <groupId>org.slf4j</groupId>
    <artifactId>slf4j-log4j12</artifactId>
  </dependency>
</dependencies>

and also dcm4che maven repo

<repositories>
  <repository>
    <id>www.dcm4che.org</id>
    <name>dcm4che Repository</name>
    <url>http://www.dcm4che.org/maven2</url>
</repository>

Hope it helps.