API Example - Extracting an image Slice

This example shows you how to create a simple programme to extract a single image slice from a multi-slice image. The image can be in UNC, Analyze, NIFTI-1, NIFTI-2 or DICOM format. To try out the programme, save the following text to a file called ExtractSlice.java. You need to make sure that the following files from the Jim installation folder are in your classpath:

For programs that use other parts of the A.P.I., you may also need to put these files from the Jim installation folder in your classpath: Then compile the program with the javac command:

javac ExtractSlice.java

Note: you must use javac version 17.
This will create a file called ExtractSlice.class. To run the programme, type (for example):

java ExtractSlice 2 input-image output-image

where input-image is the name of the image from which to extract the slice, and output-image is the image to create. This example would extract slice 2 from the input image and create a single slice output image containing just slice 2.

<--Java code Starts Here --> 

import java.io.IOException;

import com.xinapse.image.ReadableImage;
import com.xinapse.image.WritableImage;
import com.xinapse.image.ImageUtils;
import com.xinapse.image.InvalidImageException;
import com.xinapse.multisliceimage.InfoStorer;
import com.xinapse.util.InfoList;

public class ExtractSlice {

  /**
     Java program to extract a single slice from a multi-slice image.
  */
  public static void main(String argv[]) {

    int sliceToExtract = 0;
    int nFiles = argv.length - 1;

    if (nFiles != 2) {
      System.err.println("Usage: ExtractSlice slice-number input-file output-file");
      System.err.println("     - extract a slice from a multi-slice image and create a new image");
      System.exit(-1);
    }

    try {
      // The user will have supplied a slice indexed from 1.
      // getSlice works with indices from zero.
      sliceToExtract = Integer.parseInt(argv[0]) - 1;
    }
    catch (NumberFormatException e) {
      System.err.println("Couldn't get slice number to extract from " + argv[0]);
      System.exit(-1);
    }

    // Create a ReadableImage instance from the supplied file name.
    ReadableImage inputImage = null;
    try {
      inputImage = ImageUtils.getReadableImage(argv[1]);
    }
    catch (InvalidImageException iiE) {
      System.err.println("Error reading input image: " + iiE.getMessage());
      System.exit(-1);
    }

    String outputImageName = argv[2];
    
    // Get the image dimensionality.
    int nDim = inputImage.getNDim();
    if (nDim < 3) {
      System.err.println("Can't extract a slice from a " + nDim + "-dimensional image"); 
      System.exit(-1);
    }
    
    int nRows   = inputImage.getNRows();
    int nCols   = inputImage.getNCols();
    int nSlices = inputImage.getTotalNSlices();
    
    if (sliceToExtract < 0 || sliceToExtract >= nSlices) {
      System.err.println("Slice to extract out of range: " + (sliceToExtract + 1));
      System.exit(-1);
    }
    
    // Create the output image, with the same format as the input image, but with only one
    // slice. There are other methods to change the format, change the pixel data type etc.
    try {
      WritableImage outputImage = ImageUtils.getWritableImage(inputImage, 1);
      
      // Get the one slice-worth of pixels from the input image ...
      Object slicePixels = inputImage.getSlice(sliceToExtract);
      // ... and put them to slice 0 of the output image. 
      outputImage.putSlice(slicePixels, 0);
      
      if (inputImage instanceof InfoStorer && outputImage instanceof InfoStorer) {
        // Copy any slice-specific information from the right slice in the input image to
        // the general information of the output image.
        InfoList sliceInfoList = ((InfoStorer) inputImage).getInfoList(nDim-3, sliceToExtract);
        ((InfoStorer) outputImage).appendInfoList(sliceInfoList);
        // Remove any slice-specific information from the output image (for slice 0).
        ((InfoStorer) outputImage).setSliceInfoList(new InfoList(), 0);
      }
      // Save the output image to disk.
      outputImage.write(outputImageName);
      // It's good practice to close the images when we're finished with them, although
      // in this case they will be closed when the program exits.
      inputImage.close();
      outputImage.close();
    }
    catch (IOException ioE) {
      System.err.println("Error writing output image: " + ioE.getMessage());
      System.exit(-1);
    }
    catch (InvalidImageException iiE) {
      System.err.println("Error writing output image: " + iiE.getMessage());
      System.exit(-1);
    }

    System.exit(0);
  }
}
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