I know that there is a plugin for ImageJ that handles NIfTI-1 files (http://rsb.info.nih.gov/ij/plugins/nifti.html).
But all its instructions on that page is to use ImageJ as a standalone program, however I am using its API. How can I know what methods are available in this jar file without its source?
I couldn't find the source code either.
For the supported archives in imageJ (such as DICOM) is quite easy :
public class ImageJTest {
public static void main(){
String path = "res/vaca.dcm";
FileInputStream fis;
ImageView image;
try {
fis = new FileInputStream(path);
DICOM d = new DICOM(fis);
d.run(path);
// Stretches the histogram because the pictures were being
// displayed too dark.
(new ij.plugin.ContrastEnhancer()).stretchHistogram(d, 0.1);
Image picture = SwingFXUtils.toFXImage(d.getBufferedImage(),
null);
// Makes the size standard for thumbnails
image = new ImageView(picture);
} catch (FileNotFoundException e) {
e.printStackTrace();
}
}
}
How can I load the NIfTI-1 files in imageJ ?
Once you have the class files, which are embedded in the jar file (as @Alvin Thompson pointed out, these are just zip files by a different name), you can use the reflection API to mine the class files to get their methods. A sample follows for one class, cribbed from here:
Method[] methods = thisClass.getClass().getMethods(); // thisClass is an instance of the class you're working with
for(Method method : methods){
System.out.println("method = " + method.getName());
}