AWTMedical3.java

/*=========================================================================

  Program: GDCM (Grassroots DICOM). A DICOM library

  Copyright (c) 2006-2011 Mathieu Malaterre
  All rights reserved.
  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
package examples;

import vtk.*;
//import gdcm.*;

import vtk.util.VtkPanelContainer;
import vtk.util.VtkPanelUtil;
import vtk.util.VtkUtil;

import java.util.ArrayList;


import javax.swing.*;
import java.awt.*;
import java.io.File;

public class AWTMedical3  extends JComponent implements VtkPanelContainer {

  private vtkPanel renWin;

    vtkImageData ReadDataFile(File inSelectedFile){

        vtkImageData outImageData = null;
        Directory theDir = new Directory();

        String theInputDirectory = inSelectedFile.getPath();
        theDir.Load(theInputDirectory);

        Scanner theScanner = new Scanner();
        Tag theStudyTag = new Tag(0x0020,0x000d);
        Tag theSeriesTag = new Tag(0x0020,0x000e);
        theScanner.AddTag(theStudyTag);//get studies,
        theScanner.AddTag(theSeriesTag);//get studies,
        theScanner.Scan(theDir.GetFilenames());

        FilenamesType theStudyValues = theScanner.GetOrderedValues(theStudyTag);
        long theNumStudies = theStudyValues.size();
        //for now, take the first study, and nothing else.
        //and the return is actually not FilenamesType, just a
        //vector of strings
        if (theNumStudies != 1)
            return outImageData;
        String theStudyVal = theStudyValues.get(0);
        //now, get all the values from the scanner that are in that
        //study, then from that get their different series
        FilenamesType theFilenames =
                theScanner.GetAllFilenamesFromTagToValue(theStudyTag, theStudyVal);

        //from that set of filenames, isolate individual series
        //conclude that singleton series = RT struct (can do further
        //checking for things like MIPs and the like)
        //and multiple series entries = volumetric data
        theScanner.Scan(theFilenames);
        FilenamesType theSeriesValues = theScanner.GetOrderedValues(theSeriesTag);
        String studyUID = theScanner.GetValue(theScanner.GetFilenames().get(0), theStudyTag);
        long theNumSeries = theSeriesValues.size();
        for (int i = 0; i < theNumSeries; i++) {
            FilenamesType theSeriesFiles =
                theScanner.GetAllFilenamesFromTagToValue(theSeriesTag, theSeriesValues.get(i));
            long theNumFilesInSeries = theSeriesFiles.size();
            if (theNumFilesInSeries > 1) {//assume it's CT or volumetric data
                //for now, assume a single volume
                //could have multiples, like PET and CT

                IPPSorter sorter = new IPPSorter();
                sorter.SetComputeZSpacing(true);
                sorter.SetZSpacingTolerance(0.001);
                Boolean sorted = sorter.Sort(theSeriesFiles);
                if (!sorted){
                    //need some better way to handle failures here
                    return outImageData;
                }

                FilenamesType sortedFT = sorter.GetFilenames();
                long theSize = sortedFT.size();
                vtkStringArray sa = new vtkStringArray();
                ArrayList<String> theStrings = new ArrayList<String>();

                vtkGDCMImageReader gdcmReader = new vtkGDCMImageReader();
                for (int j = 0; j < theSize; j++) {
                    String theFileName = sortedFT.get(j);
                    if (gdcmReader.CanReadFile(theFileName) > 0){
                        theStrings.add(theFileName);
                        sa.InsertNextValue(theFileName);
                    } else {
                        //this is a busted series
                        //need some more appropriate error here
                        return outImageData;
                    }
                }

                gdcmReader.SetFileNames(sa);

                gdcmReader.Update();

                outImageData = gdcmReader.GetOutput();//the zeroth output should be the image
            }
        }
        String theImageInfo = "";
        if (outImageData != null){
            theImageInfo = outImageData.Print();
        }
        return outImageData;
    }

    //this function is a rewrite of Medical3 to see if data can
    //be loaded via gdcm easily
  public AWTMedical3(File inFile) {
    // Create the buttons.
    renWin = new vtkPanel();

    vtkImageData theImageData = ReadDataFile(inFile);

    // An isosurface, or contour value of 500 is known to correspond to the
    // skin of the patient. Once generated, a vtkPolyDataNormals filter is
    // is used to create normals for smooth surface shading during rendering.
    // The triangle stripper is used to create triangle strips from the
    // isosurface these render much faster on some systems.
    vtkContourFilter skinExtractor = new vtkContourFilter();
    skinExtractor.SetInput(theImageData);
    skinExtractor.SetValue(0, 500);
    vtkPolyDataNormals skinNormals = new vtkPolyDataNormals();
    skinNormals.SetInput(skinExtractor.GetOutput());
    skinNormals.SetFeatureAngle(60.0);
//        vtkStripper skinStripper = new vtkStripper();
//        skinStripper.SetInput(skinNormals.GetOutput());
    vtkPolyDataMapper skinMapper = new vtkPolyDataMapper();
    skinMapper.SetInput(skinNormals.GetOutput());
    skinMapper.ScalarVisibilityOff();
    vtkActor skin = new vtkActor();
    skin.SetMapper(skinMapper);
    skin.GetProperty().SetDiffuseColor(1, .49, .25);
    skin.GetProperty().SetSpecular(.3);
    skin.GetProperty().SetSpecularPower(20);

    // An isosurface, or contour value of 1150 is known to correspond to the
    // skin of the patient. Once generated, a vtkPolyDataNormals filter is
    // is used to create normals for smooth surface shading during rendering.
    // The triangle stripper is used to create triangle strips from the
    // isosurface these render much faster on some systems.
    vtkContourFilter boneExtractor = new vtkContourFilter();
    boneExtractor.SetInput(theImageData);
    boneExtractor.SetValue(0, 1150);
    vtkPolyDataNormals boneNormals = new vtkPolyDataNormals();
    boneNormals.SetInput(boneExtractor.GetOutput());
    boneNormals.SetFeatureAngle(60.0);
    vtkStripper boneStripper = new vtkStripper();
    boneStripper.SetInput(boneNormals.GetOutput());
    vtkPolyDataMapper boneMapper = new vtkPolyDataMapper();
    boneMapper.SetInput(boneStripper.GetOutput());
    boneMapper.ScalarVisibilityOff();
    vtkActor bone = new vtkActor();
    bone.SetMapper(boneMapper);
    bone.GetProperty().SetDiffuseColor(1, 1, .9412);

    // An outline provides context around the data.
    vtkOutlineFilter outlineData = new vtkOutlineFilter();
    outlineData.SetInput(theImageData);
    vtkPolyDataMapper mapOutline = new vtkPolyDataMapper();
    mapOutline.SetInput(outlineData.GetOutput());
    vtkActor outline = new vtkActor();
    outline.SetMapper(mapOutline);
    outline.GetProperty().SetColor(0, 0, 0);

    // Now we are creating three orthogonal planes passing through the
    // volume. Each plane uses a different texture map and therefore has
    // diferent coloration.

    // Start by creatin a black/white lookup table.
    vtkLookupTable bwLut = new vtkLookupTable();
    bwLut.SetTableRange(0, 2000);
    bwLut.SetSaturationRange(0, 0);
    bwLut.SetHueRange(0, 0);
    bwLut.SetValueRange(0, 1);
    bwLut.Build();

    // Now create a lookup table that consists of the full hue circle (from
    // HSV);.
    vtkLookupTable hueLut = new vtkLookupTable();
    hueLut.SetTableRange(0, 2000);
    hueLut.SetHueRange(0, 1);
    hueLut.SetSaturationRange(1, 1);
    hueLut.SetValueRange(1, 1);
    hueLut.Build();

    // Finally, create a lookup table with a single hue but having a range
    // in the saturation of the hue.
    vtkLookupTable satLut = new vtkLookupTable();
    satLut.SetTableRange(0, 2000);
    satLut.SetHueRange(.6, .6);
    satLut.SetSaturationRange(0, 1);
    satLut.SetValueRange(1, 1);
    satLut.Build();

    // Create the first of the three planes. The filter vtkImageMapToColors
    // maps the data through the corresponding lookup table created above.
    // The vtkImageActor is a type of vtkProp and conveniently displays an
    // image on a single quadrilateral plane. It does this using texture
    // mapping and as a result is quite fast. (Note: the input image has to
    // be unsigned char values, which the vtkImageMapToColors produces.);
    // Note also that by specifying the DisplayExtent, the pipeline
    // requests data of this extent and the vtkImageMapToColors only
    // processes a slice of data.
    vtkImageMapToColors saggitalColors = new vtkImageMapToColors();
    saggitalColors.SetInput(theImageData);
    saggitalColors.SetLookupTable(bwLut);
    vtkImageActor saggital = new vtkImageActor();
    saggital.SetInput(saggitalColors.GetOutput());
    saggital.SetDisplayExtent(32, 32, 0, 63, 0, 92);

    // Create the second (axial); plane of the three planes. We use the same
    // approach as before except that the extent differs.
    vtkImageMapToColors axialColors = new vtkImageMapToColors();
    axialColors.SetInput(theImageData);
    axialColors.SetLookupTable(hueLut);
    vtkImageActor axial = new vtkImageActor();
    axial.SetInput(axialColors.GetOutput());
    axial.SetDisplayExtent(0, 63, 0, 63, 46, 46);

    // Create the third (coronal); plane of the three planes. We use the same
    // approach as before except that the extent differs.
    vtkImageMapToColors coronalColors = new vtkImageMapToColors();
    coronalColors.SetInput(theImageData);
    coronalColors.SetLookupTable(satLut);
    vtkImageActor coronal = new vtkImageActor();
    coronal.SetInput(coronalColors.GetOutput());
    coronal.SetDisplayExtent(0, 63, 32, 32, 0, 92);

    // It is convenient to create an initial view of the data. The FocalPoint
    // and Position form a vector direction. Later on (ResetCamera() method)
    // this vector is used to position the camera to look at the data in
    // this direction.
    vtkCamera aCamera = new vtkCamera();
    aCamera.SetViewUp(0, 0, -1);
    aCamera.SetPosition(0, 1, 0);
    aCamera.SetFocalPoint(0, 0, 0);
    aCamera.ComputeViewPlaneNormal();

    // Actors are added to the renderer. An initial camera view is created.
    // The Dolly() method moves the camera towards the FocalPoint,
    // thereby enlarging the image.
    renWin.GetRenderer().AddActor(saggital);
    renWin.GetRenderer().AddActor(axial);
    renWin.GetRenderer().AddActor(coronal);
    renWin.GetRenderer().AddActor(outline);
    renWin.GetRenderer().AddActor(skin);
    renWin.GetRenderer().AddActor(bone);

    // Turn off bone for this example.
    bone.VisibilityOff();

    // Set skin to semi-transparent.
    skin.GetProperty().SetOpacity(0.5);

    // An initial camera view is created.  The Dolly() method moves
    // the camera towards the FocalPoint, thereby enlarging the image.
    renWin.GetRenderer().SetActiveCamera(aCamera);
    renWin.GetRenderer().ResetCamera();
    aCamera.Dolly(1.5);

    // Set a background color for the renderer and set the size of the
    // render window (expressed in pixels).
    renWin.GetRenderer().SetBackground(1, 1, 1);
    VtkPanelUtil.setSize(renWin, 640, 480);

    // Note that when camera movement occurs (as it does in the Dolly()
    // method), the clipping planes often need adjusting. Clipping planes
    // consist of two planes: near and far along the view direction. The
    // near plane clips out objects in front of the plane the far plane
    // clips out objects behind the plane. This way only what is drawn
    // between the planes is actually rendered.
    renWin.GetRenderer().ResetCameraClippingRange();

    // Setup panel
    setLayout(new BorderLayout());
    add(renWin, BorderLayout.CENTER);
  }



  public vtkPanel getRenWin() {
    return renWin;
  }


  public static void main(String s[]) {
    if (s.length == 0){
      return; //need a filename here
    }
    File theFile = new File(s[0]);
    //File theFile = new File("/Users/mmroden/Documents/MVSDownloadDirectory/Documents/1.2.840.113704.1.111.3384.1271766367.5/");
    AWTMedical3 panel = new AWTMedical3(theFile);

    JFrame frame = new JFrame("AWTMedical3");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    frame.getContentPane().add("Center", panel);
    frame.pack();
    frame.setVisible(true);
  }

}