Package gov.nih.mipav.view.renderer.WildMagic.ProstateFramework

Class JDialogProstateSPIEcancerChallengeNIH_train_ced

java.lang.Object
java.awt.Component
java.awt.Container
java.awt.Window
java.awt.Dialog
javax.swing.JDialog
gov.nih.mipav.view.dialogs.JDialogBase
gov.nih.mipav.view.renderer.WildMagic.ProstateFramework.JDialogProstateSPIEcancerChallengeNIH_train_ced
All Implemented Interfaces:
AlgorithmInterface, DialogDefaultsInterface, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants
public class JDialogProstateSPIEcancerChallengeNIH_train_ced extends JDialogBase implements AlgorithmInterface
The MICCAI ProstateX challenge is rolling over to prostate segmentation, which includes the whole prostate(wp) and central gland(cg). This is the first attempt to try the wp and cg segmentation. Combining the CED and MRI slices to train one HED deep learning model. NIH data only. We will try something for 2nd Journal paper on this path soon. For the challenge, we apply the whole prostate and central gland segmentation to the challenge testing data. steps: 1) From MRI image, generates the binary mask images. 2) Normalize the MRI image slices within range [0, 1000]. 3) Generate the CED slices 3) save MRI and CED slices with corresponding binary masks in png format.
Author:
Ruida Cheng
See Also:

  • Field Details

  • Constructor Details

    • JDialogProstateSPIEcancerChallengeNIH_train_ced

      public JDialogProstateSPIEcancerChallengeNIH_train_ced(Frame theParentFrame)
      Constructor.
      Parameters:
      theParentFrame -

  • Method Details

    • disposeLocal

      public void disposeLocal()
      dispose memory

    • actionPerformed

      public void actionPerformed(ActionEvent event)
      Dialog local actionPerformed handler.
      Specified by:
      actionPerformed in interface ActionListener
      Overrides:
      actionPerformed in class JDialogBase

    • recordSaveImageDir

      private void recordSaveImageDir()
      Let user specify the saved 2D slices atlas, record the save directory.

    • readKeyImageDir

      private void readKeyImageDir()
      Read 3D images atlas directory.

    • traverse_Layer_noCoil

      private void traverse_Layer_noCoil(File dir)

    • traverse_firstLayer_noCoil

      private void traverse_firstLayer_noCoil(File firstDir, String child)

    • traverse_secondLayer_noCoil

      private void traverse_secondLayer_noCoil(File firstLayer, String hashID)

    • traverse_DicomLayer

      private void traverse_DicomLayer(File lastLayer, String hashID)

    • algorithmPerformed

      public void algorithmPerformed(AlgorithmBase algorithm)
      This method is required if the AlgorithmPerformed interface is implemented. It is called by the algorithms when it has completed or failed to to complete, so that the dialog can be display the result image and/or clean up.
      Specified by:
      algorithmPerformed in interface AlgorithmInterface
      Parameters:
      algorithm - Algorithm that caused the event.

    • callAlgorithm

      public void callAlgorithm()
      Driver function to read image and VOIs, and convert each 3D image to 2D slices.

    • runScaleIntensity

      public void runScaleIntensity()

    • histoEqual

      public ModelImage histoEqual(ModelImage image)

    • scaleIntensity

      public ModelImage scaleIntensity(ModelImage image)

    • runMask

      public void runMask()

    • runCED

      public void runCED()

    • calculateTransform

      public ModelImage calculateTransform(ModelImage image)

    • calculateCoherenceEnhancingDiffusion

      private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage inImage)

    • saveTestedImages

      public void saveTestedImages()

    • train

      public void train()

    • savePNGfile

      private void savePNGfile(String dirName, String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, int xDim, int yDim, boolean isMask)

    • saveImages

      public void saveImages(String key, int[] index, String folderName, Hashtable<String,ModelImage> whichTable)

    • saveImagesTest

      public void saveImagesTest(String key, int[] index, String folderName)

    • savePNGfile

      private void savePNGfile(String dirName, String fileName, ModelImage srcImage, float minIntensity, float maxIntensity, boolean isMask)

    • smoothVOI60

      public void smoothVOI60(ModelImage maskImage, ModelImage resultImage)
      Smooth VOIs to 60 points.
      Parameters:
      maskImage -
      resultImage -

    • loadFiles

      public void loadFiles()
      load image files and voi files

    • deleteDir

      public static boolean deleteDir(File dir)
      Debugger to test dir deletion.
      Parameters:
      dir -
      Returns:

    • readFile

      public void readFile()

    • pause

      public static void pause()

    • init

      public void init()
      Initial panel

    • buildKeyImagePanel

      public void buildKeyImagePanel()
      Panel contains both the 3D image dir and saved 2D slices atlas dir.