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

Class JDialogPromise12NIHDataToNii

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.JDialogPromise12NIHDataToNii
All Implemented Interfaces:
AlgorithmInterface, DialogDefaultsInterface, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants
public class JDialogPromise12NIHDataToNii extends JDialogBase implements AlgorithmInterface
This is the first try to 3D convolution deep learning models. 3D-Unet. Miccai Promise 12 NIH data: Preprocessed after, 1. N4 correction 2. Transform to 0.35m x 0.35m x 0.355m resolution images 3. Intensity normalization Convert the image to double type. Save the images and masks in .nii.gz format. Just convert the NIH data to nii format. Those nii data will be used for 3D-Unet deep learning training.
Author:
Ruida Cheng
See Also:

  • Field Details

  • Constructor Details

    • JDialogPromise12NIHDataToNii

      public JDialogPromise12NIHDataToNii(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_folder_2

      private void traverse_folder_2(File dir, String hashID)

    • read_name_2

      private void read_name_2(File dir)

    • printImages

      public void printImages()
      Debugger for test the image and VOis reading.

    • 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.

    • saveHED2DsliceCED

      public void saveHED2DsliceCED()

    • saveImage

      public void saveImage(ModelImage image, ModelImage imageMask, String orientation)

    • scaleIntensity

      public ModelImage scaleIntensity(ModelImage image)

    • savePNGfile

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

    • loadFiles

      public void loadFiles()
      load image files and voi files

    • readFile

      public void readFile()

    • init

      public void init()
      Initial panel

    • buildKeyImagePanel

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