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

Class JDialogProstate2DSlicesAtlasPngConverterTest_JMI

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.JDialogProstate2DSlicesAtlasPngConverterTest_JMI
All Implemented Interfaces:
AlgorithmInterface, DialogDefaultsInterface, ActionListener, FocusListener, ItemListener, WindowListener, ImageObserver, MenuContainer, Serializable, EventListener, Accessible, RootPaneContainer, WindowConstants
public class JDialogProstate2DSlicesAtlasPngConverterTest_JMI extends JDialogBase implements AlgorithmInterface
For JMI 2017 paper: this class uses image processing methods that are different to the SPIE paper. 1) Read the MRI image with VOIs 2) Generate the binary masks 2) Crop the image with the 25% deduction 3) Scale image intensity to range 0 to 1000. 4) Generate the CED image. 5) Extract MRI image and CED image slices with corresponding binary image masks for HED to train the deep learning model. Different to the training, the test processing saves MRI and CED slices in one directory for each image. The training processing follows the 5 fold cross validation, in each fold, save all other fold's MRI and CED slices in order to train.
Author:
Ruida Cheng
See Also:

  • Field Details

  • Constructor Details

    • JDialogProstate2DSlicesAtlasPngConverterTest_JMI

      public JDialogProstate2DSlicesAtlasPngConverterTest_JMI(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_1

      private void traverse_folder_1(File dir)

    • processDir_folder_1

      private void processDir_folder_1(File dir)

    • sortKeyImage_1

      public void sortKeyImage_1()

    • traverse_folder_2

      private void traverse_folder_2(File dir)

    • processDir_folder_2

      private void processDir_folder_2(File dir)

    • sortKeyImage_2

      public void sortKeyImage_2()

    • traverse_folder_3

      private void traverse_folder_3(File dir)

    • processDir_folder_3

      private void processDir_folder_3(File dir)

    • sortKeyImage_3

      public void sortKeyImage_3()

    • traverse_folder_4

      private void traverse_folder_4(File dir)

    • processDir_folder_4

      private void processDir_folder_4(File dir)

    • sortKeyImage_4

      public void sortKeyImage_4()

    • traverse_folder_5

      private void traverse_folder_5(File dir)

    • processDir_folder_5

      private void processDir_folder_5(File dir)

    • sortKeyImage_5

      public void sortKeyImage_5()

    • 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.

    • crossValidationTest

      public void crossValidationTest()

    • saveImagesTest

      public void saveImagesTest(int i, int[] index, String folderName, Hashtable<Integer,ModelImage> whichTable)

    • savePNGfile

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

    • disposeMemory

      public void disposeMemory()

    • runCED_ext

      public void runCED_ext()

    • runMask_ext

      public void runMask_ext()

    • runCrop_ext

      public void runCrop_ext()

    • runScaleIntensity_ext

      public void runScaleIntensity_ext()

    • cropImage

      private ModelImage cropImage(ModelImage image)

    • cropImage_ext

      private ModelImage cropImage_ext(ModelImage image)

    • scaleIntensity

      public ModelImage scaleIntensity(ModelImage image)

    • calculateCoherenceEnhancingDiffusion

      private ModelImage calculateCoherenceEnhancingDiffusion(ModelImage inImage)

    • saveTestedImages

      public void saveTestedImages()

    • 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()

    • init

      public void init()
      Initial panel

    • buildKeyImagePanel

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