/** * 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. * * @param algorithm Algorithm that caused the event. */ public void algorithmPerformed(AlgorithmBase algorithm) { if (algorithm instanceof AlgorithmNonlocalMeansFilter) { image.clearMask(); if ((nlMeansFilterAlgo.isCompleted() == true) && (resultImage != null)) { updateFileInfo(image, resultImage); resultImage.clearMask(); // The algorithm has completed and produced a new image to be displayed. try { new ViewJFrameImage(resultImage, null, new Dimension(610, 200)); } catch (OutOfMemoryError error) { MipavUtil.displayError("Out of memory: unable to open new frame"); } } else if (resultImage == null) { // These next lines set the titles in all frames where the source image is displayed to // image name so as to indicate that the image is now unlocked! // The image frames are enabled and then registed to the userinterface. Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector(); for (int i = 0; i < imageFrames.size(); i++) { ((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]); ((Frame) (imageFrames.elementAt(i))).setEnabled(true); if (((Frame) (imageFrames.elementAt(i))) != parentFrame) { userInterface.registerFrame((Frame) (imageFrames.elementAt(i))); } } if (parentFrame != null) { userInterface.registerFrame(parentFrame); } image.notifyImageDisplayListeners(null, true); } else if (resultImage != null) { // algorithm failed but result image still has garbage resultImage.disposeLocal(); // clean up memory resultImage = null; } } if (algorithm.isCompleted()) { insertScriptLine(); } // save the completion status for later setComplete(algorithm.isCompleted()); nlMeansFilterAlgo.finalize(); nlMeansFilterAlgo = null; dispose(); }
/** * Creates a new JDialogNonlocalMeansFilter object. * * @param theParentFrame Parent frame. * @param im Source image. */ public JDialogNonlocalMeansFilter(Frame theParentFrame, ModelImage im) { super(theParentFrame, false); image = im; userInterface = ViewUserInterface.getReference(); init(); setVisible(true); }
/** {@inheritDoc} */ protected void setGUIFromParams() { image = scriptParameters.retrieveInputImage(); userInterface = ViewUserInterface.getReference(); parentFrame = image.getParentFrame(); if (scriptParameters.doOutputNewImage()) { setDisplayLocNew(); } else { setDisplayLocReplace(); } searchWindowSide = scriptParameters.getParams().getInt("search_window_side"); similarityWindowSide = scriptParameters.getParams().getInt("similarity_window_side"); noiseStandardDeviation = scriptParameters.getParams().getFloat("noise_standard_deviation"); degreeOfFiltering = scriptParameters.getParams().getFloat("degree_of_filtering"); doRician = scriptParameters.getParams().getBoolean("do_rician"); image25D = scriptParameters.doProcess3DAs25D(); }
/** {@inheritDoc} */ protected void setGUIFromParams() { image = scriptParameters.retrieveInputImage(1); userInterface = ViewUserInterface.getReference(); parentFrame = image.getParentFrame(); if (scriptParameters.doOutputNewImage()) { setDisplayLocNew(); } else { // replace processing not supported.. // setDisplayLocReplace(); setDisplayLocNew(); } subXDim = scriptParameters.getParams().getInt("sub_x_dim"); subYDim = scriptParameters.getParams().getInt("sub_y_dim"); numberOfImagesInMosaic = scriptParameters.getParams().getInt("number_of_images_in_mosaic"); }
/** * Once all the necessary variables are set, call the Nonlocal Means filter algorithm based on * what type of image this is and whether or not there is a separate destination image. */ protected void callAlgorithm() { String name = makeImageName(image.getImageName(), "_NonlocalMeans"); int[] destExtents; if (image.getNDims() == 2) { // source image is 2D destExtents = new int[2]; destExtents[0] = image.getExtents()[0]; // X dim destExtents[1] = image.getExtents()[1]; // Y dim } else { destExtents = new int[3]; destExtents[0] = image.getExtents()[0]; destExtents[1] = image.getExtents()[1]; destExtents[2] = image.getExtents()[2]; } if (displayLoc == NEW) { try { // Make result image of float type if (image.isColorImage()) { resultImage = new ModelImage(ModelImage.ARGB, destExtents, name); } else { resultImage = new ModelImage(ModelImage.FLOAT, destExtents, name); } // resultImage = (ModelImage)image.clone(); // resultImage.setImageName(name); // Make algorithm nlMeansFilterAlgo = new AlgorithmNonlocalMeansFilter( resultImage, image, searchWindowSide, similarityWindowSide, noiseStandardDeviation, degreeOfFiltering, doRician, image25D); // This is very important. Adding this object as a listener allows the algorithm to // notify this object when it has completed of failed. See algorithm performed event. // This is made possible by implementing AlgorithmedPerformed interface nlMeansFilterAlgo.addListener(this); createProgressBar(image.getImageName(), nlMeansFilterAlgo); // Hide dialog setVisible(false); if (isRunInSeparateThread()) { // Start the thread as a low priority because we wish to still have user interface work // fast if (nlMeansFilterAlgo.startMethod(Thread.MIN_PRIORITY) == false) { MipavUtil.displayError("A thread is already running on this object"); } } else { nlMeansFilterAlgo.run(); } } catch (OutOfMemoryError x) { MipavUtil.displayError("Dialog Nonlocal Means Filter: unable to allocate enough memory"); if (resultImage != null) { resultImage.disposeLocal(); // Clean up memory of result image resultImage = null; } return; } } else { try { // No need to make new image space because the user has choosen to replace the source image // Make the algorithm class nlMeansFilterAlgo = new AlgorithmNonlocalMeansFilter( null, image, searchWindowSide, similarityWindowSide, noiseStandardDeviation, degreeOfFiltering, doRician, image25D); // This is very important. Adding this object as a listener allows the algorithm to // notify this object when it has completed of failed. See algorithm performed event. // This is made possible by implementing AlgorithmedPerformed interface nlMeansFilterAlgo.addListener(this); createProgressBar(image.getImageName(), nlMeansFilterAlgo); // Hide the dialog since the algorithm is about to run. setVisible(false); // These next lines set the titles in all frames where the source image is displayed to // "locked - " image name so as to indicate that the image is now read/write locked! // The image frames are disabled and then unregisted from the userinterface until the // algorithm has completed. Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector(); titles = new String[imageFrames.size()]; for (int i = 0; i < imageFrames.size(); i++) { titles[i] = ((Frame) (imageFrames.elementAt(i))).getTitle(); ((Frame) (imageFrames.elementAt(i))).setTitle("Locked: " + titles[i]); ((Frame) (imageFrames.elementAt(i))).setEnabled(false); userInterface.unregisterFrame((Frame) (imageFrames.elementAt(i))); } if (isRunInSeparateThread()) { // Start the thread as a low priority because we wish to still have user interface work // fast if (nlMeansFilterAlgo.startMethod(Thread.MIN_PRIORITY) == false) { MipavUtil.displayError("A thread is already running on this object"); } } else { nlMeansFilterAlgo.run(); } } catch (OutOfMemoryError x) { MipavUtil.displayError("Dialog Nonlocal Means Filter: unable to allocate enough memory"); return; } } }
/** * Creates new Mosaic To Slices dialog. * * @param theParentFrame Parent frame. * @param im Source image. */ public JDialogMosaicToSlices(Frame theParentFrame, ModelImage im) { super(theParentFrame, false); image = im; userInterface = ViewUserInterface.getReference(); init(); }
/** * Once all the necessary variables are set, call the Concat algorithm based on what type of image * this is and whether or not there is a separate destination image. */ protected void callAlgorithm() { int destExtents[] = new int[3]; ModelImage destImage = null; destExtents[0] = subXDim; destExtents[1] = subYDim; destExtents[2] = numberOfImagesInMosaic; destImage = new ModelImage( image.getType(), destExtents, makeImageName(image.getImageName(), "_mosaic_to_slices")); try { // Make algorithm mathAlgo = new AlgorithmMosaicToSlices(image, destImage); // This is very important. Adding this object as a listener allows the algorithm to // notify this object when it has completed of failed. See algorithm performed event. // This is made possible by implementing AlgorithmedPerformed interface mathAlgo.addListener(this); createProgressBar(image.getImageName(), mathAlgo); // Hide dialog setVisible(false); if (displayLoc == REPLACE) { // These next lines set the titles in all frames where the source image is displayed to // "locked - " image name so as to indicate that the image is now read/write locked! // The image frames are disabled and then unregisted from the userinterface until the // algorithm has completed. Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector(); titles = new String[imageFrames.size()]; for (int i = 0; i < imageFrames.size(); i++) { titles[i] = ((Frame) (imageFrames.elementAt(i))).getTitle(); ((Frame) (imageFrames.elementAt(i))).setTitle("Locked: " + titles[i]); ((Frame) (imageFrames.elementAt(i))).setEnabled(false); userInterface.unregisterFrame((Frame) (imageFrames.elementAt(i))); } } if (isRunInSeparateThread()) { // Start the thread as a low priority because we wish to still have user interface work // fast. if (mathAlgo.startMethod(Thread.MIN_PRIORITY) == false) { MipavUtil.displayError("A thread is already running on this object"); } } else { mathAlgo.run(); } } catch (OutOfMemoryError x) { System.gc(); MipavUtil.displayError("Dialog Concatenation: unable to allocate enough memory"); return; } }
/** * 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. * * @param algorithm Algorithm that caused the event. */ public void algorithmPerformed(AlgorithmBase algorithm) { ViewJFrameImage imageFrame = null; if (algorithm instanceof AlgorithmMosaicToSlices) { if ((mathAlgo.isCompleted() == true) && (mathAlgo.getResultImage() != null)) { // The algorithm has completed and produced a new image to be displayed. if (displayLoc == NEW) { try { resultImage = mathAlgo.getResultImage(); new ViewJFrameImage(resultImage, null, new Dimension(610, 200)); } catch (OutOfMemoryError error) { System.gc(); MipavUtil.displayError("Out of memory: unable to open new frame"); } } else { // These next lines set the titles in all frames where the source image is displayed to // image name so as to indicate that the image is now unlocked! // The image frames are enabled and then registed to the userinterface. resultImage = mathAlgo.getResultImage(); Vector<ViewImageUpdateInterface> imageFrames = image.getImageFrameVector(); for (int i = 0; i < imageFrames.size(); i++) { ((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]); ((Frame) (imageFrames.elementAt(i))).setEnabled(true); if ((((Frame) (imageFrames.elementAt(i))) != parentFrame) && (parentFrame != null)) { userInterface.registerFrame((Frame) (imageFrames.elementAt(i))); } } Point pt; if (parentFrame != null) { pt = ((ViewJFrameBase) parentFrame).getLocation(); } else { pt = new Point( Toolkit.getDefaultToolkit().getScreenSize().width / 2, Toolkit.getDefaultToolkit().getScreenSize().height / 2); } imageFrame = new ViewJFrameImage(resultImage, null, new Dimension(pt.x, pt.y)); if (parentFrame != null) { ((ViewJFrameBase) parentFrame).close(); } else { ((ViewJFrameBase) image.getParentFrame()).close(); } // Not so sure about this. if (image.getLightBoxFrame() != null) { try { pt = image.getLightBoxFrame().getLocation(); image.getLightBoxFrame().close(); new ViewJFrameLightBox( imageFrame, "LightBox", resultImage, imageFrame.getComponentImage().getLUTa(), imageFrame.getComponentImage().getImageB(), imageFrame.getComponentImage().getLUTb(), imageFrame.getComponentImage().getResolutionX(), imageFrame.getComponentImage().getResolutionY(), new Dimension(pt.x, pt.y), imageFrame.getControls(), imageFrame.getVOIManager()); } catch (OutOfMemoryError error) { MipavUtil.displayError("Out of memory: unable to open new frame"); } } } } else if (resultImage == null) { // These next lines set the titles in all frames where the source image is displayed to // image name so as to indicate that the image is now unlocked! // The image frames are enabled and then registered to the userinterface. /*Vector imageFrames = imageA.getImageFrameVector(); for (int i = 0; i < imageFrames.size(); i++) { ((Frame) (imageFrames.elementAt(i))).setTitle(titles[i]); ((Frame) (imageFrames.elementAt(i))).setEnabled(true); if (((Frame) (imageFrames.elementAt(i))) != parentFrame) { userInterface.registerFrame((Frame) (imageFrames.elementAt(i))); } }*/ if (parentFrame != null) { userInterface.registerFrame(parentFrame); } image.notifyImageDisplayListeners(null, true); } else if (resultImage != null) { // algorithm failed but result image still has garbage resultImage.disposeLocal(); // clean up memory System.gc(); } } if (algorithm.isCompleted()) { insertScriptLine(); } mathAlgo.finalize(); mathAlgo = null; dispose(); }