/** Calls the algorithm. */ protected void callAlgorithm() { try { resultImage = new ModelImage(imageA.getType(), imageA.getExtents(), (imageA.getImageName() + "_isn")); resultImage.copyFileTypeInfo(imageA); // Make algorithm isnAlgo = new PlugInAlgorithmISN(resultImage, imageA); // 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 isnAlgo.addListener(this); createProgressBar(imageA.getImageName(), " ...", isnAlgo); // Hide dialog setVisible(false); if (isRunInSeparateThread()) { // Start the thread as a low priority because we wish to still have user interface work // fast. if (isnAlgo.startMethod(Thread.MIN_PRIORITY) == false) { MipavUtil.displayError("A thread is already running on this object"); } } else { isnAlgo.run(); } } catch (OutOfMemoryError x) { System.gc(); MipavUtil.displayError("AlgorithmAbsoluteValue: unable to allocate enough memory"); return; } }
/** * 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; } } }
/** * Use the GUI results to set up the variables needed to run the algorithm. * * @return <code>true</code> if parameters set successfully, <code>false</code> otherwise. */ private boolean setVariables() { String tmpStr; int i; int totLength = image.getExtents()[0]; for (i = 1; i < image.getNDims(); i++) { totLength *= image.getExtents()[i]; } tmpStr = greenMergingText.getText(); mergingDistance = Float.parseFloat(tmpStr); if (mergingDistance < 0.0f) { MipavUtil.displayError("Merging distance cannot be less than 0"); greenMergingText.requestFocus(); greenMergingText.selectAll(); return false; } tmpStr = redMinText.getText(); redMin = Integer.parseInt(tmpStr); if (redMin < 1) { MipavUtil.displayError("red minimum must be at least 1"); redMinText.requestFocus(); redMinText.selectAll(); return false; } else if (redMin > totLength) { MipavUtil.displayError("red minimum must not exceed " + totLength); redMinText.requestFocus(); redMinText.selectAll(); return false; } tmpStr = redFractionText.getText(); redFraction = Float.parseFloat(tmpStr); if (redFraction <= 0.0f) { MipavUtil.displayError("red fraction must be greater than zero"); redFractionText.requestFocus(); redFractionText.selectAll(); return false; } else if (redFraction > 1.0f) { MipavUtil.displayError("red fraction must not exceed one"); redFractionText.requestFocus(); redFractionText.selectAll(); return false; } tmpStr = greenMinText.getText(); greenMin = Integer.parseInt(tmpStr); if (greenMin < 1) { MipavUtil.displayError("green minimum must be at least 1"); greenMinText.requestFocus(); greenMinText.selectAll(); return false; } else if (greenMin > totLength) { MipavUtil.displayError("green minimum must not exceed " + totLength); greenMinText.requestFocus(); greenMinText.selectAll(); return false; } tmpStr = greenFractionText.getText(); greenFraction = Float.parseFloat(tmpStr); if (greenFraction <= 0.0f) { MipavUtil.displayError("green fraction must be greater than zero"); greenFractionText.requestFocus(); greenFractionText.selectAll(); return false; } else if (greenFraction > 1.0f) { MipavUtil.displayError("green fraction must not exceed one"); greenFractionText.requestFocus(); greenFractionText.selectAll(); return false; } tmpStr = blueMinText.getText(); blueMin = Integer.parseInt(tmpStr); if (blueMin <= 0) { MipavUtil.displayError("Number of blue pixels must be greater than 0"); blueMinText.requestFocus(); blueMinText.selectAll(); return false; } else if (blueMin > totLength) { MipavUtil.displayError("blue minimum must not exceed " + totLength); blueMinText.requestFocus(); blueMinText.selectAll(); return false; } if (oneButton.isSelected()) { greenRegionNumber = 1; } else if (twoButton.isSelected()) { greenRegionNumber = 2; } else if (threeButton.isSelected()) { greenRegionNumber = 3; } else { greenRegionNumber = 4; } twoGreenLevels = twoBox.isSelected(); tmpStr = blueValueText.getText(); blueBoundaryFraction = Float.parseFloat(tmpStr); if (blueBoundaryFraction < 0.0f) { MipavUtil.displayError("Blue boundary fraction cannot be less than 0.0"); blueValueText.requestFocus(); blueValueText.selectAll(); return false; } else if (blueBoundaryFraction > 1.0f) { MipavUtil.displayError("Blue boundary value cannot be greater than 1.0"); blueValueText.requestFocus(); blueValueText.selectAll(); return false; } blueSmooth = blueSmoothBox.isSelected(); tmpStr = interpolationText.getText(); interpolationDivisor = Float.parseFloat(tmpStr); if (interpolationDivisor <= 1.0f) { MipavUtil.displayError("Interpolation divisor must be greater than 1"); interpolationText.requestFocus(); interpolationText.selectAll(); return false; } return true; } // end setVariables()
/** * Use the GUI results to set up the variables needed to run the algorithm. * * @return <code>true</code> if parameters set successfully, <code>false</code> otherwise. */ private boolean setVariables() { String tmpStr; tmpStr = textXDim.getText(); try { subXDim = Integer.parseInt(tmpStr); } catch (NumberFormatException e) { MipavUtil.displayError("New XDIM string is not a valid integer"); textXDim.requestFocus(); textXDim.selectAll(); return false; } if (subXDim < 3) { MipavUtil.displayError("New XDIM must be at least 3"); textXDim.requestFocus(); textXDim.selectAll(); return false; } else if (subXDim > image.getExtents()[0]) { MipavUtil.displayError("New XDIM cannot exceed " + image.getExtents()[0]); textXDim.requestFocus(); textXDim.selectAll(); return false; } tmpStr = textYDim.getText(); try { subYDim = Integer.parseInt(tmpStr); } catch (NumberFormatException e) { MipavUtil.displayError("New YDIM string is not a valid integer"); textYDim.requestFocus(); textYDim.selectAll(); return false; } if (subYDim < 3) { MipavUtil.displayError("New YDIM must be at least 3"); textYDim.requestFocus(); textYDim.selectAll(); return false; } else if (subYDim > image.getExtents()[1]) { MipavUtil.displayError("New YDIM cannot exceed " + image.getExtents()[1]); textYDim.requestFocus(); textYDim.selectAll(); return false; } tmpStr = textNumberImages.getText(); try { numberOfImagesInMosaic = Integer.parseInt(tmpStr); } catch (NumberFormatException e) { MipavUtil.displayError("New numberOfImagesInMosaic string is not a valid integer"); textNumberImages.requestFocus(); textNumberImages.selectAll(); return false; } if (numberOfImagesInMosaic < 1) { MipavUtil.displayError("New numberOfImagesInMosaic must be at least 1"); textNumberImages.requestFocus(); textNumberImages.selectAll(); return false; } else if (numberOfImagesInMosaic > (subXDim * subYDim)) { MipavUtil.displayError("New numberOfImagesInMosaic cannot exceed (newXDim) * (newYDim)"); textNumberImages.requestFocus(); textNumberImages.selectAll(); return false; } displayLoc = NEW; return true; }