SE_MTF_2xNyquist.jar_ImageJ_

/************************************************************************* * Compilation: javac SE_MTF_2xNyquist.java * Execution: java SE_MTF_2xNyquist * * Calculates the Modulation Transfer Function (MTF) for an image of f rows and c columns of pixels selected. * For FFT requirements, uses a sample of power of 2 rows for both the calculation of the MTF and the SPP. * * Calcula la Función de Transferencia de Modulación (MTF) para una imagen de un tamaño f filas y * c columnas de pixels seleccionados. * Por requisitos de la fft, se utiliza una muestra de hileras potencia de 2 tanto para el calculo * de la MTF como de la SPP. * * * Limitations * ----------- * * TIFF image only * * *************************************************************************/ import ij.*; import ij.process.*; import ij.gui.*; import java.awt.*; import ij.plugin.*; import java.awt.event.*; import ij.plugin.PlugIn; import ij.plugin.frame.*; import ij.measure.*; import ij.io.*; import java.math.BigDecimal; import ij.text.*; import java.util.*; import java.lang.Object.*; import java.lang.Integer; import ij.process.ColorProcessor; import ij.process.ImageConverter; import ij.process.StackConverter; import ij.plugin.filter.*; import ij.plugin.filter.RGBStackSplitter; import ij.*; import ij.process.*; import ij.gui.*; import ij.measure.Calibration; import java.awt.*; import ij.plugin.FFT.*; import java.util.EventObject; public class SE_MTF_2xNyquist implements PlugIn,ActionListener,WindowListener,DialogListener{ Frame frame; ImagePlus imp,impOriginal; ProfilePlot plotESF; Plot plotResult; int k; int i; int selecWidth; int selecHeight; int sppLength; double[] ESFLinea; double[][] ESFArray; double[][] LSFArray; double[] Vector; double[][] Array; double[][] ArrayF; double[][] ESFArrayF; double[][] LSFArrayF; double[][] PosMax; double[]ESFVector; double[]LSFVector; double[]LSFDVector; double[]MTFVector; double[]SPPVector; double[]Max; String title; Roi roi; int optWidth; int optHeight; int sChannel; int sFrequnits; int type; boolean isStack; int roiType; int sSize; boolean cancel; int bit; int yMax; double mmSensors=0.0; int nPhotodetectors=0; double ny=1; // Message that asks the user what to do public void run(String arg){ frame = new Frame("SE_MTF"); frame.setLayout(new GridBagLayout()); frame.setBounds(100, 100, 450, 100); Button button1 = new Button("Generate MTF"); button1.addActionListener(this); GridBagConstraints c = new GridBagConstraints(); c.gridx = 1; c.gridy = 0; c.gridwidth = 1; c.gridwidth = 1; c.anchor = GridBagConstraints.NORTH; c.insets.top = 0; c.insets.left = 0; c.insets.bottom= 0; c.insets.right = 0; c.weightx = 0; c.weighty = 0; c.fill = GridBagConstraints.NONE; ((GridBagLayout)frame.getLayout()).setConstraints(button1, c); frame.add(button1); frame.validate(); frame.show(); frame.setBackground(Color.lightGray); frame.setResizable(false); frame.setLocation(0,0); frame.addWindowListener(this); } public void actionPerformed(ActionEvent e) { String command = e.getActionCommand(); if (command==null){ return; } if (command.equals("Generate MTF")){ cancel=false; openImage(); if (cancel==false){ options(); } if (cancel==false){ generateESFArray("ESF Plot",imp,roi); generateLSFArray("LSF Plot",ESFArray); calculateMax(); ESFArrayF=alignArray(ESFArray); if (cancel==false){ LSFArrayF=alignArray(LSFArray); } if (cancel==false){ ESFVector=averageVector(ESFArrayF); } if (cancel==false){ LSFVector=averageVector(LSFArrayF); int aura = (LSFVector.length * 2); LSFDVector = new double [aura]; int j = 0; int aura2 = (LSFVector.length); for(i=0;i<(LSFDVector.length-3); i++){ if(i % 2 == 0) { LSFDVector[i]= LSFVector[j]; j=j+1; }else { LSFDVector[i]= ((0.375*LSFVector[(j-1)]) + (0.75*LSFVector[(j)]) - (0.125*LSFVector[(j+1)])); } } LSFDVector[i] = ((LSFVector[j-1] + LSFVector[j])*0.5); LSFDVector[i+1] = LSFVector[j]; LSFDVector[i+2] = LSFVector[j]; int indexMax = 0; double valorMax = LSFDVector[0]; for(int i=0;i<LSFDVector.length;i++){ if(valorMax < LSFDVector[i]){ indexMax = i; valorMax = LSFDVector[i]; } } i=indexMax; LSFDVector[i-1]=((LSFDVector[i-2] + LSFDVector[i])*0.5); MTFVector=fftConversion(LSFDVector, "MTF"); Max=obtenerMax(); SPPVector=fftConversion(Max,"SPP"); //-****************************************************************-S'hauria d'intentar que no quedéssin superposats, sinó en escala, cada un 10 més avall generatePlot(MTFVector,"MTF"); generatePlot(LSFVector,"LSF"); generatePlot(ESFVector,"ESF"); generatePlot(SPPVector,"SPP"); } } cleanImage(); } } public void openImage(){ boolean opButton=true; imp = WindowManager.getCurrentImage(); if (imp==null){ IJ.showMessage("Error","There are no images open\nProcess canceled"); cancel=true; } title=imp.getTitle(); if (cancel==false){ type=imp.getType(); switch(type){ case ImagePlus.GRAY8:{ isStack=false; yMax=255; } break; case ImagePlus.GRAY16:{ isStack=false; yMax=65535; } break; case ImagePlus.GRAY32:{ isStack=false; yMax=2147483647; } break; case ImagePlus.COLOR_256:{ isStack=true; yMax=255; } break; case ImagePlus.COLOR_RGB:{ isStack=true; yMax=255; } break; default: yMax=255; } //Get the selection roi = imp.getRoi(); if (roi==null) { imp.setRoi(0, 0, imp.getWidth(), imp.getHeight()); roi = imp.getRoi(); opButton=IJ.showMessageWithCancel("Warning","All image selected"); if (opButton==false) cancel=true; } } if (cancel==false){ //Rectangular selection roiType = roi.getType(); if (!(roi.isLine() || roiType==Roi.RECTANGLE)) { IJ.showMessage("Error","Line or rectangular selection required\nProcess canceled"); cancel=true; } } } void cleanImage(){ imp.killRoi(); } void generateStack(){ if (isStack==true && sChannel!=3){ ImageConverter ic = new ImageConverter(imp); ic.convertToRGBStack(); ImageStack is; is=imp.getStack(); } } void options(){ GenericDialog gd = new GenericDialog("MTF - Options",frame); //User can choose the units gd.addDialogListener(this); String[]frequnits=new String[3]; frequnits[0]="Absolute (lp/mm)"; frequnits[1]="Relative (cycles/pixel)"; frequnits[2]="Line widths per picture height (LW/PH)"; gd.addChoice("Frequency units:",frequnits,frequnits[1]); //Input data gd.addNumericField("Sensor size (mm): ",mmSensors,1); gd.addNumericField("Number of photodetectors: ",nPhotodetectors,0); ((Component) gd.getNumericFields().get(0)).setEnabled(false); ((Component) gd.getNumericFields().get(1)).setEnabled(false); //The user can choose the sample width String[]sampleSize=new String[5]; sampleSize[0]="32"; sampleSize[1]="64"; sampleSize[2]="128"; sampleSize[3]="256"; sampleSize[4]="512"; gd.addChoice("Sample size (pixels):",sampleSize,sampleSize[0]); //If is a greyscale image there is no options avaliable if (isStack==false){ gd.addMessage("This is a greyscale image, no optio