//===================================================== // Name: GLCM_Texture // Project: Gray Level Correlation Matrix Texture Analyzer // Version: 0.4 // // Author: Julio E.

Cabrera // Date: 06/10/05 // Comment: Calculates texture features based in Gray Level Correlati on Matrices // Changes since 0.1 version: The normalization constant (R in Haralic 's paper, pixelcounter here) // now ta es in account the fact that for each pair of p ixel you ta e in account there are two entries to the // grey level co-ocurrence matrix // Changes were made also in the Correlation parameter. Now this parameter is calculated according to Wal er's paper //===================================================== //===========imports=================================== import ij.*; import ij.gui.*; import ij.plugin.filter.PlugInFilter; import ij.process.*; import java.awt.*; import ij.plugin.PlugIn; import ij.text.*; import ij.measure.ResultsTable; //===========source==================================== public class GLCM_Texture implements PlugInFilter { static int step = 1; static String selectedStep = "0 degrees"; static boolean doIcalculateASM = true; static boolean doIcalculateContrast = true; static boolean doIcalculateCorrelation = true; static boolean doIcalculateIDM = true; static boolean doIcalculateEntropy = true; ResultsTable rt = ResultsTable.getResultsTable(); public int setup(String arg, ImagePlus imp) { if (imp!=null && !showDialog()) return DONE; rt.reset(); return DOES_8G+DOES_STACKS+SUPPORTS_MASKING; } public void run(ImageProcessor ip) { // This part get al the pixel values into the pixel [ ] array via the Image Proc essor byte [] pixels =(byte []) ip.getPixels(); int width = ip.getWidth(); Rectangle r = ip.getRoi(); //}

// The variable a holds the value of the pixel where the Image Processor is sitt ing its attention // The varialbe b holds the value of the pixel which is the neighbor to the pix el where the Image Processor is sitting its attention int a; int b; double pixelCounter=0; //============================================================================== ====================== // This part computes the Gray Level Correlation Matrix based in the step select ed by the user int offset, i; double [] [] glcm= new double [257][257]; if (selectedStep.equals("0 degrees")) { for (int y=r.y; y<(r.y+r.height); y++) { offset = y*width; for (int x=r.x; x<(r.x+r.width); x++)

{ i = offset + x; a = 0xff & pixel

s[i]; b = 0xff & (ip.getPixel (x+step, y)); glcm [a][b] +=1; glcm [b][a] +=1; pixelCounter +=2 ;

} } } //float [] [] glcmf= new float [257][257]; //for (a=0; a<257; a++) { // for (b=0; b<257;b++) { // glcmf[a][b]=(float)glcm[a][b]; // } //} //new ImagePlus("glcm", new FloatProcessor(glcmf)).show(); if (selectedStep.equals("90 degrees")) { for (int y=r.y; y<(r.y+r.height); y++) { offset = y*width; for (int x=r.x; x<(r.x+r.width); x++)

{ i = offset + x; a = 0xff & pixel

s[i]; b = 0xff &

(ip.getPixel (x, y-step)); glcm [a][b] +=1; glcm [b][a] +=1; pixelCounter +=2 ; } } } if (selectedStep.equals("180 degrees")) { for (int y=r.y; y<(r.y+r.height); y++) { offset = y*width; for (int x=r.x; x<(r.x+r.width); x++)

{ i = offset + x; a = 0xff & pixel

s[i]; b = 0xff & (ip.getPixel (x-step, y)); glcm [a][b] +=1; glcm [b][a] +=1; pixelCounter +=2 ; } } } if (selectedStep.equals("270 degrees")) { for (int y=r.y; y<(r.y+r.height); y++) { offset = y*width; for (int x=r.x; x<(r.x+r.width); x++)

{ i = offset + x; a = 0xff & pixel

s[i]; b = 0xff & (ip.getPixel (x, y+step)); glcm [a][b] +=1; glcm [b][a] +=1; pixelCounter +=2 ; } } } //============================================================================== ======================= // This part divides each member of the glcm matrix by the number of pixels. The number of pixels was stored in the pixelCounter variable // The number of pixels is used as a normalizing constant for (a=0; a<257; a++) {

for (b=0; b<257;b++) { glcm[a][b]=(glcm[a][b])/(pixelCounter); } } rt.incrementCounter(); int row = rt.getCounter()-1; //============================================================================== ======================= // This part calculates the angular second moment; the value is stored in asm if (doIcalculateASM==true){ double asm=0.0; for (a=0; a<257; a++) { for (b=0; b<257;b++) { asm=asm+ (glcm[a][b]*glcm[a][b]); } } rt.setValue("Angular Second Moment", row, asm); } //============================================================================== ======================= // This part calculates the contrast; the value is stored in contrast if (doIcalculateContrast==true){ double contrast=0.0; for (a=0; a<257; a++) { for (b=0; b<257;b++) { contrast=contrast+ (a-b)*(a-b)*(glcm[a][b]); } } rt.setValue("Contrast", row, contrast); } //============================================================================== ======================= //This part calculates the correlation; the value is stored in correlation // px [] and py [] are arrays to calculate the correlation // meanx and meany are variables to calculate the correlation // stdevx and stdevy are variables to calculate the correlation if (doIcalculateCorrelation==true){ //First step in the calculations will be to calculate px [] and py [] double correlation=0.0; double px=0; double py=0; double meanx=0.0; double meany=0.0; double stdevx=0.0; double stdevy=0.0; for (a=0; a<257;a++){ for (b=0; b <257; b++){ px=px+a*glcm [a][b];

py=py+b*glcm [a][b]; } }

// Now calculate the standard deviations for (a=0; a<257; a++){ for (b=0; b <257; b++){ stdevx=stdevx+(a -px)*(a-px)*glcm [a][b]; stdevy=stdevy+(b -py)*(b-py)*glcm [a][b]; } } // Now finally calculate the correlation parameter for (a=0; a<257; a++) { for (b=0; b<257;b++) { correlat ion=correlation+( (a-px)*(b-py)*glcm [a][b]/(stdevx*stdevy)) ; } } rt.setValue("Correlation", row, correlation);

} //============================================================================== ================= // This part calculates the inverse difference moment if (doIcalculateIDM==true){ double IDM=0.0; for (a=0; a<257; a++) { for (b=0; b<257;b++) { IDM=IDM+ (glcm[a][b]/(1+(a-b)*(a-b))) ; } } rt.setValue("Inverse Difference Moment } //============================================================================== ================= // This part calculates the entropy if (doIcalculateEntropy==true){ double entropy=0.0; for (a=0; a<257; a++) { for (b=0; b<257;b++) { if (glcm[a][b]==0) {} else {entropy=entropy-(glcm[a][b]*(Math.log(glcm [a][b])));} ", row, IDM);

} } rt.setValue("Entropy", row, entropy); }

double suma=0.0; for (a=0; a<257; a++) { for (b=0; b<257;b++) { suma= suma + glcm[a][b]; } } rt.setValue("Sum of all GLCM elements", row, suma); rt.show("Results"); //============================================================================== ================= // TextWindow tw = new TextWindow("Haralic 's texture features ", "", 400, 200); // tw.append(" "); // tw.append ("Total pixels analyzed "+ pixelCounter); // tw.append ( "Selected Step " + selectedStep); // tw.append ("Size of the step "+ step); // tw.append ("3 a la quinta "+ Math.pow(3,5)); } // This part is the implementation of the Dialog box (called gd here) boolean showDialog() { GenericDialog gd = new GenericDialog("Textural features based in GLCM. Version 0.4"); gd.addMessage("This plug-in calculates textural features\n" +" b ased in Gray Level Correlation Matrices."); gd.addNumericField ("Enter the size of the step in pixels", ste p, 0); String [] stepOptions={"0 degrees", "90 degrees", "180 degrees", "270 degrees"}; gd.addChoice("Select the direction of the step", stepOptions, se lectedStep); gd.addMessage("Chec in the following boxes\n" +"for the paramet ers you want to compute \n"+"and clic OK."); gd.addChec box("Angular Second Moment ", doIcalculateASM); gd.addChec box("Contrast ", doIcalculateContrast); gd.addChec box ("Correlation ", doIcalculateCorrelation); gd.addChec box ("Inverse Difference Moment ", doIcalculateIDM); gd.addChec box ("Entropy ", doIcalculateEntropy); gd.showDialog(); if (gd.wasCanceled()) return false; step=(int) gd.getNextNumber(); selectedStep=gd.getNextChoice ();

doIcalculateASM=gd.getNextBoolean (); doIcalculateContrast=gd.getNextBoolean (); doIcalculateCorrelation=gd.getNextBoolean(); doIcalculateIDM=gd.getNextBoolean(); doIcalculateEntropy=gd.getNextBoolean(); return true; } }