package ppmrmn; import java.awt.*; import java.applet.*; import java.awt.event.*; //30 janvier 2004 public class SolomonEkoXtalJDK118 extends Graph implements Runnable { private int numVars = 3, //number of parameters to be fitted with simplex nbou = 1, //1 + number of pulse duration increment ligne = 2, //transition position in the density matrix colonne = 2, ligneST = 1; private boolean stopFit = false, showCurve = true; private double coeff = 5, //for signal normalisation use pop = 2*Math.sqrt(3), //for signal normalisation use dureePremiere = 0, //inital pulse duration dureePas = 1, //increment of the pulse duration dureeFin = 1, //final pulse duration dureePremiere1 = 0, dureePremiere2 = 0, amplitude[] = {0.0}, //FID intensity amplitudeReal[] = {0.0}, //real part of the FID intensity amplitudeImag[] = {0.0}, //imaginary part of the FID intensity listExpIntensity[] = {0.0}, //experimental intensity /*matEstimation[][] is the matrix for the initial guess values of fitting parameters*/ matEstimation[][] = new double[numVars + 1][numVars]; //같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같 // Dimensions 700LX390H of the applet to be introduced in its WEB page //같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같같 private int hautLB = 20, //label height hautBouton = 30, //button height hautPanel = 390; //panel height //PanelSpin includes panelSpinLabel, panelSpinData, // panelSpinData2, and panelSpinUnit Panel panelSpin = new Panel(); Panel panelSpinLabel = new Panel(); Panel panelSpinData = new Panel(); Panel panelSpinData2 = new Panel(); Panel panelSpinUnit = new Panel(); //panelTransition includes panelSimulation, panelCheckgroup, // and scrollPaneSimulation Panel panelTransition = new Panel(); Panel panelSimulation = new Panel(); Panel panelCheckgroup = new Panel(); ScrollPane scrollPaneSimulation = new ScrollPane(); //PanelFit includes panelFitEstim, panelFitBouton, and panelBlanc Panel panelFit = new Panel(); Panel panelFitEstim = new Panel(); Panel panelFitBouton = new Panel(); Panel panelBlanc = new Panel(); Choice choicePulseSequence = new Choice(); Choice choiceSpin = new Choice(); Choice choiceSequence = new Choice(); Choice choiceTransition = new Choice(); Choice choiceEkoPosition = new Choice(); Choice choiceSimplex = new Choice(); Button buttonRun = new Button("Run"); Button buttonFit = new Button("Fit"); Button buttonGraph = new Button("DeactivateGraph"); Button buttonPrevious = new Button("Previous"); CheckboxGroup checkboxgroup = new CheckboxGroup(); Checkbox checkboxReal = new Checkbox("real part", checkboxgroup, false); Checkbox checkboxImag = new Checkbox("imaginary part", checkboxgroup, true); Label labelDate = new Label("30-01-04"); Label labelPulse = new Label("Pulse"); Label labelDuree = new Label("Length (탎)"); Label labelLine = new Label("Line"); Label labelIntensite = new Label("Intensity"); Label labelTransition = new Label("Nature of the echo:"); Label labelPosition = new Label("Position of the echo:"); Label labelExperimental = new Label("Experimental"); Label labelExpIntensite = new Label("Intensity"); Label labelAdvice = new Label("Deactivate graph speeds up fitting!!!"); TextField textFieldOmegaQ = new TextField("0.0"); TextField textFieldOmegaRF = new TextField("50.0"); TextField textFieldDerniereDuree = new TextField("10.0"); TextField textFieldPas = new TextField("0.5"); TextField textFieldPremiereDuree = new TextField("5.0"); TextField textFieldDerniereDuree2 = new TextField("10.0"); TextField textFieldPas2 = new TextField("0.5"); TextField textFieldPremiereDuree2 = new TextField("0"); TextField textFieldOmegaQEst = new TextField("5"); TextField textFieldOmegaRFEst = new TextField("55"); //100 rows, 7 columns, 2 = SCROLLBARS_NONE TextArea textAreaDuree = new TextArea("", 100, 7, TextArea.SCROLLBARS_NONE); /*imaginary part of the echo amplitude*/ TextArea textAreaIntensite = new TextArea("", 100, 7, TextArea.SCROLLBARS_NONE); /*real part of the echo amplitude*/ TextArea textAreaIntensiteReel = new TextArea("", 100, 7, TextArea.SCROLLBARS_NONE); TextArea textAreaExpIntensite = new TextArea(12, 7); //experimental intensity TextArea textAreaParameter = new TextArea(5, 7); //fitting parameters /**Construct the applet*/ public SolomonEkoXtalJDK118() { } /**Initialize the applet*/ public void init() { try { jbInit(); } catch(Exception e) { e.printStackTrace(); } } /**Component initialization*/ private void jbInit() throws Exception { setBackground(Color.white); setLayout(null); buttonGraph.setBounds(75, 355, 150, hautBouton); add(buttonGraph); buttonGraph.setVisible(false); labelAdvice.setBounds(15, 320, 220, hautBouton); add(labelAdvice); labelAdvice.setFont(new Font("TimesRoman", Font.PLAIN, 10)); //necessary for WEB browsers other than IE5.5: labelAdvice.setBackground(Color.pink); labelAdvice.setVisible(false); //***panelSpin width + 100 panelSpin.setBounds(0, 0, 260, hautPanel); add(panelSpin); panelSpinLabel.setBounds(0, 0, 90, hautPanel-3); panelSpin.add(panelSpinLabel); panelSpinData.setBounds(90, 0, 60, hautPanel-3); panelSpin.add(panelSpinData); panelSpinData2.setBounds(150, 0, 60, hautPanel-3); panelSpin.add(panelSpinData2); panelSpinUnit.setBounds(210, 0, 50, hautPanel-3); panelSpin.add(panelSpinUnit); //***panelTransition width + 100 panelTransition.setBounds(260, 0, 220, hautPanel); add(panelTransition); //***panelFit width + 100 panelFit.setBounds(480, 0, 220, hautPanel); add(panelFit); panelFit.setVisible(false); //**************************** panelSpin ********************************* panelSpin.setBackground(Color.pink); panelSpin.setLayout(null); panelSpin.setFont(new Font("TimesRoman", Font.PLAIN, 12)); choicePulseSequence.add("X-X"); choicePulseSequence.add("Y-X"); choiceSpin.add("3/2"); choiceSpin.add("5/2"); choiceSpin.add("7/2"); choiceSpin.add("9/2"); choiceSequence.add("A(p1)B()"); choiceSequence.add("A()B(p2)"); choiceSequence.select(1); //8 lines, 1 column, 0 horizontal space, and 10 vertical spaces panelSpinLabel.setLayout(new GridLayout(8, 1, 0, 10)); panelSpinData.setLayout(new GridLayout(8, 1, 0, 10)); panelSpinData2.setLayout(new GridLayout(8, 1, 0, 10)); panelSpinUnit.setLayout(new GridLayout(8, 1, 0, 10)); panelSpinLabel.setBackground(Color.pink); panelSpinData.setBackground(Color.pink); panelSpinData2.setBackground(Color.pink); panelSpinUnit.setBackground(Color.pink); panelSpinLabel.add(choicePulseSequence); panelSpinData.add(new Label("")); panelSpinData2.add(labelDate); panelSpinUnit.add(new Label("")); panelSpinLabel.add(new Label(" Spin")); panelSpinData.add(choiceSpin); panelSpinData2.add(new Label("")); panelSpinUnit.add(new Label("")); panelSpinLabel.add(new Label(" RF field")); panelSpinData.add(textFieldOmegaRF); panelSpinData2.add(new Label(" kHz")); panelSpinUnit.add(new Label("")); panelSpinLabel.add(new Label(" OmegaQ")); panelSpinData.add(textFieldOmegaQ); panelSpinData2.add(new Label(" kHz")); panelSpinUnit.add(new Label("")); panelSpinLabel.add(choiceSequence); panelSpinData.add(new Label("Pulse-1")); panelSpinData2.add(new Label("Pulse-2")); panelSpinUnit.add(new Label("")); panelSpinLabel.add(new Label(" MinLength")); panelSpinData.add(textFieldPremiereDuree); panelSpinData2.add(textFieldPremiereDuree2); panelSpinUnit.add(new Label(" 탎")); panelSpinLabel.add(new Label(" MaxLength")); panelSpinData.add(textFieldDerniereDuree); panelSpinData2.add(textFieldDerniereDuree2); panelSpinUnit.add(new Label(" 탎")); panelSpinLabel.add(new Label(" Step")); panelSpinData.add(textFieldPas); panelSpinData2.add(textFieldPas2); panelSpinUnit.add(new Label(" 탎")); textFieldDerniereDuree.setVisible(false); textFieldPas.setVisible(false); //************************** panelTransition ***************************** panelTransition.setBackground(Color.pink); panelTransition.setLayout(null); panelTransition.setFont(new Font("TimesRoman", Font.PLAIN, 12)); //labels of the simulated line intensity labelPulse.setBounds(15, 7, 85, hautLB); panelTransition.add(labelPulse); labelDuree.setBounds(15, 27, 85, hautLB); panelTransition.add(labelDuree); labelLine.setBounds(100, 7, 85, hautLB); panelTransition.add(labelLine); labelIntensite.setBounds(100, 27, 100, hautLB); panelTransition.add(labelIntensite); //simulation scroll pane panelSimulation.setLayout(new GridLayout(1, 2)); panelSimulation.add(textAreaDuree); panelSimulation.add(textAreaIntensite); textAreaDuree.setEditable(false); textAreaIntensite.setEditable(false); scrollPaneSimulation.setBounds(10, 50, 180, 150); scrollPaneSimulation.add(panelSimulation); panelTransition.add(scrollPaneSimulation); //imaginary and real echo amplitude check group panel panelCheckgroup.setBounds(110, 215, 110, 30); panelTransition.add(panelCheckgroup); panelCheckgroup.setBackground(Color.pink); panelCheckgroup.setLayout(new GridLayout(2, 1)); //2 lines, 1 column panelCheckgroup.add(checkboxReal); panelCheckgroup.add(checkboxImag); checkboxReal.setBackground(Color.pink); checkboxImag.setBackground(Color.pink); panelCheckgroup.setVisible(false); //transition choice labelTransition.setBounds(10, 250, 180, hautLB); panelTransition.add(labelTransition); choiceTransition.add("Satellite Transitions"); choiceTransition.setBounds(10, 275, 180, 20); panelTransition.add(choiceTransition); //echo position choice labelPosition.setBounds(10, 300, 180, hautLB); panelTransition.add(labelPosition); choiceEkoPosition.add("tau2"); choiceEkoPosition.setBounds(10, 325, 180, 20); panelTransition.add(choiceEkoPosition); buttonRun.setBounds(50, 355, 100, hautBouton); panelTransition.add(buttonRun); //**************************** panelFit ********************************** panelFit.setBackground(Color.orange); panelFit.setLayout(null); panelFit.setFont(new Font("TimesRoman", Font.PLAIN, 12)); labelExperimental.setBounds(10, 7, 100, hautLB); panelFit.add(labelExperimental); labelExpIntensite.setBounds(10, 27, 100, hautLB); panelFit.add(labelExpIntensite); textAreaExpIntensite.setBounds(10, 50, 80, 160); panelFit.add(textAreaExpIntensite); textAreaParameter.setBounds(10, 212, 200, 140); panelFit.add(textAreaParameter); panelFitBouton.setBounds(10, 355, 200, hautBouton); panelFit.add(panelFitBouton); panelFitBouton.setLayout(new GridLayout(1, 2)); panelFitBouton.add(buttonPrevious); panelFitBouton.add(buttonFit); buttonPrevious.setEnabled(false); choiceSimplex.add("1.1"); choiceSimplex.add("1.2"); choiceSimplex.add("1.3"); choiceSimplex.add("1.4"); choiceSimplex.select(2); panelFitEstim.setBounds(110, 5, 100, 206); //5 lines, 2 columns, zero horizontal and vertical spaces panelFitEstim.setLayout(new GridLayout(5, 2, 0, 0)); panelFit.add(panelFitEstim); panelFitEstim.setBackground(Color.orange); panelFitEstim.setFont(new Font("TimesRoman", Font.PLAIN, 12)); panelFitEstim.add(new Label("Simplex:")); panelFitEstim.add(choiceSimplex); panelFitEstim.add(new Label("RF field:")); panelFitEstim.add(new Label("")); panelFitEstim.add(textFieldOmegaRFEst); panelFitEstim.add(new Label(" kHz")); panelFitEstim.add(new Label("OmegaQ:")); panelFitEstim.add(new Label("")); panelFitEstim.add(textFieldOmegaQEst); panelFitEstim.add(new Label(" kHz")); //valeurs exemples String s5 = 0.0+"\n"+-0.01088+"\n"+-0.04087+"\n"+-0.08264+"\n"; s5 += -0.12578+"\n"+-0.1591+"\n"+-0.17312+"\n"+-0.16219+"\n"+-0.12578+"\n"; s5 += -0.06867+"\n"+0.0+"\n"+0.06867+"\n"+0.12578+"\n"+0.16219+"\n"; s5 += 0.17312+"\n"+0.1591+"\n"+0.12578+"\n"+0.08264+"\n"; s5 += 0.04087+"\n"+0.01088+"\n"+0.0+"\n"; textAreaExpIntensite.setText(s5); }//end of JbInit() private void solomonEkoSequence(int i, Nmr myNmrTmp, double tp1, double tp2, RealMat matHD, RealMat matR, RealMat matRt, RealMat matR2) { ComplexMat matHH, matHHC, matC1, matC2, matC3, matC4, matC5, matC6, matC7, matC8, matC9, matC10, matCz; //first +x pulse matHH = myNmrTmp.matriceHamilton(matHD, tp1); matHHC = myNmrTmp.matConjugue(matHH); matC1 = myNmrTmp.mult(matR2, matHH); //action of the first +x pulse matC2 = myNmrTmp.mult(matHHC, matC1); //action of the first +x pulse matC3 = myNmrTmp.mult(matC2, matRt); //back to the matC4 = myNmrTmp.mult(matR, matC3); //rotating frame if (choicePulseSequence.getSelectedIndex() == 1) matC4 = myNmrTmp.matRotation(matC4, Math.PI/2); matCz = myNmrTmp.matQuatre(matC4, ligne, colonne); //action of the second +x pulse matC5 = myNmrTmp.mult(matCz, matR); //return to the PAS of matH matC6 = myNmrTmp.mult(matRt, matC5); //return to the PAS of matH matHH = myNmrTmp.matriceHamilton(matHD, tp2); matHHC = myNmrTmp.matConjugue(matHH); matC7 = myNmrTmp.mult(matC6, matHH); //action of the second +x pulse matC8 = myNmrTmp.mult(matHHC, matC7); //action of the second +x pulse matC9 = myNmrTmp.mult(matC8, matRt); //back to the matC10 = myNmrTmp.mult(matR, matC9); //rotating frame amplitudeImag[i] = (pop/coeff)*matC10.im[ligneST][ligneST - 1]; amplitudeReal[i] = (pop/coeff)*matC10.re[ligneST][ligneST - 1]; if (checkboxReal.getState()) { for (int ii = 0; ii < nbou + 1; ii++) amplitude[ii] = amplitudeReal[ii]; } else { for (int ii = 0; ii < nbou + 1; ii++) amplitude[ii] = amplitudeImag[ii]; } }//end of solomonEkoSequence() private void calculIntensite(double omegaQTmp, double omegaRFTmp) { RealMat matH, matHD, matR, matRt, matIz, matR1, matR2; double tp; //OmegaQTmp and omegaRFTmp in kHz unit Nmr myNmr = new Nmr(omegaQTmp, omegaRFTmp); //OmegaQ and omegaRF in radian/second unit for (int i = 0; i < nbou + 1; i++) { amplitudeReal[i] = 0.0; amplitudeImag[i] = 0.0; }//clear //first x pulse matH = myNmr.dataIn(); //find eigenvectors and eigenvalues of matH matHD = myNmr.jacRot(matH); //matHD is the eigenvalue matrix of matH matR = myNmr.getMatR(); //matR is the eigenvector matrix of matH matRt = RealMat.transpose(matR); //matRt is the transposed matrix of matR matIz = myNmr.matriceIz(); //matrix of spin operator Iz matR1 = myNmr.mult(matIz, matR); //matrix of Iz expressed in the PAS matR2 = myNmr.mult(matRt, matR1); //of matH switch (choiceSequence.getSelectedIndex()) { case 0: //A(p1)B() for (int i = 0; i <= nbou; i++) { tp = dureePremiere + i*dureePas; solomonEkoSequence(i, myNmr, tp, dureePremiere2, matHD, matR, matRt, matR2); } break; case 1: //A()B(p2) for (int i = 0; i <= nbou; i++) { tp = dureePremiere + i*dureePas; solomonEkoSequence(i, myNmr, dureePremiere1, tp, matHD, matR, matRt, matR2); } break; }//end of switch }//end of calculIntensite() private void afficheTransition() { choiceTransition.removeAll(); //clear choiceEkoPosition.removeAll(); //clear switch (choiceSpin.getSelectedIndex()) { case 0: //spin 3/2 choiceTransition.add("Satellite Transitions"); choiceEkoPosition.add("tau2"); break; case 1: //spin 5/2 choiceTransition.add("Inner Satellite Transitions"); choiceTransition.add("Outer Satellite Transitions"); choiceEkoPosition.add("tau2"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("3*tau2"); break; case 2: //spin 7/2 choiceTransition.add("Inner Satellite Transitions"); choiceTransition.add("Medium Satellite Transitions"); choiceTransition.add("Outer Satellite Transitions"); choiceEkoPosition.add("tau2"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("3*tau2-1Q"); choiceEkoPosition.add("3*tau2-nQ"); choiceEkoPosition.add("5*tau2"); choiceEkoPosition.add("6*tau2"); break; case 3: //spin 9/2 choiceTransition.add("Inner Satellite Transitions"); choiceTransition.add("Medium Satellite Transitions"); choiceTransition.add("Next Satellite Transitions"); choiceTransition.add("Outer Satellite Transitions"); choiceEkoPosition.add("tau2"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("3*tau2-1Q"); choiceEkoPosition.add("3*tau2-nQ"); choiceEkoPosition.add("4*tau2"); choiceEkoPosition.add("5*tau2"); choiceEkoPosition.add("6*tau2"); choiceEkoPosition.add("7*tau2"); choiceEkoPosition.add("9*tau2"); choiceEkoPosition.add("10*tau2"); break; }//end of switch choiceTransition.select(0); choiceEkoPosition.select(0); }//end of afficheTransition() private void eko3sur2() { ligne = 0; colonne = 1; } private void eko5sur2() { switch (choiceEkoPosition.getSelectedIndex()) { case 0: ligne = 1; colonne = 2; break; case 1: ligne = 0; colonne = 1; break; case 2: ligne = 0; colonne = 2; break; } } private void eko7sur2() { switch (choiceEkoPosition.getSelectedIndex()) { case 0: ligne = 2; colonne = 3; break; case 1: ligne = 1; colonne = 2; break; case 2: ligne = 0; colonne = 1; break; case 3: ligne = 1; colonne = 3; break; case 4: ligne = 0; colonne = 2; break; case 5: ligne = 0; colonne = 3; break; } } private void eko9sur2() { switch (choiceEkoPosition.getSelectedIndex()) { case 0: ligne = 3; colonne = 4; break; case 1: ligne = 2; colonne = 3; break; case 2: ligne = 1; colonne = 2; break; case 3: ligne = 2; colonne = 4; break; case 4: ligne = 0; colonne = 1; break; case 5: ligne = 1; colonne = 3; break; case 6: ligne = 1; colonne = 4; break; case 7: ligne = 0; colonne = 2; break; case 8: ligne = 0; colonne = 3; break; case 9: ligne = 0; colonne = 4; break; } } private void normalisationSignal() { switch (choiceSpin.getSelectedIndex()) { case 0: //spin 3/2 ComplexMat.setTailleMatrice (4); coeff = 5.0; ligneST = 1; pop = 2*Math.sqrt(3); eko3sur2(); break; case 1: //spin 5/2 ComplexMat.setTailleMatrice (6); coeff = 35.0/2.0; switch (choiceTransition.getSelectedIndex()) { case 0: ligneST = 2; pop = 2*Math.sqrt(8); break;//is case 1: ligneST = 1; pop = 2*Math.sqrt(5); break;//os } eko5sur2(); break; case 2: //spin 7/2 ComplexMat.setTailleMatrice (8); coeff = 42.0; switch (choiceTransition.getSelectedIndex()) { case 0: ligneST = 3; pop = 2*Math.sqrt(15); break;//is case 1: ligneST = 2; pop = 2*Math.sqrt(12); break;//ms case 2: ligneST = 1; pop = 2*Math.sqrt(7); break;//os } eko7sur2(); break; case 3: //spin 9/2 ComplexMat.setTailleMatrice (10); coeff = 165.0/2.0; switch (choiceTransition.getSelectedIndex()) { case 0: ligneST = 4; pop = 2*Math.sqrt(24); break;//is case 1: ligneST = 3; pop = 2*Math.sqrt(21); break;//ms case 2: ligneST = 2; pop = 2*Math.sqrt(16); break;//nm case 3: ligneST = 1; pop = 2*Math.sqrt(9); break;//os } eko9sur2(); break; }//end of switch }//end of normalisationSignal() /**Start the applet*/ public void start() { //********* //buttonRun //********* buttonRun.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { double milli = 0.001; normalisationSignal(); /*transform pulse durations from microsecond unit to millisecond unit, because the interactions are in kHz unit*/ switch (choiceSequence.getSelectedIndex()) { case 0: //A(p1)B(), V-F dureeFin = milli*Double.valueOf(textFieldDerniereDuree .getText()).doubleValue(); dureePremiere = milli*Double.valueOf(textFieldPremiereDuree .getText()).doubleValue(); dureePas = milli*Double.valueOf(textFieldPas .getText()).doubleValue(); dureePremiere2 = milli*Double.valueOf(textFieldPremiereDuree2 .getText()).doubleValue(); break; case 1: //A()B(p2), F-V dureePremiere1 = milli*Double.valueOf(textFieldPremiereDuree .getText()).doubleValue(); dureeFin = milli*Double.valueOf(textFieldDerniereDuree2 .getText()).doubleValue(); dureePremiere = milli*Double.valueOf(textFieldPremiereDuree2 .getText()).doubleValue(); dureePas = milli*Double.valueOf(textFieldPas2 .getText()).doubleValue(); break; }//end of switch nbou = (int)((dureeFin - dureePremiere)/dureePas); amplitude = new double[nbou + 1]; amplitudeReal = new double[nbou + 1]; amplitudeImag = new double[nbou + 1]; listExpIntensity = new double[nbou + 1]; calculIntensite(Double.valueOf(textFieldOmegaQ.getText()).doubleValue(), Double.valueOf(textFieldOmegaRF.getText()).doubleValue()); scrollPaneSimulation.setScrollPosition(0, 0); //top part of scrollPane afficheValeur(); panelFit.setVisible(true); panelFitEstim.setVisible(true); panelCheckgroup.setVisible(true); } }); //********* //buttonFit //********* buttonFit.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { /*thread for starting the simplex procedure with run() and for plotting the fitting curves*/ Thread th = null; if (buttonFit.getLabel() == "Fit") { //convert experimental intensities into numbers String s = textAreaExpIntensite.getText(), s1 = ""; int spaceAt = 0, startingForm = 0, ip = 0; while (true) { spaceAt = s.indexOf("\n", startingForm); if (spaceAt == -1) break; s1 = s.substring(startingForm, spaceAt); listExpIntensity[ip] = Double.valueOf(s1).doubleValue(); startingForm = spaceAt + 1; ip++; } if (ip != nbou + 1) { //check the number of data textAreaParameter.setText(""); textAreaParameter.append("The number of experimental" + "\n"); textAreaParameter.append("intensities is wrong!!!" + "\n"); textAreaParameter.append("May be type enter key" + "\n"); textAreaParameter.append("for the last intensity data!!!"); } else { //start fitting panelFit.setLocation(300, 0); setBackground(Color.pink); panelTransition.setVisible(false); panelSpin.setVisible(false); panelBlanc.setBounds(520 ,0, 240, hautPanel); add(panelBlanc); panelBlanc.setVisible(true); panelBlanc.setBackground(Color.white); buttonFit.setLabel("StopFit"); buttonPrevious.setEnabled(false); textAreaParameter.setText(""); double alpha = Double.valueOf(choiceSimplex.getSelectedItem()).doubleValue(); double val1 = Double.valueOf(textFieldOmegaQEst.getText()).doubleValue(); double val2 = Double.valueOf(textFieldOmegaRFEst.getText()).doubleValue(); //find the maximum values in listExpIntensity[] and in amplitude[] double maxExp = 0, maxCal = 0; for (int i = 0; i < nbou + 1; i++) if (Math.abs(listExpIntensity[i]) > maxExp) maxExp = Math.abs(listExpIntensity[i]); for (int i = 0; i < nbou + 1; i++) if (Math.abs(amplitude[i]) > maxCal) maxCal = Math.abs(amplitude[i]); double val3 = maxExp/maxCal; //scaling choiceSimplex.setEnabled(false); textFieldOmegaRFEst.setEnabled(false); textFieldOmegaQEst.setEnabled(false); textAreaExpIntensite.setEnabled(false); normalisationSignal(); //initial parameters for simplex procedure matEstimation[0][0] = val1; matEstimation[0][1] = val2; matEstimation[0][2] = val3; matEstimation[1][0] = alpha*val1; matEstimation[1][1] = val2; matEstimation[1][2] = val3; matEstimation[2][0] = val1; matEstimation[2][1] = alpha*val2; matEstimation[2][2] = val3; matEstimation[3][0] = val1; matEstimation[3][1] = val2; matEstimation[3][2] = alpha*val3; th = new Thread(SolomonEkoXtalJDK118.this); th.start(); buttonGraph.setLabel("DeactivateGraph"); buttonGraph.setVisible(true); buttonGraph.setEnabled(true); labelAdvice.setVisible(true); showCurve = true; stopFit = false; } } else { //stop fitting stopFit = true; th = null; buttonPrevious.setEnabled(true); buttonFit.setLabel("Fit"); choiceSimplex.setEnabled(true); textFieldOmegaRFEst.setEnabled(true); textFieldOmegaQEst.setEnabled(true); textAreaExpIntensite.setEnabled(true); buttonGraph.setEnabled(false); labelAdvice.setVisible(false); } } }); //************** //buttonPrevious //************** buttonPrevious.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { panelSpin.setVisible(true); panelBlanc.setVisible(false); //***panelTransition and panelFit widths + 100 panelTransition.setLocation(260, 0); panelTransition.setVisible(true); panelFit.setLocation(480, 0); buttonPrevious.setEnabled(false); setBackground(Color.white); panelSpin.setBackground(Color.pink); panelFit.setBackground(Color.orange); panelTransition.setBackground(Color.pink); buttonGraph.setVisible(false); buttonFit.setLabel("Fit"); buttonRun.setEnabled(true); } }); //*********** //buttonGraph //*********** buttonGraph.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { if (buttonGraph.getLabel() == "DeactivateGraph") { showCurve = false; buttonGraph.setLabel("ActivateGraph"); labelAdvice.setVisible(false); } else { showCurve = true; buttonGraph.setLabel("DeactivateGraph"); labelAdvice.setVisible(true); } } }); //************ //checkboxReal //************ checkboxReal.addItemListener(new java.awt.event.ItemListener() { public void itemStateChanged(ItemEvent e) { for (int i = 0; i < nbou + 1; i++) amplitude[i] = amplitudeReal[i]; afficheValeur(); } }); //************ //checkboxImag //************ checkboxImag.addItemListener(new java.awt.event.ItemListener() { public void itemStateChanged(ItemEvent e) { for (int i = 0; i < nbou + 1; i++) amplitude[i] = amplitudeImag[i]; afficheValeur(); } }); //********** //choiceSpin //********** choiceSpin.addItemListener(new java.awt.event.ItemListener() { public void itemStateChanged(ItemEvent e) { textAreaIntensite.setText(""); //clear intensity textAreaDuree.setText(""); //clear pulse duration panelCheckgroup.setVisible(false); afficheTransition(); } }); //************** //choiceSequence //************** choiceSequence.addItemListener(new java.awt.event.ItemListener() { public void itemStateChanged(ItemEvent e) { switch (choiceSequence.getSelectedIndex()) { //A(p1)B(), V-F case 0: textFieldPremiereDuree.setVisible(true); textFieldDerniereDuree.setVisible(true); textFieldPas.setVisible(true); textFieldPremiereDuree2.setVisible(true); textFieldDerniereDuree2.setVisible(false); textFieldPas2.setVisible(false); break; //A()B(p2), F-V case 1: textFieldPremiereDuree.setVisible(true); textFieldDerniereDuree.setVisible(false); textFieldPas.setVisible(false); textFieldPremiereDuree2.setVisible(true); textFieldDerniereDuree2.setVisible(true); textFieldPas2.setVisible(true); break; } } }); //********************* //choicePulseSequence //********************* choicePulseSequence.addItemListener(new java.awt.event.ItemListener() { public void itemStateChanged(ItemEvent e) { textAreaIntensite.setText(""); //clear textAreaDuree.setText(""); //clear panelCheckgroup.setVisible(false); } }); //**************** //choiceTransition //**************** choiceTransition.addItemListener(new java.awt.event.ItemListener() { public void itemStateChanged(ItemEvent e) { choiceEkoPosition.removeAll(); switch (choiceSpin.getSelectedIndex()) { case 0: //spin 3/2 choiceEkoPosition.add("tau2"); break; case 1: //spin 5/2 switch (choiceTransition.getSelectedIndex()) { case 0: //inner satellite choiceEkoPosition.add("tau2"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("3*tau2"); choiceEkoPosition.select(0); break; case 1: //outer satellite choiceEkoPosition.add("tau2/2"); choiceEkoPosition.add("tau2"); choiceEkoPosition.add("3*tau2/2"); choiceEkoPosition.select(1); break; } break; case 2: //spin 7/2 switch (choiceTransition.getSelectedIndex()) { case 0: //inner satellite choiceEkoPosition.add("tau2"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("3*tau2-1Q"); choiceEkoPosition.add("3*tau2-nQ"); choiceEkoPosition.add("5*tau2"); choiceEkoPosition.add("6*tau2"); choiceEkoPosition.select(0); break; case 1: //medium satellite choiceEkoPosition.add("tau2/2"); choiceEkoPosition.add("tau2"); choiceEkoPosition.add("3*tau2/2-1Q"); choiceEkoPosition.add("3*tau2/2-nQ"); choiceEkoPosition.add("5*tau2/2"); choiceEkoPosition.add("3*tau2"); choiceEkoPosition.select(1); break; case 2: //outer satellite choiceEkoPosition.add("tau2/3"); choiceEkoPosition.add("2*tau2/3"); choiceEkoPosition.add("tau2-1Q"); choiceEkoPosition.add("tau2-nQ"); choiceEkoPosition.add("5*tau2/3"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.select(2); break; } break; case 3: //spin 9/2 switch (choiceTransition.getSelectedIndex()) { case 0: //inner satellite choiceEkoPosition.add("tau2"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("3*tau2-1Q"); choiceEkoPosition.add("3*tau2-nQ"); choiceEkoPosition.add("4*tau2"); choiceEkoPosition.add("5*tau2"); choiceEkoPosition.add("6*tau2"); choiceEkoPosition.add("7*tau2"); choiceEkoPosition.add("9*tau2"); choiceEkoPosition.add("10*tau2"); choiceEkoPosition.select(0); break; case 1: //medium satellite choiceEkoPosition.add("tau2/2"); choiceEkoPosition.add("tau2"); choiceEkoPosition.add("3*tau2/2-1Q"); choiceEkoPosition.add("3*tau2/2-nQ"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("5*tau2/2"); choiceEkoPosition.add("3*tau2"); choiceEkoPosition.add("7*tau2/2"); choiceEkoPosition.add("9*tau2/2"); choiceEkoPosition.add("5*tau2"); choiceEkoPosition.select(1); break; case 2: //next medium satellite choiceEkoPosition.add("tau2/3"); choiceEkoPosition.add("2*tau2/3"); choiceEkoPosition.add("tau2-1Q"); choiceEkoPosition.add("tau2-nQ"); choiceEkoPosition.add("4*tau2/3"); choiceEkoPosition.add("5*tau2/3"); choiceEkoPosition.add("2*tau2"); choiceEkoPosition.add("7*tau2/3"); choiceEkoPosition.add("3*tau2"); choiceEkoPosition.add("10*tau2/3"); choiceEkoPosition.select(2); break; case 3: //outer satellite choiceEkoPosition.add("tau2/4"); choiceEkoPosition.add("tau2/2"); choiceEkoPosition.add("3*tau2/4-1Q"); choiceEkoPosition.add("3*tau2/4-nQ"); choiceEkoPosition.add("tau2"); choiceEkoPosition.add("5*tau2/4"); choiceEkoPosition.add("3*tau2/2"); choiceEkoPosition.add("7*tau2/4"); choiceEkoPosition.add("9*tau2/4"); choiceEkoPosition.add("5*tau2/2"); choiceEkoPosition.select(4); break; } break; } } }); }//end of start() /**Stop the applet*/ public void stop() { } /**Destroy the applet*/ public void destroy() { } /**Get Applet information*/ public String getAppletInfo() { return "Applet Information"; } /**Get parameter info*/ public String[][] getParameterInfo() { return null; } private void afficheValeur() { //show the echo amplitude versus the pulse length double tp = 0; String s = "", s2 = ""; textAreaIntensite.setText(""); //clear textAreaDuree.setText(""); //clear for (int i = 0; i <= nbou; i++) { tp = dureePremiere + i*dureePas; s = textAreaIntensite.getText() + Math.round(100000*amplitude[i])/100000.0 + "\n"; textAreaIntensite.setText(s); s2 = textAreaDuree.getText() + Math.round(100000*tp)/100.0 + "\n"; textAreaDuree.setText(s2); } }//end of afficheValeur() private double mySimplexFonction(double omegaQFit, double omegaRFFit, double norme) { double sqsum = 0; calculIntensite(omegaQFit, omegaRFFit); for (int i = 0; i <= nbou; i++) { double tmp = norme*amplitude[i] - listExpIntensity[i]; sqsum += tmp*tmp; } return sqsum; }//end of mySimplexFonction private void plotCourbe(double b0, double b1, double b2) { //plot experimental intensity data and the fitting curve verus the //pulse length String st1 = "p1 (" + (char) 181 + "s)", st2 = "p2 (" + (char) 181 + "s)"; switch (choiceSequence.getSelectedIndex()) { case 0: Graph("Solomon echo to crystal", st1, "A(p1)B()"); break; case 1: Graph("Solomon echo to crystal", st2, "A()B(p2)"); break; } double inc; setSymbol(true); setLine(false); setColor(blue); setTitle("experimental"); for (int i = 0; i <= nbou; i++) { inc = Math.round(100000*(dureePremiere + i*dureePas))/100.0; add(inc, listExpIntensity[i]); } nextGraph(); setColor(black); setTitle("fit"); calculIntensite(b0, b1); for (int i = 0; i <= nbou; i++) { inc = Math.round(100000*(dureePremiere + i*dureePas))/100.0; add(inc, b2*amplitude[i]); } repaint(); }//end of plotCourbe() public void run() { //run the simplex procedure /* The flexible simplex method allows you to find the minimum for a function * with multiple variables. The method obtains the minimum for a function * with N variables by examining the function values at N + 1 points. * This method locates the points with the best and worst values * then attempts to replace the worst-value point with a better point. * This replacement process involves expanding and contracting the simplex * near the worst-value point to determine a better replacement point. * The iterations of the method shrinks the multidimensional simplex around * the minimum point. * Given * # N variables that evaluate function f(X) * # The matrix X, which contains N + 1 rows and N columns * # The array of function values, Y(containing N + 1 values) * # The maximum number of iterations, MAXITER * # The reflection factor, which is a positive value that may be unity * # The expansion factor, which is greater than one (usually two) * # The contraction factor, a value between zero and one (ususally 0.5) */ //(1) set Iter = 0 //(2) set P = N + 1 //the 4 constants used in simplex procedure final int REFLECTFACT = 1; final int EXPANDFACT = 2; final double CONTRACTFACT = 0.5; final int MAXITER = 1000; int numIter = 0, numPoints = numVars + 1, worstI = 0, bestI = 0; double y1 = 0, y2 = 0; //(5) set the convergence flag to false boolean flag = false; double y[] = new double[numVars + 1]; //(3) allocate dynamic arrays x1, x2 and centroid to contain N elements double x1[] = new double[numVars]; double x2[] = new double[numVars]; double centroid[] = new double[numVars]; //(4)calculate the values for y() using x1() for (int i = 0; i < numPoints; i++) { for (int j = 0; j < numVars; j++) x1[j] = matEstimation[i][j]; y[i] = mySimplexFonction(x1[0], x1[1], x1[2]); } //************************* boucle while ********************************* //(6) repeat the next step while Iter < M and the convergence flag is false while ((numIter < MAXITER) && (!stopFit)) { String sx = ""; textAreaParameter.setText(""); sx = "Iteration: " + numIter + " \n"; textAreaParameter.append(sx); numIter += 1; //(6.1) increment Iter //(6.2) find the indices of the worst A and best points worstI = 0; bestI = 0; for (int i = 1; i < numPoints; i++) { if (y[i] < y[bestI]) bestI = i; else if (y[i] > y[worstI]) worstI = i; } //provide the fitting parameters sx = Math.round(1000*matEstimation[bestI][1])/1000.0 + " ( " + Math.round(1000*matEstimation[worstI][1])/1000.0 + " ) kHz\n"; textAreaParameter.append("RF field: " + sx); sx = Math.round(1000*matEstimation[bestI][0])/1000.0 + " ( " + Math.round(1000*matEstimation[worstI][0])/1000.0 + " ) kHz\n"; textAreaParameter.append("OmegaQ: " + sx); sx = Math.round(1000*matEstimation[bestI][2])/1000.0 + " ( " + Math.round(1000*matEstimation[worstI][2])/1000.0 + " )\n"; textAreaParameter.append("Scale: " + sx); sx = y[bestI] + "\n"; textAreaParameter.append(sx); sx = y[worstI] + "\n"; textAreaParameter.append(sx); if (showCurve) { try {Thread.sleep(1000);} catch (InterruptedException e) {} //plotCourbe should be located after try otherwise problem with Netscape plotCourbe(matEstimation[worstI][0], matEstimation[worstI][1], matEstimation[worstI][2]); } //(6.3) calculate centroid (exclude the worst point A) //= center of gravity G for (int i = 0; i < numVars; i++) { centroid[i] = 0; for (int j = 0; j < numPoints; j++) { if (j != worstI) centroid[i] += matEstimation[j][i]; } centroid[i] /= numVars; } //(6.4) calculate reflected point A' //(symmetrical point of A relative to G): A' = 2*G - A for (int i = 0; i < numVars; i++) x1[i] = (1 + REFLECTFACT) * centroid[i] - REFLECTFACT * matEstimation[worstI][i]; //(6.5) set y1 = function value at point x1 or f(A') y1 = mySimplexFonction(x1[0], x1[1], x1[2]); //************************** beginning of if **************************** //(6.6) if y1 or f(A') < best y, that is, //f(A') is the best value found so far if (y1 < y[bestI]) { //perform the following tasks: //(6.6.1) calculate the expandeded point x2 or A" = 2A' - G: //a point twice as far from G as A' for (int k = 0; k < numVars; k++) x2[k] = (1 + EXPANDFACT) * x1[k] - EXPANDFACT * centroid[k]; //(6.6.2) set y2 = function value at point x2, or f(A") y2 = mySimplexFonction(x2[0], x2[1], x2[2]); //(6.6.3) if y2 or f(A") < best y if (y2 < y[bestI]) { //then replace worst point matEstimation //with point x2 or A" and resume at step 7 for (int m = 0; m < numVars; m++) matEstimation[worstI][m] = x2[m]; } else { //else replace worst point matEstimation with point x1 or A' //and resume at step 7 for (int n = 0; n < numVars; n++) matEstimation[worstI][n] = x1[n]; } } //******************************* else *********************************** else { //(6.7) y1 or f(A') >= best y flag = true; for (int q = 0; q < numPoints; q++) { if ((q != worstI) && (y1 <= y[q])) { flag = false; //f(A') is between best y and the others y, except A break; //exit for } } if (flag) {//y1 or f(A') is not between best y and the others y, except A if (y1 < y[worstI]) { //f(A') is between best y and f(A), //(6.7.1) replace worst point by x1 or A' for (int p = 0; p < numVars; p++) matEstimation[worstI][p] = x1[p]; y[worstI] = y1; } //f(A') >= f(A) //(6.7.2) calculate contracted point x2 or //B = (A + G)/2 or B = (A' + G)/2 for (int s = 0; s < numVars; s ++) x2[s] = CONTRACTFACT * matEstimation[worstI][s] + (1 - CONTRACTFACT) * centroid[s]; //(6.7.3) set y2 = function value at point x2 or f(B) y2 = mySimplexFonction(x2[0], x2[1], x2[2]); if (y2 > y[worstI]) { //f(B)>f(A) or f(B)>f(A'), //ALL WE DID ARE NOT USEFUL //store best matEstimation in x2 for (int u = 0; u < numVars; u++) x2[u] = matEstimation[bestI][u]; //and build a new simplex obtained by dividing //all edges leading to the point yielding the best value by 2 for (int j = 0; j < numPoints; j++) for (int q = 0; q < numVars; q++) matEstimation[j][q] = 0.5 * (x2[q] + matEstimation[j][q]); } //resume 7 else { //(else of y2), f(B)