List of usage examples for java.lang Math log10
@HotSpotIntrinsicCandidate public static double log10(double a)
From source file:org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculatorUnitTest.java
@Test public void testManyRefSamplesDontKillGoodVariant() { final AlleleFrequencyCalculator afCalc = new AlleleFrequencyCalculator(1, 0.1, 0.1, DEFAULT_PLOIDY); final List<Allele> alleles = Arrays.asList(A, B); final Genotype AA = genotypeWithObviousCall(DIPLOID, BIALLELIC, new int[] { 0, 2 }, EXTREMELY_CONFIDENT_PL); final Genotype AB = genotypeWithObviousCall(DIPLOID, BIALLELIC, new int[] { 0, 1, 1, 1 }, EXTREMELY_CONFIDENT_PL);/*from ww w . j a v a 2 s. c om*/ for (final int numRef : new int[] { 1, 10, 100, 1000, 10000, 100000 }) { final List<Genotype> genotypeList = new ArrayList<>(Collections.nCopies(numRef, AA)); genotypeList.add(AB); final VariantContext vc = makeVC(alleles, genotypeList); final double log10PRef = afCalc.getLog10PNonRef(vc).getLog10LikelihoodOfAFEq0(); Assert.assertTrue(log10PRef < (-EXTREMELY_CONFIDENT_PL / 10) + Math.log10(numRef) + 1); } }
From source file:statisticsintegration.StatisticsLabr.java
private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton1ActionPerformed List<String> Temp = new ArrayList<String>(); List<String> check = new ArrayList<String>(); List<Double> fnl = new ArrayList<>(); List<String> frame = new ArrayList<String>(); List<String> name = new ArrayList<String>(); List<String> name2 = new ArrayList<String>(); List<Double> frame2 = new ArrayList<Double>(); List<Double> limitLeft = new ArrayList<>(); List<Double> limitRight = new ArrayList<>(); List<Double> trueLimitLeft = new ArrayList<>(); List<Double> trueLimitRight = new ArrayList<>(); List<Double> midpoint = new ArrayList<>(); List<Integer> frequency = new ArrayList<>(); List<Double> percent = new ArrayList<>(); List<Integer> cf = new ArrayList<>(); List<Double> cp = new ArrayList<>(); Integer freq = 0;//ww w. ja v a 2 s. c o m Double freqtot = 0.0; if (Categorical.isSelected() == true && Numerical.isSelected() == false) { for (int i = 0; i < jTable1.getRowCount(); i++) { frame.add((String) jTable1.getModel().getValueAt(i, 0)); } Collections.sort(frame); Integer size = frame.size(); System.out.println(size); for (Object b : frame) { String c = b + ""; Temp.add(c); } for (int i = 0; i < jTable1.getRowCount(); i++) { for (int j = 0; j < jTable1.getColumnCount(); j++) { jTable1.setValueAt("", i, j); } } int ct = 0; for (Object z : frame) { String a = z + ""; System.out.print(check.contains(a)); if (!(check.contains(a))) { for (int i = 0; i < Temp.size(); i++) { if (a.equals(Temp.get(i))) { freq++; } } Double freque = (((freq + .0) / size) * 100); fnl.add(freque); name.add(a); freqtot += freque; jTable1.getModel().setValueAt(a, ct, 0); jTable1.getModel().setValueAt(String.format("%1.1f", freque) + "%", ct, 1); ct++; freq = 0; check.add(a); } total.setText("Total :" + String.format("%1.1f", freqtot)); } if (Chart.isSelected() == true) { DefaultPieDataset chart = new DefaultPieDataset(); int h = 0; for (Double z : fnl) { chart.setValue(name.get(h) + "", new Double(z)); h++; } JFreeChart mychart = ChartFactory.createPieChart3D(Desc.getText() + "", chart, true, true, true); PiePlot3D p = (PiePlot3D) mychart.getPlot(); ChartFrame charteuFrame = new ChartFrame(Desc.getText(), mychart); charteuFrame.setVisible(true); charteuFrame.setSize(450, 500); } } else if (Numerical.isSelected() == true && Categorical.isSelected() == false) { double subtrahend = 0.5; for (int i = 0; i < jTable1.getRowCount();) { double d = Double.parseDouble((String) jTable1.getModel().getValueAt(i, 0)); frame2.add(d); i++; } double max = 0; double min = frame2.get(0); for (int j = 0; j < frame2.size(); j++) { System.out.print("Sulod"); if (max < frame2.get(j)) { max = frame2.get(j); } if (min > frame2.get(j)) { min = frame2.get(j); } } System.out.print(frame2); double range = max - min; double k = Math.ceil(1 + 3.322 * Math.log10(frame2.size())); int width = (int) Math.ceil(range / k); System.out.println("char: " + max + " " + min + " " + range + " " + k + " width: " + width); double limit = min; while (limit < max) { limitLeft.add(limit); limit += width; } for (int j = 0; j < limitLeft.size(); j++) { System.out.print(limitLeft.get(j) + " "); } double limit2 = min + width - 1; while (limit2 <= max) { limitRight.add(limit2); limit2 += width; } if (limitRight.get(limitRight.size() - 1) != max) { limitRight.add(max); } System.out.println(); for (int j = 0; j < limitRight.size(); j++) { System.out.print(limitRight.get(j) + " "); } //true limit if (((String) choice.getSelectedItem()).equals("Integer")) { for (int j = 0; j < limitLeft.size(); j++) { trueLimitLeft.add(limitLeft.get(j) - 0.5); } System.out.println(); for (int j = 0; j < trueLimitLeft.size(); j++) { System.out.print(trueLimitLeft.get(j) + " "); } for (int j = 0; j < limitRight.size(); j++) { trueLimitRight.add(limitRight.get(j) + 0.5); } System.out.println(); for (int j = 0; j < trueLimitRight.size(); j++) { System.out.print(trueLimitRight.get(j) + " "); } } else if (((String) choice.getSelectedItem()).equals("Floating")) { int count1 = 0; float diff = 0; boolean flag = false; for (int j = 0; j < frame2.size(); j++) { double value = Math.floor(frame2.get(j)); // System.out.println(frame.get(j)); diff = (float) (frame2.get(j) - value); System.out.println("diff: " + diff); String counts = String.valueOf(diff); if (diff > 0.0) { if (counts.length() - 1 > count1) { count1 = counts.length() - 1; System.out.println(count1); } } } System.out.println(count1); for (int j = 0; j < count1 - 1; j++) { subtrahend /= 10; System.out.println(subtrahend); } System.out.println("sub: " + subtrahend); for (int j = 0; j < limitLeft.size(); j++) { trueLimitLeft.add(limitLeft.get(j) - subtrahend); } for (int j = 0; j < limitRight.size(); j++) { trueLimitRight.add(limitRight.get(j) + subtrahend); } } //midpoint for (int j = 0; j < limitLeft.size(); j++) { midpoint.add((limitLeft.get(j) + limitRight.get(j)) / 2); } System.out.println(); for (int j = 0; j < midpoint.size(); j++) { System.out.print(midpoint.get(j) + " "); } //frequency for (int j = 0; j < limitLeft.size(); j++) { int count = 0; for (int m = 0; m < frame2.size(); m++) { if (frame2.get(m) >= limitLeft.get(j) && frame2.get(m) <= limitRight.get(j)) { count++; } } frequency.add(count); } System.out.println(); for (int j = 0; j < frequency.size(); j++) { System.out.print(frequency.get(j) + " "); } //percent for (int j = 0; j < frequency.size(); j++) { double pp = (((double) frequency.get(j) / frame2.size()) * 100); percent.add(pp); } System.out.println(); for (int j = 0; j < percent.size(); j++) { System.out.print(percent.get(j) + " "); } int cff = 0; for (int j = 0; j < frequency.size(); j++) { cff += frequency.get(j); cf.add(cff); } System.out.println(); for (int j = 0; j < cf.size(); j++) { System.out.print(cf.get(j) + " "); } double cpp = 0; for (int j = 0; j < percent.size(); j++) { cpp += percent.get(j); cp.add(cpp); } System.out.println(); for (int j = 0; j < cp.size(); j++) { System.out.print(cp.get(j) + " "); } DefaultTableModel dtm = (DefaultTableModel) jTable1.getModel(); dtm.setRowCount(limitLeft.size()); int ct = 0; if (collapse.isSelected() == true) { for (int j = 0; j < limitLeft.size(); j++) { if (ct == 0) { jTable1.getModel().setValueAt("< " + limitRight.get(j), ct, 1); jTable1.getModel().setValueAt("-", ct, 3); name.add("<"); } else if (ct == limitLeft.size() - 1) { jTable1.getModel().setValueAt("> " + limitLeft.get(j), ct, 1); jTable1.getModel().setValueAt("-", ct, 3); name.add(">"); } else { jTable1.getModel().setValueAt(limitLeft.get(j) + "-" + limitRight.get(j), ct, 1); jTable1.getModel().setValueAt(midpoint.get(j), ct, 3); name.add(midpoint.get(j) + ""); } jTable1.getModel().setValueAt(trueLimitLeft.get(j) + "-" + trueLimitRight.get(j), ct, 2); jTable1.getModel().setValueAt(frequency.get(j), ct, 4); jTable1.getModel().setValueAt(percent.get(j), ct, 5); jTable1.getModel().setValueAt(cf.get(j), ct, 6); jTable1.getModel().setValueAt(cp.get(j), ct, 7); ct++; } } else { for (int j = 0; j < limitLeft.size(); j++) { jTable1.getModel().setValueAt(limitLeft.get(j) + "-" + limitRight.get(j), ct, 1); jTable1.getModel().setValueAt(trueLimitLeft.get(j) + "-" + trueLimitRight.get(j), ct, 2); jTable1.getModel().setValueAt(midpoint.get(j), ct, 3); name.add(midpoint.get(j) + ""); jTable1.getModel().setValueAt(frequency.get(j), ct, 4); jTable1.getModel().setValueAt(percent.get(j), ct, 5); jTable1.getModel().setValueAt(cf.get(j), ct, 6); jTable1.getModel().setValueAt(cp.get(j), ct, 7); ct++; } } if (Chart.isSelected() == true) { DefaultCategoryDataset chart = new DefaultCategoryDataset(); int h = 0; for (Integer z : frequency) { chart.setValue(z, "Frequency", name.get(h)); h++; } JFreeChart mychart = ChartFactory.createBarChart(Desc.getText() + "", "Midpoint", "Frequency", chart, PlotOrientation.VERTICAL, true, false, false); CategoryPlot p = (CategoryPlot) mychart.getPlot(); p.setDomainGridlinesVisible(true); p.getDomainAxis().setCategoryMargin(0.0); ChartFrame charteuFrame = new ChartFrame(Desc.getText(), mychart); charteuFrame.setVisible(true); charteuFrame.setSize(450, 500); } } }
From source file:savant.snp.SNPFinderPlugin.java
/** * Call SNP for piles for current sequence. *//*from w ww.j a v a 2s . com*/ private List<Pileup> callSNPsFromPileups(List<Pileup> piles, byte[] sequence) { //addMessage("Calling SNPs"); List<Pileup> snps = new ArrayList<Pileup>(); int length = sequence.length; Pileup.Nucleotide n; Pileup p; for (int i = 0; i < length; i++) { n = Pileup.getNucleotide(sequence[i]); p = piles.get(i); //System.out.println ("I am here"); if (p.getSNPNucleotide(snpPrior) != null) { // System.out.println ("I am inside"); double snpConfidence = -10 * Math.log10(1 - p.getSNPNucleotideConfidence(snpPrior)); double z = this.confidence; //-Math.log(1 - ((double)this.confidence)/50.0); // criteria for calling snps if (snpConfidence > z) { snps.add(p); } LOG.debug("conf " + p.getSNPNucleotideConfidence(snpPrior) + "logconf " + snpConfidence + " sens " + z); } } addMessage(snps.size() + " SNPs found"); return snps; }
From source file:de.uni_erlangen.lstm.models.adm1.DAEModel.java
@Override public void computeDerivatives(double t, double[] x, double[] dx) throws MaxCountExceededException, DimensionMismatchException { for (int i = 0; i < x.length; i++) { if (x[i] < 0) { xtemp[i] = 0.0;//from w ww. j a va2s. c om } else { xtemp[i] = x[i]; } } // Adjustments for acid-base equations factor = (1.0 / (param[0]) - 1.0 / (273.15 + xtemp[36])) / (100.0 * R); K_w = Math.pow(10, -param[2]) * Math.exp(55900.0 * factor); // T adjustment for K_w K_a_co2 = Math.pow(10, -param[7]) * Math.exp(7646.0 * factor); // T adjustment for K_a_co2 K_a_IN = Math.pow(10, -param[8]) * Math.exp(51965.0 * factor); // T adjustment for K_a_IN K_H_h2 = param[9] * Math.exp(-4180.0 * factor); // T adjustment for K_H_h2 K_H_ch4 = param[10] * Math.exp(-14240.0 * factor); // T adjustment for K_H_ch4 K_H_co2 = param[11] * Math.exp(-19410.0 * factor); // T adjustment for K_H_co2 p_gas_h2o = param[12] * Math.exp(5290.0 * (1.0 / (param[0]) - 1.0 / (273.15 + xtemp[36]))); // T adjustment for water vapour saturation pressure K_a_va = Math.pow(10, -param[3]); K_a_bu = Math.pow(10, -param[4]); K_a_pro = Math.pow(10, -param[5]); K_a_ac = Math.pow(10, -param[6]); if (fix_pH >= 0) { // S_H_ion based on set pH shDAE = false; S_H_ion = Math.pow(10, -fix_pH); // Run the DAE functions runDAE(); } else { // Run the DAE functions runDAE(); // SH+ Equation (pH and ion states) if (!shDAE) { // Scat+(S_IN-Snh3)-hco3-(Sac/64)-(Spro/112)-(Sbu/160)-(Sva/208)-San phi = xtemp[24] + (xtemp[10] - xtemp[31]) - xtemp[30] - (xtemp[29] / 64.0) - (xtemp[28] / 112.0) - (xtemp[27] / 160.0) - (xtemp[26] / 208.0) - xtemp[25]; S_H_ion = (-phi * 0.5) + 0.5 * Math.sqrt(phi * phi + (4.0 * K_w)); // SH+ } } // Adjustments for gas pressure p_gas_h2 = xtemp[32] * R * (273.15 + xtemp[36]) / 16.0; p_gas_ch4 = xtemp[33] * R * (273.15 + xtemp[36]) / 64.0; p_gas_co2 = xtemp[34] * R * (273.15 + xtemp[36]); P_gas = p_gas_h2 + p_gas_ch4 + p_gas_co2 + p_gas_h2o; // pH Inhibition I_pH_aa = Math.pow(pHLim_aa, n_aa) / (Math.pow(S_H_ion, n_aa) + Math.pow(pHLim_aa, n_aa)); I_pH_ac = Math.pow(pHLim_ac, n_ac) / (Math.pow(S_H_ion, n_ac) + Math.pow(pHLim_ac, n_ac)); I_pH_h2 = Math.pow(pHLim_h2, n_h2) / (Math.pow(S_H_ion, n_h2) + Math.pow(pHLim_h2, n_h2)); I_IN_lim = 1.0 / (1.0 + param[19] / xtemp[10]); // 1.0/(1.0+K_S_IN/S_IN) I_h2_fa = 1.0 / (1.0 + xtemp[7] / param[20]); // 1.0/(1.0+S_h2/K_Ih2_fa) I_h2_c4 = 1.0 / (1.0 + xtemp[7] / param[21]); // 1.0/(1.0+S_h2/K_Ih2_c4) I_h2_pro = 1.0 / (1.0 + xtemp[7] / param[22]); // 1.0/(1.0+S_h2/K_Ih2_pro) I_nh3 = 1.0 / (1.0 + xtemp[31] / param[23]); // 1.0/(1.0+S_nh3/K_I_nh3) // Inhibitors inhib[0] = I_pH_aa * I_IN_lim; // Inhibition Equation 5 & 6 inhib[1] = inhib[0] * I_h2_fa; // Inhibition Equation 7 inhib[2] = inhib[0] * I_h2_c4; // Inhibition Equation 8 & 9 inhib[3] = inhib[0] * I_h2_pro; // Inhibition Equation 10 inhib[4] = I_pH_ac * I_IN_lim * I_nh3; // Inhibition Equation 11 inhib[5] = I_pH_h2 * I_IN_lim; // Inhibition Equation 12 // Biochemical process rates proc1 = param[24] * xtemp[12]; // k_dis*X_xc, Disintegration proc2 = param[25] * xtemp[13]; // k_hyd_ch*X_ch, Hydrolysis of carbohydrates proc3 = param[26] * xtemp[14]; // k_hyd_pr*X_pr, Hydrolysis of proteins proc4 = param[27] * xtemp[15]; // k_hyd_li*X_li, Hydrolysis of lipids proc5 = param[28] * xtemp[0] / (param[29] + xtemp[0]) * xtemp[16] * inhib[0]; // k_m_su*(S_su/(K_S_su+S_su))*X_su*inhib_5, Uptake of sugars proc6 = param[30] * xtemp[1] / (param[31] + xtemp[1]) * xtemp[17] * inhib[0]; // k_m_aa*(S_aa/(K_S_aa+S_aa))*X_aa*inhib_6, Uptake of amino acids proc7 = param[32] * xtemp[2] / (param[33] + xtemp[2]) * xtemp[18] * inhib[1]; // k_m_fa*(S_fa/(K_S_fa+S_fa))*X_aa*inhib_7, Uptake of LCFA proc8 = param[34] * xtemp[3] / (param[35] + xtemp[3]) * xtemp[19] * xtemp[3] / (xtemp[3] + xtemp[4] + eps) * inhib[2]; // k_m_c4*(S_va/(K_S_c4+S_va))*X_c4*(S_va/(S_bu+S_va+eps))*inhib_8, Uptake of valerate proc9 = param[34] * xtemp[4] / (param[35] + xtemp[4]) * xtemp[19] * xtemp[4] / (xtemp[3] + xtemp[4] + eps) * inhib[2]; // k_m_c4*(S_bu/(K_S_c4+S_bu))*X_c4*(S_bu/(S_va+S_bu+eps))*inhib_9, Uptake of butyrate proc10 = param[36] * xtemp[5] / (param[37] + xtemp[5]) * xtemp[20] * inhib[3]; // k_m_pro*(S_pro/(K_S_pro+S_pro))*X_pro*inhib_10, Uptake of propionate proc11 = param[38] * xtemp[6] / (param[39] + xtemp[6]) * xtemp[21] * inhib[4]; // k_m_ac*(S_ac/(K_S_ac+S_ac))*X_ac*inhib_11, Uptake of acetate proc12 = param[40] * xtemp[7] / (param[41] + xtemp[7]) * xtemp[22] * inhib[5]; // k_m_h2*(S_h2/(K_S_h2+S_h2))*X_h2*inhib_12, Uptake of hydrogen proc13 = param[42] * xtemp[16]; // k_dec_Xsu*X_su, Decay of X_su proc14 = param[43] * xtemp[17]; // k_dec_Xaa*X_aa, Decay of X_aa proc15 = param[44] * xtemp[18]; // k_dec_Xfa*X_fa, Decay of X_fa proc16 = param[45] * xtemp[19]; // k_dec_Xc4*X_c4, Decay of X_c4 proc17 = param[46] * xtemp[20]; // k_dec_Xpro*X_pro, Decay of X_pro proc18 = param[47] * xtemp[21]; // k_dec_Xac*X_ac, Decay of X_ac proc19 = param[48] * xtemp[22]; // k_dec_Xh2*X_h2, Decay of X_h2 // Gas transfer rates procT8 = param[55] * (xtemp[7] - 16.0 * K_H_h2 * p_gas_h2); // kLa*(S_h2-16.0*K_H_h2*p_gas_h2) procT9 = param[55] * (xtemp[8] - 64.0 * K_H_ch4 * p_gas_ch4); // kLa*(S_ch4-64.0*K_H_ch4*p_gas_ch4) procT10 = param[55] * ((xtemp[9] - xtemp[30]) - K_H_co2 * p_gas_co2); // kLa*((S_IC-S_hco3)-K_H_co2*p_gas_co2) // Reactions // reac1 = proc2+(1.0-f_fa_li)*proc4-proc5; reac1 = proc2 + (1.0 - param[69]) * proc4 - proc5; reac2 = proc3 - proc6; // reac3 = f_fa_li*proc4-proc7; reac3 = param[69] * proc4 - proc7; // reac4 = (1.0-Y_aa)*f_va_aa*proc6-proc8; reac4 = (1.0 - param[79]) * param[80] * proc6 - proc8; //reac5 = (1.0-Y_su)*f_bu_su*proc5+(1.0-Y_aa)*f_bu_aa*proc6-proc9; reac5 = (1.0 - param[71]) * param[72] * proc5 + (1.0 - param[79]) * param[82] * proc6 - proc9; // reac6 = (1.0-Y_su)*f_pro_su*proc5+(1.0-Y_aa)*f_pro_aa*proc6+(1.0-Y_c4)*0.54*proc8-proc10; reac6 = (1.0 - param[71]) * param[74] * proc5 + (1.0 - param[79]) * param[83] * proc6 + (1.0 - param[86]) * 0.54 * proc8 - proc10; // reac7 = (1.0-Y_su)*f_ac_su*proc5+(1.0-Y_aa)*f_ac_aa*proc6+(1.0-Y_fa)*0.7*proc7+(1.0-Y_c4)*0.31*proc8+(1.0-Y_c4)*0.8*proc9+(1.0-Y_pro)*0.57*proc10-proc11; reac7 = (1.0 - param[71]) * param[76] * proc5 + (1.0 - param[79]) * param[84] * proc6 + (1.0 - param[85]) * 0.7 * proc7 + (1.0 - param[86]) * 0.31 * proc8 + (1.0 - param[86]) * 0.8 * proc9 + (1.0 - param[87]) * 0.57 * proc10 - proc11; // reac8 = (1.0-Y_su)*f_h2_su*proc5+(1.0-Y_aa)*f_h2_aa*proc6+(1.0-Y_fa)*0.3*proc7+(1.0-Y_c4)*0.15*proc8+(1.0-Y_c4)*0.2*proc9+(1.0-Y_pro)*0.43*proc10-proc12-procT8; reac8 = (1.0 - param[71]) * param[91] * proc5 + (1.0 - param[79]) * param[92] * proc6 + (1.0 - param[85]) * 0.3 * proc7 + (1.0 - param[86]) * 0.15 * proc8 + (1.0 - param[86]) * 0.2 * proc9 + (1.0 - param[87]) * 0.43 * proc10 - proc12 - procT8; // reac9 = (1.0-Y_ac)*proc11+(1.0-Y_h2)*proc12-procT9; reac9 = (1.0 - param[88]) * proc11 + (1.0 - param[90]) * proc12 - procT9; reac10 = -stoich1 * proc1 - stoich2 * proc2 - stoich3 * proc3 - stoich4 * proc4 - stoich5 * proc5 - stoich6 * proc6 - stoich7 * proc7 - stoich8 * proc8 - stoich9 * proc9 - stoich10 * proc10 - stoich11 * proc11 - stoich12 * proc12 - stoich13 * proc13 - stoich13 * proc14 - stoich13 * proc15 - stoich13 * proc16 - stoich13 * proc17 - stoich13 * proc18 - stoich13 * proc19 - procT10; // reac11 = (N_xc-f_xI_xc*N_I-f_sI_xc*N_I-f_pr_xc*N_aa)*proc1-Y_su*N_bac*proc5+(N_aa-Y_aa*N_bac)*proc6-Y_fa*N_bac*proc7-Y_c4*N_bac*proc8-Y_c4*N_bac*proc9-Y_pro*N_bac*proc10-Y_ac*N_bac*proc11-Y_h2*N_bac*proc12+(N_bac-N_xc)*(proc13+proc14+proc15+proc16+proc17+proc18+proc19); reac11 = -(param[93] - param[65] * param[94] - param[57] * param[94] - param[61] * param[95]) * proc1 - param[71] * param[96] * proc5 + (param[95] - param[79] * param[96]) * proc6 - param[85] * param[96] * proc7 - param[86] * param[96] * proc8 - param[86] * param[96] * proc9 - param[87] * param[96] * proc10 - param[88] * param[96] * proc11 - param[90] * param[96] * proc12 + (param[96] - param[93]) * (proc13 + proc14 + proc15 + proc16 + proc17 + proc18 + proc19); // reac12 = f_sI_xc*proc1; reac12 = param[57] * proc1; reac13 = -proc1 + proc13 + proc14 + proc15 + proc16 + proc17 + proc18 + proc19; // reac14 = f_ch_xc*proc1-proc2; reac14 = param[59] * proc1 - proc2; // reac15 = f_pr_xc*proc1-proc3; reac15 = param[61] * proc1 - proc3; // reac16 = f_li_xc*proc1-proc4; reac16 = param[63] * proc1 - proc4; // reac17 = Y_su*proc5-proc13; reac17 = param[71] * proc5 - proc13; // reac18 = Y_aa*proc6-proc14; reac18 = param[79] * proc6 - proc14; // reac19 = Y_fa*proc7-proc15; reac19 = param[85] * proc7 - proc15; // reac20 = Y_c4*proc8+Y_c4*proc9-proc16; reac20 = param[86] * proc8 + param[86] * proc9 - proc16; // reac21 = Y_pro*proc10-proc17; reac21 = param[87] * proc10 - proc17; // reac22 = Y_ac*proc11-proc18; reac22 = param[88] * proc11 - proc18; // reac23 = Y_h2*proc12-proc19; reac23 = param[90] * proc12 - proc19; // reac24 = f_xI_xc*proc1; reac24 = param[65] * proc1; q_gas = param[97] * (P_gas - P_atm); if (q_gas < 0) q_gas = 0.0; // DE's -> Soluble matter // dSsu/dt = Qad/Vad,liq(Ssu,i-Ssu)+reac1 dx[0] = (xtemp[35] / param[98]) * (u[0] - xtemp[0]) + reac1; // Ssu dx[1] = (xtemp[35] / param[98]) * (u[1] - xtemp[1]) + reac2; // Saa dx[2] = (xtemp[35] / param[98]) * (u[2] - xtemp[2]) + reac3; // Sfa dx[3] = (xtemp[35] / param[98]) * (u[3] - xtemp[3]) + reac4; // Sva dx[4] = (xtemp[35] / param[98]) * (u[4] - xtemp[4]) + reac5; // Sbu dx[5] = (xtemp[35] / param[98]) * (u[5] - xtemp[5]) + reac6; // Spro dx[6] = (xtemp[35] / param[98]) * (u[6] - xtemp[6]) + reac7; // Sac if (!sh2DAE) { dx[7] = (xtemp[35] / param[98]) * (u[7] - xtemp[7]) + reac8; // Sh2 } dx[8] = (xtemp[35] / param[98]) * (u[8] - xtemp[8]) + reac9; // Sch4 dx[9] = (xtemp[35] / param[98]) * (u[9] - xtemp[9]) + reac10; // SIC dx[10] = (xtemp[35] / param[98]) * (u[10] - xtemp[10]) + reac11; // SIN dx[11] = (xtemp[35] / param[98]) * (u[11] - xtemp[11]) + reac12; // SI // DE's -> Particulate matter dx[12] = (xtemp[35] / param[98]) * (u[12] - xtemp[12]) + reac13; // Xc dx[13] = (xtemp[35] / param[98]) * (u[13] - xtemp[13]) + reac14; // Xch dx[14] = (xtemp[35] / param[98]) * (u[14] - xtemp[14]) + reac15; // Xpr dx[15] = (xtemp[35] / param[98]) * (u[15] - xtemp[15]) + reac16; // Xli dx[16] = (xtemp[35] / param[98]) * (u[16] - xtemp[16]) + reac17; // Xsu dx[17] = (xtemp[35] / param[98]) * (u[17] - xtemp[17]) + reac18; // Xaa dx[18] = (xtemp[35] / param[98]) * (u[18] - xtemp[18]) + reac19; // Xfa dx[19] = (xtemp[35] / param[98]) * (u[19] - xtemp[19]) + reac20; // Xc4 dx[20] = (xtemp[35] / param[98]) * (u[20] - xtemp[20]) + reac21; // Xpro dx[21] = (xtemp[35] / param[98]) * (u[21] - xtemp[21]) + reac22; // Xac dx[22] = (xtemp[35] / param[98]) * (u[22] - xtemp[22]) + reac23; // Xh2 dx[23] = (xtemp[35] / param[98]) * (u[23] - xtemp[23]) + reac24; // XI dx[24] = (xtemp[35] / param[98]) * (u[24] - xtemp[24]); // Scat+ dx[25] = (xtemp[35] / param[98]) * (u[25] - xtemp[25]); // San- // Acid-base process rates for ODE //k_A_Bva*(S_hva*(K_A_va+S_H_ion)-K_a_va*S_va) if (!shDAE && fix_pH < 0) { dx[26] = -(param[49] * (xtemp[26] * (K_a_va + S_H_ion) - K_a_va * xtemp[3])); // Sva- dx[27] = -(param[50] * (xtemp[27] * (K_a_bu + S_H_ion) - K_a_bu * xtemp[4])); // Sbu- dx[28] = -(param[51] * (xtemp[28] * (K_a_pro + S_H_ion) - K_a_pro * xtemp[5])); // Spro- dx[29] = -(param[52] * (xtemp[29] * (K_a_ac + S_H_ion) - K_a_ac * xtemp[6])); // Sac- dx[30] = -(param[53] * (xtemp[30] * (K_a_co2 + S_H_ion) - K_a_co2 * xtemp[9])); // SHCO3- dx[31] = -(param[54] * (xtemp[31] * (K_a_IN + S_H_ion) - K_a_IN * xtemp[10])); // SNH3 } dx[32] = -xtemp[32] * q_gas / param[99] + procT8 * param[98] / param[99]; // Sgas,h2 dx[33] = -xtemp[33] * q_gas / param[99] + procT9 * param[98] / param[99]; // Sgas,ch4 dx[34] = -xtemp[34] * q_gas / param[99] + procT10 * param[98] / param[99]; // Sgas,co2 dx[35] = 0; // Flow dx[36] = 0; // Temp // Correction by factor of 64.0 due to COD basis of Sgas,ch4 // Methane gas (m3/d) //xtemp[37] = (q_gas*xtemp[33])*R*(273.15+xtemp[36])/64.0; // Calculate methane production from concentration in gas phase xtemp[37] = q_gas * (p_gas_ch4 / P_gas); // Calculate methane production from partial pressures xtemp[38] = q_gas;// Gas production (m3/d) xtemp[39] = -Math.log10(S_H_ion); // pH // SCO2 = SIC - SHCO3 xtemp[40] = xtemp[9] - xtemp[30]; // SCO2 // SNH4+ = SIN - SNH3 xtemp[41] = xtemp[10] - xtemp[31]; // SNH4+ }
From source file:ubic.gemma.core.ontology.GoMetric.java
/** * @param GOFreq hashMap of GO term to its frequency in the corpus * @param N number of genes in the corpus * @return map/* ww w .j a va 2 s.c o m*/ */ private Map<String, Double> createWeightMap(Map<String, Integer> GOFreq, Integer N) { Map<String, Double> weightMap = new HashMap<>(); for (String id : GOFreq.keySet()) { Double weightedGO = Math.log10((double) N / GOFreq.get(id)); weightMap.put(id, weightedGO); } return weightMap; }
From source file:org.esa.s1tbx.calibration.gpf.calibrators.ERSCalibrator.java
/** * Called by the framework in order to compute a tile for the given target band. * <p>The default implementation throws a runtime exception with the message "not implemented".</p> * * @param targetBand The target band./* www.j a v a 2s . co m*/ * @param targetTile The current tile associated with the target band to be computed. * @param pm A progress monitor which should be used to determine computation cancelation requests. * @throws OperatorException If an error occurs during computation of the target raster. */ @Override public void computeTile(Band targetBand, Tile targetTile, ProgressMonitor pm) throws OperatorException { try { final Rectangle targetTileRectangle = targetTile.getRectangle(); final int x0 = targetTileRectangle.x; final int y0 = targetTileRectangle.y; final int w = targetTileRectangle.width; final int h = targetTileRectangle.height; //System.out.println("x0 = " + x0 + ", y0 = " + y0 + ", w = " + w + ", h = " + h); final ProductData trgData = targetTile.getDataBuffer(); Band sourceBand1 = null; Band sourceBand2 = null; Tile sourceRaster1 = null; Tile sourceRaster2 = null; ProductData srcData1 = null; ProductData srcData2 = null; final String[] srcBandNames = targetBandNameToSourceBandName.get(targetBand.getName()); if (srcBandNames.length == 1) { sourceBand1 = sourceProduct.getBand(srcBandNames[0]); sourceRaster1 = getSourceTile(sourceBand1, targetTileRectangle); srcData1 = sourceRaster1.getDataBuffer(); } else { sourceBand1 = sourceProduct.getBand(srcBandNames[0]); sourceBand2 = sourceProduct.getBand(srcBandNames[1]); sourceRaster1 = getSourceTile(sourceBand1, targetTileRectangle); sourceRaster2 = getSourceTile(sourceBand2, targetTileRectangle); srcData1 = sourceRaster1.getDataBuffer(); srcData2 = sourceRaster2.getDataBuffer(); } final Unit.UnitType tgtBandUnit = Unit.getUnitType(targetBand); final Unit.UnitType srcBandUnit = Unit.getUnitType(sourceBand1); // copy band if unit is phase if (tgtBandUnit == Unit.UnitType.PHASE) { targetTile.setRawSamples(sourceRaster1.getRawSamples()); return; } if (applyAntennaPatternCorrection && !isAntPattAvailable) { computeAntennaPatternCorrectionFactors(0, sourceImageWidth); } if (applyADCSaturationCorrection && !adcHasBeenTestedFlag) { testADC(sourceBand1, sourceBand2, srcBandUnit); } boolean applyADCSaturationCorrectionToCurrentTile = false; if (applyADCSaturationCorrection && h >= blockHeight && w >= blockWidth) { applyADCSaturationCorrectionToCurrentTile = true; } double[][] adcPowerLoss = null; if (applyADCSaturationCorrectionToCurrentTile) { adcPowerLoss = computeADCPowerLossValuesForCurrentTile(sourceBand1, sourceBand2, x0, y0, w, h, srcBandUnit); } final double k = calibrationConstant * FastMath.sin(referenceIncidenceAngle); final int maxY = y0 + h; final int maxX = x0 + w; double sigma, dn, dn2, i, q, phaseTerm = 0.0; int index; int adcJ = 0; for (int x = x0; x < maxX; x++) { final double sinIncidenceAngleByK = FastMath.sin(incidenceAngles[x]) / k; if (applyADCSaturationCorrectionToCurrentTile) { adcJ = Math.min(((x - x0) / blockWidth), adcPowerLoss[0].length - 1); } for (int y = y0; y < maxY; y++) { index = sourceRaster1.getDataBufferIndex(x, y); if (srcBandUnit == Unit.UnitType.AMPLITUDE) { dn = srcData1.getElemDoubleAt(index); dn2 = dn * dn; } else if (srcBandUnit == Unit.UnitType.INTENSITY) { dn2 = srcData1.getElemDoubleAt(index); } else if (srcBandUnit == Unit.UnitType.REAL) { i = srcData1.getElemDoubleAt(index); q = srcData2.getElemDoubleAt(index); dn2 = i * i + q * q; if (tgtBandUnit == Unit.UnitType.REAL) { phaseTerm = i / Math.sqrt(dn2); } else if (tgtBandUnit == Unit.UnitType.IMAGINARY) { phaseTerm = q / Math.sqrt(dn2); } } else if (srcBandUnit == Unit.UnitType.INTENSITY_DB) { dn2 = FastMath.pow(10, srcData1.getElemDoubleAt(index) / 10.0); // convert dB to linear scale } else { throw new OperatorException("ERS Calibration: unhandled unit"); } double calFactor = sinIncidenceAngleByK; if (applyAntennaPatternCorrection) { calFactor *= antennaPatternCorrFactor[x]; } if (applyRangeSpreadingLossCorrection) { calFactor *= rangeSpreadingLoss[x]; } if (applyReplicaPowerCorrection) { calFactor *= replicaPulseVariationsCorrectionFactor; } if (applyADCSaturationCorrectionToCurrentTile) { final int adcI = Math.min(((y - y0) / blockHeight), adcPowerLoss.length - 1); calFactor *= adcPowerLoss[adcI][adcJ]; } sigma = dn2 * calFactor; if (isComplex && outputImageInComplex) { sigma = Math.sqrt(sigma) * phaseTerm; } if (outputImageScaleInDb) { // convert calibration result to dB if (sigma < underFlowFloat) { sigma = -underFlowFloat; } else { sigma = 10.0 * Math.log10(sigma); } } trgData.setElemDoubleAt(targetTile.getDataBufferIndex(x, y), sigma); } } } catch (Throwable e) { OperatorUtils.catchOperatorException("ERSCalibrator", e); } }
From source file:com.jkoolcloud.jesl.simulator.TNT4JSimulator.java
private static int printProgress(String text, long iteration, int trcWidth) { if (numIterations == 1) return 0; int itPct = (int) ((double) iteration / numIterations * 100.0); int maxItWidth = (int) (Math.log10(numIterations) + 1); String bkSpStr = StringUtils.leftPad("", trcWidth, '\b'); String trcMsg = String.format(bkSpStr + "%" + maxItWidth + "d (%02d%%)", iteration, itPct); trcWidth = trcMsg.length() - bkSpStr.length(); System.out.print(trcMsg);//from w w w .j a v a 2s . c o m return trcWidth; }
From source file:it.cnr.isti.hpc.dexter.disambiguation.TurkishEntityDisambiguator.java
@Override public EntityMatchList disambiguate(DexterLocalParams localParams, SpotMatchList sml) { entityScoreMap = new HashMap<String, EntityScores>(); selectedEntities = new HashSet<String>(); Multiset<String> entityFrequencyMultiset = HashMultiset.create(); EntityMatchList entities = sml.getEntities(); String inputText = localParams.getParams().get("text"); String algorithm = Property.getInstance().get("algorithm"); String ambigious = Property.getInstance().get("algorithm.ambigious"); List<Token> inputTokens = Zemberek.getInstance().disambiguateFindTokens(inputText, false, true); List<Double> documentVector = DescriptionEmbeddingAverage.getAverageVectorList(inputText); Multiset<String> inputTokensMultiset = HashMultiset.create(); for (Token token : inputTokens) { inputTokensMultiset.add(token.getMorphText()); }/* w w w . j a v a 2s. c om*/ Multiset<String> domainMultiset = HashMultiset.create(); Multiset<String> typeMultiset = HashMultiset.create(); HashMap<String, Double> entitySimMap = new HashMap<String, Double>(); // if (printCandidateEntities) { // printEntities(entities); // } HashSet<String> words = new HashSet<String>(); Multiset<String> leskWords = HashMultiset.create(); // first pass for finding number of types and domains for (int i = 0; i < entities.size(); i++) { EntityMatch em = entities.get(i); String id = em.getId(); if (!entityFrequencyMultiset.contains(id)) { entityFrequencyMultiset.add(id); Entity entity = em.getEntity(); words.add(entity.getShingle().getText()); String type = entity.getPage().getType(); if (type != null && type.length() > 0) { typeMultiset.add(type); } String domain = entity.getPage().getDomain(); if (domain != null && domain.length() > 0) { domainMultiset.add(domain); } String desc = entity.getPage().getDescription(); List<Token> tokens = Zemberek.getInstance().disambiguateFindTokens(desc, false, true); for (Token token : tokens) { leskWords.add(token.getMorphText()); } } else { entityFrequencyMultiset.add(id); } } int maxDomainCount = 0; for (String domain : Multisets.copyHighestCountFirst(domainMultiset).elementSet()) { maxDomainCount = domainMultiset.count(domain); break; } int maxTypeCount = 0; for (String type : Multisets.copyHighestCountFirst(typeMultiset).elementSet()) { maxTypeCount = typeMultiset.count(type); break; } double maxSuffixScore = 0, maxLeskScore = 0, maxSimpleLeskScore = 0, maxLinkScore = 0, maxHashInfoboxScore = 0, maxwordvecDescriptionLocalScore = 0, maxHashDescriptionScore = 0, maxPopularityScore = 0, maxWordvectorAverage = 0, maxWordvecLinksScore = 0; // second pass compute similarities between entities in a window int currentSpotIndex = -1; SpotMatch currentSpot = null; for (int i = 0; i < entities.size(); i++) { EntityMatch em = entities.get(i); SpotMatch spot = em.getSpot(); if (currentSpot == null || spot != currentSpot) { currentSpotIndex++; currentSpot = spot; } String id = em.getId(); Entity entity = entities.get(i).getEntity(); EntityPage page = entities.get(i).getEntity().getPage(); String domain = page.getDomain(); String type = page.getType(); Shingle shingle = entity.getShingle(); /* windowing algorithms stars */ int left = currentSpotIndex - window; int right = currentSpotIndex + window; if (left < 0) { right -= left; left = 0; } if (right > sml.size()) { left += (sml.size()) - right; right = sml.size(); if (left < 0) { left = 0; } } double linkScore = 0, hashInfoboxScore = 0, wordvecDescriptionLocalScore = 0, hashDescriptionScore = 0, wordvecLinksScore = 0; for (int j = left; j < right; j++) { SpotMatch sm2 = sml.get(j); EntityMatchList entities2 = sm2.getEntities(); for (EntityMatch em2 : entities2) { String id2 = em2.getId(); EntityPage page2 = em2.getEntity().getPage(); int counter = 0; if (!ambigious.equals("true")) { for (EntityMatch entityMatch : entities2) { if (entityMatch.getId().startsWith("w")) { counter++; } } } if ((ambigious.equals("true") || counter == 1) && em.getSpot() != em2.getSpot() && !id.equals(id2)) { // Link Similarity calculation starts double linkSim = 0; if (id.startsWith("w") && id2.startsWith("w")) { if (entitySimMap.containsKey("link" + id + id2)) { linkSim = entitySimMap.get("link" + id + id2); } else { HashSet<String> set1 = Sets.newHashSet(page.getLinks().split(" ")); HashSet<String> set2 = Sets.newHashSet(page2.getLinks().split(" ")); linkSim = JaccardCalculator.calculateSimilarity(set1, set2); entitySimMap.put("link" + id + id2, linkSim); } linkScore += linkSim; // Link Similarity calculation ends } // Entity embedding similarity calculation starts double eeSim = 0; if (id.startsWith("w") && id2.startsWith("w")) { if (entitySimMap.containsKey("ee" + id + id2)) { eeSim = entitySimMap.get("ee" + id + id2); } else { eeSim = EntityEmbeddingSimilarity.getInstance().getSimilarity(page, page2); entitySimMap.put("ee" + id + id2, eeSim); } hashInfoboxScore += eeSim; } double w2veclinksSim = 0; if (id.startsWith("w") && id2.startsWith("w")) { if (entitySimMap.containsKey("wl" + id + id2)) { w2veclinksSim = entitySimMap.get("wl" + id + id2); } else { w2veclinksSim = AveragePooling.getInstance().getSimilarity(page.getWord2vec(), page2.getWord2vec()); entitySimMap.put("wl" + id + id2, w2veclinksSim); } wordvecLinksScore += w2veclinksSim; } // Entity embedding similarity calculation ends // Description word2vec similarity calculation // starts double word2vecSim = 0; if (entitySimMap.containsKey("w2v" + id + id2)) { word2vecSim = entitySimMap.get("w2v" + id + id2); } else { word2vecSim = AveragePooling.getInstance().getSimilarity(page2.getDword2vec(), page.getDword2vec()); entitySimMap.put("w2v" + id + id2, word2vecSim); } wordvecDescriptionLocalScore += word2vecSim; // Description word2vec similarity calculation ends // Description autoencoder similarity calculation // starts double autoVecSim = 0; if (entitySimMap.containsKey("a2v" + id + id2)) { autoVecSim = entitySimMap.get("a2v" + id + id2); } else { autoVecSim = AveragePooling.getInstance().getSimilarity(page2.getDautoencoder(), page.getDautoencoder()); entitySimMap.put("a2v" + id + id2, autoVecSim); } hashDescriptionScore += autoVecSim; // Description autoencoder similarity calculation // ends } } } if (linkScore > maxLinkScore) { maxLinkScore = linkScore; } if (hashInfoboxScore > maxHashInfoboxScore) { maxHashInfoboxScore = hashInfoboxScore; } if (wordvecDescriptionLocalScore > maxwordvecDescriptionLocalScore) { maxwordvecDescriptionLocalScore = wordvecDescriptionLocalScore; } if (hashDescriptionScore > maxHashDescriptionScore) { maxHashDescriptionScore = hashDescriptionScore; } if (wordvecLinksScore > maxWordvecLinksScore) { maxWordvecLinksScore = wordvecLinksScore; } /* windowing algorithms ends */ double domainScore = 0; if (domainMultiset.size() > 0 && maxDomainCount > 1 && domainMultiset.count(domain) > 1) { domainScore = (double) domainMultiset.count(domain) / maxDomainCount; } double typeScore = 0; if (typeMultiset.size() > 0 && maxTypeCount > 1 && typeMultiset.count(type) > 1) { typeScore = (double) typeMultiset.count(type) / maxTypeCount; } if (typeBlackList.contains(type)) { typeScore /= 10; } double typeContentScore = 0; if (type.length() > 0 && StringUtils.containsIgnoreCase(words.toString(), type)) { typeContentScore = 1; } double typeClassifierScore = TypeClassifier.getInstance().predict(page, page.getTitle(), page.getType(), entity.getShingle().getSentence()); double wordvecDescriptionScore = AveragePooling.getInstance().getSimilarity(documentVector, page.getDword2vec()); if (wordvecDescriptionScore > maxWordvectorAverage) { maxWordvectorAverage = wordvecDescriptionScore; } double suffixScore = 0; if (type != null && type.length() > 0) { Set<String> suffixes = new HashSet<String>(); String t = entity.getTitle().toLowerCase(new Locale("tr", "TR")); for (int x = 0; x < entities.size(); x++) { EntityMatch e2 = entities.get(x); if (e2.getId().equals(entity.getId())) { suffixes.add(e2.getMention()); } } suffixes.remove(t); suffixes.remove(entity.getTitle()); // String inputTextLower = inputText.toLowerCase(new // Locale("tr", // "TR")); // while (inputTextLower.contains(t)) { // int start = inputTextLower.indexOf(t); // int end = inputTextLower.indexOf(" ", start + t.length()); // if (end > start) { // String suffix = inputTextLower.substring(start, end); // // .replaceAll("\\W", ""); // if (suffix.contains("'") // || (Zemberek.getInstance().hasMorph(suffix) // && !suffix.equals(t) && suffix.length() > 4)) { // suffixes.add(suffix); // } // inputTextLower = inputTextLower.substring(end); // } else { // break; // } // } if (suffixes.size() >= minSuffix) { for (String suffix : suffixes) { double sim = gd.calculateSimilarity(suffix, type); suffixScore += sim; } } } // String entitySuffix = page.getSuffix(); // String[] inputSuffix = shingle.getSuffix().split(" "); // for (int j = 0; j < inputSuffix.length; j++) { // if (entitySuffix.contains(inputSuffix[j])) { // suffixScore += 0.25f; // } // } if (suffixScore > maxSuffixScore) { maxSuffixScore = suffixScore; } // if (id.equals("w691538")) { // LOGGER.info(""); // } double letterCaseScore = 0; int lc = page.getLetterCase(); if (StringUtils.isAllLowerCase(em.getMention()) && lc == 0 && id.startsWith("t")) { letterCaseScore = 1; } else if (StringUtils.isAllUpperCase(em.getMention()) && lc == 1 && id.startsWith("w")) { letterCaseScore = 1; } else if (Character.isUpperCase(em.getMention().charAt(0)) && lc == 2 && id.startsWith("w")) { letterCaseScore = 1; } else if (StringUtils.isAllLowerCase(em.getMention()) && id.startsWith("t")) { letterCaseScore = 1; } double nameScore = 1 - LevenshteinDistanceCalculator.calculateDistance(page.getTitle(), Zemberek.removeAfterSpostrophe(em.getMention())); double popularityScore = page.getRank(); if (id.startsWith("w")) { popularityScore = Math.log10(popularityScore + 1); if (popularityScore > maxPopularityScore) { maxPopularityScore = popularityScore; } } double leskScore = 0, simpleLeskScore = 0; String desc = em.getEntity().getPage().getDescription(); if (desc != null) { List<Token> tokens = Zemberek.getInstance().disambiguateFindTokens(desc, false, true); for (Token token : tokens) { if (inputTokensMultiset.contains(token.getMorphText()) && !TurkishNLP.isStopWord(token.getMorphText())) { simpleLeskScore += inputTokensMultiset.count(token.getMorphText()); } if (leskWords.contains(token.getMorphText()) && !TurkishNLP.isStopWord(token.getMorphText())) { leskScore += leskWords.count(token.getMorphText()); } } leskScore /= Math.log(tokens.size() + 1); simpleLeskScore /= Math.log(tokens.size() + 1); if (leskScore > maxLeskScore) { maxLeskScore = leskScore; } if (simpleLeskScore > maxSimpleLeskScore) { maxSimpleLeskScore = simpleLeskScore; } if (!entityScoreMap.containsKey(id)) { EntityScores scores = new EntityScores(em, id, popularityScore, nameScore, letterCaseScore, suffixScore, wordvecDescriptionScore, typeContentScore, typeScore, domainScore, hashDescriptionScore, wordvecDescriptionLocalScore, hashInfoboxScore, linkScore, wordvecLinksScore, leskScore, simpleLeskScore, typeClassifierScore); entityScoreMap.put(id, scores); } else { EntityScores entityScores = entityScoreMap.get(id); entityScores.setHashInfoboxScore((entityScores.getHashInfoboxScore() + hashInfoboxScore) / 2); entityScores.setHashDescriptionScore( (entityScores.getHashInfoboxScore() + hashDescriptionScore) / 2); entityScores.setLinkScore((entityScores.getLinkScore() + linkScore) / 2); entityScores.setWordvecDescriptionLocalScore( (entityScores.getWordvecDescriptionLocalScore() + wordvecDescriptionLocalScore) / 2); entityScores .setWordvecLinksScore((entityScores.getWordvecLinksScore() + wordvecLinksScore) / 2); entityScores.setLeskScore((entityScores.getLeskScore() + leskScore) / 2); } } } /* normalization and total score calculation starts */ Set<String> set = new HashSet<String>(); for (int i = 0; i < entities.size(); i++) { EntityMatch em = entities.get(i); String id = em.getId(); EntityScores entityScores = entityScoreMap.get(id); if (set.contains(id)) { continue; } if (id.startsWith("w")) { if (maxLinkScore > 0 && entityScores.getLinkScore() > 0) { entityScores.setLinkScore(entityScores.getLinkScore() / maxLinkScore); } if (maxHashInfoboxScore > 0 && entityScores.getHashInfoboxScore() > 0) { entityScores.setHashInfoboxScore(entityScores.getHashInfoboxScore() / maxHashInfoboxScore); } if (maxWordvecLinksScore > 0 && entityScores.getWordvecLinksScore() > 0) { entityScores.setWordvecLinksScore(entityScores.getWordvecLinksScore() / maxWordvecLinksScore); } if (maxPopularityScore > 0 && entityScores.getPopularityScore() > 0) { entityScores.setPopularityScore(entityScores.getPopularityScore() / maxPopularityScore); } } if (maxwordvecDescriptionLocalScore > 0 && entityScores.getWordvecDescriptionLocalScore() > 0) { entityScores.setWordvecDescriptionLocalScore( entityScores.getWordvecDescriptionLocalScore() / maxwordvecDescriptionLocalScore); } if (maxHashDescriptionScore > 0 && entityScores.getHashDescriptionScore() > 0) { entityScores .setHashDescriptionScore(entityScores.getHashDescriptionScore() / maxHashDescriptionScore); } if (maxWordvectorAverage > 0 && entityScores.getWordvecDescriptionScore() > 0) { entityScores.setWordvecDescriptionScore( entityScores.getWordvecDescriptionScore() / maxWordvectorAverage); } if (maxLeskScore > 0 && entityScores.getLeskScore() > 0) { entityScores.setLeskScore(entityScores.getLeskScore() / maxLeskScore); } if (maxSimpleLeskScore > 0 && entityScores.getSimpleLeskScore() > 0) { entityScores.setSimpleLeskScore(entityScores.getSimpleLeskScore() / maxSimpleLeskScore); } if (maxSuffixScore > 0 && entityScores.getSuffixScore() > 0) { entityScores.setSuffixScore(entityScores.getSuffixScore() / maxSuffixScore); } set.add(id); } LOGGER.info("\t" + "id\tTitle\tURL\tScore\tPopularity\tName\tLesk\tSimpeLesk\tCase\tNoun\tSuffix\tTypeContent\tType\tDomain\twordvecDescription\twordvecDescriptionLocal\thashDescription\thashInfobox\tword2vecLinks\tLink\t\ttypeClassifier\tDescription"); for (int i = 0; i < entities.size(); i++) { EntityMatch em = entities.get(i); String id = em.getId(); EntityScores e = entityScoreMap.get(id); double wikiScore = 0; if (id.startsWith("w") && Character.isUpperCase(em.getMention().charAt(0))) { wikiScore = wikiWeight; } else if (id.startsWith("t") && Character.isLowerCase(em.getMention().charAt(0))) { wikiScore = wikiWeight; } // if(id.equals("w508792")){ // LOGGER.info(""); // } double totalScore = wikiScore + e.getPopularityScore() * popularityWeight + e.getNameScore() * nameWeight + e.getLeskScore() * leskWeight + e.getSimpleLeskScore() * simpleLeskWeight + e.getLetterCaseScore() * letterCaseWeight + e.getSuffixScore() * suffixWeight + e.getTypeContentScore() * typeContentWeight + e.getTypeScore() * typeWeight + e.getDomainScore() * domainWeight + e.getWordvecDescriptionScore() * wordvecDescriptionWeight + e.getWordvecDescriptionLocalScore() * wordvecDescriptionLocalWeight + e.getHashDescriptionScore() * hashDescriptionWeight + e.getHashInfoboxScore() * hashInfoboxWeight + e.getWordvecLinksScore() * word2vecLinksWeight + e.getLinkScore() * linkWeight + e.getTypeClassifierkScore() * typeClassifierkWeight; if (ranklib == true) { totalScore = RankLib.getInstance().score(e); } if (em.getEntity().getPage().getUrlTitle().contains("(")) { totalScore /= 2; } em.setScore(totalScore); e.setScore(totalScore); LOGGER.info("\t" + id + "\t" + em.getEntity().getPage().getTitle() + "\t" + em.getEntity().getPage().getUrlTitle() + "\t" + em.getScore() + "\t" + e.getPopularityScore() * popularityWeight + "\t" + e.getNameScore() * nameWeight + "\t" + e.getLeskScore() * leskWeight + "\t" + e.getSimpleLeskScore() * simpleLeskWeight + "\t" + e.getLetterCaseScore() * letterCaseWeight + "\t" + e.getSuffixScore() * suffixWeight + "\t" + e.getTypeContentScore() * typeContentWeight + "\t" + e.getTypeScore() * typeWeight + "\t" + e.getDomainScore() * domainWeight + "\t" + e.getWordvecDescriptionScore() * wordvecDescriptionWeight + "\t" + e.getWordvecDescriptionLocalScore() * wordvecDescriptionLocalWeight + "\t" + e.getHashDescriptionScore() * hashDescriptionWeight + "\t" + e.getHashInfoboxScore() * hashInfoboxWeight + "\t" + e.getWordvecLinksScore() * word2vecLinksWeight + "\t" + e.getLinkScore() * linkWeight + "\t" + e.getTypeClassifierkScore() * typeClassifierkWeight + "\t" + em.getEntity().getPage().getDescription()); } // if (annotateEntities) { // annotateEntities(localParams.getParams().get("originalText"), sml); // } EntityMatchList eml = new EntityMatchList(); for (SpotMatch match : sml) { EntityMatchList list = match.getEntities(); if (!list.isEmpty()) { list.sort(); eml.add(list.get(0)); selectedEntities.add(list.get(0).getId()); } } return eml; }
From source file:asl.util.PlotMaker.java
public void plotSpecAmp(double freq[], double[] amp, double[] phase, String plotString) { // plotTitle = "2012074.IU_ANMO.00-BHZ " + plotString final String plotTitle = String.format("%04d%03d.%s.%s %s", date.get(Calendar.YEAR), date.get(Calendar.DAY_OF_YEAR), station, channel, plotString); // plot filename = "2012074.IU_ANMO.00-BHZ" + plotString + ".png" final String pngName = String.format("%s/%04d%03d.%s.%s.%s.png", outputDir, date.get(Calendar.YEAR), date.get(Calendar.DAY_OF_YEAR), station, channel, plotString); File outputFile = new File(pngName); // Check that we will be able to output the file without problems and if not --> return if (!checkFileOut(outputFile)) { System.out.format("== plotSpecAmp: request to output plot=[%s] but we are unable to create it " + " --> skip plot\n", pngName); return;//from w ww . j a va 2s . c o m } final XYSeries series1 = new XYSeries("Amplitude"); final XYSeries series2 = new XYSeries("Phase"); double maxdB = 0.; for (int k = 0; k < freq.length; k++) { double dB = 20. * Math.log10(amp[k]); series1.add(freq[k], dB); series2.add(freq[k], phase[k]); if (dB > maxdB) { maxdB = dB; } } //final XYItemRenderer renderer = new StandardXYItemRenderer(); final XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(); Rectangle rectangle = new Rectangle(3, 3); renderer.setSeriesShape(0, rectangle); //renderer.setSeriesShapesVisible(0, true); renderer.setSeriesShapesVisible(0, false); renderer.setSeriesLinesVisible(0, true); renderer.setSeriesShape(1, rectangle); renderer.setSeriesShapesVisible(1, true); renderer.setSeriesLinesVisible(1, false); Paint[] paints = new Paint[] { Color.red, Color.blue }; renderer.setSeriesPaint(0, paints[0]); //renderer.setSeriesPaint(1, paints[1]); final XYLineAndShapeRenderer renderer2 = new XYLineAndShapeRenderer(); renderer2.setSeriesPaint(0, paints[1]); renderer2.setSeriesShapesVisible(0, false); renderer2.setSeriesLinesVisible(0, true); // Stroke is part of Java Swing ... //renderer2.setBaseStroke( new Stroke( ... ) ); double ymax; if (maxdB < 10) { ymax = 10.; } else { ymax = maxdB + 2; ; } final NumberAxis verticalAxis = new NumberAxis("Spec Amp (dB)"); verticalAxis.setRange(new Range(-40, ymax)); verticalAxis.setTickUnit(new NumberTickUnit(5)); //final LogarithmicAxis verticalAxis = new LogarithmicAxis("Amplitude Response"); //verticalAxis.setRange( new Range(0.01 , 10) ); final LogarithmicAxis horizontalAxis = new LogarithmicAxis("Frequency (Hz)"); //horizontalAxis.setRange( new Range(0.0001 , 100.5) ); horizontalAxis.setRange(new Range(0.00009, 110)); final XYSeriesCollection seriesCollection = new XYSeriesCollection(); seriesCollection.addSeries(series1); final XYPlot xyplot = new XYPlot((XYDataset) seriesCollection, null, verticalAxis, renderer); //final XYPlot xyplot = new XYPlot((XYDataset)seriesCollection, horizontalAxis, verticalAxis, renderer); xyplot.setDomainGridlinesVisible(true); xyplot.setRangeGridlinesVisible(true); xyplot.setRangeGridlinePaint(Color.black); xyplot.setDomainGridlinePaint(Color.black); final NumberAxis phaseAxis = new NumberAxis("Phase (Deg)"); phaseAxis.setRange(new Range(-180, 180)); phaseAxis.setTickUnit(new NumberTickUnit(30)); final XYSeriesCollection seriesCollection2 = new XYSeriesCollection(); seriesCollection2.addSeries(series2); final XYPlot xyplot2 = new XYPlot((XYDataset) seriesCollection2, null, phaseAxis, renderer2); //CombinedXYPlot combinedPlot = new CombinedXYPlot( horizontalAxis, CombinedXYPlot.VERTICAL ); CombinedDomainXYPlot combinedPlot = new CombinedDomainXYPlot(horizontalAxis); combinedPlot.add(xyplot, 1); combinedPlot.add(xyplot2, 1); combinedPlot.setGap(15.); //final JFreeChart chart = new JFreeChart(xyplot); final JFreeChart chart = new JFreeChart(combinedPlot); chart.setTitle(new TextTitle(plotTitle)); // Here we need to see if test dir exists and create it if necessary ... try { //ChartUtilities.saveChartAsJPEG(new File("chart.jpg"), chart, 500, 300); //ChartUtilities.saveChartAsPNG(outputFile, chart, 500, 300); ChartUtilities.saveChartAsPNG(outputFile, chart, 1000, 800); } catch (IOException e) { System.err.println("Problem occurred creating chart."); } }
From source file:ubic.gemma.ontology.GoMetric.java
/** * @param GOFreq hashMap of GO term to its frequency in the corpus * @param N number of genes in the corpus * @return/* w ww .ja v a 2s.co m*/ */ private Map<String, Double> createWeightMap(Map<String, Integer> GOFreq, Integer N) { Map<String, Double> weightMap = new HashMap<String, Double>(); for (String id : GOFreq.keySet()) { Double weightedGO = Math.log10((double) N / GOFreq.get(id)); weightMap.put(id, weightedGO); } return weightMap; }