Examples with NumberFormatter dr.util.NumberFormatter used on opensource projects

Example 1 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class CompoundLikelihood method getReport.

public String getReport(int indent) {
    if (EVALUATION_TIMERS) {
        String message = "\n";
        boolean first = true;
        final NumberFormatter nf = new NumberFormatter(6);
        int index = 0;
        for (Likelihood lik : likelihoods) {
            if (!first) {
                message += ", ";
            } else {
                first = false;
            }
            if (indent >= 0) {
                message += "\n";
                for (int i = 0; i < indent; i++) {
                    message += " ";
                }
            }
            message += lik.prettyName() + "=";
            if (lik instanceof CompoundLikelihood) {
                final String d = ((CompoundLikelihood) lik).getReport(indent < 0 ? -1 : indent + 2);
                if (d != null && d.length() > 0) {
                    message += "(" + d;
                    if (indent >= 0) {
                        message += "\n";
                        for (int i = 0; i < indent; i++) {
                            message += " ";
                        }
                    }
                    message += ")";
                }
            } else {
                double secs = (double) evaluationTimes[index] / 1.0E9;
                message += evaluationCounts[index] + " evaluations in " + nf.format(secs) + " secs (" + nf.format(secs / evaluationCounts[index]) + " secs/eval)";
            }
            index++;
        }
        message += "\n\n";
        for (int i = 0; i < indent; i++) {
            message += " ";
        }
        message += this.getId() + " log-likelihood = " + this.getLogLikelihood();
        if (indent == 0)
            message += "\n\n";
        return message;
    } else {
        return "No evaluation timer report available";
    }
}

Example 2 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class CompoundLikelihood method getDiagnosis.

public String getDiagnosis(int indent) {
    String message = "";
    boolean first = true;
    final NumberFormatter nf = new NumberFormatter(6);
    for (Likelihood lik : likelihoods) {
        if (!first) {
            message += ", ";
        } else {
            first = false;
        }
        if (indent >= 0) {
            message += "\n";
            for (int i = 0; i < indent; i++) {
                message += " ";
            }
        }
        message += lik.prettyName() + "=";
        if (lik instanceof CompoundLikelihood) {
            final String d = ((CompoundLikelihood) lik).getDiagnosis(indent < 0 ? -1 : indent + 2);
            if (d != null && d.length() > 0) {
                message += "(" + d;
                if (indent >= 0) {
                    message += "\n";
                    for (int i = 0; i < indent; i++) {
                        message += " ";
                    }
                }
                message += ")";
            }
        } else {
            final double logLikelihood = lik.getLogLikelihood();
            if (logLikelihood == Double.NEGATIVE_INFINITY) {
                message += "-Inf";
            } else if (Double.isNaN(logLikelihood)) {
                message += "NaN";
            } else if (logLikelihood == Double.POSITIVE_INFINITY) {
                message += "+Inf";
            } else {
                message += nf.formatDecimal(logLikelihood, 4);
            }
        }
    }
    message += "\n";
    for (int i = 0; i < indent; i++) {
        message += " ";
    }
    message += "Total = " + this.getLogLikelihood();
    return message;
}

Example 3 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class ThreadedCompoundLikelihood method getDiagnosis.

public String getDiagnosis() {
    String message = "";
    boolean first = true;
    for (Likelihood lik : likelihoods) {
        if (!first) {
            message += ", ";
        } else {
            first = false;
        }
        String id = lik.getId();
        if (id == null || id.trim().length() == 0) {
            String[] parts = lik.getClass().getName().split("\\.");
            id = parts[parts.length - 1];
        }
        message += id + "=";
        if (lik instanceof ThreadedCompoundLikelihood) {
            String d = ((ThreadedCompoundLikelihood) lik).getDiagnosis();
            if (d != null && d.length() > 0) {
                message += "(" + d + ")";
            }
        } else {
            if (lik.getLogLikelihood() == Double.NEGATIVE_INFINITY) {
                message += "-Inf";
            } else if (Double.isNaN(lik.getLogLikelihood())) {
                message += "NaN";
            } else {
                NumberFormatter nf = new NumberFormatter(6);
                message += nf.formatDecimal(lik.getLogLikelihood(), 4);
            }
        }
    }
    return message;
}

Example 4 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class TestThreadedCompoundLikelihood method getDiagnosis.

public String getDiagnosis() {
    String message = "";
    boolean first = true;
    for (Likelihood lik : likelihoods) {
        if (!first) {
            message += ", ";
        } else {
            first = false;
        }
        String id = lik.getId();
        if (id == null || id.trim().length() == 0) {
            String[] parts = lik.getClass().getName().split("\\.");
            id = parts[parts.length - 1];
        }
        message += id + "=";
        if (lik instanceof TestThreadedCompoundLikelihood) {
            String d = ((TestThreadedCompoundLikelihood) lik).getDiagnosis();
            if (d != null && d.length() > 0) {
                message += "(" + d + ")";
            }
        } else {
            if (lik.getLogLikelihood() == Double.NEGATIVE_INFINITY) {
                message += "-Inf";
            } else if (Double.isNaN(lik.getLogLikelihood())) {
                message += "NaN";
            } else {
                NumberFormatter nf = new NumberFormatter(6);
                message += nf.formatDecimal(lik.getLogLikelihood(), 4);
            }
        }
    }
    return message;
}

Example 5 with NumberFormatter

use of dr.util.NumberFormatter in project beast-mcmc by beast-dev.

the class TraceAnalysisParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String fileName = xo.getStringAttribute(FILE_NAME);
    boolean withStdError = xo.getAttribute(STD_ERROR, false);
    boolean computeMSE = xo.getAttribute(COMPUTE_MSE, false);
    try {
        File file = new File(fileName);
        String name = file.getName();
        String parent = file.getParent();
        if (!file.isAbsolute()) {
            parent = System.getProperty("user.dir");
        }
        file = new File(parent + File.separator, name);
        if (file.exists()) {
            fileName = file.getName();
            // leaving the burnin attribute off will result in 10% being used
            int burnin = xo.getAttribute(BURN_IN, -1);
            TraceList traces = TraceAnalysis.report(fileName, burnin, null, withStdError);
            for (int x = 0; x < xo.getChildCount(); x++) {
                XMLObject child = (XMLObject) xo.getChild(x);
                String statName = child.getStringAttribute(Attribute.NAME);
                double expectation = child.getDoubleAttribute(Attribute.VALUE);
                NumberFormatter formatter = new NumberFormatter(6);
                formatter.setPadding(true);
                formatter.setFieldWidth(14);
                for (int i = 0; i < traces.getTraceCount(); i++) {
                    TraceDistribution distribution = traces.getDistributionStatistics(i);
                    TraceCorrelation corr = traces.getCorrelationStatistics(i);
                    if (traces.getTraceName(i).equals(statName)) {
                        double estimate = distribution.getMean();
                        double error = corr.getStdErrorOfMean();
                        System.out.print("E[" + statName + "] = " + formatter.format(expectation));
                        if (computeMSE) {
                            List values = traces.getValues(i);
                            double[] dv = new double[values.size()];
                            for (int j = 0; j < dv.length; j++) {
                                dv[j] = ((Number) values.get(j)).doubleValue();
                            }
                            double MSE = distribution.getMeanSquaredError(dv, expectation);
                            System.out.println(" MSE = " + formatter.format(MSE));
                        } else {
                            System.out.println("");
                            if (expectation > (estimate - (2 * error)) && expectation < (estimate + (2 * error))) {
                                System.out.println("OK:       " + formatter.format(estimate) + " +- " + formatter.format(error) + "\n");
                            } else {
                                System.out.print("WARNING: " + formatter.format(estimate) + " +- " + formatter.format(error) + "\n");
                            }
                        }
                    }
                }
            }
            System.out.println();
            System.out.flush();
            return traces;
        } else {
            throw new XMLParseException("Log file, " + parent + File.separator + name + " does not exist.");
        }
    } catch (FileNotFoundException fnfe) {
        throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
    } catch (java.io.IOException ioe) {
        throw new XMLParseException(ioe.getMessage());
    } catch (TraceException e) {
        throw new XMLParseException(e.toString());
    }
}