Merge branch 'master' of https://github.com/biometrics/openbr

Scott Klum
2 parents a83b5e97 bdf861b4
Showing 16 changed files with 340 additions and 169 deletions
.gitignore
app/br/br.cpp
openbr/core/eval.cpp
openbr/core/plot.cpp
openbr/core/plot.h
openbr/core/qtutils.cpp
openbr/openbr.cpp
openbr/openbr.h
openbr/openbr_export.cpp
openbr/openbr_plugin.h
openbr/plugins/frames.cpp
openbr/plugins/gallery.cpp
openbr/plugins/stream.cpp
scripts/downloadDatasets.sh
share/openbr/Doxyfile.in
share/openbr/openbr.bib
@@ -2,6 +2,7 @@
 3rdparty/LatentSDK*
 3rdparty/pittpatt*
 data/*/img
+data/*/vid
 data/PCSO/*
 build*
 scripts/results
@@ -135,11 +135,14 @@ public:
                 check(parc == 2, "Incorrect parameter count for 'evalClustering'.");
                 br_eval_clustering(parv[0], parv[1]);
             } else if (!strcmp(fun, "evalDetection")) {
-                check(parc == 2, "Incorrect parameter count for 'evalDetection'.");
-                br_eval_detection(parv[0], parv[1]);
+                check((parc >= 2) && (parc <= 3), "Incorrect parameter count for 'evalDetection'.");
+                br_eval_detection(parv[0], parv[1], parc == 3 ? parv[2] : "");
             } else if (!strcmp(fun, "evalRegression")) {
                 check(parc == 2, "Incorrect parameter count for 'evalRegression'.");
                 br_eval_regression(parv[0], parv[1]);
+            } else if (!strcmp(fun, "plotDetection")) {
+                check(parc >= 2, "Incorrect parameter count for 'plotDetection'.");
+                br_plot_detection(parc-1, parv, parv[parc-1], true);
             } else if (!strcmp(fun, "plotMetadata")) {
                 check(parc >= 2, "Incorrect parameter count for 'plotMetadata'.");
                 br_plot_metadata(parc-1, parv, parv[parc-1], true);
@@ -214,8 +217,9 @@ private:
                "-convert (Format|Gallery|Output) <input_file> {output_file}\n"
                "-evalClassification <predicted_gallery> <truth_gallery>\n"
                "-evalClustering <clusters> <gallery>\n"
-               "-evalDetection <predicted_gallery> <truth_gallery>\n"
+               "-evalDetection <predicted_gallery> <truth_gallery> [{csv}]\n"
                "-evalRegression <predicted_gallery> <truth_gallery>\n"
+               "-plotDetection <file> ... <file> {destination}\n"
                "-plotMetadata <file> ... <file> <columns>\n"
                "-getHeader <matrix>\n"
                "-setHeader {<matrix>} <target_gallery> <query_gallery>\n"
@@ -23,6 +23,8 @@ using namespace cv;
 namespace br
 {
+static const int Max_Points = 500; // Maximum number of points to render on plots
+
 struct Comparison
 {
     float score;
@@ -100,7 +102,6 @@ float Evaluate(const Mat &amp;simmat, const Mat &amp;mask, const QString &amp;csv)
         qFatal("Similarity matrix (%ix%i) differs in size from mask matrix (%ix%i).",
                simmat.rows, simmat.cols, mask.rows, mask.cols);
-    const int Max_Points = 500;
     float result = -1;
     // Make comparisons
@@ -237,7 +238,7 @@ float Evaluate(const Mat &amp;simmat, const Mat &amp;mask, const QString &amp;csv)
         if (i == Report_Retrieval) reportRetrievalRate = retrievalRate;
     }
-    if (!csv.isEmpty()) QtUtils::writeFile(csv, lines);
+    QtUtils::writeFile(csv, lines);
     qDebug("TAR @ FAR = 0.01: %.3f\nRetrieval Rate @ Rank = %d: %.3f", result, Report_Retrieval, reportRetrievalRate);
     return result;
 }
@@ -325,7 +326,7 @@ struct Detection
     float overlap(const Detection &other) const
     {
         const Detection intersection(boundingBox.intersected(other.boundingBox));
-        return intersection.area() / (area() + other.area() - 2*intersection.area());
+        return intersection.area() / (area() + other.area() - intersection.area());
     }
 };
@@ -334,14 +335,53 @@ struct Detections
     QList<Detection> predicted, truth;
 };
-struct DetectionOperatingPoint
+struct ResolvedDetection
 {
     float confidence, overlap;
-    DetectionOperatingPoint() : confidence(-1), overlap(-1) {}
-    DetectionOperatingPoint(float confidence_, float overlap_) : confidence(confidence_), overlap(overlap_) {}
-    inline bool operator<(const DetectionOperatingPoint &other) const { return confidence > other.confidence; }
+    ResolvedDetection() : confidence(-1), overlap(-1) {}
+    ResolvedDetection(float confidence_, float overlap_) : confidence(confidence_), overlap(overlap_) {}
+    inline bool operator<(const ResolvedDetection &other) const { return confidence > other.confidence; }
+};
+
+struct DetectionOperatingPoint
+{
+    float Recall, FalsePositives, Precision;
+    DetectionOperatingPoint() : Recall(-1), FalsePositives(-1), Precision(-1) {}
+    DetectionOperatingPoint(float TP, float FP, float totalPositives)
+        : Recall(TP/totalPositives), FalsePositives(FP), Precision(TP/(TP+FP)) {}
 };
+static QStringList computeDetectionResults(const QList<ResolvedDetection> &detections, int totalPositives, bool discrete)
+{
+    QList<DetectionOperatingPoint> points;
+    float TP = 0, FP = 0, prevFP = 0;
+    for (int i=0; i<detections.size(); i++) {
+        const ResolvedDetection &detection = detections[i];
+        if (discrete) {
+            if (detection.overlap >= 0.5) TP++;
+            else                          FP++;
+        } else {
+            TP += detection.overlap;
+            FP += 1 - detection.overlap;
+        }
+        if ((i == detections.size()-1) || (detection.confidence > detections[i+1].confidence)) {
+            if (FP > prevFP) {
+                points.append(DetectionOperatingPoint(TP, FP, totalPositives));
+                prevFP = FP;
+            }
+        }
+    }
+
+    const int keep = qMin(points.size(), Max_Points);
+    QStringList lines; lines.reserve(keep);
+    for (int i=0; i<keep; i++) {
+        const DetectionOperatingPoint &point = points[double(i) / double(keep-1) * double(points.size()-1)];
+        lines.append(QString("%1ROC, %2, %3").arg(discrete ? "Discrete" : "Continuous", QString::number(point.FalsePositives), QString::number(point.Recall)));
+        lines.append(QString("%1PR, %2, %3").arg(discrete ? "Discrete" : "Continuous", QString::number(point.Precision), QString::number(point.Recall)));
+    }
+    return lines;
+}
+
 float EvalDetection(const QString &predictedInput, const QString &truthInput, const QString &csv)
 {
     qDebug("Evaluating detection of %s against %s", qPrintable(predictedInput), qPrintable(truthInput));
@@ -358,18 +398,18 @@ float EvalDetection(const QString &amp;predictedInput, const QString &amp;truthInput, co
     if (detectKey.isNull()) qFatal("No suitable metadata key found.");
     else                    qDebug("Using metadata key: %s", qPrintable(detectKey));
-    QHash<QString, Detections> allDetections; // Organized by file
+    QMap<QString, Detections> allDetections; // Organized by file, QMap used to preserve order
     foreach (const Template &t, predicted)
         allDetections[t.file.baseName()].predicted.append(Detection(t.file.get<QRectF>(detectKey), t.file.get<float>("Confidence", -1)));
     foreach (const Template &t, truth)
         allDetections[t.file.baseName()].truth.append(Detection(t.file.get<QRectF>(detectKey)));
-    QList<DetectionOperatingPoint> points;
+    QList<ResolvedDetection> resolvedDetections, falseNegativeDetections;
     foreach (Detections detections, allDetections.values()) {
         while (!detections.truth.isEmpty() && !detections.predicted.isEmpty()) {
-            Detection truth = detections.truth.takeFirst();
+            const Detection truth = detections.truth.takeFirst();
             int bestIndex = -1;
-            float bestOverlap = -1;
+            float bestOverlap = -std::numeric_limits<float>::max();
             for (int i=0; i<detections.predicted.size(); i++) {
                 const float overlap = truth.overlap(detections.predicted[i]);
                 if (overlap > bestOverlap) {
@@ -377,25 +417,40 @@ float EvalDetection(const QString &amp;predictedInput, const QString &amp;truthInput, co
                     bestIndex = i;
                 }
             }
-            Detection predicted = detections.predicted.takeAt(bestIndex);
-            points.append(DetectionOperatingPoint(predicted.confidence, bestOverlap));
+            const Detection predicted = detections.predicted.takeAt(bestIndex);
+            resolvedDetections.append(ResolvedDetection(predicted.confidence, bestOverlap));
         }
         foreach (const Detection &detection, detections.predicted)
-            points.append(DetectionOperatingPoint(detection.confidence, 0));
+            resolvedDetections.append(ResolvedDetection(detection.confidence, 0));
         for (int i=0; i<detections.truth.size(); i++)
-            points.append(DetectionOperatingPoint(-std::numeric_limits<float>::max(), 0));
+            falseNegativeDetections.append(ResolvedDetection(-std::numeric_limits<float>::max(), 0));
     }
-    std::sort(points.begin(), points.end());
+    std::sort(resolvedDetections.begin(), resolvedDetections.end());
     QStringList lines;
     lines.append("Plot, X, Y");
+    lines.append(computeDetectionResults(resolvedDetections, truth.size(), true));
+    lines.append(computeDetectionResults(resolvedDetections, truth.size(), false));
+
+    float averageOverlap;
+    { // Overlap Density
+        QList<ResolvedDetection> allDetections; allDetections << resolvedDetections << falseNegativeDetections;
+        const int keep = qMin(allDetections.size(), Max_Points);
+        lines.reserve(lines.size() + keep);
+        float totalOverlap = 0;
+        for (int i=0; i<keep; i++) {
+            const float overlap = allDetections[double(i) / double(keep-1) * double(allDetections.size()-1)].overlap;
+            totalOverlap += overlap;
+            lines.append(QString("Overlap,%1,1").arg(QString::number(allDetections[double(i) / double(keep-1) * double(allDetections.size()-1)].overlap)));
+        }
+        averageOverlap = totalOverlap / keep;
+    }
-    // TODO: finish implementing
-
-    (void) csv;
-    return 0;
+    QtUtils::writeFile(csv, lines);
+    qDebug("Average Overlap = %.3f", averageOverlap);
+    return averageOverlap;
 }
 void EvalRegression(const QString &predictedInput, const QString &truthInput)
@@ -79,7 +79,7 @@ struct RPlot
     Pivot major, minor;
-    RPlot(QStringList files, const br::File &destination, bool isEvalFormat = true)
+    RPlot(QStringList files, const File &destination, bool isEvalFormat = true)
     {
         if (files.isEmpty()) qFatal("Empty file list.");
         qSort(files.begin(), files.end(), sortFiles);
@@ -214,7 +214,7 @@ struct RPlot
 };
 // Does not work if dataset folder starts with a number
-bool Plot(const QStringList &files, const br::File &destination, bool show)
+bool Plot(const QStringList &files, const File &destination, bool show)
 {
     qDebug("Plotting %d file(s) to %s", files.size(), qPrintable(destination));
@@ -272,6 +272,15 @@ bool Plot(const QStringList &amp;files, const br::File &amp;destination, bool show)
     return p.finalize(show);
 }
+bool PlotDetection(const QStringList &files, const File &destination, bool show)
+{
+    qDebug("Plotting %d detection file(s) to %s", files.size(), qPrintable(destination));
+
+    RPlot p(files, destination, false);
+
+    return p.finalize(show);
+}
+
 bool PlotMetadata(const QStringList &files, const QString &columns, bool show)
 {
     qDebug("Plotting %d metadata file(s) for columns %s", files.size(), qPrintable(columns));
@@ -24,7 +24,8 @@
 namespace br
 {
-    bool Plot(const QStringList &files, const br::File &destination, bool show = false);
+    bool Plot(const QStringList &files, const File &destination, bool show = false);
+    bool PlotDetection(const QStringList &files, const File &destination, bool show = false);
     bool PlotMetadata(const QStringList &files, const QString &destination, bool show = false);
 }
@@ -105,6 +105,7 @@ void QtUtils::writeFile(const QString &amp;file, const QString &amp;data)
 void QtUtils::writeFile(const QString &file, const QByteArray &data, int compression)
 {
+    if (file.isEmpty()) return;
     const QString baseName = QFileInfo(file).baseName();
     const QByteArray contents = (compression == 0) ? data : qCompress(data, compression);
     if (baseName == "terminal") {
@@ -82,9 +82,9 @@ void br_eval_clustering(const char *csv, const char *gallery)
     EvalClustering(csv, gallery);
 }
-void br_eval_detection(const char *predicted_gallery, const char *truth_gallery)
+float br_eval_detection(const char *predicted_gallery, const char *truth_gallery, const char *csv)
 {
-    EvalDetection(predicted_gallery, truth_gallery);
+    return EvalDetection(predicted_gallery, truth_gallery, csv);
 }
 void br_eval_regression(const char *predicted_gallery, const char *truth_gallery)
@@ -172,6 +172,11 @@ bool br_plot(int num_files, const char *files[], const char *destination, bool s
     return Plot(QtUtils::toStringList(num_files, files), destination, show);
 }
+bool br_plot_detection(int num_files, const char *files[], const char *destination, bool show)
+{
+    return PlotDetection(QtUtils::toStringList(num_files, files), destination, show);
+}
+
 bool br_plot_metadata(int num_files, const char *files[], const char *columns, bool show)
 {
     return PlotMetadata(QtUtils::toStringList(num_files, files), columns, show);
@@ -146,9 +146,8 @@ BR_EXPORT float br_eval(const char *simmat, const char *mask, const char *csv = 
 /*!
  * \brief Evaluates and prints classification accuracy to terminal.
- * \param predicted_input The predicted br::Gallery.
- * \param truth_input The ground truth br::Gallery.
- * \see br_enroll
+ * \param predicted_gallery The predicted br::Gallery.
+ * \param truth_gallery The ground truth br::Gallery.
  */
 BR_EXPORT void br_eval_classification(const char *predicted_gallery, const char *truth_gallery);
@@ -163,16 +162,16 @@ BR_EXPORT void br_eval_clustering(const char *csv, const char *gallery);
 /*!
  * \brief Evaluates and prints detection accuracy to terminal.
  * \param predicted_gallery The predicted br::Gallery.
- * \param truth_galery The ground truth br::Gallery.
- * \see br_enroll
+ * \param truth_gallery The ground truth br::Gallery.
+ * \param csv Optional \c .csv file to contain performance metrics.
+ * \return Average detection bounding box overlap.
  */
-BR_EXPORT void br_eval_detection(const char *predicted_gallery, const char *truth_gallery);
+BR_EXPORT float br_eval_detection(const char *predicted_gallery, const char *truth_gallery, const char *csv = "");
 /*!
  * \brief Evaluates regression accuracy to disk.
- * \param predicted_input The predicted br::Gallery.
- * \param truth_input The ground truth br::Gallery.
- * \see br_enroll
+ * \param predicted_gallery The predicted br::Gallery.
+ * \param truth_gallery The ground truth br::Gallery.
  */
 BR_EXPORT void br_eval_regression(const char *predicted_gallery, const char *truth_gallery);
@@ -241,7 +240,7 @@ BR_EXPORT const char *br_most_recent_message();
 BR_EXPORT const char *br_objects(const char *abstractions = ".*", const char *implementations = ".*", bool parameters = true);
 /*!
- * \brief Renders performance figures for a set of <tt>.csv</tt> files.
+ * \brief Renders recognition performance figures for a set of <tt>.csv</tt> files created by \ref br_eval.
  *
  * In order of their output, the figures are:
  * -# Metadata table
@@ -263,11 +262,17 @@ BR_EXPORT const char *br_objects(const char *abstractions = &quot;.*&quot;, const char *im
  * \return Returns \c true on success. Returns false on a failure to compile the figures due to a missing, out of date, or incomplete \c R installation.
  * \note This function requires a current <a href="http://www.r-project.org/">R</a> installation with the following packages:
  * \code install.packages(c("ggplot2", "gplots", "reshape", "scales")) \endcode
- * \see br_plot_metadata
+ * \see br_eval
  */
 BR_EXPORT bool br_plot(int num_files, const char *files[], const char *destination, bool show = false);
 /*!
+ * \brief Renders detection performance figures for a set of <tt>.csv</tt> files created by \ref br_eval_detection.
+ * \see br_plot
+ */
+BR_EXPORT bool br_plot_detection(int num_files, const char *files[], const char *destination, bool show = false);
+
+/*!
  * \brief Renders metadata figures for a set of <tt>.csv</tt> files with specified columns.
  *
  * Several files will be created:
@@ -17,7 +17,7 @@
 /*!
  * \mainpage
  * \section overview Overview
- * OpenBR \cite openbr is a framework for investigating new modalities, improving existing algorithms, interfacing with commercial systems, measuring recognition performance, and deploying automated biometric systems.
+ * OpenBR \cite klontz2013open is a framework for investigating new modalities, improving existing algorithms, interfacing with commercial systems, measuring recognition performance, and deploying automated biometric systems.
  * The project is designed to facilitate rapid algorithm prototyping, and features a mature core framework, flexible plugin system, and support for open and closed source development.
  * Off-the-shelf algorithms are also available for specific modalities including \ref cpp_face_recognition, \ref cpp_age_estimation, and \ref cpp_gender_estimation.
  *
@@ -27,14 +27,24 @@
  * \image html "abstraction.svg" "The two principal software artifacts are the shared library 'openbr' and command line application 'br'."
  *
  * \section get_started Get Started
- * - \ref installation - \copybrief installation
- * - \ref qmake_integration - \copybrief qmake_integration
+ * - \ref introduction - A high-level technical overview of OpenBR.
+ * - \ref installation - A hacker's guide to building, editing, and running OpenBR.
+ * - \ref qmake_integration - Add OpenBR to your Qt <tt>.pro</tt> project.
  *
  * \section learn_more Learn More
- * - \ref algorithm_grammar - \copybrief algorithm_grammar
- * - \ref cli - \copybrief cli
- * - \ref c_sdk - \copybrief c_sdk
- * - \ref cpp_plugin_sdk - \copybrief cpp_plugin_sdk
+ * - \ref algorithm_grammar - How algorithms are constructed from string descriptions.
+ * - \ref cli - Command line wrapper of the \ref c_sdk.
+ * - \ref c_sdk - High-level API for running algorithms and evaluating results.
+ * - \ref cpp_plugin_sdk - Plugin API for extending OpenBR functionality.
+ * - \ref bee - A <a href="http://www.nist.gov/index.html">NIST</a> standard for evaluating biometric algorithms.
+ */
+
+/*!
+ * \page introduction Introduction
+ * \brief A high-level technical overview of OpenBR.
+ *
+ * We strongly encourage users new to OpenBR to read our <a href="www.openbiometrics.org/publications/klontz2013open.pdf"><b>publication</b></a> for an introduction to the core concepts.
+ * Researchers incorporating OpenBR into their own work are kindly requested to cite this paper.
  */
 /*!
@@ -354,7 +354,7 @@ struct Template : public QList&lt;cv::Mat&gt;
     inline const cv::Mat &m() const { static const cv::Mat NullMatrix;
                                       return isEmpty() ? qFatal("Empty template."), NullMatrix : last(); } /*!< \brief Idiom to treat the template as a matrix. */
     inline cv::Mat &m() { return isEmpty() ? append(cv::Mat()), last() : last(); } /*!< \brief Idiom to treat the template as a matrix. */
-    inline const File &operator()() const { return file; }
+    inline operator const File &() const { return file; }
     inline cv::Mat &operator=(const cv::Mat &other) { return m() = other; } /*!< \brief Idiom to treat the template as a matrix. */
     inline operator const cv::Mat&() const { return m(); } /*!< \brief Idiom to treat the template as a matrix. */
     inline operator cv::Mat&() { return m(); } /*!< \brief Idiom to treat the template as a matrix. */
+#include "openbr_internal.h"
+
+namespace br
+{
+
+/*!
+ * \ingroup transforms
+ * \brief Passes along n sequential frames to the next transform.
+ * \author Josh Klontz \cite jklontz
+ *
+ * For a video with m frames, AggregateFrames would create a total of m-n+1 sequences ([0,n] ... [m-n+1, m]).
+ */
+class AggregateFrames : public TimeVaryingTransform
+{
+    Q_OBJECT
+    Q_PROPERTY(int n READ get_n WRITE set_n RESET reset_n STORED false)
+    BR_PROPERTY(int, n, 1)
+
+    TemplateList buffer;
+
+    void train(const TemplateList &data)
+    {
+        (void) data;
+    }
+
+    void projectUpdate(const Template &src, Template &dst)
+    {
+        buffer.append(src);
+        if (buffer.size() < n) return;
+        foreach (const Template &t, buffer) dst.append(t);
+        dst.file = buffer.takeFirst().file;
+    }
+
+    void store(QDataStream &stream) const
+    {
+        (void) stream;
+    }
+
+    void load(QDataStream &stream)
+    {
+        (void) stream;
+    }
+};
+
+BR_REGISTER(Transform, AggregateFrames)
+
+} // namespace br
+
+#include "frames.moc"
@@ -269,67 +269,6 @@ class matrixGallery : public Gallery
 BR_REGISTER(Gallery, matrixGallery)
 /*!
- * \ingroup galleries
-  * \brief Treat a video as a gallery, making a single template from each frame
-  * \author Charles Otto \cite caotto
-  */
-class aviGallery : public  Gallery
-{
-    Q_OBJECT
-
-    TemplateList output_set;
-    QScopedPointer<cv::VideoWriter> videoOut;
-
-    ~aviGallery()
-    {
-        if (videoOut && videoOut->isOpened()) videoOut->release();
-    }
-
-    TemplateList readBlock(bool * done)
-    {
-        std::string fname = file.name.toStdString();
-        *done = true;
-
-        TemplateList output;
-        if (!file.exists())
-            return output;
-
-        cv::VideoCapture videoReader(file.name.toStdString());
-
-        bool open = videoReader.isOpened();
-
-        while (open) {
-            cv::Mat frame;
-            
-            open = videoReader.read(frame);
-            if (!open) break;
-            output.append(Template());
-            output.back() = frame.clone();
-        }
-
-        return TemplateList();
-    }
-
-    void write(const Template & t)
-    {
-        if (videoOut.isNull() || !videoOut->isOpened()) {
-            int fourcc = OpenCVUtils::getFourcc(); 
-            videoOut.reset(new cv::VideoWriter(qPrintable(file.name), fourcc, 30, t.m().size()));
-        }
-
-        if (!videoOut->isOpened()) {
-            qWarning("Failed to open %s for writing\n", qPrintable(file.name));
-            return;
-        }
-
-        foreach(const cv::Mat & m, t) {
-            videoOut->write(m);
-        }
-    }
-};
-BR_REGISTER(Gallery, aviGallery)
-
-/*!
  * \ingroup initializers
  * \brief Initialization support for memGallery.
  * \author Josh Klontz \cite jklontz
@@ -284,8 +284,11 @@ public:
             {
                 qDebug("Video not open!");
             }
+        } else {
+            // Yes, we should specify absolute path:
+            // http://stackoverflow.com/questions/9396459/loading-a-video-in-opencv-in-python
+            video.open(QFileInfo(input.file.name).absoluteFilePath().toStdString());
         }
-        else video.open(input.file.name.toStdString());
         return video.isOpened();
     }
@@ -63,4 +63,6 @@ if [ ! -d ../data/KTH/vid ]; then
     unzip ${vidclass}.zip -d ../data/KTH/vid/${vidclass}
 	rm ${vidclass}.zip
   done
+  # this file is corrupted
+  rm ../data/KTH/vid/boxing/person01_boxing_d4_uncomp.avi
 fi
-# Doxyfile 1.8.2
+# Doxyfile 1.8.4
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
 #
+# All text after a double hash (##) is considered a comment and is placed
+# in front of the TAG it is preceding .
 # All text after a hash (#) is considered a comment and will be ignored.
 # The format is:
 #       TAG = value [value, ...]
@@ -70,9 +72,9 @@ CREATE_SUBDIRS         = NO
 # Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
 # Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
 # Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+# messages), Korean, Korean-en, Latvian, Lithuanian, Norwegian, Macedonian,
+# Persian, Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic,
+# Slovak, Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
 OUTPUT_LANGUAGE        = English
@@ -252,10 +254,10 @@ EXTENSION_MAPPING      =
 MARKDOWN_SUPPORT       = YES
-# When enabled doxygen tries to link words that correspond to documented classes,
-# or namespaces to their corresponding documentation. Such a link can be
-# prevented in individual cases by by putting a % sign in front of the word or
-# globally by setting AUTOLINK_SUPPORT to NO.
+# When enabled doxygen tries to link words that correspond to documented
+# classes, or namespaces to their corresponding documentation. Such a link can
+# be prevented in individual cases by by putting a % sign in front of the word
+# or globally by setting AUTOLINK_SUPPORT to NO.
 AUTOLINK_SUPPORT       = YES
@@ -279,7 +281,12 @@ CPP_CLI_SUPPORT        = NO
 SIP_SUPPORT            = NO
-# For Microsoft's IDL there are propget and propput attributes to indicate getter and setter methods for a property. Setting this option to YES (the default) will make doxygen replace the get and set methods by a property in the documentation. This will only work if the methods are indeed getting or setting a simple type. If this is not the case, or you want to show the methods anyway, you should set this option to NO.
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES (the
+# default) will make doxygen replace the get and set methods by a property in
+# the documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
 IDL_PROPERTY_SUPPORT   = YES
@@ -306,11 +313,11 @@ SUBGROUPING            = YES
 INLINE_GROUPED_CLASSES = NO
 # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
-# unions with only public data fields will be shown inline in the documentation
-# of the scope in which they are defined (i.e. file, namespace, or group
-# documentation), provided this scope is documented. If set to NO (the default),
-# structs, classes, and unions are shown on a separate page (for HTML and Man
-# pages) or section (for LaTeX and RTF).
+# unions with only public data fields or simple typedef fields will be shown
+# inline in the documentation of the scope in which they are defined (i.e. file,
+# namespace, or group documentation), provided this scope is documented. If set
+# to NO (the default), structs, classes, and unions are shown on a separate
+# page (for HTML and Man pages) or section (for LaTeX and RTF).
 INLINE_SIMPLE_STRUCTS  = NO
@@ -324,30 +331,14 @@ INLINE_SIMPLE_STRUCTS  = NO
 TYPEDEF_HIDES_STRUCT   = NO
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penalty.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will roughly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
-
-SYMBOL_CACHE_SIZE      = 0
-
-# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
-# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
-# their name and scope. Since this can be an expensive process and often the
-# same symbol appear multiple times in the code, doxygen keeps a cache of
-# pre-resolved symbols. If the cache is too small doxygen will become slower.
-# If the cache is too large, memory is wasted. The cache size is given by this
-# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
+# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
+# cache is used to resolve symbols given their name and scope. Since this can
+# be an expensive process and often the same symbol appear multiple times in
+# the code, doxygen keeps a cache of pre-resolved symbols. If the cache is too
+# small doxygen will become slower. If the cache is too large, memory is wasted.
+# The cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid
+# range is 0..9, the default is 0, corresponding to a cache size of 2^16 = 65536
+# symbols.
 LOOKUP_CACHE_SIZE      = 0
@@ -358,7 +349,7 @@ LOOKUP_CACHE_SIZE      = 0
 # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
 # documentation are documented, even if no documentation was available.
 # Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+# the EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES
 EXTRACT_ALL            = YES
@@ -539,7 +530,8 @@ GENERATE_BUGLIST       = YES
 GENERATE_DEPRECATEDLIST= YES
 # The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
+# documentation sections, marked by \if section-label ... \endif
+# and \cond section-label ... \endcond blocks.
 ENABLED_SECTIONS       =
@@ -597,7 +589,8 @@ LAYOUT_FILE            =
 # requires the bibtex tool to be installed. See also
 # http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
 # of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path.
+# feature you need bibtex and perl available in the search path. Do not use
+# file names with spaces, bibtex cannot handle them.
 CITE_BIB_FILES         = ${BR_SHARE_DIR}/openbr.bib
@@ -680,7 +673,8 @@ INPUT_ENCODING         = UTF-8
 # *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
 # *.f90 *.f *.for *.vhd *.vhdl
-FILE_PATTERNS          = *.h *.cpp
+FILE_PATTERNS          = *.h \
+                         *.cpp
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories
 # should be searched for input files as well. Possible values are YES and NO.
@@ -763,8 +757,10 @@ IMAGE_PATH             = ${CMAKE_SOURCE_DIR}/share/openbr
 # is the value of the INPUT_FILTER tag, and <input-file> is the name of an
 # input file. Doxygen will then use the output that the filter program writes
 # to standard output.
-# If FILTER_PATTERNS is specified, this tag will be
-# ignored.
+# If FILTER_PATTERNS is specified, this tag will be ignored.
+# Note that the filter must not add or remove lines; it is applied before the
+# code is scanned, but not when the output code is generated. If lines are added
+# or removed, the anchors will not be placed correctly.
 INPUT_FILTER           =
@@ -793,6 +789,13 @@ FILTER_SOURCE_FILES    = NO
 FILTER_SOURCE_PATTERNS =
+# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page
+# (index.html). This can be useful if you have a project on for instance GitHub
+# and want reuse the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -934,7 +937,7 @@ HTML_EXTRA_STYLESHEET  =
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
 # that these files will be copied to the base HTML output directory. Use the
-# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
+# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
 # files. In the HTML_STYLESHEET file, use the file name only. Also note that
 # the files will be copied as-is; there are no commands or markers available.
@@ -1202,6 +1205,13 @@ FORMULA_TRANSPARENT    = YES
 USE_MATHJAX            = NO
+# When MathJax is enabled you can set the default output format to be used for
+# the MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and
+# SVG. The default value is HTML-CSS, which is slower, but has the best
+# compatibility.
+
+MATHJAX_FORMAT         = HTML-CSS
+
 # When MathJax is enabled you need to specify the location relative to the
 # HTML output directory using the MATHJAX_RELPATH option. The destination
 # directory should contain the MathJax.js script. For instance, if the mathjax
@@ -1219,6 +1229,11 @@ MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
 MATHJAX_EXTENSIONS     =
+# The MATHJAX_CODEFILE tag can be used to specify a file with javascript
+# pieces of code that will be used on startup of the MathJax code.
+
+MATHJAX_CODEFILE       =
+
 # When the SEARCHENGINE tag is enabled doxygen will generate a search box
 # for the HTML output. The underlying search engine uses javascript
 # and DHTML and should work on any modern browser. Note that when using
@@ -1230,15 +1245,55 @@ MATHJAX_EXTENSIONS     =
 SEARCHENGINE           = YES
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
+# implemented using a web server instead of a web client using Javascript.
+# There are two flavours of web server based search depending on the
+# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
+# searching and an index file used by the script. When EXTERNAL_SEARCH is
+# enabled the indexing and searching needs to be provided by external tools.
+# See the manual for details.
 SERVER_BASED_SEARCH    = NO
+# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain
+# the search results. Doxygen ships with an example indexer (doxyindexer) and
+# search engine (doxysearch.cgi) which are based on the open source search
+# engine library Xapian. See the manual for configuration details.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will returned the search results when EXTERNAL_SEARCH is enabled.
+# Doxygen ships with an example search engine (doxysearch) which is based on
+# the open source search engine library Xapian. See the manual for configuration
+# details.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id
+# of to a relative location where the documentation can be found.
+# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ...
+
+EXTRA_SEARCH_MAPPINGS  =
+
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
@@ -1276,7 +1331,7 @@ COMPACT_LATEX          = NO
 # The PAPER_TYPE tag can be used to set the paper type that is used
 # by the printer. Possible values are: a4, letter, legal and
-# executive. If left blank a4wide will be used.
+# executive. If left blank a4 will be used.
 PAPER_TYPE             = a4
@@ -1299,6 +1354,13 @@ LATEX_HEADER           =
 LATEX_FOOTER           =
+# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images
+# or other source files which should be copied to the LaTeX output directory.
+# Note that the files will be copied as-is; there are no commands or markers
+# available.
+
+LATEX_EXTRA_FILES      =
+
 # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
 # is prepared for conversion to pdf (using ps2pdf). The pdf file will
 # contain links (just like the HTML output) instead of page references
@@ -1444,6 +1506,21 @@ XML_DTD                =
 XML_PROGRAMLISTING     = YES
 #---------------------------------------------------------------------------
+# configuration options related to the DOCBOOK output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_DOCBOOK tag is set to YES Doxygen will generate DOCBOOK files
+# that can be used to generate PDF.
+
+GENERATE_DOCBOOK       = NO
+
+# The DOCBOOK_OUTPUT tag is used to specify where the DOCBOOK pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
+# front of it. If left blank docbook will be used as the default path.
+
+DOCBOOK_OUTPUT         = docbook
+
+#---------------------------------------------------------------------------
 # configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
@@ -1539,7 +1616,8 @@ INCLUDE_FILE_PATTERNS  =
 # undefined via #undef or recursively expanded use the := operator
 # instead of the = operator.
-PREDEFINED             = BR_EXPORT= __cplusplus
+PREDEFINED             = BR_EXPORT= \
+                         __cplusplus
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
 # this tag can be used to specify a list of macro names that should be expanded.
@@ -1592,6 +1670,12 @@ ALLEXTERNALS           = NO
 EXTERNAL_GROUPS        = YES
+# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed
+# in the related pages index. If set to NO, only the current project's
+# pages will be listed.
+
+EXTERNAL_PAGES         = YES
+
 # The PERL_PATH should be the absolute path and name of the perl script
 # interpreter (i.e. the result of `which perl').
@@ -1688,7 +1772,7 @@ UML_LOOK               = NO
 # the class node. If there are many fields or methods and many nodes the
 # graph may become too big to be useful. The UML_LIMIT_NUM_FIELDS
 # threshold limits the number of items for each type to make the size more
-# managable. Set this to 0 for no limit. Note that the threshold may be
+# manageable. Set this to 0 for no limit. Note that the threshold may be
 # exceeded by 50% before the limit is enforced.
 UML_LIMIT_NUM_FIELDS   = 10
@@ -30,16 +30,11 @@
 	Title = {ottochar at gmail.com}}
 @misc{lbestrowden,
-	Author = {Lacey S. Best-Rowden},
+	Author = {{Lacey S. Best-Rowden}},
 	Howpublished = {https://github.com/lbestrowden},
 	Title = {bestrow1 at msu.edu}}
 % Software
-@misc{OpenBR,
-	Author = {Joshua C. Klontz and Dr. Mark J. Burge},
-	Title = {{OpenBR} - {Open} {Biometric} {Recognition}},
-	Year = {2012}}
-
 @misc{libface,
 	Howpublished = {http://libface.sourceforge.net/file/Home.html},
 	Title = {libface},
@@ -227,6 +222,14 @@
   pages={1--8},
 }
+@inproceedings{klontz2013open,
+  title={{Open Source Biometric Recognition}},
+  author={Klontz et al.},
+  booktitle={Biometrics: Theory, Applications and Systems (BTAS), 2013 IEEE Sixth International Conference on},
+  year={2013},
+  organization={IEEE}
+}
+
 @inproceedings{li2009hfb,
   title={The {HFB} face database for heterogeneous face biometrics research},
   author={Li, Stan Z and Lei, Zhen and Ao, Meng},