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

Charles Otto
2 parents 72a5968a 7dd634b3
Showing 9 changed files with 141 additions and 88 deletions
openbr/core/common.h
openbr/core/fuse.cpp
openbr/gui/imageviewer.cpp
openbr/openbr_export.cpp
openbr/openbr_plugin.cpp
openbr/plugins/distance.cpp
openbr/plugins/output.cpp
openbr/plugins/quality.cpp
share/openbr/Doxyfile.in
@@ -153,11 +153,10 @@ void MeanStdDev(const V&lt;T&gt; &amp;vals, double *mean, double *stddev)
 template<template<typename> class C, typename T>
 T Median(C<T> vals, T *q1 = 0, T *q3 = 0)
 {
-    if (vals.isEmpty()) return std::numeric_limits<float>::quiet_NaN();
     qSort(vals);
-    if (q1 != 0) *q1 = vals[1*vals.size()/4];
-    if (q3 != 0) *q3 = vals[3*vals.size()/4];
-    return vals[vals.size()/2];
+    if (q1 != 0) *q1 = vals.isEmpty() ? 0 : vals[1*vals.size()/4];
+    if (q3 != 0) *q3 = vals.isEmpty() ? 0 : vals[3*vals.size()/4];
+    return vals.isEmpty() ? 0 : vals[vals.size()/2];
 }
 /*!
@@ -14,7 +14,6 @@
  * limitations under the License.                                            *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-#include <QFile>
 #include <QList>
 #include <QStringList>
 #include <limits>
@@ -36,7 +36,8 @@ void br::ImageViewer::setDefaultText(const QString &amp;text)
 void br::ImageViewer::setImage(const QString &file, bool async)
 {
-    src = QImage(file);
+    if(file.isNull()) src = QImage(); // Gets rid of runtime FileEngine::open warning
+    else src = QImage(file);
     updatePixmap(async);
 }
@@ -24,7 +24,7 @@
  * OpenBR originated within The MITRE Corporation from a need to streamline the process of prototyping new algorithms.
  * The project was later published as open source software under the <a href="http://www.apache.org/licenses/LICENSE-2.0.html">Apache 2</a> license and is <i>free for academic and commercial use</i>.
  *
- * \image html "share/openbr/abstraction.svg" "The two principal software artifacts are the shared library 'openbr' and command line application 'br'."
+ * \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
@@ -70,13 +70,13 @@ $ export DYLD_FRAMEWORK_PATH=../lib:${DYLD_FRAMEWORK_PATH}
  *  No configuration is necessary!
  *
  * \section installation_license_dongle License Dongle
- *  If you were given a USB License Dongle, then dongle must be in the computer in order to use the SDK.
+ *  In the unlikely event that you were given a USB License Dongle, then dongle must be in the computer in order to use the SDK.
  *  No configuration of the dongle is needed.
  *
  * \section installation_done Start Working
  * To test for successful installation:
 \verbatim
-$ cd bin/
+$ cd bin
 $ br -help
 \endverbatim
  */
@@ -180,7 +180,7 @@ $ br -help
  *  $ cmake -G "MinGW Makefiles" -DBUILD_opencv_java=OFF -DBUILD_opencv_world=ON -DBUILD_PERF_TESTS=OFF -DBUILD_TESTS=OFF -DWITH_FFMPEG=OFF -DCMAKE_BUILD_TYPE=Debug ..
  *  $ mingw32-make
  *  $ mingw32-make install
- *  $ cmake -DCMAKE_BUILD_TYPE=Release
+ *  $ cmake -DCMAKE_BUILD_TYPE=Release ..
  *  $ mingw32-make
  *  $ mingw32-make install
  *  $ mingw32-make clean
@@ -244,7 +244,7 @@ $ br -help
 /*!
  * \page osx_clang OS X Mountain Lion - Clang/LLVM 3.1 - x64
  * -# Download and install the latest "Xcode" and "Command Line Tools" from the <a href="https://developer.apple.com/downloads/index.action#">Apple Developer Downloads</a> page.
- * -# <a href="http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz">Download CMake 2.8.10.2</a>.
+ * -# <a href="http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz">Download CMake 2.8.10.2</a>
  * \code
  * $ cd ~/Downloads
  * $ tar -xf cmake-2.8.10.2.tar.gz
@@ -253,22 +253,22 @@ $ br -help
  * $ make -j4
  * $ sudo make install
  * $ cd ..
- * $ rm -r cmake-2.8.10.2
+ * $ rm -rf cmake-2.8.10.2*
  * \endcode
- * -# <a href="http://downloads.sourceforge.net/project/opencvlibrary/opencv-unix/2.4.4/OpenCV-2.4.4.tar.bz2">Download OpenCV 2.4.4</a>.
+ * -# <a href="http://downloads.sourceforge.net/project/opencvlibrary/opencv-unix/2.4.5/opencv-2.4.5.tar.gz">Download OpenCV 2.4.5</a>
  * \code
  * $ cd ~/Downloads
- * $ tar -xf OpenCV-2.4.4.tar.bz2
- * $ cd OpenCV-2.4.4
+ * $ tar -xf opencv-2.4.5.tar.gz
+ * $ cd opencv-2.4.5
  * $ mkdir build
  * $ cd build
- * $ cmake -DBUILD_opencv_java=OFF -DBUILD_opencv_world=OFF -DCMAKE_BUILD_TYPE=Release ..
+ * $ cmake -DCMAKE_BUILD_TYPE=Release ..
  * $ make -j4
  * $ sudo make install
  * $ cd ../..
- * $ rm -r OpenCV-2.4.4
+ * $ rm -rf opencv-2.4.5*
  * \endcode
- * -# <a href="http://releases.qt-project.org/qt5/5.0.1/qt-mac-opensource-5.0.1-clang-offline.dmg">Download Qt 5.0.1</a> and install.
+ * -# <a href="http://download.qt-project.org/official_releases/qt/5.0/5.0.2/qt-mac-opensource-5.0.2-clang-offline.dmg">Download and install Qt 5.0.2</a>
  * -# Create a <a href="github.com">GitHub</a> account, follow their instructions for <a href="https://help.github.com/articles/set-up-git">setting up Git</a>.
  * \code
  * $ git clone https://github.com/biometrics/openbr.git
@@ -281,27 +281,34 @@ $ br -help
  * $ cd openbr
  * $ mkdir build
  * $ cd build
- * $ cmake -DCMAKE_PREFIX_PATH=~/Qt5.0.1/5.0.1/clang_64 -DCMAKE_BUILD_TYPE=Release ..
+ * $ cmake -DCMAKE_PREFIX_PATH=~/Qt5.0.2/5.0.2/clang_64 -DCMAKE_BUILD_TYPE=Release ..
  * $ make -j4
  * $ sudo make install
  * \endcode
  * -# Hack OpenBR!
  *  -# Open Qt Creator IDE
  *  \code
- *  $ open ~/Qt5.0.1/Qt\ Creator.app
+ *  $ open ~/Qt5.0.2/Qt\ Creator.app
  *  \endcode
  *  -# From the Qt Creator "File" menu select "Open File or Project...".
- *  -# Select "~/openbr/CMakeLists.txt" then "Open".
- *  -# Browse to your prexisting build directory "~/openbr/build" then select "Continue".
+ *  -# Select "openbr/CMakeLists.txt" then "Open".
+ *  -# Browse to your prexisting build directory "openbr/build" then select "Continue".
  *  -# Select "Run CMake" then "Done".
  *  -# You're all set! You can find more information on Qt Creator <a href="http://qt-project.org/doc/qtcreator">here</a> if you need.
+ * -# (Optional) Test OpenBR!
+ * \code
+ * $ cd openbr/scripts
+ * $ ./downloadDatasets.sh
+ * $ cd ../build
+ * $ make test
+ * \endcode
  * -# (Optional) Package OpenBR!
  * \code
  * $ cd openbr/build
- * $ make package
+ * $ cpack -G TGZ
  * \endcode
  * -# (Optional) Build OpenBR documentation!
- *  -# <a href="ftp://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.2.src.tar.gz">Download Doxygen 1.8.2</a> and install:
+ *  -# <a href="ftp://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.2.src.tar.gz">Download Doxygen 1.8.2</a>
  *  \code
  *  $ cd ~/Downloads
  *  $ tar -xf doxygen-1.8.2.src.tar.gz
@@ -310,9 +317,9 @@ $ br -help
  *  $ make -j4
  *  $ sudo make install
  *  $ cd ..
- *  $ rm -r doxygen-1.8.2
+ *  $ rm -rf doxygen-1.8.2*
  *  \endcode
- *  -# Modify build settings and recompile:
+ *  -# Modify build settings and recompile.
  *  \code
  *  $ cd openbr/build
  *  $ cmake -DBR_BUILD_DOCUMENTATION=ON ..
@@ -389,8 +389,6 @@ TemplateList TemplateList::fromGallery(const br::File &amp;gallery)
         if (crossValidate > 0) srand(0);
         for (int i=newTemplates.size()-1; i>=0; i--) {
-            newTemplates[i].file.append(gallery.localMetadata());
-            newTemplates[i].file.append(file.localMetadata());
             newTemplates[i].file.set("Index", i+templates.size());
             newTemplates[i].file.set("Gallery", gallery.name);
@@ -298,46 +298,6 @@ class IdenticalDistance : public Distance
 BR_REGISTER(Distance, IdenticalDistance)
-class HeatMapDistance : public Distance
-{
-    Q_OBJECT
-    Q_PROPERTY(br::Distance* distance READ get_distance WRITE set_distance RESET reset_distance STORED false)
-    BR_PROPERTY(br::Distance*, distance, make("Dist(L2)"))
-    Q_PROPERTY(int rows READ get_rows WRITE set_rows RESET reset_rows STORED false)
-    BR_PROPERTY(int, rows, -1)
-    Q_PROPERTY(int cols READ get_cols WRITE set_cols RESET reset_cols STORED false)
-    BR_PROPERTY(int, cols, -1)
-
-    void train(const TemplateList &src)
-    {
-        distance->train(src);
-    }
-
-
-    float compare(const Template &a, const Template &b) const
-    {
-        qFatal("HeatMap expects a TemplateList");
-
-        (void) a; (void) b;
-    }
-
-   void compare(const TemplateList &target, const TemplateList &query, Output *output) const
-    {
-        if (rows*cols > target.size()) qFatal("Incompatible heatmap comparison dimensionality");
-
-        int index = 0;
-        for (int col = 0; col < cols; col++) {
-            for (int row = 0; row < rows; row++) {
-                float score = distance->compare(target[index],query[index]);
-                output->setRelative(score, row, col);
-                index++;
-            }
-        }
-    }
-};
-
-BR_REGISTER(Distance, HeatMapDistance)
-
 } // namespace br
 #include "distance.moc"
@@ -97,33 +97,25 @@ BR_REGISTER(Output, csvOutput)
 class heatOutput : public MatrixOutput
 {
     Q_OBJECT
-    Q_PROPERTY(int rows READ get_rows WRITE set_rows RESET reset_rows STORED false)
-    BR_PROPERTY(int, rows, -1)
-    Q_PROPERTY(int cols READ get_cols WRITE set_cols RESET reset_cols STORED false)
-    BR_PROPERTY(int, cols, -1)
+    Q_PROPERTY(int patches READ get_patches WRITE set_patches RESET reset_patches STORED false)
+    BR_PROPERTY(int, patches, -1);
     ~heatOutput()
     {
         if (file.isNull() || targetFiles.isEmpty() || queryFiles.isEmpty()) return;
-        if (rows*cols > targetFiles.size()) qFatal("Incompatible heatmap output dimensionality");
-
         QStringList lines;
-        for (int col = 0; col < cols; col++) {
-            QStringList words;
-            for (int row = 0; row < rows; row++)
-                words.append(toString(row,col));
-            lines.append(words.join(","));
+        for (int i=0; i<data.rows; i++) {
+            lines.append(toString(i,0));
         }
         QtUtils::writeFile(file, lines);
     }
     void initialize(const FileList &targetFiles, const FileList &queryFiles)
     {
-        if (rows == -1 || cols == -1) qFatal("heatOutput requires dimensionality");
-
+        if (patches == -1) qFatal("Heat output requires the number of patches");
         Output::initialize(targetFiles, queryFiles);
-        data.create(rows, cols, CV_32FC1);
+        data.create(patches, 1, CV_32FC1);
     }
 };
@@ -150,8 +150,7 @@ class MatchProbabilityDistance : public Distance
     Q_OBJECT
     Q_PROPERTY(br::Distance* distance READ get_distance WRITE set_distance RESET reset_distance STORED false)
     Q_PROPERTY(bool gaussian READ get_gaussian WRITE set_gaussian RESET reset_gaussian STORED false)
-    BR_PROPERTY(br::Distance*, distance, make("Dist(L2)"))
-    BR_PROPERTY(bool, gaussian, true)
+    Q_PROPERTY(bool crossModality READ get_crossModality WRITE set_crossModality RESET reset_crossModality STORED false)
     MP mp;
@@ -170,6 +169,7 @@ class MatchProbabilityDistance : public Distance
             for (int j=0; j<i; j++) {
                 const float score = matrixOutput.data()->data.at<float>(i, j);
                 if (score == -std::numeric_limits<float>::max()) continue;
+                if (crossModality) if(src[i].file.get<QString>("Modality") == src[j].file.get<QString>("Modality")) continue;
                 if (labels[i] == labels[j]) genuineScores.append(score);
                 else                        impostorScores.append(score);
             }
@@ -181,9 +181,8 @@ class MatchProbabilityDistance : public Distance
     float compare(const Template &target, const Template &query) const
     {
         float rawScore = distance->compare(target, query);
-        return -log(rawScore+1);
-        //if (rawScore == -std::numeric_limits<float>::max()) return rawScore;
-        //return mp(rawScore, gaussian);
+        if (rawScore == -std::numeric_limits<float>::max()) return rawScore;
+        return mp(rawScore, gaussian);
     }
     void store(QDataStream &stream) const
@@ -197,12 +196,110 @@ class MatchProbabilityDistance : public Distance
         distance->load(stream);
         stream >> mp;
     }
+
+protected:
+    BR_PROPERTY(br::Distance*, distance, make("Dist(L2)"))
+    BR_PROPERTY(bool, gaussian, true)
+    BR_PROPERTY(bool, crossModality, false)
 };
 BR_REGISTER(Distance, MatchProbabilityDistance)
 /*!
  * \ingroup distances
+ * \brief Match Probability modification for heat maps \cite klare12
+ * \author Scott Klum \cite sklum
+ */
+class HeatMapDistance : public Distance
+{
+    Q_OBJECT
+    Q_PROPERTY(br::Distance* distance READ get_distance WRITE set_distance RESET reset_distance STORED false)
+    Q_PROPERTY(bool gaussian READ get_gaussian WRITE set_gaussian RESET reset_gaussian STORED false)
+    Q_PROPERTY(bool crossModality READ get_crossModality WRITE set_crossModality RESET reset_crossModality STORED false)
+    Q_PROPERTY(int step READ get_step WRITE set_step RESET reset_step STORED false)
+    BR_PROPERTY(br::Distance*, distance, make("Dist(L2)"))
+    BR_PROPERTY(bool, gaussian, true)
+    BR_PROPERTY(bool, crossModality, false)
+    BR_PROPERTY(int, step, 1)
+
+    QList<MP> mp;
+
+    void train(const TemplateList &src)
+    {
+        distance->train(src);
+
+        const QList<int> labels = src.indexProperty("Subject");
+
+        QList<TemplateList> patches;
+
+        // Split src into list of TemplateLists of corresponding patches across all Templates
+        for (int i=0; i<step; i++) {
+            TemplateList patchBuffer;
+            for (int j=i; j<src.size(); j+=step) {
+                patchBuffer.append(src[j]);
+            }
+            patches.append(patchBuffer);
+            patchBuffer.clear();
+        }
+
+        QScopedPointer<MatrixOutput> matrixOutput(MatrixOutput::make(FileList(patches[0].size()), FileList(patches[0].size())));
+
+        for (int i=0; i<step; i++) {
+            distance->compare(patches[i], patches[i], matrixOutput.data());
+            QList<float> genuineScores, impostorScores;
+            genuineScores.reserve(step);
+            impostorScores.reserve(step);
+            for (int j=0; j<matrixOutput.data()->data.rows; j++) {
+                for (int k=0; k<j; k++) {
+                    const float score = matrixOutput.data()->data.at<float>(j, k);
+                    if (score == -std::numeric_limits<float>::max()) continue;
+                    if (crossModality) if(src[j*step].file.get<QString>("MODALITY") == src[k*step].file.get<QString>("MODALITY")) continue;
+                    if (labels[j*step] == labels[k*step]) genuineScores.append(score);
+                    else                                                        impostorScores.append(score);
+                }
+            }
+
+            mp.append(MP(genuineScores, impostorScores));
+        }
+    }
+
+    float compare(const Template &target, const Template &query) const
+    {
+        (void) target;
+        (void) query;
+        qFatal("You did this wrong");
+
+        return 0;
+    }
+
+    // Switch this to template list version, use compare(template, template) in
+    // heat map distance, and index into the proper match probability
+    void compare(const TemplateList &target, const TemplateList &query, Output *output) const
+    {
+        for (int i=0; i<step; i++) {
+            float rawScore = distance->compare(target[i],query[i]);
+            if (rawScore == -std::numeric_limits<float>::max()) output->setRelative(rawScore, i, 0);
+            else output->setRelative(mp[i](rawScore, gaussian), i, 0);
+        }
+     }
+
+    void store(QDataStream &stream) const
+    {
+        distance->store(stream);
+        stream << mp;
+    }
+
+    void load(QDataStream &stream)
+    {
+        distance->load(stream);
+        stream >> mp;
+    }
+};
+
+BR_REGISTER(Distance, HeatMapDistance)
+
+/*!
+ * \ingroup distances
  * \brief Linear normalizes of a distance so the mean impostor score is 0 and the mean genuine score is 1.
  * \author Josh Klontz \cite jklontz
  */
@@ -755,7 +755,7 @@ EXAMPLE_RECURSIVE      = YES
 # directories that contain image that are included in the documentation (see
 # the \image command).
-IMAGE_PATH             = ${CMAKE_SOURCE_DIR}
+IMAGE_PATH             = ${CMAKE_SOURCE_DIR}/share/openbr
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program