diff --git a/openbr/core/bee.cpp b/openbr/core/bee.cpp
index facafe9..6458049 100644
--- a/openbr/core/bee.cpp
+++ b/openbr/core/bee.cpp
@@ -14,17 +14,10 @@
  * limitations under the License.                                            *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#include <QFile>
-#include <QFileInfo>
-#include <QHash>
-#include <QMap>
-#include <QRegExp>
+#include <QtCore>
 #ifndef BR_EMBEDDED
 #include <QtXml>
 #endif // BR_EMBEDDED
-#include <algorithm>
-#include <limits>
-#include <openbr/openbr_plugin.h>
 
 #include "bee.h"
 #include "opencvutils.h"
@@ -33,23 +26,21 @@
 using namespace cv;
 using namespace br;
 
-/**** BEE ****/
-FileList BEE::readSigset(const File &sigset, bool ignoreMetadata)
+namespace BEE
+{
+
+FileList readSigset(const File &sigset, bool ignoreMetadata)
 {
     FileList fileList;
 
 #ifndef BR_EMBEDDED
     QDomDocument doc(sigset.fileName());
-    QFile file(sigset.resolved());
-    bool success;
-    success = file.open(QIODevice::ReadOnly); if (!success) qFatal("Unable to open %s for reading.", qPrintable(sigset));
-    success = doc.setContent(&file);
-
-    file.close();
-
-    if (!success) {
-        qWarning("Unable to parse %s.", qPrintable(sigset));
-        return fileList;
+    {
+        QFile file(sigset.resolved());
+        if (!file.open(QIODevice::ReadOnly))
+            qFatal("Unable to open %s for reading.", qPrintable(sigset));
+        if (!doc.setContent(&file))
+            qFatal("Unable to parse %s.", qPrintable(sigset));
     }
 
     QDomElement docElem = doc.documentElement();
@@ -105,7 +96,7 @@ FileList BEE::readSigset(const File &sigset, bool ignoreMetadata)
     return fileList;
 }
 
-void BEE::writeSigset(const QString &sigset, const br::FileList &files, bool ignoreMetadata)
+void writeSigset(const QString &sigset, const FileList &files, bool ignoreMetadata)
 {
     QStringList lines; lines.reserve(3*files.size()+3);
     lines.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
@@ -137,7 +128,7 @@ void BEE::writeSigset(const QString &sigset, const br::FileList &files, bool ign
     QtUtils::writeFile(sigset, lines);
 }
 
-Mat BEE::readMat(const br::File &matrix, QString *targetSigset, QString *querySigset)
+Mat readMatrix(const File &matrix, QString *targetSigset, QString *querySigset)
 {
     QFile file(matrix);
     bool success = file.open(QFile::ReadOnly);
@@ -148,7 +139,6 @@ Mat BEE::readMat(const br::File &matrix, QString *targetSigset, QString *querySi
     bool isDistance = (format[0] == 'D');
     if (format[1] != '2') qFatal("Invalid matrix header.");
 
-
     // Read sigsets
     if (targetSigset != NULL) *targetSigset = file.readLine().simplified();
     else                      file.readLine();
@@ -156,57 +146,52 @@ Mat BEE::readMat(const br::File &matrix, QString *targetSigset, QString *querySi
     else                     file.readLine();
 
     // Get matrix size
-    QStringList words = QString(file.readLine()).split(" ");
-    int rows = words[1].toInt();
-    int cols = words[2].toInt();
-
-    bool isMask = words[0][1] == 'B';
-    int typeSize = isMask ? sizeof(BEE::Mask_t) : sizeof(BEE::Simmat_t);
+    const QStringList words = QString(file.readLine()).split(" ");
+    const int rows = words[1].toInt();
+    const int cols = words[2].toInt();
+    const bool isMask = words[0][1] == 'B';
+    const int typeSize = isMask ? sizeof(BEE::MaskValue) : sizeof(BEE::SimmatValue);
 
     // Get matrix data
     Mat m;
     if (isMask)
-        m.create(rows, cols, OpenCVType<BEE::Mask_t,1>::make());
+        m.create(rows, cols, OpenCVType<BEE::MaskValue,1>::make());
     else
-        m.create(rows, cols, OpenCVType<BEE::Simmat_t,1>::make());
+        m.create(rows, cols, OpenCVType<BEE::SimmatValue,1>::make());
 
-    qint64 bytesPerRow = m.cols * typeSize;
-
-    for (int i=0; i < m.rows;i++)
-    {
-        cv::Mat aRow = m.row(i);
+    const qint64 bytesPerRow = m.cols * typeSize;
+    for (int i=0; i<m.rows; i++) {
+        Mat aRow = m.row(i);
         qint64 bytesRead = file.read((char *)aRow.data, bytesPerRow);
         if (bytesRead != bytesPerRow)
-        {
             qFatal("Didn't read complete row!");
-        }
     }
     if (!file.atEnd())
         qFatal("Expected matrix end of file.");
     file.close();
 
     Mat result = m;
-    if (isDistance ^ matrix.get<bool>("negate", false)) m.convertTo(result, -1, -1);
-
+    if (isDistance ^ matrix.get<bool>("negate", false))
+        m.convertTo(result, -1, -1);
     return result;
 }
 
-void BEE::writeMat(const Mat &m, const QString &matrix, const QString &targetSigset, const QString &querySigset)
+void writeMatrix(const Mat &m, const QString &fileName, const QString &targetSigset, const QString &querySigset)
 {
     bool isMask = false;
-    if (m.type() == OpenCVType<BEE::Mask_t,1>::make())
+    if (m.type() == OpenCVType<BEE::MaskValue,1>::make())
         isMask = true;
-    else if (m.type() != OpenCVType<BEE::Simmat_t,1>::make())
+    else if (m.type() != OpenCVType<BEE::SimmatValue,1>::make())
         qFatal("Invalid matrix type, .mtx files can only contain single channel float or uchar matrices.");
 
-    int elemSize = isMask ? sizeof(BEE::Mask_t) : sizeof(BEE::Simmat_t);
-
-    QString matrixType = isMask ? "B" : "F";
+    const int elemSize = isMask ? sizeof(BEE::MaskValue) : sizeof(BEE::SimmatValue);
+    const QString matrixType = isMask ? "B" : "F";
 
     char buff[4];
-    QFile file(matrix);
+    QFile file(fileName);
     QtUtils::touchDir(file);
-    bool success = file.open(QFile::WriteOnly); if (!success) qFatal("Unable to open %s for writing.", qPrintable(matrix));
+    if (!file.open(QFile::WriteOnly))
+        qFatal("Unable to open %s for writing.", qPrintable(fileName));
     file.write("S2\n");
     file.write(qPrintable(targetSigset));
     file.write("\n");
@@ -219,7 +204,7 @@ void BEE::writeMat(const Mat &m, const QString &matrix, const QString &targetSig
     file.write(" ");
     file.write(qPrintable(QString::number(m.cols)));
     file.write(" ");
-    int endian = 0x12345678;
+    const int endian = 0x12345678;
     memcpy(&buff, &endian, 4);
     file.write(buff, 4);
     file.write("\n");
@@ -227,57 +212,58 @@ void BEE::writeMat(const Mat &m, const QString &matrix, const QString &targetSig
     file.close();
 }
 
-void BEE::readMatrixHeader(const QString &matrix, QString *targetSigset, QString *querySigset)
+void readMatrixHeader(const QString &matrix, QString *targetSigset, QString *querySigset)
 {
     qDebug("Reading %s header.", qPrintable(matrix));
-    readMat(matrix, targetSigset, querySigset);
+    readMatrix(matrix, targetSigset, querySigset);
 }
 
-void BEE::writeMatrixHeader(const QString &matrix, const QString &targetSigset, const QString &querySigset)
+void writeMatrixHeader(const QString &matrix, const QString &targetSigset, const QString &querySigset)
 {
     qDebug("Writing %s header to %s %s.", qPrintable(matrix), qPrintable(targetSigset), qPrintable(querySigset));
-
-    writeMat(readMat(matrix), matrix, targetSigset, querySigset);
+    writeMatrix(readMatrix(matrix), matrix, targetSigset, querySigset);
 }
 
-void BEE::makeMask(const QString &targetInput, const QString &queryInput, const QString &mask)
+void makeMask(const QString &targetInput, const QString &queryInput, const QString &mask)
 {
     qDebug("Making mask from %s and %s to %s", qPrintable(targetInput), qPrintable(queryInput), qPrintable(mask));
-    FileList targets = TemplateList::fromGallery(targetInput).files();
-    FileList queries = (queryInput == ".") ? targets : TemplateList::fromGallery(queryInput).files();
-    int partitions = targets.first().get<int>("crossValidate");
-    if (partitions == 0) writeMat(makeMask(targets, queries), mask, targetInput, queryInput);
-    else {
+    const FileList targets = TemplateList::fromGallery(targetInput).files();
+    const FileList queries = (queryInput == ".") ? targets : TemplateList::fromGallery(queryInput).files();
+    const int partitions = targets.first().get<int>("crossValidate");
+    if (partitions == 0) {
+        writeMatrix(makeMask(targets, queries), mask, targetInput, queryInput);
+    } else {
         if (!mask.contains("%1")) qFatal("Mask file name missing partition number place marker (%%1)");
         for (int i=0; i<partitions; i++) {
-            writeMat(makeMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
+            writeMatrix(makeMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
         }
     }
 }
 
-void BEE::makePairwiseMask(const QString &targetInput, const QString &queryInput, const QString &mask)
+void makePairwiseMask(const QString &targetInput, const QString &queryInput, const QString &mask)
 {
-    FileList targets = TemplateList::fromGallery(targetInput).files();
-    FileList queries = (queryInput == ".") ? targets : TemplateList::fromGallery(queryInput).files();
-    int partitions = targets.first().get<int>("crossValidate");
-    if (partitions == 0) writeMat(makePairwiseMask(targets, queries), mask, targetInput, queryInput);
-    else {
+    qDebug("Making pairwise mask from %s and %s to %s", qPrintable(targetInput), qPrintable(queryInput), qPrintable(mask));
+    const FileList targets = TemplateList::fromGallery(targetInput).files();
+    const FileList queries = (queryInput == ".") ? targets : TemplateList::fromGallery(queryInput).files();
+    const int partitions = targets.first().get<int>("crossValidate");
+    if (partitions == 0) {
+        writeMatrix(makePairwiseMask(targets, queries), mask, targetInput, queryInput);
+    } else {
         if (!mask.contains("%1")) qFatal("Mask file name missing partition number place marker (%%1)");
         for (int i=0; i<partitions; i++) {
-            writeMat(makePairwiseMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
+            writeMatrix(makePairwiseMask(targets, queries, i), mask.arg(i), targetInput, queryInput);
         }
     }
 }
 
-cv::Mat BEE::makePairwiseMask(const br::FileList &targets, const br::FileList &queries, int partition)
+Mat makePairwiseMask(const FileList &targets, const FileList &queries, int partition)
 {
-    // Direct use of "Label" isn't general, also would prefer to use indexProperty, rather than
+    // TODO: Direct use of "Label" isn't general, also would prefer to use indexProperty, rather than
     // doing string comparisons (but that isn't implemented yet for FileList) -cao
-    QList<QString> targetLabels = File::get<QString>(targets, "Label", "-1");
-    QList<QString> queryLabels = File::get<QString>(queries, "Label", "-1");
-
-    QList<int> targetPartitions = targets.crossValidationPartitions();
-    QList<int> queryPartitions = queries.crossValidationPartitions();
+    const QStringList targetLabels = File::get<QString>(targets, "Label", "-1");
+    const QStringList queryLabels = File::get<QString>(queries, "Label", "-1");
+    const QList<int> targetPartitions = targets.crossValidationPartitions();
+    const QList<int> queryPartitions = queries.crossValidationPartitions();
 
     Mat mask(queries.size(), 1, CV_8UC1);
     for (int i=0; i<queries.size(); i++) {
@@ -289,7 +275,7 @@ cv::Mat BEE::makePairwiseMask(const br::FileList &targets, const br::FileList &q
         const QString labelB = targetLabels[i];
         const int partitionB = targetPartitions[i];
 
-        Mask_t val;
+        MaskValue val;
         if      (fileA == fileB)           val = DontCare;
         else if (labelA == "-1")           val = DontCare;
         else if (labelB == "-1")           val = DontCare;
@@ -298,23 +284,21 @@ cv::Mat BEE::makePairwiseMask(const br::FileList &targets, const br::FileList &q
         else if (partitionB != partition)  val = DontCare;
         else if (labelA == labelB)         val = Match;
         else                               val = NonMatch;
-        mask.at<Mask_t>(i,0) = val;
+        mask.at<MaskValue>(i,0) = val;
     }
 
     return mask;
 }
 
-cv::Mat BEE::makeMask(const br::FileList &targets, const br::FileList &queries, int partition)
+Mat makeMask(const FileList &targets, const FileList &queries, int partition)
 {
-    // Direct use of "Label" isn't general, also would prefer to use indexProperty, rather than
+    // TODO: Direct use of "Label" isn't general, also would prefer to use indexProperty, rather than
     // doing string comparisons (but that isn't implemented yet for FileList) -cao
-    QList<QString> targetLabels = File::get<QString>(targets, "Label", "-1");
-    QList<QString> queryLabels = File::get<QString>(queries, "Label", "-1");
-
-    QList<int> targetPartitions = targets.crossValidationPartitions();
-    QList<int> queryPartitions = queries.crossValidationPartitions();
-
-    QList<bool> targetsOnly = File::get<bool>(queries, "targetOnly", false);
+    const QStringList targetLabels = File::get<QString>(targets, "Label", "-1");
+    const QStringList queryLabels = File::get<QString>(queries, "Label", "-1");
+    const QList<int> targetPartitions = targets.crossValidationPartitions();
+    const QList<int> queryPartitions = queries.crossValidationPartitions();
+    const QList<bool> targetsOnly = File::get<bool>(queries, "targetOnly", false);
 
     Mat mask(queries.size(), targets.size(), CV_8UC1);
     for (int i=0; i<queries.size(); i++) {
@@ -328,7 +312,7 @@ cv::Mat BEE::makeMask(const br::FileList &targets, const br::FileList &queries, 
             const QString labelB = targetLabels[j];
             const int partitionB = targetPartitions[j];
 
-            Mask_t val;
+            MaskValue val;
             if      (fileA == fileB)           val = DontCare;
             else if (targetOnly)               val = DontCare;
             else if (labelA == "-1")           val = DontCare;
@@ -338,14 +322,14 @@ cv::Mat BEE::makeMask(const br::FileList &targets, const br::FileList &queries, 
             else if (partitionB != partition)  val = DontCare;
             else if (labelA == labelB)         val = Match;
             else                               val = NonMatch;
-            mask.at<Mask_t>(i,j) = val;
+            mask.at<MaskValue>(i,j) = val;
         }
     }
 
     return mask;
 }
 
-void BEE::combineMasks(const QStringList &inputMasks, const QString &outputMask, const QString &method)
+void combineMasks(const QStringList &inputMasks, const QString &outputMask, const QString &method)
 {
     qDebug("Combining %d masks to %s with method %s", inputMasks.size(), qPrintable(outputMask), qPrintable(method));
 
@@ -356,12 +340,12 @@ void BEE::combineMasks(const QStringList &inputMasks, const QString &outputMask,
 
     QList<Mat> masks;
     foreach (const QString &inputMask, inputMasks)
-        masks.append(readMat(inputMask));
-    if (masks.size() < 2) qFatal("Expected at least two masks.");
+        masks.append(readMatrix(inputMask));
+    if (masks.size() < 2)
+        qFatal("Expected at least two masks.");
 
     const int rows = masks.first().rows;
     const int columns = masks.first().cols;
-
     Mat combinedMask(rows, columns, CV_8UC1);
     for (int i=0; i<rows; i++) {
         for (int j=0; j<columns; j++) {
@@ -369,7 +353,7 @@ void BEE::combineMasks(const QStringList &inputMasks, const QString &outputMask,
             int imposterCount = 0;
             int dontcareCount = 0;
             for (int k=0; k<masks.size(); k++) {
-                switch (masks[k].at<Mask_t>(i,j)) {
+                switch (masks[k].at<MaskValue>(i,j)) {
                   case Match:
                     genuineCount++;
                     break;
@@ -383,14 +367,16 @@ void BEE::combineMasks(const QStringList &inputMasks, const QString &outputMask,
             }
             if ((genuineCount != 0) && (imposterCount != 0)) qFatal("Comparison is both a genuine and an imposter.");
 
-            Mask_t val;
+            MaskValue val;
             if      (genuineCount > 0)  val = Match;
             else if (imposterCount > 0) val = NonMatch;
             else                        val = DontCare;
             if (AND && (dontcareCount > 0)) val = DontCare;
-            combinedMask.at<Mask_t>(i,j) = val;
+            combinedMask.at<MaskValue>(i,j) = val;
         }
     }
 
-    writeMat(combinedMask, outputMask, "Combined_Targets", "Combined_Queries");
+    writeMatrix(combinedMask, outputMask, "Combined_Targets", "Combined_Queries");
 }
+
+} // namespace BEE
diff --git a/openbr/core/bee.h b/openbr/core/bee.h
index 313708a..e4c7fa9 100644
--- a/openbr/core/bee.h
+++ b/openbr/core/bee.h
@@ -17,30 +17,29 @@
 #ifndef BEE_BEE_H
 #define BEE_BEE_H
 
-#include <QList>
-#include <QPair>
-#include <QHash>
 #include <QString>
 #include <QStringList>
 #include <opencv2/core/core.hpp>
 #include <openbr/openbr_plugin.h>
 
-/*** Functions for parsing BEE style data structures. ***/
+/*!
+ * Functions for parsing NIST BEE data structures.
+ */
 namespace BEE
 {
-    const uchar Match(0xff);
-    const uchar NonMatch(0x7f);
-    const uchar DontCare(0x00);
-    typedef float Simmat_t;
-    typedef uchar Mask_t;
+    typedef float SimmatValue;
+    typedef uchar MaskValue;
+    const MaskValue Match(0xff);
+    const MaskValue NonMatch(0x7f);
+    const MaskValue DontCare(0x00);
 
     // Sigset
     br::FileList readSigset(const br::File &sigset, bool ignoreMetadata = false);
     void writeSigset(const QString &sigset, const br::FileList &files, bool ignoreMetadata = false);
 
     // Matrix
-    cv::Mat readMat(const br::File & mat, QString * targetSigset = NULL, QString * querySigset = NULL);
-    void writeMat(const cv::Mat &m, const QString &simmat, const QString &targetSigset = "Unknown_Target", const QString &querySigset = "Unknown_Query");
+    cv::Mat readMatrix(const br::File &mat, QString *targetSigset = NULL, QString *querySigset = NULL);
+    void writeMatrix(const cv::Mat &m, const QString &fileName, const QString &targetSigset = "Unknown_Target", const QString &querySigset = "Unknown_Query");
     void readMatrixHeader(const QString &matrix, QString *targetSigset, QString *querySigset);
     void writeMatrixHeader(const QString &matrix, const QString &targetSigset, const QString &querySigset);
 
diff --git a/openbr/core/core.cpp b/openbr/core/core.cpp
index bf13564..20b82d4 100644
--- a/openbr/core/core.cpp
+++ b/openbr/core/core.cpp
@@ -672,7 +672,7 @@ void br::Convert(const File &fileType, const File &inputFile, const File &output
         while (!done) after->writeBlock(before->readBlock(&done));
     } else if (fileType == "Output") {
         QString target, query;
-        cv::Mat m = BEE::readMat(inputFile, &target, &query);
+        cv::Mat m = BEE::readMatrix(inputFile, &target, &query);
         const FileList targetFiles = TemplateList::fromGallery(target).files();
         const FileList queryFiles = TemplateList::fromGallery(query).files();
 
diff --git a/openbr/core/eval.cpp b/openbr/core/eval.cpp
index e71fd9c..f3bc694 100644
--- a/openbr/core/eval.cpp
+++ b/openbr/core/eval.cpp
@@ -99,7 +99,7 @@ float Evaluate(const QString &simmat, const QString &mask, const QString &csv)
     QString target, query;
     Mat scores;
     if (simmat.endsWith(".mtx")) {
-        scores = BEE::readMat(simmat, &target, &query);
+        scores = BEE::readMatrix(simmat, &target, &query);
     } else {
         QScopedPointer<Format> format(Factory<Format>::make(simmat));
         scores = format->read();
@@ -144,8 +144,8 @@ float Evaluate(const Mat &simmat, const Mat &mask, const QString &csv)
     int genuineCount = 0, impostorCount = 0, numNaNs = 0;
     for (int i=0; i<simmat.rows; i++) {
         for (int j=0; j<simmat.cols; j++) {
-            const BEE::Mask_t mask_val = mask.at<BEE::Mask_t>(i,j);
-            const BEE::Simmat_t simmat_val = simmat.at<BEE::Simmat_t>(i,j);
+            const BEE::MaskValue mask_val = mask.at<BEE::MaskValue>(i,j);
+            const BEE::SimmatValue simmat_val = simmat.at<BEE::SimmatValue>(i,j);
             if (mask_val == BEE::DontCare) continue;
             if (simmat_val != simmat_val) { numNaNs++; continue; }
             comparisons.append(Comparison(simmat_val, j, i, mask_val == BEE::Match));
@@ -315,7 +315,7 @@ float InplaceEval(const QString & simmat, const QString & target, const QString 
     qint64 cols = words[2].toLongLong();
 
     bool isMask = words[0][1] == 'B';
-    qint64 typeSize = isMask ? sizeof(BEE::Mask_t) : sizeof(BEE::Simmat_t);
+    qint64 typeSize = isMask ? sizeof(BEE::MaskValue) : sizeof(BEE::SimmatValue);
 
     // Get matrix data
     qint64 rowSize = cols * typeSize;
diff --git a/openbr/core/fuse.cpp b/openbr/core/fuse.cpp
index 146fa90..56e4782 100644
--- a/openbr/core/fuse.cpp
+++ b/openbr/core/fuse.cpp
@@ -39,7 +39,7 @@ static void normalizeMatrix(Mat &matrix, const Mat &mask, const QString &method)
     for (int i=0; i<matrix.rows; i++) {
         for (int j=0; j<matrix.cols; j++) {
             float val = matrix.at<float>(i,j);
-            if ((mask.at<BEE::Mask_t>(i,j) == BEE::DontCare) ||
+            if ((mask.at<BEE::MaskValue>(i,j) == BEE::DontCare) ||
                 (val == -std::numeric_limits<float>::max()) ||
                 (val ==  std::numeric_limits<float>::max()))
                 continue;
@@ -55,7 +55,7 @@ static void normalizeMatrix(Mat &matrix, const Mat &mask, const QString &method)
     if (method == "MinMax") {
         for (int i=0; i<matrix.rows; i++) {
             for (int j=0; j<matrix.cols; j++) {
-                if (mask.at<BEE::Mask_t>(i,j) == BEE::DontCare) continue;
+                if (mask.at<BEE::MaskValue>(i,j) == BEE::DontCare) continue;
                 float &val = matrix.at<float>(i,j);
                 if      (val == -std::numeric_limits<float>::max()) val = 0;
                 else if (val ==  std::numeric_limits<float>::max()) val = 1;
@@ -66,7 +66,7 @@ static void normalizeMatrix(Mat &matrix, const Mat &mask, const QString &method)
         if (stddev == 0) qFatal("Stddev is 0.");
         for (int i=0; i<matrix.rows; i++) {
             for (int j=0; j<matrix.cols; j++) {
-                if (mask.at<BEE::Mask_t>(i,j) == BEE::DontCare) continue;
+                if (mask.at<BEE::MaskValue>(i,j) == BEE::DontCare) continue;
                 float &val = matrix.at<float>(i,j);
                 if      (val == -std::numeric_limits<float>::max()) val = (min - mean) / stddev;
                 else if (val ==  std::numeric_limits<float>::max()) val = (max - mean) / stddev;
@@ -85,7 +85,7 @@ void br::Fuse(const QStringList &inputSimmats, const QString &normalization, con
     QString target, query, previousTarget, previousQuery;
     QList<Mat> originalMatrices;
     foreach (const QString &simmat, inputSimmats) {
-        originalMatrices.append(BEE::readMat(simmat,&target,&query));
+        originalMatrices.append(BEE::readMatrix(simmat,&target,&query));
         // Make we're fusing score matrices for the same set of targets and querys
         if (!previousTarget.isEmpty() && !previousQuery.isEmpty() && (previousTarget != target || previousQuery != query))
             qFatal("Target or query files are not the same across fused matrices.");
@@ -163,5 +163,5 @@ void br::Fuse(const QStringList &inputSimmats, const QString &normalization, con
 
     } while (partition < crossValidate);
 
-    BEE::writeMat(buffer, outputSimmat);
+    BEE::writeMatrix(buffer, outputSimmat);
 }
diff --git a/openbr/plugins/format.cpp b/openbr/plugins/format.cpp
index b573b8b..66a8f4b 100644
--- a/openbr/plugins/format.cpp
+++ b/openbr/plugins/format.cpp
@@ -293,12 +293,12 @@ class mtxFormat : public Format
 
     Template read() const
     {
-        return BEE::readMat(file);
+        return BEE::readMatrix(file);
     }
 
     void write(const Template &t) const
     {
-        BEE::writeMat(t, file);
+        BEE::writeMatrix(t, file);
     }
 };