Peter M. Groen / openbr

Commit c3e880e6c15be09cd4dae8f067aa3cdbb2d02f06

Authored by Charles Otto
1 parent 0d62d619

Refactor BEE::readMask and readSimmat to a common readMat function 

Since .mtx files include a matrix type in their header, we don't really need
separate functions to read similarity matrices and masks.

This drops special case support for creating identity matrices via readSimmat
and readMask (since in that case, there is no actual header to read to get a
matrix type).
Inline Side-by-side
Showing 7 changed files with 26 additions and 67 deletions
openbr/core/bee.cpp
  View file @c3e880e
... ... @@ -135,43 +135,8 @@ void BEE::writeSigset(const QString &sigset, const br::FileList &files, bool ign
135 135 QtUtils::writeFile(sigset, lines);
136 136 }
137 137  
138   -template <typename T>
139   -Mat readMatrix(const br::File &matrix, QString *targetSigset = NULL, QString *querySigset = NULL)
  138 +Mat BEE::readMat(const br::File &matrix, QString *targetSigset, QString *querySigset)
140 139 {
141   - // Special case matrix construction
142   - if (matrix == "Identity") {
143   - int rows = matrix.get<int>("rows", -1);
144   - int columns = matrix.get<int>("columns", -1);
145   - const int size = matrix.get<int>("size", -1);
146   - if (size != -1) {
147   - if (rows == -1) rows = size;
148   - if (columns == -1) columns = size;
149   - }
150   - const int step = matrix.get<int>("step", 1);
151   - if (rows % step != 0) qFatal("Step does not divide rows evenly.");
152   - if (columns % step != 0) qFatal("Step does not divide columns evenly.");
153   -
154   - if (sizeof(T) == sizeof(BEE::Mask_t)) {
155   - const bool selfSimilar = matrix.get<bool>("selfSimilar", false);
156   -
157   - Mat m(rows, columns, CV_8UC1);
158   - m.setTo(BEE::NonMatch);
159   - for (int i=0; i<std::min(rows, columns); i+=step)
160   - for (int j=0; j<step; j++)
161   - for (int k=0; k<step; k++)
162   - m.at<BEE::Mask_t>(i+j,i+k) = ((selfSimilar && (j == k)) ? BEE::DontCare : BEE::Match);
163   - return m;
164   - } else if (sizeof(T) == sizeof(BEE::Simmat_t)) {
165   - Mat m(rows, columns, CV_32FC1);
166   - m.setTo(0);
167   - for (int i=0; i<std::min(rows, columns); i+=step)
168   - for (int j=0; j<step; j++)
169   - for (int k=0; k<step; k++)
170   - m.at<BEE::Simmat_t>(i+j,i+k) = 1;
171   - return m;
172   - }
173   - }
174   -
175 140 QFile file(matrix);
176 141 bool success = file.open(QFile::ReadOnly);
177 142 if (!success) qFatal("Unable to open %s for reading.", qPrintable(matrix.name));
... ... @@ -181,6 +146,7 @@ Mat readMatrix(const br::File &amp;matrix, QString *targetSigset = NULL, QString *qu
181 146 bool isDistance = (format[0] == 'D');
182 147 if (format[1] != '2') qFatal("Invalid matrix header.");
183 148  
  149 +
184 150 // Read sigsets
185 151 if (targetSigset != NULL) *targetSigset = file.readLine().simplified();
186 152 else file.readLine();
... ... @@ -192,9 +158,17 @@ Mat readMatrix(const br::File &amp;matrix, QString *targetSigset = NULL, QString *qu
192 158 int rows = words[1].toInt();
193 159 int cols = words[2].toInt();
194 160  
  161 + bool isMask = words[0][1] == 'B';
  162 + int typeSize = isMask ? sizeof(BEE::Mask_t) : sizeof(BEE::Simmat_t);
  163 +
195 164 // Get matrix data
196   - qint64 bytesExpected = (qint64)rows*(qint64)cols*(qint64)sizeof(T);
197   - Mat m(rows, cols, OpenCVType<T,1>::make());
  165 + qint64 bytesExpected = (qint64)rows*(qint64)cols*(qint64)typeSize;
  166 + Mat m;
  167 + if (isMask)
  168 + m.create(rows, cols, OpenCVType<BEE::Mask_t,1>::make());
  169 + else
  170 + m.create(rows, cols, OpenCVType<BEE::Simmat_t,1>::make());
  171 +
198 172 qint64 read = file.read((char*)m.data, bytesExpected);
199 173 if (read != bytesExpected)
200 174 qFatal("Invalid matrix size.");
... ... @@ -206,16 +180,6 @@ Mat readMatrix(const br::File &amp;matrix, QString *targetSigset = NULL, QString *qu
206 180 return result;
207 181 }
208 182  
209   -Mat BEE::readSimmat(const br::File &simmat, QString *targetSigset, QString *querySigset)
210   -{
211   - return readMatrix<Simmat_t>(simmat, targetSigset, querySigset);
212   -}
213   -
214   -Mat BEE::readMask(const br::File &mask)
215   -{
216   - return readMatrix<Mask_t>(mask);
217   -}
218   -
219 183 template <typename T>
220 184 void writeMatrix(const Mat &m, const QString &matrix, const QString &targetSigset, const QString &querySigset)
221 185 {
... ... @@ -264,15 +228,15 @@ void BEE::writeMask(const Mat &amp;m, const QString &amp;mask, const QString &amp;targetSigs
264 228 void BEE::readMatrixHeader(const QString &matrix, QString *targetSigset, QString *querySigset)
265 229 {
266 230 qDebug("Reading %s header.", qPrintable(matrix));
267   - if (matrix.endsWith("mask")) readMatrix< Mask_t>(matrix, targetSigset, querySigset);
268   - else readMatrix<Simmat_t>(matrix, targetSigset, querySigset);
  231 + readMat(matrix, targetSigset, querySigset);
269 232 }
270 233  
271 234 void BEE::writeMatrixHeader(const QString &matrix, const QString &targetSigset, const QString &querySigset)
272 235 {
273 236 qDebug("Writing %s header to %s %s.", qPrintable(matrix), qPrintable(targetSigset), qPrintable(querySigset));
274   - if (matrix.endsWith("mask")) writeMatrix< Mask_t>(readMatrix< Mask_t>(matrix), matrix, targetSigset, querySigset);
275   - else writeMatrix<Simmat_t>(readMatrix<Simmat_t>(matrix), matrix, targetSigset, querySigset);
  237 +
  238 + if (matrix.endsWith("mask")) writeMatrix< Mask_t>(readMat(matrix), matrix, targetSigset, querySigset);
  239 + else writeMatrix<Simmat_t>(readMat(matrix), matrix, targetSigset, querySigset);
276 240 }
277 241  
278 242 void BEE::makeMask(const QString &targetInput, const QString &queryInput, const QString &mask)
... ... @@ -387,7 +351,7 @@ void BEE::combineMasks(const QStringList &amp;inputMasks, const QString &amp;outputMask,
387 351  
388 352 QList<Mat> masks;
389 353 foreach (const QString &inputMask, inputMasks)
390   - masks.append(readMask(inputMask));
  354 + masks.append(readMat(inputMask));
391 355 if (masks.size() < 2) qFatal("Expected at least two masks.");
392 356  
393 357 const int rows = masks.first().rows;
... ...
openbr/core/bee.h
  View file @c3e880e
... ... @@ -39,8 +39,7 @@ namespace BEE
39 39 void writeSigset(const QString &sigset, const br::FileList &files, bool ignoreMetadata = false);
40 40  
41 41 // Matrix
42   - cv::Mat readSimmat(const br::File &simmat, QString *targetSigset = NULL, QString *querySigset = NULL);
43   - cv::Mat readMask(const br::File &mask);
  42 + cv::Mat readMat(const br::File & mat, QString * targetSigset = NULL, QString * querySigset = NULL);
44 43 void writeSimmat(const cv::Mat &m, const QString &simmat, const QString &targetSigset = "Unknown_Target", const QString &querySigset = "Unknown_Query");
45 44 void writeMask(const cv::Mat &m, const QString &mask, const QString &targetSigset = "Unknown_Target", const QString &querySigset = "Unknown_Query");
46 45 void readMatrixHeader(const QString &matrix, QString *targetSigset, QString *querySigset);
... ...
openbr/core/cluster.cpp
  View file @c3e880e
... ... @@ -99,7 +99,7 @@ Neighborhood getNeighborhood(const QStringList &amp;simmats)
99 99 int currentRows = -1;
100 100 int columnOffset = 0;
101 101 for (int j=0; j<numGalleries; j++) {
102   - cv::Mat m = BEE::readSimmat(simmats[i*numGalleries+j]);
  102 + cv::Mat m = BEE::readMat(simmats[i*numGalleries+j]);
103 103 if (j==0) {
104 104 currentRows = m.rows;
105 105 allNeighbors.resize(currentRows);
... ...
openbr/core/core.cpp
  View file @c3e880e
... ... @@ -443,7 +443,7 @@ void br::Convert(const File &amp;fileType, const File &amp;inputFile, const File &amp;output
443 443 while (!done) after->writeBlock(before->readBlock(&done));
444 444 } else if (fileType == "Output") {
445 445 QString target, query;
446   - cv::Mat m = BEE::readSimmat(inputFile, &target, &query);
  446 + cv::Mat m = BEE::readMat(inputFile, &target, &query);
447 447 const FileList targetFiles = TemplateList::fromGallery(target).files();
448 448 const FileList queryFiles = TemplateList::fromGallery(query).files();
449 449  
... ...
openbr/core/eval.cpp
  View file @c3e880e
... ... @@ -81,7 +81,7 @@ float Evaluate(const QString &amp;simmat, const QString &amp;mask, const QString &amp;csv)
81 81 QString target, query;
82 82 Mat scores;
83 83 if (simmat.endsWith(".mtx")) {
84   - scores = BEE::readSimmat(simmat, &target, &query);
  84 + scores = BEE::readMat(simmat, &target, &query);
85 85 } else {
86 86 QScopedPointer<Format> format(Factory<Format>::make(simmat));
87 87 scores = format->read();
... ... @@ -99,12 +99,8 @@ float Evaluate(const QString &amp;simmat, const QString &amp;mask, const QString &amp;csv)
99 99 File maskFile(mask);
100 100 maskFile.set("rows", scores.rows);
101 101 maskFile.set("columns", scores.cols);
102   - if (mask.endsWith(".mtx"))
103   - truth = BEE::readMask(mask);
104   - else {
105   - QScopedPointer<Format> format(Factory<Format>::make(maskFile));
106   - truth = format->read();
107   - }
  102 + QScopedPointer<Format> format(Factory<Format>::make(maskFile));
  103 + truth = format->read();
108 104 }
109 105  
110 106 return Evaluate(scores, truth, csv);
... ...
openbr/core/fuse.cpp
  View file @c3e880e
... ... @@ -82,7 +82,7 @@ void br::Fuse(const QStringList &amp;inputSimmats, const QString &amp;normalization, con
82 82 QString target, query, previousTarget, previousQuery;
83 83 QList<Mat> originalMatrices;
84 84 foreach (const QString &simmat, inputSimmats) {
85   - originalMatrices.append(BEE::readSimmat(simmat,&target,&query));
  85 + originalMatrices.append(BEE::readMat(simmat,&target,&query));
86 86 // Make we're fusing score matrices for the same set of targets and querys
87 87 if (!previousTarget.isEmpty() && !previousQuery.isEmpty() && (previousTarget != target || previousQuery != query))
88 88 qFatal("Target or query files are not the same across fused matrices.");
... ...
openbr/plugins/format.cpp
  View file @c3e880e
... ... @@ -280,7 +280,7 @@ class mtxFormat : public Format
280 280  
281 281 Template read() const
282 282 {
283   - return BEE::readSimmat(file);
  283 + return BEE::readMat(file);
284 284 }
285 285  
286 286 void write(const Template &t) const
... ... @@ -302,7 +302,7 @@ class maskFormat : public Format
302 302  
303 303 Template read() const
304 304 {
305   - return BEE::readMask(file);
  305 + return BEE::readMat(file);
306 306 }
307 307  
308 308 void write(const Template &t) const
... ...