Merge branch 'master' of github.com:aportelli/LatAnalyze3

lib/Hdf5File.cpp

@@ -124,8 +124,8 @@ void Hdf5File::save(const RandGenState &state, const string &name)
     group = h5File_->createGroup(name.c_str() + nameOffset(name));
     attr  = group.createAttribute("type", PredType::NATIVE_SHORT, attrSpace);
     attr.write(PredType::NATIVE_SHORT, &rgStateType);
-    dataset = group.createDataSet("data", PredType::NATIVE_DOUBLE, dataSpace);
+    dataset = group.createDataSet("data", PredType::NATIVE_INT, dataSpace);
-    dataset.write(state.data(), PredType::NATIVE_DOUBLE);
+    dataset.write(state.data(), PredType::NATIVE_INT);
 }
 
 // read first name ////////////////////////////////////////////////////////////
@@ -262,7 +262,7 @@ void Hdf5File::load(RandGenState &state, const DataSet &d)
     dataspace.getSimpleExtentDims(dim);
     if (dim[0] != RLXG_STATE_SIZE)
     {
-        // error here
+        LATAN_ERROR(Io, "random generator state has a wrong length");
     }
     d.read(state.data(), PredType::NATIVE_INT);
 }

lib/Io.cpp

@@ -25,20 +25,9 @@ using namespace Latan;
 
 string Io::getFirstName(const string &fileName)
 {
-    string ext = extension(fileName);
+    std::unique_ptr<File> file = open(fileName);
     
-    if (ext == "h5")
+    return file->getFirstName();
-    {
-        return getFirstName<Hdf5File>(fileName);
-    }
-    else if ((ext == "dat")||(ext == "sample")||(ext == "seed"))
-    {
-        return getFirstName<AsciiFile>(fileName);
-    }
-    else
-    {
-        LATAN_ERROR(Io, "unknown file extension '" + ext + "'");
-    }
 }
 
 unique_ptr<File> Io::open(const std::string &fileName, const unsigned int mode)

lib/Io.hpp

@@ -48,7 +48,7 @@ public:
     static std::string getFirstName(const std::string &fileName);
     static std::string getFirstName(const std::string &fileName);
     static std::unique_ptr<File> open(const std::string &fileName,
-                                      const unsigned int mode = File::Mode::write);
+                                      const unsigned int mode = File::Mode::read);
 };
 
 // template implementation /////////////////////////////////////////////////////
@@ -63,20 +63,9 @@ IoT Io::load(const std::string &fileName, const std::string &name)
 template <typename IoT>
 IoT Io::load(const std::string &fileName, const std::string &name)
 {
-    std::string ext = extension(fileName);
+    std::unique_ptr<File> file = open(fileName);
     
-    if (ext == "h5")
+    return file->read<IoT>(name);
-    {
-        return load<IoT, Hdf5File>(fileName, name);
-    }
-    else if ((ext == "dat")||(ext == "sample")||(ext == "seed"))
-    {
-        return load<IoT, AsciiFile>(fileName, name);
-    }
-    else
-    {
-        LATAN_ERROR(Io, "unknown file extension '" + ext + "'");
-    }
 }
 
 template <typename IoT, typename FileType>
@@ -93,20 +82,10 @@ template <typename IoT>
 void Io::save(const IoT &data, const std::string &fileName,
               const unsigned int mode, const std::string &name)
 {
-    std::string ext = extension(fileName);
+    std::unique_ptr<File> file     = open(fileName, mode);
+    std::string           realName = (name.empty()) ? fileName : name;
     
-    if (ext == "h5")
+    file->save(data, realName);
-    {
-        save<IoT, Hdf5File>(data, fileName, mode, name);
-    }
-    else if ((ext == "dat")||(ext == "sample")||(ext == "seed"))
-    {
-        save<IoT, AsciiFile>(data, fileName, mode, name);
-    }
-    else
-    {
-        LATAN_ERROR(Io, "unknown file extension '" + ext + "'");
-    }
 }
 
 template <typename FileType>

utils/Makefile.am

@@ -15,11 +15,16 @@ endif
 endif
 
 bin_PROGRAMS =            \
+    latan_create_rg_state \
     latan_make_fake_sample\
     latan_sample_combine  \
     latan_sample_read     \
     latan_resample
 
+latan_create_rg_state_SOURCES  = create_rg_state.cpp
+latan_create_rg_state_CXXFLAGS = $(COM_CXXFLAGS)
+latan_create_rg_state_LDFLAGS  = -L../lib/.libs -lLatAnalyze
+
 latan_make_fake_sample_SOURCES  = make_fake_sample.cpp
 latan_make_fake_sample_CXXFLAGS = $(COM_CXXFLAGS)
 latan_make_fake_sample_LDFLAGS  = -L../lib/.libs -lLatAnalyze

utils/create_rg_state.cpp

@@ -0,0 +1,44 @@
+/*
+ * create_rg_state.cpp, part of LatAnalyze 3
+ *
+ * Copyright (C) 2013 - 2015 Antonin Portelli
+ *
+ * LatAnalyze 3 is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * LatAnalyze 3 is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with LatAnalyze 3.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <iostream>
+#include <LatAnalyze/Io.hpp>
+#include <LatAnalyze/RandGen.hpp>
+
+using namespace Latan;
+using namespace std;
+
+int main(int argc, char *argv[])
+{
+    string outFilename;
+    
+    if (argc != 2)
+    {
+        cerr << "usage: " << argv[0] << " <output file>" << endl;
+        
+        return EXIT_FAILURE;
+    }
+    outFilename = argv[1];
+    
+    RandGen gen;
+    
+    Io::save(gen.getState(), outFilename);
+    
+    return EXIT_SUCCESS;
+}

utils/resample.cpp

@@ -34,7 +34,7 @@ using namespace Latan;
 static void usage(const string &cmdName)
 {
     cerr << "usage: " << cmdName;
-    cerr << " [-n <nsample> -b <bin size> -r <state> -o <output dir>]";
+    cerr << " [-n <nsample> -b <bin size> -r <state> -o <output dir> -f {h5|sample}]";
     cerr << " <data list> <name list>";
     cerr << endl;
     exit(EXIT_FAILURE);
@@ -45,11 +45,12 @@ int main(int argc, char *argv[])
     // argument parsing ////////////////////////////////////////////////////////
     int    c;
     string manFileName, nameFileName, stateFileName, cmdName, outDirName = ".";
+    string ext = "h5";
     Index  binSize = 1, nSample = DEF_NSAMPLE;
     
     opterr = 0;
     cmdName = basename(argv[0]);
-    while ((c = getopt(argc, argv, "b:n:r:o:")) != -1)
+    while ((c = getopt(argc, argv, "b:n:r:o:f:")) != -1)
     {
         switch (c)
         {
@@ -65,6 +66,9 @@ int main(int argc, char *argv[])
             case 'r':
                 stateFileName = optarg;
                 break;
+            case 'f':
+                ext = optarg;
+                break;
             case '?':
                 cerr << "error parsing option -" << char(optopt) << endl;
                 usage(cmdName);
@@ -97,6 +101,7 @@ int main(int argc, char *argv[])
     cout << "     bin size= " << binSize << endl;
     cout << "      #sample= " << nSample << endl;
     cout << "   output dir: " << outDirName << endl;
+    cout << "output format: " << ext << endl;
     cout << "------------------------------------------------" << endl;
     
     // data loading ////////////////////////////////////////////////////////////
@@ -109,30 +114,13 @@ int main(int argc, char *argv[])
     }
     for (unsigned int i = 0; i < dataFileName.size(); ++i)
     {
-        std::unique_ptr<File> dataFile;
+        std::unique_ptr<File> dataFile = Io::open(dataFileName[i]);
 
-        if (extension(dataFileName[i]) == "dat")
-        {
-            dataFile.reset(new AsciiFile);
-        }
-        else if (extension(dataFileName[i]) == "h5")
-        {
-            dataFile.reset(new Hdf5File);
-        }
-        else
-        {
-            cerr << "error: '" << dataFileName[i];
-            cerr << "' has an unknown extension" << endl;
-
-            return EXIT_FAILURE;
-        }
         cout << '\r' << ProgressBar(i + 1, dataFileName.size());
-        dataFile->open(dataFileName[i], AsciiFile::Mode::read);
         for (const string &n: name)
         {
             data[n][i] = dataFile->read<DMat>(n);
         }
-        dataFile->close();
     }
     cout << endl;
     
@@ -148,7 +136,7 @@ int main(int argc, char *argv[])
     }
     for (unsigned int i = 0; i < name.size(); ++i)
     {
-        const string outFileName = name[i] + "_" + manFileName + ".sample";
+        const string outFileName = name[i] + "_" + manFileName + "." + ext;
         
         cout << '\r' << ProgressBar(i + 1, name.size());
         data[name[i]].bin(binSize);