Add support for netCDF4 and padding with NaN values.

reporting/CMakeLists.txt

@@ -6,8 +6,8 @@ IF ( BUILD_REPORTING )
     find_package(RTTPlugin REQUIRED rtt-marshalling)
 
     # This gathers all the .cpp files into the variable 'SRCS'
-    SET( SRCS ConsoleReporting.cpp FileReporting.cpp ReportingComponent.cpp )
-    SET( HPPS ConsoleReporting.hpp  FileReporting.hpp NiceHeaderMarshaller.hpp ReportingComponent.hpp TableMarshaller.hpp)
+    SET( SRCS ConsoleReporting.cpp FileReporting.cpp ReportingComponent.cpp TSVReporting.cpp )
+    SET( HPPS ConsoleReporting.hpp  FileReporting.hpp NiceHeaderMarshaller.hpp ReportingComponent.hpp TableMarshaller.hpp TSVReporting.hpp TSVMarshaller.hpp )
 
     # Reporting to a socket
     SET( SOCKET_SRCS command.cpp datasender.cpp socket.cpp socketmarshaller.cpp TcpReporting.cpp)

reporting/NetcdfHeaderMarshaller.hpp

@@ -5,6 +5,7 @@
 #include <boost/lexical_cast.hpp>
 
 #include <netcdf.h>
+#include <cmath>
 
 #define DIMENSION_VAR 1
 #define DIMENSION_ARRAY 2
@@ -25,10 +26,14 @@ namespace RTT
       int ncid;
       int dimsid;
       int ncopen;
+      float fNaN;
+      double dNaN;
 
       public:
 
-      NetcdfHeaderMarshaller(int ncid, int dimsid) : ncid( ncid ), dimsid(dimsid), ncopen(0) {}
+      NetcdfHeaderMarshaller(int ncid, int dimsid) :
+                    ncid( ncid ), dimsid(dimsid), ncopen(0),
+                    fNaN(nanf("")), dNaN(nan("")) {}
 
       virtual ~NetcdfHeaderMarshaller() {}
 
@@ -150,6 +155,7 @@ namespace RTT
           log(Error) << "Could not create variable " << sname << ", error " << retval <<endlog();
         else
           log(Info) << "Variable "<< sname << " successfully created" <<endlog();
+
       }
 
       /**
@@ -210,6 +216,8 @@ namespace RTT
           log(Error) << "Could not create variable " << sname << ", error " << retval <<endlog();
         else
           log(Info) << "Variable "<< sname << " successfully created" <<endlog();
+
+        nc_def_var_fill(ncid, varid, NC_FILL, &fNaN);
       }
 
       /**
@@ -231,6 +239,8 @@ namespace RTT
           log(Error) << "Could not create variable " << sname << ", error " << retval <<endlog();
         else
           log(Info) << "Variable "<< sname << " successfully created" <<endlog();
+
+        nc_def_var_fill(ncid, varid, NC_FILL, &dNaN);
       }
 
       /**

reporting/NetcdfReporting.cpp

@@ -18,9 +18,14 @@ namespace OCL
 
     NetcdfReporting::NetcdfReporting(const std::string& fr_name)
         : ReportingComponent( fr_name ),
-          repfile("ReportFile","Location on disc to store the reports.", "reports.nc")
+          repfile("ReportFile","Location on disc to store the reports.", "reports.nc"),
+          useNetCDF4("useNetCDF4", "This flag controls whether to use the newer netCDF4 format.\n"
+                                   "The new format supports writing NaN values where there are missing values in the reported values arrays\n"
+                                   "but does not support shared access to the netCDF (e.g. your visualizer can not read from the file while orocos writes to it.",
+                                    true)
     {
         this->properties()->addProperty( repfile );
+        this->properties()->addProperty( useNetCDF4 );
 
         if(types::TypeInfoRepository::Instance()->getTypeInfo<short>() == 0 )
         {
@@ -36,9 +41,12 @@ namespace OCL
        * Create a new netcdf dataset in the NC_CLOBBER mode.
        * This means that the nc_create function overwrites any existing dataset.
        */
-      retval = nc_create(repfile.get().c_str(), NC_CLOBBER | NC_SHARE, &ncid);
+      int cmode = NC_CLOBBER | NC_SHARE;
+      if(useNetCDF4.get())
+          cmode |= NC_NETCDF4;
+      retval = nc_create(repfile.get().c_str(), cmode, &ncid);
       if ( retval ) {
-       log(Error) << "Could not create "+repfile.get()+" for reporting."<<endlog();
+       log(Error) << "Could not create " << repfile.get() << " for reporting."<<endlog();
        return false;
       }
 
@@ -48,7 +56,7 @@ namespace OCL
        */
       retval = nc_def_dim(ncid, "time", NC_UNLIMITED, &dimsid);
       if ( retval ) {
-       log(Error) << "Could not create time dimension "+repfile.get() <<endlog();
+       log(Error) << "Could not create time dimension " << repfile.get() <<endlog();
        return false;
       }
 
@@ -57,7 +65,7 @@ namespace OCL
        */
       retval = nc_enddef( ncid );
       if ( retval ) {
-       log(Error) << "Could not leave define mode in "+repfile.get() <<endlog();
+       log(Error) << "Could not leave define mode in " << repfile.get() <<endlog();
        return false;
       }
 
@@ -83,7 +91,7 @@ namespace OCL
     if ( ncid )
       retval = nc_close (ncid);
     if ( retval )
-      log(Error) << "Could not close file "+repfile.get()+" for reporting."<<endlog();
+      log(Error) << "Could not close file " << repfile.get() << " for reporting."<<endlog();
   }
 
 }

reporting/NetcdfReporting.hpp

@@ -20,6 +20,12 @@ namespace OCL
          */
         RTT::Property<std::string>  repfile;
 
+        /**
+         * Flag to toggle the usage of the newer netCDF4 format.
+         * Beware that the new format does not shared access to the .nc file.
+         */
+        RTT::Property<bool> useNetCDF4;
+
         /**
          * Netcdf ID
          */

reporting/ReportingComponent.cpp

@@ -355,7 +355,8 @@ namespace OCL
         Ports ports   = comp->ports()->getPorts();
         for (Ports::iterator it = ports.begin(); it != ports.end() ; ++it) {
             log(Debug) << "Checking port " << (*it)->getName()<<"."<<endlog();
-            this->reportPort( component, (*it)->getName() );
+            if(!dynamic_cast<base::InputPortInterface*>(*it)) //Don't try to report input ports
+                this->reportPort( component, (*it)->getName() );
         }
         return true;
     }

reporting/TSVMarshaller.hpp

@@ -0,0 +1,129 @@
+/***************************************************************************
+  tag: Peter Soetens  Mon Jan 19 14:11:20 CET 2004  TSVMarshaller.hpp
+
+                        TSVMarshaller.hpp -  description
+                           -------------------
+    begin                : Mon January 19 2004
+    copyright            : (C) 2004 Peter Soetens
+    email                : [email protected]
+
+ ***************************************************************************
+ *   This library 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;                 *
+ *   version 2 of the License.                                             *
+ *                                                                         *
+ *   As a special exception, you may use this file as part of a free       *
+ *   software library without restriction.  Specifically, if other files   *
+ *   instantiate templates or use macros or inline functions from this     *
+ *   file, or you compile this file and link it with other files to        *
+ *   produce an executable, this file does not by itself cause the         *
+ *   resulting executable to be covered by the GNU General Public          *
+ *   License.  This exception does not however invalidate any other        *
+ *   reasons why the executable file might be covered by the GNU General   *
+ *   Public License.                                                       *
+ *                                                                         *
+ *   This library 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     *
+ *   Lesser General Public License for more details.                       *
+ *                                                                         *
+ *   You should have received a copy of the GNU General Public             *
+ *   License along with this library; if not, write to the Free Software   *
+ *   Foundation, Inc., 59 Temple Place,                                    *
+ *   Suite 330, Boston, MA  02111-1307  USA                                *
+ *                                                                         *
+ ***************************************************************************/
+
+#ifndef PI_PROPERTIES_TABLESERIALIZER
+#define PI_PROPERTIES_TABLESERIALIZER
+
+#include <fstream>
+#include <map>
+#include <rtt/Property.hpp>
+#include <rtt/base/PropertyIntrospection.hpp>
+#include <rtt/marsh/MarshallInterface.hpp>
+
+namespace RTT {
+
+/**
+ * @brief The TSVMarshaller class writes the serialized properties to a
+ * collection of TSV (tab separated values) files.
+ */
+class TSVMarshaller : public marsh::MarshallInterface {
+  std::string msep;
+  std::map<std::string, std::ofstream*> streams;
+  typedef std::map<std::string, std::ofstream*>::iterator stream_it;
+  double current_reporting_timestamp;
+
+  std::ofstream* getStream(const std::string& key, base::PropertyBase* v) {
+    if (streams.count(key) == 0) {
+      streams[key] =
+          new std::ofstream((key + ".txt").c_str(), std::ofstream::out);
+      (*streams[key]) << "ReportingTimestamp";
+      serialize(v, *streams[key], "", true);
+      (*streams[key]) << std::endl;
+    }
+    return streams[key];
+  }
+
+ public:
+
+  TSVMarshaller(std::string sep = "\t") : msep(sep) {}
+
+  virtual ~TSVMarshaller() {
+    for (stream_it it = streams.begin(); it != streams.end(); ++it) {
+      it->second->close();
+      delete it->second;
+    }
+  }
+
+  virtual void serialize(base::PropertyBase* v) {
+    if (v->getName() == "TimeStamp") {
+      Property<double>* timestamp = dynamic_cast<Property<double>*>(v);
+      current_reporting_timestamp = timestamp->rvalue();
+    } else {
+      std::ofstream& stream = *getStream(v->getName(), v);
+      stream << current_reporting_timestamp;
+      serialize(v, stream);
+      stream << std::endl;
+    }
+  }
+
+  void serialize(base::PropertyBase* v, std::ofstream& stream,
+                 const std::string& prefix = "", bool header = false) {
+    Property<PropertyBag>* bag = dynamic_cast<Property<PropertyBag>*>(v);
+    if (bag) {
+      serialize(bag->rvalue(), stream, bag->getName(), header);
+    } else {
+      if (header) {
+        stream << msep << v->getName();
+      } else {
+        stream << msep << v->getDataSource();
+      }
+    }
+  }
+
+  virtual void serialize(const PropertyBag& v) {
+    for (PropertyBag::const_iterator i = v.getProperties().begin();
+         i != v.getProperties().end(); i++) {
+      serialize(*i);
+    }
+  }
+
+  virtual void serialize(const PropertyBag& v, std::ofstream& stream,
+                         const std::string& prefix = "", bool header = false) {
+    for (PropertyBag::const_iterator i = v.getProperties().begin();
+         i != v.getProperties().end(); i++) {
+      this->serialize(*i, stream, prefix, header);
+    }
+  }
+
+  virtual void flush() {
+    for (stream_it it = streams.begin(); it != streams.end(); ++it) {
+      it->second->flush();
+    }
+  }
+};
+}
+#endif

reporting/TSVReporting.cpp

@@ -0,0 +1,35 @@
+#include <rtt/Logger.hpp>
+#include <rtt/RTT.hpp>
+
+#include "TSVReporting.hpp"
+#include "TSVMarshaller.hpp"
+
+#include "ocl/Component.hpp"
+ORO_LIST_COMPONENT_TYPE(OCL::TSVReporting)
+
+namespace OCL {
+using namespace RTT;
+using namespace std;
+
+TSVReporting::TSVReporting(const std::string& fr_name)
+    : ReportingComponent(fr_name) {
+    this->onlyNewData = true;
+}
+
+bool TSVReporting::startHook() {
+  this->addMarshaller(0, new RTT::TSVMarshaller());
+  return ReportingComponent::startHook();
+}
+
+void TSVReporting::stopHook() {
+  ReportingComponent::stopHook();
+  this->removeMarshallers();
+}
+
+bool TSVReporting::screenComponent(const std::string& comp) {
+  Logger::In in("TSVReporting::screenComponent");
+  ofstream file((comp + ".screen").c_str());
+  if (!file) return false;
+  return this->screenImpl(comp, file);
+}
+}

reporting/TSVReporting.hpp

@@ -0,0 +1,36 @@
+#ifndef ORO_COMP_TSV_REPORTING_HPP
+#define ORO_COMP_TSV_REPORTING_HPP
+
+#include <fstream>
+#include "ReportingComponent.hpp"
+
+#include <ocl/OCL.hpp>
+
+namespace OCL {
+
+/**
+ * @brief The TSVReporting class writes the reported values to a collection of
+ * TSV (Tab Separated Values) files.
+ * Each reported port ends up in its own TSV file, named after the port. This
+ * solves the problem of ports, that emit data on different frequencies. It also
+ * makes any header writing obsolete, enabling us to add new reported ports
+ * during runtime. By default reportOnlyNewData is set to true.
+ */
+class TSVReporting : public ReportingComponent {
+ protected:
+ public:
+  TSVReporting(const std::string& fr_name);
+
+  bool startHook();
+
+  void stopHook();
+
+  /**
+   * Writes the interface status of \a comp to
+   * a file 'comp.screen'.
+   */
+  bool screenComponent(const std::string& comp);
+};
+}
+
+#endif