Updated field input/output to add provenance data.

Changed FieldMetadataMap to use string values instead of NekDouble.

cmake/GetGitRevisionDescription.cmake

+# - Returns a version string from Git
+#
+# These functions force a re-configure on each git commit so that you can
+# trust the values of the variables in your build system.
+#
+#  get_git_head_revision(<refspecvar> <hashvar> [<additional arguments to git describe> ...])
+#
+# Returns the refspec and sha hash of the current head revision
+#
+#  git_describe(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe on the source tree, and adjusting
+# the output so that it tests false if an error occurs.
+#
+#  git_get_exact_tag(<var> [<additional arguments to git describe> ...])
+#
+# Returns the results of git describe --exact-match on the source tree,
+# and adjusting the output so that it tests false if there was no exact
+# matching tag.
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright Iowa State University 2009-2010.
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+if(__get_git_revision_description)
+    return()
+endif()
+set(__get_git_revision_description YES)
+
+# We must run the following at "include" time, not at function call time,
+# to find the path to this module rather than the path to a calling list file
+get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
+
+function(get_git_head_revision _refspecvar _hashvar)
+    set(GIT_PARENT_DIR "${CMAKE_SOURCE_DIR}")
+    set(GIT_DIR "${GIT_PARENT_DIR}/.git")
+    while(NOT EXISTS "${GIT_DIR}")  # .git dir not found, search parent directories
+        set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}")
+        get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH)
+        if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT)
+            # We have reached the root directory, we are not in git
+            set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
+            set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
+            return()
+        endif()
+        set(GIT_DIR "${GIT_PARENT_DIR}/.git")
+    endwhile()
+    set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
+    if(NOT EXISTS "${GIT_DATA}")
+        file(MAKE_DIRECTORY "${GIT_DATA}")
+    endif()
+
+    if(NOT EXISTS "${GIT_DIR}/HEAD")
+        return()
+    endif()
+    set(HEAD_FILE "${GIT_DATA}/HEAD")
+    configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
+
+    configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
+        "${GIT_DATA}/grabRef.cmake"
+        @ONLY)
+    include("${GIT_DATA}/grabRef.cmake")
+
+    set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE)
+    set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE)
+endfunction()
+
+function(git_describe _var)
+    if(NOT GIT_FOUND)
+        find_package(Git QUIET)
+    endif()
+    get_git_head_revision(refspec hash)
+    if(NOT GIT_FOUND)
+        set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
+        return()
+    endif()
+    if(NOT hash)
+        set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
+        return()
+    endif()
+
+    # TODO sanitize
+    #if((${ARGN}" MATCHES "&&") OR
+    #   (ARGN MATCHES "||") OR
+    #   (ARGN MATCHES "\\;"))
+    #   message("Please report the following error to the project!")
+    #   message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
+    #endif()
+
+    #message(STATUS "Arguments to execute_process: ${ARGN}")
+
+    execute_process(COMMAND
+        "${GIT_EXECUTABLE}"
+        describe
+        ${hash}
+        ${ARGN}
+        WORKING_DIRECTORY
+        "${CMAKE_SOURCE_DIR}"
+        RESULT_VARIABLE
+        res
+        OUTPUT_VARIABLE
+        out
+        ERROR_QUIET
+        OUTPUT_STRIP_TRAILING_WHITESPACE)
+    if(NOT res EQUAL 0)
+        set(out "${out}-${res}-NOTFOUND")
+    endif()
+
+    set(${_var} "${out}" PARENT_SCOPE)
+endfunction()
+
+function(git_get_exact_tag _var)
+    git_describe(out --exact-match ${ARGN})
+    set(${_var} "${out}" PARENT_SCOPE)
+endfunction()
+

cmake/GetGitRevisionDescription.cmake.in

+# 
+# Internal file for GetGitRevisionDescription.cmake
+#
+# Requires CMake 2.6 or newer (uses the 'function' command)
+#
+# Original Author:
+# 2009-2010 Ryan Pavlik <rpavlik@iastate.edu> <abiryan@ryand.net>
+# http://academic.cleardefinition.com
+# Iowa State University HCI Graduate Program/VRAC
+#
+# Copyright Iowa State University 2009-2010.
+# Distributed under the Boost Software License, Version 1.0.
+# (See accompanying file LICENSE_1_0.txt or copy at
+# http://www.boost.org/LICENSE_1_0.txt)
+
+set(HEAD_HASH)
+
+file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
+
+string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
+if(HEAD_CONTENTS MATCHES "ref")
+    # named branch
+    string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
+    if(EXISTS "@GIT_DIR@/${HEAD_REF}")
+        configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
+    elseif(EXISTS "@GIT_DIR@/logs/${HEAD_REF}")
+        configure_file("@GIT_DIR@/logs/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
+        set(HEAD_HASH "${HEAD_REF}")
+    endif()
+else()
+    # detached HEAD
+    configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
+endif()
+
+if(NOT HEAD_HASH)
+    file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
+    string(STRIP "${HEAD_HASH}" HEAD_HASH)
+endif()
+

cmake/NektarCommon.cmake

@@ -118,9 +118,22 @@ MACRO(SET_COMMON_PROPERTIES name)
                     "${CMAKE_CXX_FLAGS_DEBUG} -fpermissive")
             ENDIF()
         ENDIF( NOT MSVC)
-                        
+
+        # Attempt to retrieve git branch and SHA1 hash
+        get_git_head_revision(GIT_REFSPEC GIT_SHA1)
+
+        # Define version
+        SET_PROPERTY(TARGET ${name}
+            APPEND PROPERTY COMPILE_DEFINITIONS NEKTAR_VERSION=\"${NEKTAR_VERSION}\")
+
+        # Define the git branch and SHA1 hash if we are in a git repository
+        IF (NOT ${GIT_REFSPEC} STREQUAL "GITDIR-NOTFOUND")
+            SET_PROPERTY(TARGET ${name}
+                APPEND PROPERTY COMPILE_DEFINITIONS GIT_SHA1=\"${GIT_SHA1}\" GIT_BRANCH=\"${GIT_REFSPEC}\")
+        ENDIF ()
+
         SET(CMAKE_CXX_FLAGS_RELEASE 
-                    "${CMAKE_CXX_FLAGS_RELEASE} -DNEKTAR_RELEASE")
+                "${CMAKE_CXX_FLAGS_RELEASE} -DNEKTAR_RELEASE")
     ENDIF(NOT ${CMAKE_CXX_FLAGS_DEBUG} MATCHES ".*DNEKTAR_DEBUG.*")
         
     IF( CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64" )

library/LibUtilities/BasicUtils/FieldIO.cpp

@@ -33,12 +33,23 @@
 //
 ////////////////////////////////////////////////////////////////////////////////
 
+#include <boost/date_time/posix_time/posix_time.hpp>
+#include <boost/date_time/posix_time/posix_time_io.hpp>
+#include <boost/asio/ip/host_name.hpp>
+
 #include <LibUtilities/BasicUtils/FieldIO.h>
 #include "zlib.h"
 
 // Buffer size for zlib compression/decompression
 #define CHUNK 16384
 
+#ifndef NEKTAR_VERSION
+#define NEKTAR_VERSION "Unknown"
+#endif
+
+namespace ptime = boost::posix_time;
+namespace ip = boost::asio::ip;
+
 namespace Nektar
 {
     namespace LibUtilities
@@ -51,8 +62,8 @@ namespace Nektar
                    std::vector<std::vector<NekDouble> > &fielddata, 
                    FieldMetaDataMap &fieldmetadatamap)
         {
-           ASSERTL1(fielddefs.size() == fielddata.size(),
-                     "Length of fielddefs and fielddata incompatible");
+            ASSERTL1(fielddefs.size() == fielddata.size(),
+                      "Length of fielddefs and fielddata incompatible");
 
             TiXmlDocument doc;
             TiXmlDeclaration * decl = new TiXmlDeclaration("1.0", "utf-8", "");
@@ -63,26 +74,55 @@ namespace Nektar
             TiXmlElement * root = new TiXmlElement("NEKTAR");
             doc.LinkEndChild(root);
 
+            FieldMetaDataMap ProvenanceMap;
+
+            // Nektar++ release version from VERSION file
+            ProvenanceMap["NektarVersion"] = string(NEKTAR_VERSION);
+
+            // Date/time stamp
+            ptime::time_facet *facet = new ptime::time_facet("%d-%b-%Y %H:%M:%S");
+            std::stringstream wss;
+            wss.imbue(locale(wss.getloc(), facet));
+            wss << ptime::second_clock::local_time();
+            ProvenanceMap["Timestamp"] = wss.str();
+
+            // Hostname
+            ProvenanceMap["Hostname"] = ip::host_name();
+
+            // Git information
+            // If built from a distributed package, do not include this
+#ifdef GIT_SHA1
+            ProvenanceMap["GitSHA1"] = string(GIT_SHA1);
+#endif
+#ifdef GIT_BRANCH
+            ProvenanceMap["GitBranch"] = string(GIT_BRANCH);
+#endif
+
+            TiXmlElement * infoTag = new TiXmlElement("Metadata");
+            root->LinkEndChild(infoTag);
+
+            TiXmlElement * v;
+            FieldMetaDataMap::iterator infoit;
+
+            TiXmlElement * provTag = new TiXmlElement("Provenance");
+            infoTag->LinkEndChild(provTag);
+            for (infoit = ProvenanceMap.begin(); infoit != ProvenanceMap.end(); ++infoit)
+            {
+                v = new TiXmlElement( (infoit->first).c_str() );
+                v->LinkEndChild(new TiXmlText((infoit->second).c_str()));
+                provTag->LinkEndChild(v);
+            }
+
             //---------------------------------------------
-            // write field info section 
+            // write field info section
             if(fieldmetadatamap != NullFieldMetaDataMap)
             {
-                TiXmlElement * infoTag = new TiXmlElement("FIELDMETADATA");
-                root->LinkEndChild(infoTag);
-                
-                FieldMetaDataMap::iterator infoit;
-                
                 for(infoit = fieldmetadatamap.begin(); infoit != fieldmetadatamap.end(); ++infoit)
                 {
-                    NekDouble val = infoit->second;
-                    stringstream s;
-                    s << val; 
-                    TiXmlElement * v = new TiXmlElement( "P" );
-                    v->SetAttribute("PARAM",(infoit->first).c_str());
-                    v->LinkEndChild(new TiXmlText(s.str()));
+                    v = new TiXmlElement( (infoit->first).c_str() );
+                    v->LinkEndChild(new TiXmlText((infoit->second).c_str()));
                     infoTag->LinkEndChild(v);
                 }
-
             }
 
             for (int f = 0; f < fielddefs.size(); ++f)
@@ -346,30 +386,26 @@ namespace Nektar
         {
             
             TiXmlHandle docHandle(&doc);
-            TiXmlElement* master = NULL;    // Master tag within which all data is contained.
+            TiXmlElement* master = 0;    // Master tag within which all data is contained.
+            TiXmlElement* metadata = 0;
             
             master = doc.FirstChildElement("NEKTAR");
             ASSERTL0(master, "Unable to find NEKTAR tag in file.");
             std::string strLoop = "NEKTAR";
 
-
-            TiXmlElement* metadata = master->FirstChildElement("FIELDMETADATA");
-            
-            if(!metadata) // section not available so just exit
-            {
-                return;
-            }
-            else
+            // Retain original metadata structure for backwards compatibility
+            // TODO: Remove old metadata format
+            metadata = master->FirstChildElement("FIELDMETADATA");
+            if(metadata)
             {
-                
                 TiXmlElement *param = metadata->FirstChildElement("P");
-                    
+
                 while (param)
                 {
                     TiXmlAttribute *paramAttr = param->FirstAttribute();
                     std::string attrName(paramAttr->Name());
                     std::string paramString;
-                    
+
                     if(attrName == "PARAM")
                     {
                         paramString.insert(0,paramAttr->Value());
@@ -381,30 +417,37 @@ namespace Nektar
 
                     // Now read body of param
                     std::string paramBodyStr;
-                    
+
                     TiXmlNode *paramBody = param->FirstChild();
-                    
+
                     paramBodyStr += paramBody->ToText()->Value();
+
+                    fieldmetadatamap[paramString] = paramBodyStr;
+                    param = param->NextSiblingElement("P");
+                }
+            }
+
+            // New metadata format
+            metadata = master->FirstChildElement("Metadata");
+            if(metadata)
+            {
+                TiXmlElement *param = metadata->FirstChildElement();
                     
-                    NekDouble value;
-                    std::istringstream paramStrm(paramBodyStr.c_str());
-                    
-                    try
-                    {
-                        while(!paramStrm.fail())
-                        {
-                            paramStrm >> value;
-                        }
-                    }
-                    catch(...)
+                while (param)
+                {
+                    std::string paramString = param->Value();
+                    if (paramString != "Provenance")
                     {
-                        ASSERTL0(false,"Failied to read PARAM data");
-                    }
+                        // Now read body of param
+                        TiXmlNode *paramBody = param->FirstChild();
+                        std::string paramBodyStr = paramBody->ToText()->Value();
 
-                    fieldmetadatamap[paramString] = value; 
-                    param = param->NextSiblingElement("P");
+                        fieldmetadatamap[paramString] = paramBodyStr;
+                    }
+                    param = param->NextSiblingElement();
                 }
             }
+
         }
         
 

library/LibUtilities/BasicUtils/FieldIO.h

@@ -59,7 +59,7 @@ namespace Nektar
         static std::vector<LibUtilities::PointsType> NullPointsTypeVector;
         static std::vector<unsigned int> NullUnsignedIntVector;
 
-        typedef std::map<std::string, NekDouble>  FieldMetaDataMap;
+        typedef std::map<std::string, std::string>  FieldMetaDataMap;
         static  FieldMetaDataMap  NullFieldMetaDataMap;
         
 

library/SolverUtils/EquationSystem.cpp

@@ -1881,7 +1881,7 @@ namespace Nektar
             // Update time in field info if required
             if(m_fieldMetaDataMap.find("Time") != m_fieldMetaDataMap.end())
             {
-                m_fieldMetaDataMap["Time"] =  m_time; 
+                m_fieldMetaDataMap["Time"] = boost::lexical_cast<std::string>(m_time);
             }
 
             LibUtilities::Write(outname, FieldDef, FieldData, m_fieldMetaDataMap);

library/SolverUtils/UnsteadySystem.cpp

@@ -108,7 +108,8 @@ namespace Nektar
             m_session->LoadParameter("CFL", m_cflSafetyFactor, 0.0);
 
             // Set up time to be dumped in field information
-            m_fieldMetaDataMap["Time"] = m_time; 
+            m_fieldMetaDataMap["Time"] =
+                    boost::lexical_cast<std::string>(m_time);
 
             // Set up filters
             LibUtilities::FilterMap::const_iterator x;
@@ -810,7 +811,7 @@ namespace Nektar
                             iter = m_fieldMetaDataMap.find("Time");
                             if(iter != m_fieldMetaDataMap.end())
                             {
-                                time = iter->second; 
+                                time = boost::lexical_cast<NekDouble>(iter->second);
                             }
                         }
                         

solvers/CardiacEPSolver/CellModels/CellModel.cpp

@@ -360,7 +360,7 @@ namespace Nektar
                 iter = fieldMetaDataMap.find("Time");
                 if(iter != fieldMetaDataMap.end())
                 {
-                    m_lastTime = iter->second;
+                    m_lastTime = boost::lexical_cast<NekDouble>(iter->second);
                 }
 
                 // Extract the data into the modal coefficients

solvers/IncNavierStokesSolver/EquationSystems/IncNavierStokes.cpp

@@ -246,8 +246,8 @@ namespace Nektar
         }
 
         // Set up Field Meta Data for output files
-        m_fieldMetaDataMap["Kinvis"] = m_kinvis;
-        m_fieldMetaDataMap["TimeStep"] = m_timestep;
+        m_fieldMetaDataMap["Kinvis"] = boost::lexical_cast<std::string>(m_kinvis);
+        m_fieldMetaDataMap["TimeStep"] = boost::lexical_cast<std::string>(m_timestep);
     }
 
     IncNavierStokes::~IncNavierStokes(void)