Changeset 5364

Timestamp:

27/07/10 09:28:03 (6 weeks ago)

Author:

Martyn Gigg

Message:

Implemented run parameter reading for ISIS Nexus and Raw loading routines. Re #1416

Location:

trunk/Code/Mantid

Files:

• DataHandling/inc/MantidDataHandling/LoadRawHelper.h (modified) (3 diffs)
• DataHandling/src/LoadRaw.cpp (modified) (3 diffs)
• DataHandling/src/LoadRaw2.cpp (modified) (5 diffs)
• DataHandling/src/LoadRaw3.cpp (modified) (1 diff)
• DataHandling/src/LoadRawHelper.cpp (modified) (4 diffs)
• Nexus/inc/MantidNexus/LoadISISNexus.h (modified) (2 diffs)
• Nexus/src/LoadISISNexus.cpp (modified) (7 diffs)
• Nexus/src/LoadISISNexus2.cpp (modified) (2 diffs)

trunk/Code/Mantid/DataHandling/inc/MantidDataHandling/LoadRawHelper.h

@@ -13 +13 @@
 // Forward declaration
 //----------------------------------------------------------------------
+class ISISRAW;
 class ISISRAW2;
 
@@ -54 +55 @@
       /// Destructor
       ~LoadRawHelper();
+      ///Opens Raw File
+      FILE* openRawFile(const std::string & fileName);
+      /// Read in run parameters Public so that LoadRaw2 can use it
+      void loadRunParameters(API::MatrixWorkspace_sptr localWorkspace, ISISRAW * const = NULL) const;
     protected:
       /// Overwrites Algorithm method.
       void init();
-      ///Opens Raw File
-      FILE* openRawFile(const std::string & fileName);
       ///checks the file is an ascii file
       bool isAscii(FILE* file) const;
@@ -104 +107 @@
       void runLoadLog(const std::string& fileName,DataObjects::Workspace2D_sptr,int period=1);
 
-      /// Read in run parameters
-      void loadRunParameters(API::MatrixWorkspace_sptr localWorkspace) const;
 
       ///gets the monitor spectrum list from the workspace

trunk/Code/Mantid/DataHandling/src/LoadRaw.cpp

@@ -3 +3 @@
 //----------------------------------------------------------------------
 #include "MantidDataHandling/LoadRaw.h"
+#include "MantidDataHandling/LoadRawHelper.h"
 #include "MantidDataObjects/Workspace2D.h"
 #include "MantidKernel/UnitFactory.h"
@@ -77 +78 @@
       // Retrieve the filename from the properties
       m_filename = getPropertyValue("Filename");
-      if( isAscii(m_filename) )
-      {
-        g_log.error() << "File \"" << m_filename << "\" is not a valid RAW file.\n";
-        throw std::invalid_argument("Incorrect file type encountered.");
-      }
+
+      LoadRawHelper *helper = new LoadRawHelper;
+      FILE* file = helper->openRawFile(m_filename);
+      ISISRAW iraw;
+      iraw.ioRAW(file, true);
+
+      std::string title(iraw.hdr.hd_run, 69);
+      // Insert some spaces to tidy the string up a bit
+      title.insert(5, " ");
+      title.insert(26, " ");
+      title.insert(51, " ");
+      g_log.information("**** Run title: "+title+ "***");
       
-      ISISRAW iraw(NULL);
-      if (iraw.readFromFile(m_filename.c_str()) != 0)
-      {
-        g_log.error("Unable to open file " + m_filename);
-        throw Exception::FileError("Unable to open File:" , m_filename);
-      }
-
       // Read in the number of spectra in the RAW file
       m_numberOfSpectra = iraw.t_nsp1;
@@ -139 +140 @@
                (WorkspaceFactory::Instance().create("Workspace2D",total_specs,lengthIn,lengthIn-1));
       localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
+      localWorkspace->setTitle(title);
+      // Run parameters
+      helper->loadRunParameters(localWorkspace, &iraw);
+      delete helper;
+      helper = NULL;
+
 
       // Loop over the number of periods in the raw file, putting each period in a separate workspace

trunk/Code/Mantid/DataHandling/src/LoadRaw2.cpp

@@ -4 +4 @@
 #include "MantidDataHandling/LoadRaw2.h"
 #include "MantidDataHandling/ManagedRawFileWorkspace2D.h"
+#include "MantidDataHandling/LoadRawHelper.h"
 #include "MantidDataObjects/Workspace2D.h"
 #include "MantidAPI/XMLlogfile.h"
@@ -86 +87 @@
       // Retrieve the filename from the properties
       m_filename = getPropertyValue("Filename");
-
-      if( isAscii(m_filename) )
-      {
-        g_log.error() << "File \"" << m_filename << "\" is not a valid RAW file.\n";
-        throw std::invalid_argument("Incorrect file type encountered.");
-      }
-
-      //ISISRAW iraw(NULL);
-      FILE* file = fopen(m_filename.c_str(),"rb");
-      if (file == NULL)
-      {
-        g_log.error("Unable to open file " + m_filename);
-        throw Exception::FileError("Unable to open File:" , m_filename);
-      }
+      LoadRawHelper *helper = new LoadRawHelper;
+      FILE* file = helper->openRawFile(m_filename);
       isisRaw->ioRAW(file, true);
-      const std::string title(isisRaw->hdr.hd_title);
+      
+      std::string title(isisRaw->hdr.hd_run, 69);
+      // Insert some spaces to tidy the string up a bit
+      title.insert(5, " ");
+      title.insert(26, " ");
+      title.insert(51, " ");
       g_log.information("**** Run title: "+title+ "***");
 
@@ -196 +190 @@
       localWorkspace->setTitle(title);
       localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
-
-      //if (dhdr.d_comp == 0) throw std::runtime_error("Oops..");
+      // Run parameters
+      helper->loadRunParameters(localWorkspace, isisRaw.get());
+      delete helper;
+      helper = NULL;
+
       // Loop over the number of periods in the raw file, putting each period in a separate workspace
       for (int period = 0; period < m_numberOfPeriods; ++period) {
@@ -205 +202 @@
             localWorkspace =  boost::dynamic_pointer_cast<DataObjects::Workspace2D>
                 (WorkspaceFactory::Instance().create(localWorkspace));
-            //localWorkspace->newInstrumentParameters(); ????
         }
 
@@ -316 +312 @@
 }
 
-    /**
-     * Check if a file is a text file
-     * @param filename The file path to check
-     * @returns true if the file an ascii text file, false otherwise
-     */
-    bool LoadRaw2::isAscii(const std::string & filename) const
-    {
-      FILE* file = fopen(filename.c_str(), "rb");
-      char data[256];
-      int n = fread(data, 1, sizeof(data), file);
-      char *pend = &data[n];
-      /*
-       * Call it a binary file if we find a non-ascii character in the 
-       * first 256 bytes of the file.
-       */
-      for( char *p = data;  p < pend; ++p )
-      {
-        unsigned long ch = (unsigned long)*p;
-        if( !(ch <= 0x7F) )
-        {
-          return false;
-        }
-        
-      }
-      return true;
-    }
-
     /// Validates the optional 'spectra to read' properties, if they have been set
     void LoadRaw2::checkOptionalProperties()

trunk/Code/Mantid/DataHandling/src/LoadRaw3.cpp

@@ -84 +84 @@
   //open the raw file
   FILE* file=openRawFile(m_filename);
-
-  // Need to check that the file is not a text file as the ISISRAW routines don't deal with these very well, i.e 
-  // reading continues until a bad_alloc is encountered.
-  if( isAscii(file) )
-  {
-    g_log.error() << "File \"" << m_filename << "\" is not a valid RAW file.\n";
-        fclose(file);
-    throw std::invalid_argument("Incorrect file type encountered.");
-  }
 
   bool bLoadlogFiles = getProperty("LoadLogFiles");

trunk/Code/Mantid/DataHandling/src/LoadRawHelper.cpp

@@ -80 +80 @@
         throw Exception::FileError("Unable to open File:", fileName);
       }
+      // Need to check that the file is not a text file as the ISISRAW routines don't deal with these very well, i.e 
+      // reading continues until a bad_alloc is encountered.
+      if( isAscii(file) )
+      {
+        g_log.error() << "File \"" << fileName << "\" is not a valid RAW file.\n";
+        fclose(file);
+        throw std::invalid_argument("Incorrect file type encountered.");
+      }
+      
       return file;
 
@@ -89 +98 @@
     void LoadRawHelper::readTitle(FILE* file,std::string & title)
     {
-      ioRaw(file,true );
+      ioRaw(file, true);
       // This reads in the HDR_STRUCT run, user, title, date & time fields
       std::string header(isisRaw->hdr.hd_run, 69);
@@ -691 +700 @@
      * @param localWorkspace The workspace to attach the information to
      */
-    void LoadRawHelper::loadRunParameters(API::MatrixWorkspace_sptr localWorkspace) const
-    {
+    void LoadRawHelper::loadRunParameters(API::MatrixWorkspace_sptr localWorkspace, ISISRAW * const rawFile) const
+    {
+      ISISRAW * localISISRaw(NULL);
+      if( !rawFile )
+      {
+        localISISRaw = isisRaw.get();
+      }
+      else
+      {
+        localISISRaw = rawFile;
+      }      
+
       API::Run& runDetails = localWorkspace->mutableRun();
       // Run header is what we have set as the workspace title
@@ -698 +717 @@
       runDetails.addProperty("run_header", run_header);
       // Run title is stored in a different attribute
-      runDetails.addProperty("run_title", std::string(isisRaw->r_title,80));
+      runDetails.addProperty("run_title", std::string(localISISRaw->r_title,80));
       
       // Data details on run not the workspace
-      runDetails.addProperty("nspectra", static_cast<int>(isisRaw->t_nsp1));
-      runDetails.addProperty("nchannels", static_cast<int>(isisRaw->t_ntc1));
-      runDetails.addProperty("nperiods", static_cast<int>(isisRaw->t_nper));
+      runDetails.addProperty("nspectra", static_cast<int>(localISISRaw->t_nsp1));
+      runDetails.addProperty("nchannels", static_cast<int>(localISISRaw->t_ntc1));
+      runDetails.addProperty("nperiods", static_cast<int>(localISISRaw->t_nper));
 
       // RPB struct info
-      runDetails.addProperty("r_dur", isisRaw->rpb.r_dur);      // actual run duration
-      runDetails.addProperty("r_durunits", isisRaw->rpb.r_durunits);    // scaler for above (1=seconds)
-      runDetails.addProperty("r_dur_freq",isisRaw->rpb.r_dur_freq);  // testinterval for above (seconds)
-      runDetails.addProperty("r_dmp", isisRaw->rpb.r_dmp);       // dump interval
-      runDetails.addProperty("r_dmp_units", isisRaw->rpb.r_dmp_units);  // scaler for above
-      runDetails.addProperty("r_dmp_freq",isisRaw->rpb.r_dmp_freq);     // interval for above
-      runDetails.addProperty("r_freq",isisRaw->rpb.r_freq);     // 2**k where source frequency = 50 / 2**k
-      runDetails.addProperty("r_gd_prtn_chrg", static_cast<double>(isisRaw->rpb.r_gd_prtn_chrg));  // good proton charge (uA.hour)
-      runDetails.addProperty("r_tot_prtn_chrg", static_cast<double>(isisRaw->rpb.r_tot_prtn_chrg)); // total proton charge (uA.hour)
-      runDetails.addProperty("r_goodfrm",isisRaw->rpb.r_goodfrm);       // good frames
-      runDetails.addProperty("r_rawfrm", isisRaw->rpb.r_rawfrm);        // raw frames
-      runDetails.addProperty("r_dur_wanted",isisRaw->rpb.r_dur_wanted); // requested run duration (units as for "duration" above)
-      runDetails.addProperty("r_dur_secs",isisRaw->rpb.r_dur_secs );    // actual run duration in seconds
-      runDetails.addProperty("r_mon_sum1", isisRaw->rpb.r_mon_sum1);    // monitor sum 1
-      runDetails.addProperty("r_mon_sum2",isisRaw->rpb.r_mon_sum2);     // monitor sum 2
-      runDetails.addProperty("r_mon_sum3",isisRaw->rpb.r_mon_sum3);     // monitor sum 3
-      runDetails.addProperty("r_enddate",std::string(isisRaw->rpb.r_enddate, 11)); // format DD-MMM-YYYY
-      runDetails.addProperty("r_endtime", std::string(isisRaw->rpb.r_endtime, 8)); // format HH-MM-SS
-      runDetails.addProperty("r_prop",isisRaw->rpb.r_prop); // RB (proposal) number
+      runDetails.addProperty("dur", localISISRaw->rpb.r_dur);   // actual run duration
+      runDetails.addProperty("durunits", localISISRaw->rpb.r_durunits); // scaler for above (1=seconds)
+      runDetails.addProperty("dur_freq",localISISRaw->rpb.r_dur_freq);  // testinterval for above (seconds)
+      runDetails.addProperty("dmp", localISISRaw->rpb.r_dmp);       // dump interval
+      runDetails.addProperty("dmp_units", localISISRaw->rpb.r_dmp_units);       // scaler for above
+      runDetails.addProperty("dmp_freq",localISISRaw->rpb.r_dmp_freq);  // interval for above
+      runDetails.addProperty("freq",localISISRaw->rpb.r_freq);  // 2**k where source frequency = 50 / 2**k
+      runDetails.addProperty("gd_prtn_chrg", static_cast<double>(localISISRaw->rpb.r_gd_prtn_chrg));  // good proton charge (uA.hour)
+      runDetails.addProperty("tot_prtn_chrg", static_cast<double>(localISISRaw->rpb.r_tot_prtn_chrg)); // total proton charge (uA.hour)
+      runDetails.addProperty("goodfrm",localISISRaw->rpb.r_goodfrm);    // good frames
+      runDetails.addProperty("rawfrm", localISISRaw->rpb.r_rawfrm);     // raw frames
+      runDetails.addProperty("dur_wanted",localISISRaw->rpb.r_dur_wanted); // requested run duration (units as for "duration" above)
+      runDetails.addProperty("dur_secs",localISISRaw->rpb.r_dur_secs ); // actual run duration in seconds
+      runDetails.addProperty("mon_sum1", localISISRaw->rpb.r_mon_sum1); // monitor sum 1
+      runDetails.addProperty("mon_sum2",localISISRaw->rpb.r_mon_sum2);  // monitor sum 2
+      runDetails.addProperty("mon_sum3",localISISRaw->rpb.r_mon_sum3);  // monitor sum 3
+      runDetails.addProperty("enddate",std::string(localISISRaw->rpb.r_enddate, 11)); // format DD-MMM-YYYY
+      runDetails.addProperty("endtime", std::string(localISISRaw->rpb.r_endtime, 8)); // format HH-MM-SS
+      runDetails.addProperty("rb_proposal",localISISRaw->rpb.r_prop); // RB (proposal) number
 
     }

trunk/Code/Mantid/Nexus/inc/MantidNexus/LoadISISNexus.h

@@ -99 +99 @@
             void loadData(int, int, int&, DataObjects::Workspace2D_sptr );
             void runLoadInstrument(DataObjects::Workspace2D_sptr);
-            //     void runLoadInstrumentFromNexus(DataObjects::Workspace2D_sptr);
             void loadMappingTable(DataObjects::Workspace2D_sptr);
-            void loadProtonCharge(DataObjects::Workspace2D_sptr);
+            void loadRunDetails(DataObjects::Workspace2D_sptr localWorkspace);
+            template<class TYPE>
+            TYPE getEntryValue(const std::string & name);
+            template<class TYPE>
+            TYPE getNXData(const std::string & name);
+
             void loadLogs(DataObjects::Workspace2D_sptr,int period = 1);
 
@@ -167 +171 @@
             static double dblSqrt(double in);
         };
+      
+      /**
+       * Get a value from the nexus file. The name should be relative and the parent group already opened.
+       * @param name The name of the NX entry
+       * @returns The value of entry
+       */
+      template<class TYPE>
+      TYPE LoadISISNexus::getEntryValue(const std::string & name)
+      {
+        openNexusData(name);
+        TYPE value;
+        getNexusData(&value);
+        closeNexusData();
+        return value;
+      }
+
+      /**
+       * Get the first entry from an NX data group
+       * @param name The group name
+       * @returns The data value
+       */
+      template<class TYPE>
+      TYPE LoadISISNexus::getNXData(const std::string & name)
+      {
+        openNexusData(name);
+        TYPE value[1];
+        getNexusData(value);
+        closeNexusData();
+        return value[0];
+      }
+
+
+
 
     } // namespace NeXus

trunk/Code/Mantid/Nexus/src/LoadISISNexus.cpp

@@ -14 +14 @@
 
 #include "Poco/Path.h"
-
+#include <Poco/DateTimeFormatter.h>
+#include <Poco/DateTimeParser.h>
+#include <Poco/DateTimeFormat.h>
+
+#include "boost/lexical_cast.hpp"
 #include <cmath>
 #include <sstream>
@@ -146 +150 @@
       localWorkspace->getAxis(0)->unit() = UnitFactory::Instance().create("TOF");
       localWorkspace->setYUnit("Counts");
+      const std::string title = getNexusString("title");
+      localWorkspace->setTitle(title);
 
       Progress prog(this,0.,1.,total_specs*m_numberOfPeriods);
@@ -158 +164 @@
             runLoadInstrument(localWorkspace );
             loadMappingTable(localWorkspace );
-            loadProtonCharge(localWorkspace);
+            loadRunDetails(localWorkspace);
             loadLogs(localWorkspace );
           }
@@ -167 +173 @@
           runLoadInstrument(localWorkspace );
           loadMappingTable(localWorkspace );
-          loadProtonCharge(localWorkspace);
+          loadRunDetails(localWorkspace);
           loadLogs(localWorkspace );
         }
@@ -174 +180 @@
           localWorkspace =  boost::dynamic_pointer_cast<DataObjects::Workspace2D>
             (WorkspaceFactory::Instance().create(localWorkspace));
-          //localWorkspace->newInstrumentParameters(); ???
 
           loadLogs(localWorkspace ,period);
@@ -334 +339 @@
       }
 
-      //boost::shared_array<char> nxname( new char[NX_MAXNAMELEN] );
-      //boost::shared_array<char> nxclass( new char[NX_MAXNAMELEN] );
-      //int nxdatatype;
-
-      //int stat = NX_OK;
-      //while(stat != NX_EOD)
-      //{
-      //    stat=NXgetnextentry(m_fileID,nxname.get(),nxclass.get(),&nxdatatype);
-      //    std::cerr<<nxname.get()<<"  "<<nxclass.get()<<"  "<<nxdatatype<<"\n";
-      //}
-      //std::cerr<<'\n';
     }
 
@@ -573 +567 @@
     }
 
-    /**  Loag the proton charge from the file.
+    /**  Loag the run details from the file
     *   Group /raw_data_1 must be open.
+    * @param localWorkspace The workspace details to use
     */
-    void LoadISISNexus::loadProtonCharge(DataObjects::Workspace2D_sptr ws)
-    {
-      openNexusData("proton_charge");
-      {
-        getNexusData(&m_proton_charge);
-        ws->mutableRun().setProtonCharge(m_proton_charge);
-      }
+    void LoadISISNexus::loadRunDetails(DataObjects::Workspace2D_sptr localWorkspace)
+    {
+      API::Run & runDetails = localWorkspace->mutableRun();
+      m_proton_charge = getEntryValue<double>("proton_charge");
+      runDetails.setProtonCharge(m_proton_charge);
+      int run_number = getEntryValue<int>("run_number");
+      runDetails.addProperty("run_number", boost::lexical_cast<std::string>(run_number));
+
+
+      openNexusGroup("isis_vms_compat","IXvms");
+      char header[80];
+      openNexusData("HDR");
+      getNexusData(&header);
       closeNexusData();
+      runDetails.addProperty("run_header", std::string(header,80));
+      runDetails.addProperty("run_title", localWorkspace->getTitle());
+      
+
+      runDetails.addProperty("nspectra", getNXData<int>("NSP1"));
+      runDetails.addProperty("nchannels", getNXData<int>("NTC1"));
+      runDetails.addProperty("nperiods", getNXData<int>("NPER"));
+
+      int rpb_int[32];
+      openNexusData("IRPB");
+      getNexusData(&rpb_int[0]);
+      closeNexusData();
+
+      double rpb_dbl[32];
+      openNexusData("RRPB");
+      getNexusData(&rpb_dbl[0]);
+      closeNexusData();
+      
+      runDetails.addProperty("dur", rpb_int[0]);        // actual run duration
+      runDetails.addProperty("durunits", rpb_int[1]);   // scaler for above (1=seconds)
+      runDetails.addProperty("dur_freq", rpb_int[2]);  // testinterval for above (seconds)
+      runDetails.addProperty("dmp", rpb_int[3]);       // dump interval
+      runDetails.addProperty("dmp_units", rpb_int[4]);  // scaler for above
+      runDetails.addProperty("dmp_freq", rpb_int[5]);   // interval for above
+      runDetails.addProperty("freq", rpb_int[6]);       // 2**k where source frequency = 50 / 2**k
+      runDetails.addProperty("gd_prtn_chrg", rpb_dbl[7]);  // good proton charge (uA.hour)
+      runDetails.addProperty("tot_prtn_chrg", rpb_dbl[8]); // total proton charge (uA.hour)
+      runDetails.addProperty("goodfrm",rpb_int[9]);     // good frames
+      runDetails.addProperty("rawfrm", rpb_int[10]);    // raw frames
+      runDetails.addProperty("dur_wanted", rpb_int[11]); // requested run duration (units as for "duration" above)
+      runDetails.addProperty("dur_secs", rpb_int[12]);  // actual run duration in seconds
+      runDetails.addProperty("mon_sum1", rpb_int[13]);  // monitor sum 1
+      runDetails.addProperty("mon_sum2", rpb_int[14]);  // monitor sum 2
+      runDetails.addProperty("mon_sum3",rpb_int[15]);   // monitor sum 3
+      
+      closeNexusGroup(); // isis_vms_compat
+
+      //std::string end_time_iso = getNXData<>("end_time");
+      char strvalue[19];
+      openNexusData("end_time");
+      getNexusData(&strvalue);
+      closeNexusData();
+      std::string end_time_iso(strvalue, 19);
+      std::string end_date(""), end_time("");
+      try
+      {
+        Poco::DateTime end_time_output;
+        int timezone_diff(0);
+        Poco::DateTimeParser::parse(Poco::DateTimeFormat::ISO8601_FORMAT, end_time_iso, end_time_output, timezone_diff);
+        end_date = Poco::DateTimeFormatter::format(end_time_output, "%d-%m-%Y", timezone_diff);
+        end_time = Poco::DateTimeFormatter::format(end_time_output, "%H:%M:%S", timezone_diff);
+      }
+      catch(Poco::SyntaxException&)
+      {
+        end_date = "\?\?-\?\?-\?\?\?\?";
+        end_time = "\?\?-\?\?-\?\?";
+        g_log.warning() << "Cannot parse end time from entry in Nexus file.\n";
+      }
+      
+      runDetails.addProperty("enddate", end_date);
+      runDetails.addProperty("endtime", end_time);
+      runDetails.addProperty("rb_proposal",rpb_int[21]); // RB (proposal) number
 
       openNexusGroup("sample","NXsample");
       std::string sample_name = getNexusString("name");
-      ws->mutableSample().setName(sample_name);
+      localWorkspace->mutableSample().setName(sample_name);
       closeNexusGroup();
     }

trunk/Code/Mantid/Nexus/src/LoadISISNexus2.cpp

@@ -619 +619 @@
         int timezone_diff(0);
         Poco::DateTimeParser::parse(Poco::DateTimeFormat::ISO8601_FORMAT, end_time_iso, end_time_output, timezone_diff);
-        end_date = Poco::DateTimeFormatter::format(end_time_output, "%DD-%MM-%YYYY", timezone_diff);
-        end_time = Poco::DateTimeFormatter::format(end_time_output, "%HH-%MM-%SS", timezone_diff);
+        end_date = Poco::DateTimeFormatter::format(end_time_output, "%d-%m-%Y", timezone_diff);
+        end_time = Poco::DateTimeFormatter::format(end_time_output, "%H:%M:%S", timezone_diff);
       }
       catch(Poco::SyntaxException&)
@@ -631 +631 @@
       runDetails.addProperty("enddate", end_date);
       runDetails.addProperty("endtime", end_time);
-      runDetails.addProperty("prop",rpb_int[21]); // RB (proposal) number
+      runDetails.addProperty("rb_proposal",rpb_int[21]); // RB (proposal) number
       vms_compat.close();