Merge remote-tracking branch 'origin/feature/10374_fits_nxtomo_beam_d…

…ata'

Code/Mantid/Framework/DataHandling/CMakeLists.txt

@@ -411,6 +411,7 @@ set ( TEST_FILES
 	SaveMaskTest.h
 	SaveNISTDATTest.h
 	SaveNXSPETest.h
+	SaveNXTomoTest.h
 	SaveNexusProcessedTest.h
 	SaveNexusTest.h
 	SavePARTest.h

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/LoadFITS.h

@@ -24,6 +24,7 @@ struct FITSInfo {
   double tof;
   double timeBin;
   double scale;
+  int imageKey;
   long int countsInImage;
   long int numberOfTriggers;
   string extension;
@@ -127,6 +128,7 @@ namespace DataHandling
     string m_headerOffsetKey;
     string m_headerBitDepthKey;
     string m_headerRotationKey;
+    string m_headerImageKeyKey;
     string m_mapFile;
     std::vector<std::string> m_headerAxisNameKeys;
 

Code/Mantid/Framework/DataHandling/inc/MantidDataHandling/SaveNXTomo.h

@@ -5,10 +5,10 @@
 // Includes
 //---------------------------------------------------
 #include <vector>
+#include "MantidAPI/Algorithm.h"
 #include "MantidDataObjects/Workspace2D.h"
 #include "MantidGeometry/Instrument/RectangularDetector.h"
 
-
 namespace Mantid
 {
   namespace DataHandling
@@ -76,20 +76,19 @@ namespace Mantid
       void exec();
 
       /// Creates the format for the output file if it doesn't exist
-      ::NeXus::File setupFile(bool resizeData = false);
+      ::NeXus::File setupFile();
 
       /// Writes a single workspace into the file
-      void writeSingle(const DataObjects::Workspace2D_sptr workspace, ::NeXus::File &nxFile);
+      void writeSingleWorkspace(const DataObjects::Workspace2D_sptr workspace, ::NeXus::File &nxFile);
+
+      /// Write various pieces of data from the workspace log with checks on the structure of the nexus file
+      void writeLogValues(const DataObjects::Workspace2D_sptr workspace, ::NeXus::File &nxFile, int thisFileInd);
+      void writeIntensityValue(const DataObjects::Workspace2D_sptr workspace, ::NeXus::File &nxFile, int thisFileInd);
+      void writeImageKeyValue(const DataObjects::Workspace2D_sptr workspace, ::NeXus::File &nxFile, int thisFileInd);    
 
       /// Main exec routine, called for group or individual workspace processing.
       void processAll();
 
-      /// Fetch all rectangular Detector objects defined for an instrument
-      std::vector<boost::shared_ptr<const Mantid::Geometry::RectangularDetector>> getRectangularDetectors(const Geometry::Instrument_const_sptr &instrument);
-
-      /// Populate dims_array with the dimensions defined in the rectangular detector in the instrument
-      std::vector<int64_t> getDimensionsFromDetector(const std::vector<boost::shared_ptr<const Mantid::Geometry::RectangularDetector>> &rectDetectors, size_t useDetectorIndex = 0);
-
       // Include error data in the written file
       bool m_includeError;
       bool m_overwriteFile;
@@ -100,6 +99,8 @@ namespace Mantid
       std::string m_filename;                     
       // Dimensions for axis in nxTomo file.
       std::vector<int64_t> m_dimensions;
+      // Infinite file range dimensions / for use with makeData data and error
+      std::vector<int64_t> m_infDimensions;
 
       /// file format version
       static const std::string NXTOMO_VER;

Code/Mantid/Framework/DataHandling/src/LoadFITS.cpp

@@ -21,6 +21,7 @@ namespace
     static const std::string BIT_DEPTH_NAME = "BitDepthName";
     static const std::string ROTATION_NAME = "RotationName";
     static const std::string AXIS_NAMES_NAME = "AxisNames";
+    static const std::string IMAGE_KEY_NAME = "ImageKeyName";
     static const std::string HEADER_MAP_NAME = "HeaderMapFile";
 
   /**
@@ -74,12 +75,18 @@ namespace DataHandling
 
     declareProperty(new API::WorkspaceProperty<API::Workspace>("OutputWorkspace", "", Kernel::Direction::Output));    
 
+    declareProperty(new PropertyWithValue<int>("ImageKey", -1, Kernel::Direction::Input),
+      "Image type to set these files as. 0=data image, 1=flat field, 2=open field, -1=use the value from FITS header.");
+
     declareProperty(new PropertyWithValue<string>(BIT_DEPTH_NAME, "BITPIX", Kernel::Direction::Input),
       "Name for the pixel bit depth header key.");
     declareProperty(new PropertyWithValue<string>(ROTATION_NAME, "ROTATION", Kernel::Direction::Input),
       "Name for the rotation header key.");
     declareProperty(new PropertyWithValue<string>(AXIS_NAMES_NAME, "NAXIS1,NAXIS2", Kernel::Direction::Input),
       "Names for the axis header keys, comma separated string of all axis.");
+    declareProperty(new PropertyWithValue<string>(IMAGE_KEY_NAME, "IMAGEKEY", Kernel::Direction::Input),
+      "Names for the image type, key.");
+
 
     declareProperty(new FileProperty(HEADER_MAP_NAME, "", FileProperty::OptionalDirectory, "", Kernel::Direction::Input), 
       "A file mapping header keys to the ones used by ISIS [line separated values in the format KEY=VALUE, e.g. BitDepthName=BITPIX ");
@@ -95,6 +102,7 @@ namespace DataHandling
     m_headerScaleKey = "BSCALE";
     m_headerOffsetKey = "BZERO";
     m_headerBitDepthKey = "BITPIX";
+    m_headerImageKeyKey = "IMAGEKEY";
     m_headerRotationKey = "ROTATION";
     m_mapFile = "";
     m_headerAxisNameKeys.push_back("NAXIS1");
@@ -145,6 +153,13 @@ namespace DataHandling
             allHeaderInfo[i].isFloat = false;
           }
 
+          // Add the image key, use the property if it's not -1, otherwise use the header value
+          allHeaderInfo[i].imageKey = boost::lexical_cast<int>(getPropertyValue("ImageKey"));
+          if(allHeaderInfo[i].imageKey == -1)
+          {
+            allHeaderInfo[i].imageKey = boost::lexical_cast<int>(allHeaderInfo[i].headerKeys[m_headerImageKeyKey]);
+          }
+
           allHeaderInfo[i].bitsPerPixel = lexical_cast<int>(tmpBitPix);
           allHeaderInfo[i].numberOfAxis = static_cast<int>(m_headerAxisNameKeys.size());
 
@@ -163,7 +178,7 @@ namespace DataHandling
         catch(std::exception &)
         {
           //todo write error and fail this load with invalid data in file.
-          throw std::runtime_error("Unable to locate one or more valid BITPIX, NAXIS, TOF, TIMEBIN, N_COUNTS or N_TRIGS values in the FITS file header.");
+          throw std::runtime_error("Unable to locate one or more valid BITPIX, NAXIS or IMAGEKEY values in the FITS file header.");
         }
 
         allHeaderInfo[i].scale = (allHeaderInfo[i].headerKeys[m_headerScaleKey] == "") ? 1 : lexical_cast<double>(allHeaderInfo[i].headerKeys[m_headerScaleKey]);
@@ -286,7 +301,7 @@ namespace DataHandling
     else
     {
       // Invalid files, record error
-       throw std::runtime_error("Loader currently doesn't support FITS files with non-standard extensions, greater than two axis of data, or has detected that all the files are not similar.");
+      throw std::runtime_error("Loader currently doesn't support FITS files with non-standard extensions, greater than two axis of data, or has detected that all the files are not similar.");
     }    
   }
 
@@ -332,7 +347,15 @@ namespace DataHandling
     if(rotation != -1)
       ws->mutableRun().addLogData(new PropertyWithValue<double>("Rotation", rotation));  
 
-
+    // Add axis information to log. Clear first from copied WS
+    ws->mutableRun().removeLogData("Axis1",true);
+    ws->mutableRun().addLogData(new PropertyWithValue<int>("Axis1", static_cast<int>(fileInfo.axisPixelLengths[0])));  
+    ws->mutableRun().removeLogData("Axis2",true);
+    ws->mutableRun().addLogData(new PropertyWithValue<int>("Axis2", static_cast<int>(fileInfo.axisPixelLengths[1])));  
+
+    // Add image key data to log. Clear first from copied WS
+    ws->mutableRun().removeLogData("ImageKey",true);
+    ws->mutableRun().addLogData(new PropertyWithValue<int>("ImageKey", static_cast<int>(fileInfo.imageKey)));
 
     m_progress->report();
 
@@ -589,6 +612,11 @@ namespace DataHandling
               std::string propVal = getProperty(AXIS_NAMES_NAME);
               boost::split(m_headerAxisNameKeys, propVal, boost::is_any_of(","));
             }
+
+            if(lineSplit[0] == IMAGE_KEY_NAME && lineSplit[1] != "")
+            {              
+              m_headerImageKeyKey = lineSplit[1];
+            }
           }
 
           fStream.close(); 
@@ -619,6 +647,8 @@ namespace DataHandling
         std::string propVal = getProperty(AXIS_NAMES_NAME);
         boost::split(m_headerAxisNameKeys, propVal, boost::is_any_of(","));
       }
+      if(getPropertyValue(IMAGE_KEY_NAME) != "")
+        m_headerImageKeyKey = getPropertyValue(IMAGE_KEY_NAME);
     }