Merge branch 'tube_calibration_1' into develop re #6344

Conflicts:
	Code/Mantid/Framework/Algorithms/src/ApplyCalibration.cpp

Signed-off-by: Karl Palmen <karl.palmen@stfc.ac.uk>

Code/Mantid/Framework/Algorithms/CMakeLists.txt

@@ -442,6 +442,7 @@ set ( TEST_FILES
 	AlphaCalcTest.h
 	AnyShapeAbsorptionTest.h
 	AppendSpectraTest.h
+	ApplyCalibrationTest.h
 	ApplyDeadTimeCorrTest.h
 	ApplyDetailedBalanceTest.h
 	ApplyTransmissionCorrectionTest.h

Code/Mantid/Framework/Algorithms/src/ApplyCalibration.cpp

@@ -12,6 +12,7 @@ The PositionTable must have columns ''Detector ID'' and ''Detector Position''. T
 #include "MantidGeometry/Instrument/Component.h"
 #include "MantidAPI/FileProperty.h"
 #include "MantidAPI/MatrixWorkspace.h"
+#include "MantidGeometry/Instrument/ComponentHelper.h"
 #include <boost/scoped_ptr.hpp>
 
 namespace Mantid
@@ -33,7 +34,7 @@ namespace Mantid
     using Geometry::Instrument;
     using Geometry::Instrument_sptr;
     using Geometry::IDetector_sptr;
-    using Kernel::V3D;
+    using Geometry::IComponent_const_sptr;
 
     /// Empty default constructor
     ApplyCalibration::ApplyCalibration()
@@ -91,32 +92,14 @@ namespace Mantid
     */
     void ApplyCalibration::setDetectorPosition(const Geometry::Instrument_const_sptr & instrument, int detID, V3D pos, bool /*sameParent*/ )
     {
-       Geometry::IDetector_const_sptr det = instrument->getDetector(detID);
-       // Then find the corresponding relative position
-       boost::shared_ptr<const Geometry::IComponent> parent = det->getParent();
-       if (parent)
-       {
-         pos -= parent->getPos();
-         Quat rot = parent->getRelativeRot();
-         rot.inverse();
-         rot.rotate(pos);
-       }
-       boost::shared_ptr<const Geometry::IComponent>grandparent = parent->getParent();
-       if (grandparent)
-       {
-         Quat rot = grandparent->getRelativeRot();
-         rot.inverse();
-         rot.rotate(pos);
-         boost::shared_ptr<const Geometry::IComponent>greatgrandparent = grandparent->getParent();
-         if (greatgrandparent) {
-           Quat rot2 = greatgrandparent->getRelativeRot();
-            rot2.inverse();
-            rot2.rotate(pos);
-         }
-       }
-
-       // Add a parameter for the new position
-       m_pmap->addV3D(det.get(), "pos", pos);
+
+       IComponent_const_sptr det =instrument->getDetector(detID); ;
+       // Do the move
+       using namespace Geometry::ComponentHelper;
+       TransformType positionType = Absolute;
+       // TransformType positionType = Relative;
+       Geometry::ComponentHelper::moveComponent(*det, *m_pmap, pos, positionType);
+
     }
 
   } // namespace Algorithms

Code/Mantid/Framework/Algorithms/test/ApplyCalibrationTest.h

@@ -0,0 +1,155 @@
+#ifndef APPLYCALIBRATIONTEST_H_
+#define APPLYCALIBRATIONTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidDataHandling/LoadInstrument.h"
+#include "MantidAPI/IAlgorithm.h"
+#include "MantidAlgorithms/ApplyCalibration.h"
+#include "MantidAPI/Workspace.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidAPI/MatrixWorkspace.h"
+#include "WorkspaceCreationHelperTest.h"
+#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/ITableWorkspace.h"
+#include "MantidAPI/TableRow.h"
+#include "MantidKernel/V3D.h"
+#include "MantidGeometry/Instrument.h"
+#include "MantidGeometry/Instrument/Component.h"
+#include "MantidDataHandling/LoadEmptyInstrument.h"
+#include <stdexcept>
+
+using namespace Mantid::Algorithms;
+using namespace Mantid::API;
+using namespace Mantid::Kernel;
+using namespace Mantid::DataObjects;
+using Mantid::Geometry::IDetector_const_sptr;
+
+class ApplyCalibrationTest : public CxxTest::TestSuite
+{
+public:
+
+  void testName()
+  {
+    TS_ASSERT_EQUALS( appCalib.name(), "ApplyCalibration" )
+  }
+
+  void testInit()
+  {
+    appCalib.initialize();
+    TS_ASSERT( appCalib.isInitialized() )
+  }
+
+  void testSimple()
+  {
+
+     int ndets = 3; 
+
+     // Create workspace with paremeterised instrument and put into data store
+     Workspace2D_sptr ws = WorkspaceCreationHelper::create2DWorkspaceWithFullInstrument(ndets, 10, true);
+     const std::string wsName("ApplyCabrationWs");
+     AnalysisDataServiceImpl & dataStore = AnalysisDataService::Instance();
+     dataStore.add(wsName, ws);
+
+     // Create Calibration Table
+     ITableWorkspace_sptr posTableWs = WorkspaceFactory::Instance().createTable();
+     posTableWs->addColumn("int","Detector ID");
+     posTableWs->addColumn("V3D","Detector Position");
+
+     for(int i=0; i < ndets; ++i)
+     {
+       TableRow row = posTableWs->appendRow();
+       row << i+1 << V3D(1.0,0.01*i,2.0); 
+     }
+     TS_ASSERT_THROWS_NOTHING(appCalib.setPropertyValue("Workspace", wsName ));
+     TS_ASSERT_THROWS_NOTHING(appCalib.setProperty<ITableWorkspace_sptr>("PositionTable", posTableWs ));
+     TS_ASSERT_THROWS_NOTHING(appCalib.execute());
+
+     TS_ASSERT( appCalib.isExecuted() );
+
+     IDetector_const_sptr det = ws->getDetector(0);
+     int id = det->getID();
+     V3D newPos = det->getPos();
+     TS_ASSERT_EQUALS( id, 1);
+     TS_ASSERT_DELTA( newPos.X() , 1.0, 0.0001);
+     TS_ASSERT_DELTA( newPos.Y() , 0.0, 0.0001);
+     TS_ASSERT_DELTA( newPos.Z() , 2.0, 0.0001);
+
+     det = ws->getDetector(ndets-1);
+     id = det->getID();
+     newPos = det->getPos();
+     TS_ASSERT_EQUALS( id, ndets);
+     TS_ASSERT_DELTA( newPos.X() , 1.0, 0.0001);
+     TS_ASSERT_DELTA( newPos.Y() , 0.01*(ndets-1), 0.0001);
+     TS_ASSERT_DELTA( newPos.Z() , 2.0, 0.0001);
+  }
+
+  void testComplex()
+  {
+     /* The purpse of this test is to test the algorithm when the relative positioning and rotation
+      * of components is complicated. This is the case for the MAPS instrument and so here we
+      * load the IDF of a MAPS instrument where the number of detectors has been reduced.
+     */
+
+     int ndets = 3; 
+
+     // Create workspace with a reduced MAPS instrument (parametrised) and retrieve vfrom data store.
+     const std::string wsName("ApplyCabrationWs");
+     Mantid::DataHandling::LoadEmptyInstrument loader;
+     loader.initialize();
+     loader.setPropertyValue("Filename", "IDFs_For_UNIT_TESTING/MAPS_Definition_reduced.xml");
+     loader.setPropertyValue("OutputWorkspace", wsName);
+     loader.execute();
+     AnalysisDataServiceImpl & dataStore = AnalysisDataService::Instance();
+     MatrixWorkspace_sptr ws = dataStore.retrieveWS<MatrixWorkspace>(wsName);
+
+     // Create Calibration Table
+     int firstDetectorID = 34208002;
+     ITableWorkspace_sptr posTableWs = WorkspaceFactory::Instance().createTable();
+     posTableWs->addColumn("int","Detector ID");
+     posTableWs->addColumn("V3D","Detector Position");
+
+     for(int i=0; i < ndets; ++i)
+     {
+       TableRow row = posTableWs->appendRow();
+       row << firstDetectorID + 10*i << V3D(1.0,0.01*i,2.0); 
+     }
+     TS_ASSERT_THROWS_NOTHING(appCalib.setPropertyValue("Workspace", wsName ));
+     TS_ASSERT_THROWS_NOTHING(appCalib.setProperty<ITableWorkspace_sptr>("PositionTable", posTableWs ));
+     TS_ASSERT_THROWS_NOTHING(appCalib.execute());
+
+     TS_ASSERT( appCalib.isExecuted() );
+
+     IDetector_const_sptr det = ws->getDetector(1830);
+     int id = det->getID();
+     V3D newPos = det->getPos();
+     TS_ASSERT_EQUALS( id, firstDetectorID);
+     TS_ASSERT_DELTA( newPos.X() , 1.0, 0.0001);
+     TS_ASSERT_DELTA( newPos.Y() , 0.0, 0.0001);
+     TS_ASSERT_DELTA( newPos.Z() , 2.0, 0.0001);
+
+     det = ws->getDetector(1840);
+     id = det->getID();
+     newPos = det->getPos();
+     TS_ASSERT_EQUALS( id, firstDetectorID + 10);
+     TS_ASSERT_DELTA( newPos.X() , 1.0, 0.0001);
+     TS_ASSERT_DELTA( newPos.Y() , 0.01, 0.0001);
+     TS_ASSERT_DELTA( newPos.Z() , 2.0, 0.0001);
+
+     det = ws->getDetector(1850);
+     id = det->getID();
+     newPos = det->getPos();
+     TS_ASSERT_EQUALS( id, firstDetectorID + 20);
+     TS_ASSERT_DELTA( newPos.X() , 1.0, 0.0001);
+     TS_ASSERT_DELTA( newPos.Y() , 0.02, 0.0001);
+     TS_ASSERT_DELTA( newPos.Z() , 2.0, 0.0001);
+  }
+
+
+private:
+  ApplyCalibration appCalib;
+
+
+};
+
+#endif /*APPLYCALIBRATIONTEST_H_*/

Code/Mantid/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py

@@ -0,0 +1,73 @@
+#
+# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
+#
+# Here we run the calibration of a selected part of MAPS 
+
+#
+from mantid.api import WorkspaceFactory  # For table worskspace of calibrations
+from tube_calib_fit_params import * # To handle fit parameters
+from ideal_tube import * # For ideal tube
+from tube_calib import *  # For tube calibration functions
+from tube_spec import * # For tube specification class
+
+
+# == Set parameters for calibration ==
+
+path = r"C:/Temp/" # Path name of folder containing input and output files
+filename = 'MAPS14919.raw' # Name of calibration run
+rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper 
+rangeUpper = 10000 #
+
+
+# Set initial parameters for peak finding
+ExpectedHeight = -1000.0 # Expected Height of Peaks (initial value of fit parameter)
+ExpectedWidth = 8.0 # Expected width of centre peak (initial value of fit parameter)
+ExpectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0] # Expected positions of the edges and peak (initial values of fit parameters)
+
+# Set what we want to calibrate (e.g whole intrument or one door )
+CalibratedComponent = 'MAPS'  # Calibrate all
+
+
+# Get calibration raw file and integrate it    
+rawCalibInstWS = Load(path+filename)  #'raw' in 'rawCalibInstWS' means unintegrated.
+print "Integrating Workspace"
+CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
+DeleteWorkspace(rawCalibInstWS)
+print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate" 
+
+# == Create Objects needed for calibration ==
+
+#Create Calibration Table
+calibrationTable = CreateEmptyTableWorkspace(OutputWorkspace="CalibTable")
+calibrationTable.addColumn(type="int",name="Detector ID")  # "Detector ID" column required by ApplyCalbration
+calibrationTable.addColumn(type="V3D",name="Detector Position")  # "Detector Position" column required by ApplyCalbration
+
+# Specify component to calibrate
+thisTubeSet = TubeSpec(CalibInstWS)
+thisTubeSet.setTubeSpecByString(CalibratedComponent)
+
+# Get ideal tube
+iTube = IdealTube()
+# Set positions of where the shadows and ends should be. 
+# An intelligent guess is used here that is not correct for all tubes.
+iTube.setPositionsAndForm([-0.50,-0.16,-0.00, 0.16, 0.50 ],[2,1,1,1,2]) 
+
+# Get fitting parameters
+fitPar = TubeCalibFitParams( ExpectedPositions, ExpectedHeight, ExpectedWidth )
+
+print "Created objects needed for calibration."
+
+# == Get the calibration and put results into calibration table ==
+# also put peaks into PeakFile
+getCalibration( CalibInstWS, thisTubeSet, calibrationTable,  fitPar, iTube, PeakFile=path+'TubeDemoMaps01.txt' )
+print "Got calibration (new positions of detectors) "
+
+# == Apply the Calibation ==
+ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+print "Applied calibration"
+
+
+# == Save workspace ==
+SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+

Code/Mantid/scripts/Calibration/Examples/TubeCalibDemoMaps_B1.py

@@ -0,0 +1,72 @@
+#
+# TUBE CALIBRATION DEMONSTRATION PROGRAM FOR MAPS - Execute this
+#
+# Here we run the calibration of a selected part of MAPS 
+
+#
+from mantid.api import WorkspaceFactory  # For table worskspace of calibrations
+from tube_calib_fit_params import * # To handle fit parameters
+from ideal_tube import * # For ideal tube
+from tube_calib import *  # For tube calibration functions
+from tube_spec import * # For tube specification class
+
+
+# == Set parameters for calibration ==
+
+path = r"C:/Temp/" # Path name of folder containing input and output files
+filename = 'MAPS14919.raw' # Name of calibration run
+rangeLower = 2000 # Integrate counts in each spectra from rangeLower to rangeUpper 
+rangeUpper = 10000 #
+
+
+# Set initial parameters for peak finding
+ExpectedHeight = -1000.0 # Expected Height of Peaks (initial value of fit parameter)
+ExpectedWidth = 8.0 # Expected width of centre peak (initial value of fit parameter)
+ExpectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0] # Expected positions of the edges and peak (initial values of fit parameters)
+
+# Set what we want to calibrate (e.g whole intrument or one door )
+CalibratedComponent = 'B1_window'  # Calibrate B1 window
+
+
+# Get calibration raw file and integrate it    
+rawCalibInstWS = Load(path+filename)  #'raw' in 'rawCalibInstWS' means unintegrated.
+print "Integrating Workspace"
+CalibInstWS = Integration( rawCalibInstWS, RangeLower=rangeLower, RangeUpper=rangeUpper )
+DeleteWorkspace(rawCalibInstWS)
+print "Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate" 
+
+# == Create Objects needed for calibration ==
+
+#Create Calibration Table
+calibrationTable = CreateEmptyTableWorkspace(OutputWorkspace="CalibTable")
+calibrationTable.addColumn(type="int",name="Detector ID")  # "Detector ID" column required by ApplyCalbration
+calibrationTable.addColumn(type="V3D",name="Detector Position")  # "Detector Position" column required by ApplyCalbration
+
+# Specify component to calibrate
+thisTubeSet = TubeSpec(CalibInstWS)
+thisTubeSet.setTubeSpecByString(CalibratedComponent)
+
+# Get ideal tube
+iTube = IdealTube()
+# The positions of the shadows and ends here are an intelligent guess.
+iTube.setPositionsAndForm([-0.50,-0.165,-0.00, 0.165, 0.50 ],[2,1,1,1,2])
+
+# Get fitting parameters
+fitPar = TubeCalibFitParams( ExpectedPositions, ExpectedHeight, ExpectedWidth )
+
+print "Created objects needed for calibration."
+
+# == Get the calibration and put results into calibration table ==
+# also put peaks into PeakFile
+getCalibration( CalibInstWS, thisTubeSet, calibrationTable,  fitPar, iTube, PeakFile=path+'TubeDemoMaps01.txt' )
+print "Got calibration (new positions of detectors) "
+
+# == Apply the Calibation ==
+ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
+print "Applied calibration"
+
+
+# == Save workspace ==
+SaveNexusProcessed( CalibInstWS, path+'TubeCalibDemoMapsResult.nxs',"Result of Running TCDemoMaps.py")
+print "saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
+