Refs #11229 option for nexus output added

Code/Mantid/scripts/SCD_Reduction/ReduceSCD.config

@@ -43,6 +43,8 @@ calibration_file_2  None
 #
 data_directory    None       
 output_directory  /SNS/TOPAZ/IPTS-9890/shared/SPAnH
+# Change to true for data with lots of peaks.  Use False for ISAW ASCII output
+output_nexus      False
 
 #
 # If use_monitor_counts is True, then the integrated beam monitor

Code/Mantid/scripts/SCD_Reduction/ReduceSCD_OneRun.py

@@ -72,6 +72,7 @@
 calibration_file_2        = params_dictionary.get('calibration_file_2', None)
 data_directory            = params_dictionary[ "data_directory" ]
 output_directory          = params_dictionary[ "output_directory" ]
+output_nexus              = params_dictionary.get( "output_nexus", False)
 min_tof                   = params_dictionary[ "min_tof" ]
 max_tof                   = params_dictionary[ "max_tof" ]
 use_monitor_counts        = params_dictionary[ "use_monitor_counts" ]
@@ -145,7 +146,10 @@
 # Name the files to write for this run
 #
 run_niggli_matrix_file = output_directory + "/" + run + "_Niggli.mat"
-run_niggli_integrate_file = output_directory + "/" + run + "_Niggli.integrate"
+if output_nexus:
+    run_niggli_integrate_file = output_directory + "/" + run + "_Niggli.nxs"
+else:
+    run_niggli_integrate_file = output_directory + "/" + run + "_Niggli.integrate"
 
 #
 # Load the run data and find the total monitor counts
@@ -219,7 +223,10 @@
 # see these partial results
 #
 SaveIsawUB( InputWorkspace=peaks_ws,Filename=run_niggli_matrix_file )
-SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False,
+if output_nexus:
+	SaveNexus( InputWorkspace=peaks_ws, Filename=run_niggli_integrate_file )
+else:
+	SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False,
                Filename=run_niggli_integrate_file )
 
 #
@@ -327,7 +334,10 @@
 # This is the only file needed, for the driving script to get a combined
 # result.
 #
-SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False,
+if output_nexus:
+	SaveNexus( InputWorkspace=peaks_ws, Filename=run_niggli_integrate_file )
+else:
+	SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False,
                Filename=run_niggli_integrate_file )
 
 # Print warning if user is trying to integrate using the cylindrical method and transorm the cell
@@ -342,13 +352,20 @@
     if (not cell_type is None) and (not centering is None) :
         run_conventional_matrix_file = output_directory + "/" + run + "_" +        \
                                    cell_type + "_" + centering + ".mat"
-        run_conventional_integrate_file = output_directory + "/" + run + "_" + \
+        if output_nexus:
+            run_conventional_integrate_file = output_directory + "/" + run + "_" + \
+                                      cell_type + "_" + centering + ".nxs"
+        else:
+            run_conventional_integrate_file = output_directory + "/" + run + "_" + \
                                       cell_type + "_" + centering + ".integrate"
         SelectCellOfType( PeaksWorkspace=peaks_ws,\
                       CellType=cell_type, Centering=centering,\
                       AllowPermutations=allow_perm,\
                       Apply=True, Tolerance=tolerance )
-        SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False,\
+	if output_nexus:
+        	SaveNexus( InputWorkspace=peaks_ws, Filename=run_conventional_integrate_file )
+        else:
+        	SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False,\
                    Filename=run_conventional_integrate_file )
         SaveIsawUB( InputWorkspace=peaks_ws, Filename=run_conventional_matrix_file )
 

Code/Mantid/scripts/SCD_Reduction/ReduceSCD_Parallel.py

@@ -84,6 +84,7 @@ def run ( self ):
 
 exp_name              = params_dictionary[ "exp_name" ]
 output_directory      = params_dictionary[ "output_directory" ]
+output_nexus          = params_dictionary.get( "output_nexus", False)
 reduce_one_run_script = params_dictionary[ "reduce_one_run_script" ]
 slurm_queue_name      = params_dictionary[ "slurm_queue_name" ]
 max_processes         = int(params_dictionary[ "max_processes" ])
@@ -94,6 +95,7 @@ def run ( self ):
 centering             = params_dictionary[ "centering" ]
 allow_perm            = params_dictionary[ "allow_perm" ]
 run_nums              = params_dictionary[ "run_nums" ]
+data_directory        = params_dictionary[ "data_directory" ]
 
 use_cylindrical_integration = params_dictionary[ "use_cylindrical_integration" ]
 instrument_name       = params_dictionary[ "instrument_name" ]
@@ -153,14 +155,44 @@ def run ( self ):
 # appending them to a combined output file.
 #
 niggli_name = output_directory + "/" + exp_name + "_Niggli"
-niggli_integrate_file = niggli_name + ".integrate"
+if output_nexus:
+    niggli_integrate_file = niggli_name + ".nxs"
+else:
+    niggli_integrate_file = niggli_name + ".integrate"
 niggli_matrix_file = niggli_name + ".mat"
 
 first_time = True
+
+if output_nexus:
+    #Only need this for instrument for peaks_total
+    short_filename = "%s_%s_event.nxs" % (instrument_name, str(run_nums[0]))
+    if data_directory is not None:
+        full_name = data_directory + "/" + short_filename
+    else:
+        candidates = FileFinder.findRuns(short_filename)
+        full_name = ""
+        for item in candidates:
+            if os.path.exists(item):
+                full_name = str(item)
+
+        if not full_name.endswith('nxs'):
+            print "Exiting since the data_directory was not specified and"
+            print "findnexus failed for event NeXus file: " + instrument_name + " " + str(run)
+            exit(0)
+    #
+    # Load the first data file to find instrument
+    #
+    wksp = LoadEventNexus( Filename=full_name, FilterByTofMin=0, FilterByTofMax=0 )
+    peaks_total = CreatePeaksWorkspace(NumberOfPeaks=0, InstrumentWorkspace=wksp)
+
 if not use_cylindrical_integration:
     for r_num in run_nums:
-        one_run_file = output_directory + '/' + str(r_num) + '_Niggli.integrate'
-        peaks_ws = LoadIsawPeaks( Filename=one_run_file )
+        if output_nexus:
+            one_run_file = output_directory + '/' + str(r_num) + '_Niggli.nxs'
+            peaks_ws = Load( Filename=one_run_file )
+        else:
+            one_run_file = output_directory + '/' + str(r_num) + '_Niggli.integrate'
+            peaks_ws = LoadIsawPeaks( Filename=one_run_file )
         if first_time:
             if UseFirstLattice and not read_UB:
     # Find a UB (using FFT) for the first run to use in the FindUBUsingLatticeParameters
@@ -171,17 +203,27 @@ def run ( self ):
                 uc_alpha = peaks_ws.sample().getOrientedLattice().alpha()
                 uc_beta = peaks_ws.sample().getOrientedLattice().beta()
                 uc_gamma = peaks_ws.sample().getOrientedLattice().gamma()
-            SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False, Filename=niggli_integrate_file )
-
+		if output_nexus:
+                    peaks_total = CombinePeaksWorkspaces(LHSWorkspace=peaks_total, RHSWorkspace=peaks_ws)
+                    SaveNexus( InputWorkspace=peaks_ws, Filename=niggli_integrate_file )
+		else:
+                    SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False, Filename=niggli_integrate_file )
             first_time = False
         else:
-            SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=True, Filename=niggli_integrate_file )
+	    if output_nexus:
+                peaks_total = CombinePeaksWorkspaces(LHSWorkspace=peaks_total, RHSWorkspace=peaks_ws)
+                SaveNexus( InputWorkspace=peaks_total, Filename=niggli_integrate_file )
+	    else:
+                SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=True, Filename=niggli_integrate_file )
 
 #
 # Load the combined file and re-index all of the peaks together.
 # Save them back to the combined Niggli file (Or selcted UB file if in use...)
 #
-    peaks_ws = LoadIsawPeaks( Filename=niggli_integrate_file )
+    if output_nexus:
+        peaks_ws = Load( Filename=niggli_integrate_file )
+    else:
+        peaks_ws = LoadIsawPeaks( Filename=niggli_integrate_file )
 
 #
 # Find a Niggli UB matrix that indexes the peaks in this run
@@ -206,7 +248,10 @@ def run ( self ):
         FindUBUsingFFT( PeaksWorkspace=peaks_ws, MinD=min_d, MaxD=max_d, Tolerance=tolerance )
 
     IndexPeaks( PeaksWorkspace=peaks_ws, Tolerance=tolerance )
-    SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False, Filename=niggli_integrate_file )
+    if output_nexus:
+        SaveNexus( InputWorkspace=peaks_ws, Filename=niggli_integrate_file )
+    else:
+        SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False, Filename=niggli_integrate_file )
     SaveIsawUB( InputWorkspace=peaks_ws, Filename=niggli_matrix_file )
 
 #
@@ -216,12 +261,18 @@ def run ( self ):
 if not use_cylindrical_integration:
     if (not cell_type is None) and (not centering is None) :
         conv_name = output_directory + "/" + exp_name + "_" + cell_type + "_" + centering
-        conventional_integrate_file = conv_name + ".integrate"
+        if output_nexus:
+            conventional_integrate_file = conv_name + ".nxs"
+        else:
+            conventional_integrate_file = conv_name + ".integrate"
         conventional_matrix_file = conv_name + ".mat"
 
         SelectCellOfType( PeaksWorkspace=peaks_ws, CellType=cell_type, Centering=centering,\
                       AllowPermutations=allow_perm, Apply=True, Tolerance=tolerance )
-        SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False, Filename=conventional_integrate_file )
+        if output_nexus:
+            SaveNexus( InputWorkspace=peaks_ws, Filename=conventional_integrate_file )
+        else:
+            SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False, Filename=conventional_integrate_file )
         SaveIsawUB( InputWorkspace=peaks_ws, Filename=conventional_matrix_file )
 
 if use_cylindrical_integration: