diff --git a/Code/Mantid/scripts/SCD_Reduction/ReduceSCD.config b/Code/Mantid/scripts/SCD_Reduction/ReduceSCD.config
index 67b5014828afe4eb8502b3a4816760b39390420c..324b3883589caf24d49f3ea2b12b0f784a38cdd6 100644
--- a/Code/Mantid/scripts/SCD_Reduction/ReduceSCD.config
+++ b/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
diff --git a/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_OneRun.py b/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_OneRun.py
index da992481ba3ac2c36cd0634d9073a5a3f2989c71..8ae81127207be15b6d7bff3d4f079f5d9f55bd07 100644
--- a/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_OneRun.py
+++ b/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_OneRun.py
@@ -72,6 +72,7 @@ calibration_file_1 = params_dictionary.get('calibration_file_1', None)
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 @@ print "\nProcessing File: " + full_name + " ......\n"
# 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 @@ IndexPeaks( PeaksWorkspace=peaks_ws, Tolerance=tolerance)
# 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 @@ elif use_cylindrical_integration:
# 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 @@ else:
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 )
diff --git a/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_Parallel.py b/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_Parallel.py
index 16a978089c34d4a2f4c1ad37234f8ce01d269a62..804358531b1d668af187c5aedeea8ff4958e5339 100644
--- a/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_Parallel.py
+++ b/Code/Mantid/scripts/SCD_Reduction/ReduceSCD_Parallel.py
@@ -84,6 +84,7 @@ params_dictionary = ReduceDictionary.LoadDictionary( *config_files )
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 @@ cell_type = params_dictionary[ "cell_type" ]
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 @@ print "***********************************************************************
# 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 @@ if not use_cylindrical_integration:
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 @@ if not use_cylindrical_integration:
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 @@ if not use_cylindrical_integration:
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: