Few python files modified by hand. Refs #11293

Code/Mantid/Framework/PythonInterface/plugins/algorithms/SuggestTibHYSPEC.py

@@ -1,7 +1,7 @@
 #pylint: disable=no-init
 from mantid.api import PythonAlgorithm, AlgorithmFactory
 from mantid.kernel import FloatBoundedValidator,Direction,logger
-from numpy import sqrt,divide
+import numpy
 
 
 class SuggestTibHYSPEC(PythonAlgorithm):
@@ -33,7 +33,7 @@ def PyInit(self):
         return
 
     def e2v(self,energy):
-        return sqrt(energy/5.227e-6)
+        return numpy.sqrt(energy/5.227e-6)
 
     def PyExec(self):
         """ Main execution body
@@ -50,7 +50,7 @@ def PyExec(self):
         t_det_us = dist_mm /self.e2v(energy) * 1000 + T0_moderator
         frame_start_us = t_det_us - 16667/2
         frame_end_us = t_det_us + 16667/2
-        index_under_frame = divide(int(t_det_us),16667)
+        index_under_frame = numpy.divide(int(t_det_us),16667)
         pre_lead_us = 16667 * index_under_frame
         pre_tail_us = pre_lead_us + tail_length_us
         post_lead_us = 16667 * (1+ index_under_frame)

Code/Mantid/Testing/SystemTests/tests/analysis/ARCSReductionTest.py

@@ -32,30 +32,28 @@ def runTest(self):
         self.nxspeFile=os.path.join(config.getString('defaultsave.directory'),'ARCSsystemtest.nxspe')
         config['default.facility']="SNS"
         DgsReduction(
-          SampleInputFile="ARCS_23961_event.nxs",
-          OutputWorkspace="reduced",
-          IncidentBeamNormalisation="ByCurrent",
-          DetectorVanadiumInputFile="WBARCS.nxs",
-          UseBoundsForDetVan=True,
-          DetVanIntRangeLow=0.35,
-          DetVanIntRangeHigh=0.75,
-          DetVanIntRangeUnits="Wavelength",
-          SaveProcessedDetVan=True,
-          SaveProcDetVanFilename=self.vanFile0,
-          )
+                        SampleInputFile="ARCS_23961_event.nxs",
+                        OutputWorkspace="reduced",
+                        IncidentBeamNormalisation="ByCurrent",
+                        DetectorVanadiumInputFile="WBARCS.nxs",
+                        UseBoundsForDetVan=True,
+                        DetVanIntRangeLow=0.35,
+                        DetVanIntRangeHigh=0.75,
+                        DetVanIntRangeUnits="Wavelength",
+                        SaveProcessedDetVan=True,
+                        SaveProcDetVanFilename=self.vanFile0)
         DgsReduction(
-          SampleInputFile="ARCS_23961_event.nxs",
-          OutputWorkspace="reduced",
-          IncidentBeamNormalisation="ByCurrent",
-          DetectorVanadiumInputFile="WBARCS.nxs",
-          UseBoundsForDetVan=True,
-          DetVanIntRangeLow=0.35,
-          DetVanIntRangeHigh=0.75,
-          DetVanIntRangeUnits="Wavelength",
-          MedianTestLevelsUp=1.,
-          SaveProcessedDetVan=True,
-          SaveProcDetVanFilename=self.vanFile1,
-          )
+                        SampleInputFile="ARCS_23961_event.nxs",
+                        OutputWorkspace="reduced",
+                        IncidentBeamNormalisation="ByCurrent",
+                        DetectorVanadiumInputFile="WBARCS.nxs",
+                        UseBoundsForDetVan=True,
+                        DetVanIntRangeLow=0.35,
+                        DetVanIntRangeHigh=0.75,
+                        DetVanIntRangeUnits="Wavelength",
+                        MedianTestLevelsUp=1.,
+                        SaveProcessedDetVan=True,
+                        SaveProcDetVanFilename=self.vanFile1)
 
         Ei=mtd["reduced"].run().get("Ei").value
         SaveNXSPE(InputWorkspace="reduced",Filename=self.nxspeFile,Efixed=Ei,psi=0,KiOverKfScaling=True)
@@ -74,7 +72,7 @@ def validate(self):
         DeleteWorkspace(van0)
         DeleteWorkspace(van1)
         self.assertTrue(os.path.exists(self.nxspeFile))
-        nxspe=LoadNXSPE(self.nxspeFile)
+        LoadNXSPE(self.nxspeFile,OutputWorkspace='nxspe')
         self.disableChecking.append('Instrument')
 
         return 'nxspe','ARCSsystemtest.nxs'

Code/Mantid/Testing/SystemTests/tests/analysis/CNCSReductionTest.py

@@ -38,25 +38,23 @@ def runTest(self):
         GenerateGroupingPowder(InputWorkspace="sum",AngleStep=0.5,GroupingFilename=self.groupingFile)
         Ei=mtd['sum'].getRun()['EnergyRequest'].firstValue()
         tib=SuggestTibCNCS(Ei)
-        erange=str(-Ei)+','+str(0.01*Ei)+','+str(0.95*Ei)
 
         DgsReduction(
-                    SampleInputWorkspace="sum",
-                    OutputWorkspace="reduced",
-                    EnergyTransferRange="-0.2,0.05,2.2",
-                    GroupingFile=self.groupingFile,
-                    IncidentBeamNormalisation="ByCurrent",
-                    TimeIndepBackgroundSub=True,
-                    TibTofRangeStart=tib[0],
-                    TibTofRangeEnd=tib[1],
-                    DetectorVanadiumInputFile="CNCS_51936_event.nxs",
-                    UseBoundsForDetVan=True,
-                    DetVanIntRangeLow=52000.0,
-                    DetVanIntRangeHigh=53000.0,
-                    DetVanIntRangeUnits="TOF",
-                    SaveProcessedDetVan=True,
-                    SaveProcDetVanFilename=self.vanFile,
-                    )
+                        SampleInputWorkspace="sum",
+                        OutputWorkspace="reduced",
+                        EnergyTransferRange="-0.2,0.05,2.2",
+                        GroupingFile=self.groupingFile,
+                        IncidentBeamNormalisation="ByCurrent",
+                        TimeIndepBackgroundSub=True,
+                        TibTofRangeStart=tib[0],
+                        TibTofRangeEnd=tib[1],
+                        DetectorVanadiumInputFile="CNCS_51936_event.nxs",
+                        UseBoundsForDetVan=True,
+                        DetVanIntRangeLow=52000.0,
+                        DetVanIntRangeHigh=53000.0,
+                        DetVanIntRangeUnits="TOF",
+                        SaveProcessedDetVan=True,
+                        SaveProcDetVanFilename=self.vanFile)
 
         rotationdevice="SERotator2"
         psi=mtd["reduced"].run().get(rotationdevice).value[0]
@@ -70,7 +68,7 @@ def validate(self):
         self.assertEqual(van.getNumberHistograms(),51200)
         DeleteWorkspace(van)
         self.assertTrue(os.path.exists(self.nxspeFile))
-        nxspe=LoadNXSPE(self.nxspeFile)
+        LoadNXSPE(self.nxspeFile,OutputWorkspace='nxspe')
         self.disableChecking.append('Instrument')
 
         return 'nxspe','CNCSReduction_TIBasEvents.nxs'

Code/Mantid/Testing/SystemTests/tests/analysis/HYSPECReductionTest.py

@@ -24,9 +24,9 @@ def runTest(self):
         Load(Filename='HYS_13656-13658',OutputWorkspace='sum')
         FilterByLogValue(InputWorkspace='sum',OutputWorkspace='sum1',LogName='s1',MinimumValue='0',MaximumValue='24.5',LogBoundary='Left')
         DeleteWorkspace('sum')
-        GenerateEventsFilter(InputWorkspace='sum1',OutputWorkspace='splboth',InformationWorkspace='info',
+        GenerateEventsFilter(   InputWorkspace='sum1',OutputWorkspace='splboth',InformationWorkspace='info',
                                 UnitOfTime='Nanoseconds',LogName='s1',MaximumLogValue='24.5',LogValueInterval='3')
-        FilterEvents(InputWorkspace='sum1',OutputWorkspaceBaseName='split',InformationWorkspace='info',
+        FilterEvents(   InputWorkspace='sum1',OutputWorkspaceBaseName='split',InformationWorkspace='info',
                         SplitterWorkspace='splboth',FilterByPulseTime='1',GroupWorkspaces='1')
         DeleteWorkspace('split_unfiltered')
         DeleteWorkspace("splboth")
@@ -37,7 +37,7 @@ def runTest(self):
         self.groupingFile=os.path.join(config.getString('defaultsave.directory'),'group4x2.xml')
         GenerateGroupingSNSInelastic(AlongTubes="4",AcrossTubes="2",Instrument="HYSPEC",Filename=self.groupingFile)
         config['default.facility']="SNS"
-        DgsReduction(SampleInputWorkspace='splitc',IncidentBeamNormalisation='ByCurrent',
+        DgsReduction(   SampleInputWorkspace='splitc',IncidentBeamNormalisation='ByCurrent',
                         OutputWorkspace='reduced',GroupingFile=self.groupingFile,
                         TimeIndepBackgroundSub ='1',TibTofRangeStart =10400,TibTofRangeEnd =12400,IncidentEnergyGuess=50)
         DeleteWorkspace('splitc')
@@ -48,7 +48,7 @@ def runTest(self):
         DeleteWorkspace('reduced')
         MergeMD(InputWorkspaces='md',OutputWorkspace='merged')
         DeleteWorkspace("md")
-        BinMD(InputWorkspace='merged',AxisAligned='0',BasisVector0='[H,0,0],in 1.079 A^-1,1,0,0,0',
+        BinMD(  InputWorkspace='merged',AxisAligned='0',BasisVector0='[H,0,0],in 1.079 A^-1,1,0,0,0',
                 BasisVector1='[0,K,0],in 0.97 A^-1,0,1,0,0',BasisVector2='[0,0,L],in 1.972 A^-1,0,0,1,0',
                 BasisVector3='DeltaE,DeltaE,0,0,0,1',
                 OutputExtents='-3,3,-2,6,-4,-1.5,-3,3',OutputBins='1,100,100,1',Parallel='1',OutputWorkspace='slice')

Code/Mantid/Testing/SystemTests/tests/analysis/PEARLSystemTest.py

@@ -138,22 +138,22 @@ def PearlLoadMon(self, files,ext,outname):
 
     def PEARL_getmonitor(self, number,ext,spline_terms=20):
 
-       works="monitor"+str(number)
-       self.PearlLoadMon(number,ext,works)
-       ConvertUnits(InputWorkspace=works,OutputWorkspace=works,Target="Wavelength")
-       lmin,lmax=self.PEARL_getlambdarange()
-       CropWorkspace(InputWorkspace=works,OutputWorkspace=works,XMin=lmin,XMax=lmax)
-       ex_regions=n.zeros((2,4))
-       ex_regions[:,0]=[3.45,3.7]
-       ex_regions[:,1]=[2.96,3.2]
-       ex_regions[:,2]=[2.1,2.26]
-       ex_regions[:,3]=[1.73,1.98]
-
-       for reg in range(0,4):
-                MaskBins(InputWorkspace=works,OutputWorkspace=works,XMin=ex_regions[0,reg],XMax=ex_regions[1,reg])
-
-       SplineBackground(InputWorkspace=works,OutputWorkspace=works,WorkspaceIndex=0,NCoeff=spline_terms)
-       return works
+        works="monitor"+str(number)
+        self.PearlLoadMon(number,ext,works)
+        ConvertUnits(InputWorkspace=works,OutputWorkspace=works,Target="Wavelength")
+        lmin,lmax=self.PEARL_getlambdarange()
+        CropWorkspace(InputWorkspace=works,OutputWorkspace=works,XMin=lmin,XMax=lmax)
+        ex_regions=n.zeros((2,4))
+        ex_regions[:,0]=[3.45,3.7]
+        ex_regions[:,1]=[2.96,3.2]
+        ex_regions[:,2]=[2.1,2.26]
+        ex_regions[:,3]=[1.73,1.98]
+
+        for reg in range(0,4):
+            MaskBins(InputWorkspace=works,OutputWorkspace=works,XMin=ex_regions[0,reg],XMax=ex_regions[1,reg])
+
+        SplineBackground(InputWorkspace=works,OutputWorkspace=works,WorkspaceIndex=0,NCoeff=spline_terms)
+        return works
 
 
     def PEARL_read(self, number,ext,outname):

Code/Mantid/Testing/SystemTests/tests/analysis/ReduceOneSCD_Run.py

@@ -13,13 +13,9 @@
 #information.
 #
 #
-import os
-import sys
-import shutil
 import time
 
 import stresstesting
-import numpy
 
 
 from mantid.api import *
@@ -96,14 +92,13 @@ def runTest(self):
                            FilterByTofMin=min_tof, FilterByTofMax=max_tof )
 
         if (calibration_file_1 is not None) or (calibration_file_2 is not None):
-            LoadIsawDetCal( event_ws,
-                  Filename=calibration_file_1)
+            LoadIsawDetCal(event_ws, Filename=calibration_file_1)
 
         monitor_ws = LoadNexusMonitors( Filename=full_name )
 
-        integrated_monitor_ws = Integration( InputWorkspace=monitor_ws,
-                                     RangeLower=min_monitor_tof, RangeUpper=max_monitor_tof,
-                                     StartWorkspaceIndex=monitor_index, EndWorkspaceIndex=monitor_index )
+        integrated_monitor_ws = Integration(InputWorkspace=monitor_ws,
+                                            RangeLower=min_monitor_tof, RangeUpper=max_monitor_tof,
+                                            StartWorkspaceIndex=monitor_index, EndWorkspaceIndex=monitor_index)
 
         monitor_count = integrated_monitor_ws.dataY(0)[0]
         print "\n", run, " has calculated monitor count", monitor_count, "\n"
@@ -112,16 +107,16 @@ def runTest(self):
 # Make MD workspace using Lorentz correction, to find peaks
 #
         MDEW = ConvertToMD( InputWorkspace=event_ws, QDimensions="Q3D",
-                    dEAnalysisMode="Elastic", QConversionScales="Q in A^-1",
-    LorentzCorrection='1', MinValues="-50,-50,-50", MaxValues="50,50,50",
-                    SplitInto='2', SplitThreshold='50',MaxRecursionDepth='11' )
+                            dEAnalysisMode="Elastic", QConversionScales="Q in A^-1",
+                            LorentzCorrection='1', MinValues="-50,-50,-50", MaxValues="50,50,50",
+                            SplitInto='2', SplitThreshold='50',MaxRecursionDepth='11' )
 #
 # Find the requested number of peaks.  Once the peaks are found, we no longer
 # need the weighted MD event workspace, so delete it.
 #
         distance_threshold = 0.9 * 6.28 / float(max_d)
         peaks_ws = FindPeaksMD( MDEW, MaxPeaks=num_peaks_to_find,
-                        PeakDistanceThreshold=distance_threshold )
+                                PeakDistanceThreshold=distance_threshold )
 
         AnalysisDataService.remove( MDEW.getName() )
 #      SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False,
@@ -169,22 +164,22 @@ def runTest(self):
 # LorentzCorrection to do the raw sphere integration )
 #
             MDEW = ConvertToDiffractionMDWorkspace( InputWorkspace=event_ws,
-                 LorentzCorrection='0', OutputDimensions='Q (lab frame)',
-                 SplitInto='2', SplitThreshold='500', MaxRecursionDepth='5' )
+                                                    LorentzCorrection='0', OutputDimensions='Q (lab frame)',
+                                                    SplitInto='2', SplitThreshold='500', MaxRecursionDepth='5' )
 
-            peaks_ws = IntegratePeaksMD( InputWorkspace=MDEW, PeakRadius=peak_radius,
-	          BackgroundOuterRadius=bkg_outer_radius,
-                  BackgroundInnerRadius=bkg_inner_radius,
-	          PeaksWorkspace=peaks_ws,
-                  IntegrateIfOnEdge=integrate_if_edge_peak )
+            peaks_ws = IntegratePeaksMD(InputWorkspace=MDEW, PeakRadius=peak_radius,
+	                                    BackgroundOuterRadius=bkg_outer_radius,
+                                        BackgroundInnerRadius=bkg_inner_radius,
+	                                    PeaksWorkspace=peaks_ws,
+                                        IntegrateIfOnEdge=integrate_if_edge_peak )
 
         elif use_fit_peaks_integration:
-            event_ws = Rebin( InputWorkspace=event_ws,
-                    Params=rebin_params, PreserveEvents=preserve_events )
+            event_ws = Rebin(InputWorkspace=event_ws,
+                                Params=rebin_params, PreserveEvents=preserve_events )
             peaks_ws = PeakIntegration( InPeaksWorkspace=peaks_ws, InputWorkspace=event_ws,
-                              IkedaCarpenterTOF=use_ikeda_carpenter,
-                              MatchingRunNo=True,
-                              NBadEdgePixels=n_bad_edge_pixels )
+                                        IkedaCarpenterTOF=use_ikeda_carpenter,
+                                        MatchingRunNo=True,
+                                        NBadEdgePixels=n_bad_edge_pixels )
 #
 # Save the final integrated peaks, using the Niggli reduced cell.
 # This is the only file needed, for the driving script to get a combined
@@ -203,8 +198,8 @@ def runTest(self):
             run_conventional_integrate_file = self.output_directory + "/" + run + "_" + \
                                     cell_type + "_" + centering + ".integrate"
             SelectCellOfType( PeaksWorkspace=peaks_ws,
-                    CellType=cell_type, Centering=centering,
-                    Apply=True, Tolerance=tolerance )
+                                CellType=cell_type, Centering=centering,
+                                Apply=True, Tolerance=tolerance )
          # UNCOMMENT the line below to get new output values if an algorithm changes
          #SaveIsawPeaks( InputWorkspace=peaks_ws, AppendFile=False, Filename=run_conventional_integrate_file )
             SaveIsawUB( InputWorkspace=peaks_ws, Filename=self.run_conventional_matrix_file )