def test_get_abs_normalization_factor(self) :
mono_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000,XUnit='DeltaE',XMin=-5,XMax=15,BinWidth=0.1,function='Flat background')
LoadInstrument(mono_ws,InstrumentName='MARI', RewriteSpectraMap=True)
tReducer = DirectEnergyConversion(mono_ws.getInstrument())
tReducer.prop_man.incident_energy = 5.
tReducer.prop_man.monovan_integr_range=[-10,10]
tReducer.wb_run = mono_ws
(nf1,nf2,nf3,nf4) = tReducer.get_abs_normalization_factor(PropertyManager.wb_run,5.)
self.assertAlmostEqual(nf1,0.58561121802167193,7)
self.assertAlmostEqual(nf1,nf2)
self.assertAlmostEqual(nf2,nf3)
self.assertAlmostEqual(nf3,nf4)
# check warning. WB spectra with 0 signal indicate troubles.
mono_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000,XUnit='DeltaE',XMin=-5,XMax=15,BinWidth=0.1,function='Flat background')
LoadInstrument(mono_ws,InstrumentName='MARI', RewriteSpectraMap=True)
sig = mono_ws.dataY(0)
sig[:]=0
tReducer.wb_run = mono_ws
(nf1,nf2,nf3,nf4) = tReducer.get_abs_normalization_factor(PropertyManager.wb_run,5.)
self.assertAlmostEqual(nf1,0.585611218022,7)
self.assertAlmostEqual(nf1,nf2)
self.assertAlmostEqual(nf2,nf3)
self.assertAlmostEqual(nf3,nf4)
def __init__(self, instrumentName, web_var=None):
""" sets properties defaults for the instrument with Name
and define if wrapper runs from web services or not
"""
# internal variable, indicating if we should try to wait for input files to appear
self._wait_for_file = False
#The property defines the run number, to validate. If defined, switches reduction wrapper from
#reduction to validation mode
self._run_number_to_validate = None
# internal variable, used in system tests to validate workflow,
# with waiting for files. It is the holder to the function
# used during debugging "wait for files" workflow
# instead of Pause algorithm
self._debug_wait_for_files_operation = None
# tolerance to change in some tests if default is not working well
self._tolerr = None
# The variables which are set up from web interface or to be exported to
# web interface
if web_var:
self._run_from_web = True
else:
self._run_from_web = False
self._wvs = ReductionWrapper.var_holder(web_var)
# Initialize reduced for given instrument
self.reducer = DirectEnergyConversion(instrumentName)
#
web_vars = self._wvs.get_all_vars()
if web_vars:
self.reducer.prop_man.set_input_parameters(**web_vars)
def test_remove_empty_bg(self):
# create test workspace
wksp = CreateSampleWorkspace(Function='Multiple Peaks',
WorkspaceType='Event',
NumBanks=3,
BankPixelWidth=1,
NumEvents=100,
XUnit='TOF',
XMin=2000,
XMax=20000,
BinWidth=1)
CloneWorkspace(wksp, OutputWorkspace='bg_ws')
AddSampleLog(Workspace=wksp,
LogName='gd_prtn_chrg',
LogText='10',
LogType='Number')
AddSampleLog(Workspace='bg_ws',
LogName='gd_prtn_chrg',
LogText='100',
LogType='Number')
# Prepare reducer
tReducer = DirectEnergyConversion('MAR')
tReducer.prop_man.sample_run = wksp
tReducer.prop_man.empty_bg_run = 'bg_ws'
tReducer.remove_empty_background()
ws = PropertyManager.sample_run.get_workspace()
self.assertTrue(ws.run().hasProperty('empty_bg_removed'))
resWs = 0.9 * wksp
difr = CompareWorkspaces(resWs, ws)
self.assertTrue(difr.Result)
def test_late_rebinning(self):
run_monitors=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=4, BankPixelWidth=1, NumEvents=100000, XUnit='Energy',
XMin=3, XMax=200, BinWidth=0.1)
LoadInstrument(run_monitors,InstrumentName='MARI')
ConvertUnits(InputWorkspace='run_monitors', OutputWorkspace='run_monitors', Target='TOF')
run_monitors = mtd['run_monitors']
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace( Function='Multiple Peaks',WorkspaceType='Event',NumBanks=8, BankPixelWidth=1, NumEvents=100000,
XUnit='TOF',xMin=tMin,xMax=tMax)
LoadInstrument(run,InstrumentName='MARI')
wb_ws = Rebin(run,Params=[tMin,1,tMax],PreserveEvents=False)
# References used to test against ordinary reduction
ref_ws = Rebin(run,Params=[tMin,1,tMax],PreserveEvents=False)
ref_ws_monitors = CloneWorkspace('run_monitors')
# just in case, wb should work without clone too.
wb_clone = CloneWorkspace(wb_ws)
# Run Mono
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.energy_bins = [-20,0.2,60]
ei_guess = 67.
mono_s = tReducer.mono_sample(run, ei_guess,wb_ws)
#
mono_ref = tReducer.mono_sample(ref_ws, ei_guess,wb_clone)
rez = CheckWorkspacesMatch(mono_s,mono_ref)
self.assertEqual(rez,'Success!')
def test_sum_monitors(self):
# create test workspace
monitor_ws=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=6, BankPixelWidth=1,\
NumEvents=100000, XUnit='Energy', XMin=3, XMax=200, BinWidth=0.1)
ConvertUnits(InputWorkspace=monitor_ws, OutputWorkspace='monitor_ws', Target='TOF')
# Rebin to "formally" make common bin boundaries as it is not considered as such
#any more after converting units (Is this a bug?)
xx = monitor_ws.readX(0)
x_min = min(xx[0],xx[-1])
x_max= max(xx[0],xx[-1])
x_step = (x_max-x_min)/(len(xx)-1)
monitor_ws = Rebin(monitor_ws,Params=[x_min,x_step,x_max])
monitor_ws = mtd['monitor_ws']
#
# keep this workspace for second test below -- clone and give
# special name for RunDescriptor to recognize as monitor workspace for
# fake data workspace we will provide.
_TMPmonitor_ws_monitors = CloneWorkspace(monitor_ws)
# Estimate energy from two monitors
ei,mon1_peak,mon1_index,tzero = \
GetEi(InputWorkspace=monitor_ws, Monitor1Spec=1,Monitor2Spec=4,
EnergyEstimate=62.2,FixEi=False)
self.assertAlmostEqual(ei,62.1449,3)
# Provide instrument parameter, necessary to define
# DirectEnergyConversion class properly
SetInstrumentParameter(monitor_ws,ParameterName='fix_ei',ParameterType='Number',Value='0')
SetInstrumentParameter(monitor_ws,DetectorList=[1,2,3,6],ParameterName='DelayTime',\
ParameterType='Number',Value='0.5')
SetInstrumentParameter(monitor_ws,ParameterName='mon2_norm_spec',\
ParameterType='Number',Value='1')
# initiate test reducer
tReducer = DirectEnergyConversion(monitor_ws.getInstrument())
tReducer.prop_man.ei_mon_spectra= ([1,2,3],6)
tReducer.prop_man.normalise_method = 'current'
tReducer.prop_man.mon2_norm_spec = 2
ei_mon_spectra = tReducer.prop_man.ei_mon_spectra
ei_mon_spectra,monitor_ws = tReducer.sum_monitors_spectra(monitor_ws,ei_mon_spectra)
#
# Check GetEi with summed monitors. Try to run separately.
ei1,mon1_peak,mon1_index,tzero = \
GetEi(InputWorkspace=monitor_ws, Monitor1Spec=1,Monitor2Spec=6,
EnergyEstimate=62.2,FixEi=False)
self.assertAlmostEqual(ei1,ei,2)
# Second test Check get_ei as part of the reduction
tReducer.prop_man.ei_mon_spectra= ([1,2,3],[4,5,6])
tReducer.prop_man.fix_ei = False
# DataWorkspace == monitor_ws data workspace is not used anyway. The only thing we
# use it for is to retrieve monitor workspace from Mantid using its name
ei2,mon1_peak2=tReducer.get_ei(monitor_ws,62.2)
self.assertAlmostEqual(ei2,64.95,2)
ei2b,mon1_peak2=tReducer.get_ei(monitor_ws,62.2)
self.assertAlmostEqual(ei2b,64.95,2)
def test_sum_monitors(self):
# create test workspace
monitor_ws=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=6, BankPixelWidth=1,\
NumEvents=100000, XUnit='Energy', XMin=3, XMax=200, BinWidth=0.1)
ConvertUnits(InputWorkspace=monitor_ws, OutputWorkspace='monitor_ws', Target='TOF')
# Rebin to "formally" make common bin boundaries as it is not considered as such
#any more after converting units (Is this a bug?)
xx = monitor_ws.readX(0)
x_min = min(xx[0],xx[-1])
x_max= max(xx[0],xx[-1])
x_step = (x_max-x_min)/(len(xx)-1)
monitor_ws = Rebin(monitor_ws,Params=[x_min,x_step,x_max])
monitor_ws = mtd['monitor_ws']
#
# keep this workspace for second test below -- clone and give
# special name for RunDescriptor to recognize as monitor workspace for
# fake data workspace we will provide.
_TMPmonitor_ws_monitors = CloneWorkspace(monitor_ws)
# Estimate energy from two monitors
ei,mon1_peak,mon1_index,tzero = \
GetEi(InputWorkspace=monitor_ws, Monitor1Spec=1,Monitor2Spec=4,
EnergyEstimate=62.2,FixEi=False)
self.assertAlmostEqual(ei,62.1449,3)
# Provide instrument parameter, necessary to define
# DirectEnergyConversion class properly
SetInstrumentParameter(monitor_ws,ParameterName='fix_ei',ParameterType='Number',Value='0')
SetInstrumentParameter(monitor_ws,DetectorList=[1,2,3,6],ParameterName='DelayTime',\
ParameterType='Number',Value='0.5')
SetInstrumentParameter(monitor_ws,ParameterName='mon2_norm_spec',\
ParameterType='Number',Value='1')
# initiate test reducer
tReducer = DirectEnergyConversion(monitor_ws.getInstrument())
tReducer.prop_man.ei_mon_spectra= ([1,2,3],6)
tReducer.prop_man.normalise_method = 'current'
tReducer.prop_man.mon2_norm_spec = 2
ei_mon_spectra = tReducer.prop_man.ei_mon_spectra
ei_mon_spectra,monitor_ws = tReducer.sum_monitors_spectra(monitor_ws,ei_mon_spectra)
#
# Check GetEi with summed monitors. Try to run separately.
ei1,mon1_peak,mon1_index,tzero = \
GetEi(InputWorkspace=monitor_ws, Monitor1Spec=1,Monitor2Spec=6,
EnergyEstimate=62.2,FixEi=False)
self.assertAlmostEqual(ei1,ei,2)
# Second test Check get_ei as part of the reduction
tReducer.prop_man.ei_mon_spectra= ([1,2,3],[4,5,6])
tReducer.prop_man.fix_ei = False
# DataWorkspace == monitor_ws data workspace is not used anyway. The only thing we
# use it for is to retrieve monitor workspace from Mantid using its name
ei2,mon1_peak2=tReducer.get_ei(monitor_ws,62.2)
self.assertAlmostEqual(ei2,64.95,2)
ei2b,mon1_peak2=tReducer.get_ei(monitor_ws,62.2)
self.assertAlmostEqual(ei2b,64.95,2)
def test_do_white_wb(self) :
wb_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000)
#LoadParameterFile(Workspace=wb_ws,ParameterXML = used_parameters)
LoadInstrument(wb_ws,InstrumentName='MARI', RewriteSpectraMap=True)
tReducer = DirectEnergyConversion(wb_ws.getInstrument())
white_ws = tReducer.do_white(wb_ws, None, None)
self.assertTrue(white_ws)
def test_do_white_wb(self) :
wb_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000)
#LoadParameterFile(Workspace=wb_ws,ParameterXML = used_parameters)
LoadInstrument(wb_ws,InstrumentName='MARI', RewriteSpectraMap=True)
tReducer = DirectEnergyConversion(wb_ws.getInstrument())
white_ws = tReducer.do_white(wb_ws, None, None)
self.assertTrue(white_ws)
def test_diagnostics_wb(self):
wb_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000)
LoadInstrument(wb_ws, InstrumentName="MARI", RewriteSpectraMap=True)
tReducer = DirectEnergyConversion(wb_ws.getInstrument())
mask_workspace = tReducer.diagnose(wb_ws)
self.assertTrue(mask_workspace)
api.AnalysisDataService.clear()
def custom_operation(custom_fun):
DirectEnergyConversion.__setattr__()
def custom_fun_wrapper(*args):
# execute decorated function
ws = custom_fun(*args)
#print "in decorator: ",properties
#host = args[0]
return ws
return custom_fun_wrapper
def test_diagnostics_wb(self):
wb_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000)
LoadInstrument(wb_ws,InstrumentName='MARI', RewriteSpectraMap=True)
tReducer = DirectEnergyConversion(wb_ws.getInstrument())
mask_workspace=tReducer.diagnose(wb_ws)
self.assertTrue(mask_workspace)
api.AnalysisDataService.clear()
def test_tof_range(self):
run = CreateSampleWorkspace(Function='Multiple Peaks',
NumBanks=6,
BankPixelWidth=1,
NumEvents=10,
XUnit='Energy',
XMin=5,
XMax=75,
BinWidth=0.2)
LoadInstrument(run, InstrumentName='MARI', RewriteSpectraMap=True)
red = DirectEnergyConversion(run.getInstrument())
red.prop_man.incident_energy = 26.2
red.prop_man.energy_bins = [-20, 0.1, 20]
red.prop_man.multirep_tof_specta_list = [4, 5, 6]
MoveInstrumentComponent(Workspace='run',
ComponentName='Detector',
DetectorID=1102,
Z=3)
MoveInstrumentComponent(Workspace='run',
ComponentName='Detector',
DetectorID=1103,
Z=6)
run_tof = ConvertUnits(run, Target='TOF', EMode='Elastic')
tof_range = red.find_tof_range_for_multirep(run_tof)
self.assertEqual(len(tof_range), 3)
x = run_tof.readX(3)
xMin = min(x)
x = run_tof.readX(5)
xMax = max(x)
self.assertGreater(tof_range[0], xMin)
# self.assertAlmostEqual(tof_range[1],dt)
self.assertLess(tof_range[2], xMax)
# check another working mode
red.prop_man.multirep_tof_specta_list = 4
red.prop_man.incident_energy = 47.505
red.prop_man.energy_bins = [-20, 0.1, 45]
tof_range1 = red.find_tof_range_for_multirep(run_tof)
self.assertGreater(tof_range1[0], xMin)
self.assertLess(tof_range1[2], xMax)
self.assertLess(tof_range1[2], tof_range[2])
self.assertLess(tof_range1[0], tof_range[0])
self.assertLess(tof_range1[1], tof_range[1])
def test_tof_range(self):
run = CreateSampleWorkspace(
Function="Multiple Peaks",
NumBanks=6,
BankPixelWidth=1,
NumEvents=10,
XUnit="Energy",
XMin=5,
XMax=75,
BinWidth=0.2,
)
LoadInstrument(run, InstrumentName="MARI", RewriteSpectraMap=True)
red = DirectEnergyConversion(run.getInstrument())
red.prop_man.incident_energy = 26.2
red.prop_man.energy_bins = [-20, 0.1, 20]
red.prop_man.multirep_tof_specta_list = [4, 5, 6]
MoveInstrumentComponent(Workspace="run", ComponentName="Detector", DetectorID=1102, Z=3)
MoveInstrumentComponent(Workspace="run", ComponentName="Detector", DetectorID=1103, Z=6)
run_tof = ConvertUnits(run, Target="TOF", EMode="Elastic")
tof_range = red.find_tof_range_for_multirep(run_tof)
self.assertEqual(len(tof_range), 3)
x = run_tof.readX(3)
dx = abs(x[1:] - x[:-1])
xMin = min(x)
dt = min(dx)
x = run_tof.readX(5)
xMax = max(x)
self.assertTrue(tof_range[0] > xMin)
# self.assertAlmostEqual(tof_range[1],dt)
self.assertTrue(tof_range[2] < xMax)
# check another working mode
red.prop_man.multirep_tof_specta_list = 4
red.prop_man.incident_energy = 47.505
red.prop_man.energy_bins = [-20, 0.1, 45]
tof_range1 = red.find_tof_range_for_multirep(run_tof)
self.assertTrue(tof_range1[0] > xMin)
self.assertTrue(tof_range1[2] < xMax)
self.assertTrue(tof_range1[2] < tof_range[2])
self.assertTrue(tof_range1[0] < tof_range[0])
self.assertTrue(tof_range1[1] < tof_range[1])
def test_late_rebinning(self):
run_monitors = CreateSampleWorkspace(Function='Multiple Peaks',
NumBanks=4,
BankPixelWidth=1,
NumEvents=100000,
XUnit='Energy',
XMin=3,
XMax=200,
BinWidth=0.1)
LoadInstrument(run_monitors,
InstrumentName='MARI',
RewriteSpectraMap=True)
ConvertUnits(InputWorkspace='run_monitors',
OutputWorkspace='run_monitors',
Target='TOF')
run_monitors = mtd['run_monitors']
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace(Function='Multiple Peaks',
WorkspaceType='Event',
NumBanks=8,
BankPixelWidth=1,
NumEvents=100000,
XUnit='TOF',
xMin=tMin,
xMax=tMax)
LoadInstrument(run, InstrumentName='MARI', RewriteSpectraMap=True)
run.setMonitorWorkspace(run_monitors)
wb_ws = Rebin(run, Params=[tMin, 1, tMax], PreserveEvents=False)
# References used to test against ordinary reduction
ref_ws = Rebin(run, Params=[tMin, 1, tMax], PreserveEvents=False)
ref_ws_monitors = CloneWorkspace('run_monitors')
ref_ws.setMonitorWorkspace(ref_ws_monitors)
# just in case, wb should work without clone too.
wb_clone = CloneWorkspace(wb_ws)
# Run Mono
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.energy_bins = [-20, 0.2, 60]
ei_guess = 67.
mono_s = tReducer.mono_sample(run, ei_guess, wb_ws)
#
mono_ref = tReducer.mono_sample(ref_ws, ei_guess, wb_clone)
rez = CompareWorkspaces(mono_s, mono_ref)
self.assertTrue(rez[0])
def test_late_rebinning(self):
run_monitors = CreateSampleWorkspace(
Function="Multiple Peaks",
NumBanks=4,
BankPixelWidth=1,
NumEvents=100000,
XUnit="Energy",
XMin=3,
XMax=200,
BinWidth=0.1,
)
LoadInstrument(run_monitors, InstrumentName="MARI", RewriteSpectraMap=True)
ConvertUnits(InputWorkspace="run_monitors", OutputWorkspace="run_monitors", Target="TOF")
run_monitors = mtd["run_monitors"]
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace(
Function="Multiple Peaks",
WorkspaceType="Event",
NumBanks=8,
BankPixelWidth=1,
NumEvents=100000,
XUnit="TOF",
xMin=tMin,
xMax=tMax,
)
LoadInstrument(run, InstrumentName="MARI", RewriteSpectraMap=True)
run.setMonitorWorkspace(run_monitors)
wb_ws = Rebin(run, Params=[tMin, 1, tMax], PreserveEvents=False)
# References used to test against ordinary reduction
ref_ws = Rebin(run, Params=[tMin, 1, tMax], PreserveEvents=False)
ref_ws_monitors = CloneWorkspace("run_monitors")
ref_ws.setMonitorWorkspace(ref_ws_monitors)
# just in case, wb should work without clone too.
wb_clone = CloneWorkspace(wb_ws)
# Run Mono
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.energy_bins = [-20, 0.2, 60]
ei_guess = 67.0
mono_s = tReducer.mono_sample(run, ei_guess, wb_ws)
#
mono_ref = tReducer.mono_sample(ref_ws, ei_guess, wb_clone)
rez = CheckWorkspacesMatch(mono_s, mono_ref)
self.assertEqual(rez, "Success!")
def test_multirep_mode(self):
# create test workspace
run_monitors=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=4, BankPixelWidth=1,\
NumEvents=100000,XUnit='Energy', XMin=3, XMax=200, BinWidth=0.1)
LoadInstrument(run_monitors,InstrumentName='MARI', RewriteSpectraMap=True)
ConvertUnits(InputWorkspace='run_monitors', OutputWorkspace='run_monitors', Target='TOF')
run_monitors = mtd['run_monitors']
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace( Function='Multiple Peaks',WorkspaceType='Event',NumBanks=8, BankPixelWidth=1,\
NumEvents=100000, XUnit='TOF',xMin=tMin,xMax=tMax)
LoadInstrument(run,InstrumentName='MARI', RewriteSpectraMap=True)
MoveInstrumentComponent(Workspace='run', ComponentName='Detector', DetectorID=1102,Z=1)
# MoveInstrumentComponent(Workspace='run', ComponentName='Detector', DetectorID=1103,Z=4)
# MoveInstrumentComponent(Workspace='run', ComponentName='Detector', DetectorID=1104,Z=5)
# do second
run2 = CloneWorkspace(run)
run2_monitors = CloneWorkspace(run_monitors)
wb_ws = Rebin(run,Params=[tMin,1,tMax],PreserveEvents=False)
# Run multirep
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.prop_man.run_diagnostics=True
tReducer.hard_mask_file=None
tReducer.map_file=None
tReducer.save_format=None
tReducer.multirep_tof_specta_list = [4,5]
result = tReducer.convert_to_energy(wb_ws,run,[67.,122.],[-2,0.02,0.8])
self.assertEqual(len(result),2)
ws1=result[0]
self.assertEqual(ws1.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws1.readX(0)
self.assertAlmostEqual(x[0],-2*67.)
self.assertAlmostEqual(x[-1],0.8*67.)
ws2=result[1]
self.assertEqual(ws2.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws2.readX(0)
self.assertAlmostEqual(x[0],-2*122.)
self.assertAlmostEqual(x[-1],0.8*122.)
# test another ws
# rename samples from previous workspace to avoid deleting them on current run
for ind,item in enumerate(result):
result[ind]=RenameWorkspace(item,OutputWorkspace='SampleRez#'+str(ind))
#
result2 = tReducer.convert_to_energy(None,run2,[67.,122.],[-2,0.02,0.8])
rez = CheckWorkspacesMatch(result[0],result2[0])
self.assertEqual(rez,'Success!')
rez = CheckWorkspacesMatch(result[1],result2[1])
self.assertEqual(rez,'Success!')
def __init__(self,instrumentName,web_var=None):
""" sets properties defaults for the instrument with Name
and define if wrapper runs from web services or not
"""
# internal variable, indicating if we should try to wait for input files to appear
self._wait_for_file = False
#The property defines the run number, to validate. If defined, switches reduction wrapper from
#reduction to validation mode
self._run_number_to_validate=None
# internal variable, used in system tests to validate workflow,
# with waiting for files. It is the holder to the function
# used during debugging "wait for files" workflow
# instead of Pause algorithm
self._debug_wait_for_files_operation = None
# tolerance to change in some tests if default is not working well
self._tolerr=None
# The variables which are set up from web interface or to be exported to
# web interface
if web_var:
self._run_from_web = True
else:
self._run_from_web = False
self._wvs = ReductionWrapper.var_holder(web_var)
# Initialize reduced for given instrument
self.reducer = DirectEnergyConversion(instrumentName)
#
web_vars = self._wvs.get_all_vars()
if web_vars :
self.reducer.prop_man.set_input_parameters(**web_vars)
def test_multirep_mode(self):
# create test workspace
run_monitors=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=4, BankPixelWidth=1,\
NumEvents=100000,XUnit='Energy', XMin=3, XMax=200, BinWidth=0.1)
LoadInstrument(run_monitors,InstrumentName='MARI', RewriteSpectraMap=True)
ConvertUnits(InputWorkspace='run_monitors', OutputWorkspace='run_monitors', Target='TOF')
run_monitors = mtd['run_monitors']
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace( Function='Multiple Peaks',WorkspaceType='Event',NumBanks=8, BankPixelWidth=1,\
NumEvents=100000, XUnit='TOF',xMin=tMin,xMax=tMax)
LoadInstrument(run,InstrumentName='MARI', RewriteSpectraMap=True)
MoveInstrumentComponent(Workspace='run', ComponentName='Detector', DetectorID=1102,Z=1)
# MoveInstrumentComponent(Workspace='run', ComponentName='Detector', DetectorID=1103,Z=4)
# MoveInstrumentComponent(Workspace='run', ComponentName='Detector', DetectorID=1104,Z=5)
# do second
run2 = CloneWorkspace(run)
run2_monitors = CloneWorkspace(run_monitors)
wb_ws = Rebin(run,Params=[tMin,1,tMax],PreserveEvents=False)
# Run multirep
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.prop_man.run_diagnostics=True
tReducer.hard_mask_file=None
tReducer.map_file=None
tReducer.save_format=None
tReducer.multirep_tof_specta_list = [4,5]
result = tReducer.convert_to_energy(wb_ws,run,[67.,122.],[-2,0.02,0.8])
self.assertEqual(len(result),2)
ws1=result[0]
self.assertEqual(ws1.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws1.readX(0)
self.assertAlmostEqual(x[0],-2*67.)
self.assertAlmostEqual(x[-1],0.8*67.)
ws2=result[1]
self.assertEqual(ws2.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws2.readX(0)
self.assertAlmostEqual(x[0],-2*122.)
self.assertAlmostEqual(x[-1],0.8*122.)
# test another ws
# rename samples from previous workspace to avoid deleting them on current run
for ind,item in enumerate(result):
result[ind]=RenameWorkspace(item,OutputWorkspace='SampleRez#'+str(ind))
#
result2 = tReducer.convert_to_energy(None,run2,[67.,122.],[-2,0.02,0.8])
rez = CompareWorkspaces(result[0],result2[0])
self.assertTrue(rez[0])
rez = CompareWorkspaces(result[1],result2[1])
self.assertTrue(rez[0])
def test_energy_to_TOF_range(self):
ws = Load(Filename='MAR11001.raw',LoadMonitors='Include')
en_range = [0.8*13,13,1.2*13]
detIDs=[1,2,3,10]
red = DirectEnergyConversion()
TRange = red.get_TOF_for_energies(ws,en_range,detIDs)
for ind,detID in enumerate(detIDs):
tof = TRange[ind]
y = [1]*(len(tof)-1)
ind = ws.getIndexFromSpectrumNumber(detID)
ExtractSingleSpectrum(InputWorkspace=ws, OutputWorkspace='_ws_template', WorkspaceIndex=ind)
CreateWorkspace(OutputWorkspace='TOF_WS',NSpec = 1,DataX=tof,DataY=y,UnitX='TOF',ParentWorkspace='_ws_template')
EnWs=ConvertUnits(InputWorkspace='TOF_WS',Target='Energy',EMode='Elastic')
eni = EnWs.dataX(0)
for samp,rez in zip(eni,en_range): self.assertAlmostEqual(samp,rez)
# Now Test shifted:
ei,mon1_peak,mon1_index,tzero = GetEi(InputWorkspace=ws, Monitor1Spec=int(2), Monitor2Spec=int(3),EnergyEstimate=13)
ScaleX(InputWorkspace='ws',OutputWorkspace='ws',Operation="Add",Factor=-mon1_peak,InstrumentParameter="DelayTime",Combine=True)
ws = mtd['ws']
mon1_det = ws.getDetector(1)
mon1_pos = mon1_det.getPos()
src_name = ws.getInstrument().getSource().getName()
MoveInstrumentComponent(Workspace='ws',ComponentName= src_name, X=mon1_pos.getX(), Y=mon1_pos.getY(), Z=mon1_pos.getZ(), RelativePosition=False)
# Does not work for monitor 2 as it has been moved to mon2 position and there all tof =0
detIDs=[1,3,10]
TRange1 = red.get_TOF_for_energies(ws,en_range,detIDs)
for ind,detID in enumerate(detIDs):
tof = TRange1[ind]
y = [1]*(len(tof)-1)
ind = ws.getIndexFromSpectrumNumber(detID)
ExtractSingleSpectrum(InputWorkspace=ws, OutputWorkspace='_ws_template', WorkspaceIndex=ind)
CreateWorkspace(OutputWorkspace='TOF_WS',NSpec = 1,DataX=tof,DataY=y,UnitX='TOF',ParentWorkspace='_ws_template')
EnWs=ConvertUnits(InputWorkspace='TOF_WS',Target='Energy',EMode='Elastic')
eni = EnWs.dataX(0)
for samp,rez in zip(eni,en_range): self.assertAlmostEqual(samp,rez)
def test_energy_to_TOF_range(self):
ws = Load(Filename='MAR11001.raw',LoadMonitors='Include')
en_range = [0.8*13,13,1.2*13]
detIDs=[1,2,3,10]
red = DirectEnergyConversion()
TRange = red.get_TOF_for_energies(ws,en_range,detIDs)
for ind,detID in enumerate(detIDs):
tof = TRange[ind]
y = [1]*(len(tof)-1)
ind = ws.getIndexFromSpectrumNumber(detID)
ExtractSingleSpectrum(InputWorkspace=ws, OutputWorkspace='_ws_template', WorkspaceIndex=ind)
CreateWorkspace(OutputWorkspace='TOF_WS',NSpec = 1,DataX=tof,DataY=y,UnitX='TOF',ParentWorkspace='_ws_template')
EnWs=ConvertUnits(InputWorkspace='TOF_WS',Target='Energy',EMode='Elastic')
eni = EnWs.dataX(0)
for samp,rez in zip(eni,en_range): self.assertAlmostEqual(samp,rez)
# Now Test shifted:
ei,mon1_peak,mon1_index,tzero = GetEi(InputWorkspace=ws, Monitor1Spec=int(2), Monitor2Spec=int(3),EnergyEstimate=13)
ScaleX(InputWorkspace='ws',OutputWorkspace='ws',Operation="Add",Factor=-mon1_peak,InstrumentParameter="DelayTime",Combine=True)
ws = mtd['ws']
mon1_det = ws.getDetector(1)
mon1_pos = mon1_det.getPos()
src_name = ws.getInstrument().getSource().getName()
MoveInstrumentComponent(Workspace='ws',ComponentName= src_name, X=mon1_pos.getX(), Y=mon1_pos.getY(), Z=mon1_pos.getZ(), RelativePosition=False)
# Does not work for monitor 2 as it has been moved to mon2 position and there all tof =0
detIDs=[1,3,10]
TRange1 = red.get_TOF_for_energies(ws,en_range,detIDs)
for ind,detID in enumerate(detIDs):
tof = TRange1[ind]
y = [1]*(len(tof)-1)
ind = ws.getIndexFromSpectrumNumber(detID)
ExtractSingleSpectrum(InputWorkspace=ws, OutputWorkspace='_ws_template', WorkspaceIndex=ind)
CreateWorkspace(OutputWorkspace='TOF_WS',NSpec = 1,DataX=tof,DataY=y,UnitX='TOF',ParentWorkspace='_ws_template')
EnWs=ConvertUnits(InputWorkspace='TOF_WS',Target='Energy',EMode='Elastic')
eni = EnWs.dataX(0)
for samp,rez in zip(eni,en_range): self.assertAlmostEqual(samp,rez)
def test_get_abs_normalization_factor(self) :
mono_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000,XUnit='DeltaE',XMin=-5,XMax=15,BinWidth=0.1,function='Flat background')
LoadInstrument(mono_ws,InstrumentName='MARI', RewriteSpectraMap=True)
tReducer = DirectEnergyConversion(mono_ws.getInstrument())
tReducer.prop_man.incident_energy = 5.
tReducer.prop_man.monovan_integr_range=[-10,10]
tReducer.wb_run = mono_ws
(nf1,nf2,nf3,nf4) = tReducer.get_abs_normalization_factor(PropertyManager.wb_run,5.)
self.assertAlmostEqual(nf1,0.58561121802167193,7)
self.assertAlmostEqual(nf1,nf2)
self.assertAlmostEqual(nf2,nf3)
self.assertAlmostEqual(nf3,nf4)
# check warning. WB spectra with 0 signal indicate troubles.
mono_ws = CreateSampleWorkspace(NumBanks=1, BankPixelWidth=4, NumEvents=10000,XUnit='DeltaE',XMin=-5,XMax=15,BinWidth=0.1,function='Flat background')
LoadInstrument(mono_ws,InstrumentName='MARI', RewriteSpectraMap=True)
sig = mono_ws.dataY(0)
sig[:]=0
tReducer.wb_run = mono_ws
(nf1,nf2,nf3,nf4) = tReducer.get_abs_normalization_factor(PropertyManager.wb_run,5.)
self.assertAlmostEqual(nf1,0.585611218022,7)
self.assertAlmostEqual(nf1,nf2)
self.assertAlmostEqual(nf2,nf3)
self.assertAlmostEqual(nf3,nf4)
def __init__(self,instrumentName,web_var=None):
""" sets properties defaults for the instrument with Name
and define if wrapper runs from web services or not
"""
# internal variable, indicating if we should try to wait for input files to appear
self._wait_for_file=False
# The variables which are set up from web interface or to be exported to
# web interface
if web_var:
self._run_from_web = True
self._wvs = web_var
else:
self._run_from_web = False
self._wvs = ReductionWrapper.var_holder()
# Initialize reduced for given instrument
self.reducer = DirectEnergyConversion(instrumentName)
self._validation_fname=None
def setUp(self):
if self.reducer == None or type(self.reducer) != type(DirectEnergyConversion):
self.reducer = DirectEnergyConversion("MAR")
def test_multirep_abs_units_mode(self):
# create test workspace
run_monitors = CreateSampleWorkspace(
Function="Multiple Peaks",
NumBanks=4,
BankPixelWidth=1,
NumEvents=100000,
XUnit="Energy",
XMin=3,
XMax=200,
BinWidth=0.1,
)
LoadInstrument(run_monitors, InstrumentName="MARI", RewriteSpectraMap=True)
ConvertUnits(InputWorkspace="run_monitors", OutputWorkspace="run_monitors", Target="TOF")
run_monitors = mtd["run_monitors"]
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace(
Function="Multiple Peaks",
WorkspaceType="Event",
NumBanks=8,
BankPixelWidth=1,
NumEvents=100000,
XUnit="TOF",
xMin=tMin,
xMax=tMax,
)
LoadInstrument(run, InstrumentName="MARI", RewriteSpectraMap=True)
# build "monovanadium"
mono = CloneWorkspace(run)
mono_monitors = CloneWorkspace(run_monitors)
# build "White-beam"
wb_ws = Rebin(run, Params=[tMin, 1, tMax], PreserveEvents=False)
# build "second run" to ensure repeated execution
run2 = CloneWorkspace(run)
run2_monitors = CloneWorkspace(run_monitors)
# Run multirep
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.prop_man.run_diagnostics = True
tReducer.hard_mask_file = None
tReducer.map_file = None
tReducer.prop_man.background_range = [0.99 * tMax, tMax]
tReducer.prop_man.monovan_mapfile = None
tReducer.save_format = None
tReducer.prop_man.normalise_method = "monitor-1"
tReducer.norm_mon_integration_range = [tMin, tMax]
result = tReducer.convert_to_energy(wb_ws, run, [67.0, 122.0], [-2, 0.02, 0.8], None, mono)
self.assertEqual(len(result), 2)
ws1 = result[0]
self.assertEqual(ws1.getAxis(0).getUnit().unitID(), "DeltaE")
x = ws1.readX(0)
self.assertAlmostEqual(x[0], -2 * 67.0)
self.assertAlmostEqual(x[-1], 0.8 * 67.0)
ws2 = result[1]
self.assertEqual(ws2.getAxis(0).getUnit().unitID(), "DeltaE")
x = ws2.readX(0)
self.assertAlmostEqual(x[0], -2 * 122.0)
self.assertAlmostEqual(x[-1], 0.8 * 122.0)
# test another ws
# rename samples from previous workspace to avoid deleting them on current run
for ind, item in enumerate(result):
result[ind] = RenameWorkspace(item, OutputWorkspace="SampleRez#" + str(ind))
#
result2 = tReducer.convert_to_energy(None, run2)
rez = CheckWorkspacesMatch(result[0], result2[0])
self.assertEqual(rez, "Success!")
rez = CheckWorkspacesMatch(result[1], result2[1])
self.assertEqual(rez, "Success!")
class ReductionWrapper(object):
""" Abstract class provides interface to direct inelastic reduction
allowing it to be run from Mantid, web services, or system tests
using the same interface and the same run file placed in different
locations.
"""
class var_holder(object):
""" A simple wrapper class to keep web variables"""
def __init__(self,Web_vars=None):
if Web_vars:
self.standard_vars = Web_vars.standard_vars
self.advanced_vars = Web_vars.advanced_vars
else:
self.standard_vars = None
self.advanced_vars = None
#
def get_all_vars(self):
"""Return dictionary with all defined variables
combined together
"""
web_vars = {}
if self.advanced_vars:
web_vars = self.advanced_vars.copy()
if self.standard_vars:
if len(web_vars)>0:
web_vars.update(self.standard_vars)
else:
web_vars = self.standard_vars.copy()
return web_vars
def __init__(self,instrumentName,web_var=None):
""" sets properties defaults for the instrument with Name
and define if wrapper runs from web services or not
"""
# internal variable, indicating if we should try to wait for input files to appear
self._wait_for_file = False
#The property defines the run number, to validate. If defined, switches reduction wrapper from
#reduction to validation mode
self._run_number_to_validate=None
# internal variable, used in system tests to validate workflow,
# with waiting for files. It is the holder to the function
# used during debugging "wait for files" workflow
# instead of Pause algorithm
self._debug_wait_for_files_operation = None
# tolerance to change in some tests if default is not working well
self._tolerr=None
# The variables which are set up from web interface or to be exported to
# web interface
if web_var:
self._run_from_web = True
else:
self._run_from_web = False
self._wvs = ReductionWrapper.var_holder(web_var)
# Initialize reduced for given instrument
self.reducer = DirectEnergyConversion(instrumentName)
#
web_vars = self._wvs.get_all_vars()
if web_vars :
self.reducer.prop_man.set_input_parameters(**web_vars)
@property
def wait_for_file(self):
""" If this variable set to positive value, this value
is interpreted as time to wait until check for specified run file
if this file have not been find immediately.
if this variable is 0 or false and the file have not been found,
reduction will fail
"""
return self._wait_for_file
@wait_for_file.setter
def wait_for_file(self,value):
if value > 0:
self._wait_for_file = value
else:
self._wait_for_file = False
#
def save_web_variables(self,FileName=None):
""" Method to write simple and advanced properties and help
information into dictionary, to use by web reduction
interface
If no file is provided, reduce_var.py file will be written
to the folder, containing current script
"""
if not FileName:
FileName = 'reduce_vars.py'
f = open(FileName,'w')
f.write("standard_vars = {\n")
str_wrapper = ' '
for key,val in self._wvs.standard_vars.iteritems():
if isinstance(val,str):
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper,key,val)
else:
row = "{0}\'{1}\':{2}".format(str_wrapper,key,val)
f.write(row)
str_wrapper = ',\n '
f.write("\n}\nadvanced_vars={\n")
#print advances variables
str_wrapper = ' '
for key,val in self._wvs.advanced_vars.iteritems():
if isinstance(val,str):
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper,key,val)
else:
row = "{0}\'{1}\':{2}".format(str_wrapper,key,val)
f.write(row)
str_wrapper = ',\n '
def write_help_block(fhandle,block_name,block_dict):
str_wrapper = ' '
row = "{0}\'{1}\' : {{\n".format(str_wrapper,block_name)
fhandle.write(row)
for key in block_dict:
try:
prop = getattr(PropertyManager,key)
docstring = prop.__doc__
if not docstring:
continue
except:
continue
contents = self._do_format(docstring)
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper,key,contents)
fhandle.write(row)
str_wrapper = ',\n '
fhandle.write('{0} }},\n'.format(str_wrapper))
f.write("\n}\nvariable_help={\n")
write_help_block(f,"standard_vars",self._wvs.standard_vars)
write_help_block(f,"advanced_vars",self._wvs.advanced_vars)
f.write("}\n")
f.close()
def _do_format(self,docstring):
"""Format docstring to write it as string in the reduce_var file"""
contents = re.sub(" +"," ",docstring)
contents = contents.split('\n')
contents = '\\n'.join(contents)
return contents
@property
def validate_run_number(self):
"""The property defines the run number to validate. If defined, switches reduction wrapper from
reduction to validation mode, where reduction tries to load result, previously calculated,
for this run and then compare this result with the result, defined earlier"""
return self._run_number_to_validate
@validate_run_number.setter
def validate_run_number(self,val):
if val is None:
self._run_number_to_validate = None
else:
self._run_number_to_validate = int(val)
def validate_settings(self):
""" method validates initial parameters, provided for reduction"""
self.def_advanced_properties()
self.def_main_properties()
if self._run_from_web:
web_vars = self._wvs.get_all_vars()
self.reducer.prop_man.set_input_parameters(**web_vars)
else:
pass # we should already set up these variables using
# def_main_properties & def_advanced_properties
# validate properties and report result
return self.reducer.prop_man.validate_properties(False)
#
def validation_file_name(self):
""" the name of the file, used as reference to
validate the run, specified as the class property
The method can be overloaded to return a workspace
or workspace name to validate results against.
"""
if not PropertyManager.save_file_name._file_name is None:
file_name = PropertyManager.save_file_name._file_name
if isinstance(file_name,api.Workspace):
return file_name
else:
instr = self.reducer.prop_man.instr_name
run_n = self.validate_run_number
ei = PropertyManager.incident_energy.get_current()
file_name = '{0}{1}_{2:<3.2f}meV_VALIDATION_file.nxs'.format(instr,run_n,ei)
run_dir = self.validation_file_place()
full_name = os.path.join(run_dir,file_name)
return full_name
def validation_file_place(self):
"""Redefine this to the place, where validation file, used in conjunction with
'validate_run' property, located. Here it defines the place to this script folder.
By default it looks for/places it in a default save directory"""
return config['defaultsave.directory']
#
def validate_result(self,Error=1.e-6,ToleranceRelErr=True):
"""Method to validate result against existing validation file
or workspace
Change this method to verify different results or validate results differently"""
rez,message = ReductionWrapper.build_or_validate_result(self,
Error,ToleranceRelErr)
return rez,message
#
def set_custom_output_filename(self):
""" define custom name of output files if standard one is not satisfactory
User expected to overload this method within class instantiation """
return None
def build_or_validate_result(self,Error=1.e-6,ToleranceRelErr=True):
""" Method validates results of the reduction against reference file or workspace.
Inputs:
sample_run -- the run number to reduce or validate against existing result
validation_file -- The name of nxs file, containing workspace, produced by reducing SampleRun,
or the pointer to the workspace, which is the reference workspace
for SampleRun reduction.
Returns:
True if reduction for sample_run produces result within Error from the reference file
as reported by CheckWorkspaceMatch.
False if CheckWorkspaceMatch comparison between sample and reduction is unsuccessful
True if was not able to load reference file. In this case, algorithm builds validation
file and returns True if the reduction and saving of this file is successful
"""
# this row defines location of the validation file
validation_file = self.validation_file_name()
sample_run = self.validate_run_number
if isinstance(validation_file,str):
path,name = os.path.split(validation_file)
if name in mtd:
reference_ws = mtd[name]
build_validation = False
fileName = "workspace:"+reference_ws.name()
else:
if len(path)>0:
config.appendDataSearchDir(path)
# it there bug in getFullPath? It returns the same string if given full path
# but file has not been found
name,fext=os.path.splitext(name)
fileName = FileFinder.getFullPath(name+'.nxs')
if len(fileName)>0:
build_validation = False
try:
reference_ws = Load(fileName)
except:
build_validation = True
else:
build_validation = True
elif isinstance(validation_file,api.Workspace):
# its workspace:
reference_ws = validation_file
build_validation = False
fileName = "workspace:"+reference_ws.name()
else:
build_validation = True
#--------------------------------------------------------
if build_validation:
self.reducer.prop_man.save_file_name = validation_file
self.reducer.prop_man.log\
("*** WARNING:can not find or load validation file {0}\n"\
" Building validation file for run N:{1}".format(validation_file,sample_run),'warning')
else:
self.reducer.prop_man.log\
("*** FOUND VALIDATION FILE: {0}\n"\
" Validating run {1} against this file".format(fileName,sample_run),'warning')
# just in case, to be sure
current_web_state = self._run_from_web
current_wait_state = self.wait_for_file
# disable wait for input and
self._run_from_web = False
self.wait_for_file = False
#
self.def_advanced_properties()
self.def_main_properties()
#
self.reducer.sample_run = sample_run
self.reducer.prop_man.save_format = None
reduced = self.reduce()
if build_validation:
self.reducer.prop_man.save_file_name = None
result_name = os.path.splitext(validation_file)[0]
self.reducer.prop_man.log("*** Saving validation file with name: {0}.nxs".format(result_name),'notice')
SaveNexus(reduced,Filename=result_name + '.nxs')
return True,'Created validation file {0}.nxs'.format(result_name)
else:
if isinstance(reduced,list): # check only first result in multirep
reduced = reduced[0]
# Cheat! Counterintuitive!
if self._tolerr:
TOLL=self._tolerr
else:
TOLL = Error
result = CheckWorkspacesMatch(Workspace1=reference_ws,Workspace2=reduced,\
Tolerance=TOLL,CheckSample=False,\
CheckInstrument=False,ToleranceRelErr=ToleranceRelErr)
self.wait_for_file = current_wait_state
self._run_from_web = current_web_state
if result == 'Success!':
return True,'Reference file and reduced workspace are equal with accuracy {0:<3.2f}'\
.format(TOLL)
else:
fname,ext = os.path.splitext(fileName)
filename = fname+'-mismatch.nxs'
self.reducer.prop_man.log("***WARNING: can not get results matching the reference file.\n"\
" Saving new results to file {0}".format(filename),'warning')
SaveNexus(reduced,Filename=filename)
return False,result
@abstractmethod
def def_main_properties(self):
""" Define properties which considered to be main properties changeable by user
Should be overwritten by special reduction and decorated with @MainProperties decorator.
Should return dictionary with key are the properties names and values -- the default
values these properties should have.
"""
raise NotImplementedError('def_main_properties has to be implemented')
@abstractmethod
def def_advanced_properties(self):
""" Define properties which considered to be advanced but still changeable by instrument scientist or advanced user
Should be overwritten by special reduction and decorated with @AdvancedProperties decorator.
Should return dictionary with key are the properties names and values -- the default
values these properties should have.
"""
raise NotImplementedError('def_advanced_properties has to be implemented')
#
def _run_pause(self,timeToWait=0):
""" a wrapper around pause algorithm allowing to run something
instead of pause in debug mode
"""
if not self._debug_wait_for_files_operation is None:
self._debug_wait_for_files_operation()
else:
Pause(timeToWait)
#
def reduce(self,input_file=None,output_directory=None):
""" The method performs all main reduction operations over
single run file
Wrap it into @iliad wrapper to switch input for
reduction properties between script and web variables
"""
if input_file:
self.reducer.sample_run = str(input_file)
if output_directory:
config['defaultsave.directory'] = str(output_directory)
timeToWait = self._wait_for_file
wait_counter=0
if timeToWait > 0:
Found,input_file = PropertyManager.sample_run.find_file(be_quet=True)
while not Found:
file_hint,fext = PropertyManager.sample_run.file_hint()
self.reducer.prop_man.log("*** Waiting {0} sec for file {1} to appear on the data search path"\
.format(timeToWait,file_hint),'notice')
self._run_pause(timeToWait)
Found,input_file = PropertyManager.sample_run.find_file(file_hint=file_hint,be_quet=True)
if Found:
file,found_ext=os.path.splitext(input_file)
if found_ext != fext:
wait_counter+=1
if wait_counter<2:
timeToWait =60
self.reducer.prop_man.log(\
"*** Requested file with extension {0} but found one with extension {1}\n"\
" The target may not have been delivered from the DAE machine\n".format(fext,found_ext))
Found = False
else:
wait_counter = 0
else:
pass # not found, wait more
#endWhile
converted_to_energy_transfer_ws = self.reducer.convert_to_energy(None,input_file)
else:
converted_to_energy_transfer_ws = self.reducer.convert_to_energy(None,input_file)
return converted_to_energy_transfer_ws
#
def sum_and_reduce(self):
""" procedure used to sum and reduce runs in case when not all files
are available and user have to wait for these files to appear
"""
if not PropertyManager.sample_run._run_list:
raise RuntimeError("sum_and_reduce expects run file list to be defined")
self.reducer.prop_man.sum_runs = True
timeToWait = self._wait_for_file
self._wait_for_file = 0
if timeToWait > 0:
run_files = PropertyManager.sample_run.get_run_list()
num_files_to_sum = len(PropertyManager.sample_run)
ok,missing,found = self.reducer.prop_man.find_files_to_sum()
n_found = len(found)
if not ok:
# necessary to cache intermediate sums in memory
self.reducer.prop_man.cashe_sum_ws = True
while not ok:
while n_found > 0:
last_found = found[-1]
self.reducer.prop_man.sample_run = last_found # request to reduce all up to last found
# Note that here we run convert to energy instead of user (may be) reloaded reduction!
# This would cause problem for user-defined reduction, which pre-process rather than
# post-process resulting workspace
ws = self.reducer.convert_to_energy()
# reset search to whole file list again
self.reducer.prop_man.sample_run = run_files[num_files_to_sum - 1]
ok,missing,found = self.reducer.prop_man.find_files_to_sum()
n_found = len(found)
if ok: # no need to cache sum any more. All necessary files found
self.reducer.prop_man.cashe_sum_ws = False
self.reducer.prop_man.log("*** Waiting {0} sec for runs {1} to appear on the data search path"\
.format(timeToWait,str(missing)),'notice')
self._run_pause(timeToWait)
ok,missing,found = self.reducer.prop_man.find_files_to_sum()
n_found = len(found)
#end not(ok)
if n_found > 0:
# cash sum can be dropped now if it has not been done before
self.reducer.prop_man.cashe_sum_ws = False
ws = self.reduce()
else:
ws = self.reduce()
self._wait_for_file = timeToWait
return ws
#
def run_reduction(self):
"""" Reduces runs one by one or sum all them together and reduce after this
if wait_for_file time is > 0, it will until missing files appear on the
data search path
"""
try:
n,r = funcreturns.lhs_info('both')
out_ws_name = r[0]
except:
out_ws_name = None
# if this is not None, we want to run validation not reduction
if self.validate_run_number:
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
rez,mess=self.build_or_validate_result()
if rez:
self.reducer.prop_man.log("*** SUCCESS! {0}".format(mess))
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
else:
self.reducer.prop_man.log("*** VALIDATION FAILED! {0}".format(mess))
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
raise RuntimeError("Validation against old data file failed")
self.validate_run_number=None
return rez,mess
if self.reducer.sum_runs:
# --------### sum runs provided ------------------------------------###
if out_ws_name is None:
self.sum_and_reduce()
return None
else:
red_ws = self.sum_and_reduce()
RenameWorkspace(InputWorkspace=red_ws,OutputWorkspace=out_ws_name)
return mtd[out_ws_name]
else:
# --------### reduce list of runs one by one ----------------------------###
runfiles = PropertyManager.sample_run.get_run_file_list()
if out_ws_name is None:
for file in runfiles:
self.reduce(file)
return None
else:
results = []
nruns = len(runfiles)
for num,file in enumerate(runfiles):
red_ws = self.reduce(file)
if isinstance(red_ws,list):
for ws in red_ws:
results.append(ws)
else:
if nruns == 1:
if red_ws.name() != out_ws_name:
RenameWorkspace(InputWorkspace=red_ws,OutputWorkspace=out_ws_name)
results.append(mtd[out_ws_name])
else:
OutWSName = '{0}#{1}of{2}'.format(out_ws_name,num+1,nruns)
if red_ws.name() != out_ws_name:
RenameWorkspace(InputWorkspace=red_ws,OutputWorkspace=OutWSName)
results.append(mtd[OutWSName])
#end
if len(results) == 1:
return results[0]
else:
return results
def test_abs_multirep_with_bkg_and_bleed(self):
# create test workspace
run_monitors=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=4, BankPixelWidth=1,\
NumEvents=100000, XUnit='Energy', XMin=3, XMax=200, BinWidth=0.1)
LoadInstrument(run_monitors,InstrumentName='MARI', RewriteSpectraMap=True)
ConvertUnits(InputWorkspace='run_monitors', OutputWorkspace='run_monitors', Target='TOF')
run_monitors = mtd['run_monitors']
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace( Function='Multiple Peaks',WorkspaceType='Event',NumBanks=8, BankPixelWidth=1,\
NumEvents=100000, XUnit='TOF',xMin=tMin,xMax=tMax)
LoadInstrument(run,InstrumentName='MARI', RewriteSpectraMap=True)
AddSampleLog(run,LogName='gd_prtn_chrg',LogText='1.',LogType='Number')
run.setMonitorWorkspace(run_monitors)
# build "monovanadium"
mono = CloneWorkspace(run)
mono_monitors = CloneWorkspace(run_monitors)
mono.setMonitorWorkspace(mono_monitors)
# build "White-beam"
wb_ws = Rebin(run,Params=[tMin,1,tMax],PreserveEvents=False)
# build "second run" to ensure repeated execution
run2 = CloneWorkspace(run)
run2_monitors = CloneWorkspace(run_monitors)
run2.setMonitorWorkspace(run2_monitors)
# Run multirep
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.prop_man.run_diagnostics=True
tReducer.hard_mask_file=None
tReducer.map_file=None
tReducer.prop_man.check_background = True
tReducer.prop_man.background_range=[0.99*tMax,tMax]
tReducer.prop_man.monovan_mapfile=None
tReducer.save_format=None
tReducer.prop_man.normalise_method='monitor-2'
tReducer.prop_man.bleed = True
tReducer.norm_mon_integration_range=[tMin,tMax]
AddSampleLog(run,LogName='good_frames',LogText='1.',LogType='Number Series')
result = tReducer.convert_to_energy(wb_ws,run,[67.,122.],[-2,0.02,0.8],None,mono)
self.assertEqual(len(result),2)
ws1=result[0]
self.assertEqual(ws1.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws1.readX(0)
self.assertAlmostEqual(x[0],-2*67.)
self.assertAlmostEqual(x[-1],0.8*67.)
ws2=result[1]
self.assertEqual(ws2.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws2.readX(0)
self.assertAlmostEqual(x[0],-2*122.)
self.assertAlmostEqual(x[-1],0.8*122.)
# test another ws
# rename samples from previous workspace to avoid deleting them on current run
for ind,item in enumerate(result):
result[ind]=RenameWorkspace(item,OutputWorkspace='SampleRez#'+str(ind))
#
AddSampleLog(run2,LogName='goodfrm',LogText='1',LogType='Number')
result2 = tReducer.convert_to_energy(None,run2)
rez = CheckWorkspacesMatch(result[0],result2[0])
self.assertEqual(rez,'Success!')
rez = CheckWorkspacesMatch(result[1],result2[1])
self.assertEqual(rez,'Success!')
class ReductionWrapper(object):
""" Abstract class provides interface to direct inelastic reduction
allowing it to be run from Mantid, web services, or system tests
using the same interface and the same run file placed in different
locations.
"""
#pylint: disable=too-few-public-methods
class var_holder(object):
""" A simple wrapper class to keep web variables"""
def __init__(self, Web_vars=None):
if Web_vars:
self.standard_vars = Web_vars.standard_vars
self.advanced_vars = Web_vars.advanced_vars
else:
self.standard_vars = None
self.advanced_vars = None
#
def get_all_vars(self):
"""Return dictionary with all defined variables
combined together
"""
web_vars = {}
if self.advanced_vars:
web_vars = self.advanced_vars.copy()
if self.standard_vars:
if len(web_vars) > 0:
web_vars.update(self.standard_vars)
else:
web_vars = self.standard_vars.copy()
return web_vars
def __init__(self, instrumentName, web_var=None):
""" sets properties defaults for the instrument with Name
and define if wrapper runs from web services or not
"""
# internal variable, indicating if we should try to wait for input files to appear
self._wait_for_file = False
#The property defines the run number, to validate. If defined, switches reduction wrapper from
#reduction to validation mode
self._run_number_to_validate = None
# internal variable, used in system tests to validate workflow,
# with waiting for files. It is the holder to the function
# used during debugging "wait for files" workflow
# instead of Pause algorithm
self._debug_wait_for_files_operation = None
# tolerance to change in some tests if default is not working well
self._tolerr = None
# The variables which are set up from web interface or to be exported to
# web interface
if web_var:
self._run_from_web = True
else:
self._run_from_web = False
self._wvs = ReductionWrapper.var_holder(web_var)
# Initialize reduced for given instrument
self.reducer = DirectEnergyConversion(instrumentName)
#
web_vars = self._wvs.get_all_vars()
if web_vars:
self.reducer.prop_man.set_input_parameters(**web_vars)
@property
def wait_for_file(self):
""" If this variable set to positive value, this value
is interpreted as time to wait until check for specified run file
if this file have not been find immediately.
if this variable is 0 or false and the file have not been found,
reduction will fail
"""
return self._wait_for_file
@wait_for_file.setter
def wait_for_file(self, value):
if value > 0:
self._wait_for_file = value
else:
self._wait_for_file = False
#
def save_web_variables(self, FileName=None):
""" Method to write simple and advanced properties and help
information into dictionary, to use by web reduction
interface
If no file is provided, reduce_var.py file will be written
to the folder, containing current script
"""
if not FileName:
FileName = 'reduce_vars.py'
f = open(FileName, 'w')
f.write("standard_vars = {\n")
str_wrapper = ' '
for key, val in iteritems(self._wvs.standard_vars):
if isinstance(val, string_types):
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper, key, val)
else:
row = "{0}\'{1}\':{2}".format(str_wrapper, key, val)
f.write(row)
str_wrapper = ',\n '
f.write("\n}\nadvanced_vars={\n")
#print advances variables
str_wrapper = ' '
for key, val in iteritems(self._wvs.advanced_vars):
if isinstance(val, string_types):
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper, key, val)
else:
row = "{0}\'{1}\':{2}".format(str_wrapper, key, val)
f.write(row)
str_wrapper = ',\n '
def write_help_block(fhandle, block_name, block_dict):
str_wrapper = ' '
row = "{0}\'{1}\' : {{\n".format(str_wrapper, block_name)
fhandle.write(row)
for key in block_dict:
try:
prop = getattr(PropertyManager, key)
docstring = prop.__doc__
if not docstring:
continue
#pylint: disable=bare-except
except:
continue
contents = self._do_format(docstring)
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper, key, contents)
fhandle.write(row)
str_wrapper = ',\n '
fhandle.write('{0} }},\n'.format(str_wrapper))
f.write("\n}\nvariable_help={\n")
write_help_block(f, "standard_vars", self._wvs.standard_vars)
write_help_block(f, "advanced_vars", self._wvs.advanced_vars)
f.write("}\n")
f.close()
def _do_format(self, docstring):
"""Format docstring to write it as string in the reduce_var file"""
contents = re.sub(" +", " ", docstring)
contents = contents.split('\n')
contents = '\\n'.join(contents)
return contents
@property
def validate_run_number(self):
"""The property defines the run number to validate. If defined, switches reduction wrapper from
reduction to validation mode, where reduction tries to load result, previously calculated,
for this run and then compare this result with the result, defined earlier"""
return self._run_number_to_validate
@validate_run_number.setter
def validate_run_number(self, val):
if val is None:
self._run_number_to_validate = None
else:
self._run_number_to_validate = int(val)
def validate_settings(self):
""" method validates initial parameters, provided for reduction"""
self.def_advanced_properties()
self.def_main_properties()
if self._run_from_web:
web_vars = self._wvs.get_all_vars()
self.reducer.prop_man.set_input_parameters(**web_vars)
else:
pass # we should already set up these variables using
# def_main_properties & def_advanced_properties
# validate properties and report result
return self.reducer.prop_man.validate_properties(False)
#
def validation_file_name(self):
""" the name of the file, used as reference to
validate the run, specified as the class property
The method can be overloaded to return a workspace
or workspace name to validate results against.
"""
#pylint: disable=protected-access
if PropertyManager.save_file_name._file_name is not None:
#pylint: disable=protected-access
file_name = PropertyManager.save_file_name._file_name
if isinstance(file_name, api.Workspace):
return file_name
else:
instr = self.reducer.prop_man.instr_name
run_n = self.validate_run_number
ei = PropertyManager.incident_energy.get_current()
file_name = '{0}{1}_{2:<3.2f}meV_VALIDATION_file.nxs'.format(
instr, run_n, ei)
run_dir = self.validation_file_place()
full_name = os.path.join(run_dir, file_name)
return full_name
def validation_file_place(self):
"""Redefine this to the place, where validation file, used in conjunction with
'validate_run' property, located. Here it defines the place to this script folder.
By default it looks for/places it in a default save directory"""
return config['defaultsave.directory']
#
def validate_result(self, Error=1.e-6, ToleranceRelErr=True):
"""Method to validate result against existing validation file
or workspace
Change this method to verify different results or validate results differently"""
rez, message = ReductionWrapper.build_or_validate_result(
self, Error, ToleranceRelErr)
return rez, message
#
def set_custom_output_filename(self):
""" define custom name of output files if standard one is not satisfactory
User expected to overload this method within class instantiation """
return None
def evaluate_abs_corrections(self, test_ws, spectra_to_correct):
""" Evaluate absorption corrections from the input workspace
Input:
test_ws -- the workspace to calculate corrections for.
The corrections themselves should be defined by
the following data reduction properties:
propmen.correct_absorption_on = TheShapeOfTheSample -- define sample parameters
propmen.abs_corr_info = {} Dictionary with additional correction parameters
(can be empty)
spectra_to_correct -- list of the spectra to correct absorption for.
If this list is empty, the corrections are calculated for the whole workspace,
which can cause problems for plotting.
Returns:
corrections -- the workspace containing the absorption corrections
for the spectra, specified in spectra_to_correct variable.
"""
n_spectra = test_ws.getNumberHistograms()
decrement = len(spectra_to_correct)
if decrement > 0:
red_ws = ExtractSpectra(test_ws,
WorkspaceIndexList=spectra_to_correct)
else:
decrement = n_spectra
prop_man = self.reducer.prop_man
abs_shape = prop_man.correct_absorption_on
start_time = time.time()
ws, corrections = abs_shape.correct_absorption(red_ws,
prop_man.abs_corr_info)
end_time = time.time()
estimated_time = (end_time - start_time) * n_spectra / decrement
prop_man.log(
"**************************************************************************************************",
'notice')
prop_man.log(
"*** Estimated time to run absorption corrections on the final workspace is: {0:.1f}sec"
.format(estimated_time), 'notice')
prop_man.log(
"**************************************************************************************************",
'notice')
return (corrections, estimated_time)
#pylint: disable=too-many-branches
def build_or_validate_result(self, Error=1.e-6, ToleranceRelErr=True):
""" Method validates results of the reduction against reference file or workspace.
Inputs:
sample_run -- the run number to reduce or validate against existing result
validation_file -- The name of nxs file, containing workspace, produced by reducing SampleRun,
or the pointer to the workspace, which is the reference workspace
for SampleRun reduction.
Returns:
True if reduction for sample_run produces result within Error from the reference file
as reported by CompareWorkspaces.
False if CheckWorkspaceMatch comparison between sample and reduction is unsuccessful
True if was not able to load reference file. In this case, algorithm builds validation
file and returns True if the reduction and saving of this file is successful
"""
# this row defines location of the validation file
validation_file = self.validation_file_name()
sample_run = self.validate_run_number
if isinstance(validation_file, string_types):
path, name = os.path.split(validation_file)
if name in mtd:
reference_ws = mtd[name]
build_validation = False
fileName = "workspace:" + reference_ws.name()
else:
if len(path) > 0:
config.appendDataSearchDir(path)
# it there bug in getFullPath? It returns the same string if given full path
# but file has not been found
#pylint: disable=unused-variable
name, fext = os.path.splitext(name)
fileName = FileFinder.getFullPath(name + '.nxs')
if len(fileName) > 0:
build_validation = False
try:
reference_ws = Load(fileName)
#pylint: disable=bare-except
except:
build_validation = True
else:
build_validation = True
elif isinstance(validation_file, api.Workspace):
# its workspace:
reference_ws = validation_file
build_validation = False
fileName = "workspace:" + reference_ws.name()
else:
build_validation = True
#--------------------------------------------------------
if build_validation:
self.reducer.prop_man.save_file_name = validation_file
self.reducer.prop_man.log\
("*** WARNING:can not find or load validation file {0}\n"
" Building validation file for run N:{1}".format(validation_file,sample_run),'warning')
else:
self.reducer.prop_man.log\
("*** FOUND VALIDATION FILE: {0}\n"
" Validating run {1} against this file".format(fileName,sample_run),'warning')
# just in case, to be sure
current_web_state = self._run_from_web
current_wait_state = self.wait_for_file
# disable wait for input and
self._run_from_web = False
self.wait_for_file = False
#
self.def_advanced_properties()
self.def_main_properties()
#
self.reducer.sample_run = sample_run
self.reducer.prop_man.save_format = None
reduced = self.reduce()
if build_validation:
self.reducer.prop_man.save_file_name = None
result_name = os.path.splitext(validation_file)[0]
self.reducer.prop_man.log(
"*** Saving validation file with name: {0}.nxs".format(
result_name), 'notice')
SaveNexus(reduced, Filename=result_name + '.nxs')
return True, 'Created validation file {0}.nxs'.format(result_name)
else:
if isinstance(reduced,
list): # check only first result in multirep
reduced = reduced[0]
# Cheat! Counterintuitive!
if self._tolerr:
TOLL = self._tolerr
else:
TOLL = Error
result = CompareWorkspaces(Workspace1=reference_ws,
Workspace2=reduced,
Tolerance=TOLL,
CheckSample=False,
CheckInstrument=False,
ToleranceRelErr=ToleranceRelErr)
self.wait_for_file = current_wait_state
self._run_from_web = current_web_state
if result[0]:
return True,'Reference file and reduced workspace are equal with accuracy {0:<3.2f}'\
.format(TOLL)
else:
fname, _ = os.path.splitext(fileName)
filename = fname + '-mismatch.nxs'
self.reducer.prop_man.log(
"***WARNING: can not get results matching the reference file.\n"
" Saving new results to file {0}".format(filename),
'warning')
SaveNexus(reduced, Filename=filename)
return False, result
@abstractmethod
def def_main_properties(self):
""" Define properties which considered to be main properties changeable by user
Should be overwritten by special reduction and decorated with @MainProperties decorator.
Should return dictionary with key are the properties names and values -- the default
values these properties should have.
"""
raise NotImplementedError('def_main_properties has to be implemented')
@abstractmethod
def def_advanced_properties(self):
""" Define properties which considered to be advanced but still changeable by instrument scientist or advanced user
Should be overwritten by special reduction and decorated with @AdvancedProperties decorator.
Should return dictionary with key are the properties names and values -- the default
values these properties should have.
"""
raise NotImplementedError(
'def_advanced_properties has to be implemented')
#
def _run_pause(self, timeToWait=0):
""" a wrapper around pause algorithm allowing to run something
instead of pause in debug mode
"""
if self._debug_wait_for_files_operation is not None:
# it is callable and the main point of this method is that it is callable
#pylint: disable=E1102
self._debug_wait_for_files_operation()
else:
Pause(timeToWait)
#
def _check_access_granted(self, input_file):
""" Check if the access to the found nxs file is granted
Created to fix issue on ISIS archive, when file
is copied through the network for ~2min and become available
2 minutes after it has been found.
"""
_, found_ext = os.path.splitext(input_file)
if found_ext != '.nxs': # problem solution for nxs files only. Others are seems ok
return
if not h5py_installed: # well this check is not available. Sad, but it available on
# all our working systems. Inform user about the problem
self.reducer.prop_man.log \
('*** Can not verify if file is accessible. Install h5py to be able to check file access in waiting mode',
'notice')
return
ic = 0
#ok = os.access(input_file,os.R_OK) # does not work in this case
try:
f = h5py.File(input_file, 'r')
ok = True
except IOError:
ok = False
while not ok:
self.reducer.prop_man.log \
('*** File found but access can not be gained. Waiting for 10 sec','notice')
time.sleep(10)
ic = ic + 1
try:
f = h5py.File(input_file, 'r')
ok = True
except IOError:
ok = False
if ic > 24:
raise IOError\
("Can not get read access to input file: "+input_file+" after 4 min of trying")
if ok:
f.close()
def reduce(self, input_file=None, output_directory=None):
""" The method performs all main reduction operations over
single run file
Wrap it into @iliad wrapper to switch input for
reduction properties between script and web variables
"""
if input_file:
# attribute-defined-outside-init -- wrong, it is not
#pylint: disable=W0201
self.reducer.sample_run = str(input_file)
if output_directory:
config['defaultsave.directory'] = str(output_directory)
timeToWait = self._wait_for_file
wait_counter = 0
if timeToWait > 0:
Found, input_file = PropertyManager.sample_run.find_file(
self.reducer.prop_man, be_quet=True)
while not Found:
file_hint, fext = PropertyManager.sample_run.file_hint()
self.reducer.prop_man.log(
"*** Waiting {0} sec for file {1} to appear on the data search path"
.format(timeToWait, file_hint), 'notice')
self._run_pause(timeToWait)
Found, input_file = PropertyManager.sample_run.find_file(
self.reducer.prop_man, file_hint=file_hint, be_quet=True)
if Found:
_, found_ext = os.path.splitext(input_file)
if found_ext != fext:
wait_counter += 1
if wait_counter < 2:
timeToWait = 60
self.reducer.prop_man.log(
"*** Requested file with extension {0} but found one with extension {1}\n"
" The target may not have been delivered from the DAE machine\n"
.format(fext, found_ext))
Found = False
else:
wait_counter = 0
else:
pass
else:
pass # not found, wait more
#endWhile
# found but let's give it some time to finish possible IO operations
self._check_access_granted(input_file)
#
converted_to_energy_transfer_ws = self.reducer.convert_to_energy(
None, input_file)
else:
converted_to_energy_transfer_ws = self.reducer.convert_to_energy(
None, input_file)
return converted_to_energy_transfer_ws
#
def sum_and_reduce(self):
""" procedure used to sum and reduce runs in case when not all files
are available and user have to wait for these files to appear
"""
#pylint: disable=protected-access
if not PropertyManager.sample_run._run_list:
raise RuntimeError(
"sum_and_reduce expects run file list to be defined")
self.reducer.prop_man.sum_runs = True
timeToWait = self._wait_for_file
self._wait_for_file = 0
if timeToWait > 0:
run_files = PropertyManager.sample_run.get_run_list()
num_files_to_sum = len(PropertyManager.sample_run)
ok, missing, found = self.reducer.prop_man.find_files_to_sum()
n_found = len(found)
if not ok:
# necessary to cache intermediate sums in memory
self.reducer.prop_man.cashe_sum_ws = True
while not ok:
while n_found > 0:
last_found = found[-1]
self.reducer.prop_man.sample_run = last_found # request to reduce all up to last found
# Note that here we run convert to energy instead of user (may be) reloaded reduction!
# This would cause problem for user-defined reduction, which pre-process rather than
# post-process resulting workspace
ws = self.reducer.convert_to_energy()
# reset search to whole file list again
self.reducer.prop_man.sample_run = run_files[
num_files_to_sum - 1]
ok, missing, found = self.reducer.prop_man.find_files_to_sum(
)
n_found = len(found)
if ok: # no need to cache sum any more. All necessary files found
self.reducer.prop_man.cashe_sum_ws = False
self.reducer.prop_man.log(
"*** Waiting {0} sec for runs {1} to appear on the data search path"
.format(timeToWait, str(missing)), 'notice')
self._run_pause(timeToWait)
ok, missing, found = self.reducer.prop_man.find_files_to_sum()
n_found = len(found)
#end not(ok)
if n_found > 0:
# cash sum can be dropped now if it has not been done before
self.reducer.prop_man.cashe_sum_ws = False
for run in found:
# here we have run numbers. Let's get real file names
prop_man = self.reducer.prop_man
instr_name = prop_man.short_instr_name
is_found, fname = PropertyManager.sample_run.find_file(
prop_man, instr_name, run)
if not is_found:
raise RuntimeError(
"File has been found earlier but can not been retrieved now. Logical bug"
)
else:
# found but let's give it some time to finish possible IO operations
self._check_access_granted(fname)
ws = self.reduce()
else:
ws = self.reduce()
self._wait_for_file = timeToWait
return ws
#
def run_reduction(self):
"""" Reduces runs one by one or sum all them together and reduce after this
if wait_for_file time is > 0, it will until missing files appear on the
data search path
"""
try:
_, r = funcinspect.lhs_info('both')
out_ws_name = r[0]
# no-exception-type(s) specified. Who knows what exception this internal procedure rises...
#pylint: disable=W0702
except:
out_ws_name = None
# if this is not None, we want to run validation not reduction
if self.validate_run_number:
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
rez, mess = self.build_or_validate_result()
if rez:
self.reducer.prop_man.log("*** SUCCESS! {0}".format(mess))
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
else:
self.reducer.prop_man.log(
"*** VALIDATION FAILED! {0}".format(mess))
self.reducer.prop_man.log\
("**************************************************************************************",'warning')
raise RuntimeError("Validation against old data file failed")
self.validate_run_number = None
return rez, mess
if self.reducer.sum_runs:
# --------### sum runs provided ------------------------------------###
if out_ws_name is None:
self.sum_and_reduce()
return None
else:
red_ws = self.sum_and_reduce()
RenameWorkspace(InputWorkspace=red_ws,
OutputWorkspace=out_ws_name)
return mtd[out_ws_name]
else:
# --------### reduce list of runs one by one ----------------------------###
runfiles = PropertyManager.sample_run.get_run_file_list()
if out_ws_name is None:
for file_name in runfiles:
self.reduce(file_name)
return None
else:
results = []
nruns = len(runfiles)
for num, file_name in enumerate(runfiles):
red_ws = self.reduce(file_name)
if isinstance(red_ws, list):
for ws in red_ws:
results.append(ws)
else:
if nruns == 1:
if red_ws.name() != out_ws_name:
RenameWorkspace(InputWorkspace=red_ws,
OutputWorkspace=out_ws_name)
results.append(mtd[out_ws_name])
else:
OutWSName = '{0}#{1}of{2}'.format(
out_ws_name, num + 1, nruns)
if red_ws.name() != out_ws_name:
RenameWorkspace(InputWorkspace=red_ws,
OutputWorkspace=OutWSName)
results.append(mtd[OutWSName])
#end
if len(results) == 1:
return results[0]
else:
return results
def test_abs_multirep_with_bkg_and_bleed(self):
# create test workspace
run_monitors=CreateSampleWorkspace(Function='Multiple Peaks', NumBanks=4, BankPixelWidth=1,\
NumEvents=100000, XUnit='Energy', XMin=3, XMax=200, BinWidth=0.1)
LoadInstrument(run_monitors,InstrumentName='MARI', RewriteSpectraMap=True)
ConvertUnits(InputWorkspace='run_monitors', OutputWorkspace='run_monitors', Target='TOF')
run_monitors = mtd['run_monitors']
tof = run_monitors.dataX(3)
tMin = tof[0]
tMax = tof[-1]
run = CreateSampleWorkspace( Function='Multiple Peaks',WorkspaceType='Event',NumBanks=8, BankPixelWidth=1,\
NumEvents=100000, XUnit='TOF',xMin=tMin,xMax=tMax)
LoadInstrument(run,InstrumentName='MARI', RewriteSpectraMap=True)
AddSampleLog(run,LogName='gd_prtn_chrg',LogText='1.',LogType='Number')
run.setMonitorWorkspace(run_monitors)
# build "monovanadium"
mono = CloneWorkspace(run)
mono_monitors = CloneWorkspace(run_monitors)
mono.setMonitorWorkspace(mono_monitors)
# build "White-beam"
wb_ws = Rebin(run,Params=[tMin,1,tMax],PreserveEvents=False)
# build "second run" to ensure repeated execution
run2 = CloneWorkspace(run)
run2_monitors = CloneWorkspace(run_monitors)
run2.setMonitorWorkspace(run2_monitors)
# Run multirep
tReducer = DirectEnergyConversion(run.getInstrument())
tReducer.prop_man.run_diagnostics=True
tReducer.hard_mask_file=None
tReducer.map_file=None
tReducer.prop_man.check_background = True
tReducer.prop_man.background_range=[0.99*tMax,tMax]
tReducer.prop_man.monovan_mapfile=None
tReducer.save_format=None
tReducer.prop_man.normalise_method='monitor-2'
tReducer.prop_man.bleed = True
tReducer.norm_mon_integration_range=[tMin,tMax]
AddSampleLog(run,LogName='good_frames',LogText='1.',LogType='Number Series')
result = tReducer.convert_to_energy(wb_ws,run,[67.,122.],[-2,0.02,0.8],None,mono)
self.assertEqual(len(result),2)
ws1=result[0]
self.assertEqual(ws1.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws1.readX(0)
self.assertAlmostEqual(x[0],-2*67.)
self.assertAlmostEqual(x[-1],0.8*67.)
ws2=result[1]
self.assertEqual(ws2.getAxis(0).getUnit().unitID(),'DeltaE')
x = ws2.readX(0)
self.assertAlmostEqual(x[0],-2*122.)
self.assertAlmostEqual(x[-1],0.8*122.)
# test another ws
# rename samples from previous workspace to avoid deleting them on current run
for ind,item in enumerate(result):
result[ind]=RenameWorkspace(item,OutputWorkspace='SampleRez#'+str(ind))
#
AddSampleLog(run2,LogName='goodfrm',LogText='1',LogType='Number')
result2 = tReducer.convert_to_energy(None,run2)
rez = CompareWorkspaces(result[0],result2[0])
self.assertTrue(rez[0])
rez = CompareWorkspaces(result[1],result2[1])
self.assertTrue(rez[0])
class ReductionWrapper(object):
""" Abstract class provides interface to direct inelastic reduction
allowing it to be run from Mantid, web services, or system tests
using the same interface and the same run file placed in different
locations.
"""
class var_holder(object):
""" A simple wrapper class to keep web variables"""
def __init__(self):
self.standard_vars = None
self.advanced_vars = None
pass
def __init__(self,instrumentName,web_var=None):
""" sets properties defaults for the instrument with Name
and define if wrapper runs from web services or not
"""
# internal variable, indicating if we should try to wait for input files to appear
self._wait_for_file=False
# The variables which are set up from web interface or to be exported to
# web interface
if web_var:
self._run_from_web = True
self._wvs = web_var
else:
self._run_from_web = False
self._wvs = ReductionWrapper.var_holder()
# Initialize reduced for given instrument
self.reducer = DirectEnergyConversion(instrumentName)
self._validation_fname=None
#
def get_validation_file_name(self,ReferenceFile=None):
""" function provides name of the file with mantid
workspace reduced earlier and which should be validated
against results of current reduction
Should be overloaded to return real file name for particular
reduction
"""
if ReferenceFile:
self._validation_fname = ReferenceFile
return self._validation_fname
@property
def wait_for_file(self):
""" If this variable set to positive value, this value
is interpreted as time to wait until check for specified run file
if this file have not been find immediately.
if this variable is 0 or false and the the file have not been found,
reduction will fail
"""
return self._wait_for_file
@wait_for_file.setter
def wait_for_file(self,value):
if value>0:
self._wait_for_file = value
else:
self._wait_for_file = False
#
def save_web_variables(self,FileName=None):
""" Method to write simple and advanced properties and help
information into dictionary, to use by web reduction
interface
If no file is provided, reduce_var.py file will be written
to
"""
if not FileName:
FileName = 'reduce_vars.py'
f=open(FileName,'w')
f.write("standard_vars = {\n")
str_wrapper = ' '
for key,val in self._wvs.standard_vars.iteritems():
if isinstance(val,str):
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper,key,val)
else:
row = "{0}\'{1}\':{2}".format(str_wrapper,key,val)
f.write(row)
str_wrapper=',\n '
f.write("\n}\nadvanced_vars={\n")
str_wrapper=' '
for key,val in self._wvs.advanced_vars.iteritems():
if isinstance(val,str):
row = "{0}\'{1}\':\'{2}\'".format(str_wrapper,key,val)
else:
row = "{0}\'{1}\':{2}".format(str_wrapper,key,val)
f.write(row)
str_wrapper=',\n '
f.write("\n}\n")
f.close()
#
#
def validate_result(self,build_validation=False,Error=1.e-3,ToleranceRelErr=True):
""" Overload this using build_or_validate_result to have possibility to run or validate result """
return True
def build_or_validate_result(self,sample_run,validationFile,build_validation=False,Error=1.e-3,ToleranceRelErr=True):
""" Method validates results of the reduction against reference file provided
by get_validation_file_name() method
At the moment, get_validation_file_name method should return the name of a file,
where workspace sample reduced workspace with default properties
is stored.
CheckWorkspaceMatch method is applied to verify if current reduced workspace is
equivalent to the workspace, stored in the reference file.
"""
if not build_validation:
if validationFile:
sample = Load(validationFile)
else:
build_validation=True
# just in case, to be sure
current_web_state = self._run_from_web
current_wait_state= self.wait_for_file
# disable wait for input and
self._run_from_web = False
self.wait_for_file = False
#
self.def_advanced_properties()
self.def_main_properties()
#
self.reducer.sample_run = sample_run
self.reducer.prop_man.save_format=None
reduced = self.reduce()
if build_validation:
if validationFile:
result_name = os.path.splitext(validationFile)[0]
else:
result_name = self.reducer.prop_man.save_file_name
self.reducer.prop_man.log("*** Saving validation file with name: {0}.nxs".format(result_name),'notice')
SaveNexus(reduced,Filename=result_name+'.nxs')
return True,'Created validation file {0}.nxs'.format(result_name)
else:
result = CheckWorkspacesMatch(Workspace1=sample,Workspace2=reduced,
Tolerance=Error,CheckSample=False,
CheckInstrument=False,ToleranceRelErr=ToleranceRelErr)
self.wait_for_file = current_wait_state
self._run_from_web = current_web_state
if result == 'Success!':
return True,'Reference file and reduced workspace are equivalent'
else:
return False,result
@abstractmethod
def def_main_properties(self):
""" Define properties which considered to be main properties changeable by user
Should be overwritten by special reduction and decorated with @MainProperties decorator.
Should return dictionary with key are the properties names and values -- the default
values these properties should have.
"""
raise NotImplementedError('def_main_properties has to be implemented')
@abstractmethod
def def_advanced_properties(self):
""" Define properties which considered to be advanced but still changeable by instrument scientist or advanced user
Should be overwritten by special reduction and decorated with @AdvancedProperties decorator.
Should return dictionary with key are the properties names and values -- the default
values these properties should have.
"""
raise NotImplementedError('def_advanced_properties has to be implemented')
def reduce(self,input_file=None,output_directory=None):
""" The method performs all main reduction operations over
single run file
Wrap it into @iliad wrapper to switch input for
reduction properties between script and web variables
"""
if input_file:
self.reducer.sample_run = input_file
timeToWait = self._wait_for_file
if timeToWait:
file = PropertyManager.sample_run.find_file(be_quet=True)
while file.find('ERROR:')>=0:
file_hint,fext = PropertyManager.sample_run.file_hint()
self.reducer.prop_man.log("*** Waiting {0} sec for file {1} to appear on the data search path"\
.format(timeToWait,file_hint),'notice')
Pause(timeToWait)
file = PropertyManager.sample_run.find_file(be_quet=True)
ws = self.reducer.convert_to_energy(None,input_file)
else:
ws = self.reducer.convert_to_energy(None,input_file)
return ws