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Move the isis_reduction_steps to Python V2
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re #6578
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@gesnerpassos
gesnerpassos committed Mar 5, 2013
1 parent b1dfe74 commit d9fdded
Showing 1 changed file with 68 additions and 58 deletions.
126 changes: 68 additions & 58 deletions Code/Mantid/scripts/SANS/isis_reduction_steps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from reduction import ReductionStep
import isis_reducer
import reduction.instruments.sans.sans_reduction_steps as sans_reduction_steps
from mantidsimple import *
from mantid.simpleapi import *
import SANSUtility
import isis_instrument
import os
Expand All @@ -22,15 +22,15 @@ def _issueWarning(msg):
@param msg: message to be issued
"""
print msg
mantid.sendWarningMessage('::SANS::Warning: ' + msg)
logger.warning('::SANS::Warning: ' + msg)

def _issueInfo(msg):
"""
Prints a message to the log
@param msg: message to be issued
"""
print msg
mantid.sendLogMessage(msg)
logger.notice(msg)


class LoadRun(object):
Expand Down Expand Up @@ -78,20 +78,30 @@ def _load(self, inst = None, is_can=False):

if os.path.splitext(self._data_file)[1].lower().startswith('.r') or os.path.splitext(self._data_file)[1].lower().startswith('.s'):
try:
alg = LoadRaw(self._data_file, workspace, SpectrumMin=self._spec_min, SpectrumMax=self._spec_max)
outWs = LoadRaw(Filename=self._data_file,
OutputWorkspace=workspace,
SpectrumMin=self._spec_min,
SpectrumMax=self._spec_max)
except ValueError:
# MG - 2011-02-24: Temporary fix to load .sav or .s* files. Lets the file property
# work it out
file_hint = os.path.splitext(self._data_file)[0]
alg = LoadRaw(file_hint, workspace, SpectrumMin=self._spec_min, SpectrumMax=self._spec_max)
self._data_file = alg.getPropertyValue("Filename")

LoadSampleDetailsFromRaw(workspace, self._data_file)
outWs = LoadRaw(Filename=file_hint,
OutputWorkspace=workspace,
SpectrumMin=self._spec_min,
SpectrumMax=self._spec_max)

alg = outWs.getHistory().lastAlgorithm()
self._data_file = alg.getPropertyValue("Filename")
LoadSampleDetailsFromRaw(InputWorkspace=workspace, Filename=self._data_file)

workspace = self._leaveSinglePeriod(workspace, period)
else:
alg = LoadNexus(self._data_file, workspace,
SpectrumMin=self._spec_min, SpectrumMax=self._spec_max, EntryNumber=period)
outWs = LoadNexus(Filename=self._data_file,
OutputWorkspace=workspace,
SpectrumMin=self._spec_min, SpectrumMax=self._spec_max,
EntryNumber=period)
alg = outWs.getHistory().lastAlgorithm()
self._data_file = alg.getPropertyValue("Filename")

SANS2D_log_file = mtd[workspace]
Expand All @@ -102,7 +112,7 @@ def _load(self, inst = None, is_can=False):
#get the workspace name, a period number of 1 is only included if the file has more than 1 period
period_definitely_inc = self._get_workspace_name(self._period)
if period_definitely_inc != workspace:
RenameWorkspace(workspace, period_definitely_inc)
RenameWorkspace(InputWorkspace=workspace,OutputWorkspace= period_definitely_inc)
workspace = period_definitely_inc

log = None
Expand Down Expand Up @@ -180,13 +190,13 @@ def _assignHelper(self, reducer):
self._spec_max = 8
self.periods_in_file, logs = self._load(reducer.instrument)
except RuntimeError, err:
mantid.sendLogMessage("::SANS::Warning: "+str(err))
logger.notice("::SANS::Warning: "+str(err))
return '', -1
else:
try:
self.periods_in_file, logs = self._load(reducer.instrument)
except RuntimeError, details:
mantid.sendLogMessage("::SANS::Warning: "+str(details))
logger.notice("::SANS::Warning: "+str(details))
self.wksp_name = ''
return '', -1

Expand Down Expand Up @@ -217,16 +227,16 @@ def _leaveSinglePeriod(self, workspace, period):
newName += '_'+discriptors[i]

if oldName != newName:
RenameWorkspace(oldName, newName)
RenameWorkspace(InputWorkspace=oldName,OutputWorkspace= newName)

#remove the rest of the group
mantid.deleteWorkspace(groupW.getName())
DeleteWorkspace(groupW.getName())
return newName

def _clearPrevious(self, inWS, others = []):
if inWS != None:
if mantid.workspaceExists(inWS) and (not inWS in others):
mantid.deleteWorkspace(inWS)
if inWs in mtd and (not inWS in others):
DeleteWorkspace(inWs)


def _extract_run_details(self, run_string, is_trans=False, prefix='', run_number_width=-1):
Expand Down Expand Up @@ -292,7 +302,7 @@ def _find_workspace_num_periods(self, workspace):

#the logs have the definitive information on the number of periods, if it is in the logs
try:
samp = pWorksp.getSampleDetails()
samp = pWorksp.getRun()
numPeriods = samp.getLogData('nperiods').value
except:
#it's OK for there not to be any logs
Expand Down Expand Up @@ -405,7 +415,7 @@ def assign_can(self, reducer):
logs = self.workspace._assignHelper(reducer)

if self.workspace.wksp_name == '':
mantid.sendLogMessage('::SANS::Warning: Unable to load SANS can run, cannot continue.')
logger.notice('::SANS::Warning: Unable to load SANS can run, cannot continue.')
return '()'

if logs:
Expand All @@ -429,14 +439,14 @@ def execute(self, reducer, workspace):
"""
#remain the sample workspace, its name will be restored to the original once the subtraction has been done
tmp_smp = workspace+"_sam_tmp"
RenameWorkspace(workspace, tmp_smp)
RenameWorkspace(InputWorkspace=workspace,OutputWorkspace= tmp_smp)

tmp_can = workspace+"_can_tmp"
#do same corrections as were done to the sample
reducer.reduce_can(tmp_can)

#we now have the can workspace, use it
Minus(tmp_smp, tmp_can, workspace)
Minus(LHSWorkspace=tmp_smp,RHSWorkspace= tmp_can,OutputWorkspace= workspace)

#clean up the workspaces ready users to see them if required
if reducer.to_Q.output_type == '1D':
Expand Down Expand Up @@ -834,18 +844,18 @@ def execute(self, reducer, workspace):
sans_reduction_steps.Mask.execute(self, reducer, workspace)

if len(self.spec_list)>0:
MaskDetectors(workspace, SpectraList = self.spec_list)
MaskDetectors(Workspace=workspace, SpectraList = self.spec_list)

if self._lim_phi_xml != '' and self.mask_phi:
MaskDetectorsInShape(workspace, self._lim_phi_xml)
MaskDetectorsInShape(Workspace=workspace,ShapeXML= self._lim_phi_xml)

if self.arm_width and self.arm_angle:
if instrument.name() == "SANS2D":
ws = mtd[str(workspace)]
det = ws.getInstrument().getComponentByName('rear-detector')
det_Z = det.getPos().getZ()
start_point = [0, 0, det_Z]
MaskDetectorsInShape(workspace,
MaskDetectorsInShape(Workspace=workspace,ShapeXML=
self._mask_line(start_point, 1e6, self.arm_width, self.arm_angle))

def view(self, instrum):
Expand All @@ -869,7 +879,7 @@ def view(self, instrum):
instrum.setDetector(original)

# Mark up "dead" detectors with error value
FindDeadDetectors(wksp_name, wksp_name, DeadValue=500)
FindDeadDetectors(InputWorkspace=wksp_name,OutputWorkspace= wksp_name, DeadValue=500)

#opens an instrument showing the contents of the workspace (i.e. the instrument with masked detectors)
instrum.view(wksp_name)
Expand All @@ -894,11 +904,11 @@ def display(self, wksp, reducer, counts=None):
instrum.setDetector(original)

if counts:
Power(counts, 'ones', 0)
Plus(wksp, 'ones', wksp)
Power(InputWorkspace=counts,OutputWorkspace= 'ones',Exponent= 0)
Plus(LHSWorkspace=wksp,RHSWorkspace= 'ones',OutputWorkspace= wksp)

# Mark up "dead" detectors with error value
FindDeadDetectors(wksp, wksp, LiveValue = 0, DeadValue=1)
FindDeadDetectors(InputWorkspace=wksp,OutputWorkspace= wksp, LiveValue = 0, DeadValue=1)

#check if we have a workspace to superimpose the mask on to
if counts:
Expand Down Expand Up @@ -929,13 +939,13 @@ def display(self, wksp, reducer, counts=None):
if Ys[i] != 0:
Ys[i] = maxval*Ys[i] + vals.readY(i)[0]

CreateWorkspace(wksp, Xs, Ys, Es, len(Ys), UnitX='TOF', VerticalAxisValues=Ys)
CreateWorkspace(OutputWorkspace=wksp,DataX= Xs,DataY= Ys,DataE= Es,NSpec= len(Ys), UnitX='TOF', VerticalAxisValues=Ys)
#change the units on the workspace so it is compatible with the workspace containing counts data
Multiply('ones', wksp, 'units')
Multiply(LHSWorkspace='ones',RHSWorkspace= wksp,OutputWorkspace= 'units')
#do the super-position and clean up
Minus(counts, 'units', wksp)
mantid.deleteWorkspace('ones')
mantid.deleteWorkspace('units')
Minus(LHSWorkspace=counts,RHSWorkspace= 'units',OutputWorkspace= wksp)
DeleteWorkspace('ones')
DeleteWorkspace('units')

#opens an instrument showing the contents of the workspace (i.e. the instrument with masked detectors)
instrum.view(wksp)
Expand Down Expand Up @@ -991,20 +1001,20 @@ def execute(self, reducer, workspace):
p_run_ws = p_run_ws[0]

try:
run_num = p_run_ws.getSampleDetails().getLogData('run_number').value
run_num = p_run_ws.getRun().getLogData('run_number').value
except RuntimeError:
# if the run number is not stored in the workspace, try to take it from the filename
run_num = os.path.basename(self._data_file).split('.')[0].split('-')[0].split('0')[-1]
try:
dummy = int(run_num)
except ValueError:
mantid.sendLogMessage('Could not extract run number from file name ' + self._data_file)
logger.notice('Could not extract run number from file name ' + self._data_file)

reducer.instrument.set_up_for_run(run_num)

if reducer.instrument.name() == 'SANS2D':
if logs == None:
mantid.deleteWorkspace(self.wksp_name)
DeleteWorkspace(self.wksp_name)
raise RuntimeError('Sample logs cannot be loaded, cannot continue')
reducer.instrument.apply_detector_logs(logs)

Expand Down Expand Up @@ -1070,22 +1080,22 @@ def execute(self, reducer, workspace):
if raw_ws is None:
raw_ws = reducer.get_sample().wksp_name

mantid.sendLogMessage('::SANS::Normalizing to monitor ' + str(normalization_spectrum))
logger.notice('::SANS::Normalizing to monitor ' + str(normalization_spectrum))

self.output_wksp = 'Monitor'
CropWorkspace(raw_ws, self.output_wksp,
CropWorkspace(InputWorkspace=raw_ws,OutputWorkspace= self.output_wksp,
StartWorkspaceIndex = normalization_spectrum-1,
EndWorkspaceIndex = normalization_spectrum-1)

if reducer.instrument.name() == 'LOQ':
RemoveBins(self.output_wksp, self.output_wksp, reducer.transmission_calculator.loq_removePromptPeakMin,
RemoveBins(InputWorkspace=self.output_wksp,OutputWorkspace= self.output_wksp,XMin= reducer.transmission_calculator.loq_removePromptPeakMin,XMax=
reducer.transmission_calculator.loq_removePromptPeakMax, Interpolation="Linear")

# Remove flat background
TOF_start, TOF_end = reducer.inst.get_TOFs(
self.NORMALISATION_SPEC_NUMBER)
if TOF_start and TOF_end:
FlatBackground(self.output_wksp, self.output_wksp, StartX=TOF_start, EndX=TOF_end,
FlatBackground(InputWorkspace=self.output_wksp,OutputWorkspace= self.output_wksp, StartX=TOF_start, EndX=TOF_end,
WorkspaceIndexList=self.NORMALISATION_SPEC_INDEX, Mode='Mean')

#perform the same conversion on the monitor spectrum as was applied to the workspace but with a possibly different rebin
Expand Down Expand Up @@ -1221,27 +1231,27 @@ def setup_wksp(self, inputWS, inst, wavbining, pre_monitor, post_monitor):
#exclude unused spectra because the sometimes empty/sometimes not spectra can cause errors with interpolate
spectrum1 = min(pre_monitor, post_monitor)
spectrum2 = max(pre_monitor, post_monitor)
CropWorkspace(inputWS, tmpWS,
CropWorkspace(InputWorkspace=inputWS,OutputWorkspace= tmpWS,
StartWorkspaceIndex=self._get_index(spectrum1),
EndWorkspaceIndex=self._get_index(spectrum2))

if inst.name() == 'LOQ':
RemoveBins(tmpWS, tmpWS, self.loq_removePromptPeakMin, self.loq_removePromptPeakMax,
RemoveBins(InputWorkspace=tmpWS,OutputWorkspace= tmpWS,XMin= self.loq_removePromptPeakMin,XMax= self.loq_removePromptPeakMax,
Interpolation='Linear')

for spectra_number in [pre_monitor, post_monitor]:
back_start, back_end = inst.get_TOFs(spectra_number)
if back_start and back_end:
index = spectra_number - spectrum1
FlatBackground(tmpWS, tmpWS, StartX=back_start, EndX=back_end,
FlatBackground(InputWorkspace=tmpWS,OutputWorkspace= tmpWS, StartX=back_start, EndX=back_end,
WorkspaceIndexList=index, Mode='Mean')

ConvertUnits(tmpWS, tmpWS,"Wavelength")
ConvertUnits(InputWorkspace=tmpWS,OutputWorkspace= tmpWS,Target="Wavelength")

if self.interpolate:
InterpolatingRebin(tmpWS, tmpWS, wavbining)
InterpolatingRebin(InputWorkspace=tmpWS,OutputWorkspace= tmpWS,Params= wavbining)
else :
Rebin(tmpWS, tmpWS, wavbining)
Rebin(InputWorkspace=tmpWS,OutputWorkspace= tmpWS,Params= wavbining)

return tmpWS

Expand Down Expand Up @@ -1343,17 +1353,17 @@ def calculate(self, reducer):

# If no fitting is required just use linear and get unfitted data from CalculateTransmission algorithm
fit_type = self.CALC_TRANS_FIT_PARAMS[fit_meth]
CalculateTransmission(trans_tmp_out,direct_tmp_out, fittedtransws,
pre_sample, post_sample, reducer.to_wavelen.get_rebin(), FitMethod=fit_type, OutputUnfittedData=True)
CalculateTransmission(SampleRunWorkspace=trans_tmp_out,DirectRunWorkspace=direct_tmp_out,OutputWorkspace= fittedtransws,IncidentBeamMonitor=
pre_sample,TransmissionMonitor= post_sample,RebinParams= reducer.to_wavelen.get_rebin(), FitMethod=fit_type, OutputUnfittedData=True)

# Remove temporaries
DeleteWorkspace(trans_tmp_out)
DeleteWorkspace(Workspace=trans_tmp_out)
if direct_tmp_out != trans_tmp_out:
DeleteWorkspace(direct_tmp_out)
DeleteWorkspace(Workspace=direct_tmp_out)

if fit_meth == 'Off':
result = unfittedtransws
mantid.deleteWorkspace(fittedtransws)
DeleteWorkspace(fittedtransws)
else:
result = fittedtransws

Expand Down Expand Up @@ -1448,7 +1458,7 @@ def getPixelCorrFile(self, detector ):
elif detector in ("REAR","MAIN","MAIN-DETECTOR-BANK",""):
return self._low_angle_pixel_file
else :
mantid.sendWarningMessage("ASK GETPIXELCORRFILE WITHOUT ARGUMENT: + "+ str(detector))
logger.warning("ASK GETPIXELCORRFILE WITHOUT ARGUMENT: + "+ str(detector))
return self._pixel_file

def calculate(self, reducer, wave_wks=[]):
Expand All @@ -1461,11 +1471,11 @@ def calculate(self, reducer, wave_wks=[]):
#use the instrument's correction file
corr_file = reducer.instrument.cur_detector().correction_file
if corr_file:
LoadRKH(corr_file, self.TMP_ISIS_NAME, "Wavelength")
LoadRKH(Filename=corr_file,OutputWorkspace= self.TMP_ISIS_NAME,FirstColumnValue= "Wavelength")
wave_wks.append(self.TMP_ISIS_NAME)

if self._is_point_data(self.TMP_ISIS_NAME):
ConvertToHistogram(self.TMP_ISIS_NAME, self.TMP_ISIS_NAME)
ConvertToHistogram(InputWorkspace=self.TMP_ISIS_NAME,OutputWorkspace= self.TMP_ISIS_NAME)
## try to redefine self._pixel_file to pass to CalculateNORM method calculate.
detect_pixel_file = self.getPixelCorrFile(reducer.instrument.cur_detector().name())
if (detect_pixel_file != ""):
Expand Down Expand Up @@ -1518,10 +1528,10 @@ def execute(self, reducer, workspace):

try:
if self._Q_alg == 'Q1D':
Q1D(workspace, workspace, OutputBinning=self.binning, WavelengthAdj=wave_adj, PixelAdj=pixel_adj, AccountForGravity=self._use_gravity, RadiusCut=self.r_cut*1000.0, WaveCut=self.w_cut, OutputParts=self.outputParts, WavePixelAdj = wavepixeladj)
Q1D(DetBankWorkspace=workspace,OutputWorkspace= workspace, OutputBinning=self.binning, WavelengthAdj=wave_adj, PixelAdj=pixel_adj, AccountForGravity=self._use_gravity, RadiusCut=self.r_cut*1000.0, WaveCut=self.w_cut, OutputParts=self.outputParts, WavePixelAdj = wavepixeladj)
elif self._Q_alg == 'Qxy':
Qxy(workspace, workspace, reducer.QXY2, reducer.DQXY, WavelengthAdj=wave_adj, PixelAdj=pixel_adj, AccountForGravity=self._use_gravity, RadiusCut=self.r_cut*1000.0, WaveCut=self.w_cut, OutputParts=self.outputParts)
ReplaceSpecialValues(workspace, workspace, NaNValue="0", InfinityValue="0")
Qxy(InputWorkspace=workspace,OutputWorkspace= workspace,MaxQxy= reducer.QXY2,DeltaQ= reducer.DQXY, WavelengthAdj=wave_adj, PixelAdj=pixel_adj, AccountForGravity=self._use_gravity, RadiusCut=self.r_cut*1000.0, WaveCut=self.w_cut, OutputParts=self.outputParts)
ReplaceSpecialValues(InputWorkspace=workspace,OutputWorkspace= workspace, NaNValue="0", InfinityValue="0")
else:
raise NotImplementedError('The type of Q reduction has not been set, e.g. 1D or 2D')
except:
Expand Down Expand Up @@ -1558,7 +1568,7 @@ def execute(self, reducer, workspace, bin_alg=None):
@param workspace: the name of the workspace to convert
@param workspace: the name of the workspace to convert
"""
ConvertUnits(workspace, workspace, self._units)
ConvertUnits(InputWorkspace=workspace,OutputWorkspace= workspace,Target= self._units)

low_wav = self.wav_low
high_wav = self.wav_high
Expand Down

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