diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
index 25c63b44818b7b3e450eae5c5b5317ea86080647..68743b9527ee1658c5f5bc19ae89089ab21a95e1 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
@@ -1972,8 +1972,9 @@ void SANSRunWindow::handleReduceButtonClick(const QString & typeStr)
csv_file = saveBatchGrid(selected_file);
}
py_code.prepend("import SANSBatchMode as batch\n");
- py_code += "\nbatch.BatchReduce('" + csv_file + "','" + m_uiForm.file_opt->itemData(m_uiForm.file_opt->currentIndex()).toString() + "',";
- py_code += m_uiForm.transFit_ck->isChecked() ? "True" : "False";
+ const int fileFormat = m_uiForm.file_opt->currentIndex();
+ py_code += "\nbatch.BatchReduce('" + csv_file + "','" +
+ m_uiForm.file_opt->itemData(fileFormat).toString() + "'";
if( m_uiForm.plot_check->isChecked() )
{
py_code += ", plotresults=True";
diff --git a/Code/Mantid/instrument/SANS2D_Definition.xml b/Code/Mantid/instrument/SANS2D_Definition.xml
index 501f632a8035b90b7c4b96e380afcb6136a7d5b3..aa7379421a7c62bdafa6a613befcbf451a43f3bb 100644
--- a/Code/Mantid/instrument/SANS2D_Definition.xml
+++ b/Code/Mantid/instrument/SANS2D_Definition.xml
@@ -58,16 +58,16 @@
<type name="monitors">
<component type="monitor-tbd" mark-as="monitor">
<!-- better positions and shapes will be defined later -->
- <location z="7.217" name="Monitor 1"/>
- <location z="17.937" name="Monitor 2"/>
+ <location z="7.217" name="monitor1"/>
+ <location z="17.937" name="monitor2"/>
</component>
<component type="Moderator-Monitor3" mark-as="monitor">
<!-- transmisssion detector, either in or out of beam -->
- <location z="19.497"/>
+ <location z="19.497" name="monitor3"/>
</component>
<component type="monitor-tbd" mark-as="monitor">
<!-- better positions and shapes will be defined later -->
- <location z="30.0" name="Monitor 4"/>
+ <location z="30.0" name="monitor4"/>
</component>
</type>
diff --git a/Code/Mantid/scripts/SANS/SANSBatchMode.py b/Code/Mantid/scripts/SANS/SANSBatchMode.py
index 37b6f2a5a6d6d70fca3a0a8823c03ce871523aff..10db4f12e68cd83808a96b97613de2756f1244b3 100644
--- a/Code/Mantid/scripts/SANS/SANSBatchMode.py
+++ b/Code/Mantid/scripts/SANS/SANSBatchMode.py
@@ -90,11 +90,10 @@ def addRunToStore(parts, run_store):
run_store.append(inputdata)
return 0
-def BatchReduce(filename, format, full_trans_wav=True, plotresults=False, saveAlgs={'SaveRKH':'txt'},verbose=False, centreit=False, reducer=None):
+def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},verbose=False, centreit=False, reducer=None):
"""
@param filename: the CSV file with the list of runs to analyse
@param format: type of file to load, nxs for Nexus, etc.
- @param full_trans_wav: when set to true (default) a wider range of wavelengths are used in the transmission correction calculation
@param plotresults: if true and this function is run from Mantidplot a graph will be created for the results of each reduction
@param save: this named algorithm will be passed the name of the results workspace and filename (default = 'SaveRKH'). Pass a tuple of strings to save to multiple file formats
@param verbose: set to true to write more information to the log (default=False)
@@ -142,7 +141,7 @@ def BatchReduce(filename, format, full_trans_wav=True, plotresults=False, saveAl
# WavRangeReduction runs the reduction for the specified wavelength range where the final argument can either be DefaultTrans or CalcTrans:
- reduced = WavRangeReduction(full_trans_wav=full_trans_wav)
+ reduced = WavRangeReduction()
except SkipEntry, reason:
#this means that a load step failed, the warning and the fact that the results aren't there is enough for the user
diff --git a/Code/Mantid/scripts/SANS/SANSReduction.py b/Code/Mantid/scripts/SANS/SANSReduction.py
deleted file mode 100644
index 4b99e4e7411d71fdfdff35e2b34e814eb6f3c157..0000000000000000000000000000000000000000
--- a/Code/Mantid/scripts/SANS/SANSReduction.py
+++ /dev/null
@@ -1,1731 +0,0 @@
-###########################################################################
-# This is the template analysis script for reducing the SANS data. #
-# It has place holders so that the appropriate data can be filled in at #
-# run time by the SANS GUI #
-# #
-# Authors: Russell Taylor, Tessella plc (Original script) #
-# Martyn Gigg, Tessella plc (Adapted to GUI use) #
-# with major input from Richard Heenan #
-###########################################################################
-#
-#
-# README:
-# This script contains a list of function definitions to perform the SANS data reduction.
-# It was primarily designed as a back end to the GUI. When being used from the GUI, MantidPlot
-# automatically replaces all of the information at the top of this module
-#
-
-#
-# Set up for cycle 09/02 for which the spectra are now by rows, right to left
-# from top right, and start at 9 after 8 monitors !
-#
-import SANSUtility
-import isis_instrument as SANSInsts
-import math
-from mantidsimple import *
-##START REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
-# disable plotting if running outside Mantidplot
-try:
- from mantidplot import plotSpectrum, mergePlots
-except ImportError:
- def plotSpectrum(a,b):
- pass
- def mergePlots(a,b):
- pass
-
-try:
- from PyQt4.QtGui import qApp
- def appwidgets():
- return qApp.allWidgets()
-except ImportError:
- def appwidgets():
- return []
-##END REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
-
-NORMALISATION_FILE = None
-# The workspaces
-SCATTER_SAMPLE = None
-SCATTER_CAN = SANSUtility.WorkspaceDetails('', -1)
-TRANS_SAMPLE = ''
-TRANS_CAN = ''
-PERIOD_NOS = { "SCATTER_SAMPLE":1, "SCATTER_CAN":1 }
-DIRECT_SAMPLE = ''
-DIRECT_CAN = ''
-DIRECT_CAN = ''
-# if the workspaces come from multi-period i.e. group workspaces, the number of periods in that group will be stored in the following variables. These variables corrospond with those above
-_SAMPLE_N_PERIODS = -1
-_CAN_N_PERIODS =-1
-_TRANS_SAMPLE_N_PERIODS = -1
-DIRECT_SAMPLE_N_PERIODS = -1
-TRANS_SAMPLE_N_CAN = -1
-DIRECT_SAMPLE_N_CAN = -1
-
-#This is stored as UserFile in the output workspace
-MASKFILE = '_ no file'
-# Now the mask string (can be empty)
-# These apply to both detectors
-SPECMASKSTRING = ''
-TIMEMASKSTRING = ''
-# These are for the separate detectors (R = main & F = HAB for LOQ)
-SPECMASKSTRING_R = ''
-SPECMASKSTRING_F = ''
-TIMEMASKSTRING_R = ''
-TIMEMASKSTRING_F = ''
-
-# Instrument information
-INSTR_DIR = mtd.getConfigProperty('instrumentDefinition.directory')
-
-# Instrument object. Start with a default
-#TODO: get rid of all those globals
-INSTRUMENT = SANSInsts.SANS2D()
-
-# Beam centre in metres
-XBEAM_CENTRE = None
-YBEAM_CENTRE = None
-
-# Analysis tab values
-RMIN = None
-RMAX = None
-DEF_RMIN = None
-DEF_RMAX = None
-WAV1 = None
-WAV2 = None
-DWAV = None
-Q_REBIN = None
-QXY2 = None
-DQXY = None
-DIRECT_BEAM_FILE_R = None
-DIRECT_BEAM_FILE_F = None
-GRAVITY = False
-# This indicates whether a 1D or a 2D analysis is performed
-CORRECTION_TYPE = '1D'
-# Component positions
-PHIMIN=-90.0
-PHIMAX=90.0
-PHIMIRROR=True
-
-# Scaling values
-RESCALE = 100. # percent
-SAMPLE_GEOM = 3
-SAMPLE_WIDTH = 1.0
-SAMPLE_HEIGHT = 1.0
-SAMPLE_THICKNESS = 1.0
-
-# These values are used for the start and end bins for FlatBackground removal.
-BACKMON_START = None
-BACKMON_END = None
-
-# Transmission variables
-TRANS_FIT_DEF = 'Log'
-TRANS_FIT = TRANS_FIT_DEF
-# Map input values to Mantid options
-TRANS_FIT_OPTIONS = {
-'YLOG' : 'Log',
-'STRAIGHT' : 'Linear',
-'CLEAR' : 'Off',
-# Add Mantid ones as well
-'LOG' : 'Log',
-'LINEAR' : 'Linear',
-'LIN' : 'Linear',
-'OFF' : 'Off'
-}
-TRANS_WAV1 = None
-TRANS_WAV2 = None
-TRANS_WAV1_FULL = None
-TRANS_WAV2_FULL = None
-
-###################################################################################################################
-#
-# Interface functions (to be called from scripts or the GUI)
-#
-###################################################################################################################
-DefaultTrans = True
-NewTrans = False
-##START REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
-_NOPRINT_ = False
-_VERBOSE_ = False
-def SetNoPrintMode(quiet = True):
- global _NOPRINT_
- _NOPRINT_ = quiet
-
-def SetVerboseMode(state):
- global _VERBOSE_
- _VERBOSE_ = state
-
-# Print a message and log it if the
-def _printMessage(msg, log = True):
- if log == True and _VERBOSE_ == True:
- mantid.sendLogMessage('::SANS::' + msg)
- if _NOPRINT_ == True:
- return
- print msg
-##END REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
-# Warn the user
-def _issueWarning(msg):
- mantid.sendLogMessage('::SANS::Warning: ' + msg)
- if _NOPRINT_ == True:
- return
- print 'WARNING: ' + msg
-
-# Fatal error
-def _fatalError(msg):
- exit(msg)
-
-DATA_PATH = ''
-# Set the data directory
-def DataPath(directory):
- _printMessage('DataPath("' + directory + '") - Will look for raw data here')
- if os.path.exists(directory) == False:
- _issueWarning("Data directory does not exist")
- return
- global DATA_PATH
- DATA_PATH = directory
-
-USER_PATH = ''
-# Set the user directory
-def UserPath(directory):
- _printMessage('UserPath("' + directory + '") #Will look for mask file here')
- if os.path.exists(directory) == False:
- _issueWarning("Data directory does not exist")
- return
- global USER_PATH
- USER_PATH = directory
-
-#####################################################
-# Access function for retrieving parameters
-#####################################################
-def printParameter(var):
- try:
- exec('print ' + var + ',')
- except:
- _issueWarning("Could not find parameter " + var + ", trying instrument object")
- exec('print INSTRUMENT.' + var)
-
-###########################
-# Instrument
-###########################
-def SANS2D():
- _printMessage('SANS2D()')
- global INSTRUMENT, TRANS_WAV1, TRANS_WAV2, TRANS_WAV1_FULL, TRANS_WAV2_FULL
- INSTRUMENT = SANSInsts.SANS2D()
-
- TRANS_WAV1_FULL = TRANS_WAV1 = 2.0
- TRANS_WAV2_FULL = TRANS_WAV2 = 14.0
- INSTRUMENT.lowAngDetSet = True
-
-def LOQ():
- _printMessage('LOQ()')
- global INSTRUMENT, TRANS_WAV1, TRANS_WAV2, TRANS_WAV1_FULL, TRANS_WAV2_FULL
- INSTRUMENT = SANSInsts.LOQ()
-
- TRANS_WAV1_FULL = TRANS_WAV1 = 2.2
- TRANS_WAV2_FULL = TRANS_WAV2 = 10.0
- INSTRUMENT.lowAngDetSet = True
-
-def Detector(det_name):
- _printMessage('Detector("' + det_name + '")')
- global INSTRUMENT
- if not INSTRUMENT.setDetector(det_name) :
- _issueWarning('Detector not found')
- _issueWarning('Detector set to ' + INSTRUMENT.cur_detector().name() + ' in ' + INSTRUMENT.name())
-
-def Set1D():
- _printMessage('Set1D()')
- global CORRECTION_TYPE
- CORRECTION_TYPE = '1D'
-
-def Set2D():
- _printMessage('Set2D()')
- global CORRECTION_TYPE
- CORRECTION_TYPE = '2D'
-
-###########################
-# Set the scattering sample raw workspace
-###########################
-_SAMPLE_SETUP = None
-_SAMPLE_RUN = ''
-def AssignSample(sample_run, reload = True, period = -1):
- _printMessage('AssignSample("' + sample_run + '")')
- global SCATTER_SAMPLE, _SAMPLE_SETUP, _SAMPLE_RUN, _SAMPLE_N_PERIODS, PERIOD_NOS
-
- __clearPrevious(SCATTER_SAMPLE,others=[SCATTER_CAN,TRANS_SAMPLE,TRANS_CAN,DIRECT_SAMPLE,DIRECT_CAN])
- _SAMPLE_N_PERIODS = -1
-
- if( sample_run.startswith('.') or sample_run == '' or sample_run == None):
- _SAMPLE_SETUP = None
- _SAMPLE_RUN = ''
- SCATTER_SAMPLE = None
- return '', '()'
-
- _SAMPLE_RUN = sample_run
- SCATTER_SAMPLE,reset,logname,filepath, _SAMPLE_N_PERIODS = _assignHelper(sample_run, False, reload, period)
- if SCATTER_SAMPLE.getName() == '':
- _issueWarning('Unable to load SANS sample run, cannot continue.')
- return '','()'
- if reset == True:
- _SAMPLE_SETUP = None
-
- try:
- logvalues = INSTRUMENT.load_detector_logs(logname,filepath)
- if logvalues == None:
- mtd.deleteWorkspace(SCATTER_SAMPLE.getName())
- _issueWarning("Sample logs cannot be loaded, cannot continue")
- return '','()'
- except AttributeError:
- if not INSTRUMENT.name() == 'LOQ': raise
-
- PERIOD_NOS["SCATTER_SAMPLE"] = period
-
- if (INSTRUMENT.name() == 'LOQ'):
- return SCATTER_SAMPLE.getName(), None
-
- #global FRONT_DET_Z, FRONT_DET_X, FRONT_DET_ROT, REAR_DET_Z, REAR_DET_X
- INSTRUMENT.FRONT_DET_Z = float(logvalues['Front_Det_Z'])
- INSTRUMENT.FRONT_DET_X = float(logvalues['Front_Det_X'])
- INSTRUMENT.FRONT_DET_ROT = float(logvalues['Front_Det_Rot'])
- INSTRUMENT.REAR_DET_Z = float(logvalues['Rear_Det_Z'])
- INSTRUMENT.REAR_DET_X = float(logvalues['Rear_Det_X'])
-
- return SCATTER_SAMPLE.getName(), logvalues
-
-###########################
-# Set the scattering can raw workspace
-###########################
-_CAN_SETUP = None
-_CAN_RUN = ''
-def AssignCan(can_run, reload = True, period = -1):
- _printMessage('AssignCan("' + can_run + '")')
- global SCATTER_CAN, _CAN_SETUP, _CAN_RUN, _CAN_N_PERIODS, PERIOD_NOS
-
- __clearPrevious(SCATTER_CAN,others=[SCATTER_SAMPLE,TRANS_SAMPLE,TRANS_CAN,DIRECT_SAMPLE,DIRECT_CAN])
- _CAN_N_PERIODS = -1
-
- if( can_run.startswith('.') or can_run == '' or can_run == None):
- SCATTER_CAN.reset()
- _CAN_RUN = ''
- _CAN_SETUP = None
- return '', '()'
-
- _CAN_RUN = can_run
- SCATTER_CAN ,reset, logname,filepath, _CAN_N_PERIODS = \
- _assignHelper(can_run, False, reload, period)
- if SCATTER_CAN.getName() == '':
- _issueWarning('Unable to load sans can run, cannot continue.')
- return '','()'
- if reset == True:
- _CAN_SETUP = None
-
-
- try:
- logvalues = INSTRUMENT.load_detector_logs(logname,filepath)
- if logvalues == None:
- _issueWarning("Can logs could not be loaded, using sample values.")
- return SCATTER_CAN.getName(), "()"
- except AttributeError:
- if not INSTRUMENT.name() == 'LOQ' : raise
-
- PERIOD_NOS["SCATTER_CAN"] = period
-
- if (INSTRUMENT.name() == 'LOQ'):
- return SCATTER_CAN.getName(), ""
-
- smp_values = []
- front_det = INSTRUMENT.getDetector('front')
- smp_values.append(INSTRUMENT.FRONT_DET_Z + front_det.z_corr)
- smp_values.append(INSTRUMENT.FRONT_DET_X + front_det.x_corr)
- smp_values.append(INSTRUMENT.FRONT_DET_ROT + front_det.rot_corr)
- rear_det = INSTRUMENT.getDetector('rear')
- smp_values.append(INSTRUMENT.REAR_DET_Z + rear_det.z_corr)
- smp_values.append(INSTRUMENT.REAR_DET_X + rear_det.x_corr)
-
-
- # Check against sample values and warn if they are not the same but still continue reduction
- if len(logvalues) == 0:
- return SCATTER_CAN.getName(), logvalues
-
- can_values = []
- can_values.append(float(logvalues['Front_Det_Z']) + front_det.z_corr)
- can_values.append(float(logvalues['Front_Det_X']) + front_det.x_corr)
- can_values.append(float(logvalues['Front_Det_Rot']) + front_det.rot_corr)
- can_values.append(float(logvalues['Rear_Det_Z']) + rear_det.z_corr)
- can_values.append(float(logvalues['Rear_Det_X']) + rear_det.x_corr)
-
-
- det_names = ['Front_Det_Z', 'Front_Det_X','Front_Det_Rot', 'Rear_Det_Z', 'Rear_Det_X']
- for i in range(0, 5):
- if math.fabs(smp_values[i] - can_values[i]) > 5e-04:
- _issueWarning(det_names[i] + " values differ between sample and can runs. Sample = " + str(smp_values[i]) + \
- ' , Can = ' + str(can_values[i]))
- INSTRUMENT.append_marked(det_names[i])
-
- return SCATTER_CAN.getName(), logvalues
-
-###########################
-# Set the trans sample and measured raw workspaces
-###########################
-def TransmissionSample(sample, direct, reload = True, period = -1):
- _printMessage('TransmissionSample("' + sample + '","' + direct + '")')
- global TRANS_SAMPLE, DIRECT_SAMPLE, _TRANS_SAMPLE_N_PERIODS, DIRECT_SAMPLE_N_PERIODS
-
- __clearPrevious(TRANS_SAMPLE,others=[SCATTER_SAMPLE,SCATTER_CAN,TRANS_CAN,DIRECT_SAMPLE,DIRECT_CAN])
- __clearPrevious(DIRECT_SAMPLE,others=[SCATTER_SAMPLE,SCATTER_CAN,TRANS_SAMPLE,TRANS_CAN,DIRECT_CAN])
-
- trans_ws, dummy1, dummy2, dummy3, _TRANS_SAMPLE_N_PERIODS = \
- _assignHelper(sample, True, reload, period)
- TRANS_SAMPLE = trans_ws.getName()
-
- direct_sample_ws, dummy1, dummy2, dummy3, DIRECT_SAMPLE_N_PERIODS = \
- _assignHelper(direct, True, reload, period)
- DIRECT_SAMPLE = direct_sample_ws.getName()
-
- return TRANS_SAMPLE, DIRECT_SAMPLE
-
-##########################
-# Set the trans sample and measured raw workspaces
-##########################
-def TransmissionCan(can, direct, reload = True, period = -1):
- _printMessage('TransmissionCan("' + can + '","' + direct + '")')
- global TRANS_CAN, DIRECT_CAN, TRANS_CAN_N_PERIODS, DIRECT_CAN_N_PERIODS
-
- __clearPrevious(TRANS_CAN,others=[SCATTER_SAMPLE,SCATTER_CAN,TRANS_SAMPLE,DIRECT_SAMPLE,DIRECT_CAN])
- __clearPrevious(DIRECT_CAN,others=[SCATTER_SAMPLE,SCATTER_CAN,TRANS_SAMPLE,TRANS_CAN,DIRECT_SAMPLE])
-
- can_ws, dummy1, dummy2, dummy3, TRANS_CAN_N_PERIODS = \
- _assignHelper(can, True, reload, period)
- TRANS_CAN = can_ws.getName()
- if direct == '' or direct == None:
- DIRECT_CAN, DIRECT_CAN_N_PERIODS = DIRECT_SAMPLE, DIRECT_SAMPLE_N_PERIODS
- else:
- direct_can_ws, dummy1, dummy2, dummy3, DIRECT_CAN_N_PERIODS = \
- _assignHelper(direct, True, reload, period)
- DIRECT_CAN = direct_can_ws.getName()
- return TRANS_CAN, DIRECT_CAN
-
-# Helper function
-def _assignHelper(run_string, is_trans, reload = True, period = -1):
- if run_string == '' or run_string.startswith('.'):
- return SANSUtility.WorkspaceDetails('', -1),True,'','', -1
- pieces = run_string.split('.')
- if len(pieces) != 2 :
- _fatalError("Invalid run specified: " + run_string + ". Please use RUNNUMBER.EXT format")
- else:
- run_no = pieces[0]
- ext = pieces[1]
- if run_no == '':
- return SANSUtility.WorkspaceDetails('', -1),True,'','', -1
-
- if INSTRUMENT.name() == 'LOQ':
- field_width = 5
- else:
- field_width = 8
-
- fullrun_no,logname,shortrun_no = padRunNumber(run_no, field_width)
-
- if is_trans:
- wkspname = shortrun_no + '_trans_' + ext.lower()
- else:
- wkspname = shortrun_no + '_sans_' + ext.lower()
-
- if reload == False and mtd.workspaceExists(wkspname):
- return WorkspaceDetails(wkspname, shortrun_no),False,'','', -1
-
- basename = INSTRUMENT.name() + fullrun_no
- filename = os.path.join(DATA_PATH,basename)
- # Workaround so that the FileProperty does the correct searching of data paths if this file doesn't exist
- if not os.path.exists(filename + '.' + ext):
- filename = basename
- if period <= 0:
- period = 1
- if is_trans:
- try:
- if INSTRUMENT.name() == 'SANS2D' and int(shortrun_no) < 568:
- dimension = SANSUtility.GetInstrumentDetails(INSTRUMENT)[0]
- specmin = dimension*dimension*2
- specmax = specmin + 4
- else:
- specmin = None
- specmax = 8
-
- [filepath, wkspname, nPeriods] = \
- _loadRawData(filename, wkspname, ext, specmin, specmax, period)
- except RuntimeError, err:
- _issueWarning(str(err))
- return SANSUtility.WorkspaceDetails('', -1),True,'','', -1
- else:
- try:
- [filepath, wkspname, nPeriods] = _loadRawData(filename, wkspname, ext, None, None, period)
- except RuntimeError, details:
- _issueWarning(str(details))
- return SANSUtility.WorkspaceDetails('', -1),True,'','', -1
-
-
- inWS = SANSUtility.WorkspaceDetails(wkspname, shortrun_no)
- return inWS,True, INSTRUMENT.name() + logname, filepath, nPeriods
-
-def padRunNumber(run_no, field_width):
- nchars = len(run_no)
- digit_end = 0
- for i in range(0, nchars):
- if run_no[i].isdigit():
- digit_end += 1
- else:
- break
-
- if digit_end == nchars:
- filebase = run_no.rjust(field_width, '0')
- return filebase, filebase, run_no
- else:
- filebase = run_no[:digit_end].rjust(field_width, '0')
- return filebase + run_no[digit_end:], filebase, run_no[:digit_end]
-
-def __clearPrevious(inWS, others = []):
- if inWS != None:
- if type(inWS) == SANSUtility.WorkspaceDetails:
- inWS = inWS.getName()
- if mtd.workspaceExists(inWS) and (not inWS in others):
- mtd.deleteWorkspace(inWS)
-
-##########################
-# Loader function
-##########################
-def _loadRawData(filename, wsName, ext, spec_min = None, spec_max = None, period=1):
- if ext.lower().startswith('n'):
- alg = LoadNexus(filename + '.' + ext, wsName,SpectrumMin=spec_min,SpectrumMax=spec_max)
- else:
- alg = LoadRaw(filename + '.' + ext, wsName, SpectrumMin = spec_min,SpectrumMax = spec_max)
- LoadSampleDetailsFromRaw(wsName, filename + '.' + ext)
-
- pWorksp = mtd[wsName]
-
- if pWorksp.isGroup() :
- #get the number of periods in a group using the fact that each period has a different name
- nNames = len(pWorksp.getNames())
- numPeriods = nNames - 1
- wsName = _leaveSinglePeriod(pWorksp, period)
- pWorksp = mtd[wsName]
- else :
- #if the work space isn't a group there is only one period
- numPeriods = 1
-
- if (period > numPeriods) or (period < 1):
- raise ValueError('_loadRawData: Period number ' + str(period) + ' doesn\'t exist in workspace ' + pWorksp.getName())
-
- sample_details = pWorksp.getSampleInfo()
- SampleGeometry(sample_details.getGeometryFlag())
- SampleThickness(sample_details.getThickness())
- SampleHeight(sample_details.getHeight())
- SampleWidth(sample_details.getWidth())
-
- # Return the filepath actually used to load the data
- fullpath = alg.getPropertyValue("Filename")
- return [ os.path.dirname(fullpath), wsName, numPeriods]
-
-##REMOVED STEVE 08 September 2010
-def _leaveSinglePeriod(groupW, period):
- #get the name of the individual workspace in the group
- oldName = groupW.getName()+'_'+str(period)
- #move this workspace out of the group (this doesn't delete it)
- groupW.remove(oldName)
-
- discriptors = groupW.getName().split('_') #information about the run (run number, if it's 1D or 2D, etc) is listed in the workspace name between '_'s
- for i in range(0, len(discriptors) ): #insert the period name after the run number
- if i == 0 : #the run number is the first part of the name
- newName = discriptors[0]+'p'+str(period)#so add the period number here
- else :
- newName += '_'+discriptors[i]
-
- RenameWorkspace(oldName, newName)
-
- #remove the rest of the group
- mtd.deleteWorkspace(groupW.getName())
- return newName
-# Return the list of mismatched detector names
-def GetMismatchedDetList():
- return INSTRUMENT.get_marked_dets()
-
-#########################
-# Limits
-def LimitsR(rmin, rmax):
- _printMessage('LimitsR(' + str(rmin) + ',' +str(rmax) + ')')
- _readLimitValues('L/R ' + str(rmin) + ' ' + str(rmax) + ' 1')
-
-def LimitsWav(lmin, lmax, step, type):
- _printMessage('LimitsWav(' + str(lmin) + ',' + str(lmax) + ',' + str(step) + ',' + type + ')')
- _readLimitValues('L/WAV ' + str(lmin) + ' ' + str(lmax) + ' ' + str(step) + '/' + type)
-
-def LimitsQ(*args):
- # If given one argument it must be a rebin string
- if len(args) == 1:
- val = args[0]
- if type(val) == str:
- _printMessage("LimitsQ(" + val + ")")
- _readLimitValues("L/Q " + val)
- else:
- _issueWarning("LimitsQ can only be called with a single string or 4 values")
- elif len(args) == 4:
- qmin,qmax,step,step_type = args
- _printMessage('LimitsQ(' + str(qmin) + ',' + str(qmax) +',' + str(step) + ',' + str(step_type) + ')')
- _readLimitValues('L/Q ' + str(qmin) + ' ' + str(qmax) + ' ' + str(step) + '/' + step_type)
- else:
- _issueWarning("LimitsQ called with " + str(len(args)) + " arguments, 1 or 4 expected.")
-
-def LimitsQXY(qmin, qmax, step, type):
- _printMessage('LimitsQXY(' + str(qmin) + ',' + str(qmax) +',' + str(step) + ',' + str(type) + ')')
- _readLimitValues('L/QXY ' + str(qmin) + ' ' + str(qmax) + ' ' + str(step) + '/' + type)
-
-def LimitsPhi(phimin, phimax, use_mirror=True):
- if use_mirror :
- _printMessage("LimitsPHI(" + str(phimin) + ' ' + str(phimax) + 'use_mirror=True)')
- _readLimitValues('L/PHI ' + str(phimin) + ' ' + str(phimax))
- else :
- _printMessage("LimitsPHI(" + str(phimin) + ' ' + str(phimax) + 'use_mirror=False)')
- _readLimitValues('L/PHI/NOMIRROR ' + str(phimin) + ' ' + str(phimax))
-
-def Gravity(flag):
- _printMessage('Gravity(' + str(flag) + ')')
- if isinstance(flag, bool) or isinstance(flag, int):
- global GRAVITY
- GRAVITY = flag
- else:
- _issueWarning("Invalid GRAVITY flag passed, try True/False. Setting kept as " + str(GRAVITY))
-
-def TransFit(mode,lambdamin=None,lambdamax=None):
- global TRANS_WAV1, TRANS_WAV2, TRANS_FIT
- mode = mode.upper()
-
- if mode in TRANS_FIT_OPTIONS.keys():
- TRANS_FIT = TRANS_FIT_OPTIONS[mode]
- else:
- _issueWarning("Invalid fit mode passed to TransFit, using default LOG method")
- TRANS_FIT = mode = TRANS_FIT_DEF
-
- if lambdamin is None or lambdamax is None:
- _printMessage("TransFit(\"" + str(mode) + "\")")
- TRANS_WAV1 = TRANS_WAV1_FULL
- TRANS_WAV2 = TRANS_WAV2_FULL
- else:
- _printMessage("TransFit(\"" + str(mode) + "\"," + str(lambdamin) + "," + str(lambdamax) + ")")
- TRANS_WAV1 = lambdamin
- TRANS_WAV2 = lambdamax
-
-
-###################################
-# Scaling value
-###################################
-def _SetScales(scalefactor):
- global RESCALE
- RESCALE = scalefactor * 100.0
-##START REMOVED STEVE (ISISCOmmandInterface.py)
-#########################
-# Sample geometry flag
-#########################
-def SampleGeometry(geom_id):
- if geom_id > 3 or geom_id < 1:
- _issueWarning("Invalid geometry type for sample: " + str(geom_id) + ". Setting default to 3.")
- geom_id = 3
- global SAMPLE_GEOM
- SAMPLE_GEOM = geom_id
-
-#########################
-# Sample width
-#########################
-def SampleWidth(width):
- if SAMPLE_GEOM == None:
- _fatalError('Attempting to set width without setting geometry flag. Please set geometry type first')
- global SAMPLE_WIDTH
- SAMPLE_WIDTH = width
- # For a disk the height=width
- if SAMPLE_GEOM == 3:
- global SAMPLE_HEIGHT
- SAMPLE_HEIGHT = width
-
-#########################
-# Sample height
-#########################
-def SampleHeight(height):
- if SAMPLE_GEOM == None:
- _fatalError('Attempting to set height without setting geometry flag. Please set geometry type first')
- global SAMPLE_HEIGHT
- SAMPLE_HEIGHT = height
- # For a disk the height=width
- if SAMPLE_GEOM == 3:
- global SAMPLE_WIDTH
- SAMPLE_WIDTH = height
-
-#########################
-# Sample thickness
-#########################
-def SampleThickness(thickness):
- global SAMPLE_THICKNESS
- SAMPLE_THICKNESS = thickness
-
-#############################
-# Print sample geometry
-###########################
-def displayGeometry():
- print 'Beam centre: [' + str(XBEAM_CENTRE) + ',' + str(YBEAM_CENTRE) + ']'
- print '-- Sample Geometry --\n' + \
- ' ID: ' + str(SAMPLE_GEOM) + '\n' + \
- ' Width: ' + str(SAMPLE_WIDTH) + '\n' + \
- ' Height: ' + str(SAMPLE_HEIGHT) + '\n' + \
- ' Thickness: ' + str(SAMPLE_THICKNESS) + '\n'
-######################################
-# Set the centre in mm
-####################################
-def SetCentre(XVAL, YVAL):
- _printMessage('SetCentre(' + str(XVAL) + ',' + str(YVAL) + ')')
- global XBEAM_CENTRE, YBEAM_CENTRE
- XBEAM_CENTRE = XVAL/1000.
- YBEAM_CENTRE = YVAL/1000.
-
-#####################################
-# Set the phi limit
-#####################################
-def SetPhiLimit(phimin,phimax, phimirror=True):
- if phimirror :
- if phimin > phimax:
- phimin, phimax = phimax, phimin
- if abs(phimin) > 180.0 :
- phimin = -90.0
- if abs(phimax) > 180.0 :
- phimax = 90.0
-
- if phimax - phimin == 180.0 :
- phimin = -90.0
- phimax = 90.0
- else:
- phimin = SANSUtility.normalizePhi(phimin)
- phimax = SANSUtility.normalizePhi(phimax)
-
-
- global PHIMIN, PHIMAX, PHIMIRROR
- PHIMIN = phimin
- PHIMAX = phimax
- PHIMIRROR = phimirror
-##END REMOVED STEVE (ISISCOmmandInterface.py)
-##START REMOVED STEVE 13 September 2010 (ISISSANSReductionSteps.py)
-def _restore_defaults():
-
- Mask('MASK/CLEAR')
- Mask('MASK/CLEAR/TIME')
- SetRearEfficiencyFile(None)
- SetFrontEfficiencyFile(None)
- global RMIN,RMAX, DEF_RMIN, DEF_RMAX
- RMIN = RMAX = DEF_RMIN = DEF_RMAX = None
- global WAV1, WAV2, DWAV, Q_REBIN, QXY2, DQY
- WAV1 = WAV2 = DWAV = Q_REBIN = QXY = DQY = None
- global RESCALE, SAMPLE_GEOM, SAMPLE_WIDTH, SAMPLE_HEIGHT, SAMPLE_THICKNESS
- # Scaling values
- RESCALE = 100. # percent
- SAMPLE_GEOM = 3
- SAMPLE_WIDTH = SAMPLE_HEIGHT = SAMPLE_THICKNESS = 1.0
- front_det = INSTRUMENT.getDetector('rear')
- front_det.z_corr = front_det.y_corr = front_det.x_corr = front_det.rot_corr = 0.0
- rear_det = INSTRUMENT.getDetector('rear')
- rear_det.z_corr = rear_det.x_corr = 0.0
-
- global BACKMON_START, BACKMON_END
- BACKMON_START = BACKMON_END = None
-
- global NORMALISATION_FILE
- NORMALISATION_FILE = None
-##START REMOVED STEVE 13 September 2010 (ISISSANSReductionSteps.py)
-####################################
-# Add a mask to the correct string
-###################################
-def Mask(details):
- _printMessage('Mask("' + details + '")')
- details = details.lstrip()
- details_compare = details.upper()
- if not details_compare.startswith('MASK'):
- _issueWarning('Ignoring malformed mask line ' + details)
- return
-
- global TIMEMASKSTRING, TIMEMASKSTRING_R, TIMEMASKSTRING_F,SPECMASKSTRING, SPECMASKSTRING_R, SPECMASKSTRING_F
- parts = details_compare.split('/')
- # A spectrum mask or mask range applied to the rear detector
- if len(parts) == 1:
- spectra = details[4:].lstrip()
- if len(spectra.split()) == 1:
- SPECMASKSTRING_R += ',' + spectra
- elif len(parts) == 2:
- type = parts[1]
- detname = type.split()
- if type == 'CLEAR':
- SPECMASKSTRING = ''
- SPECMASKSTRING_R = ''
- SPECMASKSTRING_F = ''
- elif type.startswith('T'):
- if type.startswith('TIME'):
- bin_range = type[4:].lstrip()
- else:
- bin_range = type[1:].lstrip()
- TIMEMASKSTRING += ';' + bin_range
- elif len(detname) == 2:
- det_type = detname[0]
- if INSTRUMENT.isDetectorName(det_type) :
- spectra = detname[1]
- if INSTRUMENT.isHighAngleDetector(det_type) :
- SPECMASKSTRING_F += ',' + spectra
- else:
- SPECMASKSTRING_R += ',' + spectra
- else:
- _issueWarning('Detector \'' + det_type + '\' not found in currently selected instrument ' + INSTRUMENT.name() + '. Skipping line.')
- else:
- _issueWarning('Unrecognized masking option "' + details + '"')
- elif len(parts) == 3:
- type = parts[1]
- if type == 'CLEAR':
- TIMEMASKSTRING = ''
- TIMEMASKSTRING_R = ''
- TIMEMASKSTRING_F = ''
- elif (type == 'TIME' or type == 'T'):
- parts = parts[2].split()
- if len(parts) == 3:
- detname = parts[0].rstrip()
- bin_range = parts[1].rstrip() + ' ' + parts[2].lstrip()
- if INSTRUMENT.detectorExists(detname) :
- if INSTRUMENT.isHighAngleDetector(detname) :
- TIMEMASKSTRING_F += ';' + bin_range
- else:
- TIMEMASKSTRING_R += ';' + bin_range
- else:
- _issueWarning('Detector \'' + det_type + '\' not found in currently selected instrument ' + INSTRUMENT.name() + '. Skipping line.')
- else:
- _issueWarning('Unrecognized masking option "' + details + '"')
- else:
- pass
-##START REMOVED (ISISReducer.py)
-def MaskFile(filename):
- _printMessage('#Opening "'+filename+'"')
- if os.path.isabs(filename) == False:
- filename = os.path.join(USER_PATH, filename)
-
- if os.path.exists(filename) == False:
- _fatalError("Cannot read mask file '" + filename + "', path does not exist.")
-
- _restore_defaults()
-
- file_handle = open(filename, 'r')
- for line in file_handle:
- if line.startswith('!'):
- continue
- # This is so that I can be sure all EOL characters have been removed
- line = line.lstrip().rstrip()
- upper_line = line.upper()
- if upper_line.startswith('L/'):
- _readLimitValues(line)
-
- elif upper_line.startswith('MON/'):
- _readMONValues(line)
-
- elif upper_line.startswith('MASK'):
- Mask(upper_line)
-
- elif upper_line.startswith('SET CENTRE'):
- values = upper_line.split()
- SetCentre(float(values[2]), float(values[3]))
-
- elif upper_line.startswith('SET SCALES'):
- values = upper_line.split()
- _SetScales(float(values[2]))
-
- elif upper_line.startswith('SAMPLE/OFFSET'):
- values = upper_line.split()
- SetSampleOffset(values[1])
-
- elif upper_line.startswith('DET/'):
- type = upper_line[4:]
- if type.startswith('CORR'):
- _readDetectorCorrections(upper_line[8:])
- else:
- # This checks whether the type is correct and issues warnings if it is not
- Detector(type)
-
- elif upper_line.startswith('GRAVITY'):
- flag = upper_line[8:]
- if flag == 'ON':
- Gravity(True)
- elif flag == 'OFF':
- Gravity(False)
- else:
- _issueWarning("Gravity flag incorrectly specified, disabling gravity correction")
- Gravity(False)
-
- elif upper_line.startswith('BACK/MON/TIMES'):
- tokens = upper_line.split()
- global BACKMON_START, BACKMON_END
- if len(tokens) == 3:
- BACKMON_START = int(tokens[1])
- BACKMON_END = int(tokens[2])
- else:
- _issueWarning('Incorrectly formatted BACK/MON/TIMES line, not running FlatBackground.')
- BACKMON_START = None
- BACKMON_END = None
-
- elif upper_line.startswith("FIT/TRANS/"):
- params = upper_line[10:].split()
- if len(params) == 3:
- fit_type, lambdamin, lambdamax = params
- TransFit(fit_type, lambdamin, lambdamax)
- elif len(params) == 1:
- TransFit(params[0])
- else:
- _issueWarning('Incorrectly formatted FIT/TRANS line, setting defaults to LOG and full range')
- TransFit(TRANS_FIT_DEF)
-
- else:
- continue
-
- # Close the handle
- file_handle.close()
- # Check if one of the efficency files hasn't been set and assume the other is to be used
- if DIRECT_BEAM_FILE_R == None and DIRECT_BEAM_FILE_F != None:
- SetRearEfficiencyFile(DIRECT_BEAM_FILE_F)
- if DIRECT_BEAM_FILE_F == None and DIRECT_BEAM_FILE_R != None:
- SetFrontEfficiencyFile(DIRECT_BEAM_FILE_R)
-
- # just print thhe name, remove the path
- filename = os.path.basename(filename)
- global MASKFILE
- MASKFILE = filename
- _printMessage('#Successfully read "'+filename+'"')
- return True
-
-# Read a limit line of a mask file
-def _readLimitValues(limit_line):
- limits = limit_line.split('L/')
- if len(limits) != 2:
- _issueWarning("Incorrectly formatted limit line ignored \"" + limit_line + "\"")
- return
- limits = limits[1]
- limit_type = ''
- if not ',' in limit_line:
- # Split with no arguments defaults to any whitespace character and in particular
- # multiple spaces are include
- elements = limits.split()
- if len(elements) == 4:
- limit_type, minval, maxval, step = elements[0], elements[1], elements[2], elements[3]
- rebin_str = None
- step_details = step.split('/')
- if len(step_details) == 2:
- step_size = step_details[0]
- step_type = step_details[1]
- if step_type.upper() == 'LIN':
- step_type = ''
- else:
- step_type = '-'
- else:
- step_size = step_details[0]
- step_type = ''
- elif len(elements) == 3:
- limit_type, minval, maxval = elements[0], elements[1], elements[2]
- else:
- # We don't use the L/SP line
- if not 'L/SP' in limit_line:
- _issueWarning("Incorrectly formatted limit line ignored \"" + limit_line + "\"")
- return
- else:
- limit_type = limits[0].lstrip().rstrip()
- rebin_str = limits[1:].lstrip().rstrip()
- minval = maxval = step_type = step_size = None
-
- if limit_type.upper() == 'WAV':
- global WAV1, WAV2, DWAV
- WAV1 = float(minval)
- WAV2 = float(maxval)
- DWAV = float(step_type + step_size)
- elif limit_type.upper() == 'Q':
- global Q_REBIN
- if not rebin_str is None:
- Q_REBIN = rebin_str
- else:
- Q_REBIN = minval + "," + step_type + step_size + "," + maxval
- elif limit_type.upper() == 'QXY':
- global QXY2, DQXY
- QXY2 = float(maxval)
- DQXY = float(step_type + step_size)
- elif limit_type.upper() == 'R':
- global RMIN, RMAX, DEF_RMIN, DEF_RMAX
- RMIN = float(minval)/1000.
- RMAX = float(maxval)/1000.
- DEF_RMIN = RMIN
- DEF_RMAX = RMAX
- elif limit_type.upper() == 'PHI':
- SetPhiLimit(float(minval), float(maxval), True)
- elif limit_type.upper() == 'PHI/NOMIRROR':
- SetPhiLimit(float(minval), float(maxval), False)
- else:
- pass
-
-def _readMONValues(line):
- details = line[4:]
-
- #MON/LENTH, MON/SPECTRUM and MON/TRANS all accept the INTERPOLATE option
- interpolate = False
- interPlace = details.upper().find('/INTERPOLATE')
- if interPlace != -1 :
- interpolate = True
- details = details[0:interPlace]
-
- if details.upper().startswith('LENGTH'):
- SuggestMonitorSpectrum(int(details.split()[1]), interpolate)
-
- elif details.upper().startswith('SPECTRUM'):
- SetMonitorSpectrum(int(details.split('=')[1]), interpolate)
-
- elif details.upper().startswith('TRANS'):
- parts = details.split('=')
- if len(parts) < 2 or parts[0].upper() != 'TRANS/SPECTRUM' :
- _issueWarning('Unable to parse MON/TRANS line, needs MON/TRANS/SPECTRUM=')
- SetTransSpectrum(int(parts[1]), interpolate)
-
- elif 'DIRECT' in details.upper() or details.upper().startswith('FLAT'):
- parts = details.split("=")
- if len(parts) == 2:
- filepath = parts[1].rstrip()
- if '[' in filepath:
- idx = filepath.rfind(']')
- filepath = filepath[idx + 1:]
- if not os.path.isabs(filepath):
- filepath = os.path.join(USER_PATH, filepath)
- type = parts[0]
- parts = type.split("/")
- if len(parts) == 1:
- if parts[0].upper() == 'DIRECT':
- SetRearEfficiencyFile(filepath)
- SetFrontEfficiencyFile(filepath)
- elif parts[0].upper() == 'HAB':
- SetFrontEfficiencyFile(filepath)
- elif parts[0].upper() == 'FLAT':
- SetDetectorFloodFile(filepath)
- else:
- pass
- elif len(parts) == 2:
- detname = parts[1]
- if detname.upper() == 'REAR':
- SetRearEfficiencyFile(filepath)
- elif detname.upper() == 'FRONT' or detname.upper() == 'HAB':
- SetFrontEfficiencyFile(filepath)
- else:
- _issueWarning('Incorrect detector specified for efficiency file "' + line + '"')
- else:
- _issueWarning('Unable to parse monitor line "' + line + '"')
- else:
- _issueWarning('Unable to parse monitor line "' + line + '"')
-
-def _readDetectorCorrections(details):
- values = details.split()
- det_name = values[0]
- det_axis = values[1]
- shift = float(values[2])
-
- detector = INSTRUMENT.getDetector(det_name)
- if det_axis == 'X':
- detector.x_corr = shift
- elif det_axis == 'Y':
- detector.y_corr = shift
- elif det_axis == 'Z':
- detector.z_corr = shift
- elif det_axis == 'ROT':
- detector.rot_corr = shift
- else:
- raise NotImplemented('Detector correction on "'+det_axis+'" is not supported')
-##END REMOVED (ISISReducer.py)
-##START REMOVED STEVE 13 September 2010 (ISISSANSReductionSteps.py)
-def SetSampleOffset(value):
- INSTRUMENT.set_sample_offset(value)
-
-def SetMonitorSpectrum(specNum, interp=False):
- INSTRUMENT.set_incident_mon(specNum)
- #if interpolate is stated once in the file, that is enough it wont be unset (until a file is loaded again)
- if interp :
- INSTRUMENT.set_interpolating_norm()
-
-def SuggestMonitorSpectrum(specNum, interp=False):
- INSTRUMENT.suggest_incident_mntr(specNum)
- #if interpolate is stated once in the file, that is enough it wont be unset (until a file is loaded again)
- if interp :
- INSTRUMENT.suggest_interpolating_norm()
-
-def SetTransSpectrum(specNum, interp=False):
- INSTRUMENT.incid_mon_4_trans_calc = int(specNum)
- #if interpolate is stated once in the file, that is enough it wont be unset (until a file is loaded again)
- if interp :
- INSTRUMENT.use_interpol_trans_calc = True
-
-def SetRearEfficiencyFile(filename):
- global DIRECT_BEAM_FILE_R
- DIRECT_BEAM_FILE_R = filename
-
-def SetFrontEfficiencyFile(filename):
- global DIRECT_BEAM_FILE_F
- DIRECT_BEAM_FILE_F = filename
-
-def SetDetectorFloodFile(filename):
- global NORMALISATION_FILE
- NORMALISATION_FILE = filename
-
-def displayMaskFile():
- print '-- Mask file defaults --'
- print ' Wavelength range: ',WAV1, WAV2, DWAV
- print ' Q range: ', Q_REBIN
- print ' QXY range: ', QXY2, DQXY
- print ' radius', RMIN, RMAX
- print ' direct beam file rear:', DIRECT_BEAM_FILE_R
- print ' direct beam file front:', DIRECT_BEAM_FILE_F
- print ' global spectrum mask: ', SPECMASKSTRING
- print ' rear spectrum mask: ', SPECMASKSTRING_R
- print ' front spectrum mask: ', SPECMASKSTRING_F
- print ' global time mask: ', TIMEMASKSTRING
- print ' rear time mask: ', TIMEMASKSTRING_R
- print ' front time mask: ', TIMEMASKSTRING_F
-# ---------------------------------------------------------------------------------------
-
-##
-# Set up the sample and can detectors and calculate the transmission if available
-##
-def _initReduction(xcentre = None, ycentre = None):
- # *** Sample setup first ***
- if SCATTER_SAMPLE == None:
- exit('Error: No sample run has been set')
-
- if xcentre == None or ycentre == None:
- xcentre = XBEAM_CENTRE
- ycentre = YBEAM_CENTRE
-
- global _SAMPLE_SETUP
- if _SAMPLE_SETUP == None:
- _SAMPLE_SETUP = _init_run(SCATTER_SAMPLE, [xcentre, ycentre], False)
-
- global _CAN_SETUP
- if SCATTER_CAN.getName() != '' and _CAN_SETUP == None:
- _CAN_SETUP = _init_run(SCATTER_CAN, [xcentre, ycentre], True)
-
- # Instrument specific information using function in utility file
- global DIMENSION, SPECMIN, SPECMAX, INSTRUMENT
- DIMENSION, SPECMIN, SPECMAX = SANSUtility.GetInstrumentDetails(INSTRUMENT)
-
- return _SAMPLE_SETUP, _CAN_SETUP
-##END REMOVED STEVE 13 September 2010 (ISISSANSReductionSteps.py)
-##START REMOVED STEVE 14 September 2010 (ISISSANSReductionSteps.py)
-##
-# Run the reduction for a given wavelength range
-##
-def WavRangeReduction(wav_start = None, wav_end = None, use_def_trans = DefaultTrans, finding_centre = False):
- if wav_start == None:
- wav_start = WAV1
- if wav_end == None:
- wav_end = WAV2
-
- if finding_centre == False:
- _printMessage('WavRangeReduction(' + str(wav_start) + ',' + str(wav_end) + ',' + str(use_def_trans) + ',' + str(finding_centre) + ')')
- _printMessage("Running reduction for wavelength range " + str(wav_start) + '-' + str(wav_end))
- # This only performs the init if it needs to
- sample_setup, can_setup = _initReduction(XBEAM_CENTRE, YBEAM_CENTRE)
-
- wsname_cache = sample_setup.getReducedWorkspace()
- # Run correction function
- if finding_centre == True:
- final_workspace = wsname_cache.split('_')[0] + '_quadrants'
- else:
- final_workspace = wsname_cache + '_' + str(wav_start) + '_' + str(wav_end)
- sample_setup.setReducedWorkspace(final_workspace)
- # Perform correction
- Correct(sample_setup, wav_start, wav_end, use_def_trans, finding_centre)
-##END REMOVED STEVE 14 September 2010 (ISISSANSReductionSteps.py)
- if can_setup != None:
- tmp_smp = final_workspace+"_sam_tmp"
- RenameWorkspace(final_workspace, tmp_smp)
- # Run correction function
- # was Correct(SCATTER_CAN, can_setup[0], can_setup[1], wav_start, wav_end, can_setup[2], can_setup[3], finding_centre)
- tmp_can = final_workspace+"_can_tmp"
- can_setup.setReducedWorkspace(tmp_can)
- # Can correction
- Correct(can_setup, wav_start, wav_end, use_def_trans, finding_centre)
- Minus(tmp_smp, tmp_can, final_workspace)
-
- # Due to rounding errors, small shifts in detector encoders and poor stats in highest Q bins need "minus" the
- # workspaces before removing nan & trailing zeros thus, beware, _sc, _sam_tmp and _can_tmp may NOT have same Q bins
- if finding_centre == False:
- ReplaceSpecialValues(InputWorkspace = tmp_smp,OutputWorkspace = tmp_smp, NaNValue="0", InfinityValue="0")
- ReplaceSpecialValues(InputWorkspace = tmp_can,OutputWorkspace = tmp_can, NaNValue="0", InfinityValue="0")
- if CORRECTION_TYPE == '1D':
- SANSUtility.StripEndZeroes(tmp_smp)
- SANSUtility.StripEndZeroes(tmp_can)
- else:
- mantid.deleteWorkspace(tmp_smp)
- mantid.deleteWorkspace(tmp_can)
- mantid.deleteWorkspace(final_workspace)
-
- # Crop Workspace to remove leading and trailing zeroes
- if finding_centre == False:
- # Replaces NANs with zeroes
- ReplaceSpecialValues(InputWorkspace = final_workspace, OutputWorkspace = final_workspace, NaNValue="0", InfinityValue="0")
- if CORRECTION_TYPE == '1D':
- SANSUtility.StripEndZeroes(final_workspace)
- # Store the mask file within the final workspace so that it is saved to the CanSAS file
- AddSampleLog(final_workspace, "UserFile", MASKFILE)
- else:
- quadrants = {1:'Left', 2:'Right', 3:'Up',4:'Down'}
- for key, value in quadrants.iteritems():
- old_name = final_workspace + '_' + str(key)
- RenameWorkspace(old_name, value)
- AddSampleLog(value, "UserFile", MASKFILE)
-
- # Revert the name change so that future calls with different wavelengths get the correct name
- sample_setup.setReducedWorkspace(wsname_cache)
- return final_workspace
-##REMOVED STEVE 08 September 2010
-def _init_run(raw_ws, beamcoords, emptycell):
- if raw_ws == '':
- return None
-
- if emptycell:
- _printMessage('Initializing can workspace to [' + str(beamcoords[0]) + ',' + str(beamcoords[1]) + ']' )
- else:
- _printMessage('Initializing sample workspace to [' + str(beamcoords[0]) + ',' + str(beamcoords[1]) + ']' )
-
- if emptycell == True:
- final_ws = "can_temp_workspace"
- else:
- final_ws = raw_ws.getName().split('_')[0]
- final_ws += INSTRUMENT.cur_detector().name('short')
- final_ws += '_' + CORRECTION_TYPE
-
- # Put the components in the correct positions
- currentDet = INSTRUMENT.cur_detector().name()
- maskpt_rmin, maskpt_rmax = INSTRUMENT.set_component_positions(raw_ws.getName(), beamcoords[0], beamcoords[1])
-
- # Create a run details object
- if emptycell == True:
- return SANSUtility.RunDetails(raw_ws, final_ws, TRANS_CAN, DIRECT_CAN, maskpt_rmin, maskpt_rmax, 'can')
- else:
- return SANSUtility.RunDetails(raw_ws, final_ws, TRANS_SAMPLE, DIRECT_SAMPLE, maskpt_rmin, maskpt_rmax, 'sample')
-##REMOVED STEVE 08 September 2010
-##START REMOVED ISISReductionSteps
-# Setup the transmission workspace
-##
-def CalculateTransmissionCorrection(run_setup, lambdamin, lambdamax, use_def_trans):
- trans_raw = run_setup.getTransRaw()
- direct_raw = run_setup.getDirectRaw()
- if trans_raw == '' or direct_raw == '':
- return None
-
- if use_def_trans == DefaultTrans:
- wavbin = str(TRANS_WAV1_FULL) + ',' + str(DWAV) + ',' + str(TRANS_WAV2_FULL)
- translambda_min = TRANS_WAV1_FULL
- translambda_max = TRANS_WAV2_FULL
- else:
- translambda_min = TRANS_WAV1
- translambda_max = TRANS_WAV2
- wavbin = str(lambdamin) + ',' + str(DWAV) + ',' + str(lambdamax)
-
- fittedtransws = trans_raw.split('_')[0] + '_trans_' + run_setup.getSuffix() + '_' + str(translambda_min) + '_' + str(translambda_max)
- unfittedtransws = fittedtransws + "_unfitted"
- if use_def_trans == False or \
- (TRANS_FIT != 'Off' and mtd.workspaceExists(fittedtransws) == False) or \
- (TRANS_FIT == 'Off' and mtd.workspaceExists(unfittedtransws) == False):
- # If no fitting is required just use linear and get unfitted data from CalculateTransmission algorithm
- if TRANS_FIT == 'Off':
- fit_type = 'Linear'
- else:
- fit_type = TRANS_FIT
- #retrieve the user setting that tells us whether Rebin or InterpolatingRebin will be used during the normalisation
- if INSTRUMENT.name() == 'LOQ':
- # Change the instrument definition to the correct one in the LOQ case
- LoadInstrument(trans_raw, INSTR_DIR + "/LOQ_trans_Definition.xml", RewriteSpectraMap=False)
- LoadInstrument(direct_raw, INSTR_DIR + "/LOQ_trans_Definition.xml", RewriteSpectraMap=False)
-
- trans_tmp_out = SANSUtility.SetupTransmissionWorkspace(trans_raw,
- '1,2', BACKMON_START, BACKMON_END, wavbin,
- INSTRUMENT.use_interpol_trans_calc, True)
-
- direct_tmp_out = SANSUtility.SetupTransmissionWorkspace(direct_raw,
- '1,2', BACKMON_START, BACKMON_END, wavbin,
- INSTRUMENT.use_interpol_trans_calc, True)
-
- CalculateTransmission(trans_tmp_out,direct_tmp_out, fittedtransws, MinWavelength = translambda_min, MaxWavelength = translambda_max, \
- FitMethod = fit_type, OutputUnfittedData=True)
- else:
- trans_tmp_out = SANSUtility.SetupTransmissionWorkspace(trans_raw,
- '1,2', BACKMON_START, BACKMON_END, wavbin,
- INSTRUMENT.use_interpol_trans_calc, False)
-
- direct_tmp_out = SANSUtility.SetupTransmissionWorkspace(direct_raw,
- '1,2', BACKMON_START, BACKMON_END, wavbin,
- INSTRUMENT.use_interpol_trans_calc, False)
-
- CalculateTransmission(trans_tmp_out,direct_tmp_out, fittedtransws,
- INSTRUMENT.incid_mon_4_trans_calc, INSTRUMENT.default_trans_spec,
- MinWavelength = translambda_min, MaxWavelength = translambda_max,
- FitMethod = fit_type, OutputUnfittedData=True)
- # Remove temporaries
- mantid.deleteWorkspace(trans_tmp_out)
- mantid.deleteWorkspace(direct_tmp_out)
-
- if TRANS_FIT == 'Off':
- result = unfittedtransws
- mantid.deleteWorkspace(fittedtransws)
- else:
- result = fittedtransws
-
- if use_def_trans == DefaultTrans:
- tmp_ws = 'trans_' + run_setup.getSuffix() + '_' + str(lambdamin) + '_' + str(lambdamax)
- CropWorkspace(result, tmp_ws, XMin = str(lambdamin), XMax = str(lambdamax))
- return tmp_ws
- else:
- return result
-##END REMOVE (ISISReductionSteps
-##REMOVED STEVE 08 September 2010
-##
-# Apply the spectrum and time masks to one detector in a given workspace
-##
-def _applyMasking(workspace, firstspec, dimension, inst, orientation=SANSUtility.Orientation.Horizontal,limitphi = True, useActiveDetector=True):
-
- #Time mask
- SANSUtility.MaskByBinRange(workspace,TIMEMASKSTRING)
-
- #this function only masks one detector, find out which one that should be
- setLowAngle = inst.lowAngDetSet
- if not useActiveDetector :
- setLowAngle = not inst.lowAngDetSet
-
- if setLowAngle :
- specstring = SPECMASKSTRING_R
- timestring = TIMEMASKSTRING_R
- else:
- specstring = SPECMASKSTRING_F
- timestring = TIMEMASKSTRING_F
-
- speclist = SANSUtility.ConvertToSpecList(specstring, firstspec, dimension,orientation)
- _printMessage(str(speclist))
- SANSUtility.MaskBySpecNumber(workspace, speclist)
-
- SANSUtility.MaskByBinRange(workspace, timestring)
-##END REMOVED STEVE
-##START REMOVED STEVE
- # Finally apply masking to get the correct phi range
- if limitphi == True:
- # Detector has been moved such that beam centre is at [0,0,0]
- SANSUtility.LimitPhi(workspace, [0,0,0], PHIMIN,PHIMAX,PHIMIRROR)
-##END REMOVED STEVE
-##START REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
-def Correct(run_setup, wav_start, wav_end, use_def_trans, finding_centre = False):
- '''Performs the data reduction steps'''
- global SPECMIN, SPECMAX
- sample_raw = run_setup.getRawWorkspace()
-#but does the full run still exist at this point, doesn't matter I'm changing the meaning of RawWorkspace get all references to it
-#but then what do we call the workspaces?
-
-# period = run_setup.getPeriod()
- orientation = orientation=SANSUtility.Orientation.Horizontal
- if INSTRUMENT.name() == "SANS2D":
- base_runno = sample_raw.getRunNumber()
- if base_runno < 568:
- INSTRUMENT.set_incident_mon(73730)
- orientation=SANSUtility.Orientation.Vertical
- if INSTRUMENT.cur_detector().name() == 'front-detector':
- SPECMIN = DIMENSION*DIMENSION + 1
- SPECMAX = DIMENSION*DIMENSION*2
- else:
- SPECMIN = 1
- SPECMAX = DIMENSION*DIMENSION
- elif (base_runno >= 568 and base_runno < 684):
- orientation = SANSUtility.Orientation.Rotated
- else:
- pass
-
- ############################# Setup workspaces ######################################
- monitorWS = "Monitor"
- montorSpecNum = INSTRUMENT.get_incident_mon()
- _printMessage('monitor ' + str(montorSpecNum), True)
- sample_name = sample_raw.getName()
- # Get the monitor ( StartWorkspaceIndex is off by one with cropworkspace)
- CropWorkspace(sample_name, monitorWS,
- StartWorkspaceIndex= montorSpecNum-1, EndWorkspaceIndex=montorSpecNum-1)
- if INSTRUMENT.name() == 'LOQ':
- RemoveBins(monitorWS, monitorWS, '19900', '20500',
- Interpolation="Linear")
-
- # Remove flat background
- if BACKMON_START != None and BACKMON_END != None:
- FlatBackground(monitorWS, monitorWS, StartX = BACKMON_START, EndX = BACKMON_END, WorkspaceIndexList = '0', Mode='Mean')
-
- final_result = run_setup.getReducedWorkspace()
- to_crop = sample_name
- if not NORMALISATION_FILE is None:
- if not NORMALISATION_FILE == "":
- to_crop = final_result
- CorrectToFile(sample_name, NORMALISATION_FILE, to_crop, 'SpectrumNumber', 'Divide')
-
- # Get the bank we are looking at
- CropWorkspace(to_crop, final_result,
- StartWorkspaceIndex = (SPECMIN - 1), EndWorkspaceIndex = str(SPECMAX - 1))
- #####################################################################################
-
- ########################## Masking ################################################
- # Mask the corners and beam stop if radius parameters are given
- maskpt_rmin = run_setup.getMaskPtMin()
- maskpt_rmax = run_setup.getMaskPtMax()
- if finding_centre == True:
- if RMIN > 0.0:
- SANSUtility.MaskInsideCylinder(final_result, RMIN, maskpt_rmin[0], maskpt_rmin[1])
- if RMAX > 0.0:
- SANSUtility.MaskOutsideCylinder(final_result, RMAX, maskpt_rmin[0], maskpt_rmin[1])
- else:
- if RMIN > 0.0:
- SANSUtility.MaskInsideCylinder(final_result, RMIN, maskpt_rmin[0], maskpt_rmin[1])
- if RMAX > 0.0:
- SANSUtility.MaskOutsideCylinder(final_result, RMAX, maskpt_rmax[0], maskpt_rmax[1])
-
- _applyMasking(final_result, SPECMIN, DIMENSION, INSTRUMENT, orientation)
- ####################################################################################
-
- ######################## Unit change and rebin #####################################
- # Convert all of the files to wavelength and rebin
- # ConvertUnits does have a rebin option, but it's crude. In particular it rebins on linear scale.
- ConvertUnits(monitorWS, monitorWS, "Wavelength")
- wavbin = str(wav_start) + "," + str(DWAV) + "," + str(wav_end)
- if INSTRUMENT.is_interpolating_norm() :
- InterpolatingRebin(monitorWS, monitorWS,wavbin)
- else :
- Rebin(monitorWS, monitorWS,wavbin)
-
- ConvertUnits(final_result,final_result,"Wavelength")
- Rebin(final_result,final_result,wavbin)
- ####################################################################################
-
- ####################### Correct by incident beam monitor ###########################
- # At this point need to fork off workspace name to keep a workspace containing raw counts
- tmpWS = "reduce_temp_workspace"
- Divide(final_result, monitorWS, tmpWS)
- mantid.deleteWorkspace(monitorWS)
- ###################################################################################
-
- ############################ Transmission correction ##############################
- trans_ws = CalculateTransmissionCorrection(run_setup, wav_start, wav_end, use_def_trans)
- if trans_ws != None:
- Divide(tmpWS, trans_ws, tmpWS)
- ##################################################################################
-
- ############################ Efficiency correction ################################
- if INSTRUMENT.lowAngDetSet :
- CorrectToFile(tmpWS, DIRECT_BEAM_FILE_R, tmpWS, "Wavelength", "Divide")
- else:
- CorrectToFile(tmpWS, DIRECT_BEAM_FILE_F, tmpWS, "Wavelength", "Divide")
- ###################################################################################
-
- ############################# Scale by volume #####################################
- scalefactor = RESCALE
- # Data reduced with Mantid is a factor of ~pi higher than colette.
- # For LOQ only, divide by this until we understand why.
- if INSTRUMENT.name() == 'LOQ':
- rescaleToColette = math.pi
- scalefactor /= rescaleToColette
-
- SANSUtility.ScaleByVolume(tmpWS, scalefactor, SAMPLE_GEOM, SAMPLE_WIDTH, SAMPLE_HEIGHT, SAMPLE_THICKNESS)
- ################################################## ################################
-
- ################################ Correction in Q space ############################
- # 1D
- if CORRECTION_TYPE == '1D':
- if finding_centre == True:
- GroupIntoQuadrants(tmpWS, final_result, maskpt_rmin[0], maskpt_rmin[1], Q_REBIN)
- return
- else:
- Q1D(tmpWS,final_result,final_result,Q_REBIN, AccountForGravity=GRAVITY)
- # 2D
- else:
- if finding_centre == True:
- raise Exception('Running center finding in 2D analysis is not possible, set1D() first.')
- # Run 2D algorithm
- Qxy(tmpWS, final_result, QXY2, DQXY)
-
- mantid.deleteWorkspace(tmpWS)
- return
-##END REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
-##REMOVED STEVE 08 September 2010 (ISISCommandInterface.py)
-# These variables keep track of the centre coordinates that have been used so that we can calculate a relative shift of the
-# detector
-XVAR_PREV = 0.0
-YVAR_PREV = 0.0
-ITER_NUM = 0
-RESIDUE_GRAPH = None
-
-# Create a workspace with a quadrant value in it
-def CreateQuadrant(reduced_ws, rawcount_ws, quadrant, xcentre, ycentre, q_bins, output):
- # Need to create a copy because we're going to mask 3/4 out and that's a one-way trip
- CloneWorkspace(reduced_ws,output)
- objxml = SANSUtility.QuadrantXML([xcentre, ycentre, 0.0], RMIN, RMAX, quadrant)
- # Mask out everything outside the quadrant of interest
- MaskDetectorsInShape(output,objxml)
- # Q1D ignores masked spectra/detectors. This is on the InputWorkspace, so we don't need masking of the InputForErrors workspace
- Q1D(output,rawcount_ws,output,q_bins,AccountForGravity=GRAVITY)
-
- flag_value = -10.0
- ReplaceSpecialValues(InputWorkspace=output,OutputWorkspace=output,NaNValue=flag_value,InfinityValue=flag_value)
- if CORRECTION_TYPE == '1D':
- SANSUtility.StripEndZeroes(output, flag_value)
-
-# Create 4 quadrants for the centre finding algorithm and return their names
-def GroupIntoQuadrants(reduced_ws, final_result, xcentre, ycentre, q_bins):
- tmp = 'quad_temp_holder'
- pieces = ['Left', 'Right', 'Up', 'Down']
- to_group = ''
- counter = 0
- for q in pieces:
- counter += 1
- to_group += final_result + '_' + str(counter) + ','
- CreateQuadrant(reduced_ws, final_result, q, xcentre, ycentre, q_bins, final_result + '_' + str(counter))
-
- # We don't need these now
- mantid.deleteWorkspace(reduced_ws)
-
-# Calcluate the sum squared difference of the given workspaces. This assumes that a workspace with
-# one spectrum for each of the quadrants. The order should be L,R,U,D.
-def CalculateResidue():
- global XVAR_PREV, YVAR_PREV, RESIDUE_GRAPH
- yvalsA = mtd.getMatrixWorkspace('Left').readY(0)
- yvalsB = mtd.getMatrixWorkspace('Right').readY(0)
- qvalsA = mtd.getMatrixWorkspace('Left').readX(0)
- qvalsB = mtd.getMatrixWorkspace('Right').readX(0)
- qrange = [len(yvalsA), len(yvalsB)]
- nvals = min(qrange)
- residueX = 0
- indexB = 0
- for indexA in range(0, nvals):
- if qvalsA[indexA] < qvalsB[indexB]:
- mantid.sendLogMessage("::SANS::LR1 "+str(indexA)+" "+str(indexB))
- continue
- elif qvalsA[indexA] > qvalsB[indexB]:
- while qvalsA[indexA] > qvalsB[indexB]:
- mantid.sendLogMessage("::SANS::LR2 "+str(indexA)+" "+str(indexB))
- indexB += 1
- if indexA > nvals - 1 or indexB > nvals - 1:
- break
- residueX += pow(yvalsA[indexA] - yvalsB[indexB], 2)
- indexB += 1
-
- yvalsA = mtd.getMatrixWorkspace('Up').readY(0)
- yvalsB = mtd.getMatrixWorkspace('Down').readY(0)
- qvalsA = mtd.getMatrixWorkspace('Up').readX(0)
- qvalsB = mtd.getMatrixWorkspace('Down').readX(0)
- qrange = [len(yvalsA), len(yvalsB)]
- nvals = min(qrange)
- residueY = 0
- indexB = 0
- for indexA in range(0, nvals):
- if qvalsA[indexA] < qvalsB[indexB]:
- mantid.sendLogMessage("::SANS::UD1 "+str(indexA)+" "+str(indexB))
- continue
- elif qvalsA[indexA] > qvalsB[indexB]:
- while qvalsA[indexA] > qvalsB[indexB]:
- mantid.sendLogMessage("::SANS::UD2 "+str(indexA)+" "+str(indexB))
- indexB += 1
- if indexA > nvals - 1 or indexB > nvals - 1:
- break
- residueY += pow(yvalsA[indexA] - yvalsB[indexB], 2)
- indexB += 1
-
- try :
- if RESIDUE_GRAPH is None or (not RESIDUE_GRAPH in appwidgets()):
- RESIDUE_GRAPH = plotSpectrum('Left', 0)
- mergePlots(RESIDUE_GRAPH, plotSpectrum(['Right','Up'],0))
- mergePlots(RESIDUE_GRAPH, plotSpectrum(['Down'],0))
- RESIDUE_GRAPH.activeLayer().setTitle("Itr " + str(ITER_NUM)+" "+str(XVAR_PREV*1000.)+","+str(YVAR_PREV*1000.)+" SX "+str(residueX)+" SY "+str(residueY))
- except :
- #if plotting is not available it probably means we are running outside a GUI, in which case do everything but don't plot
- pass
-
- mantid.sendLogMessage("::SANS::Itr: "+str(ITER_NUM)+" "+str(XVAR_PREV*1000.)+","+str(YVAR_PREV*1000.)+" SX "+str(residueX)+" SY "+str(residueY))
- return residueX, residueY
-##END REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
-def RunReduction(coords):
- '''Compute the value of (L-R)^2+(U-D)^2 a circle split into four quadrants'''
- global XVAR_PREV, YVAR_PREV
- xcentre = coords[0]
- ycentre= coords[1]
-
- xshift = -xcentre + XVAR_PREV
- yshift = -ycentre + YVAR_PREV
- XVAR_PREV = xcentre
- YVAR_PREV = ycentre
-
- # Do the correction
- if xshift != 0.0 or yshift != 0.0:
- currentDet = INSTRUMENT.cur_detector().name()
- MoveInstrumentComponent(SCATTER_SAMPLE.getName(),
- ComponentName=currentDet, X=xshift, Y=yshift, RelativePosition="1")
- if SCATTER_CAN.getName() != '':
- MoveInstrumentComponent(SCATTER_CAN.getName(),
- ComponentName=currentDet, X=xshift, Y=yshift, RelativePosition="1")
-##START REMOVED
- _SAMPLE_SETUP.setMaskPtMin([0.0,0.0])
- _SAMPLE_SETUP.setMaskPtMax([xcentre, ycentre])
- if _CAN_SETUP != None:
- _CAN_SETUP.setMaskPtMin([0.0, 0.0])
- _CAN_SETUP.setMaskPtMax([xcentre, ycentre])
-##END REMOVED
-
- WavRangeReduction(WAV1, WAV2, DefaultTrans, finding_centre = True)
- return CalculateResidue()
-
-def FindBeamCentre(rlow, rupp, MaxIter = 10, xstart = None, ystart = None):
- global XVAR_PREV, YVAR_PREV, ITER_NUM, RMIN, RMAX, XBEAM_CENTRE, YBEAM_CENTRE
- RMIN = float(rlow)/1000.
- RMAX = float(rupp)/1000.
-
- if xstart == None or ystart == None:
- XVAR_PREV = XBEAM_CENTRE
- YVAR_PREV = YBEAM_CENTRE
- else:
- XVAR_PREV = xstart
- YVAR_PREV = ystart
-
- mantid.sendLogMessage("::SANS:: xstart,ystart="+str(XVAR_PREV*1000.)+" "+str(YVAR_PREV*1000.))
- _printMessage("Starting centre finding routine ...")
- # Initialize the workspace with the starting coordinates. (Note that this moves the detector to -x,-y)
- _initReduction(XVAR_PREV, YVAR_PREV)
-
- ITER_NUM = 0
- # Run reduction, returning the X and Y sum-squared difference values
- _printMessage("Running initial reduction: " + str(XVAR_PREV*1000.)+ " "+ str(YVAR_PREV*1000.))
- oldX2,oldY2 = RunReduction([XVAR_PREV, YVAR_PREV])
- XSTEP = INSTRUMENT.cen_find_step
- YSTEP = INSTRUMENT.cen_find_step
-
- # take first trial step
- XNEW = XVAR_PREV + XSTEP
- YNEW = YVAR_PREV + YSTEP
- for ITER_NUM in range(1, MaxIter+1):
- _printMessage("Iteration " + str(ITER_NUM) + ": " + str(XNEW*1000.)+ " "+ str(YNEW*1000.))
- newX2,newY2 = RunReduction([XNEW, YNEW])
- if newX2 > oldX2:
- XSTEP = -XSTEP/2.
- if newY2 > oldY2:
- YSTEP = -YSTEP/2.
- if abs(XSTEP) < 0.1251/1000. and abs(YSTEP) < 0.1251/1000. :
- _printMessage("::SANS:: Converged - check if stuck in local minimum!")
- break
- oldX2 = newX2
- oldY2 = newY2
- XNEW += XSTEP
- YNEW += YSTEP
-
- if ITER_NUM == MaxIter:
- _printMessage("::SANS:: Out of iterations, new coordinates may not be the best!")
- XNEW -= XSTEP
- YNEW -= YSTEP
-
-
- XBEAM_CENTRE = XNEW
- YBEAM_CENTRE = YNEW
- _printMessage("Centre coordinates updated: [" + str(XBEAM_CENTRE*1000.)+ ","+ str(YBEAM_CENTRE*1000.) + ']')
-
- # Reload the sample and can and reset the radius range
- global _SAMPLE_SETUP
- _assignHelper(_SAMPLE_RUN, False, PERIOD_NOS["SCATTER_SAMPLE"])
- _SAMPLE_SETUP = None
- if _CAN_RUN != '':
- _assignHelper(_CAN_RUN, False, PERIOD_NOS["SCATTER_CAN"])
- global _CAN_SETUP
- _CAN_SETUP = None
-
- RMIN = DEF_RMIN
- RMAX = DEF_RMAX
-##START REMOVED STEVE 08 September 2010 (ISISCommandInterface.py)
-##
-# Plot the results on the correct type of plot
-##
-def PlotResult(workspace):
- if CORRECTION_TYPE == '1D':
- plotSpectrum(workspace,0)
- else:
- qti.app.mantidUI.importMatrixWorkspace(workspace).plotGraph2D()
-
-##################### View mask details #####################################################
-
-def ViewCurrentMask():
- inst_name = INSTRUMENT.name()
- top_layer = 'CurrentMask'
- inst = eval('SANSInsts.'+inst_name+'("'+top_layer+'")')
-
- if RMIN > 0.0:
- SANSUtility.MaskInsideCylinder(top_layer, RMIN, XBEAM_CENTRE, YBEAM_CENTRE)
- if RMAX > 0.0:
- SANSUtility.MaskOutsideCylinder(top_layer, RMAX, 0.0, 0.0)
-
- dimension = SANSUtility.GetInstrumentDetails(inst)[0]
-
- #_applyMasking() must be called on both detectors, the detector is specified by passing the index of it's first spectrum
- #start with the currently selected detector
- firstSpec1 = inst.cur_detector().get_first_spec_num()
- _applyMasking(top_layer, firstSpec1, dimension, inst, SANSUtility.Orientation.Horizontal, False, True)
- #now the other detector
- firstSpec2 = inst.other_detector().get_first_spec_num()
- _applyMasking(top_layer, firstSpec2, dimension, inst, SANSUtility.Orientation.Horizontal, False, False)
-
- # Mark up "dead" detectors with error value
- FindDeadDetectors(top_layer, top_layer, DeadValue=500)
-
- # Visualise the result
- instrument_win = qti.app.mantidUI.getInstrumentView(top_layer)
- instrument_win.showWindow()
-
-############################################################################################################################
-
-############################################################################################
-# Print a test script for Colette if asked
-def createColetteScript(inputdata, format, reduced, centreit , plotresults, csvfile = '', savepath = ''):
- script = ''
- if csvfile != '':
- script += '[COLETTE] @ ' + csvfile + '\n'
- file_1 = inputdata['sample_sans'] + format
- script += '[COLETTE] ASSIGN/SAMPLE ' + file_1 + '\n'
- file_1 = inputdata['sample_trans'] + format
- file_2 = inputdata['sample_direct_beam'] + format
- if file_1 != format and file_2 != format:
- script += '[COLETTE] TRANSMISSION/SAMPLE/MEASURED ' + file_1 + ' ' + file_2 + '\n'
- file_1 = inputdata['can_sans'] + format
- if file_1 != format:
- script +='[COLETTE] ASSIGN/CAN ' + file_1 + '\n'
- file_1 = inputdata['can_trans'] + format
- file_2 = inputdata['can_direct_beam'] + format
- if file_1 != format and file_2 != format:
- script += '[COLETTE] TRANSMISSION/CAN/MEASURED ' + file_1 + ' ' + file_2 + '\n'
- if centreit:
- script += '[COLETTE] FIT/MIDDLE'
- # Parameters
- script += '[COLETTE] LIMIT/RADIUS ' + str(RMIN) + ' ' + str(RMAX) + '\n'
- script += '[COLETTE] LIMIT/WAVELENGTH ' + str(WAV1) + ' ' + str(WAV2) + '\n'
- if DWAV < 0:
- script += '[COLETTE] STEP/WAVELENGTH/LOGARITHMIC ' + str(DWAV)[1:] + '\n'
- else:
- script += '[COLETTE] STEP/WAVELENGTH/LINEAR ' + str(DWAV) + '\n'
- # For the moment treat the rebin string as min/max/step
- qbins = q_REBEIN.split(",")
- nbins = len(qbins)
- if CORRECTION_TYPE == '1D':
- script += '[COLETTE] LIMIT/Q ' + str(qbins[0]) + ' ' + str(qbins[nbins-1]) + '\n'
- dq = float(qbins[1])
- if dq < 0:
- script += '[COLETTE] STEP/Q/LOGARITHMIC ' + str(dq)[1:] + '\n'
- else:
- script += '[COLETTE] STEP/Q/LINEAR ' + str(dq) + '\n'
- else:
- script += '[COLETTE] LIMIT/QXY ' + str(0.0) + ' ' + str(QXY2) + '\n'
- if DQXY < 0:
- script += '[COLETTE] STEP/QXY/LOGARITHMIC ' + str(DQXY)[1:] + '\n'
- else:
- script += '[COLETTE] STEP/QXY/LINEAR ' + str(DQXY) + '\n'
-
- # Correct
- script += '[COLETTE] CORRECT\n'
- if plotresults:
- script += '[COLETTE] DISPLAY/HISTOGRAM ' + reduced + '\n'
- if savepath != '':
- script += '[COLETTE] WRITE/LOQ ' + reduced + ' ' + savepath + '\n'
-
- return script
-##END REMOVED STEVE 13 September 2010 (ISISCommandInterface.py)
diff --git a/Code/Mantid/scripts/SANS/isis_reducer.py b/Code/Mantid/scripts/SANS/isis_reducer.py
index 6b4818a7de80b43f84594803911b16624ff6761c..8c11c225919b9093d1991c1f55365c5cca8a6765 100644
--- a/Code/Mantid/scripts/SANS/isis_reducer.py
+++ b/Code/Mantid/scripts/SANS/isis_reducer.py
@@ -77,7 +77,7 @@ class ISISReducer(SANSReducer):
proc_wav = [self.norm_mon]
proc_wav.append(self.transmission_calculator)
proc_wav.append(self._corr_and_scale)
- proc_wav.append(self._geo_corr)
+ proc_wav.append(self.geometry_correcter)
self._can = [self.background_subtracter]
@@ -115,7 +115,7 @@ class ISISReducer(SANSReducer):
self.to_Q = sans_reduction_steps.ConvertToQ(
self.prep_normalize)
self.background_subtracter = None
- self._geo_corr = sans_reduction_steps.SampleGeomCor(
+ self.geometry_correcter = sans_reduction_steps.SampleGeomCor(
self._sample_run.geometry)
# self._zero_error_flags=isis_reduction_steps.ReplaceErrors()
self._rem_nans = sans_reduction_steps.StripEndNans()