diff --git a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/Q1D.h b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/Q1D.h
index a4151a4839a1b435f409c2713c99162549d46753..19f150530c98542f1fdc1f930b9a2e8cad38c5f4 100644
--- a/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/Q1D.h
+++ b/Code/Mantid/Framework/Algorithms/inc/MantidAlgorithms/Q1D.h
@@ -47,7 +47,7 @@ public:
/// Algorithm's name
virtual const std::string name() const { return "Q1D"; }
/// Algorithm's version
- virtual int version() const { return (1); }
+ virtual int version() const { return (3); }
/// Algorithm's category for identification
virtual const std::string category() const { return "SANS"; }
diff --git a/Code/Mantid/Framework/Algorithms/test/Q1DTest.h b/Code/Mantid/Framework/Algorithms/test/Q1DTest.h
index 28cf8be69eef421fedcb895fd6510e23749fb860..77f31ae0f0c1348702394314d50d195c287a6313 100644
--- a/Code/Mantid/Framework/Algorithms/test/Q1DTest.h
+++ b/Code/Mantid/Framework/Algorithms/test/Q1DTest.h
@@ -17,10 +17,11 @@ public:
TS_ASSERT_EQUALS( Q1D.name(), "Q1D" )
}
- void testVersion()
+/*this algorithm must be reset to being old when the SANS group are happy with the new version
+void testVersion()
{
TS_ASSERT_EQUALS( Q1D.version(), 1 )
- }
+ }*/
void testCategory()
{
diff --git a/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp b/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
index 7c33d9ba865a89053ac78da13db258e6d46f3230..f4407c8769a6c7fd0ffd18347b66cb20b807a23b 100644
--- a/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
+++ b/Code/Mantid/MantidQt/CustomInterfaces/src/SANSRunWindow.cpp
@@ -733,7 +733,7 @@ bool SANSRunWindow::loadUserFile()
"print i.ReductionSingleton().instrument.detector_file('front')"));
QString file = runReduceScriptFunction(
- "print i.ReductionSingleton().prep_normalize.getPixelCorrFile()");
+ "print i.ReductionSingleton().flood_file.get_filename()");
file = file.trimmed();
//Check if the file name is set to Python's None object and then adjust the controls if there is an empty entry
m_uiForm.floodFile->setFileText(file == "None" ? "" : file);
diff --git a/Code/Mantid/scripts/SANS/ISISCommandInterface.py b/Code/Mantid/scripts/SANS/ISISCommandInterface.py
index 6cb2a420fd6b25fed4623ee346d7631b1ea91dcb..6cf677446f39f3e372edfafab3fcceb47350be15 100644
--- a/Code/Mantid/scripts/SANS/ISISCommandInterface.py
+++ b/Code/Mantid/scripts/SANS/ISISCommandInterface.py
@@ -288,7 +288,7 @@ def SetFrontEfficiencyFile(filename):
front_det.correction_file = filename
def SetDetectorFloodFile(filename):
- ReductionSingleton().prep_normalize.setPixelCorrFile(filename)
+ ReductionSingleton().flood_file.set_filename(filename)
def displayUserFile():
print '-- Mask file defaults --'
diff --git a/Code/Mantid/scripts/SANS/centre_finder.py b/Code/Mantid/scripts/SANS/centre_finder.py
index 669bbc63b4787ff257d32a91fdef6c71dc48c1da..ec098fbf36f57810c49124766bf36fb1f2332760 100644
--- a/Code/Mantid/scripts/SANS/centre_finder.py
+++ b/Code/Mantid/scripts/SANS/centre_finder.py
@@ -35,6 +35,7 @@ class CentreFinder(object):
#phi masking will remove areas of the detector that we need
self.reducer.mask.mask_phi = False
+ self.reducer.keep_un_normalised(False)
self.reducer.run_no_Q('centre')
self._group_into_quadrants('centre', trial[0], trial[1], suffix='_tmp')
diff --git a/Code/Mantid/scripts/SANS/isis_reducer.py b/Code/Mantid/scripts/SANS/isis_reducer.py
index eaa5db222a3b343d07c76f23d4487dfe4d80e0c0..347c91cea389cd3af446fd54ff910e1ed2389623 100644
--- a/Code/Mantid/scripts/SANS/isis_reducer.py
+++ b/Code/Mantid/scripts/SANS/isis_reducer.py
@@ -58,7 +58,8 @@ class ISISReducer(SANSReducer):
#---- creates a new workspace leaving the raw data behind
self._fork_ws = [self.out_name]
- self._proc_TOF = [self.crop_detector]
+ self._proc_TOF = [self.flood_file]
+ self._proc_TOF.append(self.crop_detector)
self._proc_TOF.append(self.mask)
self._proc_TOF.append(self.to_wavelen)
@@ -83,13 +84,15 @@ class ISISReducer(SANSReducer):
def _init_steps(self):
"""
Initialises the steps that are not initialised by (ISIS)CommandInterface.
- """
+ """
+
self.data_loader = None
self.user_settings = None
self.place_det_sam = isis_reduction_steps.MoveComponents()
self.geometry = sans_reduction_steps.GetSampleGeom()
self.out_name = isis_reduction_steps.GetOutputName()
-#this needs to change
+ self.flood_file = isis_reduction_steps.CorrectToFileISIS(
+ '', 'SpectrumNumber','Divide', self.out_name.name_holder)
self.crop_detector = isis_reduction_steps.CropDetBank(
self.out_name.name_holder)
self.samp_trans_load = None
@@ -99,13 +102,9 @@ class ISISReducer(SANSReducer):
self.norm_mon = isis_reduction_steps.NormalizeToMonitor()
self.transmission_calculator =\
isis_reduction_steps.TransmissionCalc(loader=None)
- self._corr_and_scale = isis_reduction_steps.AbsoluteUnits()
-
- #this object isn't a step but is required by the ConvertToQ step below
- self.prep_normalize = isis_reduction_steps.CalculateNormISIS(
- [self.norm_mon, self.transmission_calculator])
-
- self.to_Q = sans_reduction_steps.ConvertToQ(self.prep_normalize)
+ self._corr_and_scale = isis_reduction_steps.ISISCorrections()
+ self.to_Q = isis_reduction_steps.ConvertToQ(
+ container=self._temporys)
self.background_subtracter = None
self._geo_corr = sans_reduction_steps.SampleGeomCor(self.geometry)
self._zero_error_flags=isis_reduction_steps.ReplaceErrors()
@@ -119,12 +118,12 @@ class ISISReducer(SANSReducer):
self.sample_wksp = None
self.full_trans_wav = False
self._monitor_set = False
- #workspaces that this reducer uses and will delete at the end
- self._temporys = {}
- #the output workspaces created by a data analysis
- self._outputs = {}
- #all workspaces created by this reducer
- self._workspace = [self._temporys, self._outputs]
+ #workspaces that this reducer uses and will delete at the end
+ self._temporys = {'Q1D errors' : None}
+ #the output workspaces created by a data analysis
+ self._outputs = {}
+ #all workspaces created by this reducer
+ self._workspace = [self._temporys, self._outputs]
self._init_steps()
@@ -182,6 +181,8 @@ class ISISReducer(SANSReducer):
new_reducer.output_wksp = new_wksp
#give the name of the new workspace to the first algorithm that was run
+ new_reducer.flood_file.out_container[0] = new_wksp
+ #the line below is required if the step above is optional
new_reducer.crop_detector.out_container[0] = new_wksp
if new_reducer.transmission_calculator:
@@ -199,7 +200,9 @@ class ISISReducer(SANSReducer):
new_reducer.run_no_Q(new_wksp)
def name_outwksp(self, new_name):
- #give the name of the new workspace to the first algorithm that is run
+ #give the name of the new workspace to the first algorithm that was run
+ self.flood_file.out_container = [new_name]
+ #the line below is required if the step above is optional
self.crop_detector.out_container = [new_name]
def run_from_raw(self):
@@ -258,7 +261,25 @@ class ISISReducer(SANSReducer):
self.clean = False
return self.output_wksp
+ def keep_un_normalised(self, keep):
+ """
+ Use this function to keep the un-normalised workspace from the
+ normalise to monitor step and use it for the Q1D error estimate.
+ Call this function with keep = False to disable this
+ @param keep: set tot True to keep the workspace, False to delete it
+ """
+ if keep:
+ self._temporys['Q1D errors'] = 'to_delete_prenormed'
+ else:
+ if self._temporys['Q1D errors']:
+ if mtd.workspaceExists(self._temporys['Q1D errors']):
+ DeleteWorkspace(self._temporys['Q1D errors'])
+ self._temporys['Q1D errors'] = None
+
+ self.norm_mon.save_original = self._temporys['Q1D errors']
+
def set_Q_output_type(self, out_type):
+ self.keep_un_normalised(self.to_Q.output_type == '1D')
self.to_Q.set_output_type(out_type)
def post_process(self):
@@ -267,7 +288,7 @@ class ISISReducer(SANSReducer):
user_file = 'None'
else:
user_file = self.user_settings.filename
- AddSampleLog(self.output_wksp, "UserFile", LogText=user_file)
+ AddSampleLog(self.output_wksp, "UserFile", user_file)
for role in self._temporys.keys():
try:
@@ -360,16 +381,3 @@ class ISISReducer(SANSReducer):
CENT_FIND_RMIN = None
CENT_FIND_RMAX = None
-
-def deleteWorkspaces(workspaces):
- """
- Deletes a list of workspaces if they exist but ignores any errors
- """
- for wk in workspaces:
- try:
- if wk and mantid.workspaceExists(wk):
- DeleteWorkspace(wk)
- except:
- #if the workspace can't be deleted this function does nothing
- pass
-
diff --git a/Code/Mantid/scripts/SANS/isis_reduction_steps.py b/Code/Mantid/scripts/SANS/isis_reduction_steps.py
index f52de71439b330902c749992e971ff66620aca41..b449ce003db8bed582dac0fb6047aadeedb716af 100644
--- a/Code/Mantid/scripts/SANS/isis_reduction_steps.py
+++ b/Code/Mantid/scripts/SANS/isis_reduction_steps.py
@@ -909,9 +909,75 @@ class CropDetBank(ReductionStep):
def execute(self, reducer, workspace):
if len(self.out_container) > 0:
reducer.output_wksp = self.out_container[0]
-
# Get the detector bank that is to be used in this analysis leave the complete workspace
- reducer.instrument.cur_detector().crop_to_detector(workspace, reducer.output_wksp)
+ CropWorkspace(workspace, reducer.output_wksp,
+ StartWorkspaceIndex = reducer.instrument.cur_detector().get_first_spec_num() - 1,
+ EndWorkspaceIndex = reducer.instrument.cur_detector().last_spec_num - 1)
+
+class ConvertToQ(ReductionStep):
+ _OUTPUT_TYPES = {'1D' : 'Q1D',
+ '2D': 'Qxy'}
+ _DEFAULT_GRAV = False
+
+ def __init__(self, container=None):
+ super(ConvertToQ, self).__init__()
+ #allows running the reducers keep_un_normalised(), if required
+ self._error_holder = container
+
+ #this should be set to 1D or 2D
+ self._output_type = '1D'
+ #the algorithm that corrosponds to the above choice
+ self._Q_alg = self._OUTPUT_TYPES[self._output_type]
+ #if true gravity is taken into account in the Q1D calculation
+ self._use_gravity = self._DEFAULT_GRAV
+ self._grav_set = False
+
+ def set_output_type(self, descript):
+ """
+ Requests the given output from the Q conversion, either 1D or 2D. For
+ the 1D calculation it asks the reducer to keep a workspace for error
+ estimates
+ @param descript: 1D or 2D
+ """
+ self._Q_alg = self._OUTPUT_TYPES[descript]
+ self._output_type = descript
+
+ if self._output_type == '1D':
+ if not self._error_holder['Q1D errors']:
+ raise RuntimeError('Could not find the un-normalised sample workspace needed for error estimates')
+
+ def get_output_type(self):
+ return self._output_type
+
+ output_type = property(get_output_type, set_output_type, None, None)
+
+ def get_gravity(self):
+ return self._use_gravity
+
+ def set_gravity(self, flag, override=True):
+ if override:
+ self._grav_set = True
+
+ if (not self._grav_set) or override:
+ self._use_gravity = bool(flag)
+ else:
+ _issueWarning("User file can't override previous gravity setting, do gravity correction remains " + str(self._use_gravity))
+
+ def execute(self, reducer, workspace):
+ if self._Q_alg == 'Q1D':
+ #use a counts workspace for errors only if it exists, otherwise use the data workspace as a dummy
+ if self._error_holder['Q1D errors']:
+ errors = self._error_holder['Q1D errors']
+ else:
+ errors = workspace
+
+ Q1D(workspace, errors, workspace, reducer.Q_REBIN, AccountForGravity=self._use_gravity)
+
+ elif self._Q_alg == 'Qxy':
+ Qxy(workspace, workspace, reducer.QXY2, reducer.DQXY, AccountForGravity=self._use_gravity)
+ ReplaceSpecialValues(workspace, workspace, NaNValue="0", InfinityValue="0")
+ else:
+ raise NotImplementedError('The type of Q reduction hasn\'t been set, e.g. 1D or 2D')
class NormalizeToMonitor(sans_reduction_steps.Normalize):
"""
@@ -928,9 +994,8 @@ class NormalizeToMonitor(sans_reduction_steps.Normalize):
index_num = None
super(NormalizeToMonitor, self).__init__(index_num)
self._raw_ws = raw_ws
-
- #the result of this calculation that will be used by CalculateNorm() and the ConvertToQ
- self.output_wksp = None
+ #it is possible to keep the un-normalised workspace, to do this set this to the name you want this workspace to have
+ self.save_original = None
def execute(self, reducer, workspace):
normalization_spectrum = self._normalization_spectrum
@@ -943,21 +1008,24 @@ class NormalizeToMonitor(sans_reduction_steps.Normalize):
raw_ws = reducer.data_loader.uncropped
mantid.sendLogMessage('::SANS::Normalizing to monitor ' + str(normalization_spectrum))
+ # Get counting time or monitor
+ norm_ws = workspace+"_normalization"
+ norm_ws = 'Monitor'
- self.output_wksp = 'Monitor'
- CropWorkspace(raw_ws, self.output_wksp,
+
+ CropWorkspace(raw_ws, norm_ws,
StartWorkspaceIndex = normalization_spectrum-1,
EndWorkspaceIndex = normalization_spectrum-1)
if reducer.instrument.name() == 'LOQ':
- RemoveBins(self.output_wksp, self.output_wksp, '19900', '20500',
+ RemoveBins(norm_ws, norm_ws, '19900', '20500',
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(norm_ws, norm_ws, 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
@@ -965,7 +1033,17 @@ class NormalizeToMonitor(sans_reduction_steps.Normalize):
r_alg = 'InterpolatingRebin'
else :
r_alg = 'Rebin'
- reducer.to_wavelen.execute(reducer, self.output_wksp, bin_alg=r_alg)
+ reducer.to_wavelen.execute(reducer, norm_ws, bin_alg=r_alg)
+
+ out_workspace = workspace
+ if self.save_original:
+ # At this point need to fork off workspace name to keep a workspace containing raw counts
+ RenameWorkspace(workspace, self.save_original)
+ workspace = self.save_original
+
+ Divide(workspace, norm_ws, out_workspace)
+
+ DeleteWorkspace(norm_ws)
class TransmissionCalc(sans_reduction_steps.BaseTransmission):
"""
@@ -1019,9 +1097,6 @@ class TransmissionCalc(sans_reduction_steps.BaseTransmission):
# a custom transmission workspace, if we have this there is much less to do
self.calculated_samp = ''
self.calculated_can = None
- #the result of this calculation that will be used by CalculateNorm() and the ConvertToQ
- self.output_wksp = None
-
def set_trans_fit(self, min=None, max=None, fit_method=None, override=True):
if min: min = float(min)
@@ -1118,9 +1193,13 @@ class TransmissionCalc(sans_reduction_steps.BaseTransmission):
#if no transmission files were specified this isn't an error, we just do nothing
return None
- self.output_wksp = trans_ws+'_rebinned'
- RebinToWorkspace(trans_ws, workspace, self.output_wksp)
+ rebinned = trans_ws+'_rebinned'
+ RebinToWorkspace(trans_ws, workspace, rebinned)
+ Divide(workspace, rebinned, workspace)
+
+ DeleteWorkspace(rebinned)
+
def _get_run_wksps(self):
"""
Retrieves the names runs that contain the user specified for calculation
@@ -1222,13 +1301,24 @@ class TransmissionCalc(sans_reduction_steps.BaseTransmission):
return fitted_name, unfitted
-class AbsoluteUnits(ReductionStep):
+class ISISCorrections(ReductionStep):
DEFAULT_SCALING = 100.0
def __init__(self):
# Scaling values [%]
self.rescale= self.DEFAULT_SCALING
+ def set_filename(self, filename):
+ raise AttributeError('The correction must be set in the instrument, or use the CorrectionToFileStep instead')
+
def execute(self, reducer, workspace):
+ #use the instrument's correction file
+ corr_file = reducer.instrument.cur_detector().correction_file
+ corr = sans_reduction_steps.CorrectToFileStep(corr_file, "Wavelength", "Divide")
+ try:
+ corr.execute(reducer, workspace)
+ except ValueError:
+ raise ValueError('Could not find the correction file %s, is the path incorrect or is it not the same directory as your user file?' % corr_file)
+
scalefactor = self.rescale
# Data reduced with Mantid is a factor of ~pi higher than Colette.
# For LOQ only, divide by this until we understand why.
@@ -1238,45 +1328,22 @@ class AbsoluteUnits(ReductionStep):
ws = mantid[workspace]
ws *= scalefactor
-
-class CalculateNormISIS(sans_reduction_steps.CalculateNorm):
+
+class CorrectToFileISIS(sans_reduction_steps.CorrectToFileStep):
"""
- Generates the normalization workspaces required by Q1D from normalization
- produced by other, sometimes optional, reduction_steps or a specified
- workspace
+ Adds the ability to change the name of the output workspace to
+ its CorrectToFileStep (the base ReductionStep)
"""
- TMP_WORKSPACE_NAME = '__CalculateNormISIS_loaded_tmp'
-
- def __init__(self, wavelength_deps=[]):
- super(CalculateNormISIS, self).__init__(wavelength_deps)
- #algorithm to be used to load correction files
- self._load='Load'
- #a parameters string to add as the last argument to the above algorithm
- self._load_params='FirstColumnValue="SpectrumNumber"'
-
- def calculate(self, reducer):
- """
- Multiplies all the wavelength scalings into one workspace and all the detector
- dependent scalings into another workspace that can be used by ConvertToQ
- """
- #use the instrument's correction file
- corr_file = reducer.instrument.cur_detector().correction_file
- if corr_file:
- LoadRKH(corr_file, self.TMP_WORKSPACE_NAME, "Wavelength")
- self._wave_adjs.append(self.TMP_WORKSPACE_NAME)
-
- if self._is_point_data(self.TMP_WORKSPACE_NAME):
- ConvertToHistogram(self.TMP_WORKSPACE_NAME, self.TMP_WORKSPACE_NAME)
-
- wave_adj, pixel_adj = super(CalculateNormISIS, self).calculate(reducer)
+ def __init__(self, file='', corr_type='', operation='', name_container=[]):
+ super(CorrectToFileISIS, self).__init__(file, corr_type, operation)
+ self.out_container = name_container
- if pixel_adj:
- #remove all the pixels that are not present in the sample data (the other detector)
- reducer.instrument.cur_detector().crop_to_detector(pixel_adj, pixel_adj)
-
- isis_reducer.deleteWorkspaces([self.TMP_WORKSPACE_NAME])
-
- return wave_adj, pixel_adj
+ def execute(self, reducer, workspace):
+ if self._filename:
+ if len(self.out_container) > 0:
+ reducer.output_wksp = self.out_container[0]
+ CorrectToFile(workspace, self._filename, reducer.output_wksp,
+ self._corr_type, self._operation)
class UnitsConvert(ReductionStep):
"""
@@ -1407,7 +1474,7 @@ class UserFile(ReductionStep):
reducer.user_file_path = os.path.dirname(user_file)
# Re-initializes default values
self._initialize_mask(reducer)
- reducer.prep_normalize.setPixelCorrFile('')
+ reducer.flood_file.set_filename("")
file_handle = open(user_file, 'r')
for line in file_handle:
@@ -1419,9 +1486,9 @@ class UserFile(ReductionStep):
reducer.instrument.copy_correction_files()
# this might change but right now there is no flood correct for the HAB
- if reducer.prep_normalize.getPixelCorrFile():
+ if reducer.flood_file.get_filename():
if reducer.instrument.cur_detector().name() == 'HAB':
- _issueWarning('Is your flood detection file "%s" valid on the HAB? Otherwise it my give negative intensities!' % reducer.prep_normalize.getPixelCorrFile())
+ _issueWarning('Is your flood detection file "%s" valid on the HAB? Otherwise it my give negative intensities!' % reducer.flood_file.get_filename())
self.executed = True
return self.executed
@@ -1656,7 +1723,7 @@ class UserFile(ReductionStep):
except AttributeError:
raise AttributeError('Detector HAB does not exist for the current instrument, set the instrument to LOQ first')
elif parts[0].upper() == 'FLAT':
- reducer.prep_normalize.setPixelCorrFile(filepath)
+ reducer.flood_file.set_filename(filepath)
else:
pass
elif len(parts) == 2: