""" Conversion class defined for conversion to deltaE for 'direct' inelastic geometry instruments The class defines various methods to allow users to convert their files to DeltaE. Example: Assuming we have the follwing data files for MARI. NOTE: This assumes that the data path for these runs is in the Mantid preferences. mono-sample: 11015 white: 11060 mono-van: 11001 with sample mass 10g and RMM 435.96 reducer = DirectEnergyConversion('MARI') # Alter defaults if necessary reducer.normalise_method = 'monitor-2' reducer.background = False reducer.fix_ei = True reducer.save_formats = ['.spe'] # Set parameters for these runs reducer.map_file = 'mari_res.map' reducer.energy_bins = '-10,0.1,80' Run the conversion deltaE_wkspace = reducer.convert_to_energy(11015, 85, 11060, 11001) """ import CommonFunctions as common import diagnostics from mantidsimple import * import glob import os.path def setup_reducer(inst_name): """ Given an instrument name or prefix this sets up a converter object for the reduction """ try: return DirectEnergyConversion(inst_name) except RuntimeError: raise RuntimeError('Unknown instrument "%s", cannot continue' % inst_name) class DirectEnergyConversion(object): """ Performs a convert to energy assuming the provided instrument is an elastic instrument """ def diagnose(self, white_run, sample_run=None, other_white=None, remove_zero=None, tiny=None, large=None, median_lo=None, median_hi=None, signif=None, bkgd_threshold=None, bkgd_range=None, variation=None, hard_mask=None, print_results=False): """ A pass through method to the 'real' one in diagnostics.py Run diagnostics on the provided run and white beam files. There are 3 possible tests, depending on the input given: White beam diagnosis Background tests Second white beam Required inputs: white_run - The run number or filepath of the white beam run Optional inputs: sample_run - The run number or filepath of the sample run for the background test (default = None) other_white - If provided an addional set of tests is performed on this file. (default = None) remove_zero - If true then zeroes in the data will count as failed (default = False) tiny - Minimum threshold for acceptance (default = 1e-10) large - Maximum threshold for acceptance (default = 1e10) median_lo - Fraction of median to consider counting low (default = 0.1) median_hi - Fraction of median to consider counting high (default = 3.0) signif - Counts within this number of multiples of the standard dev will be kept (default = 3.3) bkgd_threshold - High threshold for background removal in multiples of median (default = 5.0) bkgd_range - The background range as a list of 2 numbers: [min,max]. If not present then they are taken from the parameter file. (default = None) variation - The number of medians the ratio of the first/second white beam can deviate from the average by (default=1.1) hard_mask - A file specifying those spectra that should be masked without testing print_results - If True then the results are printed to std out inst_name - The name of the instrument to perform the diagnosis. If it is not provided then the default instrument is used (default = None) """ return diagnostics.diagnose(white_run, sample_run, other_white, remove_zero, tiny, large, median_lo, median_hi, signif, bkgd_threshold, bkgd_range, variation, hard_mask, print_results, self.instr_name) def do_white(self, white_run, spectra_masks, map_file): """ Normalise to a specified white-beam run """ whitews_name = common.create_resultname(white_run, prefix = self.instr_name, suffix='-white') if mtd.workspaceExists(whitews_name): return mtd[whitews_name] # Load white_data = self.load_data(white_run, 'white-beam') # Normalise white_ws = self.normalise(white_data, whitews_name, self.normalise_method) # Units conversion ConvertUnits(white_ws, white_ws, "Energy", AlignBins=0) # This both integrates the workspace into one bin spectra and sets up common bin boundaries for all spectra low = self.wb_integr_range[0] upp = self.wb_integr_range[1] if low > upp: raise ValueError("White beam integration range is inconsistent. low=%d, upp=%d" % (low,upp)) delta = 2.0*(upp - low) Rebin(white_ws, white_ws, [low, delta, upp]) # Masking and grouping white_ws = self.remap(white_ws, spectra_masks, map_file) # White beam scale factor white_ws *= self.wb_scale_factor return white_ws def mono_van(self, mono_van, ei_guess, white_run=None, map_file=None, spectra_masks=None, result_name = None, Tzero=None): """Convert a mono vanadium run to DeltaE. If multiple run files are passed to this function, they are summed into a run and then processed """ # Load data sample_data = self.load_data(mono_van, 'mono-van') # Create the result name if necessary if result_name is None: result_name = common.create_resultname(mono_van, prefix=self.instr_name) return self._do_mono(sample_data, sample_data, result_name, ei_guess, white_run, map_file, spectra_masks, Tzero) def mono_sample(self, mono_run, ei_guess, white_run=None, map_file=None, spectra_masks=None, result_name = None, Tzero=None): """Convert a mono-chromatic sample run to DeltaE. If multiple run files are passed to this function, they are summed into a run and then processed """ # Load data sample_data = self.load_data(mono_run, 'mono-sample') # Create the result name if necessary if result_name is None: result_name = common.create_resultname(mono_run, prefix=self.instr_name) return self._do_mono(sample_data, sample_data, result_name, ei_guess, white_run, map_file, spectra_masks, Tzero) # ------------------------------------------------------------------------------------------- # This actually does the conversion for the mono-sample and mono-vanadium runs # # ------------------------------------------------------------------------------------------- def _do_mono(self, data_ws, monitor_ws, result_name, ei_guess, white_run=None, map_file=None, spectra_masks=None, Tzero=None): """ Convert units of a given workspace to deltaE, including possible normalisation to a white-beam vanadium run. """ # Special load monitor stuff. if (self.instr_name == "CNCS"): self.fix_ei = True ei_value = ei_guess if (Tzero is None): tzero = (0.1982*(1+ei_value)**(-0.84098))*1000.0 else: tzero = Tzero # apply T0 shift ChangeBinOffset(data_ws, result_name, -tzero) mon1_peak = 0.0 self.apply_detector_eff = True elif (self.instr_name == "ARCS" or self.instr_name == "SEQUOIA"): mono_run = common.loaded_file('mono-sample') if mono_run.endswith("_event.nxs"): loader=LoadNexusMonitors(Filename=mono_run, OutputWorkspace="monitor_ws") elif mono_run.endswith("_event.dat"): InfoFilename = mono_run.replace("_neutron_event.dat", "_runinfo.xml") loader=LoadPreNeXusMonitors(RunInfoFilename=InfoFilename,OutputWorkspace="monitor_ws") monitor_ws = loader.workspace() alg = GetEi(monitor_ws, int(self.ei_mon_spectra[0]), int(self.ei_mon_spectra[1]), ei_guess, False) Tzero = float(alg.getPropertyValue("Tzero")) if (self.fix_ei): ei_value = ei_guess else: ei_value = monitor_ws.getRun().getLogData("Ei").value if (Tzero is None): tzero = 0.0 else: tzero = Tzero mon1_peak = 0.0 # apply T0 shift ChangeBinOffset(data_ws, result_name, -tzero) self.apply_detector_eff = True else: # Do ISIS stuff for Ei # Both are these should be run properties really ei_value, mon1_peak = self.get_ei(monitor_ws, result_name, ei_guess) # As we've shifted the TOF so that mon1 is at t=0.0 we need to account for this in FlatBackground and normalisation bin_offset = -mon1_peak # Get the workspace the converted data will end up in result_ws = mtd[result_name] # For event mode, we are going to histogram in energy first, then go back to TOF if (self.facility == "SNS"): if self.background == True: # Extract the time range for the background determination before we throw it away background_bins = "%s,%s,%s" % (self.background_range[0] + bin_offset, (self.background_range[1]-self.background_range[0]), self.background_range[1] + bin_offset) Rebin(result_ws, "background_origin_ws", background_bins) # Convert to Et ConvertUnits(result_ws, "_tmp_energy_ws", Target="DeltaE",EMode="Direct", EFixed=ei_value) RenameWorkspace("_tmp_energy_ws", result_ws) # Histogram Rebin(result_ws, "_tmp_rebin_ws", self.energy_bins) RenameWorkspace("_tmp_rebin_ws", result_ws) # Convert back to TOF ConvertUnits(result_ws, result_ws, Target="TOF",EMode="Direct", EFixed=ei_value) else: # TODO: This algorithm needs to be separated so that it doesn't actually # do the correction as well so that it can be moved next to LoadRaw where # it belongs LoadDetectorInfo(result_ws, common.loaded_file('mono')) if self.background == True: # Remove the count rate seen in the regions of the histograms defined as the background regions, if the user defined a region ConvertToDistribution(result_ws) if (self.facility == "SNS"): FlatBackground("background_origin_ws", "background_ws", self.background_range[0] + bin_offset, self.background_range[1] + bin_offset, '', 'Mean', 'Return Background') # Delete the raw data background region workspace mtd.deleteWorkspace("background_origin_ws") # Convert to distribution to make it compatible with the data workspace (result_ws). ConvertToDistribution("background_ws") # Subtract the background Minus(result_ws, "background_ws", result_ws) # Delete the determined background mtd.deleteWorkspace("background_ws") else: FlatBackground(result_ws, result_ws, self.background_range[0] + bin_offset, self.background_range[1] + bin_offset, '', 'Mean') ConvertFromDistribution(result_ws) # Normalise using the chosen method # TODO: This really should be done as soon as possible after loading self.normalise(result_ws, result_ws, self.normalise_method, range_offset=bin_offset) ConvertUnits(result_ws, result_ws, Target="DeltaE",EMode='Direct') if not self.energy_bins is None: Rebin(result_ws, result_ws, self.energy_bins) if self.apply_detector_eff: if (self.facility == "SNS"): # Need to be in lambda for detector efficiency correction ConvertUnits(result_ws, result_ws, Target="Wavelength", EMode="Direct") He3TubeEfficiency(result_ws, result_ws) ConvertUnits(result_ws, result_ws, Target="DeltaE",EMode='Direct') else: DetectorEfficiencyCor(result_ws, result_ws) # Ki/Kf Scaling... CorrectKiKf(result_ws, result_ws, EMode='Direct') # Make sure that our binning is consistent if not self.energy_bins is None: Rebin(result_ws, result_ws, self.energy_bins) # Masking and grouping result_ws = self.remap(result_ws, spectra_masks, map_file) ConvertToDistribution(result_ws) # White beam correction if white_run is not None: white_ws = self.do_white(white_run, spectra_masks, map_file) result_ws /= white_ws # Overall scale factor result_ws *= self.scale_factor return result_ws #------------------------------------------------------------------------------- def convert_to_energy(self, mono_run, ei, white_run=None, mono_van=None,\ abs_ei=None, abs_white_run=None, save_path=None, Tzero=None): """ One-shot function to convert the given runs to energy """ # Check if we need to perform the absolute normalisation first if not mono_van is None: if abs_ei is None: abs_ei = ei mapping_file = self.abs_map_file spectrum_masks = self.spectra_masks monovan_wkspace = self.mono_van(mono_van, abs_ei, abs_white_run, mapping_file, spectrum_masks) # TODO: Need a better check than this... if (abs_white_run is None): self.log("Performing Normalisation to Mono Vanadium.") norm_factor = self.calc_average(monovan_wkspace) else: self.log("Performing Absolute Units Normalisation.") # Perform Abs Units... norm_factor = self.monovan_abs(monovan_wkspace) mtd.deleteWorkspace(monovan_wkspace.getName()) else: norm_factor = None # Figure out what to call the workspace result_name = save_path if not result_name is None: result_name = common.create_resultname(save_path) # Main run file conversion sample_wkspace = self.mono_sample(mono_run, ei, white_run, self.map_file, self.spectra_masks, result_name, Tzero) if not norm_factor is None: sample_wkspace /= norm_factor # Save then finish self.save_results(sample_wkspace, save_path) return sample_wkspace #---------------------------------------------------------------------------------- # Reduction steps #---------------------------------------------------------------------------------- def get_ei(self, input_ws, resultws_name, ei_guess): """ Calculate incident energy of neutrons """ fix_ei = str(self.fix_ei).lower() if fix_ei == 'true': fix_ei = True elif fix_ei == 'false': fix_ei = False elif fix_ei == 'fixei': fix_ei = True else: raise TypeError('Unknown option passed to get_ei "%s"' % fix_ei) # Calculate the incident energy alg = GetEi(input_ws, int(self.ei_mon_spectra[0]), int(self.ei_mon_spectra[1]), ei_guess, fix_ei) mon1_peak = float(alg.getPropertyValue("FirstMonitorPeak")) mon1_index = int(alg.getPropertyValue("FirstMonitorIndex")) ei = input_ws.getSampleDetails().getLogData("Ei").value # Adjust the TOF such that the first monitor peak is at t=0 ChangeBinOffset(input_ws, resultws_name, -mon1_peak) mon1_det = input_ws.getDetector(mon1_index) mon1_pos = mon1_det.getPos() src_name = input_ws.getInstrument().getSource().getName() MoveInstrumentComponent(resultws_name, src_name, X=mon1_pos.getX(), Y=mon1_pos.getY(), Z=mon1_pos.getZ(), RelativePosition=False) return ei, mon1_peak def remap(self, result_ws, spec_masks, map_file): """ Mask and group detectors based on input parameters """ if not spec_masks is None: MaskDetectors(result_ws, MaskedWorkspace=spec_masks) if not map_file is None: GroupDetectors(result_ws, result_ws, map_file, KeepUngroupedSpectra=0) return mtd[str(result_ws)] def normalise(self, data_ws, result_ws, method, range_offset=0.0): """ Apply normalisation using specified source """ method = method.lower() if method == 'monitor-1': range_min = self.mon1_norm_range[0] + range_offset range_max = self.mon1_norm_range[1] + range_offset NormaliseToMonitor(InputWorkspace=data_ws, OutputWorkspace=result_ws, MonitorSpectrum=int(self.mon1_norm_spec), IntegrationRangeMin=range_min, IntegrationRangeMax=range_max,IncludePartialBins=True) output = mtd[str(result_ws)] elif method == 'current': NormaliseByCurrent(InputWorkspace=data_ws, OutputWorkspace=result_ws) output = mtd[str(result_ws)] elif method == 'none': if str(data_ws) != str(result_ws): CloneWorkspace(InputWorkspace=data_ws, OutputWorkspace=result_ws) output = mtd[str(result_ws)] else: raise RuntimeError('Normalisation scheme ' + reference + ' not found. It must be one of monitor-1, current, peak or none') return output def calc_average(self, data_ws): """ Compute the average Y value of a workspace. The average is computed by collapsing the workspace to a single bin per spectra then masking masking out detectors given by the FindDetectorsOutsideLimits and MedianDetectorTest algorithms. The average is then the computed as the using the remainder and factoring in their errors as weights, i.e. average = sum(Yvalue[i]*weight[i]) / sum(weights) where only those detectors that are unmasked are used and the weight[i] = 1/errorValue[i]. """ e_low = self.monovan_integr_range[0] e_upp = self.monovan_integr_range[1] if e_low > e_upp: raise ValueError("Inconsistent mono-vanadium integration range defined!") Rebin(data_ws, data_ws, [e_low, 2.*(e_upp-e_low), e_upp]) min_value = self.abs_min_value max_value = self.abs_max_value median_lbound = self.abs_median_lbound median_ubound = self.abs_median_ubound median_frac_low = self.abs_median_frac_low median_frac_hi = self.abs_median_frac_hi median_sig = self.abs_median_sig self.mask_detectors_outside_range(data_ws, min_value, max_value, median_lbound, median_ubound, median_frac_low, median_frac_hi, median_sig) ConvertFromDistribution(data_ws) nhist = data_ws.getNumberHistograms() average_value = 0.0 weight_sum = 0.0 for i in range(nhist): try: det = data_ws.getDetector(i) except Exception: continue if det.isMasked(): continue y_value = data_ws.readY(i)[0] if y_value != y_value: continue weight = 1.0/data_ws.readE(i)[0] average_value += y_value * weight weight_sum += weight return average_value / weight_sum def monovan_abs(self, ei_workspace): """Calculates the scaling factor required for normalisation to absolute units. The given workspace must contain an Ei value. This will have happened if GetEi has been run """ averageY = self.calc_average(ei_workspace) absnorm_factor = averageY * (self.van_rmm/self.van_mass) # Scale by vanadium cross-section which is energy dependent up to a point run = ei_workspace.getRun() try: ei_prop = run['Ei'] except KeyError: raise RuntimeError('The given workspace "%s" does not contain an Ei value. Run GetEi first.' % str(ei_workspace)) ei_value = ei_prop.value if ei_value >= 200.0: xsection = 421.0 else: xsection = 400.0 + (ei_value/10.0) absnorm_factor /= xsection return absnorm_factor * (self.sample_mass/self.sample_rmm) def mask_detectors_outside_range(self, data_ws, min_value, max_value, median_lbound, median_ubound, median_frac_lo, median_frac_hi, median_sig): """ Masks detecrors on the given workspace according the ranges given where: min_value - lower bound of meaningful value; max_value - upper bound of meaningful value; median_lbound - lower bound defining outliers as fraction of median value; median_ubound - upper bound defining outliers as fraction of median value; median_frac_lo - lower acceptable bound as fraction of median value; median_frac_hi - upper acceptable bound as fraction of median value; media_sig - error criterion as a multiple of error bar i.e. to fail the test, the magnitude of the difference with respect to the median value must also exceed this number of error bars. """ # Limit test median_tests_ws = '_tmp_abs_median_tests' fdol_alg = FindDetectorsOutsideLimits(data_ws, median_tests_ws, HighThreshold=max_value, LowThreshold=min_value) MaskDetectors(data_ws, MaskedWorkspace=fdol_alg.workspace()) # Median tests median_test_alg = MedianDetectorTest(data_ws, median_tests_ws, LowThreshold=median_lbound, HighThreshold=median_ubound) MaskDetectors(data_ws, MaskedWorkspace=median_test_alg.workspace()) median_test_alg = MedianDetectorTest(data_ws, median_tests_ws, SignificanceTest=median_sig, LowThreshold=median_frac_lo, HighThreshold=median_frac_hi) MaskDetectors(data_ws, MaskedWorkspace=median_test_alg.workspace()) mtd.deleteWorkspace(median_tests_ws) def save_results(self, workspace, save_path, formats = None): """ Save the result workspace to the specfied filename using the list of formats specified in formats. If formats is None then the default list is used """ if save_path is None: save_path = workspace.getName() elif os.path.isdir(save_path): save_path = os.path.join(save_path, workspace.getName()) elif save_path == '': raise ValueError('Empty filename is not allowed for saving') else: pass if formats is None: formats = self.save_formats if type(formats) == str: formats = [formats] #Make sure we just have a file stem save_path = os.path.splitext(save_path)[0] for ext in formats: filename = save_path + ext if ext == '.spe': SaveSPE(workspace, filename) elif ext == '.nxs': SaveNexus(workspace, filename) elif ext == '.nxspe': SaveNXSPE(workspace, filename) else: self.log('Unknown file format "%s" encountered while saving results.') #------------------------------------------------------------------------------- def load_data(self, runs, file_type): """ Load a run or list of runs. If a list of runs is given then they are summed into one. """ if type(runs) == list: result_ws = common.load_run(runs[0], file_type) if len(runs) > 1: del runs[0] common.sum_files(result_ws.getName(), runs) RenameWorkspace(result_ws, 'summed-' + file_type) elif type(str): result_ws = common.load_run(runs, file_type) else: raise TypeError("Run number must be a list or a string") self.setup_mtd_instrument(result_ws) return result_ws #--------------------------------------------------------------------------- # Behind the scenes stuff #--------------------------------------------------------------------------- def __init__(self, instr_name): """ Constructor """ self._to_stdout = True self._log_to_mantid = False self._idf_values_read = False # Instrument and default parameter setup self.initialise(instr_name) def initialise(self, instr_name): """ Initialise the attributes of the class """ # Instrument name might be a prefix, query Mantid for the full name self.instr_name = mtd.settings.facility().instrument(instr_name).name() mtd.settings['default.instrument'] = self.instr_name self.setup_mtd_instrument() # Initialize the default parameters from the instrument as attributes of the # class self.init_params() def setup_mtd_instrument(self, workspace = None): if workspace != None: self.instrument = workspace.getInstrument() else: # Load an empty instrument idf_dir = mtd.getConfigProperty('instrumentDefinition.directory') instr_pattern = os.path.join(idf_dir,self.instr_name + '*_Definition.xml') idf_files = glob.glob(instr_pattern) if len(idf_files) > 0: tmp_ws_name = '_tmp_empty_instr' LoadEmptyInstrument(idf_files[0],tmp_ws_name) self.instrument = mtd[tmp_ws_name].getInstrument() # Instrument is cached so this is fine mtd.deleteWorkspace(tmp_ws_name) else: self.instrument = None raise RuntimeError('Cannot load instrument for prefix "%s"' % self.instr_name) # Initialise IDF parameters self.init_idf_params() def init_params(self): """ Attach analysis arguments that are particular to the ElasticConversion """ self.save_formats = ['.spe','.nxs','.nxspe'] self.fix_ei=False self.energy_bins = None self.background = False self.normalise_method = 'monitor-1' self.map_file = None if (self.instr_name == "CNCS" or self.instr_name == "ARCS" or self.instr_name == "SEQUOIA"): self.facility = "SNS" self.normalise_method = 'current' else: self.facility = str(mtd.settings.facility()) # The Ei requested self.ei_requested = None self.monitor_workspace = None self.time_bins = None # Detector diagnosis self.spectra_masks = None # Absolute normalisation self.abs_map_file = None self.abs_spectra_masks = None self.sample_mass = 1.0 self.sample_rmm = 1.0 self.apply_detector_eff = True def init_idf_params(self): """ Initialise the parameters from the IDF file if necessary """ if self._idf_values_read == True: return self.ei_mon_spectra = [int(self.get_default_parameter("ei-mon1-spec")), int(self.get_default_parameter("ei-mon2-spec"))] self.scale_factor = self.get_default_parameter("scale-factor") self.wb_scale_factor = self.get_default_parameter("wb-scale-factor") self.wb_integr_range = [self.get_default_parameter("wb-integr-min"), self.get_default_parameter("wb-integr-max")] self.mon1_norm_spec = int(self.get_default_parameter("norm-mon1-spec")) self.mon1_norm_range = [self.get_default_parameter("norm-mon1-min"), self.get_default_parameter("norm-mon1-max")] self.background_range = [self.get_default_parameter("bkgd-range-min"), self.get_default_parameter("bkgd-range-max")] self.monovan_integr_range = [self.get_default_parameter("monovan-integr-min"), self.get_default_parameter("monovan-integr-max")] self.van_mass = self.get_default_parameter("vanadium-mass") self.van_rmm = self.get_default_parameter("vanadium-rmm") self.abs_min_value = self.get_default_parameter('abs-average-min') self.abs_max_value = self.get_default_parameter('abs-average-max') self.abs_median_lbound = self.get_default_parameter('abs-median-lbound') self.abs_median_ubound = self.get_default_parameter('abs-median-ubound') self.abs_median_frac_low = self.get_default_parameter('abs-median-lo-frac') self.abs_median_frac_hi = self.get_default_parameter('abs-median-hi-frac') self.abs_median_sig = self.get_default_parameter('abs-median-signif') # Mark IDF files as read self._idf_values_read = True def get_default_parameter(self, name): if self.instrument is None: raise ValueError("Cannot init default parameter, instrument has not been loaded.") values = self.instrument.getNumberParameter(name) if len(values) != 1: raise ValueError('Instrument parameter file does not contain a definition for "%s". Cannot continue' % name) return values[0] def log(self, msg): """Send a log message to the location defined """ if self._to_stdout: print msg if self._log_to_mantid: mtd.sendLogMessage(msg) #-----------------------------------------------------------------