""" File contains Descriptors used describe run for direct inelastic reduction """
from mantid.simpleapi import *
from PropertiesDescriptors import *
class RunDescriptor(PropDescriptor):
""" descriptor supporting a run and a workspace """
# the host class referencing contained all instantiated descriptors.
# Descriptors methods rely on it to work (e.g. to extract file loader
# preferences)
# so it has to be set up manually by PropertyManager __init__ method
_holder = None
_logger = None
# class level reference to the property manager
_PropMan = None
#--------------------------------------------------------------------------------------------------------------------
def __init__(self,prop_name,DocString=None):
""" """
# Run number
self._run_number = None
# Extension of the file to load data from
#
self._prop_name = prop_name
self._run_file_path = ''
self._run_ext = None
# Workspace name which corresponds to the run
self._ws_name = None # none if not loaded
# String used to identify the workspace related to this property w.r.t.
# other workspaces
self._ws_cname = ''
self._ws_suffix = ''
self._bind_to_sum = False
#
if not DocString is None:
self.__doc__ = DocString
#--------------------------------------------------------------------------------------------------------------------
def __get__(self,instance,owner):
""" return current run number or workspace if it is loaded"""
if not RunDescriptor._PropMan:
RunDescriptor._PropMan = owner
if instance is None:
return self
if self._ws_name and self._ws_name in mtd:
return mtd[self._ws_name]
else:
return self._run_number
#--------------------------------------------------------------------------------------------------------------------
def __set__(self,instance,value):
""" Set up Run number and define workspace name from any source """
#
if not RunDescriptor._PropMan:
from PropertyManager import PropertyManager
RunDescriptor._PropMan = PropertyManager
old_ws_name = self._ws_name
clear_fext = True
#end
if value == None: # clear current run number
self._run_number = None
self._ws_name = None
self._ws_cname = ''
self._ws_suffix = ''
# only one RunDescriptor can be summed under current approach.
# To disentangle one run descriptor from another -- set up binding
self._bind_to_sum = False
self._clear_old_ws(old_ws_name,self._ws_name,clear_fext)
RunDescriptor._PropMan.sum_runs.clear_sum()
return
if isinstance(value, api.Workspace):
#if 'SumOfRuns:' in value.getRun():
# TODO: not implemented
#else:
self._set_source_ws(value)
self._clear_old_ws(old_ws_name,self._ws_name,clear_fext)
self._bind_to_sum = False
RunDescriptor._PropMan.sum_runs.clear_sum()
return
#return
if isinstance(value,str): # it may be run number as string or it may be a workspace name
if value in mtd: # workspace name
ws = mtd[value]
self.__set__(instance,ws)
return
else:
file_path,run_num,fext = prop_helpers.parse_run_file_name(value)
if isinstance(run_num,list):
RunDescriptor._PropMan.sum_runs.set_list2add(run_num,file_path,fext)
self._bind_to_sum = True
if instance.sum_runs:
last_run_ind = RunDescriptor._PropMan.sum_runs.get_last_ind2sum()
main_fext = fext[last_run_ind].lower()
self._run_file_path = file_path[last_run_ind].lower()
else:
self.__set__(instance,run_num)
self._run_file_path = file_path
main_fext = fext.lower()
#
if len(main_fext) > 0:
self._run_ext = main_fext
else: # will be default file extension
self._run_ext = None
clear_fext = False
elif isinstance(value,list):
if len(value) == 1:
self.__set__(instance,value[0])
return
self._bind_to_sum = True
RunDescriptor._PropMan.sum_runs.set_list2add(value)
if instance.sum_runs:
last_run_ind = RunDescriptor._PropMan.sum_runs.get_last_ind2sum()
self._run_number = value[last_run_ind]
else:
self._run_number = value[0]
clear_fext = True
else:
clear_fext = True
self._run_number = int(value)
if self._bind_to_sum and instance and instance.sum_runs:
num2_sum = RunDescriptor._PropMan.sum_runs.set_last_ind2sum(self._run_number)
if num2_sum == 0:
self._bind_to_sum = False
instance.sum_runs = False
self._ws_cname = ''
self._ws_name = None
self._clear_old_ws(old_ws_name,None,clear_fext)
#--------------------------------------------------------------------------------------------------------------------
def run_number(self):
""" Return run number regardless of workspace is loaded or not"""
if self._ws_name and self._ws_name in mtd:
ws = mtd[self._ws_name]
return ws.getRunNumber()
else:
return self._run_number
#--------------------------------------------------------------------------------------------------------------------
def is_monws_separate(self):
""" """
mon_ws = self.get_monitors_ws()
if mon_ws:
name = mon_ws.name()
else:
return False
if name.endswith('_monitors'):
return True
else:
return False
#--------------------------------------------------------------------------------------------------------------------
def get_run_list(self):
""" Returns list of the files, assigned to current property """
current_run = self.run_number()
if self._bind_to_sum:
runs = RunDescriptor._PropMan.sum_runs.get_runs()
if current_run in runs:
return runs
else:
return [current_run]
else:
return [current_run]
#--------------------------------------------------------------------------------------------------------------------
def set_action_suffix(self,suffix=None):
""" method to set part of the workspace name, which indicate some action performed over this workspace
e.g.: default suffix of a loaded workspace is 'RAW' but we can set it to SPE to show that conversion to
energy will be performed for this workspace.
method returns the name of the workspace is will have with this suffix. Algorithms would later
work on the initial workspace and modify it in-place or to produce workspace with new name (depending if one
wants to keep initial workspace)
synchronize_ws(ws_pointer) then should synchronize workspace and its name.
TODO: This method should be automatically invoked by an algorithm decorator
Until implemented, one have to ensure that it is correctly used together with synchronize_ws
to ensue one can always get workspace from its name
"""
if suffix:
self._ws_suffix = suffix
else: # return to default
self._ws_suffix = ''
return self._build_ws_name()
#--------------------------------------------------------------------------------------------------------------------
def synchronize_ws(self,workspace=None):
""" Synchronize workspace name (after workspace may have changed due to algorithm)
with internal run holder name. Accounts for the situation when
TODO: This method should be automatically invoked by an algorithm decorator
Until implemented, one have to ensure that it is correctly used together with
set_action_suffix to ensue one can always get expected workspace from its name
outside of a method visibility
"""
if not workspace:
workspace = mtd[self._ws_name]
new_name = self._build_ws_name()
old_name = workspace.name()
if new_name != old_name:
if new_name in mtd:
DeleteWorkspace(new_name)
RenameWorkspace(InputWorkspace=old_name,OutputWorkspace=new_name)
old_mon_name = old_name + '_monitors'
new_mon_name = new_name + '_monitors'
if new_mon_name in mtd:
DeleteWorkspace(new_mon_name)
if old_mon_name in mtd:
RenameWorkspace(InputWorkspace=old_mon_name,OutputWorkspace=new_mon_name)
self._ws_name = new_name
#--------------------------------------------------------------------------------------------------------------------
def get_file_ext(self):
""" Method returns current file extension for file to load workspace from
e.g. .raw or .nxs extension
"""
if self._run_ext:
return self._run_ext
else: # return IDF default
return RunDescriptor._holder.data_file_ext
#--------------------------------------------------------------------------------------------------------------------
def set_file_ext(self,val):
""" set non-default file extension """
if isinstance(val,str):
if val[0] != '.':
value = '.' + val
else:
value = val
self._run_ext = value
else:
raise AttributeError('Source file extension can be only a string')
#--------------------------------------------------------------------------------------------------------------------
@staticmethod
def _check_claibration_source():
""" if user have not specified calibration as input to the script,
try to retrieve calibration stored in file with run properties"""
changed_prop = RunDescriptor._holder.getChangedProperties()
if 'det_cal_file' in changed_prop:
use_workspace_calibration = False
else:
use_workspace_calibration = True
return use_workspace_calibration
#--------------------------------------------------------------------------------------------------------------------
def get_workspace(self):
""" Method returns workspace correspondent to current run number(s)
and loads this workspace if it has not been loaded
Returns Mantid pointer to the workspace, corresponding to this run number
"""
if not self._ws_name:
self._ws_name = self._build_ws_name()
if self._ws_name in mtd:
ws = mtd[self._ws_name]
if ws.run().hasProperty("calibrated"):
return ws # already calibrated
else:
prefer_ws_calibration = self._check_claibration_source()
self.apply_calibration(ws,RunDescriptor._holder.det_cal_file,prefer_ws_calibration)
return ws
else:
if self._run_number:
prefer_ws_calibration = self._check_claibration_source()
inst_name = RunDescriptor._holder.short_inst_name
calibration = RunDescriptor._holder.det_cal_file
if self._bind_to_sum and RunDescriptor._holder.sum_runs : # Sum runs
ws = RunDescriptor._PropMan.sum_runs.load_and_sum_runs(inst_name,RunDescriptor._holder.load_monitors_with_workspace)
else: # load current workspace
ws = self.load_run(inst_name, calibration,False, RunDescriptor._holder.load_monitors_with_workspace,prefer_ws_calibration)
self.synchronize_ws(ws)
self.apply_calibration(ws,calibration,prefer_ws_calibration)
return ws
else:
return None
#--------------------------------------------------------------------------------------------------------------------
def get_ws_clone(self,clone_name='ws_clone'):
""" Get unbounded clone of existing Run workspace """
ws = self.get_workspace()
CloneWorkspace(InputWorkspace=ws,OutputWorkspace=clone_name)
mon_ws_name = self.get_ws_name() + '_monitors'
if mon_ws_name in mtd:
cl_mon_name = clone_name + '_monitors'
CloneWorkspace(InputWorkspace=mon_ws_name,OutputWorkspace=cl_mon_name)
return mtd[clone_name]
#--------------------------------------------------------------------------------------------------------------------
def _set_ws_as_source(value):
""" assign all parts of the run if input value is workspace """
self._run_number = value.getRunNumber()
ws_name = value.name()
self._split_ws_name(ws_name)
self.synchronize_ws(value)
#--------------------------------------------------------------------------------------------------------------------
def chop_ws_part(self,origin,tof_range,rebin,chunk_num,n_chunks):
""" chop part of the original workspace and sets it up as new original.
Return the old one"""
if not(origin):
origin = self.get_workspace()
origin_name = origin.name()
if chunk_num == n_chungs:
target_name = origin_name
else:
target_name = '#{0}/{1}_'.format(chunk_num,n_chunks)+origin_name
if rebin: # debug and compatibility mode with old reduction
Rebin(origin_name,OutputWorkspace=target_name,Params=[tof_range[0],tof_range[1],tof_range[2]],PreserveEvents=False)
else:
CropWorkspace(origin,OutputWorkspace=target_name,XMin=tof_range[0],XMax=tof_range[2])
self._set_ws_as_source(mtd[target_name])
return mtd[origin_name]
#--------------------------------------------------------------------------------------------------------------------
def get_monitors_ws(self,monitor_ID=None):
""" get pointer to a workspace containing monitors.
Explores different ways of finding monitor workspace in Mantid and returns the python pointer to the
workspace which contains monitors.
"""
data_ws = self.get_workspace()
monWS_name = self.get_ws_name() + '_monitors'
if monWS_name in mtd:
mon_ws = mtd[monWS_name]
monitors_separate = True
else:
mon_ws = data_ws
monitors_separate = False
spec_to_mon = RunDescriptor._holder.spectra_to_monitors_list
if monitors_separate and spec_to_mon :
for specID in spec_to_mon:
mon_ws = self.copy_spectrum2monitors(data_ws,mon_ws,specID)
if monitor_ID:
try:
ws_index = mon_ws.getIndexFromSpectrumNumber(monitor_ID)
except: #
mon_ws = None
else:
mon_list = self._holder.get_used_monitors_list()
for monID in mon_list:
try:
ws_ind = mon_ws.getIndexFromSpectrumNumber(int(monID))
except:
mon_ws = None
break
return mon_ws
#--------------------------------------------------------------------------------------------------------------------
def get_ws_name(self):
""" return workspace name. If ws name is not defined, build it first and set up as the target ws name
"""
if self._ws_name:
if self._ws_name in mtd:
return self._ws_name
else:
raise RuntimeError('Getting workspace name {0} for undefined workspace. Run get_workspace first'.format(self._ws_name))
self._ws_name = self._build_ws_name()
return self._ws_name
#--------------------------------------------------------------------------------------------------------------------
def file_hint(self,run_num_str=None,filePath=None,fileExt=None,**kwargs):
""" procedure to provide run file guess name from run properties
main purpose -- to support customized order of file extensions
"""
if not run_num_str:
run_num_str = str(self.run_number())
inst_name = RunDescriptor._holder.short_inst_name
if 'file_hint' in kwargs:
hint = kwargs['file_hint']
fname,old_ext = os.path.splitext(hint)
if len(old_ext) == 0:
old_ext = self.get_file_ext()
else:
if fileExt:
old_ext = fileExt
else:
old_ext = self.get_file_ext()
hint = inst_name + run_num_str + old_ext
if not filePath:
filePath = self._run_file_path
if os.path.exists(filePath):
hint = os.path.join(filePath,hint)
if os.path.exists(hint):
return hint,old_ext
else:
fp,hint = os.path.split(hint)
return hint,old_ext
#--------------------------------------------------------------------------------------------------------------------
def find_file(self,inst_name=None,run_num=None,filePath=None,fileExt=None,**kwargs):
"""Use Mantid to search for the given run. """
if not inst_name:
inst_name = RunDescriptor._holder.short_inst_name
if run_num:
run_num_str = str(run_num)
else:
run_num_str = str(self.run_number())
#
file_hint,old_ext = self.file_hint(run_num_str,filePath,fileExt,**kwargs)
try:
file = FileFinder.findRuns(file_hint)[0]
fname,fex = os.path.splitext(file)
self._run_ext = fex
if old_ext != fex:
message = ' Cannot find run-file with extension {0}.\n'\
' Found file {1} instead'.format(old_ext,file)
RunDescriptor._logger(message,'notice')
self._run_file_path = os.path.dirname(fname)
return file
except RuntimeError:
message = 'Cannot find file matching hint {0} on current search paths ' \
'for instrument {1}'.format(file_hint,inst_name)
if not ('be_quet' in kwargs):
RunDescriptor._logger(message,'warning')
return 'ERROR:find_file: ' + message
#--------------------------------------------------------------------------------------------------------------------
def load_file(self,inst_name,ws_name,run_number=None,load_mon_with_workspace=False,filePath=None,fileExt=None,**kwargs):
""" load run for the instrument name provided. If run_numner is None, look for the current run"""
data_file = self.find_file(None,filePath,fileExt,**kwargs)
if data_file.find('ERROR') > -1:
self._ws_name = None
raise IOError(data_file)
if load_mon_with_workspace:
mon_load_option = 'Include'
else:
mon_load_option = 'Separate'
#
try: # Hack: LoadEventNexus does not understand Separate at the moment and throws.
# And event loader always loads monitors separately
Load(Filename=data_file, OutputWorkspace=ws_name,LoadMonitors = mon_load_option)
except ValueError:
#mon_load_option =str(int(load_mon_with_workspace))
Load(Filename=data_file, OutputWorkspace=ws_name,LoadMonitors = '1',MonitorsAsEvents='0')
RunDescriptor._logger("Loaded {0}".format(data_file),'information')
loaded_ws = mtd[ws_name]
return loaded_ws
#--------------------------------------------------------------------------------------------------------------------
def load_run(self,inst_name, calibration=None, force=False, mon_load_option=False,use_ws_calibration=True,\
filePath=None,fileExt=None,**kwargs):
"""Loads run into workspace with name provided.
If force is true then the file is loaded regardless of whether this workspace already exists
"""
# If a workspace with this name exists, then assume it is to be used in
# place of a file
if 'ws_name' in kwargs:
ws_name = kwargs['ws_name']
del kwargs['ws_name']
else:
try:
ws_name = self.get_ws_name()
except RuntimeError:
self._ws_name = None
ws_name = self.get_ws_name()
#-----------------------------------
if ws_name in mtd and not(force):
RunDescriptor._logger("{0} already loaded as workspace.".format(ws_name),'information')
else:
# If it doesn't exists as a workspace assume we have to try and
# load a file
loaded_ws = self.load_file(inst_name,ws_name,None,mon_load_option,filePath,fileExt,**kwargs)
######## Now we have the workspace
self.apply_calibration(loaded_ws,calibration,use_ws_calibration)
return loaded_ws
#--------------------------------------------------------------------------------------------------------------------
def apply_calibration(self,loaded_ws,calibration=None,use_ws_calibration=True):
""" If calibration is present, apply it to the workspace
use_ws_calibration -- if true, retrieve workspace property, which defines
calibration option (e.g. det_cal_file used a while ago) and try to use it
"""
if not (calibration or use_ws_calibration):
return
if not isinstance(loaded_ws, api.Workspace):
raise RuntimeError(' Calibration can be applied to a workspace only and got object of type {0}'.format(type(loaded_ws)))
if loaded_ws.run().hasProperty("calibrated"):
return # already calibrated
ws_calibration = calibration
if use_ws_calibration:
try:
ws_calibration = prop_helpers.get_default_parameter(loaded_ws.getInstrument(),'det_cal_file')
if ws_calibration is None:
ws_calibration = calibration
if isinstance(ws_calibration,str) and ws_calibration.lower() == 'none':
ws_calibration = calibration
if ws_calibration :
test_name = ws_calibration
ws_calibration = FileFinder.getFullPath(ws_calibration)
if len(ws_calibration) == 0:
raise RuntimeError('Can not find defined in run {0} calibration file {1}\n'\
'Define det_cal_file reduction parameter properly'.format(loaded_ws.name(),test_name))
RunDescriptor._logger('*** load_data: Calibrating data using workspace defined calibration file: {0}'.format(ws_calibration),'notice')
except KeyError: # no det_cal_file defined in workspace
if calibration:
ws_calibration = calibration
else:
return
if type(ws_calibration) == str : # It can be only a file (got it from calibration property)
RunDescriptor._logger('load_data: Moving detectors to positions specified in cal file {0}'.format(ws_calibration),'debug')
# Pull in pressures, thicknesses & update from cal file
LoadDetectorInfo(Workspace=loaded_ws, DataFilename=ws_calibration, RelocateDets=True)
AddSampleLog(Workspace=loaded_ws,LogName="calibrated",LogText=str(ws_calibration))
elif isinstance(ws_calibration, api.Workspace):
RunDescriptor._logger('load_data: Copying detectors positions from workspace {0}: '.format(ws_calibration.name()),'debug')
CopyInstrumentParameters(InputWorkspace=ws_calibration,OutputWorkspace=loaded_ws)
AddSampleLog(Workspace=loaded_ws,LogName="calibrated",LogText=str(ws_calibration))
#--------------------------------------------------------------------------------------------------------------------
@staticmethod
def copy_spectrum2monitors(data_ws,mon_ws,spectraID):
"""
this routine copies a spectrum form workspace to monitor workspace and rebins it according to monitor workspace binning
@param data_ws -- the event workspace which detector is considered as monitor or Mantid pointer to this workspace
@param mon_ws -- the histogram workspace with monitors where one needs to place the detector's spectra
@param spectraID-- the ID of the spectra to copy.
"""
# ----------------------------
try:
ws_index = mon_ws.getIndexFromSpectrumNumber(spectraID)
# Spectra is already in the monitor workspace
return mon_ws
except:
ws_index = data_ws.getIndexFromSpectrumNumber(spectraID)
#
x_param = mon_ws.readX(0)
bins = [x_param[0],x_param[1] - x_param[0],x_param[-1]]
ExtractSingleSpectrum(InputWorkspace=data_ws,OutputWorkspace='tmp_mon',WorkspaceIndex=ws_index)
Rebin(InputWorkspace='tmp_mon',OutputWorkspace='tmp_mon',Params=bins,PreserveEvents='0')
# should be vice versa but Conjoin invalidate ws pointers and hopefully
# nothing could happen with workspace during conjoining
#AddSampleLog(Workspace=monWS,LogName=done_log_name,LogText=str(ws_index),LogType='Number')
mon_ws_name = mon_ws.getName()
ConjoinWorkspaces(InputWorkspace1=mon_ws,InputWorkspace2='tmp_mon')
mon_ws = mtd[mon_ws_name]
if 'tmp_mon' in mtd:
DeleteWorkspace(WorkspaceName='tmp_mon')
return mon_ws
#--------------------------------------------------------------------------------------------------------------------
def _build_ws_name(self):
instr_name = self._instr_name()
sum_ext = RunDescriptor._PropMan.sum_runs.sum_ext()
if self._run_number:
ws_name = '{0}{1}{2}{3:0>#6d}{4}{5}'.format(self._prop_name,instr_name,self._ws_cname,self._run_number,sum_ext,self._ws_suffix)
else:
ws_name = '{0}{1}{2}{3}'.format(self._prop_name,self._ws_cname,sum_ext,self._ws_suffix)
return ws_name
#--------------------------------------------------------------------------------------------------------------------
@staticmethod
def rremove(thestr, trailing):
thelen = len(trailing)
if thestr[-thelen:] == trailing:
return thestr[:-thelen]
return thestr
def _split_ws_name(self,ws_name):
""" Method to split existing workspace name
into parts, in such a way that _build_name would restore the same name
"""
# Remove suffix
name = self.rremove(ws_name,self._ws_suffix)
sumExt = RunDescriptor._PropMan.sum_runs.sum_ext()
if len(sumExt) > 0:
name = self.rremove(ws_name,sumExt)
# remove _prop_name:
name = name.replace(self._prop_name,'',1)
if self._run_number:
instr_name = self._instr_name()
name = name.replace(instr_name,'',1)
self._ws_cname = filter(lambda c: not c.isdigit(), name)
else:
self._ws_cname = name
#
def _instr_name(self):
if RunDescriptor._holder:
instr_name = RunDescriptor._holder.short_inst_name
else:
instr_name = '_test_instrument'
return instr_name
def _clear_old_ws(self,old_ws_name,new_name,clear_fext=False):
""" helper method used in __set__. When new data (run or wod) """
if old_ws_name:
if new_name != old_ws_name:
if old_ws_name in mtd:
DeleteWorkspace(old_ws_name)
old_mon_ws = old_ws_name + '_monitors'
if old_mon_ws in mtd:
DeleteWorkspace(old_mon_ws)
if clear_fext:
self._run_ext = None
self._run_file_path = ''
#-------------------------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------------------------
#-------------------------------------------------------------------------------------------------------------------------------
class RunDescriptorDependent(RunDescriptor):
""" Simple RunDescriptor class dependent on another RunDescriptor,
providing the host descriptor if current descriptor value is not defined
or usual descriptor functionality if somebody sets current descriptor up
"""
def __init__(self,host_run,ws_preffix,DocString=None):
RunDescriptor.__init__(self,ws_preffix,DocString)
self._host = host_run
self._this_run_defined = False
def __get__(self,instance,owner=None):
""" return dependent run number which is host run number if this one has not been set or this run number if it was"""
if self._this_run_defined:
if instance is None:
return self
else:
return super(RunDescriptorDependent,self).__get__(instance,owner)
else:
return self._host.__get__(instance,owner)
def __set__(self,instance,value):
if value is None:
self._this_run_defined = False
return
self._this_run_defined = True
super(RunDescriptorDependent,self).__set__(instance,value)
#def __del__(self):
# # destructor removes bounded workspace
# # Probably better not to at current approach
# if self._ws_name in mtd:
# DeleteWorkspace(self._ws_name)
# object.__del__(self)