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Hahn, Steven authoredHahn, Steven authored
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ExportSpectraMask.py 7.33 KiB
#pylint: disable=invalid-name, no-init
from __future__ import (absolute_import, division, print_function)
import os
from mantid import config
from mantid.api import PythonAlgorithm, AlgorithmFactory, WorkspaceProperty, mtd, FileProperty, FileAction
from mantid.kernel import Direction, logger, IntArrayProperty
def export_masks(ws,fileName='',returnMasksOnly=False):
"""Exports masks applied to Mantid workspace
(e.g. drawn using the instrument view) and write these masks
into the old fashioned ASCII .msk file containing masked spectra numbers.
The file is Libisis/Mantid old ISIS format compatible and can be read by Libisis
or Mantid LoadMasks algorithm
If optional parameter fileName is present, the masks are saved
in the file with this name
Otherwise, the file with the name equal to the workspace
name and the extension .msk is used.
If returnMasks is set to True, the function does not write to file but returns
list of masks instead.
"""
# get pointer to the workspace
if isinstance(ws, str):
pws = mtd[ws]
else:
pws = ws
ws_name=pws.name()
nhist = pws.getNumberHistograms()
no_detectors = 0
masks = []
specInfo = pws.spectrumInfo()
for i in range(nhist):
# set provisional spectra ID
ms = i+1
try:
sp = pws.getSpectrum(i)
# got real spectra ID, which would correspond real spectra num to spectra ID map
ms = sp.getSpectrumNo()
#pylint: disable=W0703
except Exception:
logger.notice("Can not retrieve spectra No: " + str(i) + ". Have masked it")
masks.append(ms)
continue
try:
if specInfo.isMasked(i):
masks.append(ms)
#pylint: disable=W0703
except Exception:
no_detectors = no_detectors +1
masks.append(ms)
continue
filename=''
if len(fileName)==0 :
filename = os.path.join(config.getString('defaultsave.directory'),ws_name+'.msk')
else:
filename = fileName
nMasks = len(masks)
if nMasks == 0:
if returnMasksOnly:
logger.warning("Workspace {0} have no masked spectra. File {1} have not been created".format(ws_name,filename))
else:
logger.notice("Workspace "+ws_name+" have no masked spectra")
return masks
logger.notice("Workspace {0} has {1} masked spectra, including {2} spectra without detectors".format(ws_name,nMasks,no_detectors))
if not returnMasksOnly :
writeISISmasks(filename,masks,8)
return masks
def flushOutString(f,OutString,BlockSize,BlockLimit):
"""Internal function for writeISISmasks procedure,
which writes down specified number of mask blocks,
not to exceed the specified number of masks in row.
"""
BlockSize+=1
if BlockSize >= BlockLimit:
if len(OutString)>0:
f.write(OutString+'\n')
OutString = ''
BlockSize = 0
return (f,BlockSize,OutString)
def writeISISmasks(filename,masks,nSpectraInRow=8):
"""Function writes input array in the form of ISSI mask file array
This is the helper function for export_mask procedure,
which can be used separately
namely, if one have array 1,2,3,4, 20, 30,31,32
file will have the following ASCII stings:
1-4 20 30-32
nSpectaInRow indicates the number of the separate spectra ID (numbers) which the program
needs to fit into one row. For the example above the number has to be 5 or more
to fit all spectra into a single row. Setting it to one will produce 8 rows with single number in each.
Usage:
>>writeISISmasks(fileName,masks)
where:
fileName -- the name of the output file
masks -- the array with data
"""
ext = os.path.splitext(filename)[1]
if len(ext) == 0 :
filename=filename+'.msk'
OutString = ''
LastSpectraN= ''
BlockSize = 0
iDash = 0
im1=masks[0]
with open(filename,'w') as f:
# prepare and write mask data in conventional msk format
# where adjusted spectra are separated by "-" sign
for i in masks:
if len(OutString)== 0:
OutString = str(i)
(f,BlockSize,OutString) = flushOutString(f,OutString,BlockSize,nSpectraInRow)
im1 = i
continue
# if the current spectra is different from the previous one by 1 only, we may want to skip it
if im1+1 == i :
LastSpectraN = str(i)
iDash += 1
else : # it is different and should be dealt separately
if iDash > 0 :
OutString = OutString+'-'+LastSpectraN
iDash = 0
LastSpectraN=''
# write the string if it is finished
(f,BlockSize,OutString) = flushOutString(f,OutString,BlockSize,nSpectraInRow)
if len(OutString) == 0:
OutString = str(i)
else:
OutString = OutString + ' ' + str(i)
# write the string if it is finished
(f,BlockSize,OutString) = flushOutString(f,OutString,BlockSize,nSpectraInRow)
#endif
# current spectra is the previous now
im1 = i
# end masks loop
if iDash > 0 :
OutString = OutString+'-'+LastSpectraN
(f,OutString,BlockSize)=flushOutString(f,OutString,BlockSize,0)
class ExportSpectraMask(PythonAlgorithm):
""" Export workspace's mask
"""
def category(self):
""" Return category
"""
return "DataHandling\\Masking"
def name(self):
""" Return name
"""
return "ExportSpectraMask"
def summary(self):
return "Returns list of spectra numbers which are masked on a workspace"\
" and can save these numbers as legacy .msk file."
def PyInit(self):
""" Declare properties
"""
self.declareProperty(WorkspaceProperty("Workspace", "",Direction.Input), "The workspace to export masks from.")
self.declareProperty(FileProperty(name="Filename",defaultValue="",action=FileAction.OptionalSave,
extensions = [".msk"],direction=Direction.Input),
doc="The name or full path to the file to save mask to."
" If empty, the name of the input workspace and default save directory are used.")
self.declareProperty("ExportMaskOnly",False,"If true, algorithm will not save mask in a file"
"and only returns the list containing numbers of masked spectra.",
Direction.Input)
self.declareProperty(IntArrayProperty(name="SpectraMasks",direction = Direction.Output),
doc="List of the masked spectra numbers.")
return
def PyExec(self):
""" Main execution body
"""
#get parameters
ws = self.getProperty("Workspace").value
out_file_name = self.getProperty("Filename").value
export_masks_only = self.getProperty("ExportMaskOnly").value
masks = export_masks(ws,out_file_name ,export_masks_only)
self.setProperty("SpectraMasks", masks)
return
AlgorithmFactory.subscribe(ExportSpectraMask)