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Refs #11625. Encapsulating whole definition in try/catch block
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Just the registration did not seem to be enough, as the parser class depends on pyparsing. Encapsulating everything into one try/catch block solves the issue.
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Michael Wedel committed Apr 23, 2015
1 parent f482f80 commit 64df36a
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303 changes: 151 additions & 152 deletions Code/Mantid/Framework/PythonInterface/plugins/algorithms/PoldiCreatePeaksFromFile.py
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Expand Up @@ -4,217 +4,216 @@
from mantid.api import *
from mantid.geometry import *

from pyparsing import *

import os

try:
from pyparsing import *

class PoldiCompound(object):
"""Small helper class to handle the results from PoldiCrystalFileParser."""
_name = ""
_spacegroup = ""
_atomString = ""
_cellDict = ""
class PoldiCompound(object):
"""Small helper class to handle the results from PoldiCrystalFileParser."""
_name = ""
_spacegroup = ""
_atomString = ""
_cellDict = ""

def __init__(self, name, elements):
self._name = name
def __init__(self, name, elements):
self._name = name

self.assign(elements)
self.assign(elements)

def assign(self, elements):
for c in elements:
if c[0] == "atoms":
self._atomString = ';'.join(c[1:])
elif c[0] == "lattice":
cellNames = ['a', 'b', 'c', 'alpha', 'beta', 'gamma']
self._cellDict = dict(zip(cellNames, c[1:]))
elif c[0] == "spacegroup":
self._spacegroup = c[1]
def assign(self, elements):
for c in elements:
if c[0] == "atoms":
self._atomString = ';'.join(c[1:])
elif c[0] == "lattice":
cellNames = ['a', 'b', 'c', 'alpha', 'beta', 'gamma']
self._cellDict = dict(zip(cellNames, c[1:]))
elif c[0] == "spacegroup":
self._spacegroup = c[1]

def getAtomString(self):
return self._atomString
def getAtomString(self):
return self._atomString

def getCellParameters(self):
return self._cellDict
def getCellParameters(self):
return self._cellDict

def getSpaceGroup(self):
return self._spacegroup
def getSpaceGroup(self):
return self._spacegroup

def getName(self):
return self._name
def getName(self):
return self._name


def raiseParseErrorException(message):
raise ParseException(message)
def raiseParseErrorException(message):
raise ParseException(message)


class PoldiCrystalFileParser(object):
"""Small parser for crystal structure files used at POLDI
class PoldiCrystalFileParser(object):
"""Small parser for crystal structure files used at POLDI
This class encapsulates a small parser for crystal structure files that are used at
POLDI. The files contains information about the lattice, the space group and the basis (atoms
in the asymmetric unit).
This class encapsulates a small parser for crystal structure files that are used at
POLDI. The files contains information about the lattice, the space group and the basis (atoms
in the asymmetric unit).
The file format is defined as follows:
The file format is defined as follows:
Compound_1 {
Lattice: [1 - 6 floats] => a, b, c, alpha, beta, gamma
Spacegroup: [valid space group symbol]
Atoms; {
Element x y z [occupancy [U_eq]]
Element x y z [occupancy [U_eq]]
Compound_1 {
Lattice: [1 - 6 floats] => a, b, c, alpha, beta, gamma
Spacegroup: [valid space group symbol]
Atoms; {
Element x y z [occupancy [U_eq]]
Element x y z [occupancy [U_eq]]
}
}
}
Compound_2 {
...
}
Compound_2 {
...
}
The parser returns a list of PoldiCompound objects with the compounds that were found
in the file. These are then processed by PoldiCreatePeaksFromFile to generate arguments
for calling PoldiCreatePeaksFromCell.
"""
elementSymbol = Word(alphas, min=1, max=2).setFailAction(
lambda o, s, loc, token: raiseParseErrorException("Element symbol must be one or two characters."))
integerNumber = Word(nums)
decimalSeparator = Literal('.')
floatNumber = Combine(
integerNumber +
Optional(decimalSeparator + Optional(integerNumber))
)
The parser returns a list of PoldiCompound objects with the compounds that were found
in the file. These are then processed by PoldiCreatePeaksFromFile to generate arguments
for calling PoldiCreatePeaksFromCell.
"""
elementSymbol = Word(alphas, min=1, max=2).setFailAction(
lambda o, s, loc, token: raiseParseErrorException("Element symbol must be one or two characters."))
integerNumber = Word(nums)
decimalSeparator = Literal('.')
floatNumber = Combine(
integerNumber +
Optional(decimalSeparator + Optional(integerNumber))
)

whiteSpace = Suppress(White())
whiteSpace = Suppress(White())

atomLine = Combine(
elementSymbol + whiteSpace +
delimitedList(floatNumber, delim=White()),
joinString=' '
)
atomLine = Combine(
elementSymbol + whiteSpace +
delimitedList(floatNumber, delim=White()),
joinString=' '
)

keyValueSeparator = Suppress(Literal(":"))
keyValueSeparator = Suppress(Literal(":"))

groupOpener = Suppress(Literal('{'))
groupCloser = Suppress(Literal('}'))
groupOpener = Suppress(Literal('{'))
groupCloser = Suppress(Literal('}'))

atomsGroup = Group(CaselessLiteral("atoms") + keyValueSeparator +
groupOpener + delimitedList(atomLine, delim=lineEnd) + groupCloser)
atomsGroup = Group(CaselessLiteral("atoms") + keyValueSeparator +
groupOpener + delimitedList(atomLine, delim=lineEnd) + groupCloser)

unitCell = Group(CaselessLiteral("lattice") + keyValueSeparator + delimitedList(
floatNumber, delim=White()))
unitCell = Group(CaselessLiteral("lattice") + keyValueSeparator + delimitedList(
floatNumber, delim=White()))

spaceGroup = Group(CaselessLiteral("spacegroup") + keyValueSeparator + Word(
alphanums + "-" + ' '))
spaceGroup = Group(CaselessLiteral("spacegroup") + keyValueSeparator + Word(
alphanums + "-" + ' '))

compoundContent = Each([atomsGroup, unitCell, spaceGroup]).setFailAction(
lambda o, s, loc, token: raiseParseErrorException(
"One of 'Lattice', 'SpaceGroup', 'Atoms' is missing or contains errors."))
compoundContent = Each([atomsGroup, unitCell, spaceGroup]).setFailAction(
lambda o, s, loc, token: raiseParseErrorException(
"One of 'Lattice', 'SpaceGroup', 'Atoms' is missing or contains errors."))

compoundName = Word(alphanums + '_')
compoundName = Word(alphanums + '_')

compound = Group(compoundName + Optional(whiteSpace) + \
groupOpener + compoundContent + groupCloser)
compound = Group(compoundName + Optional(whiteSpace) + \
groupOpener + compoundContent + groupCloser)

comment = Suppress(Literal('#') + restOfLine)
comment = Suppress(Literal('#') + restOfLine)

compounds = Optional(comment) + OneOrMore(compound).ignore(comment) + stringEnd
compounds = Optional(comment) + OneOrMore(compound).ignore(comment) + stringEnd

def __call__(self, contentString):
parsedContent = None
def __call__(self, contentString):
parsedContent = None

if os.path.isfile(contentString):
parsedContent = self._parseFile(contentString)
else:
parsedContent = self._parseString(contentString)
if os.path.isfile(contentString):
parsedContent = self._parseFile(contentString)
else:
parsedContent = self._parseString(contentString)

return [PoldiCompound(x[0], x[1:]) for x in parsedContent]
return [PoldiCompound(x[0], x[1:]) for x in parsedContent]

def _parseFile(self, filename):
return self.compounds.parseFile(filename)
def _parseFile(self, filename):
return self.compounds.parseFile(filename)

def _parseString(self, stringContent):
return self.compounds.parseString(stringContent)
def _parseString(self, stringContent):
return self.compounds.parseString(stringContent)


class PoldiCreatePeaksFromFile(PythonAlgorithm):
_parser = PoldiCrystalFileParser()
class PoldiCreatePeaksFromFile(PythonAlgorithm):
_parser = PoldiCrystalFileParser()

def category(self):
return "SINQ\\POLDI"
def category(self):
return "SINQ\\POLDI"

def name(self):
return "PoldiLoadCrystalData"
def name(self):
return "PoldiLoadCrystalData"

def summary(self):
return ("The algorithm reads a POLDI crystal structure file and creates a WorkspaceGroup that contains tables"
"with the expected reflections.")
def summary(self):
return ("The algorithm reads a POLDI crystal structure file and creates a WorkspaceGroup that contains tables"
"with the expected reflections.")

def PyInit(self):
self.declareProperty(
FileProperty(name="InputFile",
defaultValue="",
action=FileAction.Load,
extensions=["dat"]),
doc="A file with POLDI crystal data.")
def PyInit(self):
self.declareProperty(
FileProperty(name="InputFile",
defaultValue="",
action=FileAction.Load,
extensions=["dat"]),
doc="A file with POLDI crystal data.")

self.declareProperty("LatticeSpacingMin", 0.5,
direction=Direction.Input,
doc="Lowest allowed lattice spacing.")
self.declareProperty("LatticeSpacingMin", 0.5,
direction=Direction.Input,
doc="Lowest allowed lattice spacing.")

self.declareProperty("LatticeSpacingMax", 0.0,
direction=Direction.Input,
doc="Largest allowed lattice spacing.")
self.declareProperty("LatticeSpacingMax", 0.0,
direction=Direction.Input,
doc="Largest allowed lattice spacing.")

self.declareProperty(
WorkspaceProperty(name="OutputWorkspace",
defaultValue="", direction=Direction.Output),
doc="WorkspaceGroup with reflection tables.")
self.declareProperty(
WorkspaceProperty(name="OutputWorkspace",
defaultValue="", direction=Direction.Output),
doc="WorkspaceGroup with reflection tables.")


def PyExec(self):
crystalFileName = self.getProperty("InputFile").value
try:
# Try parsing the supplied file using PoldiCrystalFileParser
compounds = self._parser(crystalFileName)
def PyExec(self):
crystalFileName = self.getProperty("InputFile").value
try:
# Try parsing the supplied file using PoldiCrystalFileParser
compounds = self._parser(crystalFileName)

dMin = self.getProperty("LatticeSpacingMin").value
dMax = self.getProperty("LatticeSpacingMax").value
dMin = self.getProperty("LatticeSpacingMin").value
dMax = self.getProperty("LatticeSpacingMax").value

workspaces = []
workspaces = []

# Go through found compounds and run "_createPeaksFromCell" for each of them
# If two compounds have the same name, a warning is written to the log.
for compound in compounds:
if compound.getName() in workspaces:
self.log().warning("A compound with the name '" + compound.getName() + \
"' has already been created. Please check the file '" + crystalFileName + "'")
else:
workspaces.append(self._createPeaksFromCell(compound, dMin, dMax))
# Go through found compounds and run "_createPeaksFromCell" for each of them
# If two compounds have the same name, a warning is written to the log.
for compound in compounds:
if compound.getName() in workspaces:
self.log().warning("A compound with the name '" + compound.getName() + \
"' has already been created. Please check the file '" + crystalFileName + "'")
else:
workspaces.append(self._createPeaksFromCell(compound, dMin, dMax))

self.setProperty("OutputWorkspace", GroupWorkspaces(workspaces))
self.setProperty("OutputWorkspace", GroupWorkspaces(workspaces))

# All parse errors are caught here and logged as errors
except ParseException as error:
errorString = "Could not parse input file '" + crystalFileName + "'.\n"
errorString += "The parser reported the following error:\n\t" + str(error)
# All parse errors are caught here and logged as errors
except ParseException as error:
errorString = "Could not parse input file '" + crystalFileName + "'.\n"
errorString += "The parser reported the following error:\n\t" + str(error)

self.log().error(errorString)
self.log().error(errorString)


def _createPeaksFromCell(self, compound, dMin, dMax):
if not SpaceGroupFactory.isSubscribedSymbol(compound.getSpaceGroup()):
raise RuntimeError("SpaceGroup '" + compound.getSpaceGroup() + "' is not registered.")
def _createPeaksFromCell(self, compound, dMin, dMax):
if not SpaceGroupFactory.isSubscribedSymbol(compound.getSpaceGroup()):
raise RuntimeError("SpaceGroup '" + compound.getSpaceGroup() + "' is not registered.")

PoldiCreatePeaksFromCell(SpaceGroup=compound.getSpaceGroup(),
Atoms=compound.getAtomString(),
LatticeSpacingMin=dMin,
LatticeSpacingMax=dMax,
OutputWorkspace=compound.getName(),
**compound.getCellParameters())
PoldiCreatePeaksFromCell(SpaceGroup=compound.getSpaceGroup(),
Atoms=compound.getAtomString(),
LatticeSpacingMin=dMin,
LatticeSpacingMax=dMax,
OutputWorkspace=compound.getName(),
**compound.getCellParameters())

return compound.getName()

return compound.getName()

try:
import pyparsing
AlgorithmFactory.subscribe(PoldiCreatePeaksFromFile)
except:
logger.debug('Failed to subscribe algorithm PoldiCreatePeaksFromFile; Python package pyparsing'\
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