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Add the ability to read a data file from the python library
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@ -86,6 +86,18 @@ class dataFileBase(object):
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count=countlst.count(countitem)
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count=countlst.count(countitem)
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lst.append((state(count,item[0],item[1]),item[2],item[3]))
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lst.append((state(count,item[0],item[1]),item[2],item[3]))
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return lst
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return lst
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def _OnReadMetaPair(self, key, value):
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if key == "molecule":
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self.molecule = value
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elif key == "comment":
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self.comment = value
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elif key == "code":
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self.code = code.fromString(value)
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elif key == "method":
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self.method = method.fromString(value)
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elif key == "article":
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self.article = value
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@staticmethod
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@staticmethod
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def readFromTable(table,TexOps, commands=[]):
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def readFromTable(table,TexOps, commands=[]):
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for formatName,Cls in getFormatHandlers():
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for formatName,Cls in getFormatHandlers():
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@ -104,6 +116,59 @@ class dataFileBase(object):
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dic["article"]="" if self.article is None else self.article
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dic["article"]="" if self.article is None else self.article
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return dic
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return dic
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def _OnReadMeta(self,line,dataType):
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#get key value
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match = dataFileBase._GetMetaRexEx().match(line)
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# normalize key to lower
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key = match.group(1).lower()
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# if data has value
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if match.group(2):
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val = match.group(2)
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self._OnReadMetaPair(key, val)
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@staticmethod
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def _OnReadRow(line):
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vals = re.findall(r"\([^\)]+\)|\S+",line)
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start = state(int(vals[0]), int(vals[1]), vals[2])
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end = state(int(vals[3]), int(vals[4]), vals[5])
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Type = vals[6] if (len(vals) >= 7) else None
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if Type == "_":
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Type = None
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if Type:
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m = re.match(r"^\(([^\)]*)\)$",Type)
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if m:
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Type = m[1]
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val = vals[7] if len(vals) >= 8 else str(np.NaN)
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T1 = vals[8] if len(vals) >= 9 else str(np.NaN)
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oscilatorForces = vals[9] if len(vals) >= 10 else str(np.NaN)
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isUnsafe = vals[10] == json.dumps(True) if len(vals) >= 11 else False
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ex = excitationValue(start, end, val, Type,T1,isUnsafe,oscilatorForces)
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return ex
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@staticmethod
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def _GetMetaRexEx():
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#metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas)
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return re.compile(r"^#\s*([A-Za-z_]+)\s*:\s*(.*)$")
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@staticmethod
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def readFile(stream,dataType):
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lines = stream.readlines()
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# for each line with metadata
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ismetaArea = True
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dat = datafileSelector(dataType)()
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for line in lines:
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#if it's not empty line
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line = line.strip()
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if line:
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# if # may be metadata or comment
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if line[0] == "#":
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# if it's metadata
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if ismetaArea and dataFileBase._GetMetaRexEx().match(line):
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dat._OnReadMeta(line,dataType)
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else: # else its row
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ismetaArea = False
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dat.excitations.append(dat._OnReadRow(line))
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return dat
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def toFile(self,datadir,suffix=None):
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def toFile(self,datadir,suffix=None):
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subpath=datadir/self.GetFileType().name.lower()
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subpath=datadir/self.GetFileType().name.lower()
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if not subpath.exists():
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if not subpath.exists():
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@ -169,6 +234,11 @@ class code:
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self.name = name
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self.name = name
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self.version = version
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self.version = version
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@staticmethod
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def fromString(string):
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vals = string.split(",")
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return method(*vals)
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def toDataString(self):
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def toDataString(self):
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string=self.name
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string=self.name
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if (self.version):
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if (self.version):
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@ -179,6 +249,12 @@ class oneStateDataFileBase(dataFileBase):
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def __init__(self):
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def __init__(self):
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super(oneStateDataFileBase,self).__init__()
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super(oneStateDataFileBase,self).__init__()
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self.geometry = None
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self.geometry = None
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def _OnReadMetaPair(self, key, value):
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if key == "geom":
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self.geometry = method.fromString(value)
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else:
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super(oneStateDataFileBase,self)._OnReadMetaPair(key, value)
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def getMetadata(self):
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def getMetadata(self):
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dic=super(oneStateDataFileBase,self).getMetadata()
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dic=super(oneStateDataFileBase,self).getMetadata()
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