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Add suport of F in table to specify fluorescence data
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f66d0c8be7
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@ -7,12 +7,12 @@ from pathlib import Path
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from lib import LaTeX
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from lib.Orientation import Orientation
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from TexSoup import TexSoup
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from lib.data import AbsDataFile,ZPEDataFile,FluoDataFile,dataType
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from lib.data import dataFileBase,dataType
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import argparse
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DEBUG=True
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DEBUG=False
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parser = argparse.ArgumentParser()
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parser.add_argument('--file', type=argparse.FileType('r'))
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parser.add_argument('--type', type=str, choices=[t.name for t in list(dataType)])
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parser.add_argument('--defaultType', type=str, choices=[t.name for t in list(dataType)])
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parser.add_argument('--MoleculeOrentation',type=str, choices=[t.name for t in list(Orientation)],default=Orientation.LINE.name)
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args = parser.parse_args()
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print(args)
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@ -26,12 +26,6 @@ if DEBUG:
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datapath=datapath/"test"
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if not datapath.exists():
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datapath.mkdir()
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switcher={
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dataType.ABS: AbsDataFile,
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dataType.FLUO: FluoDataFile,
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dataType.ZPE: ZPEDataFile
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}
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filecls=switcher.get(dataType[args.type])
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datalst=filecls.readFromTable(dat,Orientation[args.MoleculeOrentation])
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datalst=dataFileBase.readFromTable(dat,orientation=Orientation[args.MoleculeOrentation],default=dataType[args.defaultType])
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for data in datalst:
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data.toFile(datapath)
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@ -30,37 +30,56 @@ class dataFileBase(object):
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pass
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@staticmethod
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def convertState(StateTablelist,firstState=state(1,1,"A_1")):
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def convertState(StateTablelist,default=dataType.ABS,firstState=state(1,1,"A_1")):
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tmplst=[]
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for TexState in StateTablelist:
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trtype=default
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lst=list(TexState.find("$").contents)
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st=str(lst[0])
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m=re.match(r"^\^(?P<multiplicity>\d)(?P<symm>[^\s\[(]*)\s*(?:\[(?:\\mathrm{)?(?P<special>\w)(?:})\])?\s*\((?P<type>[^\)]*)\)",st)
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seq=m.group("multiplicity","symm")
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tmplst.append(seq)
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spgrp=m.group("special")
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if spgrp is not None and spgrp=="F":
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trtype=dataType.FLUO
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tmplst.append((*seq,trtype))
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lst=[]
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for index,item in enumerate(tmplst):
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unformfirststate=(str(firstState.multiplicity),firstState.symetry)
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count=([unformfirststate]+tmplst[:index+1]).count(item)
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lst.append(state(count,int(item[0]),item[1]))
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lst.append((state(count,int(item[0]),item[1]),item[2]))
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return lst
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@classmethod
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def readFromTable(cls, table,orientation=Orientation.LINE ,firstState=state(1,1,"A_1")):
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@staticmethod
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def readFromTable(table,orientation=Orientation.LINE,default=dataType.ABS ,firstState=state(1,1,"A_1")):
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datalist=list()
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switcher={
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dataType.ABS:AbsDataFile,
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dataType.FLUO:FluoDataFile,
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dataType.ZPE:ZPEDataFile
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}
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if orientation==Orientation.LINE:
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for col in range(1,np.size(table,1)):
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data=cls()
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col=table[:,col]
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data.molecule=str(col[0])
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data.method=method(str(col[2]),str(col[1]))
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finsts=cls.convertState(table[3:,0],firstState)
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mymolecule=str(col[0])
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mymethod=method(str(col[2]),str(col[1]))
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finsts=dataFileBase.convertState(table[3:,0],firstState)
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datacls=dict()
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for index,cell in enumerate(col[3:]):
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if str(cell)!="":
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val= list(cell.contents)[0]
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val=float(str(val))
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data.excitations.append(excitationValue(firstState,finsts[index],val))
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datalist.append(data)
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finst=finsts[index]
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dt=finst[1]
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if dt in datacls:
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data=datacls[dt]
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else:
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cl=switcher[dt]
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data=cl()
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data.molecule=mymolecule
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data.method=mymethod
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data.excitations.append(excitationValue(firstState,finst[0],val))
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for value in datacls.values():
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datalist.append(value)
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return datalist
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else:
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subtablesindex=list()
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@ -71,17 +90,33 @@ class dataFileBase(object):
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firstindex=i
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for first, last in subtablesindex:
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for col in range(2,np.size(table,1)):
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data=cls()
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col=table[:,col]
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data.molecule=str(table[first,0])
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data.method=method(str(col[1]),str(col[0]))
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finsts=cls.convertState(table[first:last+1,1],firstState)
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mymolecule=str(table[first,0])
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mymethod=method(str(col[1]),str(col[0]))
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finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState)
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for col in range(2,np.size(table,1)):
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datacls=dict()
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col=table[:,col]
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mymolecule=str(table[first,0])
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mymethod=method(str(col[1]),str(col[0]))
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finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState)
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for index,cell in enumerate(col[first:last+1]):
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if str(cell)!="":
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val= list(cell.contents)[0]
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val=float(str(val))
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data.excitations.append(excitationValue(firstState,finsts[index],val))
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datalist.append(data)
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finst=finsts[index]
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dt=finst[1]
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if dt in datacls:
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data=datacls[dt]
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else:
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cl=switcher[dt]
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data=cl()
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data.molecule=mymolecule
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data.method=mymethod
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datacls[dt]=data
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data.excitations.append(excitationValue(firstState,finst[0],val))
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for value in datacls.values():
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datalist.append(value)
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return datalist
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def getMetadata(self):
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dic=OrderedDict()
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@ -156,10 +191,6 @@ class oneStateDataFileBase(dataFileBase):
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dic.move_to_end("DOI")
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return dic
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@classmethod
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def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,orientation,firstState=firstState)
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return data
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class AbsDataFile(oneStateDataFileBase):
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def __init__(self):
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super(AbsDataFile,self).__init__()
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@ -182,10 +213,6 @@ class twoStateDataFileBase(dataFileBase):
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self.GS=None
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self.ES=None
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@classmethod
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def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,Orientation,firstState=firstState)
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return data
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def getMetadata(self):
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dic=super(twoStateDataFileBase,self).getMetadata()
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dic["GS"]= "" if self.GS is None else self.GS.toDataString()
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