mirror of
https://github.com/LCPQ/QUESTDB_website.git
synced 2024-07-22 18:57:38 +02:00
Add suport of F in table to specify fluorescence data
This commit is contained in:
parent
f66d0c8be7
commit
9c18598f82
@ -7,12 +7,12 @@ from pathlib import Path
|
||||
from lib import LaTeX
|
||||
from lib.Orientation import Orientation
|
||||
from TexSoup import TexSoup
|
||||
from lib.data import AbsDataFile,ZPEDataFile,FluoDataFile,dataType
|
||||
from lib.data import dataFileBase,dataType
|
||||
import argparse
|
||||
DEBUG=True
|
||||
DEBUG=False
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument('--file', type=argparse.FileType('r'))
|
||||
parser.add_argument('--type', type=str, choices=[t.name for t in list(dataType)])
|
||||
parser.add_argument('--defaultType', type=str, choices=[t.name for t in list(dataType)])
|
||||
parser.add_argument('--MoleculeOrentation',type=str, choices=[t.name for t in list(Orientation)],default=Orientation.LINE.name)
|
||||
args = parser.parse_args()
|
||||
print(args)
|
||||
@ -26,12 +26,6 @@ if DEBUG:
|
||||
datapath=datapath/"test"
|
||||
if not datapath.exists():
|
||||
datapath.mkdir()
|
||||
switcher={
|
||||
dataType.ABS: AbsDataFile,
|
||||
dataType.FLUO: FluoDataFile,
|
||||
dataType.ZPE: ZPEDataFile
|
||||
}
|
||||
filecls=switcher.get(dataType[args.type])
|
||||
datalst=filecls.readFromTable(dat,Orientation[args.MoleculeOrentation])
|
||||
datalst=dataFileBase.readFromTable(dat,orientation=Orientation[args.MoleculeOrentation],default=dataType[args.defaultType])
|
||||
for data in datalst:
|
||||
data.toFile(datapath)
|
||||
@ -30,37 +30,56 @@ class dataFileBase(object):
|
||||
pass
|
||||
|
||||
@staticmethod
|
||||
def convertState(StateTablelist,firstState=state(1,1,"A_1")):
|
||||
def convertState(StateTablelist,default=dataType.ABS,firstState=state(1,1,"A_1")):
|
||||
tmplst=[]
|
||||
for TexState in StateTablelist:
|
||||
trtype=default
|
||||
lst=list(TexState.find("$").contents)
|
||||
st=str(lst[0])
|
||||
m=re.match(r"^\^(?P<multiplicity>\d)(?P<symm>[^\s\[(]*)\s*(?:\[(?:\\mathrm{)?(?P<special>\w)(?:})\])?\s*\((?P<type>[^\)]*)\)",st)
|
||||
seq=m.group("multiplicity","symm")
|
||||
tmplst.append(seq)
|
||||
spgrp=m.group("special")
|
||||
if spgrp is not None and spgrp=="F":
|
||||
trtype=dataType.FLUO
|
||||
tmplst.append((*seq,trtype))
|
||||
lst=[]
|
||||
for index,item in enumerate(tmplst):
|
||||
unformfirststate=(str(firstState.multiplicity),firstState.symetry)
|
||||
count=([unformfirststate]+tmplst[:index+1]).count(item)
|
||||
lst.append(state(count,int(item[0]),item[1]))
|
||||
lst.append((state(count,int(item[0]),item[1]),item[2]))
|
||||
return lst
|
||||
|
||||
@classmethod
|
||||
def readFromTable(cls, table,orientation=Orientation.LINE ,firstState=state(1,1,"A_1")):
|
||||
@staticmethod
|
||||
def readFromTable(table,orientation=Orientation.LINE,default=dataType.ABS ,firstState=state(1,1,"A_1")):
|
||||
datalist=list()
|
||||
switcher={
|
||||
dataType.ABS:AbsDataFile,
|
||||
dataType.FLUO:FluoDataFile,
|
||||
dataType.ZPE:ZPEDataFile
|
||||
}
|
||||
if orientation==Orientation.LINE:
|
||||
for col in range(1,np.size(table,1)):
|
||||
data=cls()
|
||||
col=table[:,col]
|
||||
data.molecule=str(col[0])
|
||||
data.method=method(str(col[2]),str(col[1]))
|
||||
finsts=cls.convertState(table[3:,0],firstState)
|
||||
mymolecule=str(col[0])
|
||||
mymethod=method(str(col[2]),str(col[1]))
|
||||
finsts=dataFileBase.convertState(table[3:,0],firstState)
|
||||
datacls=dict()
|
||||
for index,cell in enumerate(col[3:]):
|
||||
if str(cell)!="":
|
||||
val= list(cell.contents)[0]
|
||||
val=float(str(val))
|
||||
data.excitations.append(excitationValue(firstState,finsts[index],val))
|
||||
datalist.append(data)
|
||||
finst=finsts[index]
|
||||
dt=finst[1]
|
||||
if dt in datacls:
|
||||
data=datacls[dt]
|
||||
else:
|
||||
cl=switcher[dt]
|
||||
data=cl()
|
||||
data.molecule=mymolecule
|
||||
data.method=mymethod
|
||||
data.excitations.append(excitationValue(firstState,finst[0],val))
|
||||
for value in datacls.values():
|
||||
datalist.append(value)
|
||||
return datalist
|
||||
else:
|
||||
subtablesindex=list()
|
||||
@ -71,17 +90,33 @@ class dataFileBase(object):
|
||||
firstindex=i
|
||||
for first, last in subtablesindex:
|
||||
for col in range(2,np.size(table,1)):
|
||||
data=cls()
|
||||
col=table[:,col]
|
||||
data.molecule=str(table[first,0])
|
||||
data.method=method(str(col[1]),str(col[0]))
|
||||
finsts=cls.convertState(table[first:last+1,1],firstState)
|
||||
mymolecule=str(table[first,0])
|
||||
mymethod=method(str(col[1]),str(col[0]))
|
||||
finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState)
|
||||
for col in range(2,np.size(table,1)):
|
||||
datacls=dict()
|
||||
col=table[:,col]
|
||||
mymolecule=str(table[first,0])
|
||||
mymethod=method(str(col[1]),str(col[0]))
|
||||
finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState)
|
||||
for index,cell in enumerate(col[first:last+1]):
|
||||
if str(cell)!="":
|
||||
val= list(cell.contents)[0]
|
||||
val=float(str(val))
|
||||
data.excitations.append(excitationValue(firstState,finsts[index],val))
|
||||
datalist.append(data)
|
||||
finst=finsts[index]
|
||||
dt=finst[1]
|
||||
if dt in datacls:
|
||||
data=datacls[dt]
|
||||
else:
|
||||
cl=switcher[dt]
|
||||
data=cl()
|
||||
data.molecule=mymolecule
|
||||
data.method=mymethod
|
||||
datacls[dt]=data
|
||||
data.excitations.append(excitationValue(firstState,finst[0],val))
|
||||
for value in datacls.values():
|
||||
datalist.append(value)
|
||||
return datalist
|
||||
def getMetadata(self):
|
||||
dic=OrderedDict()
|
||||
@ -156,10 +191,6 @@ class oneStateDataFileBase(dataFileBase):
|
||||
dic.move_to_end("DOI")
|
||||
return dic
|
||||
|
||||
@classmethod
|
||||
def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
|
||||
data=super().readFromTable(table,orientation,firstState=firstState)
|
||||
return data
|
||||
class AbsDataFile(oneStateDataFileBase):
|
||||
def __init__(self):
|
||||
super(AbsDataFile,self).__init__()
|
||||
@ -182,10 +213,6 @@ class twoStateDataFileBase(dataFileBase):
|
||||
self.GS=None
|
||||
self.ES=None
|
||||
|
||||
@classmethod
|
||||
def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
|
||||
data=super().readFromTable(table,Orientation,firstState=firstState)
|
||||
return data
|
||||
def getMetadata(self):
|
||||
dic=super(twoStateDataFileBase,self).getMetadata()
|
||||
dic["GS"]= "" if self.GS is None else self.GS.toDataString()
|
||||
|
||||
Loading…
Reference in New Issue
Block a user