Source code for nexus.pwscf_data_reader
##################################################################
## (c) Copyright 2015- by Jaron T. Krogel ##
##################################################################
#====================================================================#
# pwscf_data_reader.py #
# Supports data processing of PWSCF's xml output. #
# #
# Content summary: #
# read_qexml #
# Read a data-file.xml and convert to nested object structure. #
# #
# QEXML #
# Class to represent an xml element. #
# #
# readval #
# Function converts an attribute value string to numeric form. #
# #
#====================================================================#
import numpy as np
from .developer import DevBase, obj
from . import numpy_extensions as npe
[docs]
class QEXML(DevBase):
def __init__(self):
self._value = []
#end def __init__
array_keys = set('type size columns len _value'.split())
[docs]
def finalize(self):
keys = list(self.keys())
enums = obj()
for k in keys:
v = self[k]
if isinstance(k,str) and '.' in k and k.split('.',1)[1].isdigit():
name,index = k.split('.',1)
index = int(index)
if name not in enums:
enums[name] = QEXML()
#end if
enums[name][index] = v
del self[k]
continue
#end if
if isinstance(v,QEXML):
if len(set(v.keys())-self.array_keys)==0:
a = np.array(v._value)
if len(a)==1:
a = a[0]
elif 'columns' in v and v.size%v.columns==0:
npe.reshape_inplace(a, (v.size//v.columns, v.columns))
#end if
self[k] = a
else:
v.finalize()
#end if
#end if
#end for
for k,v in enums.items():
self[k] = v
v.finalize()
#end for
if len(self._value)==0:
del self._value
elif 'value' not in self:
if len(self._value)==1:
self.value = self._value[0]
else:
self.value = np.array(self._value)
#end if
del self._value
else:
if len(self._value)==1:
self._value = self._value[0]
else:
self._value = np.array(self._value)
#end if
#end if
#end def finalize
#end class QEXML
bools = obj(F=False,T=True)
[docs]
def readval(s):
s = s.strip()
v = None
if s in bools:
v = bools[s]
else:
try:
v = int(s)
except:
try:
v = float(s)
except:
if ' ' not in s:
v=s
else:
s = s.split()
try:
v=list(np.array(s,dtype=int))
except:
try:
v=list(np.array(s,dtype=float))
except:
v=s
#end try
#end try
#end if
#end try
#end try
#end if
return v
#end readval
[docs]
def read_qexml(inp):
if isinstance(inp,list):
rawlines = inp
elif isinstance(inp,str):# and os.path.exists(inp):
with open(inp, "r") as f:
rawlines = f.read().splitlines()
else:
print('read_qexml error: input can only be filename or list of lines')
print(' input received: ',inp)
return None
#end if
lines = []
incomment = False
for line in rawlines:
ls = line.strip()
if ls.startswith('<!--'):
incomment = True
#end if
if ls.endswith('-->'):
incomment = False
continue
#end if
if not ls.startswith('<?') and not incomment and ls!='':
lines.append(ls)
#end if
#end for
root = QEXML()
stack = [root]
name = ''
level = -1
if len(lines)>0:
for line in lines:
if line.startswith('</'):
#print level*' '+'end',line.strip('</>').lower()
level-=1
stack.pop()
cur = stack[-1]
elif line.startswith('<'):
level+=1
base = stack[level]
ls = line.strip('<>')
ended = ls.endswith('/')
if ended:
ls = ls[0:-1]
#end if
instr=False
lsl = list(tuple(ls))
ls = ''
for i in range(len(lsl)):
c = lsl[i]
if c=='"':
instr = not instr
elif c==' ' and instr:
c='@'
#end if
ls+=c
#end for
tokens = ls.split()
name = tokens[0].lower().replace('-','_')
attrs = tokens[1:]
cur = QEXML()
base[name] = cur
for attr in attrs:
n,v = attr.replace('@',' ').split('=',1)
v=readval(v.strip('"'))
cur[n.lower()]=v
#end for
if not ended:
#print level*' '+name
stack.append(cur)
else:
#print level*' '+name+' end',name
level-=1
cur = base
#end if
else:
v = readval(line)
#print level*' ',v
if isinstance(v,list):
cur._value.extend(v)
else:
cur._value.append(v)
#end if
#end if
#end for
#end if
root.finalize()
return root
#end def read_qexml
