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uio.py
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uio.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Oct 29 2013
@author: Kolja Glogowski
Modified: René Salhab (10.03.2017)
- Put functions into corresponding classes
- Introduced compatibility with .eos files
"""
import os
import re
import collections
import numpy as np
from struct import Struct
_uint_from_bytes = Struct('>I')
class _EntryMapping(collections.Mapping):
def __init__(self, entries):
self._entries = entries
def __getitem__(self, key):
for e in self._entries:
if e.name == key:
return e
raise KeyError('%s' % key)
def __iter__(self):
for e in self._entries:
yield e.name
def __len__(self):
return len(self._entries)
def values(self):
return self._entries
def items(self):
return [(e.name, e) for e in self._entries]
def iteritems(self):
for e in self._entries:
yield (e.name, e)
def itervalues(self):
for e in self._entries:
yield e
class Entry(object):
def __init__(self, fd, pos, type, name, params, dtype, shape):
self._fd = fd
self.pos = pos
self.type = type
self.name = name
self.params = params
self.dtype = dtype
self.shape = shape
def __repr__(self):
slist = [self.type, self.name]
for k in ['b', 'd', 'u']:
if k in self.params:
v = self.params[k]
if ' ' in v:
v = "'%s'" % v
slist.append('%s=%s' % (k, v))
return '<%s>' % (' '.join(slist))
@property
def data(self):
self._fd.seek(self.pos)
a = self._read_array()
if self.type != 'character':
return a.reshape(self.shape) if self.shape != None else a[0]
else:
if self.shape == None:
return a[0].rstrip()
elif len(self.shape) == 1:
return [s.rstrip() for s in a]
else:
return a.reshape(self.shape)
def _read_array(self):
dt = np.dtype(self.dtype).newbyteorder('>')
nbytes = self._read_block_size()
data = np.fromfile(self._fd, dtype=dt, count=nbytes // dt.itemsize)
if nbytes != self._read_block_size():
raise IOError('error reading array')
return data.astype(data.dtype.newbyteorder('='))
def _read_block_size(self):
data = self._fd.read(4)
if len(data) != 4:
raise EOFError()
return _uint_from_bytes.unpack(data)[0]
class Block(_EntryMapping):
def __init__(self, pos, params, entries):
self.pos = pos
self.params = params
super(Block, self).__init__(entries)
def __repr__(self):
slist = [ 'block' ]
slist.append('entries=%d' % len(self._entries))
return '<%s>' % (' '.join(slist))
class Box(_EntryMapping):
def __init__(self, pos, params, entries):
self.pos = pos
self.params = params
super(Box, self).__init__(entries)
def __repr__(self):
slist = [ 'box' ]
slist.append('entries=%d' % len(self._entries))
return '<%s>' % (' '.join(slist))
class DataSet(_EntryMapping):
def __init__(self, pos, params, entries, box):
self.pos = pos
self.params = params
self.box = box
super(DataSet, self).__init__(entries)
def __repr__(self):
slist = [ 'dataset' ]
slist.append('entries=%d' % len(self._entries))
slist.append('boxes=%d' % len(self.box))
return '<%s>' % (' '.join(slist))
class File(_EntryMapping):
def __init__(self, filename):
_, fend = os.path.splitext(filename)
self._fd = open(os.path.abspath(filename), 'rb')
self._re_params = re.compile(r"\w+=(?:(?:'[^']*')|(?:\S+))")
self._re_desc = re.compile(r"^(\w+) (\w+) ?(.*)$")
self._re_dims = re.compile('\d+:\d+')
self._fd.seek(0)
ff, uio, self.header = self._parse_descriptor()
if ff != 'fileform' or uio != 'uio':
raise IOError('unknown file format')
entries = []
if fend == ".eos":
self.block = []
self.dataset = None
else:
self.block = None
self.dataset = []
for x in self._read_file_entries():
if isinstance(x, DataSet):
self.dataset.append(x)
elif isinstance(x, Entry):
entries.append(x)
elif isinstance(x, Block):
self.block.append(x)
super(File, self).__init__(entries)
def __repr__(self):
slist = [ 'uio' ]
slist.append('entries=%d' % len(self._entries))
if isinstance(self.block, list):
slist.append('blocks=%d' % len(self.block))
elif isinstance(self.dataset, list):
slist.append('datasets=%d' % len(self.dataset))
return '<%s>' % (' '.join(slist))
def __enter__(self):
return self
def __exit__(self, exc_type, exc_val, exc_tb):
self._fd.close()
def close(self):
self._fd.close()
@property
def closed(self):
return self._fd.closed
@property
def name(self):
return self._fd.name
def _read_file_entries(self):
entries = []
while True:
try:
entry = self._read_entry()
except EOFError:
break
if entry.type == 'label' and entry.name == 'dataset':
ds_box = []
ds_entries = []
for ei in self._read_dataset_entries():
if isinstance(ei, Box):
ds_box.append(ei)
elif isinstance(ei, Entry):
ds_entries.append(ei)
ds = DataSet(pos=self._fd.tell(), params=entry.params, entries=ds_entries, box=ds_box)
entries.append(ds)
elif entry.type == 'label' and entry.name == 'block':
ds_entries = []
for ei in self._read_box_entries():
if isinstance(ei, Entry):
ds_entries.append(ei)
ds = Block(pos=self._fd.tell(), params=entry.params, entries=ds_entries)
entries.append(ds)
else:
entries.append(entry)
self._skip_block()
return entries
def _read_dataset_entries(self):
while True:
entry = self._read_entry()
if entry.type == 'label':
if entry.name == 'enddataset':
break
elif entry.name == 'box':
yield Box(pos=self._fd.tell(), params=entry.params, entries=self._read_box_entries())
elif entry.name == 'block':
yield Block(pos=self._fd.tell(), params=entry.params, entries=self._read_box_entries())
else:
yield entry
self._skip_block()
def _read_box_entries(self):
box = []
while True:
entry = self._read_entry()
if entry.type == 'label' and (entry.name == 'endbox' or entry.name == 'endblock'):
break
box.append(entry)
self._skip_block()
return box
def _read_entry(self):
etype, name, params = self._parse_descriptor()
if etype == 'table':
raise IOError('uio files containing tables are not supported')
pos = self._fd.tell()
dtype = None
if 'b' in params:
nbytes = int(params['b'])
if etype == 'real':
dtype = 'f%d' % nbytes
elif etype == 'integer':
dtype = 'i%d' % nbytes
elif etype == 'character':
dtype = 'S%d' % nbytes
elif etype == 'complex':
dtype = 'c%d' % nbytes
shape = None
if 'd' in params:
fshape = []
for x in self._re_dims.findall(params['d']):
x1, x2 = x.split(':')
fshape.append(int(x2) - int(x1) + 1)
shape = tuple(reversed(fshape))
return Entry(fd=self._fd, pos=pos, type=etype, name=name, params=params, dtype=dtype, shape=shape)
def _read_string(self):
s = self._read_block()
while s.rstrip().endswith(b'&'):
s = s.rstrip()[:-1] + self._read_block()
return s.rstrip()
def _read_block(self):
nbytes = self._read_block_size()
data = self._fd.read(nbytes)
if nbytes != self._read_block_size():
raise IOError('error reading block')
return data
def _skip_block(self):
nbytes = self._read_block_size()
self._fd.seek(nbytes, 1)
if nbytes != self._read_block_size():
raise IOError('error skipping block')
def _read_block_size(self):
data = self._fd.read(4)
if len(data) != 4:
raise EOFError()
return _uint_from_bytes.unpack(data)[0]
def _parse_descriptor(self):
m = self._re_desc.match(self._read_string().decode())
if not m:
return None
etype, name, pstr = m.groups()
params = {}
for it in self._re_params.findall(pstr):
key, value = it.split('=', 1)
params[key] = value.strip("'")
return etype, name, params
if __name__ == '__main__':
from numpy import *
fname = os.path.join("Z:\cobold\scratchy\job_d3gt57g44v100rsn01_400x400x188", "rhd010.mean")
f = File(fname)