def _read_header_config(fh, header_maxlines=HEADER_MAXLINES,
header_comment=HEADER_COMMENT):
"""Read a ini-style file from the header of a text file. Return a
ConfigParser object.
Parameters
----------
fh : file handle, readable
header_maxlines : max lines to read down from top of the file
header_comment : comment sign w/ which the header must be prefixed
Returns
-------
ConfigParser object
Examples
--------
>>> !cat foo.txt
# [array]
# shape = 3
# axis = -1
1
2
3
>>> _get_header_config('foo.txt')
<pwtools.common.ConfigParser instance at 0x2c52320>
"""
fn = common.get_filename(fh)
verbose("[_read_header_config]: reading header from '%s'" %fn)
header = ''
for i in range(header_maxlines):
try:
line = next(fh).strip()
except StopIteration:
break
if line.startswith(header_comment):
header += line.replace(header_comment, '').strip() + '\n'
# Read one more line to see if the header is bigger than header_maxlines.
try:
if next(fh).strip().startswith(header_comment):
raise Exception("header seems to be > header_maxlines (%i)"
%header_maxlines)
except StopIteration:
pass
c = ConfigParser()
c.read_file(StringIO(header))
# If header_maxlines > header size, we read beyond the header into the data. That
# causes havoc for all functions that read fh afterwards.
fh.seek(0)
return c
def _read_header_config(fh, header_maxlines=HEADER_MAXLINES,
header_comment=HEADER_COMMENT):
"""Read a ini-style file from the header of a text file. Return a
PydosConfigParser object.
Parameters
----------
fh : file handle, readable
header_maxlines : max lines to read down from top of the file
header_comment : comment sign w/ which the header must be prefixed
Returns
-------
PydosConfigParser object
Examples
--------
>>> !cat foo.txt
# [array]
# shape = 3
# axis = -1
1
2
3
>>> _get_header_config('foo.txt')
<pwtools.common.PydosConfigParser instance at 0x2c52320>
"""
fn = common.get_filename(fh)
verbose("[_read_header_config]: reading header from '%s'" %fn)
header = ''
for i in range(header_maxlines):
try:
line = fh.next().strip()
except StopIteration:
break
if line.startswith(header_comment):
header += line.replace(header_comment, '').strip() + '\n'
# Read one more line to see if the header is bigger than header_maxlines.
try:
if fh.next().strip().startswith(header_comment):
raise StandardError("header seems to be > header_maxlines (%i)"
%header_maxlines)
except StopIteration:
pass
c = PydosConfigParser()
c.readfp(StringIO(header))
# If header_maxlines > header size, we read beyond the header into the data. That
# causes havoc for all functions that read fh afterwards.
fh.seek(0)
return c
def _write_header_config(fh, config, header_comment=HEADER_COMMENT,
header_maxlines=HEADER_MAXLINES):
"""Write ini-style config file from `config` prefixed with `header_comment` to
file handle `fh`."""
fn = common.get_filename(fh)
verbose("[_write_header_config]: writing header to '%s'" %fn)
# write config to dummy file
ftmp = StringIO()
config.write(ftmp)
# write with comment signs to actual file
ftmp.seek(0)
lines = ftmp.readlines()
common.assert_cond(len(lines) <= header_maxlines,
"header has more then header_maxlines (%i) lines" \
%header_maxlines)
for line in lines:
fh.write((header_comment + ' ' + line).encode())
ftmp.close()
def _write_header_config(fh, config, header_comment=HEADER_COMMENT,
header_maxlines=HEADER_MAXLINES):
"""Write ini-style config file from `config` prefixed with `header_comment` to
file handle `fh`."""
fn = common.get_filename(fh)
verbose("[_write_header_config]: writing header to '%s'" %fn)
# write config to dummy file
ftmp = StringIO()
config.write(ftmp)
# write with comment signs to actual file
ftmp.seek(0)
lines = ftmp.readlines()
common.assert_cond(len(lines) <= header_maxlines,
"header has more then header_maxlines (%i) lines" \
%header_maxlines)
for line in lines:
fh.write(header_comment + ' ' + line)
ftmp.close()
def readtxt(fh, axis=None, shape=None, header_maxlines=HEADER_MAXLINES,
header_comment=HEADER_COMMENT, maxdim=TXT_MAXDIM, **kwargs):
"""Read arrays from .txt file using np.loadtxt().
If the file stores a 3d array as consecutive 2d arrays (e.g. output from
molecular dynamics code) the file header (see writetxt()) is used to
determine the shape of the original 3d array and the array is reshaped
accordingly.
If `axis` or `shape` is not None, then these are used instead and
the header, if existing, will be ignored. This has the potential to shoot
yourself in the foot. Use with care.
If `axis` and `shape` are None, then this function does not work with
normal text files which have no special header. Use np.loadtxt() in this
case.
Parameters
----------
fh : file_like
axis : int
shape : tuple
**kwargs : keyword args passed to numpy.loadtxt(), e.g. comments='@@' to
ignore weird lines etc.
Returns
-------
nd array
"""
fn = common.get_filename(fh)
verbose("[readtxt] reading: %s" %fn)
verbose("[readtxt] axis: %s" %str(axis))
verbose("[readtxt] shape: %s" %str(shape))
if shape is None or axis is None:
c = _read_header_config(fh)
sec = 'array'
if shape is None:
shape = common.str2tup(c.get(sec, 'shape'))
if axis is None:
axis = int(c.get(sec, 'axis'))
ndim = len(shape)
common.assert_cond(ndim <= maxdim, 'no rank > %i arrays supported' %maxdim)
# axis = -1 means the last dim
if axis == -1:
axis = ndim - 1
# handle empty files (no data, only special header or nothing at all)
header_lines = []
for i in range(header_maxlines):
try:
line = next(fh).strip()
if not line.startswith(header_comment) and line != '':
header_lines.append(line)
except StopIteration:
break
fh.seek(0)
if header_lines == []:
verbose("[readtxt] WARNING: empty file: %s" %fn)
return np.array([])
else:
fh.seek(0)
read_arr = np.loadtxt(fh, **kwargs)
# 1d and 2d
if ndim <= 2:
arr = read_arr
# 3d
else:
arr = arr2d_to_3d(read_arr, shape=shape, axis=axis)
verbose("[readtxt] returning shape: %s" %str(arr.shape))
return arr
def readtxt(fh, axis=None, shape=None, header_maxlines=HEADER_MAXLINES,
header_comment=HEADER_COMMENT, maxdim=TXT_MAXDIM, **kwargs):
"""Read arrays from .txt file using np.loadtxt().
If the file stores a 3d array as consecutive 2d arrays (e.g. output from
molecular dynamics code) the file header (see writetxt()) is used to
determine the shape of the original 3d array and the array is reshaped
accordingly.
If `axis` or `shape` is not None, then these are used instead and
the header, if existing, will be ignored. This has the potential to shoot
yourself in the foot. Use with care.
If `axis` and `shape` are None, then this function does not work with
normal text files which have no special header. Use np.loadtxt() in this
case.
Parameters
----------
fh : file_like
axis : int
shape : tuple
**kwargs : keyword args passed to numpy.loadtxt(), e.g. comments='@@' to
ignore weird lines etc.
Returns
-------
nd array
"""
fn = common.get_filename(fh)
verbose("[readtxt] reading: %s" %fn)
verbose("[readtxt] axis: %s" %str(axis))
verbose("[readtxt] shape: %s" %str(shape))
if shape is None or axis is None:
c = _read_header_config(fh)
sec = 'array'
if shape is None:
shape = common.str2tup(c.get(sec, 'shape'))
if axis is None:
axis = int(c.get(sec, 'axis'))
ndim = len(shape)
common.assert_cond(ndim <= maxdim, 'no rank > %i arrays supported' %maxdim)
# axis = -1 means the last dim
if axis == -1:
axis = ndim - 1
# handle empty files (no data, only special header or nothing at all)
header_lines = []
for i in range(header_maxlines):
try:
line = fh.next().strip()
if not line.startswith(header_comment) and line != '':
header_lines.append(line)
except StopIteration:
break
fh.seek(0)
if header_lines == []:
verbose("[readtxt] WARNING: empty file: %s" %fn)
return np.array([])
else:
fh.seek(0)
read_arr = np.loadtxt(fh, **kwargs)
# 1d and 2d
if ndim <= 2:
arr = read_arr
# 3d
else:
arr = arr2d_to_3d(read_arr, shape=shape, axis=axis)
verbose("[readtxt] returning shape: %s" %str(arr.shape))
return arr
