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 _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 arr2d_to_3d(arr, shape, axis=-1):
"""Reshape 2d array `arr` to 3d array of `shape`, with 2d chunks aligned
along `axis`.
Parameters
----------
arr : 2d array
shape : tuple
Target shape of 3d array
axis : int
Axis of 3d arr along which 2d chunks are placed.
Returns
-------
arr3d : 3d array
Examples
--------
>>> axis = 1
>>> shape = (50, 1000, 3)
>>> shape_2d_chunk = (50, 3)
>>> arr.shape = (1000*50,3)
"""
assert arr.ndim == 2, "input must be 2d array"
assert len(shape) == TXT_MAXDIM
shape_2d_chunk = shape[:axis] + shape[(axis+1):]
# arr: (50*1000, 3)
# arr3d: (50, 1000, 3) : natoms = 50, nstep = 1000, 3 = x,y,z
expect_shape = (shape_2d_chunk[0]*shape[axis],) + (shape_2d_chunk[1],)
common.assert_cond(arr.shape == expect_shape,
"input 2d array has not the correct "
"shape, got %s, expect %s" %(str(arr.shape),
str(expect_shape)))
arr3d = np.empty(shape, dtype=arr.dtype)
sl = [slice(None)]*3
for ind in range(shape[axis]):
sl[axis] = ind
arr3d[sl] = arr[ind*shape_2d_chunk[0]:(ind+1)*shape_2d_chunk[0], :]
return arr3d
def arr2d_to_3d(arr, shape, axis=-1):
"""Reshape 2d array `arr` to 3d array of `shape`, with 2d chunks aligned
along `axis`.
Parameters
----------
arr : 2d array
shape : tuple
Target shape of 3d array
axis : int
Axis of 3d arr along which 2d chunks are placed.
Returns
-------
arr3d : 3d array
Examples
--------
>>> axis = 1
>>> shape = (50, 1000, 3)
>>> shape_2d_chunk = (50, 3)
>>> arr.shape = (1000*50,3)
"""
assert arr.ndim == 2, "input must be 2d array"
assert len(shape) == TXT_MAXDIM
shape_2d_chunk = shape[:axis] + shape[(axis+1):]
# arr: (50*1000, 3)
# arr3d: (50, 1000, 3) : natoms = 50, nstep = 1000, 3 = x,y,z
expect_shape = (shape_2d_chunk[0]*shape[axis],) + (shape_2d_chunk[1],)
common.assert_cond(arr.shape == expect_shape,
"input 2d array has not the correct "
"shape, got %s, expect %s" %(str(arr.shape),
str(expect_shape)))
arr3d = np.empty(shape, dtype=arr.dtype)
sl = [slice(None)]*3
for ind in range(shape[axis]):
sl[axis] = ind
arr3d[sl] = arr[ind*shape_2d_chunk[0]:(ind+1)*shape_2d_chunk[0], :]
return arr3d
def writetxt(fn, arr, axis=-1, maxdim=TXT_MAXDIM, header=True):
"""Write 1d, 2d or 3d arrays to txt file.
If 3d, write as 2d chunks. Take the 2d chunks along `axis`. Write a
commented out ini-style header in the file with infos needed by readtxt()
to restore the right shape.
Parameters
----------
fn : filename
arr : nd array
axis : axis along which 2d chunks are written
maxdim : highest number of dims that `arr` is allowed to have
header : bool
Write ini style header. Can be used by readtxt().
"""
verbose("[writetxt] writing: %s" %fn)
common.assert_cond(arr.ndim <= maxdim, 'no rank > %i arrays supported' %maxdim)
fh = open(fn, 'wb+')
if header:
c = ConfigParser()
sec = 'array'
c.add_section(sec)
c.set(sec, 'shape', common.seq2str(arr.shape))
c.set(sec, 'axis', str(axis))
_write_header_config(fh, c)
# 1d and 2d case
if arr.ndim < maxdim:
np.savetxt(fh, arr)
# 3d
else:
# TODO get rid of loop?
# write 2d arrays, one by one
sl = [slice(None)]*arr.ndim
for ind in range(arr.shape[axis]):
sl[axis] = ind
np.savetxt(fh, arr[sl])
fh.close()
def writetxt(fn, arr, axis=-1, maxdim=TXT_MAXDIM, header=True):
"""Write 1d, 2d or 3d arrays to txt file.
If 3d, write as 2d chunks. Take the 2d chunks along `axis`. Write a
commented out ini-style header in the file with infos needed by readtxt()
to restore the right shape.
Parameters
----------
fn : filename
arr : nd array
axis : axis along which 2d chunks are written
maxdim : highest number of dims that `arr` is allowed to have
header : bool
Write ini style header. Can be used by readtxt().
"""
verbose("[writetxt] writing: %s" %fn)
common.assert_cond(arr.ndim <= maxdim, 'no rank > %i arrays supported' %maxdim)
fh = open(fn, 'w+')
if header:
c = PydosConfigParser()
sec = 'array'
c.add_section(sec)
c.set(sec, 'shape', common.seq2str(arr.shape))
c.set(sec, 'axis', axis)
_write_header_config(fh, c)
# 1d and 2d case
if arr.ndim < maxdim:
np.savetxt(fh, arr)
# 3d
else:
# TODO get rid of loop?
# write 2d arrays, one by one
sl = [slice(None)]*arr.ndim
for ind in range(arr.shape[axis]):
sl[axis] = ind
np.savetxt(fh, arr[sl])
fh.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
