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 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()