from __future__ import print_function
import re
import numpy as np
# Import sile objects
import sisl._array as _a
from .sile import Sile, add_sile, Sile_fh_open, sile_raise_write
__all__ = ['tableSile', 'TableSile']
[docs]class tableSile(Sile):
""" ASCII tabular formatted data
A generic table data which will easily accommodate the most common write-outs of data
Examples
--------
>>> a = np.arange(6).reshape(3, 2)
>>> tbl = tableSile('test.dat', 'w')
>>> tbl.write_data(a)
>>> print(''.join(open('test.dat').readlines())) # doctest: +NORMALIZE_WHITESPACE
0.00000e+00 2.00000e+00 4.00000e+00
1.00000e+00 3.00000e+00 5.00000e+00
<BLANKLINE>
>>> a = np.arange(6).reshape(3, 2)
>>> tbl = tableSile('test.dat', 'w')
>>> tbl.write_data(a, comment='Hello')
>>> print(''.join(open('test.dat').readlines())) # doctest: +NORMALIZE_WHITESPACE
# Hello
0.00000e+00 2.00000e+00 4.00000e+00
1.00000e+00 3.00000e+00 5.00000e+00
<BLANKLINE>
>>> a = np.arange(6).reshape(3, 2)
>>> tbl = tableSile('test.dat', 'w')
>>> tbl.write_data(a, header=['x', 'y'])
>>> print(''.join(open('test.dat').readlines())) # doctest: +NORMALIZE_WHITESPACE
#x y
0.00000e+00 2.00000e+00 4.00000e+00
1.00000e+00 3.00000e+00 5.00000e+00
<BLANKLINE>
>>> a = np.arange(6).reshape(3, 2)
>>> tbl = tableSile('test.dat', 'w')
>>> tbl.write_data(a.T)
>>> print(''.join(open('test.dat').readlines())) # doctest: +NORMALIZE_WHITESPACE
0.00000e+00 1.00000e+00
2.00000e+00 3.00000e+00
4.00000e+00 5.00000e+00
<BLANKLINE>
>>> x = np.arange(4)
>>> y = np.arange(8).reshape(2, 4) + 4
>>> tbl = tableSile('test.dat', 'w')
>>> tbl.write_data(x, y)
>>> print(''.join(open('test.dat').readlines())) # doctest: +NORMALIZE_WHITESPACE
0.00000e+00 4.00000e+00 8.00000e+00
1.00000e+00 5.00000e+00 9.00000e+00
2.00000e+00 6.00000e+00 1.00000e+01
3.00000e+00 7.00000e+00 1.10000e+01
<BLANKLINE>
"""
def _setup(self, *args, **kwargs):
""" Setup the `tableSile` after initialization """
self._comment = ['#']
[docs] @Sile_fh_open
def write_data(self, *args, **kwargs):
""" Write tabular data to the file with optional header.
Parameters
----------
*args : array_like or list of array_like
the different columns in the tabular data.
This may either be several 1D data, or 2D arrays.
Internally the data is stacked via `numpy.vstack` and for
any dimension higher than 2 it gets separated by two newline
characters (like gnuplot acceptable data).
fmt : str, optional
The formatting string, defaults to ``.5e``.
fmts : str, optional
The formatting string (for all columns), defaults to ``fmt * len(args)``.
`fmts` has precedence over `fmt`.
newline : str, optional
Defaults to ``\n``.
delimiter : str, optional
Defaults to ``\t``.
comment : str or list of str, optional
A pre-header text at the top of the file.
This comment is automatically prepended a ``#`` at the
start of new lines, for lists each item corresponds to a newline
which is automatically appended.
header : str or list of str, optional
A header for the data (this will be prepended a comment if not present).
footer : str or list of str, optional
A footer written at the end of the file.
Examples
--------
>>> tbl = tableSile('test.dat', 'w')
>>> tbl.write_data(range(2), range(1, 3), comment='A comment', header=['index', 'value'])
>>> print(''.join(open('test.dat').readlines())) # doctest: +NORMALIZE_WHITESPACE
# A comment
#index value
0.00000e+00 1.00000e+00
1.00000e+00 2.00000e+00
<BLANKLINE>
"""
sile_raise_write(self)
fmt = kwargs.get('fmt', '.5e')
newline = kwargs.get('newline', '\n')
delimiter = kwargs.get('delimiter', '\t')
comment = kwargs.get('comment', None)
if comment is None:
comment = ''
elif isinstance(comment, (list, tuple)):
comment = (newline + self._comment[0] + ' ').join(comment)
if len(comment) > 0:
comment = self._comment[0] + ' ' + comment + newline
header = kwargs.get('header', None)
if isinstance(header, (list, tuple)):
header = delimiter.join(header)
if header is not None:
# Ensure no "dangling" spaces
header = header.strip()
if not header.startswith(self._comment[0]):
header = self._comment[0] + header
if not header.endswith('\n'):
header += '\n'
else:
header = ''
header = comment + header
footer = kwargs.get('footer', None)
if footer is None:
footer = ''
elif isinstance(footer, (list, tuple)):
footer = newline.join(footer)
# Create a unified data table
# This is rather difficult because we have to guess the
# input size
if len(args) == 1:
dat = np.vstack(args[0])
else:
dat = np.vstack(args)
_fmt = '{:' + fmt + '}'
# Reshape
if len(dat.shape) > 2:
dat.shape = (-1, dat.shape[-2], dat.shape[-1])
# Now we are ready to write
self._write(header)
if len(dat.shape) > 2:
_fmt = kwargs.get('fmts', (_fmt + delimiter) * (dat.shape[1] - 1) + _fmt + newline)
for i in range(dat.shape[0]):
for j in range(dat.shape[2]):
self._write(_fmt.format(*dat[i, :, j]))
self._write(newline * 2)
else:
_fmt = kwargs.get('fmts', (_fmt + delimiter) * (dat.shape[0] - 1) + _fmt + newline)
for i in range(dat.shape[1]):
self._write(_fmt.format(*dat[:, i]))
if len(footer) > 0:
self._write(newline * 2 + footer)
[docs] @Sile_fh_open
def read_data(self, *args, **kwargs):
""" Read tabular data from the file.
Parameters
----------
columns : list of int, optional
only return the indices of the columns that are provided
delimiter : str, optional
the delimiter used in the file, will automatically try to guess if not specified
ret_comment : bool, optional
also return the comments at the top of the file (if queried)
ret_header : bool, optional
also return the header information (if queried)
comment : str, optional
lines starting with this are discarded as comments
"""
# Override the comment in the file
self._comment = [kwargs.get('comment', self._comment[0])]
# Skip to next line
comment = []
header = ''
# Also read comments
line = self.readline(True)
while line.startswith(self._comment[0] + ' '):
comment.append(line)
line = self.readline(True)
if line.startswith(self._comment[0]):
header = line
line = self.readline()
# Now we are ready to read the data
dat = [[]]
# First we need to figure out the separator:
len_sep = 0
sep = kwargs.get('delimiter', '')
if len(sep) == 0:
for cur_sep in ['\t', ' ', ',']:
s = line.split(cur_sep)
if len(s) > len_sep:
len_sep = len(s)
sep = cur_sep
if len(sep) == 0:
raise ValueError(self.__class__.__name__ + '.read_data could not determine '
'column separator...')
empty = re.compile(r'\s*\n')
while len(line) > 0:
# If we start a line by a comment, or a newline
# then we have a new data set
if empty.match(line) is not None:
if len(dat[-1]) > 0:
dat[-1] = _a.asarrayd(dat[-1])
dat.append([])
else:
line = [l for l in line.split(sep) if len(l) > 0]
dat[-1].append(_a.fromiterd(map(float, line)))
line = self.readline()
if len(dat[-1]) > 0:
dat[-1] = _a.asarrayd(dat[-1])
# Ensure we have no false positives
dat = _a.asarrayd([d for d in dat if len(d) > 0])
if dat.shape[0] == 1:
s = list(dat.shape)
s.pop(0)
dat.shape = tuple(s)
dat = np.swapaxes(dat, -2, -1)
if kwargs.get('ret_comment', False):
if kwargs.get('ret_header', False):
return dat, comment, header
return dat, comment
return dat
# Specify the default write function
_write_default = write_data
TableSile = tableSile
add_sile('table', tableSile, case=False, gzip=True)
add_sile('dat', tableSile, case=False, gzip=True)