Source code for astropy.io.ascii.latex

# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""An extensible ASCII table reader and writer.

latex.py:
  Classes to read and write LaTeX tables

:Copyright: Smithsonian Astrophysical Observatory (2011)
:Author: Tom Aldcroft ([email protected])
"""


import re

from . import core

latexdicts = {'AA': {'tabletype': 'table',
                     'header_start': r'\hline \hline', 'header_end': r'\hline',
                     'data_end': r'\hline'},
              'doublelines': {'tabletype': 'table',
                              'header_start': r'\hline \hline', 'header_end': r'\hline\hline',
                              'data_end': r'\hline\hline'},
              'template': {'tabletype': 'tabletype', 'caption': 'caption',
                           'tablealign': 'tablealign',
                           'col_align': 'col_align', 'preamble': 'preamble',
                           'header_start': 'header_start',
                           'header_end': 'header_end', 'data_start': 'data_start',
                           'data_end': 'data_end', 'tablefoot': 'tablefoot',
                           'units': {'col1': 'unit of col1', 'col2': 'unit of col2'}}
              }


RE_COMMENT = re.compile(r'(?<!\\)%')  # % character but not \%


def add_dictval_to_list(adict, key, alist):
    '''
    Add a value from a dictionary to a list

    Parameters
    ----------
    adict : dictionary
    key : hashable
    alist : list
        List where value should be added
    '''
    if key in adict:
        if isinstance(adict[key], str):
            alist.append(adict[key])
        else:
            alist.extend(adict[key])


def find_latex_line(lines, latex):
    '''
    Find the first line which matches a patters

    Parameters
    ----------
    lines : list
        List of strings
    latex : str
        Search pattern

    Returns
    -------
    line_num : int, None
        Line number. Returns None, if no match was found

    '''
    re_string = re.compile(latex.replace('\\', '\\\\'))
    for i, line in enumerate(lines):
        if re_string.match(line):
            return i
    else:
        return None


class LatexInputter(core.BaseInputter):

    def process_lines(self, lines):
        return [lin.strip() for lin in lines]


class LatexSplitter(core.BaseSplitter):
    '''Split LaTeX table date. Default delimiter is `&`.
    '''
    delimiter = '&'

    def __call__(self, lines):
        last_line = RE_COMMENT.split(lines[-1])[0].strip()
        if not last_line.endswith(r'\\'):
            lines[-1] = last_line + r'\\'

        return super().__call__(lines)

    def process_line(self, line):
        """Remove whitespace at the beginning or end of line. Also remove
        \\ at end of line"""
        line = RE_COMMENT.split(line)[0]
        line = line.strip()
        if line.endswith(r'\\'):
            line = line.rstrip(r'\\')
        else:
            raise core.InconsistentTableError(r'Lines in LaTeX table have to end with \\')
        return line

    def process_val(self, val):
        """Remove whitespace and {} at the beginning or end of value."""
        val = val.strip()
        if val and (val[0] == '{') and (val[-1] == '}'):
            val = val[1:-1]
        return val

    def join(self, vals):
        '''Join values together and add a few extra spaces for readability'''
        delimiter = ' ' + self.delimiter + ' '
        return delimiter.join(x.strip() for x in vals) + r' \\'


class LatexHeader(core.BaseHeader):
    '''Class to read the header of Latex Tables'''
    header_start = r'\begin{tabular}'
    splitter_class = LatexSplitter

    def start_line(self, lines):
        line = find_latex_line(lines, self.header_start)
        if line is not None:
            return line + 1
        else:
            return None

    def _get_units(self):
        units = {}
        col_units = [col.info.unit for col in self.cols]
        for name, unit in zip(self.colnames, col_units):
            if unit:
                try:
                    units[name] = unit.to_string(format='latex_inline')
                except AttributeError:
                    units[name] = unit
        return units

    def write(self, lines):
        if 'col_align' not in self.latex:
            self.latex['col_align'] = len(self.cols) * 'c'
        if 'tablealign' in self.latex:
            align = '[' + self.latex['tablealign'] + ']'
        else:
            align = ''
        if self.latex['tabletype'] is not None:
            lines.append(r'\begin{' + self.latex['tabletype'] + r'}' + align)
        add_dictval_to_list(self.latex, 'preamble', lines)
        if 'caption' in self.latex:
            lines.append(r'\caption{' + self.latex['caption'] + '}')
        lines.append(self.header_start + r'{' + self.latex['col_align'] + r'}')
        add_dictval_to_list(self.latex, 'header_start', lines)
        lines.append(self.splitter.join(self.colnames))
        units = self._get_units()
        if 'units' in self.latex:
            units.update(self.latex['units'])
        if units:
            lines.append(self.splitter.join([units.get(name, ' ') for name in self.colnames]))
        add_dictval_to_list(self.latex, 'header_end', lines)


class LatexData(core.BaseData):
    '''Class to read the data in LaTeX tables'''
    data_start = None
    data_end = r'\end{tabular}'
    splitter_class = LatexSplitter

    def start_line(self, lines):
        if self.data_start:
            return find_latex_line(lines, self.data_start)
        else:
            start = self.header.start_line(lines)
            if start is None:
                raise core.InconsistentTableError(r'Could not find table start')
            return start + 1

    def end_line(self, lines):
        if self.data_end:
            return find_latex_line(lines, self.data_end)
        else:
            return None

    def write(self, lines):
        add_dictval_to_list(self.latex, 'data_start', lines)
        core.BaseData.write(self, lines)
        add_dictval_to_list(self.latex, 'data_end', lines)
        lines.append(self.data_end)
        add_dictval_to_list(self.latex, 'tablefoot', lines)
        if self.latex['tabletype'] is not None:
            lines.append(r'\end{' + self.latex['tabletype'] + '}')


[docs]class Latex(core.BaseReader): r'''Write and read LaTeX tables. This class implements some LaTeX specific commands. Its main purpose is to write out a table in a form that LaTeX can compile. It is beyond the scope of this class to implement every possible LaTeX command, instead the focus is to generate a syntactically valid LaTeX tables. This class can also read simple LaTeX tables (one line per table row, no ``\multicolumn`` or similar constructs), specifically, it can read the tables that it writes. Reading a LaTeX table, the following keywords are accepted: **ignore_latex_commands** : Lines starting with these LaTeX commands will be treated as comments (i.e. ignored). When writing a LaTeX table, the some keywords can customize the format. Care has to be taken here, because python interprets ``\\`` in a string as an escape character. In order to pass this to the output either format your strings as raw strings with the ``r`` specifier or use a double ``\\\\``. Examples:: caption = r'My table \label{mytable}' caption = 'My table \\\\label{mytable}' **latexdict** : Dictionary of extra parameters for the LaTeX output * tabletype : used for first and last line of table. The default is ``\\begin{table}``. The following would generate a table, which spans the whole page in a two-column document:: ascii.write(data, sys.stdout, Writer = ascii.Latex, latexdict = {'tabletype': 'table*'}) If ``None``, the table environment will be dropped, keeping only the ``tabular`` environment. * tablealign : positioning of table in text. The default is not to specify a position preference in the text. If, e.g. the alignment is ``ht``, then the LaTeX will be ``\\begin{table}[ht]``. * col_align : Alignment of columns If not present all columns will be centered. * caption : Table caption (string or list of strings) This will appear above the table as it is the standard in many scientific publications. If you prefer a caption below the table, just write the full LaTeX command as ``latexdict['tablefoot'] = r'\caption{My table}'`` * preamble, header_start, header_end, data_start, data_end, tablefoot: Pure LaTeX Each one can be a string or a list of strings. These strings will be inserted into the table without any further processing. See the examples below. * units : dictionary of strings Keys in this dictionary should be names of columns. If present, a line in the LaTeX table directly below the column names is added, which contains the values of the dictionary. Example:: from astropy.io import ascii data = {'name': ['bike', 'car'], 'mass': [75,1200], 'speed': [10, 130]} ascii.write(data, Writer=ascii.Latex, latexdict = {'units': {'mass': 'kg', 'speed': 'km/h'}}) If the column has no entry in the ``units`` dictionary, it defaults to the **unit** attribute of the column. If this attribute is not specified (i.e. it is None), the unit will be written as ``' '``. Run the following code to see where each element of the dictionary is inserted in the LaTeX table:: from astropy.io import ascii data = {'cola': [1,2], 'colb': [3,4]} ascii.write(data, Writer=ascii.Latex, latexdict=ascii.latex.latexdicts['template']) Some table styles are predefined in the dictionary ``ascii.latex.latexdicts``. The following generates in table in style preferred by A&A and some other journals:: ascii.write(data, Writer=ascii.Latex, latexdict=ascii.latex.latexdicts['AA']) As an example, this generates a table, which spans all columns and is centered on the page:: ascii.write(data, Writer=ascii.Latex, col_align='|lr|', latexdict={'preamble': r'\begin{center}', 'tablefoot': r'\end{center}', 'tabletype': 'table*'}) **caption** : Set table caption Shorthand for:: latexdict['caption'] = caption **col_align** : Set the column alignment. If not present this will be auto-generated for centered columns. Shorthand for:: latexdict['col_align'] = col_align ''' _format_name = 'latex' _io_registry_format_aliases = ['latex'] _io_registry_suffix = '.tex' _description = 'LaTeX table' header_class = LatexHeader data_class = LatexData inputter_class = LatexInputter def __init__(self, ignore_latex_commands=['hline', 'vspace', 'tableline', 'toprule', 'midrule', 'bottomrule'], latexdict={}, caption='', col_align=None): super().__init__() self.latex = {} # The latex dict drives the format of the table and needs to be shared # with data and header self.header.latex = self.latex self.data.latex = self.latex self.latex['tabletype'] = 'table' self.latex.update(latexdict) if caption: self.latex['caption'] = caption if col_align: self.latex['col_align'] = col_align self.ignore_latex_commands = ignore_latex_commands self.header.comment = '%|' + '|'.join( [r'\\' + command for command in self.ignore_latex_commands]) self.data.comment = self.header.comment
[docs] def write(self, table=None): self.header.start_line = None self.data.start_line = None return core.BaseReader.write(self, table=table)
class AASTexHeaderSplitter(LatexSplitter): r'''Extract column names from a `deluxetable`_. This splitter expects the following LaTeX code **in a single line**: \tablehead{\colhead{col1} & ... & \colhead{coln}} ''' def __call__(self, lines): return super(LatexSplitter, self).__call__(lines) def process_line(self, line): """extract column names from tablehead """ line = line.split('%')[0] line = line.replace(r'\tablehead', '') line = line.strip() if (line[0] == '{') and (line[-1] == '}'): line = line[1:-1] else: raise core.InconsistentTableError(r'\tablehead is missing {}') return line.replace(r'\colhead', '') def join(self, vals): return ' & '.join([r'\colhead{' + str(x) + '}' for x in vals]) class AASTexHeader(LatexHeader): r'''In a `deluxetable <http://fits.gsfc.nasa.gov/standard30/deluxetable.sty>`_ some header keywords differ from standard LaTeX. This header is modified to take that into account. ''' header_start = r'\tablehead' splitter_class = AASTexHeaderSplitter def start_line(self, lines): return find_latex_line(lines, r'\tablehead') def write(self, lines): if 'col_align' not in self.latex: self.latex['col_align'] = len(self.cols) * 'c' if 'tablealign' in self.latex: align = '[' + self.latex['tablealign'] + ']' else: align = '' lines.append(r'\begin{' + self.latex['tabletype'] + r'}{' + self.latex['col_align'] + r'}' + align) add_dictval_to_list(self.latex, 'preamble', lines) if 'caption' in self.latex: lines.append(r'\tablecaption{' + self.latex['caption'] + '}') tablehead = ' & '.join([r'\colhead{' + name + '}' for name in self.colnames]) units = self._get_units() if 'units' in self.latex: units.update(self.latex['units']) if units: tablehead += r'\\ ' + self.splitter.join([units.get(name, ' ') for name in self.colnames]) lines.append(r'\tablehead{' + tablehead + '}') class AASTexData(LatexData): r'''In a `deluxetable`_ the data is enclosed in `\startdata` and `\enddata` ''' data_start = r'\startdata' data_end = r'\enddata' def start_line(self, lines): return find_latex_line(lines, self.data_start) + 1 def write(self, lines): lines.append(self.data_start) lines_length_initial = len(lines) core.BaseData.write(self, lines) # To remove extra space(s) and // appended which creates an extra new line # in the end. if len(lines) > lines_length_initial: # we compile separately because py2.6 doesn't have a flags keyword in re.sub re_final_line = re.compile(r'\s* \\ \\ \s* $', flags=re.VERBOSE) lines[-1] = re.sub(re_final_line, '', lines[-1]) lines.append(self.data_end) add_dictval_to_list(self.latex, 'tablefoot', lines) lines.append(r'\end{' + self.latex['tabletype'] + r'}')
[docs]class AASTex(Latex): '''Write and read AASTeX tables. This class implements some AASTeX specific commands. AASTeX is used for the AAS (American Astronomical Society) publications like ApJ, ApJL and AJ. It derives from the ``Latex`` reader and accepts the same keywords. However, the keywords ``header_start``, ``header_end``, ``data_start`` and ``data_end`` in ``latexdict`` have no effect. ''' _format_name = 'aastex' _io_registry_format_aliases = ['aastex'] _io_registry_suffix = '' # AASTex inherits from Latex, so override this class attr _description = 'AASTeX deluxetable used for AAS journals' header_class = AASTexHeader data_class = AASTexData def __init__(self, **kwargs): super().__init__(**kwargs) # check if tabletype was explicitly set by the user if not (('latexdict' in kwargs) and ('tabletype' in kwargs['latexdict'])): self.latex['tabletype'] = 'deluxetable'