Source code for astropy.io.ascii.fixedwidth

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

fixedwidth.py:
  Read or write a table with fixed width columns.

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


from . import core
from .core import InconsistentTableError, DefaultSplitter
from . import basic


[docs]class FixedWidthSplitter(core.BaseSplitter): """ Split line based on fixed start and end positions for each ``col`` in ``self.cols``. This class requires that the Header class will have defined ``col.start`` and ``col.end`` for each column. The reference to the ``header.cols`` gets put in the splitter object by the base Reader.read() function just in time for splitting data lines by a ``data`` object. Note that the ``start`` and ``end`` positions are defined in the pythonic style so line[start:end] is the desired substring for a column. This splitter class does not have a hook for ``process_lines`` since that is generally not useful for fixed-width input. """ delimiter_pad = '' bookend = False delimiter = '|'
[docs] def __call__(self, lines): for line in lines: vals = [line[x.start:x.end] for x in self.cols] if self.process_val: yield [self.process_val(x) for x in vals] else: yield vals
[docs] def join(self, vals, widths): pad = self.delimiter_pad or '' delimiter = self.delimiter or '' padded_delim = pad + delimiter + pad if self.bookend: bookend_left = delimiter + pad bookend_right = pad + delimiter else: bookend_left = '' bookend_right = '' vals = [' ' * (width - len(val)) + val for val, width in zip(vals, widths)] return bookend_left + padded_delim.join(vals) + bookend_right
class FixedWidthHeaderSplitter(DefaultSplitter): '''Splitter class that splits on ``|``.''' delimiter = '|'
[docs]class FixedWidthHeader(basic.BasicHeader): """ Fixed width table header reader. """ splitter_class = FixedWidthHeaderSplitter """ Splitter class for splitting data lines into columns """ position_line = None # secondary header line position """ row index of line that specifies position (default = 1) """ set_of_position_line_characters = set(r'`~!#$%^&*-_+=\|":' + "'")
[docs] def get_line(self, lines, index): for i, line in enumerate(self.process_lines(lines)): if i == index: break else: # No header line matching raise InconsistentTableError('No header line found in table') return line
[docs] def get_cols(self, lines): """ Initialize the header Column objects from the table ``lines``. Based on the previously set Header attributes find or create the column names. Sets ``self.cols`` with the list of Columns. Parameters ---------- lines : list List of table lines """ # See "else" clause below for explanation of start_line and position_line start_line = core._get_line_index(self.start_line, self.process_lines(lines)) position_line = core._get_line_index(self.position_line, self.process_lines(lines)) # If start_line is none then there is no header line. Column positions are # determined from first data line and column names are either supplied by user # or auto-generated. if start_line is None: if position_line is not None: raise ValueError("Cannot set position_line without also setting header_start") # data.data_lines attribute already set via self.data.get_data_lines(lines) # in BaseReader.read(). This includes slicing for data_start / data_end. data_lines = self.data.data_lines if not data_lines: raise InconsistentTableError( 'No data lines found so cannot autogenerate column names') vals, starts, ends = self.get_fixedwidth_params(data_lines[0]) self.names = [self.auto_format.format(i) for i in range(1, len(vals) + 1)] else: # This bit of code handles two cases: # start_line = <index> and position_line = None # Single header line where that line is used to determine both the # column positions and names. # start_line = <index> and position_line = <index2> # Two header lines where the first line defines the column names and # the second line defines the column positions if position_line is not None: # Define self.col_starts and self.col_ends so that the call to # get_fixedwidth_params below will use those to find the header # column names. Note that get_fixedwidth_params returns Python # slice col_ends but expects inclusive col_ends on input (for # more intuitive user interface). line = self.get_line(lines, position_line) if len(set(line) - set([self.splitter.delimiter, ' '])) != 1: raise InconsistentTableError('Position line should only contain delimiters and one other character, e.g. "--- ------- ---".') # The line above lies. It accepts white space as well. # We don't want to encourage using three different # characters, because that can cause ambiguities, but white # spaces are so common everywhere that practicality beats # purity here. charset = self.set_of_position_line_characters.union(set([self.splitter.delimiter, ' '])) if not set(line).issubset(charset): raise InconsistentTableError(f'Characters in position line must be part of {charset}') vals, self.col_starts, col_ends = self.get_fixedwidth_params(line) self.col_ends = [x - 1 if x is not None else None for x in col_ends] # Get the header column names and column positions line = self.get_line(lines, start_line) vals, starts, ends = self.get_fixedwidth_params(line) self.names = vals self._set_cols_from_names() # Set column start and end positions. for i, col in enumerate(self.cols): col.start = starts[i] col.end = ends[i]
[docs] def get_fixedwidth_params(self, line): """ Split ``line`` on the delimiter and determine column values and column start and end positions. This might include null columns with zero length (e.g. for ``header row = "| col1 || col2 | col3 |"`` or ``header2_row = "----- ------- -----"``). The null columns are stripped out. Returns the values between delimiters and the corresponding start and end positions. Parameters ---------- line : str Input line Returns ------- vals : list List of values. starts : list List of starting indices. ends : list List of ending indices. """ # If column positions are already specified then just use those. # If neither column starts or ends are given, figure out positions # between delimiters. Otherwise, either the starts or the ends have # been given, so figure out whichever wasn't given. if self.col_starts is not None and self.col_ends is not None: starts = list(self.col_starts) # could be any iterable, e.g. np.array ends = [x + 1 if x is not None else None for x in self.col_ends] # user supplies inclusive endpoint if len(starts) != len(ends): raise ValueError('Fixed width col_starts and col_ends must have the same length') vals = [line[start:end].strip() for start, end in zip(starts, ends)] elif self.col_starts is None and self.col_ends is None: # There might be a cleaner way to do this but it works... vals = line.split(self.splitter.delimiter) starts = [0] ends = [] for val in vals: if val: ends.append(starts[-1] + len(val)) starts.append(ends[-1] + 1) else: starts[-1] += 1 starts = starts[:-1] vals = [x.strip() for x in vals if x] if len(vals) != len(starts) or len(vals) != len(ends): raise InconsistentTableError('Error parsing fixed width header') else: # exactly one of col_starts or col_ends is given... if self.col_starts is not None: starts = list(self.col_starts) ends = starts[1:] + [None] # Assume each col ends where the next starts else: # self.col_ends is not None ends = [x + 1 for x in self.col_ends] starts = [0] + ends[:-1] # Assume each col starts where the last ended vals = [line[start:end].strip() for start, end in zip(starts, ends)] return vals, starts, ends
[docs] def write(self, lines): # Header line not written until data are formatted. Until then it is # not known how wide each column will be for fixed width. pass
[docs]class FixedWidthData(basic.BasicData): """ Base table data reader. """ splitter_class = FixedWidthSplitter """ Splitter class for splitting data lines into columns """
[docs] def write(self, lines): vals_list = [] col_str_iters = self.str_vals() for vals in zip(*col_str_iters): vals_list.append(vals) for i, col in enumerate(self.cols): col.width = max([len(vals[i]) for vals in vals_list]) if self.header.start_line is not None: col.width = max(col.width, len(col.info.name)) widths = [col.width for col in self.cols] if self.header.start_line is not None: lines.append(self.splitter.join([col.info.name for col in self.cols], widths)) if self.header.position_line is not None: char = self.header.position_char if len(char) != 1: raise ValueError('Position_char="{}" must be a single ' 'character'.format(char)) vals = [char * col.width for col in self.cols] lines.append(self.splitter.join(vals, widths)) for vals in vals_list: lines.append(self.splitter.join(vals, widths)) return lines
[docs]class FixedWidth(basic.Basic): """Fixed width table with single header line defining column names and positions. Examples:: # Bar delimiter in header and data | Col1 | Col2 | Col3 | | 1.2 | hello there | 3 | | 2.4 | many words | 7 | # Bar delimiter in header only Col1 | Col2 | Col3 1.2 hello there 3 2.4 many words 7 # No delimiter with column positions specified as input Col1 Col2Col3 1.2hello there 3 2.4many words 7 See the :ref:`fixed_width_gallery` for specific usage examples. """ _format_name = 'fixed_width' _description = 'Fixed width' header_class = FixedWidthHeader data_class = FixedWidthData def __init__(self, col_starts=None, col_ends=None, delimiter_pad=' ', bookend=True): super().__init__() self.data.splitter.delimiter_pad = delimiter_pad self.data.splitter.bookend = bookend self.header.col_starts = col_starts self.header.col_ends = col_ends
class FixedWidthNoHeaderHeader(FixedWidthHeader): '''Header reader for fixed with tables with no header line''' start_line = None class FixedWidthNoHeaderData(FixedWidthData): '''Data reader for fixed width tables with no header line''' start_line = 0
[docs]class FixedWidthNoHeader(FixedWidth): """Fixed width table which has no header line. When reading, column names are either input (``names`` keyword) or auto-generated. Column positions are determined either by input (``col_starts`` and ``col_stops`` keywords) or by splitting the first data line. In the latter case a ``delimiter`` is required to split the data line. Examples:: # Bar delimiter in header and data | 1.2 | hello there | 3 | | 2.4 | many words | 7 | # Compact table having no delimiter and column positions specified as input 1.2hello there3 2.4many words 7 This class is just a convenience wrapper around the ``FixedWidth`` reader but with ``header.start_line = None`` and ``data.start_line = 0``. See the :ref:`fixed_width_gallery` for specific usage examples. """ _format_name = 'fixed_width_no_header' _description = 'Fixed width with no header' header_class = FixedWidthNoHeaderHeader data_class = FixedWidthNoHeaderData def __init__(self, col_starts=None, col_ends=None, delimiter_pad=' ', bookend=True): super().__init__(col_starts, col_ends, delimiter_pad=delimiter_pad, bookend=bookend)
class FixedWidthTwoLineHeader(FixedWidthHeader): '''Header reader for fixed width tables splitting on whitespace. For fixed width tables with several header lines, there is typically a white-space delimited format line, so splitting on white space is needed. ''' splitter_class = DefaultSplitter class FixedWidthTwoLineDataSplitter(FixedWidthSplitter): '''Splitter for fixed width tables splitting on ``' '``.''' delimiter = ' ' class FixedWidthTwoLineData(FixedWidthData): '''Data reader for fixed with tables with two header lines.''' splitter_class = FixedWidthTwoLineDataSplitter
[docs]class FixedWidthTwoLine(FixedWidth): """Fixed width table which has two header lines. The first header line defines the column names and the second implicitly defines the column positions. Examples:: # Typical case with column extent defined by ---- under column names. col1 col2 <== header_start = 0 ----- ------------ <== position_line = 1, position_char = "-" 1 bee flies <== data_start = 2 2 fish swims # Pretty-printed table +------+------------+ | Col1 | Col2 | +------+------------+ | 1.2 | "hello" | | 2.4 | there world| +------+------------+ See the :ref:`fixed_width_gallery` for specific usage examples. """ _format_name = 'fixed_width_two_line' _description = 'Fixed width with second header line' data_class = FixedWidthTwoLineData header_class = FixedWidthTwoLineHeader def __init__(self, position_line=1, position_char='-', delimiter_pad=None, bookend=False): super().__init__(delimiter_pad=delimiter_pad, bookend=bookend) self.header.position_line = position_line self.header.position_char = position_char self.data.start_line = position_line + 1