Reading Tables

The majority of commonly encountered ASCII tables can be read with the read() function:

>>> from astropy.io import ascii
>>> data = ascii.read(table)  

Here table is the name of a file, a string representation of a table, or a list of table lines. The return value (data in this case) is a Table object.

By default, read() will try to guess the table format by trying all of the supported formats.

Warning

Guessing the file format is often slow for large files because the reader tries parsing the file with every allowed format until one succeeds. For large files it is recommended to disable guessing with guess=False.

For unusually formatted tables where guessing does not work, give additional hints about the format:

>>> lines = ['objID                   & osrcid            & xsrcid       ',
...          '----------------------- & ----------------- & -------------',
...          '              277955213 & S000.7044P00.7513 & XS04861B6_005',
...          '              889974380 & S002.9051P14.7003 & XS03957B7_004']
>>> data = ascii.read(lines, data_start=2, delimiter='&')
>>> print(data)
  objID         osrcid          xsrcid
--------- ----------------- -------------
277955213 S000.7044P00.7513 XS04861B6_005
889974380 S002.9051P14.7003 XS03957B7_004

Other examples are as follows:

>>> data = astropy.io.ascii.read('data/nls1_stackinfo.dbout', data_start=2, delimiter='|')  
>>> data = astropy.io.ascii.read('data/simple.txt', quotechar="'")  
>>> data = astropy.io.ascii.read('data/simple4.txt', format='no_header', delimiter='|')  
>>> data = astropy.io.ascii.read('data/tab_and_space.txt', delimiter=r'\s')  

If the format of a file is known (e.g., it is a fixed-width table or an IPAC table), then it is more efficient and reliable to provide a value for the format argument from one of the values in the Supported Formats. For example:

>>> data = ascii.read(lines, format='fixed_width_two_line', delimiter='&')

See the Guess Table Format section for additional details on format guessing.

For simpler formats such as CSV, read() will automatically try reading with the Cython/C parsing engine, which is significantly faster than the ordinary Python implementation (described in Fast ASCII I/O). If the fast engine fails, read() will fall back on the Python reader by default. The argument fast_reader can be specified to control this behavior. For example, to disable the fast engine:

>>> data = ascii.read(lines, format='csv', fast_reader=False)

For reading very large tables see the section on Reading Large Tables in Chunks or use pandas (see Note below).

Note

Reading a table which contains unicode characters is supported with the pure Python readers by specifying the encoding parameter. The fast C-readers do not support unicode. For large data files containing unicode, we recommend reading the file using pandas and converting to a Table via the Table - Pandas interface.

The read() function accepts a number of parameters that specify the detailed table format. Different formats can define different defaults, so the descriptions below sometimes mention “typical” default values. This refers to the Basic format reader and other similar character-separated formats.

Parameters for read()

tableinput table

There are four ways to specify the table to be read:

• Path to a file (string)

• Single string containing all table lines separated by newlines

• File-like object with a callable read() method

• List of strings where each list element is a table line

The first two options are distinguished by the presence of a newline in the string. This assumes that valid file names will not normally contain a newline, and a valid table input will at least contain two rows. Note that a table read in no_header format can legitimately consist of a single row; in this case passing the string as a list with a single item will ensure that it is not interpreted as a file name.

formatfile format (default=’basic’)

This specifies the top-level format of the ASCII table; for example, if it is a basic character delimited table, fixed format table, or a CDS-compatible table, etc. The value of this parameter must be one of the Supported Formats.

guesstry to guess table format (default=None)

If set to True, then read() will try to guess the table format by cycling through a number of possible table format permutations and attempting to read the table in each case. See the Guess table format section for further details.

delimitercolumn delimiter string

A one-character string used to separate fields which typically defaults to the space character. Other common values might be “\s” (whitespace), “,” or “|” or “\t” (tab). A value of “\s” allows any combination of the tab and space characters to delimit columns.

commentregular expression defining a comment line in table

If the comment regular expression matches the beginning of a table line then that line will be discarded from header or data processing. For the basic format this defaults to “\s*#” (any whitespace followed by #).

quotecharone-character string to quote fields containing special characters

This specifies the quote character and will typically be either the single or double quote character. This is can be useful for reading text fields with spaces in a space-delimited table. The default is typically the double quote.

header_startline index for the header line

This includes only significant non-comment lines and counting starts at 0. If set to None this indicates that there is no header line and the column names will be auto-generated. See Specifying header and data location for more details.

data_startline index for the start of data counting

This includes only significant non-comment lines and counting starts at 0. See Specifying header and data location for more details.

data_endline index for the end of data

This includes only significant non-comment lines and can be negative to count from end. See Specifying header and data location for more details.

encoding: encoding to read the file (default=None)

When None use locale.getpreferredencoding as an encoding. This matches the default behavior of the built-in open when no mode argument is provided.

convertersdict specifying output data types

See the Converters for Specifying Dtype section for examples. Each key in the dictionary is a column name or else a name matching pattern including wildcards. The value is one of:

• Python data type or numpy dtype such as int or np.float32

• list of such types which is tried in order until conversion is successful

• list of converter tuples (this is not common, but see the convert_numpy function for an example).

nameslist of names corresponding to each data column

Define the complete list of names for each data column. This will override names found in the header (if it exists). If not supplied then use names from the header or auto-generated names if there is no header.

include_nameslist of names to include in output

From the list of column names found from the header or the names parameter, select for output only columns within this list. If not supplied, then include all names.

exclude_nameslist of names to exclude from output

Exclude these names from the list of output columns. This is applied after the include_names filtering. If not specified then no columns are excluded.

fill_valueslist of fill value specifiers

Specify input table entries which should be masked in the output table because they are bad or missing. See the Bad or missing values section for more information and examples. The default is that any blank table values are treated as missing.

fill_include_nameslist of column names affected by fill_values

This is a list of column names (found from the header or the names parameter) for all columns where values will be filled. None (the default) will apply fill_values to all columns.

fill_exclude_nameslist of column names not affected by fill_values

This is a list of column names (found from the header or the names parameter) for all columns where values will be not be filled. This parameter takes precedence over fill_include_names. A value of None (default) does not exclude any columns.

outputter_clsOutputter class

This converts the raw data tables value into the output object that gets returned by read(). The default is TableOutputter, which returns a Table object (see Data Tables).

inputter_clsInputter class

This is generally not specified.

data_splitter_cls : Splitter class to split data columns

header_splitter_cls : Splitter class to split header columns

fast_readerwhether to use the C engine

This can be True or False, and also be a dict with options. (see Fast ASCII I/O)

ReaderReader class (deprecated in favor of format)

This specifies the top-level format of the ASCII table; for example, if it is a basic character delimited table, fixed format table, or a CDS-compatible table, etc. The value of this parameter must be a Reader class. For basic usage this means one of the built-in Extension Reader Classes.

Specifying Header and Data Location

The three parameters header_start, data_start, and data_end make it possible to read a table file that has extraneous non-table data included. This is a case where you need to help out astropy.io.ascii and tell it where to find the header and data.

When a file is processed into a header and data components, any blank lines (which might have whitespace characters) and commented lines (starting with the comment character, typically #) are stripped out before the header and data parsing code sees the table content.

Example

To use the parameters header_start, data_start, and data_end to read a table with non-table data included, take the file below. The column on the left is not part of the file but instead shows how astropy.io.ascii is viewing each line and the line count index.

Index    Table content
------ ----------------------------------------------------------------
   -  | # This is the start of my data file
   -  |
   0  | Automatically generated by my_script.py at 2012-01-01T12:13:14
   1  | Run parameters: None
   2  | Column header line:
   -  |
   3  | x y z
   -  |
   4  | Data values section:
   -  |
   5  | 1 2 3
   6  | 4 5 6
   -  |
   7  | Run completed at 2012:01-01T12:14:01

In this case you would have header_start=3, data_start=5, and data_end=7. The convention for data_end follows the normal Python slicing convention where to select data rows 5 and 6 you would do rows[5:7]. For data_end you can also supply a negative index to count backward from the end, so data_end=-1 (like rows[5:-1]) would work in this case.

Bad or Missing Values

ASCII data tables can contain bad or missing values. A common case is when a table contains blank entries with no available data.

Examples

Take this example of a table with blank entries:

>>> weather_data = """
...   day,precip,type
...   Mon,1.5,rain
...   Tues,,
...   Wed,1.1,snow
...   """

By default, read() will interpret blank entries as being bad/missing and output a masked Table with those entries masked out by setting the corresponding mask value set to True:

>>> dat = ascii.read(weather_data)
>>> print(dat)
day  precip type
---- ------ ----
 Mon    1.5 rain
Tues     --   --
 Wed    1.1 snow

If you want to replace the masked (missing) values with particular values, set the masked column fill_value attribute and then get the “filled” version of the table. This looks like the following:

>>> dat['precip'].fill_value = -999
>>> dat['type'].fill_value = 'N/A'
>>> print(dat.filled())
day  precip type
---- ------ ----
 Mon    1.5 rain
Tues -999.0  N/A
 Wed    1.1 snow

ASCII tables may have other indicators of bad or missing data as well. For example, a table may contain string values that are not a valid representation of a number (e.g., "..."), or a table may have special values like -999 that are chosen to indicate missing data. The read() function has a flexible system to accommodate these cases by marking specified character sequences in the input data as “missing data” during the conversion process. Whenever missing data is found the output will be a masked table.

This is done with the fill_values keyword argument, which can be set to a single missing-value specification <missing_spec> or a list of <missing_spec> tuples:

fill_values = <missing_spec> | [<missing_spec1>, <missing_spec2>, ...]
<missing_spec> = (<match_string>, '0', <optional col name 1>, <optional col name 2>, ...)

When reading a table, the second element of a <missing_spec> should always be the string '0', otherwise you may get unexpected behavior [1]. By default, the <missing_spec> is applied to all columns unless column name strings are supplied. An alternate way to limit the columns is via the fill_include_names and fill_exclude_names keyword arguments in read().

In the example below we read back the weather table after filling the missing values in with typical placeholders:

>>> table = ['day   precip  type',
...          ' Mon     1.5  rain',
...          'Tues  -999.0   N/A',
...          ' Wed     1.1  snow']
>>> t = ascii.read(table, fill_values=[('-999.0', '0', 'precip'), ('N/A', '0', 'type')])
>>> print(t)
day  precip type
---- ------ ----
 Mon    1.5 rain
Tues     --   --
 Wed    1.1 snow

Note

The default in read() is fill_values=('','0'). This marks blank entries as being missing for any data type (int, float, or string). If fill_values is explicitly set in the call to read() then the default behavior of marking blank entries as missing no longer applies. For instance setting fill_values=None will disable this auto-masking without setting any other fill values. This can be useful for a string column where one of values happens to be "".

[1]

The requirement to put the '0' there is the legacy of an old interface which is maintained for backward compatibility and also to match the format of fill_value for reading with the format of fill_value used for writing tables. On reading, the second element of the <missing_spec> tuple can actually be an arbitrary string value which replaces occurrences of the <match_string> string in the input stream prior to type conversion. This ends up being the value “behind the mask”, which should never be directly accessed. Only the value '0' is neutral when attempting to detect the column data type and perform type conversion. For instance if you used 'nan' for the <match_string> value then integer columns would wind up as float.

Selecting columns for masking

The read() function provides the parameters fill_include_names and fill_exclude_names to select which columns will be used in the fill_values masking process described above.

The use of these parameters is not common but in some cases can considerably simplify the code required to read a table. The following gives a simple example to illustrate how fill_include_names and fill_exclude_names can be used in the most basic and typical cases:

>>> from astropy.io import ascii
>>> lines = ['a,b,c,d', '1.0,2.0,3.0,4.0', ',,,']
>>> ascii.read(lines)
<Table length=2>
   a       b       c       d
float64 float64 float64 float64
------- ------- ------- -------
    1.0     2.0     3.0     4.0
     --      --      --      --

>>> ascii.read(lines, fill_include_names=['a', 'c'])
<Table length=2>
   a     b      c     d
float64 str3 float64 str3
------- ---- ------- ----
    1.0  2.0     3.0  4.0
     --           --

>>> ascii.read(lines, fill_exclude_names=['a', 'c'])
<Table length=2>
 a      b     c      d
str3 float64 str3 float64
---- ------- ---- -------
 1.0     2.0  3.0     4.0
          --           --

Guess Table Format

If the guess parameter in read() is set to True, then read() will try to guess the table format by cycling through a number of possible table format permutations and attempting to read the table in each case. The first format which succeeds will be used to read the table. To succeed, the table must be successfully parsed by the Reader and satisfy the following column requirements:

• At least two table columns.

• No column names are a float or int number.

• No column names begin or end with space, comma, tab, single quote, double quote, or a vertical bar (|).

These requirements reduce the chance for a false positive where a table is successfully parsed with the wrong format. A common situation is a table with numeric columns but no header row, and in this case astropy.io.ascii will auto-assign column names because of the restriction on column names that look like a number.

Guess Order

The order of guessing is shown by this Python code:

for format in ("ecsv", "fixed_width_two_line", "rst", "fast_basic", "basic",
               "fast_rdb", "rdb", "fast_tab", "tab", "cds", "daophot", "sextractor",
               "ipac", "latex", "aastex"):
    read(format=format)

for format in ("commented_header", "fast_basic", "basic", "fast_noheader", ""noheader"):
    for delimiter in ("|", ",", " ", "\\s"):
        for quotechar in ('"', "'"):
            read(format=format, delimiter=delimiter, quotechar=quotechar)

Note that the FixedWidth derived-readers are not included in the default guess sequence (this causes problems), so to read such tables you must explicitly specify the format with the format keyword. Also notice that formats compatible with the fast reading engine attempt to use the fast engine before the ordinary reading engine.

If none of the guesses succeed in reading the table (subject to the column requirements), a final try is made using just the user-supplied parameters but without checking the column requirements. In this way, a table with only one column or column names that look like a number can still be successfully read.

The guessing process respects any values of the format, delimiter, and quotechar parameters as well as options for the fast reader that were supplied to the read() function. Any guesses that would conflict are skipped. For example, the call:

>>> data = ascii.read(table, format="no_header", quotechar="'")

would only try the four delimiter possibilities, skipping all the conflicting format and quotechar combinations. Similarly, with any setting of fast_reader that requires use of the fast engine, only the fast variants in the format list above will be tried.

Disabling

Guessing can be disabled in two ways:

import astropy.io.ascii
data = astropy.io.ascii.read(table)               # guessing enabled by default
data = astropy.io.ascii.read(table, guess=False)  # disable for this call
astropy.io.ascii.set_guess(False)                 # set default to False globally
data = astropy.io.ascii.read(table)               # guessing disabled

Debugging

In order to get more insight into the guessing process and possibly debug if something is not working as expected, use the get_read_trace() function. This returns a traceback of the attempted read formats for the last call to read().

Comments and Metadata

Any comment lines detected during reading are inserted into the output table via the comments key in the table’s .meta dictionary.

Example

Comment lines detected during reading are inserted into the output table as such:

>>> table='''# TELESCOPE = 30 inch
...          # TARGET = PV Ceph
...          # BAND = V
...          MJD mag
...          55555 12.3
...          55556 12.4'''
>>> dat = ascii.read(table)
>>> print(dat.meta['comments'])
['TELESCOPE = 30 inch', 'TARGET = PV Ceph', 'BAND = V']

While astropy.io.ascii will not do any post-processing on comment lines, custom post-processing can be accomplished by rereading with the metadata line comments. Here is one example, where comments are of the form “# KEY = VALUE”:

>>> header = ascii.read(dat.meta['comments'], delimiter='=',
...                     format='no_header', names=['key', 'val'])
>>> print(header)
   key      val
--------- -------
TELESCOPE 30 inch
   TARGET PV Ceph
     BAND       V

Converters for Specifying Dtype

astropy.io.ascii converts the raw string values from the table into numeric data types by using converter functions such as the Python int and float functions or numpy dtype types such as np.float64.

The default converters are:

default_converters = [int, float, str]

The default converters for each column can be overridden with the converters keyword:

>>> import numpy as np
>>> converters = {'col1': np.uint,
...               'col2': np.float32}
>>> ascii.read('file.dat', converters=converters)  

In addition to single column names you can use wildcards via fnmatch to select multiple columns. For example, we can set the format for all columns with a name starting with “col” to an unsigned integer while applying default converters to all other columns in the table:

>>> import numpy as np
>>> converters = {'col*': np.uint}
>>> ascii.read('file.dat', converters=converters)  

The value in the converters dict can also be a list of types, in which case these will be tried in order. This allows for flexible type conversions. For example, imagine you get read the following table:

>>> txt = """\
...   a   b    c
... --- --- -----
...   1 3.5  True
...   2 4.0 False"""
>>> t = ascii.read(txt, format='fixed_width_two_line')

By default the True and False values will be interpreted as strings. However, if you want those values to be read as booleans you can do the following:

>>> converters = {'*': [int, float, bool, str]}
>>> t = ascii.read(txt, format='fixed_width_two_line', converters=converters)
>>> print(t['c'].dtype)
bool

Advanced usage

Internally type conversion uses the convert_numpy() function which returns a two-element tuple (converter_func, converter_type). This two-element tuple can be used as the value in a converters dict. The type provided to convert_numpy() must be a valid NumPy type such as numpy.int, numpy.uint, numpy.int8, numpy.int64, numpy.float, numpy.float64, or numpy.str.

It is also possible to directly pass an arbitrary conversion function as the converter_func element of the two-element tuple.

Fortran-Style Exponents

The fast converter available with the C input parser provides an exponent_style option to define a custom character instead of the standard 'e' for exponential formats in the input file, to read, for example, Fortran-style double precision numbers like '1.495978707D+13':

>>> ascii.read('double.dat', format='basic', guess=False,
...            fast_reader={'exponent_style': 'D'})  

The special setting 'fortran' is provided to allow for the auto-detection of any valid Fortran exponent character ('E', 'D', 'Q'), as well as of triple-digit exponents prefixed with no character at all (e.g., '2.1127123261674622-107'). All values and exponent characters in the input data are case-insensitive; any value other than the default 'E' implies the automatic setting of 'use_fast_converter': True.

Advanced Customization

Here we provide a few examples that demonstrate how to extend the base functionality to handle special cases. To go beyond these examples, the best reference is to read the code for the existing Extension Reader Classes.

Examples

For special cases, these examples demonstrate how to extend the base functionality of astropy.io.ascii.

Define custom readers by class inheritance

The most useful way to define a new reader class is by inheritance. This is the way all of the built-in readers are defined, so there are plenty of examples in the code.

In most cases, you will define one class to handle the header, one class that handles the data, and a reader class that ties it all together. Here is an example from the code that defines a reader that is just like the basic reader, but header and data start in different lines of the file:

# Note: NoHeader is already included in astropy.io.ascii for convenience.
class NoHeaderHeader(BasicHeader):
    """Reader for table header without a header

    Set the start of header line number to `None`, which tells the basic
    reader there is no header line.
    """
    start_line = None

class NoHeaderData(BasicData):
    """Reader for table data without a header

    Data starts at first uncommented line since there is no header line.
    """
    start_line = 0

class NoHeader(Basic):
    """Read a table with no header line.  Columns are autonamed using
    header.auto_format which defaults to "col%d".  Otherwise this reader
    the same as the :class:`Basic` class from which it is derived.  Example::

      # Table data
      1 2 "hello there"
      3 4 world
    """
    _format_name = 'no_header'
    _description = 'Basic table with no headers'
    header_class = NoHeaderHeader
    data_class = NoHeaderData

In a slightly more involved case, the implementation can also override some of the methods in the base class:

# Note: CommentedHeader is already included in astropy.io.ascii for convenience.
class CommentedHeaderHeader(BasicHeader):
    """Header class for which the column definition line starts with the
    comment character.  See the :class:`CommentedHeader` class  for an example.
    """
    def process_lines(self, lines):
        """Return only lines that start with the comment regexp.  For these
        lines strip out the matching characters."""
        re_comment = re.compile(self.comment)
        for line in lines:
            match = re_comment.match(line)
            if match:
                yield line[match.end():]

    def write(self, lines):
        lines.append(self.write_comment + self.splitter.join(self.colnames))


class CommentedHeader(Basic):
    """Read a file where the column names are given in a line that begins with
    the header comment character. ``header_start`` can be used to specify the
    line index of column names, and it can be a negative index (for example -1
    for the last commented line).  The default delimiter is the <space>
    character.::

      # col1 col2 col3
      # Comment line
      1 2 3
      4 5 6
    """
    _format_name = 'commented_header'
    _description = 'Column names in a commented line'

    header_class = CommentedHeaderHeader
    data_class = NoHeaderData

Define a custom reader functionally

Instead of defining a new class, it is also possible to obtain an instance of a reader, and then to modify the properties of this one reader instance in a function:

def read_rdb_table(table):
    reader = astropy.io.ascii.Basic()
    reader.header.splitter.delimiter = '\t'
    reader.data.splitter.delimiter = '\t'
    reader.header.splitter.process_line = None
    reader.data.splitter.process_line = None
    reader.data.start_line = 2

    return reader.read(table)

Create a custom splitter.process_val function

# The default process_val() normally just strips whitespace.
# In addition have it replace empty fields with -999.
def process_val(x):
    """Custom splitter process_val function: Remove whitespace at the beginning
    or end of value and substitute -999 for any blank entries."""
    x = x.strip()
    if x == '':
        x = '-999'
    return x

# Create an RDB reader and override the splitter.process_val function
rdb_reader = astropy.io.ascii.get_reader(reader_cls=astropy.io.ascii.Rdb)
rdb_reader.data.splitter.process_val = process_val

Reading Large Tables in Chunks

The default process for reading ASCII tables is not memory efficient and may temporarily require much more memory than the size of the file (up to a factor of 5 to 10). In cases where the temporary memory requirement exceeds available memory this can cause significant slowdown when disk cache gets used.

In this situation, there is a way to read the table in smaller chunks which are limited in size. There are two possible ways to do this:

• Read the table in chunks and aggregate the final table along the way. This uses only somewhat more memory than the final table requires.

• Use a Python generator function to return a Table object for each chunk of the input table. This allows for scanning through arbitrarily large tables since it never returns the final aggregate table.

The chunk reading functionality is most useful for very large tables, so this is available only for the Fast ASCII I/O readers. The following formats are supported: tab, csv, no_header, rdb, and basic. The commented_header format is not directly supported, but as a workaround one can read using the no_header format and explicitly supply the column names using the names argument.

In order to read a table in chunks you must provide the fast_reader keyword argument with a dict that includes the chunk_size key with the value being the approximate size (in bytes) of each chunk of the input table to read. In addition, if you provide a chunk_generator key which is set to True, then instead of returning a single table for the whole input it returns an iterator that provides a table for each chunk of the input.

Examples

To read an entire table while limiting peak memory usage:

# Read a large CSV table in 100 Mb chunks.

tbl = ascii.read('large_table.csv', format='csv', guess=False,
                 fast_reader={'chunk_size': 100 * 1000000})

To read the table in chunks with an iterator, we iterate over a CSV table and select all rows where the Vmag column is less than 8.0 (e.g., all stars in table brighter than 8.0 mag). We collect all of these subtables and then stack them at the end.

from astropy.table import vstack

# tbls is an iterator over the chunks (no actual reading done yet)
tbls = ascii.read('large_table.csv', format='csv', guess=False,
                  fast_reader={'chunk_size': 100 * 1000000,
                               'chunk_generator': True})

out_tbls = []

# At this point the file is actually read in chunks.
for tbl in tbls:
    bright = tbl['Vmag'] < 8.0
    if np.count_nonzero(bright):
        out_tbls.append(tbl[bright])

out_tbl = vstack(out_tbls)

Note

Performance

Specifying the format explicitly and using guess=False is a good idea for large tables. This prevents unnecessary guessing in the typical case where the format is already known.

The chunk_size should generally be set to the largest value that is reasonable given available system memory. There is overhead associated with processing each chunk, so the fewer chunks the better.

How to Find and Fix Problems Reading a Table

The purpose of this section is to provide a few examples how we can deal with tables that fail to read.

Obtain the Data Table in a Different Format

Sometimes it is easy to obtain the data in a more structured format that more clearly defines columns and metadata, e.g. a FITS or VO/XML table, or an ASCII table that uses a different column separator (e.g. comma instead of white space) or fixed-width columns. In that case, the fastest solution can be to simply download or export the data again in a different format.

Find the Problem

Usually, astropy.io.ascii.read tries many different formats until one succeeds in reading. If it works, that saves you from finding and setting right options for reading. However, if it fails to find any combination of format and format options that correctly parses the file, then you will get a long exception message which shows every format that was tried and ends with this advice:

************************************************************************
** ERROR: Unable to guess table format with the guesses listed above. **
**                                                                    **
** To figure out why the table did not read, use guess=False and      **
** fast_reader=False, along with any appropriate arguments to read(). **
** In particular specify the format and any known attributes like the **
** delimiter.                                                         **
************************************************************************

To expand on this a bit, you probably know from looking at the file what format it is in, which must be one of the Supported Formats. For instance maybe it is a basic space-delimited file but has the header line as a comment like below, which corresponds to the commented_header format:

>>> table = """# name id
... Jill 1232
... Jack Johnson 456"""

In order to find the actual problem with the reading this file, you would do:

>>> ascii.read(table, format='commented_header', delimiter=' ', guess=False, fast_reader=False)
Traceback (most recent call last):
  ...
astropy.io.ascii.core.InconsistentTableError: Number of header columns (2) inconsistent with data columns (3) at data line 1
Header values: ['name', 'id']
Data values: ['Jack', 'Johnson', '456']

At this point you can see that the problem is that the 2nd data line has 3 columns while the header says there should be only 2. You might be initially confused by the data line 1 since the problem was in the 3rd line of the file. There are two things happening here. First, data line 1 refers to the count of data lines and does not include any header lines, blank lines, or commented out lines. Second, the count starts from zero, so that 1 is the 2nd data line. See the Guess Table Format section for additional details on format guessing.

Make the Table Easier to Read

Sometimes, the parameters for astropy.io.ascii.read to specify, for example format, delimiter, comment, quote_char, header_start, data_start, data_end, and encoding are not enough. To read just a single table that has a format close to, but not identical with, any of the Supported Formats, the fastest solution may be to open that one table file in a text editor to modify it until it does conform to a format that can be read. On the other hand, if we need to read tables of that specific format again and again, it is better to find a way to read them with ascii without modifying every file by hand.

Badly formatted header line

The following table will fail to parse (raising an InconsistentTableError) because the header line looks as if there were three columns, while in fact, there are only two:

Name spectral type
Vega A0
Altair A7

Opening this file in a text editor to fix the format is easy:

Name "spectral type"
Vega A0
Altair A7

or:

Name spectral_type
Vega A0
Altair A7

With either of the above changes you can read the file with no problem using default settings.

To read the table without editing the files, we need to ignore the badly formatted header line and pass in the names of the column ourselves. That can be done without any modification of the table file by setting the data_start parameter:

>>> table = """
... Star spectral type
... Vega A0
... Altair A7
... """
>>> ascii.read(table, names=["Star", "spectral type"], data_start=1)
<Table length=2>
 Star  spectral type
 str6       str2
------ -------------
  Vega            A0
Altair            A7

Badly formatted data line

Similar principles apply to badly formatted data lines. Here is a table where the number of columns is not consistent (alpha Cen should be written as "alpha Cen" to make clear that the two words “alpha” and “Cen” are part of the same column):

Star SpT
Vega A0
alpha Cen G2V+K1

When we try to read that with guess=False, astropy throws an astropy.io.ascii.InconsistentTableError:

>>> from astropy.io import ascii
>>> table = '''
... Star SpT
... Vega A0
... alpha Cen G2V+K1
... '''
>>> ascii.read(table, guess=False)
Traceback (most recent call last):
    ...
astropy.io.ascii.core.InconsistentTableError: Number of header columns (2) inconsistent with data columns in data line 1

This points us to the line with the problem, here line 1 (starting to count after the header lines and counting the data lines from 0 as usual in Python). In this table with just two lines the problem is easy to spot, but for longer tables, the line number is very helpful. We can now fix that line by hand in the file by adding quotes around "alpha Cen". Then we can try to read the table again and see if it works or if there is a another badly formatted data line.

Reading Gaia Data Tables

Note

The recommended way to access Gaia is via its astroquery.gaia module. However, if you need to access its data file separately via astropy, then read on.

Gaia data tables are available in ECSV format including detailed metadata for the tables and columns (e.g., column descriptions, units, and data types). For example the DR3 tables are at http://cdn.gea.esac.esa.int/Gaia/gdr3/gaia_source/.

The DR3 data files are not strictly compliant with the ECSV standard because they use the marker null to indicate a missing value instead of the required "". In order to read these files correctly with the full metadata, we need to tell the ECSV reader to treat null as the missing value:

>>> from astropy.table import QTable
>>> dat = QTable.read(
...     "GaiaSource_000000-003111.csv.gz",
...     format="ascii.ecsv",
...     fill_values=("null", "0")
... )