# Licensed under a 3-clause BSD style license - see PYFITS.rst
import contextlib
import csv
import operator
import os
import re
import sys
import textwrap
import warnings
from contextlib import suppress
import numpy as np
from numpy import char as chararray
# This module may have many dependencies on astropy.io.fits.column, but
# astropy.io.fits.column has fewer dependencies overall, so it's easier to
# keep table/column-related utilities in astropy.io.fits.column
from astropy.io.fits.column import (
ATTRIBUTE_TO_KEYWORD,
FITS2NUMPY,
KEYWORD_NAMES,
KEYWORD_TO_ATTRIBUTE,
TDEF_RE,
ColDefs,
Column,
_AsciiColDefs,
_cmp_recformats,
_convert_format,
_FormatP,
_FormatQ,
_makep,
_parse_tformat,
_scalar_to_format,
)
from astropy.io.fits.fitsrec import FITS_rec, _get_recarray_field, _has_unicode_fields
from astropy.io.fits.header import Header, _pad_length
from astropy.io.fits.util import _is_int, _str_to_num, path_like
from astropy.utils import lazyproperty
from astropy.utils.exceptions import AstropyDeprecationWarning
from .base import DELAYED, ExtensionHDU, _ValidHDU
class FITSTableDumpDialect(csv.excel):
"""
A CSV dialect for the Astropy format of ASCII dumps of FITS tables.
"""
delimiter = " "
lineterminator = "\n"
quotechar = '"'
quoting = csv.QUOTE_ALL
skipinitialspace = True
class _TableLikeHDU(_ValidHDU):
"""
A class for HDUs that have table-like data. This is used for both
Binary/ASCII tables as well as Random Access Group HDUs (which are
otherwise too dissimilar for tables to use _TableBaseHDU directly).
"""
_data_type = FITS_rec
_columns_type = ColDefs
# TODO: Temporary flag representing whether uints are enabled; remove this
# after restructuring to support uints by default on a per-column basis
_uint = False
@classmethod
def match_header(cls, header):
"""
This is an abstract HDU type for HDUs that contain table-like data.
This is even more abstract than _TableBaseHDU which is specifically for
the standard ASCII and Binary Table types.
"""
raise NotImplementedError
@classmethod
def from_columns(
cls,
columns,
header=None,
nrows=0,
fill=False,
character_as_bytes=False,
**kwargs,
):
"""
Given either a `ColDefs` object, a sequence of `Column` objects,
or another table HDU or table data (a `FITS_rec` or multi-field
`numpy.ndarray` or `numpy.recarray` object, return a new table HDU of
the class this method was called on using the column definition from
the input.
See also `FITS_rec.from_columns`.
Parameters
----------
columns : sequence of `Column`, `ColDefs` -like
The columns from which to create the table data, or an object with
a column-like structure from which a `ColDefs` can be instantiated.
This includes an existing `BinTableHDU` or `TableHDU`, or a
`numpy.recarray` to give some examples.
If these columns have data arrays attached that data may be used in
initializing the new table. Otherwise the input columns will be
used as a template for a new table with the requested number of
rows.
header : `Header`
An optional `Header` object to instantiate the new HDU yet. Header
keywords specifically related to defining the table structure (such
as the "TXXXn" keywords like TTYPEn) will be overridden by the
supplied column definitions, but all other informational and data
model-specific keywords are kept.
nrows : int
Number of rows in the new table. If the input columns have data
associated with them, the size of the largest input column is used.
Otherwise the default is 0.
fill : bool
If `True`, will fill all cells with zeros or blanks. If `False`,
copy the data from input, undefined cells will still be filled with
zeros/blanks.
character_as_bytes : bool
Whether to return bytes for string columns when accessed from the
HDU. By default this is `False` and (unicode) strings are returned,
but for large tables this may use up a lot of memory.
Notes
-----
Any additional keyword arguments accepted by the HDU class's
``__init__`` may also be passed in as keyword arguments.
"""
coldefs = cls._columns_type(columns)
data = FITS_rec.from_columns(
coldefs, nrows=nrows, fill=fill, character_as_bytes=character_as_bytes
)
hdu = cls(
data=data, header=header, character_as_bytes=character_as_bytes, **kwargs
)
coldefs._add_listener(hdu)
return hdu
@lazyproperty
def columns(self):
"""
The :class:`ColDefs` objects describing the columns in this table.
"""
# The base class doesn't make any assumptions about where the column
# definitions come from, so just return an empty ColDefs
return ColDefs([])
@property
def _nrows(self):
"""
table-like HDUs must provide an attribute that specifies the number of
rows in the HDU's table.
For now this is an internal-only attribute.
"""
raise NotImplementedError
def _get_tbdata(self):
"""Get the table data from an input HDU object."""
columns = self.columns
# TODO: Details related to variable length arrays need to be dealt with
# specifically in the BinTableHDU class, since they're a detail
# specific to FITS binary tables
if (
any(type(r) in (_FormatP, _FormatQ) for r in columns._recformats)
and self._data_size is not None
and self._data_size > self._theap
):
# We have a heap; include it in the raw_data
raw_data = self._get_raw_data(self._data_size, np.uint8, self._data_offset)
tbsize = self._header["NAXIS1"] * self._header["NAXIS2"]
data = raw_data[:tbsize].view(dtype=columns.dtype, type=np.rec.recarray)
else:
raw_data = self._get_raw_data(self._nrows, columns.dtype, self._data_offset)
if raw_data is None:
# This can happen when a brand new table HDU is being created
# and no data has been assigned to the columns, which case just
# return an empty array
raw_data = np.array([], dtype=columns.dtype)
data = raw_data.view(np.rec.recarray)
self._init_tbdata(data)
data = data.view(self._data_type)
columns._add_listener(data)
return data
def _init_tbdata(self, data):
columns = self.columns
data.dtype = data.dtype.newbyteorder(">")
# hack to enable pseudo-uint support
data._uint = self._uint
# pass datLoc, for P format
data._heapoffset = self._theap
data._heapsize = self._header["PCOUNT"]
tbsize = self._header["NAXIS1"] * self._header["NAXIS2"]
data._gap = self._theap - tbsize
# pass the attributes
for idx, col in enumerate(columns):
# get the data for each column object from the rec.recarray
col.array = data.field(idx)
# delete the _arrays attribute so that it is recreated to point to the
# new data placed in the column object above
del columns._arrays
def _update_load_data(self):
"""Load the data if asked to."""
if not self._data_loaded:
self.data
def _update_column_added(self, columns, column):
"""
Update the data upon addition of a new column through the `ColDefs`
interface.
"""
# recreate data from the columns
self.data = FITS_rec.from_columns(
self.columns,
nrows=self._nrows,
fill=False,
character_as_bytes=self._character_as_bytes,
)
def _update_column_removed(self, columns, col_idx):
"""
Update the data upon removal of a column through the `ColDefs`
interface.
"""
# recreate data from the columns
self.data = FITS_rec.from_columns(
self.columns,
nrows=self._nrows,
fill=False,
character_as_bytes=self._character_as_bytes,
)
class _TableBaseHDU(ExtensionHDU, _TableLikeHDU):
"""
FITS table extension base HDU class.
Parameters
----------
data : array
Data to be used.
header : `Header` instance
Header to be used. If the ``data`` is also specified, header keywords
specifically related to defining the table structure (such as the
"TXXXn" keywords like TTYPEn) will be overridden by the supplied column
definitions, but all other informational and data model-specific
keywords are kept.
name : str
Name to be populated in ``EXTNAME`` keyword.
uint : bool, optional
Set to `True` if the table contains unsigned integer columns.
ver : int > 0 or None, optional
The ver of the HDU, will be the value of the keyword ``EXTVER``.
If not given or None, it defaults to the value of the ``EXTVER``
card of the ``header`` or 1.
(default: None)
character_as_bytes : bool
Whether to return bytes for string columns. By default this is `False`
and (unicode) strings are returned, but this does not respect memory
mapping and loads the whole column in memory when accessed.
"""
_manages_own_heap = False
"""
This flag implies that when writing VLA tables (P/Q format) the heap
pointers that go into P/Q table columns should not be reordered or
rearranged in any way by the default heap management code.
This is included primarily as an optimization for compressed image HDUs
which perform their own heap maintenance.
"""
def __init__(
self,
data=None,
header=None,
name=None,
uint=False,
ver=None,
character_as_bytes=False,
):
super().__init__(data=data, header=header, name=name, ver=ver)
self._uint = uint
self._character_as_bytes = character_as_bytes
if data is DELAYED:
# this should never happen
if header is None:
raise ValueError("No header to setup HDU.")
# if the file is read the first time, no need to copy, and keep it
# unchanged
else:
self._header = header
else:
# construct a list of cards of minimal header
cards = [
("XTENSION", self._extension, self._ext_comment),
("BITPIX", 8, "array data type"),
("NAXIS", 2, "number of array dimensions"),
("NAXIS1", 0, "length of dimension 1"),
("NAXIS2", 0, "length of dimension 2"),
("PCOUNT", 0, "number of group parameters"),
("GCOUNT", 1, "number of groups"),
("TFIELDS", 0, "number of table fields"),
]
if header is not None:
# Make a "copy" (not just a view) of the input header, since it
# may get modified. the data is still a "view" (for now)
hcopy = header.copy(strip=True)
cards.extend(hcopy.cards)
self._header = Header(cards)
if isinstance(data, np.ndarray) and data.dtype.fields is not None:
# self._data_type is FITS_rec.
if isinstance(data, self._data_type):
self.data = data
else:
self.data = self._data_type.from_columns(data)
# TEMP: Special column keywords are normally overwritten by attributes
# from Column objects. In Astropy 3.0, several new keywords are now
# recognized as being special column keywords, but we don't
# automatically clear them yet, as we need to raise a deprecation
# warning for at least one major version.
if header is not None:
future_ignore = set()
for keyword in header.keys():
match = TDEF_RE.match(keyword)
try:
base_keyword = match.group("label")
except Exception:
continue # skip if there is no match
if base_keyword in {
"TCTYP",
"TCUNI",
"TCRPX",
"TCRVL",
"TCDLT",
"TRPOS",
}:
future_ignore.add(base_keyword)
if future_ignore:
keys = ", ".join(x + "n" for x in sorted(future_ignore))
warnings.warn(
"The following keywords are now recognized as special "
"column-related attributes and should be set via the "
"Column objects: {}. In future, these values will be "
"dropped from manually specified headers automatically "
"and replaced with values generated based on the "
"Column objects.".format(keys),
AstropyDeprecationWarning,
)
# TODO: Too much of the code in this class uses header keywords
# in making calculations related to the data size. This is
# unreliable, however, in cases when users mess with the header
# unintentionally--code that does this should be cleaned up.
self._header["NAXIS1"] = self.data._raw_itemsize
self._header["NAXIS2"] = self.data.shape[0]
self._header["TFIELDS"] = len(self.data._coldefs)
self.columns = self.data._coldefs
self.columns._add_listener(self.data)
self.update()
with suppress(TypeError, AttributeError):
# Make the ndarrays in the Column objects of the ColDefs
# object of the HDU reference the same ndarray as the HDU's
# FITS_rec object.
for idx, col in enumerate(self.columns):
col.array = self.data.field(idx)
# Delete the _arrays attribute so that it is recreated to
# point to the new data placed in the column objects above
del self.columns._arrays
elif data is None:
pass
else:
raise TypeError("Table data has incorrect type.")
# Ensure that the correct EXTNAME is set on the new header if one was
# created, or that it overrides the existing EXTNAME if different
if name:
self.name = name
if ver is not None:
self.ver = ver
@classmethod
def match_header(cls, header):
"""
This is an abstract type that implements the shared functionality of
the ASCII and Binary Table HDU types, which should be used instead of
this.
"""
raise NotImplementedError
@lazyproperty
def columns(self):
"""
The :class:`ColDefs` objects describing the columns in this table.
"""
if self._has_data and hasattr(self.data, "_coldefs"):
return self.data._coldefs
return self._columns_type(self)
@lazyproperty
def data(self):
data = self._get_tbdata()
data._coldefs = self.columns
data._character_as_bytes = self._character_as_bytes
# Columns should now just return a reference to the data._coldefs
del self.columns
return data
@data.setter
def data(self, data):
if "data" in self.__dict__:
if self.__dict__["data"] is data:
return
else:
self._data_replaced = True
else:
self._data_replaced = True
self._modified = True
if data is None and self.columns:
# Create a new table with the same columns, but empty rows
formats = ",".join(self.columns._recformats)
data = np.rec.array(
None, formats=formats, names=self.columns.names, shape=0
)
if isinstance(data, np.ndarray) and data.dtype.fields is not None:
# Go ahead and always make a view, even if the data is already the
# correct class (self._data_type) so we can update things like the
# column defs, if necessary
data = data.view(self._data_type)
if not isinstance(data.columns, self._columns_type):
# This would be the place, if the input data was for an ASCII
# table and this is binary table, or vice versa, to convert the
# data to the appropriate format for the table type
new_columns = self._columns_type(data.columns)
data = FITS_rec.from_columns(new_columns)
if "data" in self.__dict__:
self.columns._remove_listener(self.__dict__["data"])
self.__dict__["data"] = data
self.columns = self.data.columns
self.columns._add_listener(self.data)
self.update()
with suppress(TypeError, AttributeError):
# Make the ndarrays in the Column objects of the ColDefs
# object of the HDU reference the same ndarray as the HDU's
# FITS_rec object.
for idx, col in enumerate(self.columns):
col.array = self.data.field(idx)
# Delete the _arrays attribute so that it is recreated to
# point to the new data placed in the column objects above
del self.columns._arrays
elif data is None:
pass
else:
raise TypeError("Table data has incorrect type.")
# returning the data signals to lazyproperty that we've already handled
# setting self.__dict__['data']
return data
@property
def _nrows(self):
if not self._data_loaded:
return self._header.get("NAXIS2", 0)
else:
return len(self.data)
@lazyproperty
def _theap(self):
size = self._header["NAXIS1"] * self._header["NAXIS2"]
return self._header.get("THEAP", size)
# TODO: Need to either rename this to update_header, for symmetry with the
# Image HDUs, or just at some point deprecate it and remove it altogether,
# since header updates should occur automatically when necessary...
def update(self):
"""
Update header keywords to reflect recent changes of columns.
"""
self._header.set("NAXIS1", self.data._raw_itemsize, after="NAXIS")
self._header.set("NAXIS2", self.data.shape[0], after="NAXIS1")
self._header.set("TFIELDS", len(self.columns), after="GCOUNT")
self._clear_table_keywords()
self._populate_table_keywords()
def copy(self):
"""
Make a copy of the table HDU, both header and data are copied.
"""
# touch the data, so it's defined (in the case of reading from a
# FITS file)
return self.__class__(data=self.data.copy(), header=self._header.copy())
def _prewriteto(self, checksum=False, inplace=False):
if self._has_data:
self.data._scale_back(update_heap_pointers=not self._manages_own_heap)
# check TFIELDS and NAXIS2
self._header["TFIELDS"] = len(self.data._coldefs)
self._header["NAXIS2"] = self.data.shape[0]
# calculate PCOUNT, for variable length tables
tbsize = self._header["NAXIS1"] * self._header["NAXIS2"]
heapstart = self._header.get("THEAP", tbsize)
self.data._gap = heapstart - tbsize
pcount = self.data._heapsize + self.data._gap
if pcount > 0:
self._header["PCOUNT"] = pcount
# update the other T****n keywords
self._populate_table_keywords()
# update TFORM for variable length columns
for idx in range(self.data._nfields):
format = self.data._coldefs._recformats[idx]
if isinstance(format, _FormatP):
_max = self.data.field(idx).max
# May be either _FormatP or _FormatQ
format_cls = format.__class__
format = format_cls(format.dtype, repeat=format.repeat, max=_max)
self._header["TFORM" + str(idx + 1)] = format.tform
return super()._prewriteto(checksum, inplace)
def _verify(self, option="warn"):
"""
_TableBaseHDU verify method.
"""
errs = super()._verify(option=option)
if len(self._header) > 1:
if not (
isinstance(self._header[0], str)
and self._header[0].rstrip() == self._extension
):
err_text = "The XTENSION keyword must match the HDU type."
fix_text = f"Converted the XTENSION keyword to {self._extension}."
def fix(header=self._header):
header[0] = (self._extension, self._ext_comment)
errs.append(
self.run_option(
option, err_text=err_text, fix_text=fix_text, fix=fix
)
)
self.req_cards("NAXIS", None, lambda v: (v == 2), 2, option, errs)
self.req_cards("BITPIX", None, lambda v: (v == 8), 8, option, errs)
self.req_cards(
"TFIELDS",
7,
lambda v: (_is_int(v) and v >= 0 and v <= 999),
0,
option,
errs,
)
tfields = self._header["TFIELDS"]
for idx in range(tfields):
self.req_cards("TFORM" + str(idx + 1), None, None, None, option, errs)
return errs
def _summary(self):
"""
Summarize the HDU: name, dimensions, and formats.
"""
class_name = self.__class__.__name__
# if data is touched, use data info.
if self._data_loaded:
if self.data is None:
nrows = 0
else:
nrows = len(self.data)
ncols = len(self.columns)
format = self.columns.formats
# if data is not touched yet, use header info.
else:
nrows = self._header["NAXIS2"]
ncols = self._header["TFIELDS"]
format = ", ".join(
[self._header["TFORM" + str(j + 1)] for j in range(ncols)]
)
format = f"[{format}]"
dims = f"{nrows}R x {ncols}C"
ncards = len(self._header)
return (self.name, self.ver, class_name, ncards, dims, format)
def _update_column_removed(self, columns, idx):
super()._update_column_removed(columns, idx)
# Fix the header to reflect the column removal
self._clear_table_keywords(index=idx)
def _update_column_attribute_changed(
self, column, col_idx, attr, old_value, new_value
):
"""
Update the header when one of the column objects is updated.
"""
# base_keyword is the keyword without the index such as TDIM
# while keyword is like TDIM1
base_keyword = ATTRIBUTE_TO_KEYWORD[attr]
keyword = base_keyword + str(col_idx + 1)
if keyword in self._header:
if new_value is None:
# If the new value is None, i.e. None was assigned to the
# column attribute, then treat this as equivalent to deleting
# that attribute
del self._header[keyword]
else:
self._header[keyword] = new_value
else:
keyword_idx = KEYWORD_NAMES.index(base_keyword)
# Determine the appropriate keyword to insert this one before/after
# if it did not already exist in the header
for before_keyword in reversed(KEYWORD_NAMES[:keyword_idx]):
before_keyword += str(col_idx + 1)
if before_keyword in self._header:
self._header.insert(
before_keyword, (keyword, new_value), after=True
)
break
else:
for after_keyword in KEYWORD_NAMES[keyword_idx + 1 :]:
after_keyword += str(col_idx + 1)
if after_keyword in self._header:
self._header.insert(after_keyword, (keyword, new_value))
break
else:
# Just append
self._header[keyword] = new_value
def _clear_table_keywords(self, index=None):
"""
Wipe out any existing table definition keywords from the header.
If specified, only clear keywords for the given table index (shifting
up keywords for any other columns). The index is zero-based.
Otherwise keywords for all columns.
"""
# First collect all the table structure related keyword in the header
# into a single list so we can then sort them by index, which will be
# useful later for updating the header in a sensible order (since the
# header *might* not already be written in a reasonable order)
table_keywords = []
for idx, keyword in enumerate(self._header.keys()):
match = TDEF_RE.match(keyword)
try:
base_keyword = match.group("label")
except Exception:
continue # skip if there is no match
if base_keyword in KEYWORD_TO_ATTRIBUTE:
# TEMP: For Astropy 3.0 we don't clear away the following keywords
# as we are first raising a deprecation warning that these will be
# dropped automatically if they were specified in the header. We
# can remove this once we are happy to break backward-compatibility
if base_keyword in {
"TCTYP",
"TCUNI",
"TCRPX",
"TCRVL",
"TCDLT",
"TRPOS",
}:
continue
num = int(match.group("num")) - 1 # convert to zero-base
table_keywords.append((idx, match.group(0), base_keyword, num))
# First delete
rev_sorted_idx_0 = sorted(
table_keywords, key=operator.itemgetter(0), reverse=True
)
for idx, keyword, _, num in rev_sorted_idx_0:
if index is None or index == num:
del self._header[idx]
# Now shift up remaining column keywords if only one column was cleared
if index is not None:
sorted_idx_3 = sorted(table_keywords, key=operator.itemgetter(3))
for _, keyword, base_keyword, num in sorted_idx_3:
if num <= index:
continue
old_card = self._header.cards[keyword]
new_card = (base_keyword + str(num), old_card.value, old_card.comment)
self._header.insert(keyword, new_card)
del self._header[keyword]
# Also decrement TFIELDS
if "TFIELDS" in self._header:
self._header["TFIELDS"] -= 1
def _populate_table_keywords(self):
"""Populate the new table definition keywords from the header."""
for idx, column in enumerate(self.columns):
for keyword, attr in KEYWORD_TO_ATTRIBUTE.items():
val = getattr(column, attr)
if val is not None:
keyword = keyword + str(idx + 1)
self._header[keyword] = val
[docs]class TableHDU(_TableBaseHDU):
"""
FITS ASCII table extension HDU class.
Parameters
----------
data : array or `FITS_rec`
Data to be used.
header : `Header`
Header to be used.
name : str
Name to be populated in ``EXTNAME`` keyword.
ver : int > 0 or None, optional
The ver of the HDU, will be the value of the keyword ``EXTVER``.
If not given or None, it defaults to the value of the ``EXTVER``
card of the ``header`` or 1.
(default: None)
character_as_bytes : bool
Whether to return bytes for string columns. By default this is `False`
and (unicode) strings are returned, but this does not respect memory
mapping and loads the whole column in memory when accessed.
"""
_extension = "TABLE"
_ext_comment = "ASCII table extension"
_padding_byte = " "
_columns_type = _AsciiColDefs
__format_RE = re.compile(r"(?P<code>[ADEFIJ])(?P<width>\d+)(?:\.(?P<prec>\d+))?")
def __init__(
self, data=None, header=None, name=None, ver=None, character_as_bytes=False
):
super().__init__(
data, header, name=name, ver=ver, character_as_bytes=character_as_bytes
)
def _get_tbdata(self):
columns = self.columns
names = [n for idx, n in enumerate(columns.names)]
# determine if there are duplicate field names and if there
# are throw an exception
dup = np.rec.find_duplicate(names)
if dup:
raise ValueError(f"Duplicate field names: {dup}")
# TODO: Determine if this extra logic is necessary--I feel like the
# _AsciiColDefs class should be responsible for telling the table what
# its dtype should be...
itemsize = columns.spans[-1] + columns.starts[-1] - 1
dtype = {}
for idx in range(len(columns)):
data_type = "S" + str(columns.spans[idx])
if idx == len(columns) - 1:
# The last column is padded out to the value of NAXIS1
if self._header["NAXIS1"] > itemsize:
data_type = "S" + str(
columns.spans[idx] + self._header["NAXIS1"] - itemsize
)
dtype[columns.names[idx]] = (data_type, columns.starts[idx] - 1)
raw_data = self._get_raw_data(self._nrows, dtype, self._data_offset)
data = raw_data.view(np.rec.recarray)
self._init_tbdata(data)
return data.view(self._data_type)
def _calculate_datasum(self):
"""
Calculate the value for the ``DATASUM`` card in the HDU.
"""
if self._has_data:
# We have the data to be used.
# We need to pad the data to a block length before calculating
# the datasum.
bytes_array = self.data.view(type=np.ndarray, dtype=np.ubyte)
padding = np.frombuffer(_pad_length(self.size) * b" ", dtype=np.ubyte)
d = np.append(bytes_array, padding)
cs = self._compute_checksum(d)
return cs
else:
# This is the case where the data has not been read from the file
# yet. We can handle that in a generic manner so we do it in the
# base class. The other possibility is that there is no data at
# all. This can also be handled in a generic manner.
return super()._calculate_datasum()
def _verify(self, option="warn"):
"""
`TableHDU` verify method.
"""
errs = super()._verify(option=option)
self.req_cards("PCOUNT", None, lambda v: (v == 0), 0, option, errs)
tfields = self._header["TFIELDS"]
for idx in range(tfields):
self.req_cards("TBCOL" + str(idx + 1), None, _is_int, None, option, errs)
return errs
[docs]class BinTableHDU(_TableBaseHDU):
"""
Binary table HDU class.
Parameters
----------
data : array, `FITS_rec`, or `~astropy.table.Table`
Data to be used.
header : `Header`
Header to be used.
name : str
Name to be populated in ``EXTNAME`` keyword.
uint : bool, optional
Set to `True` if the table contains unsigned integer columns.
ver : int > 0 or None, optional
The ver of the HDU, will be the value of the keyword ``EXTVER``.
If not given or None, it defaults to the value of the ``EXTVER``
card of the ``header`` or 1.
(default: None)
character_as_bytes : bool
Whether to return bytes for string columns. By default this is `False`
and (unicode) strings are returned, but this does not respect memory
mapping and loads the whole column in memory when accessed.
"""
_extension = "BINTABLE"
_ext_comment = "binary table extension"
def __init__(
self,
data=None,
header=None,
name=None,
uint=False,
ver=None,
character_as_bytes=False,
):
from astropy.table import Table
if isinstance(data, Table):
from astropy.io.fits.convenience import table_to_hdu
hdu = table_to_hdu(data)
if header is not None:
hdu.header.update(header)
data = hdu.data
header = hdu.header
super().__init__(
data,
header,
name=name,
uint=uint,
ver=ver,
character_as_bytes=character_as_bytes,
)
def _calculate_datasum_with_heap(self):
"""
Calculate the value for the ``DATASUM`` card given the input data
"""
with _binary_table_byte_swap(self.data) as data:
dout = data.view(type=np.ndarray, dtype=np.ubyte)
csum = self._compute_checksum(dout)
# Now add in the heap data to the checksum (we can skip any gap
# between the table and the heap since it's all zeros and doesn't
# contribute to the checksum
if data._get_raw_data() is None:
# This block is still needed because
# test_variable_length_table_data leads to ._get_raw_data
# returning None which means _get_heap_data doesn't work.
# Which happens when the data is loaded in memory rather than
# being unloaded on disk
for idx in range(data._nfields):
if isinstance(data.columns._recformats[idx], _FormatP):
for coldata in data.field(idx):
# coldata should already be byteswapped from the call
# to _binary_table_byte_swap
if not len(coldata):
continue
csum = self._compute_checksum(coldata, csum)
else:
csum = self._compute_checksum(data._get_heap_data(), csum)
return csum
def _calculate_datasum(self):
"""
Calculate the value for the ``DATASUM`` card in the HDU.
"""
if self._has_data:
# This method calculates the datasum while incorporating any
# heap data, which is obviously not handled from the base
# _calculate_datasum
return self._calculate_datasum_with_heap()
else:
# This is the case where the data has not been read from the file
# yet. We can handle that in a generic manner so we do it in the
# base class. The other possibility is that there is no data at
# all. This can also be handled in a generic manner.
return super()._calculate_datasum()
def _writedata_internal(self, fileobj):
size = 0
if self.data is None:
return size
with _binary_table_byte_swap(self.data) as data:
if _has_unicode_fields(data):
# If the raw data was a user-supplied recarray, we can't write
# unicode columns directly to the file, so we have to switch
# to a slower row-by-row write
self._writedata_by_row(fileobj)
else:
fileobj.writearray(data)
# write out the heap of variable length array columns this has
# to be done after the "regular" data is written (above)
# to avoid a bug in the lustre filesystem client, don't
# write 0-byte objects
if data._gap > 0:
fileobj.write((data._gap * "\0").encode("ascii"))
nbytes = data._gap
if not self._manages_own_heap:
# Write the heap data one column at a time, in the order
# that the data pointers appear in the column (regardless
# if that data pointer has a different, previous heap
# offset listed)
for idx in range(data._nfields):
if not isinstance(data.columns._recformats[idx], _FormatP):
continue
field = self.data.field(idx)
for row in field:
if len(row) > 0:
nbytes += row.nbytes
fileobj.writearray(row)
else:
heap_data = data._get_heap_data()
if len(heap_data) > 0:
nbytes += len(heap_data)
fileobj.writearray(heap_data)
data._heapsize = nbytes - data._gap
size += nbytes
size += self.data.size * self.data._raw_itemsize
return size
def _writedata_by_row(self, fileobj):
fields = [self.data.field(idx) for idx in range(len(self.data.columns))]
# Creating Record objects is expensive (as in
# `for row in self.data:` so instead we just iterate over the row
# indices and get one field at a time:
for idx in range(len(self.data)):
for field in fields:
item = field[idx]
field_width = None
if field.dtype.kind == "U":
# Read the field *width* by reading past the field kind.
i = field.dtype.str.index(field.dtype.kind)
field_width = int(field.dtype.str[i + 1 :])
item = np.char.encode(item, "ascii")
fileobj.writearray(item)
if field_width is not None:
j = item.dtype.str.index(item.dtype.kind)
item_length = int(item.dtype.str[j + 1 :])
# Fix padding problem (see #5296).
padding = "\x00" * (field_width - item_length)
fileobj.write(padding.encode("ascii"))
_tdump_file_format = textwrap.dedent(
"""
- **datafile:** Each line of the data file represents one row of table
data. The data is output one column at a time in column order. If
a column contains an array, each element of the column array in the
current row is output before moving on to the next column. Each row
ends with a new line.
Integer data is output right-justified in a 21-character field
followed by a blank. Floating point data is output right justified
using 'g' format in a 21-character field with 15 digits of
precision, followed by a blank. String data that does not contain
whitespace is output left-justified in a field whose width matches
the width specified in the ``TFORM`` header parameter for the
column, followed by a blank. When the string data contains
whitespace characters, the string is enclosed in quotation marks
(``""``). For the last data element in a row, the trailing blank in
the field is replaced by a new line character.
For column data containing variable length arrays ('P' format), the
array data is preceded by the string ``'VLA_Length= '`` and the
integer length of the array for that row, left-justified in a
21-character field, followed by a blank.
.. note::
This format does *not* support variable length arrays using the
('Q' format) due to difficult to overcome ambiguities. What this
means is that this file format cannot support VLA columns in
tables stored in files that are over 2 GB in size.
For column data representing a bit field ('X' format), each bit
value in the field is output right-justified in a 21-character field
as 1 (for true) or 0 (for false).
- **cdfile:** Each line of the column definitions file provides the
definitions for one column in the table. The line is broken up into
8, sixteen-character fields. The first field provides the column
name (``TTYPEn``). The second field provides the column format
(``TFORMn``). The third field provides the display format
(``TDISPn``). The fourth field provides the physical units
(``TUNITn``). The fifth field provides the dimensions for a
multidimensional array (``TDIMn``). The sixth field provides the
value that signifies an undefined value (``TNULLn``). The seventh
field provides the scale factor (``TSCALn``). The eighth field
provides the offset value (``TZEROn``). A field value of ``""`` is
used to represent the case where no value is provided.
- **hfile:** Each line of the header parameters file provides the
definition of a single HDU header card as represented by the card
image.
"""
)
[docs] def dump(self, datafile=None, cdfile=None, hfile=None, overwrite=False):
"""
Dump the table HDU to a file in ASCII format. The table may be dumped
in three separate files, one containing column definitions, one
containing header parameters, and one for table data.
Parameters
----------
datafile : path-like or file-like, optional
Output data file. The default is the root name of the
fits file associated with this HDU appended with the
extension ``.txt``.
cdfile : path-like or file-like, optional
Output column definitions file. The default is `None`, no
column definitions output is produced.
hfile : path-like or file-like, optional
Output header parameters file. The default is `None`,
no header parameters output is produced.
overwrite : bool, optional
If ``True``, overwrite the output file if it exists. Raises an
``OSError`` if ``False`` and the output file exists. Default is
``False``.
Notes
-----
The primary use for the `dump` method is to allow viewing and editing
the table data and parameters in a standard text editor.
The `load` method can be used to create a new table from the three
plain text (ASCII) files.
"""
if isinstance(datafile, path_like):
datafile = os.path.expanduser(datafile)
if isinstance(cdfile, path_like):
cdfile = os.path.expanduser(cdfile)
if isinstance(hfile, path_like):
hfile = os.path.expanduser(hfile)
# check if the output files already exist
exist = []
files = [datafile, cdfile, hfile]
for f in files:
if isinstance(f, path_like):
if os.path.exists(f) and os.path.getsize(f) != 0:
if overwrite:
os.remove(f)
else:
exist.append(f)
if exist:
raise OSError(
" ".join([f"File '{f}' already exists." for f in exist])
+ " If you mean to "
"replace the file(s) "
"then use the argument "
"'overwrite=True'."
)
# Process the data
self._dump_data(datafile)
# Process the column definitions
if cdfile:
self._dump_coldefs(cdfile)
# Process the header parameters
if hfile:
self._header.tofile(hfile, sep="\n", endcard=False, padding=False)
if isinstance(dump.__doc__, str):
dump.__doc__ += _tdump_file_format.replace("\n", "\n ")
[docs] def load(cls, datafile, cdfile=None, hfile=None, replace=False, header=None):
"""
Create a table from the input ASCII files. The input is from up to
three separate files, one containing column definitions, one containing
header parameters, and one containing column data.
The column definition and header parameters files are not required.
When absent the column definitions and/or header parameters are taken
from the header object given in the header argument; otherwise sensible
defaults are inferred (though this mode is not recommended).
Parameters
----------
datafile : path-like or file-like
Input data file containing the table data in ASCII format.
cdfile : path-like or file-like, optional
Input column definition file containing the names,
formats, display formats, physical units, multidimensional
array dimensions, undefined values, scale factors, and
offsets associated with the columns in the table. If
`None`, the column definitions are taken from the current
values in this object.
hfile : path-like or file-like, optional
Input parameter definition file containing the header
parameter definitions to be associated with the table. If
`None`, the header parameter definitions are taken from
the current values in this objects header.
replace : bool, optional
When `True`, indicates that the entire header should be
replaced with the contents of the ASCII file instead of
just updating the current header.
header : `~astropy.io.fits.Header`, optional
When the cdfile and hfile are missing, use this Header object in
the creation of the new table and HDU. Otherwise this Header
supersedes the keywords from hfile, which is only used to update
values not present in this Header, unless ``replace=True`` in which
this Header's values are completely replaced with the values from
hfile.
Notes
-----
The primary use for the `load` method is to allow the input of ASCII
data that was edited in a standard text editor of the table data and
parameters. The `dump` method can be used to create the initial ASCII
files.
"""
# Process the parameter file
if header is None:
header = Header()
if hfile:
if replace:
header = Header.fromtextfile(hfile)
else:
header.extend(
Header.fromtextfile(hfile), update=True, update_first=True
)
coldefs = None
# Process the column definitions file
if cdfile:
coldefs = cls._load_coldefs(cdfile)
# Process the data file
data = cls._load_data(datafile, coldefs)
if coldefs is None:
coldefs = ColDefs(data)
# Create a new HDU using the supplied header and data
hdu = cls(data=data, header=header)
hdu.columns = coldefs
return hdu
if isinstance(load.__doc__, str):
load.__doc__ += _tdump_file_format.replace("\n", "\n ")
load = classmethod(load)
# Have to create a classmethod from this here instead of as a decorator;
# otherwise we can't update __doc__
def _dump_data(self, fileobj):
"""
Write the table data in the ASCII format read by BinTableHDU.load()
to fileobj.
"""
if not fileobj and self._file:
root = os.path.splitext(self._file.name)[0]
fileobj = root + ".txt"
close_file = False
if isinstance(fileobj, str):
fileobj = open(fileobj, "w")
close_file = True
linewriter = csv.writer(fileobj, dialect=FITSTableDumpDialect)
# Process each row of the table and output one row at a time
def format_value(val, format):
if format[0] == "S":
itemsize = int(format[1:])
return "{:{size}}".format(val, size=itemsize)
elif format in np.typecodes["AllInteger"]:
# output integer
return f"{val:21d}"
elif format in np.typecodes["Complex"]:
return f"{val.real:21.15g}+{val.imag:.15g}j"
elif format in np.typecodes["Float"]:
# output floating point
return f"{val:#21.15g}"
for row in self.data:
line = [] # the line for this row of the table
# Process each column of the row.
for column in self.columns:
# format of data in a variable length array
# where None means it is not a VLA:
vla_format = None
format = _convert_format(column.format)
if isinstance(format, _FormatP):
# P format means this is a variable length array so output
# the length of the array for this row and set the format
# for the VLA data
line.append("VLA_Length=")
line.append(f"{len(row[column.name]):21d}")
_, dtype, option = _parse_tformat(column.format)
vla_format = FITS2NUMPY[option[0]][0]
if vla_format:
# Output the data for each element in the array
for val in row[column.name].flat:
line.append(format_value(val, vla_format))
else:
# The column data is a single element
dtype = self.data.dtype.fields[column.name][0]
array_format = dtype.char
if array_format == "V":
array_format = dtype.base.char
if array_format == "S":
array_format += str(dtype.itemsize)
if dtype.char == "V":
for value in row[column.name].flat:
line.append(format_value(value, array_format))
else:
line.append(format_value(row[column.name], array_format))
linewriter.writerow(line)
if close_file:
fileobj.close()
def _dump_coldefs(self, fileobj):
"""
Write the column definition parameters in the ASCII format read by
BinTableHDU.load() to fileobj.
"""
close_file = False
if isinstance(fileobj, str):
fileobj = open(fileobj, "w")
close_file = True
# Process each column of the table and output the result to the
# file one at a time
for column in self.columns:
line = [column.name, column.format]
attrs = ["disp", "unit", "dim", "null", "bscale", "bzero"]
line += [
"{!s:16s}".format(value if value else '""')
for value in (getattr(column, attr) for attr in attrs)
]
fileobj.write(" ".join(line))
fileobj.write("\n")
if close_file:
fileobj.close()
@classmethod
def _load_data(cls, fileobj, coldefs=None):
"""
Read the table data from the ASCII file output by BinTableHDU.dump().
"""
close_file = False
if isinstance(fileobj, path_like):
fileobj = os.path.expanduser(fileobj)
fileobj = open(fileobj)
close_file = True
initialpos = fileobj.tell() # We'll be returning here later
linereader = csv.reader(fileobj, dialect=FITSTableDumpDialect)
# First we need to do some preprocessing on the file to find out how
# much memory we'll need to reserve for the table. This is necessary
# even if we already have the coldefs in order to determine how many
# rows to reserve memory for
vla_lengths = []
recformats = []
names = []
nrows = 0
if coldefs is not None:
recformats = coldefs._recformats
names = coldefs.names
def update_recformats(value, idx):
fitsformat = _scalar_to_format(value)
recformat = _convert_format(fitsformat)
if idx >= len(recformats):
recformats.append(recformat)
else:
if _cmp_recformats(recformats[idx], recformat) < 0:
recformats[idx] = recformat
# TODO: The handling of VLAs could probably be simplified a bit
for row in linereader:
nrows += 1
if coldefs is not None:
continue
col = 0
idx = 0
while idx < len(row):
if row[idx] == "VLA_Length=":
if col < len(vla_lengths):
vla_length = vla_lengths[col]
else:
vla_length = int(row[idx + 1])
vla_lengths.append(vla_length)
idx += 2
while vla_length:
update_recformats(row[idx], col)
vla_length -= 1
idx += 1
col += 1
else:
if col >= len(vla_lengths):
vla_lengths.append(None)
update_recformats(row[idx], col)
col += 1
idx += 1
# Update the recformats for any VLAs
for idx, length in enumerate(vla_lengths):
if length is not None:
recformats[idx] = str(length) + recformats[idx]
dtype = np.rec.format_parser(recformats, names, None).dtype
# TODO: In the future maybe enable loading a bit at a time so that we
# can convert from this format to an actual FITS file on disk without
# needing enough physical memory to hold the entire thing at once
hdu = BinTableHDU.from_columns(
np.recarray(shape=1, dtype=dtype), nrows=nrows, fill=True
)
# TODO: It seems to me a lot of this could/should be handled from
# within the FITS_rec class rather than here.
data = hdu.data
for idx, length in enumerate(vla_lengths):
if length is not None:
arr = data.columns._arrays[idx]
dt = recformats[idx][len(str(length)) :]
# NOTE: FormatQ not supported here; it's hard to determine
# whether or not it will be necessary to use a wider descriptor
# type. The function documentation will have to serve as a
# warning that this is not supported.
recformats[idx] = _FormatP(dt, max=length)
data.columns._recformats[idx] = recformats[idx]
name = data.columns.names[idx]
data._cache_field(name, _makep(arr, arr, recformats[idx]))
def format_value(col, val):
# Special formatting for a couple particular data types
if recformats[col] == FITS2NUMPY["L"]:
return bool(int(val))
elif recformats[col] == FITS2NUMPY["M"]:
# For some reason, in arrays/fields where numpy expects a
# complex it's not happy to take a string representation
# (though it's happy to do that in other contexts), so we have
# to convert the string representation for it:
return complex(val)
else:
return val
# Jump back to the start of the data and create a new line reader
fileobj.seek(initialpos)
linereader = csv.reader(fileobj, dialect=FITSTableDumpDialect)
for row, line in enumerate(linereader):
col = 0
idx = 0
while idx < len(line):
if line[idx] == "VLA_Length=":
vla_len = vla_lengths[col]
idx += 2
slice_ = slice(idx, idx + vla_len)
data[row][col][:] = line[idx : idx + vla_len]
idx += vla_len
elif dtype[col].shape:
# This is an array column
array_size = int(np.multiply.reduce(dtype[col].shape))
slice_ = slice(idx, idx + array_size)
idx += array_size
else:
slice_ = None
if slice_ is None:
# This is a scalar row element
data[row][col] = format_value(col, line[idx])
idx += 1
else:
data[row][col].flat[:] = [
format_value(col, val) for val in line[slice_]
]
col += 1
if close_file:
fileobj.close()
return data
@classmethod
def _load_coldefs(cls, fileobj):
"""
Read the table column definitions from the ASCII file output by
BinTableHDU.dump().
"""
close_file = False
if isinstance(fileobj, path_like):
fileobj = os.path.expanduser(fileobj)
fileobj = open(fileobj)
close_file = True
columns = []
for line in fileobj:
words = line[:-1].split()
kwargs = {}
for key in ["name", "format", "disp", "unit", "dim"]:
kwargs[key] = words.pop(0).replace('""', "")
for key in ["null", "bscale", "bzero"]:
word = words.pop(0).replace('""', "")
if word:
word = _str_to_num(word)
kwargs[key] = word
columns.append(Column(**kwargs))
if close_file:
fileobj.close()
return ColDefs(columns)
@contextlib.contextmanager
def _binary_table_byte_swap(data):
"""
Ensures that all the data of a binary FITS table (represented as a FITS_rec
object) is in a big-endian byte order. Columns are swapped in-place one
at a time, and then returned to their previous byte order when this context
manager exits.
Because a new dtype is needed to represent the byte-swapped columns, the
new dtype is temporarily applied as well.
"""
orig_dtype = data.dtype
names = []
formats = []
offsets = []
to_swap = []
if sys.byteorder == "little":
swap_types = ("<", "=")
else:
swap_types = ("<",)
for idx, name in enumerate(orig_dtype.names):
field = _get_recarray_field(data, idx)
field_dtype, field_offset = orig_dtype.fields[name]
names.append(name)
formats.append(field_dtype)
offsets.append(field_offset)
if isinstance(field, chararray.chararray):
continue
# only swap unswapped
# must use field_dtype.base here since for multi-element dtypes,
# the .str with be '|V<N>' where <N> is the total bytes per element
if field.itemsize > 1 and field_dtype.base.str[0] in swap_types:
to_swap.append(field)
# Override the dtype for this field in the new record dtype with
# the byteswapped version
formats[-1] = field_dtype.newbyteorder()
# deal with var length table
recformat = data.columns._recformats[idx]
if isinstance(recformat, _FormatP):
coldata = data.field(idx)
for c in coldata:
if (
not isinstance(c, chararray.chararray)
and c.itemsize > 1
and c.dtype.str[0] in swap_types
):
to_swap.append(c)
for arr in reversed(to_swap):
arr.byteswap(True)
data.dtype = np.dtype({"names": names, "formats": formats, "offsets": offsets})
yield data
for arr in to_swap:
arr.byteswap(True)
data.dtype = orig_dtype