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import re
import copy
import warnings
from ..util import _stypes, _itypes, _ftypes, FITSRuntimeWarning
from ..header import FITSHDR
INVALID_HDR_CHARS_RE = re.compile(r"(\?|\*|#)+")
INVALID_HDR_CHARS = {"?", "*", "#"}
ANY_HDU = -1
IMAGE_HDU = 0
ASCII_TBL = 1
BINARY_TBL = 2
_hdu_type_map = {
IMAGE_HDU: 'IMAGE_HDU',
ASCII_TBL: 'ASCII_TBL',
BINARY_TBL: 'BINARY_TBL',
'IMAGE_HDU': IMAGE_HDU,
'ASCII_TBL': ASCII_TBL,
'BINARY_TBL': BINARY_TBL}
class HDUBase(object):
"""
A representation of a FITS HDU
parameters
----------
fits: FITS object
An instance of a _fistio_wrap.FITS object. This is the low-level
python object, not the FITS object defined above.
ext: integer
The extension number.
"""
def __init__(self, fits, ext, **keys):
if keys:
import warnings
warnings.warn(
"The keyword arguments '%s' are being ignored! This warning "
"will be an error in a future version of `fitsio`!" % keys,
DeprecationWarning, stacklevel=2)
self._FITS = fits
self._ext = ext
self._ignore_scaling = False
self._update_info()
self._filename = self._FITS.filename()
@property
def ignore_scaling(self):
"""
:return: Flag to indicate whether scaling (BZERO/BSCALE) values should
be ignored.
"""
return self._ignore_scaling
@ignore_scaling.setter
def ignore_scaling(self, ignore_scaling_flag):
"""
Set the flag to ignore scaling.
"""
old_val = self._ignore_scaling
self._ignore_scaling = ignore_scaling_flag
# Only endure the overhead of updating the info if the new value is
# actually different.
if old_val != self._ignore_scaling:
self._update_info()
def get_extnum(self):
"""
Get the extension number
"""
return self._ext
def get_extname(self):
"""
Get the name for this extension, can be an empty string
"""
name = self._info['extname']
if name.strip() == '':
name = self._info['hduname']
return name.strip()
def get_extver(self):
"""
Get the version for this extension.
Used when a name is given to multiple extensions
"""
ver = self._info['extver']
if ver == 0:
ver = self._info['hduver']
return ver
def get_exttype(self, num=False):
"""
Get the extension type
By default the result is a string that mirrors
the enumerated type names in cfitsio
'IMAGE_HDU', 'ASCII_TBL', 'BINARY_TBL'
which have numeric values
0 1 2
send num=True to get the numbers. The values
fitsio.IMAGE_HDU .ASCII_TBL, and .BINARY_TBL
are available for comparison
parameters
----------
num: bool, optional
Return the numeric values.
"""
if num:
return self._info['hdutype']
else:
name = _hdu_type_map[self._info['hdutype']]
return name
def get_offsets(self):
"""
returns
-------
a dictionary with these entries
header_start:
byte offset from beginning of the file to the start
of the header
data_start:
byte offset from beginning of the file to the start
of the data section
data_end:
byte offset from beginning of the file to the end
of the data section
Note these are also in the information dictionary, which
you can access with get_info()
"""
return dict(
header_start=self._info['header_start'],
data_start=self._info['data_start'],
data_end=self._info['data_end'],
)
def get_info(self):
"""
Get a copy of the internal dictionary holding extension information
"""
return copy.deepcopy(self._info)
def get_filename(self):
"""
Get a copy of the filename for this fits file
"""
return copy.copy(self._filename)
def write_checksum(self):
"""
Write the checksum into the header for this HDU.
Computes the checksum for the HDU, both the data portion alone (DATASUM
keyword) and the checksum complement for the entire HDU (CHECKSUM).
returns
-------
A dict with keys 'datasum' and 'hdusum'
"""
return self._FITS.write_checksum(self._ext+1)
def verify_checksum(self):
"""
Verify the checksum in the header for this HDU.
"""
res = self._FITS.verify_checksum(self._ext+1)
if res['dataok'] != 1:
raise ValueError("data checksum failed")
if res['hduok'] != 1:
raise ValueError("hdu checksum failed")
def write_comment(self, comment):
"""
Write a comment into the header
"""
self._FITS.write_comment(self._ext+1, str(comment))
def write_history(self, history):
"""
Write history text into the header
"""
self._FITS.write_history(self._ext+1, str(history))
def _write_continue(self, value):
"""
Write history text into the header
"""
self._FITS.write_continue(self._ext+1, str(value))
def write_key(self, name, value, comment=""):
"""
Write the input value to the header
parameters
----------
name: string
Name of keyword to write/update
value: scalar
Value to write, can be string float or integer type,
including numpy scalar types.
comment: string, optional
An optional comment to write for this key
Notes
-----
Write COMMENT and HISTORY using the write_comment and write_history
methods
"""
if name is None:
# we write a blank keyword and the rest is a comment
# string
if not isinstance(comment, _stypes):
raise ValueError('when writing blank key the value '
'must be a string')
# this might be longer than 80 but that's ok, the routine
# will take care of it
# card = ' ' + str(comment)
card = ' ' + str(comment)
self._FITS.write_record(
self._ext+1,
card,
)
elif value is None:
self._FITS.write_undefined_key(self._ext+1,
str(name),
str(comment))
elif isinstance(value, bool):
if value:
v = 1
else:
v = 0
self._FITS.write_logical_key(self._ext+1,
str(name),
v,
str(comment))
elif isinstance(value, _stypes):
self._FITS.write_string_key(self._ext+1,
str(name),
str(value),
str(comment))
elif isinstance(value, _ftypes):
self._FITS.write_double_key(self._ext+1,
str(name),
float(value),
str(comment))
elif isinstance(value, _itypes):
self._FITS.write_long_long_key(self._ext+1,
str(name),
int(value),
str(comment))
elif isinstance(value, (tuple, list)):
vl = [str(el) for el in value]
sval = ','.join(vl)
self._FITS.write_string_key(self._ext+1,
str(name),
sval,
str(comment))
else:
sval = str(value)
mess = (
"warning, keyword '%s' has non-standard "
"value type %s, "
"Converting to string: '%s'")
warnings.warn(mess % (name, type(value), sval), FITSRuntimeWarning)
self._FITS.write_string_key(self._ext+1,
str(name),
sval,
str(comment))
def write_keys(self, records_in, clean=True):
"""
Write the keywords to the header.
parameters
----------
records: FITSHDR or list or dict
Can be one of these:
- FITSHDR object
- list of dictionaries containing 'name','value' and optionally
a 'comment' field; the order is preserved.
- a dictionary of keyword-value pairs; no comments are written
in this case, and the order is arbitrary.
clean: boolean
If True, trim out the standard fits header keywords that are
created on HDU creation, such as EXTEND, SIMPLE, STTYPE, TFORM,
TDIM, XTENSION, BITPIX, NAXIS, etc.
Notes
-----
Input keys named COMMENT and HISTORY are written using the
write_comment and write_history methods.
"""
if isinstance(records_in, FITSHDR):
hdr = records_in
else:
hdr = FITSHDR(records_in)
if clean:
is_table = hasattr(self, '_table_type_str')
# is_table = isinstance(self, TableHDU)
hdr.clean(is_table=is_table)
for r in hdr.records():
name = r['name']
if name is not None:
name = name.upper()
if INVALID_HDR_CHARS_RE.search(name):
raise RuntimeError(
"header key '%s' has invalid characters! "
"Characters in %s are not allowed!" % (
name, INVALID_HDR_CHARS
)
)
value = r['value']
if name == 'COMMENT':
self.write_comment(value)
elif name == 'HISTORY':
self.write_history(value)
elif name == 'CONTINUE':
self._write_continue(value)
else:
comment = r.get('comment', '')
self.write_key(name, value, comment=comment)
def read_header(self):
"""
Read the header as a FITSHDR
The FITSHDR allows access to the values and comments by name and
number.
"""
# note converting strings
return FITSHDR(self.read_header_list())
def read_header_list(self):
"""
Read the header as a list of dictionaries.
You will usually use read_header instead, which just sends the output
of this functioin to the constructor of a FITSHDR, which allows access
to the values and comments by name and number.
Each dictionary is
'name': the keyword name
'value': the value field as a string
'comment': the comment field as a string.
"""
return self._FITS.read_header(self._ext+1)
def _update_info(self):
"""
Update metadata for this HDU
"""
try:
self._FITS.movabs_hdu(self._ext+1)
except IOError:
raise RuntimeError("no such hdu")
self._info = self._FITS.get_hdu_info(self._ext+1, self._ignore_scaling)
def _get_repr_list(self):
"""
Get some representation data common to all HDU types
"""
spacing = ' '*2
text = ['']
text.append("%sfile: %s" % (spacing, self._filename))
text.append("%sextension: %d" % (spacing, self._info['hdunum']-1))
text.append(
"%stype: %s" % (spacing, _hdu_type_map[self._info['hdutype']]))
extname = self.get_extname()
if extname != "":
text.append("%sextname: %s" % (spacing, extname))
extver = self.get_extver()
if extver != 0:
text.append("%sextver: %s" % (spacing, extver))
return text, spacing
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