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"""
header classes for fitslib, part of the fitsio package.
See the main docs at https://github.com/esheldon/fitsio
Copyright (C) 2011 Erin Sheldon, BNL. erin dot sheldon at gmail dot com
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
"""
from __future__ import with_statement, print_function
import warnings
from . import _fitsio_wrap
from .util import isstring, FITSRuntimeWarning, IS_PY3
# for python3 compat
if IS_PY3:
xrange = range
TYP_STRUC_KEY = 10
TYP_CMPRS_KEY = 20
TYP_SCAL_KEY = 30
TYP_NULL_KEY = 40
TYP_DIM_KEY = 50
TYP_RANG_KEY = 60
TYP_UNIT_KEY = 70
TYP_DISP_KEY = 80
TYP_HDUID_KEY = 90
TYP_CKSUM_KEY = 100
TYP_WCS_KEY = 110
TYP_REFSYS_KEY = 120
TYP_COMM_KEY = 130
TYP_CONT_KEY = 140
TYP_USER_KEY = 150
class FITSHDR(object):
"""
A class representing a FITS header.
parameters
----------
record_list: optional
A list of dicts, or dict, or another FITSHDR
- 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.
- another FITSHDR object; the order is preserved.
examples:
hdr=FITSHDR()
# set a simple value
hdr['blah'] = 35
# set from a dict to include a comment.
rec={'name':'fromdict', 'value':3, 'comment':'my comment'}
hdr.add_record(rec)
# can do the same with a full FITSRecord
rec=FITSRecord( {'name':'temp', 'value':35, 'comment':'temp in C'} )
hdr.add_record(rec)
# in the above, the record is replaced if one with the same name
# exists, except for COMMENT and HISTORY, which can exist as
# duplicates
# print the header
print(hdr)
# print a single record
print(hdr['fromdict'])
# can also set from a card
hdr.add_record('test = 77')
# using a FITSRecord object (internally uses FITSCard)
card=FITSRecord('test = 77')
hdr.add_record(card)
# can also construct with a record list
recs=[{'name':'test', 'value':35, 'comment':'a comment'},
{'name':'blah', 'value':'some string'}]
hdr=FITSHDR(recs)
# if you have no comments, you can construct with a simple dict
recs={'day':'saturday',
'telescope':'blanco'}
hdr=FITSHDR(recs)
"""
def __init__(self, record_list=None):
self._record_list = []
self._record_map = {}
self._index_map = {}
if isinstance(record_list, FITSHDR):
for r in record_list.records():
self.add_record(r)
elif isinstance(record_list, dict):
for k in record_list:
r = {'name': k, 'value': record_list[k]}
self.add_record(r)
elif isinstance(record_list, list):
for r in record_list:
self.add_record(r)
elif record_list is not None:
raise ValueError("expected a dict or list of dicts or FITSHDR")
def add_record(self, record_in):
"""
Add a new record. Strip quotes from around strings.
This will over-write if the key already exists, except
for COMMENT and HISTORY fields
parameters
-----------
record:
The record, either a dict or a header card string
or a FITSRecord or FITSCard
"""
if (isinstance(record_in, dict) and
'name' in record_in and 'value' in record_in):
record = {}
record.update(record_in)
else:
record = FITSRecord(record_in)
# only append when this name already exists if it is
# a comment or history field, otherwise simply over-write
key = record['name']
if key is not None:
key = key.upper()
key_exists = key in self._record_map
if not key_exists or key in ('COMMENT', 'HISTORY', 'CONTINUE', None):
# append new record
self._record_list.append(record)
index = len(self._record_list)-1
self._index_map[key] = index
else:
# over-write existing
index = self._index_map[key]
self._record_list[index] = record
self._record_map[key] = record
def _add_to_map(self, record):
key = record['name'].upper()
self._record_map[key] = record
def get_comment(self, item):
"""
Get the comment for the requested entry
"""
key = item.upper()
if key not in self._record_map:
raise KeyError("unknown record: %s" % key)
if 'comment' not in self._record_map[key]:
return None
else:
return self._record_map[key]['comment']
def records(self):
"""
Return the list of full records as a list of dictionaries.
"""
return self._record_list
def keys(self):
"""
Return a copy of the current key list.
"""
return [e['name'] for e in self._record_list]
def delete(self, name):
"""
Delete the specified entry if it exists.
"""
if isinstance(name, (list, tuple)):
for xx in name:
self.delete(xx)
else:
if name in self._record_map:
del self._record_map[name]
# Store current index value
cur_index = self._index_map[name]
# Delete in index map
del self._index_map[name]
self._record_list = [
r for r in self._record_list if r['name'] != name]
# Change index map for superior indexes, only
for k, v in self._index_map.items():
if v > cur_index:
self._index_map[k] = v - 1
def clean(self, is_table=False):
"""
Remove reserved keywords from the header.
These are keywords that the fits writer must write in order
to maintain consistency between header and data.
keywords
--------
is_table: bool, optional
Set True if this is a table, so extra keywords will be cleaned
"""
rmnames = [
'SIMPLE', 'EXTEND', 'XTENSION', 'BITPIX', 'PCOUNT', 'GCOUNT',
'THEAP',
'EXTNAME',
# 'BLANK',
'ZQUANTIZ', 'ZDITHER0', 'ZIMAGE', 'ZCMPTYPE',
'ZSIMPLE', 'ZTENSION', 'ZPCOUNT', 'ZGCOUNT',
'ZBITPIX', 'ZEXTEND',
# 'FZTILELN','FZALGOR',
'CHECKSUM', 'DATASUM']
if is_table:
# these are not allowed in tables
rmnames += [
'BUNIT', 'BSCALE', 'BZERO',
]
self.delete(rmnames)
r = self._record_map.get('NAXIS', None)
if r is not None:
naxis = int(r['value'])
self.delete('NAXIS')
rmnames = ['NAXIS%d' % i for i in xrange(1, naxis+1)]
self.delete(rmnames)
r = self._record_map.get('ZNAXIS', None)
self.delete('ZNAXIS')
if r is not None:
znaxis = int(r['value'])
rmnames = ['ZNAXIS%d' % i for i in xrange(1, znaxis+1)]
self.delete(rmnames)
rmnames = ['ZTILE%d' % i for i in xrange(1, znaxis+1)]
self.delete(rmnames)
rmnames = ['ZNAME%d' % i for i in xrange(1, znaxis+1)]
self.delete(rmnames)
rmnames = ['ZVAL%d' % i for i in xrange(1, znaxis+1)]
self.delete(rmnames)
r = self._record_map.get('TFIELDS', None)
if r is not None:
tfields = int(r['value'])
self.delete('TFIELDS')
if tfields > 0:
nbase = [
'TFORM', 'TTYPE', 'TDIM', 'TUNIT', 'TSCAL', 'TZERO',
'TNULL', 'TDISP', 'TDMIN', 'TDMAX', 'TDESC', 'TROTA',
'TRPIX', 'TRVAL', 'TDELT', 'TCUNI',
# 'FZALG'
]
for i in xrange(1, tfields+1):
names = ['%s%d' % (n, i) for n in nbase]
self.delete(names)
def get(self, item, default_value=None):
"""
Get the requested header entry by keyword name
"""
found, name = self._contains_and_name(item)
if found:
return self._record_map[name]['value']
else:
return default_value
def __len__(self):
return len(self._record_list)
def __contains__(self, item):
found, _ = self._contains_and_name(item)
return found
def _contains_and_name(self, item):
if isinstance(item, FITSRecord):
name = item['name']
elif isinstance(item, dict):
name = item.get('name', None)
if name is None:
raise ValueError("dict record must have 'name' field")
else:
name = item
found = False
if name is None:
if None in self._record_map:
found = True
else:
name = name.upper()
if name in self._record_map:
found = True
elif name[0:8] == 'HIERARCH':
if len(name) > 9:
name = name[9:]
if name in self._record_map:
found = True
return found, name
def __setitem__(self, item, value):
if isinstance(value, (dict, FITSRecord)):
if item.upper() != value['name'].upper():
raise ValueError("when setting using a FITSRecord, the "
"name field must match")
rec = value
else:
rec = {'name': item, 'value': value}
try:
# the entry may already exist; if so, preserve the comment
comment = self.get_comment(item)
rec['comment'] = comment
except KeyError:
pass
self.add_record(rec)
def __getitem__(self, item):
if item not in self:
raise KeyError("unknown record: %s" % item)
return self.get(item)
def __iter__(self):
self._current = 0
return self
def next(self):
"""
for iteration over the header entries
"""
if self._current < len(self._record_list):
rec = self._record_list[self._current]
key = rec['name']
self._current += 1
return key
else:
raise StopIteration
__next__ = next
def _record2card(self, record):
"""
when we add new records they don't have a card,
this sort of fakes it up similar to what cfitsio
does, just for display purposes. e.g.
DBL = 23.299843
LNG = 3423432
KEYSNC = 'hello '
KEYSC = 'hello ' / a comment for string
KEYDC = 3.14159265358979 / a comment for pi
KEYLC = 323423432 / a comment for long
basically,
- 8 chars, left aligned, for the keyword name
- a space
- 20 chars for value, left aligned for strings, right aligned for
numbers
- if there is a comment, one space followed by / then another space
then the comment out to 80 chars
"""
name = record['name']
value = record['value']
comment = record.get('comment', '')
v_isstring = isstring(value)
if name is None:
card = ' %s' % comment
elif name == 'COMMENT':
card = 'COMMENT %s' % comment
elif name == 'CONTINUE':
card = 'CONTINUE %s' % value
elif name == 'HISTORY':
card = 'HISTORY %s' % value
else:
if len(name) > 8:
card = 'HIERARCH %s= ' % name
else:
card = '%-8s= ' % name[0:8]
# these may be string representations of data, or actual strings
if v_isstring:
value = str(value)
if len(value) > 0:
if value[0] != "'":
# this is a string representing a string header field
# make it look like it will look in the header
value = "'" + value + "'"
vstr = '%-20s' % value
else:
vstr = "%20s" % value
else:
vstr = "''"
else:
if value is True:
value = 'T'
elif value is False:
value = 'F'
# upper for things like 1.0E20 rather than 1.0e20
vstr = ('%20s' % value).upper()
card += vstr
if 'comment' in record:
card += ' / %s' % record['comment']
if v_isstring and len(card) > 80:
card = card[0:79] + "'"
else:
card = card[0:80]
return card
def __repr__(self):
rep = ['']
for r in self._record_list:
card = self._record2card(r)
# if 'card_string' not in r:
# card = self._record2card(r)
# else:
# card = r['card_string']
rep.append(card)
return '\n'.join(rep)
class FITSRecord(dict):
"""
Class to represent a FITS header record
parameters
----------
record: string or dict
If a string, it should represent a FITS header card
If a dict it should have 'name' and 'value' fields.
Can have a 'comment' field.
examples
--------
# from a dict. Can include a comment
rec=FITSRecord( {'name':'temp', 'value':35, 'comment':'temperature in C'} )
# from a card
card=FITSRecord('test = 77 / My comment')
"""
def __init__(self, record):
self.set_record(record)
def set_record(self, record, **keys):
"""
check the record is valid and set keys in the dict
parameters
----------
record: string
Dict representing a record or a string representing a FITS header
card
"""
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)
if isstring(record):
card = FITSCard(record)
self.update(card)
self.verify()
else:
if isinstance(record, FITSRecord):
self.update(record)
elif isinstance(record, dict):
if 'name' in record and 'value' in record:
self.update(record)
elif 'card_string' in record:
self.set_record(record['card_string'])
else:
raise ValueError('record must have name,value fields '
'or a card_string field')
else:
raise ValueError("record must be a string card or "
"dictionary or FITSRecord")
def verify(self):
"""
make sure name,value exist
"""
if 'name' not in self:
raise ValueError("each record must have a 'name' field")
if 'value' not in self:
raise ValueError("each record must have a 'value' field")
_BLANK = ' '
class FITSCard(FITSRecord):
"""
class to represent ordinary FITS cards.
CONTINUE not supported
examples
--------
# from a card
card=FITSRecord('test = 77 / My comment')
"""
def __init__(self, card_string):
self.set_card(card_string)
def set_card(self, card_string):
self['card_string'] = card_string
self._check_hierarch()
if self._is_hierarch:
self._set_as_key()
else:
self._check_equals()
self._check_type()
self._check_len()
front = card_string[0:7]
if (not self.has_equals() or
front in ['COMMENT', 'HISTORY', 'CONTINU', _BLANK]):
if front == 'HISTORY':
self._set_as_history()
elif front == 'CONTINU':
self._set_as_continue()
elif front == _BLANK:
self._set_as_blank()
else:
# note anything without an = and not history and not blank
# key comment is treated as COMMENT; this is built into
# cfitsio as well
self._set_as_comment()
if self.has_equals():
mess = (
"warning: It is not FITS-compliant for a %s header "
"card to include an = sign. There may be slight "
"inconsistencies if you write this back out to a "
"file.")
mess = mess % (card_string[:8])
warnings.warn(mess, FITSRuntimeWarning)
else:
self._set_as_key()
def has_equals(self):
"""
True if = is in position 8
"""
return self._has_equals
def _check_hierarch(self):
card_string = self['card_string']
if card_string[0:8].upper() == 'HIERARCH':
self._is_hierarch = True
else:
self._is_hierarch = False
def _check_equals(self):
"""
check for = in position 8, set attribute _has_equals
"""
card_string = self['card_string']
if len(card_string) < 9:
self._has_equals = False
elif card_string[8] == '=':
self._has_equals = True
else:
self._has_equals = False
def _set_as_key(self):
card_string = self['card_string']
res = _fitsio_wrap.parse_card(card_string)
if len(res) == 5:
keyclass, name, value, dtype, comment = res
else:
keyclass, name, dtype, comment = res
value = None
if keyclass == TYP_CONT_KEY:
raise ValueError("bad card '%s'. CONTINUE not "
"supported" % card_string)
self['class'] = keyclass
self['name'] = name
self['value_orig'] = value
self['value'] = self._convert_value(value)
self['dtype'] = dtype
self['comment'] = comment
def _set_as_blank(self):
self['class'] = TYP_USER_KEY
self['name'] = None
self['value'] = None
self['comment'] = self['card_string'][8:]
def _set_as_comment(self):
comment = self._extract_comm_or_hist_value()
self['class'] = TYP_COMM_KEY
self['name'] = 'COMMENT'
self['value'] = comment
def _set_as_history(self):
history = self._extract_comm_or_hist_value()
self['class'] = TYP_COMM_KEY
self['name'] = 'HISTORY'
self['value'] = history
def _set_as_continue(self):
value = self._extract_comm_or_hist_value()
self['class'] = TYP_CONT_KEY
self['name'] = 'CONTINUE'
self['value'] = value
def _convert_value(self, value_orig):
"""
things like 6 and 1.25 are converted with ast.literal_value
Things like 'hello' are stripped of quotes
"""
import ast
if value_orig is None:
return value_orig
if value_orig.startswith("'") and value_orig.endswith("'"):
value = value_orig[1:-1]
else:
try:
avalue = ast.parse(value_orig).body[0].value
if isinstance(avalue, ast.BinOp):
# this is probably a string that happens to look like
# a binary operation, e.g. '25-3'
value = value_orig
else:
value = ast.literal_eval(value_orig)
except Exception:
value = self._convert_string(value_orig)
if isinstance(value, int) and '_' in value_orig:
value = value_orig
return value
def _convert_string(self, s):
if s == 'T':
return True
elif s == 'F':
return False
else:
return s
def _extract_comm_or_hist_value(self):
card_string = self['card_string']
if self._has_equals:
if len(card_string) >= 9:
value = card_string[9:]
else:
value = ''
else:
if len(card_string) >= 8:
# value=card_string[7:]
value = card_string[8:]
else:
value = ''
return value
def _check_type(self):
card_string = self['card_string']
if not isstring(card_string):
raise TypeError(
"card must be a string, got type %s" % type(card_string))
def _check_len(self):
ln = len(self['card_string'])
if ln > 80:
mess = "len(card) is %d. cards must have length < 80"
raise ValueError(mess)
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