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"""
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 os
import numpy
from . import _fitsio_wrap
from .util import IS_PY3, mks, array_to_native, isstring
from .header import FITSHDR
from .hdu import (
ANY_HDU, IMAGE_HDU, BINARY_TBL, ASCII_TBL,
ImageHDU, AsciiTableHDU, TableHDU,
_table_npy2fits_form, _npy2fits, _hdu_type_map)
# for python3 compat
if IS_PY3:
xrange = range
READONLY = 0
READWRITE = 1
NOCOMPRESS = 0
RICE_1 = 11
GZIP_1 = 21
GZIP_2 = 22
PLIO_1 = 31
HCOMPRESS_1 = 41
NO_DITHER = -1
SUBTRACTIVE_DITHER_1 = 1
SUBTRACTIVE_DITHER_2 = 2
# defaults follow fpack
DEFAULT_QLEVEL = 4.0
DEFAULT_QMETHOD = 'SUBTRACTIVE_DITHER_1'
DEFAULT_HCOMP_SCALE = 0.0
def read(filename, ext=None, extver=None, columns=None, rows=None,
header=False, case_sensitive=False, upper=False, lower=False,
vstorage='fixed', verbose=False, trim_strings=False, **keys):
"""
Convenience function to read data from the specified FITS HDU
By default, all data are read. For tables, send columns= and rows= to
select subsets of the data. Table data are read into a recarray; use a
FITS object and read_column() to get a single column as an ordinary array.
For images, create a FITS object and use slice notation to read subsets.
Under the hood, a FITS object is constructed and data are read using
an associated FITSHDU object.
parameters
----------
filename: string
A filename.
ext: number or string, optional
The extension. Either the numerical extension from zero
or a string extension name. If not sent, data is read from
the first HDU that has data.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname). These
extensions can optionally specify an EXTVER version number in the
header. Send extver= to select a particular version. If extver is not
sent, the first one will be selected. If ext is an integer, the extver
is ignored.
columns: list or array, optional
An optional set of columns to read from table HDUs. Default is to
read all. Can be string or number.
rows: optional
An optional list of rows to read from table HDUS. Default is to
read all.
header: bool, optional
If True, read the FITS header and return a tuple (data,header)
Default is False.
case_sensitive: bool, optional
Match column names and extension names with case-sensitivity. Default
is False.
lower: bool, optional
If True, force all columns names to lower case in output. Default is
False.
upper: bool, optional
If True, force all columns names to upper case in output. Default is
False.
vstorage: string, optional
Set the default method to store variable length columns. Can be
'fixed' or 'object'. See docs on fitsio.FITS for details. Default is
'fixed'.
trim_strings: bool, optional
If True, trim trailing spaces from strings. Will over-ride the
trim_strings= keyword from constructor.
verbose: bool, optional
If True, print more info when doing various FITS operations.
"""
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)
kwargs = {
'lower': lower,
'upper': upper,
'vstorage': vstorage,
'case_sensitive': case_sensitive,
'verbose': verbose,
'trim_strings': trim_strings
}
read_kwargs = {}
if columns is not None:
read_kwargs['columns'] = columns
if rows is not None:
read_kwargs['rows'] = rows
with FITS(filename, **kwargs) as fits:
if ext is None:
for i in xrange(len(fits)):
if fits[i].has_data():
ext = i
break
if ext is None:
raise IOError("No extensions have data")
item = _make_item(ext, extver=extver)
data = fits[item].read(**read_kwargs)
if header:
h = fits[item].read_header()
return data, h
else:
return data
def read_header(filename, ext=0, extver=None, case_sensitive=False, **keys):
"""
Convenience function to read the header from the specified FITS HDU
The FITSHDR allows access to the values and comments by name and
number.
parameters
----------
filename: string
A filename.
ext: number or string, optional
The extension. Either the numerical extension from zero
or a string extension name. Default read primary header.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname). These
extensions can optionally specify an EXTVER version number in the
header. Send extver= to select a particular version. If extver is not
sent, the first one will be selected. If ext is an integer, the extver
is ignored.
case_sensitive: bool, optional
Match extension names with case-sensitivity. Default is False.
"""
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)
filename = extract_filename(filename)
dont_create = 0
try:
hdunum = ext+1
except TypeError:
hdunum = None
_fits = _fitsio_wrap.FITS(filename, READONLY, dont_create)
if hdunum is None:
extname = mks(ext)
if extver is None:
extver_num = 0
else:
extver_num = extver
if not case_sensitive:
# the builtin movnam_hdu is not case sensitive
hdunum = _fits.movnam_hdu(ANY_HDU, extname, extver_num)
else:
# for case sensitivity we'll need to run through
# all the hdus
found = False
current_ext = 0
while True:
hdunum = current_ext+1
try:
hdu_type = _fits.movabs_hdu(hdunum) # noqa - not used
name, vers = _fits.get_hdu_name_version(hdunum)
if name == extname:
if extver is None:
# take the first match
found = True
break
else:
if extver_num == vers:
found = True
break
except OSError:
break
current_ext += 1
if not found:
raise IOError(
'hdu not found: %s (extver %s)' % (extname, extver))
return FITSHDR(_fits.read_header(hdunum))
def read_scamp_head(fname, header=None):
"""
read a SCAMP .head file as a fits header FITSHDR object
parameters
----------
fname: string
The path to the SCAMP .head file
header: FITSHDR, optional
Optionally combine the header with the input one. The input can
be any object convertable to a FITSHDR object
returns
-------
header: FITSHDR
A fits header object of type FITSHDR
"""
with open(fname) as fobj:
lines = fobj.readlines()
lines = [line.strip() for line in lines if line[0:3] != 'END']
# if header is None an empty FITSHDR is created
hdr = FITSHDR(header)
for line in lines:
hdr.add_record(line)
return hdr
def _make_item(ext, extver=None):
if extver is not None:
# e
item = (ext, extver)
else:
item = ext
return item
def write(filename, data, extname=None, extver=None, header=None,
clobber=False, ignore_empty=False, units=None, table_type='binary',
names=None, write_bitcols=False, compress=None, tile_dims=None,
qlevel=DEFAULT_QLEVEL,
qmethod=DEFAULT_QMETHOD,
hcomp_scale=DEFAULT_HCOMP_SCALE,
hcomp_smooth=False,
**keys):
"""
Convenience function to create a new HDU and write the data.
Under the hood, a FITS object is constructed. If you want to append rows
to an existing HDU, or modify data in an HDU, please construct a FITS
object.
parameters
----------
filename: string
A filename.
data: numpy.ndarray or recarray
Either a normal n-dimensional array or a recarray. Images are written
to a new IMAGE_HDU and recarrays are written to BINARY_TBl or
ASCII_TBL hdus.
extname: string, optional
An optional name for the new header unit.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname).
These extensions can optionally specify an EXTVER version number in
the header. Send extver= to set a particular version, which will
be represented in the header with keyname EXTVER. The extver must
be an integer > 0. If extver is not sent, the first one will be
selected. If ext is an integer, the extver is ignored.
header: FITSHDR, list, dict, optional
A set of header keys to write. The keys are written before the data
is written to the table, preventing a resizing of the table area.
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.
Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
clobber: bool, optional
If True, overwrite any existing file. Default is to append
a new extension on existing files.
ignore_empty: bool, optional
Default False. Unless set to True, only allow
empty HDUs in the zero extension.
table-only keywords
-------------------
units: list
A list of strings representing units for each column.
table_type: string, optional
Either 'binary' or 'ascii', default 'binary'
Matching is case-insensitive
write_bitcols: bool, optional
Write boolean arrays in the FITS bitcols format, default False
names: list, optional
If data is a list of arrays, you must send `names` as a list
of names or column numbers.
image-only keywords
-------------------
compress: string, optional
A string representing the compression algorithm for images,
default None.
Can be one of
'RICE'
'GZIP'
'GZIP_2'
'PLIO' (no unsigned or negative integers)
'HCOMPRESS'
(case-insensitive) See the cfitsio manual for details.
tile_dims: tuple of ints, optional
The size of the tiles used to compress images.
qlevel: float, optional
Quantization level for floating point data. Lower generally result in
more compression, we recommend one reads the FITS standard or cfitsio
manual to fully understand the effects of quantization. None or 0
means no quantization, and for gzip also implies lossless. Default is
4.0 which follows the fpack defaults
qmethod: string or int
The quantization method as string or integer.
'NO_DITHER' or fitsio.NO_DITHER (-1)
No dithering is performed
'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
Standard dithering
'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
Preserves zeros
Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
hcomp_scale: float
Scale value for HCOMPRESS, 0.0 means lossless compression. Default is
0.0 following the fpack defaults.
hcomp_smooth: bool
If True, apply smoothing when decompressing. Default False
"""
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)
kwargs = {
'clobber': clobber,
'ignore_empty': ignore_empty
}
with FITS(filename, 'rw', **kwargs) as fits:
fits.write(
data,
table_type=table_type,
units=units,
extname=extname,
extver=extver,
header=header,
names=names,
write_bitcols=write_bitcols,
compress=compress,
tile_dims=tile_dims,
qlevel=qlevel,
qmethod=qmethod,
hcomp_scale=hcomp_scale,
hcomp_smooth=hcomp_smooth,
)
class FITS(object):
"""
A class to read and write FITS images and tables.
This class uses the cfitsio library for almost all relevant work.
parameters
----------
filename: string
The filename to open.
mode: int/string, optional
The mode, either a string or integer.
For reading only
'r' or 0
For reading and writing
'rw' or 1
You can also use fitsio.READONLY and fitsio.READWRITE.
Default is 'r'
clobber: bool, optional
If the mode is READWRITE, and clobber=True, then remove any existing
file before opening.
case_sensitive: bool, optional
Match column names and extension names with case-sensitivity. Default
is False.
lower: bool, optional
If True, force all columns names to lower case in output
upper: bool, optional
If True, force all columns names to upper case in output
vstorage: string, optional
A string describing how, by default, to store variable length columns
in the output array. This can be over-ridden when reading by using the
using vstorage keyword to the individual read methods. The options are
'fixed': Use a fixed length field in the array, with
dimensions equal to the max possible size for column.
Arrays are padded with zeros.
'object': Use an object for the field in the array.
Each element will then be an array of the right type,
but only using the memory needed to hold that element.
Default is 'fixed'. The rationale is that this is the option
of 'least surprise'
iter_row_buffer: integer
Number of rows to buffer when iterating over table HDUs.
Default is 1.
ignore_empty: bool, optional
Default False. Unless set to True, only allow
empty HDUs in the zero extension.
verbose: bool, optional
If True, print more info when doing various FITS operations.
See the docs at https://github.com/esheldon/fitsio
"""
def __init__(self, filename, mode='r', lower=False, upper=False,
trim_strings=False, vstorage='fixed', case_sensitive=False,
iter_row_buffer=1, write_bitcols=False, ignore_empty=False,
verbose=False, clobber=False, **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.lower = lower
self.upper = upper
self.trim_strings = trim_strings
self.vstorage = vstorage
self.case_sensitive = case_sensitive
self.iter_row_buffer = iter_row_buffer
self.write_bitcols = write_bitcols
filename = extract_filename(filename)
self._filename = filename
# self.mode=keys.get('mode','r')
self.mode = mode
self.ignore_empty = ignore_empty
self.verbose = verbose
if self.mode not in _int_modemap:
raise IOError("mode should be one of 'r', 'rw', "
"READONLY,READWRITE")
self.charmode = _char_modemap[self.mode]
self.intmode = _int_modemap[self.mode]
# Will not test existence when reading, let cfitsio
# do the test and report an error. This allows opening
# urls etc.
create = 0
if self.mode in [READWRITE, 'rw']:
if clobber:
create = 1
if filename[0] != '!':
filename = '!' + filename
else:
if os.path.exists(filename):
create = 0
else:
create = 1
self._did_create = (create == 1)
self._FITS = _fitsio_wrap.FITS(filename, self.intmode, create)
def close(self):
"""
Close the fits file and set relevant metadata to None
"""
if hasattr(self, '_FITS'):
if self._FITS is not None:
self._FITS.close()
self._FITS = None
self._filename = None
self.mode = None
self.charmode = None
self.intmode = None
self.hdu_list = None
self.hdu_map = None
def movabs_ext(self, ext):
"""
Move to the indicated zero-offset extension.
In general, it is not necessary to use this method explicitly.
"""
return self._FITS.movabs_hdu(ext+1)
def movabs_hdu(self, hdunum):
"""
Move to the indicated one-offset hdu number.
In general, it is not necessary to use this method explicitly.
"""
return self._FITS.movabs_hdu(hdunum)
def movnam_ext(self, extname, hdutype=ANY_HDU, extver=0):
"""
Move to the indicated extension by name
In general, it is not necessary to use this method explicitly.
returns the zero-offset extension number
"""
extname = mks(extname)
hdu = self._FITS.movnam_hdu(hdutype, extname, extver)
return hdu-1
def movnam_hdu(self, extname, hdutype=ANY_HDU, extver=0):
"""
Move to the indicated HDU by name
In general, it is not necessary to use this method explicitly.
returns the one-offset extension number
"""
extname = mks(extname)
hdu = self._FITS.movnam_hdu(hdutype, extname, extver)
return hdu
def reopen(self):
"""
close and reopen the fits file with the same mode
"""
self._FITS.close()
del self._FITS
self._FITS = _fitsio_wrap.FITS(self._filename, self.intmode, 0)
self.update_hdu_list()
def write(self, data, units=None, extname=None, extver=None,
compress=None,
tile_dims=None,
qlevel=DEFAULT_QLEVEL,
qmethod=DEFAULT_QMETHOD,
hcomp_scale=DEFAULT_HCOMP_SCALE,
hcomp_smooth=False,
header=None, names=None,
table_type='binary', write_bitcols=False, **keys):
"""
Write the data to a new HDU.
This method is a wrapper. If this is an IMAGE_HDU, write_image is
called, otherwise write_table is called.
parameters
----------
data: ndarray
An n-dimensional image or an array with fields.
extname: string, optional
An optional extension name.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname).
These extensions can optionally specify an EXTVER version number in
the header. Send extver= to set a particular version, which will
be represented in the header with keyname EXTVER. The extver must
be an integer > 0. If extver is not sent, the first one will be
selected. If ext is an integer, the extver is ignored.
header: FITSHDR, list, dict, optional
A set of header keys to write. 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.
Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
image-only keywords
-------------------
compress: string, optional
A string representing the compression algorithm for images,
default None.
Can be one of
'RICE'
'GZIP'
'GZIP_2'
'PLIO' (no unsigned or negative integers)
'HCOMPRESS'
(case-insensitive) See the cfitsio manual for details.
tile_dims: tuple of ints, optional
The size of the tiles used to compress images.
qlevel: float, optional
Quantization level for floating point data. Lower generally result
in more compression, we recommend one reads the FITS standard or
cfitsio manual to fully understand the effects of quantization.
None or 0 means no quantization, and for gzip also implies
lossless. Default is 4.0 which follows the fpack defaults
qmethod: string or int
The quantization method as string or integer.
'NO_DITHER' or fitsio.NO_DITHER (-1)
No dithering is performed
'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
Standard dithering
'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
Preserves zeros
Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
hcomp_scale: float
Scale value for HCOMPRESS, 0.0 means lossless compression. Default
is 0.0 following the fpack defaults.
hcomp_smooth: bool
If True, apply smoothing when decompressing. Default False
table-only keywords
-------------------
units: list/dec, optional:
A list of strings with units for each column.
table_type: string, optional
Either 'binary' or 'ascii', default 'binary'
Matching is case-insensitive
write_bitcols: bool, optional
Write boolean arrays in the FITS bitcols format, default False
names: list, optional
If data is a list of arrays, you must send `names` as a list
of names or column numbers.
restrictions
------------
The File must be opened READWRITE
"""
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)
isimage = False
if data is None:
isimage = True
elif isinstance(data, numpy.ndarray):
if data.dtype.fields == None: # noqa - probably should be is None
isimage = True
if isimage:
self.write_image(data, extname=extname, extver=extver,
compress=compress,
tile_dims=tile_dims,
qlevel=qlevel,
qmethod=qmethod,
hcomp_scale=hcomp_scale,
hcomp_smooth=hcomp_smooth,
header=header)
else:
self.write_table(data, units=units,
extname=extname, extver=extver, header=header,
names=names,
table_type=table_type,
write_bitcols=write_bitcols)
def write_image(self, img, extname=None, extver=None,
compress=None, tile_dims=None,
qlevel=DEFAULT_QLEVEL,
qmethod=DEFAULT_QMETHOD,
hcomp_scale=DEFAULT_HCOMP_SCALE,
hcomp_smooth=False,
header=None):
"""
Create a new image extension and write the data.
parameters
----------
img: ndarray
An n-dimensional image.
extname: string, optional
An optional extension name.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname).
These extensions can optionally specify an EXTVER version number in
the header. Send extver= to set a particular version, which will
be represented in the header with keyname EXTVER. The extver must
be an integer > 0. If extver is not sent, the first one will be
selected. If ext is an integer, the extver is ignored.
compress: string, optional
A string representing the compression algorithm for images,
default None.
Can be one of
'RICE'
'GZIP'
'GZIP_2'
'PLIO' (no unsigned or negative integers)
'HCOMPRESS'
(case-insensitive) See the cfitsio manual for details.
tile_dims: tuple of ints, optional
The size of the tiles used to compress images.
qlevel: float, optional
Quantization level for floating point data. Lower generally result
in more compression, we recommend one reads the FITS standard or
cfitsio manual to fully understand the effects of quantization.
None or 0 means no quantization, and for gzip also implies
lossless. Default is 4.0 which follows the fpack defaults
qmethod: string or int
The quantization method as string or integer.
'NO_DITHER' or fitsio.NO_DITHER (-1)
No dithering is performed
'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
Standard dithering
'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
Preserves zeros
Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
hcomp_scale: float
Scale value for HCOMPRESS, 0.0 means lossless compression. Default
is 0.0 following the fpack defaults.
hcomp_smooth: bool
If True, apply smoothing when decompressing. Default False
header: FITSHDR, list, dict, optional
A set of header keys to write. 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.
Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
restrictions
------------
The File must be opened READWRITE
"""
self.create_image_hdu(
img,
header=header,
extname=extname,
extver=extver,
compress=compress,
tile_dims=tile_dims,
qlevel=qlevel,
qmethod=qmethod,
hcomp_scale=hcomp_scale,
hcomp_smooth=hcomp_smooth,
)
if header is not None:
self[-1].write_keys(header)
self[-1]._update_info()
# if img is not None:
# self[-1].write(img)
def create_image_hdu(self,
img=None,
dims=None,
dtype=None,
extname=None,
extver=None,
compress=None,
tile_dims=None,
qlevel=DEFAULT_QLEVEL,
qmethod=DEFAULT_QMETHOD,
hcomp_scale=DEFAULT_HCOMP_SCALE,
hcomp_smooth=False,
header=None):
"""
Create a new, empty image HDU and reload the hdu list. Either
create from an input image or from input dims and dtype
fits.create_image_hdu(image, ...)
fits.create_image_hdu(dims=dims, dtype=dtype)
If an image is sent, the data are also written.
You can write data into the new extension using
fits[extension].write(image)
Alternatively you can skip calling this function and instead just use
fits.write(image)
or
fits.write_image(image)
which will create the new image extension for you with the appropriate
structure, and write the data.
parameters
----------
img: ndarray, optional
An image with which to determine the properties of the HDU. The
data will be written.
dims: sequence, optional
A sequence describing the dimensions of the image to be created
on disk. You must also send a dtype=
dtype: numpy data type
When sending dims= also send the data type. Can be of the
various numpy data type declaration styles, e.g. 'f8',
numpy.float64.
extname: string, optional
An optional extension name.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname).
These extensions can optionally specify an EXTVER version number in
the header. Send extver= to set a particular version, which will
be represented in the header with keyname EXTVER. The extver must
be an integer > 0. If extver is not sent, the first one will be
selected. If ext is an integer, the extver is ignored.
compress: string, optional
A string representing the compression algorithm for images,
default None.
Can be one of
'RICE'
'GZIP'
'GZIP_2'
'PLIO' (no unsigned or negative integers)
'HCOMPRESS'
(case-insensitive) See the cfitsio manual for details.
tile_dims: tuple of ints, optional
The size of the tiles used to compress images.
qlevel: float, optional
Quantization level for floating point data. Lower generally result
in more compression, we recommend one reads the FITS standard or
cfitsio manual to fully understand the effects of quantization.
None or 0 means no quantization, and for gzip also implies
lossless. Default is 4.0 which follows the fpack defaults.
qmethod: string or int
The quantization method as string or integer.
'NO_DITHER' or fitsio.NO_DITHER (-1)
No dithering is performed
'SUBTRACTIVE_DITHER_1' or fitsio.SUBTRACTIVE_DITHER_1 (1)
Standard dithering
'SUBTRACTIVE_DITHER_2' or fitsio.SUBTRACTIVE_DITHER_2 (2)
Preserves zeros
Defaults to 'SUBTRACTIVE_DITHER_1' which follows the fpack defaults
hcomp_scale: float
Scale value for HCOMPRESS, 0.0 means lossless compression. Default
is 0.0 following the fpack defaults.
hcomp_smooth: bool
If True, apply smoothing when decompressing. Default False
header: FITSHDR, list, dict, optional
This is only used to determine how many slots to reserve for
header keywords
restrictions
------------
The File must be opened READWRITE
"""
if (img is not None) or (img is None and dims is None):
from_image = True
elif dims is not None:
from_image = False
if from_image:
img2send = img
if img is not None:
dims = img.shape
dtstr = img.dtype.descr[0][1][1:]
if img.size == 0:
raise ValueError("data must have at least 1 row")
# data must be c-contiguous and native byte order
if not img.flags['C_CONTIGUOUS']:
# this always makes a copy
img2send = numpy.ascontiguousarray(img)
array_to_native(img2send, inplace=True)
else:
img2send = array_to_native(img, inplace=False)
if IS_PY3 and img2send.dtype.char == 'U':
# for python3, we convert unicode to ascii
# this will error if the character is not in ascii
img2send = img2send.astype('S', copy=False)
else:
self._ensure_empty_image_ok()
compress = None
tile_dims = None
# we get dims from the input image
dims2send = None
else:
# img was None and dims was sent
if dtype is None:
raise ValueError("send dtype= with dims=")
# this must work!
dtype = numpy.dtype(dtype)
dtstr = dtype.descr[0][1][1:]
# use the example image to build the type in C
img2send = numpy.zeros(1, dtype=dtype)
# sending an array simplifies access
dims2send = numpy.array(dims, dtype='i8', ndmin=1)
if img2send is not None:
if img2send.dtype.fields is not None:
raise ValueError(
"got record data type, expected regular ndarray")
if extname is None:
# will be ignored
extname = ""
else:
if not isstring(extname):
raise ValueError("extension name must be a string")
extname = mks(extname)
if extname is not None and extver is not None:
extver = check_extver(extver)
if extver is None:
# will be ignored
extver = 0
comptype = get_compress_type(compress)
qmethod = get_qmethod(qmethod)
tile_dims = get_tile_dims(tile_dims, dims)
if qlevel is None:
# 0.0 is the sentinel value for "no quantization" in cfitsio
qlevel = 0.0
else:
qlevel = float(qlevel)
if img2send is not None:
check_comptype_img(comptype, dtstr)
if header is not None:
nkeys = len(header)
else:
nkeys = 0
if hcomp_smooth:
hcomp_smooth = 1
else:
hcomp_smooth = 0
self._FITS.create_image_hdu(
img2send,
nkeys,
dims=dims2send,
comptype=comptype,
tile_dims=tile_dims,
qlevel=qlevel,
qmethod=qmethod,
hcomp_scale=hcomp_scale,
hcomp_smooth=hcomp_smooth,
extname=extname,
extver=extver,
)
# don't rebuild the whole list unless this is the first hdu
# to be created
self.update_hdu_list(rebuild=False)
def _ensure_empty_image_ok(self):
"""
If ignore_empty was not set to True, we only allow empty HDU for first
HDU and if there is no data there already
"""
if self.ignore_empty:
return
if len(self) > 1:
raise RuntimeError(
"Cannot write None image at extension %d" % len(self))
if 'ndims' in self[0]._info:
raise RuntimeError("Can only write None images to extension zero, "
"which already exists")
def write_table(self, data, table_type='binary',
names=None, formats=None, units=None,
extname=None, extver=None, header=None,
write_bitcols=False):
"""
Create a new table extension and write the data.
The table definition is taken from the fields in the input array. If
you want to append new rows to the table, access the HDU directly and
use the write() function, e.g.
fits[extension].append(data)
parameters
----------
data: recarray
A numpy array with fields. The table definition will be
determined from this array.
table_type: string, optional
Either 'binary' or 'ascii', default 'binary'
Matching is case-insensitive
extname: string, optional
An optional string for the extension name.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname).
These extensions can optionally specify an EXTVER version number in
the header. Send extver= to set a particular version, which will
be represented in the header with keyname EXTVER. The extver must
be an integer > 0. If extver is not sent, the first one will be
selected. If ext is an integer, the extver is ignored.
units: list/dec, optional:
A list of strings with units for each column.
header: FITSHDR, list, dict, optional
A set of header keys to write. The keys are written before the data
is written to the table, preventing a resizing of the table area.
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.
Note required keywords such as NAXIS, XTENSION, etc are cleaed out.
write_bitcols: boolean, optional
Write boolean arrays in the FITS bitcols format, default False
restrictions
------------
The File must be opened READWRITE
"""
"""
if data.dtype.fields == None:
raise ValueError("data must have fields")
if data.size == 0:
raise ValueError("data must have at least 1 row")
"""
self.create_table_hdu(data=data,
header=header,
names=names,
units=units,
extname=extname,
extver=extver,
table_type=table_type,
write_bitcols=write_bitcols)
if header is not None:
self[-1].write_keys(header)
self[-1]._update_info()
self[-1].write(data, names=names)
def read_raw(self):
"""
Reads the raw FITS file contents, returning a Python string.
"""
return self._FITS.read_raw()
def create_table_hdu(self, data=None, dtype=None,
header=None,
names=None, formats=None,
units=None, dims=None, extname=None, extver=None,
table_type='binary', write_bitcols=False):
"""
Create a new, empty table extension and reload the hdu list.
There are three ways to do it:
1) send a numpy dtype, from which the formats in the fits file will
be determined.
2) Send an array in data= keyword. this is required if you have
object fields for writing to variable length columns.
3) send the names,formats and dims yourself
You can then write data into the new extension using
fits[extension].write(array)
If you want to write to a single column
fits[extension].write_column(array)
But be careful as the other columns will be left zeroed.
Often you will instead just use write_table to do this all
atomically.
fits.write_table(recarray)
write_table will create the new table extension for you with the
appropriate fields.
parameters
----------
dtype: numpy dtype or descriptor, optional
If you have an array with fields, you can just send arr.dtype. You
can also use a list of tuples, e.g. [('x','f8'),('index','i4')] or
a dictionary representation.
data: a numpy array with fields, optional
or a dictionary
An array or dict from which to determine the table definition. You
must use this instead of sending a descriptor if you have object
array fields, as this is the only way to determine the type and max
size.
names: list of strings, optional
The list of field names
formats: list of strings, optional
The TFORM format strings for each field.
dims: list of strings, optional
An optional list of dimension strings for each field. Should
match the repeat count for the formats fields. Be careful of
the order since FITS is more like fortran. See the descr2tabledef
function.
table_type: string, optional
Either 'binary' or 'ascii', default 'binary'
Matching is case-insensitive
units: list of strings, optional
An optional list of unit strings for each field.
extname: string, optional
An optional extension name.
extver: integer, optional
FITS allows multiple extensions to have the same name (extname).
These extensions can optionally specify an EXTVER version number in
the header. Send extver= to set a particular version, which will
be represented in the header with keyname EXTVER. The extver must
be an integer > 0. If extver is not sent, the first one will be
selected. If ext is an integer, the extver is ignored.
write_bitcols: bool, optional
Write boolean arrays in the FITS bitcols format, default False
header: FITSHDR, list, dict, optional
This is only used to determine how many slots to reserve for
header keywords
restrictions
------------
The File must be opened READWRITE
"""
# record this for the TableHDU object
write_bitcols = self.write_bitcols or write_bitcols
# can leave as turn
table_type_int = _extract_table_type(table_type)
if data is not None:
if isinstance(data, numpy.ndarray):
names, formats, dims = array2tabledef(
data, table_type=table_type, write_bitcols=write_bitcols)
elif isinstance(data, (list, dict)):
names, formats, dims = collection2tabledef(
data, names=names, table_type=table_type,
write_bitcols=write_bitcols)
else:
raise ValueError(
"data must be an ndarray with fields or a dict")
elif dtype is not None:
dtype = numpy.dtype(dtype)
names, formats, dims = descr2tabledef(
dtype.
descr,
write_bitcols=write_bitcols,
table_type=table_type,
)
else:
if names is None or formats is None:
raise ValueError(
"send either dtype=, data=, or names= and formats=")
if not isinstance(names, list) or not isinstance(formats, list):
raise ValueError("names and formats should be lists")
if len(names) != len(formats):
raise ValueError("names and formats must be same length")
if dims is not None:
if not isinstance(dims, list):
raise ValueError("dims should be a list")
if len(dims) != len(names):
raise ValueError("names and dims must be same length")
if units is not None:
if not isinstance(units, list):
raise ValueError("units should be a list")
if len(units) != len(names):
raise ValueError("names and units must be same length")
if extname is None:
# will be ignored
extname = ""
else:
if not isstring(extname):
raise ValueError("extension name must be a string")
extname = mks(extname)
if extname is not None and extver is not None:
extver = check_extver(extver)
if extver is None:
# will be ignored
extver = 0
if extname is None:
# will be ignored
extname = ""
if header is not None:
nkeys = len(header)
else:
nkeys = 0
# note we can create extname in the c code for tables, but not images
self._FITS.create_table_hdu(table_type_int, nkeys,
names, formats, tunit=units, tdim=dims,
extname=extname, extver=extver)
# don't rebuild the whole list unless this is the first hdu
# to be created
self.update_hdu_list(rebuild=False)
def update_hdu_list(self, rebuild=True):
"""
Force an update of the entire HDU list
Normally you don't need to call this method directly
if rebuild is false or the hdu_list is not yet set, the list is
rebuilt from scratch
"""
if not hasattr(self, 'hdu_list'):
rebuild = True
if rebuild:
self.hdu_list = []
self.hdu_map = {}
# we don't know how many hdus there are, so iterate
# until we can't open any more
ext_start = 0
else:
# start from last
ext_start = len(self)
ext = ext_start
while True:
try:
self._append_hdu_info(ext)
except IOError:
break
except RuntimeError:
break
ext = ext + 1
def _append_hdu_info(self, ext):
"""
internal routine
append info for indiciated extension
"""
# raised IOError if not found
hdu_type = self._FITS.movabs_hdu(ext+1)
if hdu_type == IMAGE_HDU:
hdu = ImageHDU(self._FITS, ext)
elif hdu_type == BINARY_TBL:
hdu = TableHDU(
self._FITS, ext,
lower=self.lower, upper=self.upper,
trim_strings=self.trim_strings,
vstorage=self.vstorage, case_sensitive=self.case_sensitive,
iter_row_buffer=self.iter_row_buffer,
write_bitcols=self.write_bitcols)
elif hdu_type == ASCII_TBL:
hdu = AsciiTableHDU(
self._FITS, ext,
lower=self.lower, upper=self.upper,
trim_strings=self.trim_strings,
vstorage=self.vstorage, case_sensitive=self.case_sensitive,
iter_row_buffer=self.iter_row_buffer,
write_bitcols=self.write_bitcols)
else:
mess = ("extension %s is of unknown type %s "
"this is probably a bug")
mess = mess % (ext, hdu_type)
raise IOError(mess)
self.hdu_list.append(hdu)
self.hdu_map[ext] = hdu
extname = hdu.get_extname()
if not self.case_sensitive:
extname = extname.lower()
if extname != '':
# this will guarantee we default to *first* version,
# if version is not requested, using __getitem__
if extname not in self.hdu_map:
self.hdu_map[extname] = hdu
ver = hdu.get_extver()
if ver > 0:
key = '%s-%s' % (extname, ver)
self.hdu_map[key] = hdu
def __iter__(self):
"""
begin iteration over HDUs
"""
if not hasattr(self, 'hdu_list'):
self.update_hdu_list()
self._iter_index = 0
return self
def next(self):
"""
Move to the next iteration
"""
if self._iter_index == len(self.hdu_list):
raise StopIteration
hdu = self.hdu_list[self._iter_index]
self._iter_index += 1
return hdu
__next__ = next
def __len__(self):
"""
get the number of extensions
"""
if not hasattr(self, 'hdu_list'):
self.update_hdu_list()
return len(self.hdu_list)
def _extract_item(self, item):
"""
utility function to extract an "item", meaning
a extension number,name plus version.
"""
ver = 0
if isinstance(item, tuple):
ver_sent = True
nitem = len(item)
if nitem == 1:
ext = item[0]
elif nitem == 2:
ext, ver = item
else:
ver_sent = False
ext = item
return ext, ver, ver_sent
def __getitem__(self, item):
"""
Get an hdu by number, name, and possibly version
"""
if not hasattr(self, 'hdu_list'):
if self._did_create:
# we created the file and haven't written anything yet
raise ValueError("Requested hdu '%s' not present" % item)
self.update_hdu_list()
if len(self) == 0:
raise ValueError("Requested hdu '%s' not present" % item)
ext, ver, ver_sent = self._extract_item(item)
try:
# if it is an int
hdu = self.hdu_list[ext]
except Exception:
# might be a string
ext = mks(ext)
if not self.case_sensitive:
mess = '(case insensitive)'
ext = ext.lower()
else:
mess = '(case sensitive)'
if ver > 0:
key = '%s-%s' % (ext, ver)
if key not in self.hdu_map:
raise IOError("extension not found: %s, "
"version %s %s" % (ext, ver, mess))
hdu = self.hdu_map[key]
else:
if ext not in self.hdu_map:
raise IOError("extension not found: %s %s" % (ext, mess))
hdu = self.hdu_map[ext]
return hdu
def __contains__(self, item):
"""
tell whether specified extension exists, possibly
with version sent as well
"""
try:
hdu = self[item] # noqa
return True
except Exception:
return False
def __repr__(self):
"""
Text representation of some fits file metadata
"""
spacing = ' '*2
rep = ['']
rep.append("%sfile: %s" % (spacing, self._filename))
rep.append("%smode: %s" % (spacing, _modeprint_map[self.intmode]))
rep.append('%sextnum %-15s %s' % (spacing, "hdutype", "hduname[v]"))
if not hasattr(self, 'hdu_list'):
if not self._did_create:
# we expect some stuff
self.update_hdu_list()
for i, hdu in enumerate(self.hdu_list):
t = hdu._info['hdutype']
name = hdu.get_extname()
if name != '':
ver = hdu.get_extver()
if ver != 0:
name = '%s[%s]' % (name, ver)
rep.append(
"%s%-6d %-15s %s" % (
spacing, i, _hdu_type_map[t], name
)
)
rep = '\n'.join(rep)
return rep
def __enter__(self):
return self
def __exit__(self, exception_type, exception_value, traceback):
self.close()
def check_extver(extver):
if extver is None:
return 0
extver = int(extver)
if extver <= 0:
raise ValueError("extver must be > 0")
return extver
def extract_filename(filename):
filename = mks(filename)
filename = filename.strip()
if filename[0] == "!":
filename = filename[1:]
filename = os.path.expandvars(filename)
filename = os.path.expanduser(filename)
return filename
def array2tabledef(data, table_type='binary', write_bitcols=False):
"""
Similar to descr2tabledef but if there are object columns a type
and max length will be extracted and used for the tabledef
"""
is_ascii = (table_type == 'ascii')
if data.dtype.fields is None:
raise ValueError("data must have fields")
names = []
names_nocase = {}
formats = []
dims = []
descr = data.dtype.descr
for d in descr:
# these have the form '<f4' or '|S25', etc. Extract the pure type
npy_dtype = d[1][1:]
if is_ascii:
if npy_dtype in ['u1', 'i1']:
raise ValueError(
"1-byte integers are not supported for "
"ascii tables: '%s'" % npy_dtype)
if npy_dtype in ['u2']:
raise ValueError(
"unsigned 2-byte integers are not supported for "
"ascii tables: '%s'" % npy_dtype)
if npy_dtype[0] == 'O':
# this will be a variable length column 1Pt(len) where t is the
# type and len is max length. Each element must be convertible to
# the same type as the first
name = d[0]
form, dim = npy_obj2fits(data, name)
elif npy_dtype[0] == "V":
continue
else:
name, form, dim = _npy2fits(
d, table_type=table_type, write_bitcols=write_bitcols)
if name == '':
raise ValueError("field name is an empty string")
"""
if is_ascii:
if dim is not None:
raise ValueError("array columns are not supported for "
"ascii tables")
"""
name_nocase = name.upper()
if name_nocase in names_nocase:
raise ValueError(
"duplicate column name found: '%s'. Note "
"FITS column names are not case sensitive" % name_nocase)
names.append(name)
names_nocase[name_nocase] = name_nocase
formats.append(form)
dims.append(dim)
return names, formats, dims
def collection2tabledef(
data, names=None, table_type='binary', write_bitcols=False):
if isinstance(data, dict):
if names is None:
names = list(data.keys())
isdict = True
elif isinstance(data, list):
if names is None:
raise ValueError("For list of array, send names=")
isdict = False
else:
raise ValueError("expected a dict")
is_ascii = (table_type == 'ascii')
formats = []
dims = []
for i, name in enumerate(names):
if isdict:
this_data = data[name]
else:
this_data = data[i]
dt = this_data.dtype.descr[0]
dname = dt[1][1:]
if is_ascii:
if dname in ['u1', 'i1']:
raise ValueError(
"1-byte integers are not supported for "
"ascii tables: '%s'" % dname)
if dname in ['u2']:
raise ValueError(
"unsigned 2-byte integers are not supported for "
"ascii tables: '%s'" % dname)
if dname[0] == 'O':
# this will be a variable length column 1Pt(len) where t is the
# type and len is max length. Each element must be convertible to
# the same type as the first
form, dim = npy_obj2fits(this_data)
else:
send_dt = dt
if len(this_data.shape) > 1:
send_dt = list(dt) + [this_data.shape[1:]]
_, form, dim = _npy2fits(
send_dt, table_type=table_type, write_bitcols=write_bitcols)
formats.append(form)
dims.append(dim)
return names, formats, dims
def descr2tabledef(descr, table_type='binary', write_bitcols=False):
"""
Create a FITS table def from the input numpy descriptor.
parameters
----------
descr: list
A numpy recarray type descriptor array.dtype.descr
returns
-------
names, formats, dims: tuple of lists
These are the ttyp, tform and tdim header entries
for each field. dim entries may be None
"""
names = []
formats = []
dims = []
for d in descr:
"""
npy_dtype = d[1][1:]
if is_ascii and npy_dtype in ['u1','i1']:
raise ValueError("1-byte integers are not supported for "
"ascii tables")
"""
if d[1][1] == 'O':
raise ValueError(
'cannot automatically declare a var column without '
'some data to determine max len')
name, form, dim = _npy2fits(
d, table_type=table_type, write_bitcols=write_bitcols)
if name == '':
raise ValueError("field name is an empty string")
"""
if is_ascii:
if dim is not None:
raise ValueError("array columns are not supported "
"for ascii tables")
"""
names.append(name)
formats.append(form)
dims.append(dim)
return names, formats, dims
def npy_obj2fits(data, name=None):
# this will be a variable length column 1Pt(len) where t is the
# type and len is max length. Each element must be convertible to
# the same type as the first
if name is None:
d = data.dtype.descr
first = data[0]
else:
d = data[name].dtype.descr # noqa - not used
first = data[name][0]
# note numpy._string is an instance of str in python2, bytes
# in python3
if isinstance(first, str) or (IS_PY3 and isinstance(first, bytes)):
if IS_PY3:
if isinstance(first, str):
fits_dtype = _table_npy2fits_form['U']
else:
fits_dtype = _table_npy2fits_form['S']
else:
fits_dtype = _table_npy2fits_form['S']
else:
arr0 = numpy.array(first, copy=False)
dtype0 = arr0.dtype
npy_dtype = dtype0.descr[0][1][1:]
if npy_dtype[0] == 'S' or npy_dtype[0] == 'U':
raise ValueError("Field '%s' is an arrays of strings, this is "
"not allowed in variable length columns" % name)
if npy_dtype not in _table_npy2fits_form:
raise ValueError(
"Field '%s' has unsupported type '%s'" % (name, npy_dtype))
fits_dtype = _table_npy2fits_form[npy_dtype]
# Q uses 64-bit addressing, should try at some point but the cfitsio manual
# says it is experimental
# form = '1Q%s' % fits_dtype
form = '1P%s' % fits_dtype
dim = None
return form, dim
def get_tile_dims(tile_dims, imshape):
"""
Just make sure the tile dims has the appropriate number of dimensions
"""
if tile_dims is None:
td = None
else:
td = numpy.array(tile_dims, dtype='i8')
nd = len(imshape)
if td.size != nd:
msg = "expected tile_dims to have %d dims, got %d" % (td.size, nd)
raise ValueError(msg)
return td
def get_compress_type(compress):
if compress is not None:
compress = str(compress).upper()
if compress not in _compress_map:
raise ValueError(
"compress must be one of %s" % list(_compress_map.keys()))
return _compress_map[compress]
def get_qmethod(qmethod):
if qmethod not in _qmethod_map:
if isinstance(qmethod, str):
qmethod = qmethod.upper()
elif isinstance(qmethod, bytes):
# in py27, bytes are str, so we can safely assume
# py3 here
qmethod = str(qmethod, 'ascii').upper()
if qmethod not in _qmethod_map:
raise ValueError(
"qmethod must be one of %s" % list(_qmethod_map.keys()))
return _qmethod_map[qmethod]
def check_comptype_img(comptype, dtype_str):
if comptype == NOCOMPRESS:
return
# if dtype_str == 'i8':
# no i8 allowed for tile-compressed images
# raise ValueError("8-byte integers not supported when "
# "using tile compression")
if comptype == PLIO_1:
# no unsigned u4/u8 for plio
if dtype_str == 'u4' or dtype_str == 'u8':
raise ValueError("Unsigned 4/8-byte integers currently not "
"allowed when writing using PLIO "
"tile compression")
def _extract_table_type(type):
"""
Get the numerical table type
"""
if isinstance(type, str):
type = type.lower()
if type[0:7] == 'binary':
table_type = BINARY_TBL
elif type[0:6] == 'ascii':
table_type = ASCII_TBL
else:
raise ValueError(
"table type string should begin with 'binary' or 'ascii' "
"(case insensitive)")
else:
type = int(type)
if type not in [BINARY_TBL, ASCII_TBL]:
raise ValueError(
"table type num should be BINARY_TBL (%d) or "
"ASCII_TBL (%d)" % (BINARY_TBL, ASCII_TBL))
table_type = type
return table_type
_compress_map = {
None: NOCOMPRESS,
'RICE': RICE_1,
'RICE_1': RICE_1,
'GZIP': GZIP_1,
'GZIP_1': GZIP_1,
'GZIP_2': GZIP_2,
'PLIO': PLIO_1,
'PLIO_1': PLIO_1,
'HCOMPRESS': HCOMPRESS_1,
'HCOMPRESS_1': HCOMPRESS_1,
NOCOMPRESS: None,
RICE_1: 'RICE_1',
GZIP_1: 'GZIP_1',
GZIP_2: 'GZIP_2',
PLIO_1: 'PLIO_1',
HCOMPRESS_1: 'HCOMPRESS_1',
}
_qmethod_map = {
None: NO_DITHER,
'NO_DITHER': NO_DITHER,
'SUBTRACTIVE_DITHER_1': SUBTRACTIVE_DITHER_1,
'SUBTRACTIVE_DITHER_2': SUBTRACTIVE_DITHER_2,
NO_DITHER: NO_DITHER,
SUBTRACTIVE_DITHER_1: SUBTRACTIVE_DITHER_1,
SUBTRACTIVE_DITHER_2: SUBTRACTIVE_DITHER_2,
}
_modeprint_map = {
'r': 'READONLY', 'rw': 'READWRITE', 0: 'READONLY', 1: 'READWRITE'}
_char_modemap = {
'r': 'r', 'rw': 'rw',
READONLY: 'r', READWRITE: 'rw'}
_int_modemap = {
'r': READONLY, 'rw': READWRITE, READONLY: READONLY, READWRITE: READWRITE}
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