# Licensed under a 3-clause BSD style license - see PYFITS.rst

import errno

import gzip

import http.client

import io

import math

import mmap

import os

import re

import sys

import tempfile

import warnings

import zipfile

import numpy as np

# NOTE: Python can be built without bz2.

from astropy.utils.compat.optional_deps import HAS_BZ2, HAS_LZMA, HAS_UNCOMPRESSPY

from astropy.utils.data import (

_requires_fsspec,

download_file,

get_readable_fileobj,

is_url,

)

from astropy.utils.decorators import classproperty

from astropy.utils.exceptions import AstropyUserWarning

from astropy.utils.misc import NOT_OVERWRITING_MSG

from .util import (

_array_from_file,

_array_to_file,

_write_string,

fileobj_closed,

fileobj_mode,

fileobj_name,

isfile,

isreadable,

iswritable,

path_like,

)

if HAS_BZ2:

import bz2

if HAS_LZMA:

import lzma

if HAS_UNCOMPRESSPY:

import uncompresspy

# Maps astropy.io.fits-specific file mode names to the appropriate file

# modes to use for the underlying raw files.

IO_FITS_MODES = {

"readonly": "rb",

"copyonwrite": "rb",

"update": "rb+",

"append": "ab+",

"ostream": "wb",

"denywrite": "rb",

}

# Maps OS-level file modes to the appropriate astropy.io.fits specific mode

# to use when given file objects but no mode specified; obviously in

# IO_FITS_MODES there are overlaps; for example 'readonly' and 'denywrite'

# both require the file to be opened in 'rb' mode. But 'readonly' is the

# default behavior for such files if not otherwise specified.

# Note: 'ab' is only supported for 'ostream' which is output-only.

FILE_MODES = {

"rb": "readonly",

"rb+": "update",

"wb": "ostream",

"wb+": "update",

"ab": "ostream",

"ab+": "append",

}

# A match indicates the file was opened in text mode, which is not allowed

TEXT_RE = re.compile(r"^[rwa]((t?\+?)|(\+?t?))$")

# readonly actually uses copyonwrite for mmap so that readonly without mmap and

# with mmap still have to same behavior with regard to updating the array. To

# get a truly readonly mmap use denywrite

# the name 'denywrite' comes from a deprecated flag to mmap() on Linux--it

# should be clarified that 'denywrite' mode is not directly analogous to the

# use of that flag; it was just taken, for lack of anything better, as a name

# that means something like "read only" but isn't readonly.

MEMMAP_MODES = {

"readonly": mmap.ACCESS_COPY,

"copyonwrite": mmap.ACCESS_COPY,

"update": mmap.ACCESS_WRITE,

"append": mmap.ACCESS_COPY,

"denywrite": mmap.ACCESS_READ,

}

# TODO: Eventually raise a warning, and maybe even later disable the use of

# 'copyonwrite' and 'denywrite' modes unless memmap=True. For now, however,

# that would generate too many warnings for too many users. If nothing else,

# wait until the new logging system is in place.

GZIP_MAGIC = b"\x1f\x8b\x08"

PKZIP_MAGIC = b"\x50\x4b\x03\x04"

BZIP2_MAGIC = b"\x42\x5a"

LZMA_MAGIC = b"\xfd7zXZ\x00"

LZW_MAGIC = b"\x1f\x9d"

def _is_bz2file(fileobj):

if HAS_BZ2:

return isinstance(fileobj, bz2.BZ2File)

else:

return False

def _is_lzmafile(fileobj):

if HAS_LZMA:

return isinstance(fileobj, lzma.LZMAFile)

else:

return False

def _is_lzwfile(fileobj):

if HAS_UNCOMPRESSPY:

return isinstance(fileobj, uncompresspy.LZWFile)

else:

return False

def _normalize_fits_mode(mode):

if mode is not None and mode not in IO_FITS_MODES:

if TEXT_RE.match(mode):

raise ValueError(

f"Text mode '{mode}' not supported: files must be opened in binary mode"

)

new_mode = FILE_MODES.get(mode)

if new_mode not in IO_FITS_MODES:

raise ValueError(f"Mode '{mode}' not recognized")

mode = new_mode

return mode

class _File:

"""

Represents a FITS file on disk (or in some other file-like object).

"""

def __init__(

self,

fileobj=None,

mode=None,

memmap=None,

overwrite=False,

cache=True,

*,

use_fsspec=None,

fsspec_kwargs=None,

decompress_in_memory=False,

):

self.strict_memmap = bool(memmap)

memmap = True if memmap is None else memmap

self._file = None

self.closed = False

self.binary = True

self.mode = mode

self.memmap = memmap

self.compression = None

self.readonly = False

self.writeonly = False

# Should the object be closed on error: see

# https://github.com/astropy/astropy/issues/6168

self.close_on_error = False

# Holds mmap instance for files that use mmap

self._mmap = None

if fileobj is None:

self.simulateonly = True

return

else:

self.simulateonly = False

if isinstance(fileobj, os.PathLike):

fileobj = os.fspath(fileobj)

if mode is not None and mode not in IO_FITS_MODES:

raise ValueError(f"Mode '{mode}' not recognized")

if isfile(fileobj):

objmode = _normalize_fits_mode(fileobj_mode(fileobj))

if mode is not None and mode != objmode:

raise ValueError(

f"Requested FITS mode '{mode}' not compatible with open file "

f"handle mode '{objmode}'"

)

mode = objmode

if mode is None:

mode = "readonly"

# Handle cloud-hosted files using the optional ``fsspec`` dependency

if (use_fsspec or _requires_fsspec(fileobj)) and mode != "ostream":

# Note: we don't use `get_readable_fileobj` as a context manager

# because io.fits takes care of closing files itself

fileobj = get_readable_fileobj(

fileobj,

encoding="binary",

use_fsspec=use_fsspec,

fsspec_kwargs=fsspec_kwargs,

close_files=False,

).__enter__()

# Handle raw URLs

if (

isinstance(fileobj, (str, bytes))

and mode not in ("ostream", "append", "update")

and is_url(fileobj)

):

self.name = download_file(fileobj, cache=cache)

# Handle responses from URL requests that have already been opened

elif isinstance(fileobj, http.client.HTTPResponse):

if mode in ("ostream", "append", "update"):

raise ValueError(f"Mode {mode} not supported for HTTPResponse")

fileobj = io.BytesIO(fileobj.read())

else:

if isinstance(fileobj, path_like):

fileobj = os.path.expanduser(fileobj)

self.name = fileobj_name(fileobj)

self.mode = mode

# Underlying fileobj is a file-like object, but an actual file object

self.file_like = False

# Initialize the internal self._file object

if isfile(fileobj):

self._open_fileobj(fileobj, mode, overwrite)

elif isinstance(fileobj, (str, bytes)):

self._open_filename(fileobj, mode, overwrite)

else:

self._open_filelike(fileobj, mode, overwrite)

self.fileobj_mode = fileobj_mode(self._file)

if isinstance(fileobj, gzip.GzipFile):

self.compression = "gzip"

elif isinstance(fileobj, zipfile.ZipFile):

# Reading from zip files is supported but not writing (yet)

self.compression = "zip"

elif _is_bz2file(fileobj):

self.compression = "bzip2"

elif _is_lzmafile(fileobj):

self.compression = "lzma"

elif _is_lzwfile(fileobj):

self.compression = "lzw"

if (

self.compression is not None

and decompress_in_memory

and mode in ("readonly", "copyonwrite", "denywrite")

):

# By default blocks are decompressed on the fly, when calling

# self.read. This is good for memory usage, avoiding decompression

# of the whole file, but it can be slow. With

# decompress_in_memory=True it is possible to decompress instead

# the whole file in memory.

fd = self._file

self._file = io.BytesIO(self._file.read())

fd.close()

if mode in ("readonly", "copyonwrite", "denywrite") or (

self.compression and mode == "update"

):

self.readonly = True

elif mode == "ostream" or (self.compression and mode == "append"):

self.writeonly = True

# For 'ab+' mode, the pointer is at the end after the open in

# Linux, but is at the beginning in Solaris.

if mode == "ostream" or self.compression or not hasattr(self._file, "seek"):

# For output stream start with a truncated file.

# For compressed files we can't really guess at the size

self.size = 0

else:

pos = self._file.tell()

self._file.seek(0, 2)

self.size = self._file.tell()

self._file.seek(pos)

if self.memmap:

if not isfile(self._file):

self.memmap = False

elif not self.readonly and not self._mmap_available:

# Test mmap.flush--see

# https://github.com/astropy/astropy/issues/968

self.memmap = False

elif not self.readonly and sys.platform == "emscripten":

# Emscripten's munmap writes a writeable shared mapping back

# to whichever file currently holds the file descriptor number

# the mapping was created with, so once that descriptor is

# closed and reused (as happens when a resized file is

# rewritten in update mode), another file gets overwritten.

# Emscripten's mmap is an in-memory copy anyway, so nothing is

# lost by not using it.

self.memmap = False

def __repr__(self):

return f"<{self.__module__}.{self.__class__.__name__} {self._file}>"

# Support the 'with' statement

def __enter__(self):

return self

def __exit__(self, type, value, traceback):

self.close()

def readable(self):

if self.writeonly:

return False

return isreadable(self._file)

def read(self, size=None):

if not hasattr(self._file, "read"):

raise EOFError

try:

return self._file.read(size)

except OSError:

# On some versions of Python, it appears, GzipFile will raise an

# OSError if you try to read past its end (as opposed to just

# returning '')

if self.compression == "gzip":

return ""

raise

def readarray(self, size=None, offset=0, dtype=np.uint8, shape=None):

"""

Similar to file.read(), but returns the contents of the underlying

file as a numpy array (or mmap'd array if memmap=True) rather than a

string.

Usually it's best not to use the `size` argument with this method, but

it's provided for compatibility.

"""

if not hasattr(self._file, "read"):

raise EOFError

if not isinstance(dtype, np.dtype):

dtype = np.dtype(dtype)

if size and size % dtype.itemsize != 0:

raise ValueError(f"size {size} not a multiple of {dtype}")

if isinstance(shape, int):

shape = (shape,)

if not (size or shape):

warnings.warn(

"No size or shape given to readarray(); assuming a shape of (1,)",

AstropyUserWarning,

)

shape = (1,)

if size and not shape:

shape = (size // dtype.itemsize,)

if size and shape:

actualsize = math.prod(shape) * dtype.itemsize

if actualsize > size:

raise ValueError(

f"size {size} is too few bytes for a {shape} array of {dtype}"

)

elif actualsize < size:

raise ValueError(

f"size {size} is too many bytes for a {shape} array of {dtype}"

)

filepos = self._file.tell()

try:

if self.memmap:

if self._mmap is None:

# Instantiate Memmap array of the file offset at 0 (so we

# can return slices of it to offset anywhere else into the

# file)

access_mode = MEMMAP_MODES[self.mode]

# For reasons unknown the file needs to point to (near)

# the beginning or end of the file. No idea how close to

# the beginning or end.

# If I had to guess there is some bug in the mmap module

# of CPython or perhaps in microsoft's underlying code

# for generating the mmap.

self._file.seek(0, 0)

# This would also work:

# self._file.seek(0, 2) # moves to the end

try:

self._mmap = mmap.mmap(

self._file.fileno(), 0, access=access_mode, offset=0

)

except OSError as exc:

# NOTE: mode='readonly' results in the memory-mapping

# using the ACCESS_COPY mode in mmap so that users can

# modify arrays. However, on some systems, the OS raises

# a '[Errno 12] Cannot allocate memory' OSError if the

# address space is smaller than the file. Also on windows

# a '[WinError 1455] The paging file is too small for

# this operation to complete' Windows error is raised or

# equiivalent a '[Errno 22] Invalid argument. The solution

# is to open the file in mode='denywrite', which at

# least allows the file to be opened even if the

# resulting arrays will be truly read-only.

if (

exc.errno == errno.ENOMEM

or (

exc.errno == errno.EINVAL

and getattr(exc, "winerror", 0) == 1455

)

) and self.mode == "readonly":

warnings.warn(

"Could not memory map array with "

"mode='readonly', falling back to "

"mode='denywrite', which means that "

"the array will be read-only",

AstropyUserWarning,

)

self._mmap = mmap.mmap(

self._file.fileno(),

0,

access=MEMMAP_MODES["denywrite"],

offset=0,

)

elif not self.strict_memmap:

# mmap failed but wasn't explicitly requested,

# fall back to non-mmap reading

warnings.warn(

"Could not memory map array; falling back to "

"non-memory-mapped file reading. You can disable "

"this warning by setting memmap=False",

AstropyUserWarning,

)

self.memmap = False

else:

raise

if self._mmap is not None:

return np.ndarray(

shape=shape, dtype=dtype, offset=offset, buffer=self._mmap

)

# Non-mmap path (also used as fallback when mmap fails)

count = math.prod(shape)

self._file.seek(offset)

data = _array_from_file(self._file, dtype, count)

return data.reshape(shape)

finally:

# Make sure we leave the file in the position we found it; on

# some platforms (e.g. Windows) mmaping a file handle can also

# reset its file pointer.

# Also for Windows when using mmap seek() may return weird

# negative values, which is fixed by calling tell() before.

self._file.tell()

self._file.seek(filepos)

def writable(self):

if self.readonly:

return False

return iswritable(self._file)

def write(self, string):

if self.simulateonly:

return

if hasattr(self._file, "write"):

_write_string(self._file, string)

def writearray(self, array):

"""

Similar to file.write(), but writes a numpy array instead of a string.

Also like file.write(), a flush() or close() may be needed before

the file on disk reflects the data written.

"""

if self.simulateonly:

return

if hasattr(self._file, "write"):

_array_to_file(array, self._file)

def flush(self):

if self.simulateonly:

return

if hasattr(self._file, "flush"):

self._file.flush()

def seek(self, offset, whence=0):

if not hasattr(self._file, "seek"):

return

self._file.seek(offset, whence)

pos = self._file.tell()

if self.size and pos > self.size:

warnings.warn(

"File may have been truncated: actual file length "

f"({self.size}) is smaller than the expected size ({pos})",

AstropyUserWarning,

)

def tell(self):

if self.simulateonly:

raise OSError

if not hasattr(self._file, "tell"):

raise EOFError

return self._file.tell()

def truncate(self, size=None):

if hasattr(self._file, "truncate"):

self._file.truncate(size)

def close(self):

"""

Close the 'physical' FITS file.

"""

if hasattr(self._file, "close"):

self._file.close()

self._maybe_close_mmap()

# Set self._memmap to None anyways since no new .data attributes can be

# loaded after the file is closed

self._mmap = None

self.closed = True

self.close_on_error = False

def _maybe_close_mmap(self, refcount_delta=0):

"""

When mmap is in use these objects hold a reference to the mmap of the

file (so there is only one, shared by all HDUs that reference this

file).

This will close the mmap if there are no arrays referencing it.

"""

# sys.getrefcount is CPython specific and not on PyPy.

if (

self._mmap is not None

and hasattr(sys, "getrefcount")

and sys.getrefcount(self._mmap) == 2 + refcount_delta

):

self._mmap.close()

self._mmap = None

def _overwrite_existing(self, overwrite, fileobj, closed):

"""Overwrite an existing file if ``overwrite`` is ``True``, otherwise

raise an OSError. The exact behavior of this method depends on the

_File object state and is only meant for use within the ``_open_*``

internal methods.

"""

# The file will be overwritten...

if (self.file_like and hasattr(fileobj, "len") and fileobj.len > 0) or (

os.path.exists(self.name) and os.path.getsize(self.name) != 0

):

if overwrite:

if self.file_like and hasattr(fileobj, "truncate"):

fileobj.truncate(0)

else:

if not closed:

fileobj.close()

os.remove(self.name)

else:

raise OSError(NOT_OVERWRITING_MSG.format(self.name))

def _try_read_compressed(self, obj_or_name, magic, mode, ext=""):

"""Attempt to determine if the given file is compressed."""

is_ostream = mode == "ostream"

if (is_ostream and ext == ".gz") or magic.startswith(GZIP_MAGIC):

if mode == "append":

raise OSError(

"'append' mode is not supported with gzip files."

"Use 'update' mode instead"

)

# Handle gzip files

kwargs = {"mode": IO_FITS_MODES[mode]}

if isinstance(obj_or_name, str):

kwargs["filename"] = obj_or_name

else:

kwargs["fileobj"] = obj_or_name

self._file = gzip.GzipFile(**kwargs)

self.compression = "gzip"

elif (is_ostream and ext == ".zip") or magic.startswith(PKZIP_MAGIC):

# Handle zip files

self._open_zipfile(self.name, mode)

self.compression = "zip"

elif (is_ostream and ext == ".bz2") or magic.startswith(BZIP2_MAGIC):

# Handle bzip2 files

if mode in ["update", "append"]:

raise OSError(

"update and append modes are not supported with bzip2 files"

)

if not HAS_BZ2:

raise ModuleNotFoundError(

"This Python installation does not provide the bz2 module."

)

# bzip2 only supports 'w' and 'r' modes

bzip2_mode = "w" if is_ostream else "r"

self._file = bz2.BZ2File(obj_or_name, mode=bzip2_mode)

self.compression = "bzip2"

elif (is_ostream and ext == ".xz") or magic.startswith(LZMA_MAGIC):

# Handle lzma files

if mode in ["update", "append"]:

raise OSError(

"update and append modes are not supported with lzma files"

)

if not HAS_LZMA:

raise ModuleNotFoundError(

"This Python installation does not provide the lzma module."

)

lzma_mode = "w" if is_ostream else "r"

self._file = lzma.LZMAFile(obj_or_name, mode=lzma_mode)

self.compression = "lzma"

elif (is_ostream and ext == ".Z") or magic.startswith(LZW_MAGIC):

# Handle LZW files

if mode in ["update", "append", "ostream"]:

raise OSError(f"{mode} mode not supported with LZW files")

if not HAS_UNCOMPRESSPY:

raise ModuleNotFoundError(

"The optional package uncompresspy is necessary for reading"

" LZW compressed files (.Z extension)."

)

self._file = uncompresspy.LZWFile(obj_or_name, mode="rb")

self.compression = "lzw"

return self.compression is not None

def _open_fileobj(self, fileobj, mode, overwrite):

"""Open a FITS file from a file object (including compressed files)."""

closed = fileobj_closed(fileobj)

# FIXME: this variable was unused, check if it was useful

# fmode = fileobj_mode(fileobj) or IO_FITS_MODES[mode]

if mode == "ostream":

self._overwrite_existing(overwrite, fileobj, closed)

if not closed:

self._file = fileobj

elif isfile(fileobj):

self._file = open(self.name, IO_FITS_MODES[mode])

# Attempt to determine if the file represented by the open file object

# is compressed

try:

# We need to account for the possibility that the underlying file

# handle may have been opened with either 'ab' or 'ab+', which

# means that the current file position is at the end of the file.

if mode in ["ostream", "append"]:

self._file.seek(0)

magic = self._file.read(6)

# No matter whether the underlying file was opened with 'ab' or

# 'ab+', we need to return to the beginning of the file in order

# to properly process the FITS header (and handle the possibility

# of a compressed file).

self._file.seek(0)

except OSError:

return

self._try_read_compressed(fileobj, magic, mode)

def _open_filelike(self, fileobj, mode, overwrite):

"""Open a FITS file from a file-like object, i.e. one that has

read and/or write methods.

"""

self.file_like = True

self._file = fileobj

if fileobj_closed(fileobj):

raise OSError(

f"Cannot read from/write to a closed file-like object ({fileobj!r})."

)

if isinstance(fileobj, zipfile.ZipFile):

self._open_zipfile(fileobj, mode)

# We can bypass any additional checks at this point since now

# self._file points to the temp file extracted from the zip

return

# If there is not seek or tell methods then set the mode to

# output streaming.

if not hasattr(self._file, "seek") or not hasattr(self._file, "tell"):

self.mode = mode = "ostream"

if mode == "ostream":

self._overwrite_existing(overwrite, fileobj, False)

# Any "writeable" mode requires a write() method on the file object

if self.mode in ("update", "append", "ostream") and not hasattr(

self._file, "write"

):

raise OSError(

"File-like object does not have a 'write' "

f"method, required for mode '{self.mode}'."

)

# Any mode except for 'ostream' requires readability

if self.mode != "ostream" and not hasattr(self._file, "read"):

raise OSError(

"File-like object does not have a 'read' "

f"method, required for mode {self.mode!r}."

)

def _open_filename(self, filename, mode, overwrite):

"""Open a FITS file from a filename string."""

if mode == "ostream":

self._overwrite_existing(overwrite, None, True)

if os.path.exists(self.name):

with open(self.name, "rb") as f:

magic = f.read(6)

else:

magic = b""

ext = os.path.splitext(self.name)[1]

if not self._try_read_compressed(self.name, magic, mode, ext=ext):

self._file = open(self.name, IO_FITS_MODES[mode])

self.close_on_error = True

# Make certain we're back at the beginning of the file

# BZ2File does not support seek when the file is open for writing, but

# when opening a file for write, bz2.BZ2File always truncates anyway.

if not (

(_is_bz2file(self._file) or (_is_lzmafile(self._file)))

and mode == "ostream"

):

self._file.seek(0)

@classproperty(lazy=True)

def _mmap_available(cls):

"""Tests that mmap, and specifically mmap.flush works. This may

be the case on some uncommon platforms (see

https://github.com/astropy/astropy/issues/968).

If mmap.flush is found not to work, ``self.memmap = False`` is

set and a warning is issued.

"""

tmpfd, tmpname = tempfile.mkstemp()

try:

# Windows does not allow mappings on empty files

os.write(tmpfd, b" ")

os.fsync(tmpfd)

try:

mm = mmap.mmap(tmpfd, 1, access=mmap.ACCESS_WRITE)

except OSError as exc:

warnings.warn(

f"Failed to create mmap: {exc}; mmap use will be disabled",

AstropyUserWarning,

)

del exc

return False

try:

mm.flush()

except OSError:

warnings.warn(

"mmap.flush is unavailable on this platform; "

"using mmap in writeable mode will be disabled",

AstropyUserWarning,

)

return False

finally:

mm.close()

finally:

os.close(tmpfd)

os.remove(tmpname)

return True

def _open_zipfile(self, fileobj, mode):

"""Limited support for zipfile.ZipFile objects containing a single

a file. Allows reading only for now by extracting the file to a

tempfile.

"""

if mode in ("update", "append"):

raise OSError("Writing to zipped fits files is not currently supported")

if not isinstance(fileobj, zipfile.ZipFile):

zfile = zipfile.ZipFile(fileobj)

close = True

else:

zfile = fileobj

close = False

namelist = zfile.namelist()

if len(namelist) != 1:

raise OSError("Zip files with multiple members are not supported.")

self._file = tempfile.NamedTemporaryFile(suffix=".fits")

self._file.write(zfile.read(namelist[0]))

if close:

zfile.close()

# We just wrote the contents of the first file in the archive to a new

# temp file, which now serves as our underlying file object. So it's

# necessary to reset the position back to the beginning

self._file.seek(0)