python3-pyfits 1:3.2-1build2 / usr / lib / python3 / dist-packages / pyfits / file.py

import gzip
import mmap
import os
import tempfile
import urllib.request, urllib.parse, urllib.error
import warnings
import zipfile

import numpy as np
from numpy import memmap as Memmap

from pyfits.util import (isreadable, iswritable, isfile, fileobj_open,
                         fileobj_name, fileobj_closed, fileobj_mode,
                         _array_from_file, _array_to_file, _write_string,
                         encode_ascii)
from functools import reduce


# Maps PyFITS-specific file mode names to the appropriate file modes to use
# for the underlying raw files
PYFITS_MODES = {
    'readonly': 'rb',
    'copyonwrite': 'rb',
    'update': 'rb+',
    'append': 'ab+',
    'ostream': 'wb',
    'denywrite': 'rb'}

# This is the old name of the PYFITS_MODES dict; it is maintained here for
# backwards compatibility and should be removed no sooner than PyFITS 3.4
PYTHON_MODES = PYFITS_MODES

# Maps OS-level file modes to the appropriate PyFITS specific mode to use
# when given file objects but no mode specified; obviously in PYFITS_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'}


# 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': 'c', 'copyonwrite': 'c', 'update': 'r+',
                'append': 'c', 'denywrite': 'r'}

# 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 = '\x1f\x8b\x08'.encode('raw-unicode-escape')
PKZIP_MAGIC = '\x50\x4b\x03\x04'.encode('raw-unicode-escape')


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

    # See self._test_mmap
    _mmap_available = None

    def __init__(self, fileobj=None, mode=None, memmap=False, clobber=False):
        if fileobj is None:
            self.__file = None
            self.closed = False
            self.binary = True
            self.mode = mode
            self.memmap = memmap
            self.compression = None
            self.readonly = False
            self.writeonly = False
            self.simulateonly = True
            return
        else:
            self.simulateonly = False

        if mode is None:
            if _is_random_access_file_backed(fileobj):
                fmode = fileobj_mode(fileobj)
                # If the mode is unsupported just leave it as None; we'll
                # catch this case below
                mode = FILE_MODES.get(fmode)
            else:
                mode = 'readonly'  # The default

        if mode not in PYFITS_MODES:
            raise ValueError("Mode '%s' not recognized" % mode)

        if (isinstance(fileobj, str) and
                mode not in ('ostream', 'append') and
                not os.path.exists(fileobj)):

            # Not writing file and file does not exist on local machine and
            # name does not begin with a drive letter (Windows), try to get it
            # over the web.
            try:
                if not os.path.splitdrive(fileobj)[0]:
                    # Basically if the filename (on Windows anyways) doesn't
                    # have a drive letter try to open it as a URL
                    self.name, _ = urllib.request.urlretrieve(fileobj)
                else:
                    # Otherwise the file was already not found so just raise
                    # a ValueError
                    raise ValueError("File not found")
            except (TypeError, ValueError, IOError):
                # A couple different exceptions can occur here when passing a
                # filename into urlretrieve in Python 3
                raise IOError('File does not exist: %r' % fileobj)
        else:
            self.name = fileobj_name(fileobj)

        self.closed = False
        self.binary = True
        self.mode = mode
        self.memmap = memmap

        # Underlying fileobj is a file-like object, but an actual file object
        self.file_like = False

        # More defaults to be adjusted below as necessary
        self.compression = None
        self.readonly = False
        self.writeonly = False

        # Initialize the internal self.__file object
        if _is_random_access_file_backed(fileobj):
            self._open_fileobj(fileobj, mode, clobber)
        elif isinstance(fileobj, str):
            self._open_filename(fileobj, mode, clobber)
        else:
            self._open_filelike(fileobj, mode, clobber)

        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'

        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._test_mmap():
                # Test mmap.flush--see
                # https://github.com/astropy/astropy/issues/968
                self.memmap = False

    def __repr__(self):
        return '<%s.%s %s>' % (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 IOError:
            # On some versions of Python, it appears, GzipFile will raise an
            # IOError 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('size %d not a multiple of %s' % (size, dtype))

        if isinstance(shape, int):
            shape = (shape,)

        if size and shape:
            actualsize = sum(dim * dtype.itemsize for dim in shape)
            if actualsize < size:
                raise ValueError('size %d is too few bytes for a %s array of '
                                 '%s' % (size, shape, dtype))
            if actualsize < size:
                raise ValueError('size %d is too many bytes for a %s array of '
                                 '%s' % (size, shape, dtype))

        if size and not shape:
            shape = (size // dtype.itemsize,)

        if not (size or shape):
            warnings.warn('No size or shape given to readarray(); assuming a '
                          'shape of (1,)')
            shape = (1,)

        if self.memmap:
            return Memmap(self.__file, offset=offset,
                          mode=MEMMAP_MODES[self.mode], dtype=dtype,
                          shape=shape).view(np.ndarray)
        else:
            count = reduce(lambda x, y: x * y, shape)
            pos = self.__file.tell()
            self.__file.seek(offset)
            data = _array_from_file(self.__file, dtype, count, '')
            data.shape = shape
            self.__file.seek(pos)
            return data

    def writable(self):
        if self.readonly:
            return False
        return iswritable(self.__file)

    def write(self, string):
        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 hasattr(self.__file, 'write'):
            _array_to_file(array, self.__file)

    def flush(self):
        if hasattr(self.__file, 'flush'):
            self.__file.flush()

    def seek(self, offset, whence=0):
        # In newer Python versions, GzipFiles support the whence argument, but
        # I don't think it was added until 2.6; instead of assuming it's
        # present, we implement our own support for it here
        if not hasattr(self.__file, 'seek'):
            return
        if isinstance(self.__file, gzip.GzipFile):
            if whence:
                if whence == 1:
                    offset = self.__file.offset + offset
                else:
                    raise ValueError('Seek from end not supported')
            self.__file.seek(offset)
        else:
            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 '
                          '(%i) is smaller than the expected size (%i)' %
                          (self.size, pos))

    def tell(self):
        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.closed = True

    def _overwrite_existing(self, clobber, fileobj, closed):
        """Overwrite an existing file if ``clobber`` is ``True``, otherwise
        raise an IOError.  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 clobber:
                warnings.warn("Overwriting existing file %r." % self.name)
                if self.file_like and hasattr(fileobj, 'truncate'):
                    fileobj.truncate(0)
                else:
                    if not closed:
                        fileobj.close()
                    os.remove(self.name)
            else:
                raise IOError("File %r already exists." % self.name)

    def _open_fileobj(self, fileobj, mode, clobber):
        """Open a FITS file from a file object or a GzipFile object."""

        closed = fileobj_closed(fileobj)
        fmode = fileobj_mode(fileobj) or PYFITS_MODES[mode]

        if mode == 'ostream':
            self._overwrite_existing(clobber, fileobj, closed)

        if not closed:
            # Although we have a specific mapping in PYFITS_MODES from our
            # custom file modes to raw file object modes, many of the latter
            # can be used appropriately for the former.  So determine whether
            # the modes match up appropriately
            if ((mode in ('readonly', 'denywrite', 'copyonwrite') and
                    not ('r' in fmode or '+' in fmode)) or
                    (mode == 'append' and fmode not in ('ab+', 'rb+')) or
                    (mode == 'ostream' and
                     not ('w' in fmode or 'a' in fmode or '+' in fmode)) or
                    (mode == 'update' and fmode not in ('rb+', 'wb+'))):
                raise ValueError(
                    "Mode argument '%s' does not match mode of the input "
                    "file (%s)." % (mode, fmode))
            self.__file = fileobj
        elif isfile(fileobj):
            self.__file = fileobj_open(self.name, PYFITS_MODES[mode])
        else:
            self.__file = gzip.open(self.name, PYFITS_MODES[mode])

        if fmode == 'ab+':
            # Return to the beginning of the file--in Python 3 when opening in
            # append mode the file pointer is at the end of the file
            self.__file.seek(0)

    def _open_filelike(self, fileobj, mode, clobber):
        """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 IOError("Cannot read from/write to a closed file-like "
                          "object (%r)." % fileobj)

        if isinstance(fileobj, zipfile.ZipFile):
            self._open_zipfile(fileobj, mode)
            self.__file.seek(0)
            # 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(clobber, 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 IOError("File-like object does not have a 'write' "
                          "method, required for mode '%s'."
                          % self.mode)

        # Any mode except for 'ostream' requires readability
        if self.mode != 'ostream' and not hasattr(self.__file, 'read'):
            raise IOError("File-like object does not have a 'read' "
                          "method, required for mode %r."
                          % self.mode)

    def _open_filename(self, filename, mode, clobber):
        """Open a FITS file from a filename string."""

        if mode == 'ostream':
            self._overwrite_existing(clobber, None, True)

        if os.path.exists(self.name):
            with fileobj_open(self.name, 'rb') as f:
                magic = f.read(4)
        else:
            magic = ''.encode('raw-unicode-escape')

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

        if ext == '.gz' or magic.startswith(GZIP_MAGIC):
            # Handle gzip files
            self.__file = gzip.open(self.name, PYFITS_MODES[mode])
            self.compression = 'gzip'
        elif ext == '.zip' or magic.startswith(PKZIP_MAGIC):
            # Handle zip files
            self._open_zipfile(self.name, mode)
        else:
            self.__file = fileobj_open(self.name, PYFITS_MODES[mode])
            # Make certain we're back at the beginning of the file
        self.__file.seek(0)

    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 IOError(
                  "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 IOError(
              "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()
        self.compression = 'zip'

    def _test_mmap(self):
        """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.
        """

        if self._mmap_available is not None:
            return self._mmap_available

        tmpfd, tmpname = tempfile.mkstemp()
        try:
            # Windows does not allow mappings on empty files
            os.write(tmpfd, encode_ascii(' '))
            os.fsync(tmpfd)
            try:
                mm = mmap.mmap(tmpfd, 1, access=mmap.ACCESS_WRITE)
            except mmap.error as e:
                warnings.warn('Failed to create mmap: %s; mmap use will be '
                              'disabled' % str(e))
                _File._mmap_available = False
                return False
            try:
                mm.flush()
            except mmap.error:
                warnings.warn('mmap.flush is unavailable on this platform; '
                              'using mmap in writeable mode will be disabled')
                _File._mmap_available = False
                return False
            finally:
                mm.close()
        finally:
            os.close(tmpfd)
            os.remove(tmpname)

        _File._mmap_available = True
        return True


def _is_random_access_file_backed(fileobj):
    """Returns `True` if fileobj is a `file` or `io.FileIO` object or a
    `gzip.GzipFile` object.

    Although reading from a zip file is supported, this does not include
    support for random access, and we do not yet support reading directly
    from an already opened `zipfile.ZipFile` object.
    """

    return isfile(fileobj) or isinstance(fileobj, gzip.GzipFile)