# Licensed under a 3-clause BSD style license - see PYFITS.rst from __future__ import division, with_statement import bz2 import gzip import mmap import operator import os import sys import tempfile import warnings import zipfile from functools import reduce import numpy as np from numpy import memmap as Memmap from .util import (isreadable, iswritable, isfile, fileobj_open, fileobj_name, fileobj_closed, fileobj_mode, _array_from_file, _array_to_file, _write_string) from ...extern.six import b, string_types from ...utils.data import download_file, _is_url from ...utils.decorators import classproperty, deprecated_renamed_argument from ...utils.exceptions import AstropyUserWarning # 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'} # 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 = b('\x1f\x8b\x08') PKZIP_MAGIC = b('\x50\x4b\x03\x04') BZIP2_MAGIC = b('\x42\x5a') try: import pathlib except ImportError: HAS_PATHLIB = False else: HAS_PATHLIB = True class _File(object): """ Represents a FITS file on disk (or in some other file-like object). """ @deprecated_renamed_argument('clobber', 'overwrite', '2.0') def __init__(self, fileobj=None, mode=None, memmap=None, overwrite=False, cache=True): self.strict_memmap = bool(memmap) memmap = True if memmap is None else memmap 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 self.close_on_error = False return else: self.simulateonly = False # If fileobj is of type pathlib.Path if HAS_PATHLIB and isinstance(fileobj, pathlib.Path): fileobj = str(fileobj) # Holds mmap instance for files that use mmap self._mmap = None 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 IO_FITS_MODES: raise ValueError("Mode '{}' not recognized".format(mode)) if (isinstance(fileobj, string_types) and mode not in ('ostream', 'append') and _is_url(fileobj)): # This is an URL. self.name = download_file(fileobj, cache=cache) 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 # Should the object be closed on error: see # https://github.com/astropy/astropy/issues/6168 self.close_on_error = 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, overwrite) elif isinstance(fileobj, string_types): 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 isinstance(fileobj, bz2.BZ2File): self.compression = 'bzip2' 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 def __repr__(self): return '<{}.{} {}>'.format(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 {} not a multiple of {}'.format(size, 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 = np.prod(shape) * dtype.itemsize if actualsize > size: raise ValueError('size {} is too few bytes for a {} array of ' '{}'.format(size, shape, dtype)) elif actualsize < size: raise ValueError('size {} is too many bytes for a {} array of ' '{}'.format(size, shape, 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) memmap = Memmap(self._file, mode=MEMMAP_MODES[self.mode], dtype=np.uint8) # Now we immediately discard the memmap array; we are # really just using it as a factory function to instantiate # the mmap object in a convenient way (may later do away # with this usage) self._mmap = memmap.base # Prevent dorking with self._memmap._mmap by memmap.__del__ # in Numpy 1.6 (see # https://github.com/numpy/numpy/commit/dcc355a0b179387eeba10c95baf2e1eb21d417c7) memmap._mmap = None del memmap return np.ndarray(shape=shape, dtype=dtype, offset=offset, buffer=self._mmap) else: count = reduce(operator.mul, shape) self._file.seek(offset) data = _array_from_file(self._file, dtype, count) data.shape = shape return data 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 self._file.seek(filepos) 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 ' '({}) is smaller than the expected size ({})'.format( self.size, pos), AstropyUserWarning) 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._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. """ if (self._mmap is not None 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 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 overwrite: 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.".format(self.name)) def _open_fileobj(self, fileobj, mode, overwrite): """Open a FITS file from a file object or a GzipFile object.""" closed = fileobj_closed(fileobj) fmode = fileobj_mode(fileobj) or IO_FITS_MODES[mode] if mode == 'ostream': self._overwrite_existing(overwrite, fileobj, closed) if not closed: # Although we have a specific mapping in IO_FITS_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 '{}' does not match mode of the input " "file ({}).".format(mode, fmode)) self._file = fileobj elif isfile(fileobj): self._file = fileobj_open(self.name, IO_FITS_MODES[mode]) else: self._file = gzip.open(self.name, IO_FITS_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, 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 IOError("Cannot read from/write to a closed file-like " "object ({!r}).".format(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(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 IOError("File-like object does not have a 'write' " "method, required for mode '{}'.".format(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}.".format(self.mode)) 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 fileobj_open(self.name, 'rb') as f: magic = f.read(4) else: magic = b('') ext = os.path.splitext(self.name)[1] if ext == '.gz' or magic.startswith(GZIP_MAGIC): # Handle gzip files self._file = gzip.open(self.name, IO_FITS_MODES[mode]) self.compression = 'gzip' elif ext == '.zip' or magic.startswith(PKZIP_MAGIC): # Handle zip files self._open_zipfile(self.name, mode) elif ext == '.bz2' or magic.startswith(BZIP2_MAGIC): # Handle bzip2 files if mode in ['update', 'append']: raise IOError("update and append modes are not supported " "with bzip2 files") # bzip2 only supports 'w' and 'r' modes bzip2_mode = 'w' if mode == 'ostream' else 'r' self._file = bz2.BZ2File(self.name, bzip2_mode) else: self._file = fileobj_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 isinstance(self._file, bz2.BZ2File) and mode == 'ostream': pass else: 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 mmap.error as exc: warnings.warn('Failed to create mmap: {}; mmap use will be ' 'disabled'.format(str(exc)), AstropyUserWarning) del exc 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', 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 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 _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)