/usr/lib/python2.7/dist-packages/nibabel/filebasedimages.py is in python-nibabel 2.1.0-1.
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#
# See COPYING file distributed along with the NiBabel package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
''' Common interface for any image format--volume or surface, binary or xml.'''
from .externals.six import string_types
from .fileholders import FileHolder
from .filename_parser import (types_filenames, TypesFilenamesError,
splitext_addext)
from .openers import ImageOpener
from .deprecated import deprecate_with_version
class ImageFileError(Exception):
pass
class FileBasedHeader(object):
''' Template class to implement header protocol '''
@classmethod
def from_header(klass, header=None):
if header is None:
return klass()
# I can't do isinstance here because it is not necessarily true
# that a subclass has exactly the same interface as its parent
# - for example Nifti1Images inherit from Analyze, but have
# different field names
if type(header) == klass:
return header.copy()
raise NotImplementedError("Header class requires a conversion"
" from %s to %s" % (klass, type(header)))
@classmethod
def from_fileobj(klass, fileobj):
raise NotImplementedError
def write_to(self, fileobj):
raise NotImplementedError
def __eq__(self, other):
raise NotImplementedError
def __ne__(self, other):
return not self == other
def copy(self):
''' Copy object to independent representation
The copy should not be affected by any changes to the original
object.
'''
raise NotImplementedError
class FileBasedImage(object):
'''
Abstract image class with interface for loading/saving images from disk.
The class doesn't define any image properties.
It has:
attributes:
* extra
properties:
* shape
* header
methods:
* .get_header() (deprecated, use header property instead)
* .to_filename(fname) - writes data to filename(s) derived from
``fname``, where the derivation may differ between formats.
* to_file_map() - save image to files with which the image is already
associated.
classmethods:
* from_filename(fname) - make instance by loading from filename
* from_file_map(fmap) - make instance from file map
* instance_to_filename(img, fname) - save ``img`` instance to
filename ``fname``.
It also has a ``header`` - some standard set of meta-data that is specific
to the image format, and ``extra`` - a dictionary container for any other
metadata.
You cannot slice an image, and trying to slice an image generates an
informative TypeError.
**There are several ways of writing data**
There is the usual way, which is the default::
img.to_filename(fname)
and that is, to take the data encapsulated by the image and cast it to
the datatype the header expects, setting any available header scaling
into the header to help the data match.
You can load the data into an image from file with::
img.from_filename(fname)
The image stores its associated files in its ``file_map`` attribute. In
order to just save an image, for which you know there is an associated
filename, or other storage, you can do::
img.to_file_map()
You can get the data out again with::
img.get_data()
Less commonly, for some image types that support it, you might want to
fetch out the unscaled array via the object containing the data::
unscaled_data = img.dataoobj.get_unscaled()
Analyze-type images (including nifti) support this, but others may not
(MINC, for example).
Sometimes you might to avoid any loss of precision by making the
data type the same as the input::
hdr = img.header
hdr.set_data_dtype(data.dtype)
img.to_filename(fname)
**Files interface**
The image has an attribute ``file_map``. This is a mapping, that has keys
corresponding to the file types that an image needs for storage. For
example, the Analyze data format needs an ``image`` and a ``header``
file type for storage:
>>> import numpy as np
>>> import nibabel as nib
>>> data = np.arange(24, dtype='f4').reshape((2,3,4))
>>> img = nib.AnalyzeImage(data, np.eye(4))
>>> sorted(img.file_map)
['header', 'image']
The values of ``file_map`` are not in fact files but objects with
attributes ``filename``, ``fileobj`` and ``pos``.
The reason for this interface, is that the contents of files has to
contain enough information so that an existing image instance can save
itself back to the files pointed to in ``file_map``. When a file holder
holds active file-like objects, then these may be affected by the
initial file read; in this case, the contains file-like objects need to
carry the position at which a write (with ``to_files``) should place the
data. The ``file_map`` contents should therefore be such, that this will
work:
'''
header_class = FileBasedHeader
_meta_sniff_len = 0
files_types = (('image', None),)
valid_exts = ()
_compressed_suffixes = ()
makeable = True # Used in test code
rw = True # Used in test code
def __init__(self, header=None, extra=None, file_map=None):
''' Initialize image
The image is a combination of (header), with
optional metadata in `extra`, and filename / file-like objects
contained in the `file_map` mapping.
Parameters
----------
header : None or mapping or header instance, optional
metadata for this image format
extra : None or mapping, optional
metadata to associate with image that cannot be stored in the
metadata of this image type
file_map : mapping, optional
mapping giving file information for this image format
'''
if header or self.header_class:
self._header = self.header_class.from_header(header)
else:
self._header = None
if extra is None:
extra = {}
self.extra = extra
if file_map is None:
file_map = self.__class__.make_file_map()
self.file_map = file_map
@property
def header(self):
return self._header
def __getitem__(self):
''' No slicing or dictionary interface for images
'''
raise TypeError("Cannot slice image objects.")
@deprecate_with_version('get_header method is deprecated.\n'
'Please use the ``img.header`` property '
'instead.',
'2.1', '4.0')
def get_header(self):
""" Get header from image
"""
return self.header
def get_filename(self):
''' Fetch the image filename
Parameters
----------
None
Returns
-------
fname : None or str
Returns None if there is no filename, or a filename string.
If an image may have several filenames assoctiated with it
(e.g Analyze ``.img, .hdr`` pair) then we return the more
characteristic filename (the ``.img`` filename in the case of
Analyze')
'''
# which filename is returned depends on the ordering of the
# 'files_types' class attribute - we return the name
# corresponding to the first in that tuple
characteristic_type = self.files_types[0][0]
return self.file_map[characteristic_type].filename
def set_filename(self, filename):
''' Sets the files in the object from a given filename
The different image formats may check whether the filename has
an extension characteristic of the format, and raise an error if
not.
Parameters
----------
filename : str
If the image format only has one file associated with it,
this will be the only filename set into the image
``.file_map`` attribute. Otherwise, the image instance will
try and guess the other filenames from this given filename.
'''
self.file_map = self.__class__.filespec_to_file_map(filename)
@classmethod
def from_filename(klass, filename):
file_map = klass.filespec_to_file_map(filename)
return klass.from_file_map(file_map)
@classmethod
def from_file_map(klass, file_map):
raise NotImplementedError
@classmethod
@deprecate_with_version('from_files class method is deprecated.\n'
'Please use the ``from_file_map`` class method '
'instead.',
'1.0', '3.0')
def from_files(klass, file_map):
return klass.from_file_map(file_map)
@classmethod
def filespec_to_file_map(klass, filespec):
""" Make `file_map` for this class from filename `filespec`
Class method
Parameters
----------
filespec : str
Filename that might be for this image file type.
Returns
-------
file_map : dict
`file_map` dict with (key, value) pairs of (``file_type``,
FileHolder instance), where ``file_type`` is a string giving the
type of the contained file.
Raises
------
ImageFileError
if `filespec` is not recognizable as being a filename for this
image type.
"""
try:
filenames = types_filenames(
filespec, klass.files_types,
trailing_suffixes=klass._compressed_suffixes)
except TypesFilenamesError:
raise ImageFileError(
'Filespec "{0}" does not look right for class {1}'.format(
filespec, klass))
file_map = {}
for key, fname in filenames.items():
file_map[key] = FileHolder(filename=fname)
return file_map
@classmethod
@deprecate_with_version('filespec_to_files class method is deprecated.\n'
'Please use the "filespec_to_file_map" class '
'method instead.',
'1.0', '3.0')
def filespec_to_files(klass, filespec):
return klass.filespec_to_file_map(filespec)
def to_filename(self, filename):
''' Write image to files implied by filename string
Parameters
----------
filename : str
filename to which to save image. We will parse `filename`
with ``filespec_to_file_map`` to work out names for image,
header etc.
Returns
-------
None
'''
self.file_map = self.filespec_to_file_map(filename)
self.to_file_map()
@deprecate_with_version('to_filespec method is deprecated.\n'
'Please use the "to_filename" method instead.',
'1.0', '3.0')
def to_filespec(self, filename):
self.to_filename(filename)
def to_file_map(self, file_map=None):
raise NotImplementedError
@deprecate_with_version('to_files method is deprecated.\n'
'Please use the "to_file_map" method instead.',
'1.0', '3.0')
def to_files(self, file_map=None):
self.to_file_map(file_map)
@classmethod
def make_file_map(klass, mapping=None):
''' Class method to make files holder for this image type
Parameters
----------
mapping : None or mapping, optional
mapping with keys corresponding to image file types (such as
'image', 'header' etc, depending on image class) and values
that are filenames or file-like. Default is None
Returns
-------
file_map : dict
dict with string keys given by first entry in tuples in
sequence klass.files_types, and values of type FileHolder,
where FileHolder objects have default values, other than
those given by `mapping`
'''
if mapping is None:
mapping = {}
file_map = {}
for key, ext in klass.files_types:
file_map[key] = FileHolder()
mapval = mapping.get(key, None)
if isinstance(mapval, string_types):
file_map[key].filename = mapval
elif hasattr(mapval, 'tell'):
file_map[key].fileobj = mapval
return file_map
load = from_filename
@classmethod
def instance_to_filename(klass, img, filename):
''' Save `img` in our own format, to name implied by `filename`
This is a class method
Parameters
----------
img : ``any FileBasedImage`` instance
filename : str
Filename, implying name to which to save image.
'''
img = klass.from_image(img)
img.to_filename(filename)
@classmethod
def from_image(klass, img):
''' Class method to create new instance of own class from `img`
Parameters
----------
img : ``spatialimage`` instance
In fact, an object with the API of ``FileBasedImage``.
Returns
-------
cimg : ``spatialimage`` instance
Image, of our own class
'''
raise NotImplementedError()
@classmethod
def _sniff_meta_for(klass, filename, sniff_nbytes, sniff=None):
""" Sniff metadata for image represented by `filename`
Parameters
----------
filename : str
Filename for an image, or an image header (metadata) file.
If `filename` points to an image data file, and the image type has
a separate "header" file, we work out the name of the header file,
and read from that instead of `filename`.
sniff_nbytes : int
Number of bytes to read from the image or metadata file
sniff : (bytes, fname), optional
The result of a previous call to `_sniff_meta_for`. If fname
matches the computed header file name, `sniff` is returned without
rereading the file.
Returns
-------
sniff : None or (bytes, fname)
None if we could not read the image or metadata file. `sniff[0]`
is either length `sniff_nbytes` or the length of the image /
metadata file, whichever is the shorter. `fname` is the name of
the sniffed file.
"""
froot, ext, trailing = splitext_addext(filename,
klass._compressed_suffixes)
# Determine the metadata location
t_fnames = types_filenames(
filename,
klass.files_types,
trailing_suffixes=klass._compressed_suffixes)
meta_fname = t_fnames.get('header', filename)
# Do not re-sniff if it would be from the same file
if sniff is not None and sniff[1] == meta_fname:
return sniff
# Attempt to sniff from metadata location
try:
with ImageOpener(meta_fname, 'rb') as fobj:
binaryblock = fobj.read(sniff_nbytes)
except IOError:
return None
return (binaryblock, meta_fname)
@classmethod
def path_maybe_image(klass, filename, sniff=None, sniff_max=1024):
""" Return True if `filename` may be image matching this class
Parameters
----------
filename : str
Filename for an image, or an image header (metadata) file.
If `filename` points to an image data file, and the image type has
a separate "header" file, we work out the name of the header file,
and read from that instead of `filename`.
sniff : None or (bytes, filename), optional
Bytes content read from a previous call to this method, on another
class, with metadata filename. This allows us to read metadata
bytes once from the image or header, and pass this read set of
bytes to other image classes, therefore saving a repeat read of the
metadata. `filename` is used to validate that metadata would be
read from the same file, re-reading if not. None forces this
method to read the metadata.
sniff_max : int, optional
The maximum number of bytes to read from the metadata. If the
metadata file is long enough, we read this many bytes from the
file, otherwise we read to the end of the file. Longer values
sniff more of the metadata / image file, making it more likely that
the returned sniff will be useful for later calls to
``path_maybe_image`` for other image classes.
Returns
-------
maybe_image : bool
True if `filename` may be valid for an image of this class.
sniff : None or (bytes, filename)
Read bytes content from found metadata. May be None if the file
does not appear to have useful metadata.
"""
froot, ext, trailing = splitext_addext(filename,
klass._compressed_suffixes)
if ext.lower() not in klass.valid_exts:
return False, sniff
if not hasattr(klass.header_class, 'may_contain_header'):
return True, sniff
# Force re-sniff on too-short sniff
if sniff is not None and len(sniff[0]) < klass._meta_sniff_len:
sniff = None
sniff = klass._sniff_meta_for(filename,
max(klass._meta_sniff_len, sniff_max),
sniff)
if sniff is None or len(sniff[0]) < klass._meta_sniff_len:
return False, sniff
return klass.header_class.may_contain_header(sniff[0]), sniff
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