python-nibabel 1.2.2-1 / usr / share / pyshared / nibabel / spatialimages.py

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''' Very simple spatial image class

The image class maintains the association between a 3D (or greater)
array, and an affine transform that maps voxel coordinates to some real
world space.  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.

It has attributes:

   * extra

methods:

   * .get_data()
   * .get_affine()
   * .get_header()
   * .set_shape(shape)
   * .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.
   * .get_shape() (Deprecated)

properties:

   * shape

classmethods:

   * from_filename(fname) - make instance by loading from filename
   * instance_to_filename(img, fname) - save ``img`` instance to
     filename ``fname``.

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 ``files`` 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 of::

    img.get_data()

Less commonly, for some image types that support it, you might want to
fetch out the unscaled array via the header::

    unscaled_data = img.get_unscaled_data()

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.get_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 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:

   >>> # write an image to files
   >>> from StringIO import StringIO #23dt : BytesIO
   >>> file_map = nib.AnalyzeImage.make_file_map()
   >>> file_map['image'].fileobj = StringIO() #23dt : BytesIO
   >>> file_map['header'].fileobj = StringIO() #23dt : BytesIO
   >>> img = nib.AnalyzeImage(data, np.eye(4))
   >>> img.file_map = file_map
   >>> img.to_file_map()
   >>> # read it back again from the written files
   >>> img2 = nib.AnalyzeImage.from_file_map(file_map)
   >>> np.all(img2.get_data() == data)
   True
   >>> # write, read it again
   >>> img2.to_file_map()
   >>> img3 = nib.AnalyzeImage.from_file_map(file_map)
   >>> np.all(img3.get_data() == data)
   True

'''

import warnings

import numpy as np

from .filename_parser import types_filenames, TypesFilenamesError
from .fileholders import FileHolder
from .volumeutils import shape_zoom_affine


class HeaderDataError(Exception):
    ''' Class to indicate error in getting or setting header data '''
    pass


class HeaderTypeError(Exception):
    ''' Class to indicate error in parameters into header functions '''
    pass


class Header(object):
    ''' Template class to implement header protocol '''
    default_x_flip = True

    def __init__(self,
                 data_dtype=np.float32,
                 shape=(0,),
                 zooms=None):
        self.set_data_dtype(data_dtype)
        self._zooms = ()
        self.set_data_shape(shape)
        if not zooms is None:
            self.set_zooms(zooms)

    @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 it's parent
        # - for example Nifti1Images inherit from Analyze, but have
        # different field names
        if type(header) == klass:
            return header.copy()
        return klass(header.get_data_dtype(),
                     header.get_data_shape(),
                     header.get_zooms())

    @classmethod
    def from_fileobj(klass, fileobj):
        raise NotImplementedError

    def write_to(self, fileobj):
        raise NotImplementedError

    def __eq__(self, other):
        return ((self.get_data_dtype(),
                 self.get_data_shape(),
                 self.get_zooms()) ==
                (other.get_data_dtype(),
                 other.get_data_shape(),
                 other.get_zooms()))

    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.
        '''
        return self.__class__(self._dtype, self._shape, self._zooms)

    def get_data_dtype(self):
        return self._dtype

    def set_data_dtype(self, dtype):
        self._dtype = np.dtype(dtype)

    def get_data_shape(self):
        return self._shape

    def set_data_shape(self, shape):
        ndim = len(shape)
        if ndim == 0:
            self._shape = (0,)
            self._zooms = (1.0,)
            return
        self._shape = tuple([int(s) for s in shape])
        # set any unset zooms to 1.0
        nzs = min(len(self._zooms), ndim)
        self._zooms = self._zooms[:nzs] + (1.0,) * (ndim-nzs)

    def get_zooms(self):
        return self._zooms

    def set_zooms(self, zooms):
        zooms = tuple([float(z) for z in zooms])
        shape = self.get_data_shape()
        ndim = len(shape)
        if len(zooms) != ndim:
            raise HeaderDataError('Expecting %d zoom values for ndim %d'
                                  % (ndim, ndim))
        if len([z for z in zooms if z < 0]):
            raise HeaderDataError('zooms must be positive')
        self._zooms = zooms

    def get_base_affine(self):
        shape = self.get_data_shape()
        zooms = self.get_zooms()
        return shape_zoom_affine(shape, zooms,
                                 self.default_x_flip)

    get_default_affine = get_base_affine

    def data_to_fileobj(self, data, fileobj):
        ''' Write image data to file in fortran order '''
        dtype = self.get_data_dtype()
        fileobj.write(data.astype(dtype).tostring(order='F'))

    def data_from_fileobj(self, fileobj):
        ''' Read data in fortran order '''
        dtype = self.get_data_dtype()
        shape = self.get_data_shape()
        data_size = int(np.prod(shape) * dtype.itemsize)
        data_bytes = fileobj.read(data_size)
        return np.ndarray(shape, dtype, data_bytes, order='F')


class ImageDataError(Exception):
    pass


class ImageFileError(Exception):
    pass


class SpatialImage(object):
    header_class = Header
    files_types = (('image', None),)
    _compressed_exts = ()

    ''' Template class for images '''
    def __init__(self, data, affine, header=None,
                 extra=None, file_map=None):
        ''' Initialize image

        The image is a combination of (array, affine matrix, header), with
        optional metadata in `extra`, and filename / file-like objects contained
        in the `file_map` mapping.

        Parameters
        ----------
        data : object
           image data.  It should be some object that retuns an array
           from ``np.asanyarray``.  It should have a ``shape`` attribute or
           property
        affine : None or (4,4) array-like
           homogenous affine giving relationship between voxel coordinates and
           world coordinates.  Affine can also be None.  In this case,
           ``obj.get_affine()`` also returns None, and the affine as written to
           disk will depend on the file format.
        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
        '''
        self._data = data
        if not affine is None:
            # Check that affine is array-like 4,4.  Maybe this is too strict at
            # this abstract level, but so far I think all image formats we know
            # do need 4,4.
            # Copy affine to  isolate from environment.  Specify float type to
            # avoid surprising integer rounding when setting values into affine
            affine = np.array(affine, dtype=np.float64, copy=True)
            if not affine.shape == (4,4):
                raise ValueError('Affine should be shape 4,4')
        self._affine = affine
        if extra is None:
            extra = {}
        self.extra = extra
        self._header = self.header_class.from_header(header)
        # if header not specified, get data type from input array
        if header is None:
            if hasattr(data, 'dtype'):
                self._header.set_data_dtype(data.dtype)
        # make header correspond with image and affine
        self.update_header()
        if file_map is None:
            file_map = self.__class__.make_file_map()
        self.file_map = file_map
        self._load_cache = None

    def update_header(self):
        ''' Update header from information in image'''
        self._header.set_data_shape(self._data.shape)

    def __str__(self):
        shape = self.shape
        affine = self.get_affine()
        return '\n'.join((
                str(self.__class__),
                'data shape %s' % (shape,),
                'affine: ',
                '%s' % affine,
                'metadata:',
                '%s' % self._header))

    def get_data(self):
        return np.asanyarray(self._data)

    @property
    def shape(self):
        return self._data.shape

    def get_shape(self):
        """ Return shape for image

        This function deprecated; please use the ``shape`` property instead
        """
        warnings.warn('Please use the shape property instead of get_shape',
                      DeprecationWarning,
                      stacklevel=2)
        return self.shape

    def get_data_dtype(self):
        return self._header.get_data_dtype()

    def set_data_dtype(self, dtype):
        self._header.set_data_dtype(dtype)

    def get_affine(self):
        return self._affine

    def get_header(self):
        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_filespec(klass, filespec):
        warnings.warn('``from_filespec`` class method is deprecated\n'
                      'Please use the ``from_filename`` class method '
                      'instead',
                      DeprecationWarning, stacklevel=2)
        klass.from_filename(filespec)

    @classmethod
    def from_file_map(klass, file_map):
        raise NotImplementedError

    @classmethod
    def from_files(klass, file_map):
        warnings.warn('``from_files`` class method is deprecated\n'
                      'Please use the ``from_file_map`` class method '
                      'instead',
                      DeprecationWarning, stacklevel=2)
        return klass.from_file_map(file_map)

    @classmethod
    def filespec_to_file_map(klass, filespec):
        try:
            filenames = types_filenames(filespec,
                                        klass.files_types,
                                        trailing_suffixes=klass._compressed_exts)
        except TypesFilenamesError:
            raise ImageFileError('Filespec "%s" does not look right for '
                             'class %s ' % (filespec, klass))
        file_map = {}
        for key, fname in filenames.items():
            file_map[key] = FileHolder(filename=fname)
        return file_map

    @classmethod
    def filespec_to_files(klass, filespec):
        warnings.warn('``filespec_to_files`` class method is deprecated\n'
                      'Please use the ``filespec_to_file_map`` class method '
                      'instead',
                      DeprecationWarning, stacklevel=2)
        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()

    def to_filespec(self, filename):
        warnings.warn('``to_filespec`` is deprecated, please '
                      'use ``to_filename`` instead',
                      DeprecationWarning, stacklevel=2)
        self.to_filename(filename)

    def to_file_map(self, file_map=None):
        raise NotImplementedError

    def to_files(self, file_map=None):
        warnings.warn('``to_files`` method is deprecated\n'
                      'Please use the ``to_file_map`` method '
                      'instead',
                      DeprecationWarning, stacklevel=2)
        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, basestring):
                file_map[key].filename = mapval
            elif hasattr(mapval, 'tell'):
                file_map[key].fileobj = mapval
        return file_map

    @classmethod
    def load(klass, filename):
        return klass.from_filename(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 : ``spatialimage`` instance
           In fact, an object with the API of ``spatialimage`` -
           specifically ``get_data``, ``get_affine``, ``get_header`` and
           ``extra``.
        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 ``spatialimage`` -
           specifically ``get_data``, ``get_affine``, ``get_header`` and
           ``extra``.

        Returns
        -------
        cimg : ``spatialimage`` instance
           Image, of our own class
        '''
        return klass(img.get_data(),
                     img.get_affine(),
                     klass.header_class.from_header(img.get_header()),
                     extra=img.extra.copy())