# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## # # See COPYING file distributed along with the NiBabel package for the # copyright and license terms. # ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## ''' 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())