.. -*- rst -*- 

.. _image-formats:

=====================
 Images and  formats
=====================

The Image object contains (*has a*) Format object.

The Image and the Format objects form a `bridge pattern
<http://en.wikipedia.org/wiki/Bridge_pattern>`_.  In the `wikipedia
diagram
<http://en.wikipedia.org/wiki/File:Bridge_UML_class_diagram.svg>`_ the
Image class plays the role of the Abstraction, and the Format plays the
role of the implementor.

The Format object provides an interface to the underlying file format. 

The Image has the following methods:

* img.get_data()
* img.save(fname)

It has attributes:

* affine
* world
* io_dtype
* format

We get the data with ``get_data()``, rather than via an attribute, to
reflect that fact that the data is read-only, and to flag the common
case where the data load is delayed until the data is used.  The object
can decide what it does about data caching between calls of
``get_data()``.  Another option is to make the data a cached property or
single-shot data descriptor; I prefer using the method call, for
simplicity, and to make clear that the data load may take a long time.

Example code::

   import numpy as np
   from nibabel import Image
   from nibabel.formats import Nifti1
   from nibabel.ref import mni
   arr = np.arange(24).reshape(2,3,4)
   img = Image(data = arr)
   assert img.affine is None
   assert img.world is None
   img.affine = np.eye(4)
   img.world = mni
   data = img.get_data()
   assert data.shape == (2,3,4)
   assert np.all(data == arr)
   # The format object is Nifti1 by default.  It's also empty
   assert img.format.fields == Nifti1().fields
   img.save('some_file.nii')


Note the decoupling between the information carried by the format, and
the information in the ``img`` instance.  The format instance, carries
the format, as instantiated by loading from disk, or object creation,
and is only updated on ``img.save(fname)``.  This is to allow formats
that cannot encode either affine or world information.  If you want to
manipulate fields or other information in the specific format, you
probably want to instantiate the format object directly (see below).


Format objects
==============

The API of the format object encapsulates two things:

* the shared interface to underlying image formats that is used by ``Image``
* format-specific attributes and calls

The API required by ``Image`` is:

* fmt.get_affine()
* fmt.set_affine(aff)
* fmt.get_world()
* fmt.set_world(world)
* fmt.get_io_dtype()
* fmt.set_io_dtype(dtype)
* fmt.read_data()
* fmt.write_data(arr)
* fmt.to_filename(fname)
* fmt.from_filename()

The last to save the format to the file(s) given by ``fname``.  We may
also want the ability to write to sets of file objects, for testing, and
for abstraction of the base writing layer.

* fmt.to_filemap(fmap)
* fmt.from_filemap(fmap)

where ``fmap`` is a class, currently called ``FileTuple`` that contains
mappings of file meanings (like ``image`` or ``header``) to file
objects.

With this model, we may often find ourselves using the Format object for
format-specific tasks::

   from nibabel.formats import Nifti1
   fmt = Nifti1.from_filename('some_file.nii')
   fmt.set_qform(np.eye(4))
   fmt.set_sform(np.eye(4) * 2)
   fmt.fields['descrip'] = 'some information'
   fmt.to_filename('another_file.nii')



