Frame

PIMS returns images as Frame objects. Frames can be treated precisely the same as numpy arrays.

They are a subclass of numpy.ndarray, adding two new attributes:

• frame_no, an integer

• metadata, a dictionary

These can be used by the PIMS readers to provide any metadata stored in the image files. Setting these attributes is optional.

IPython Rich Display

Frame objects hook into IPython’s rich display framework. In IPython notebooks, 2D Frames are displayed as actual images. 3D Frames (“Z stacks”) are displayed as a stack of images. The user can scroll through the images with the scroll wheel.

Caveats

As with a numpy array, if some mathematical operation reduces a Frame to a scalar, the output is a standard Python scalar. Any extra attributes are discarded.

In [1]: from pims import Frame

In [2]: frame = Frame(np.ones((5, 5)))

In [3]: frame
Out[3]: 
Frame([[1., 1., 1., 1., 1.],
       [1., 1., 1., 1., 1.],
       [1., 1., 1., 1., 1.],
       [1., 1., 1., 1., 1.],
       [1., 1., 1., 1., 1.]])

In [4]: frame.sum()
Out[4]: 25.0

Warning

Propagating metadata is a hard problem, and it is not one that PIMS has not yet solved. If you combine two Frames in, for example, addition, the metadata of the left object is propagated. This will be addressed in a future release of PIMS.