figured out how to decode the binary data in an nd2 file
Info below also present in the readme for anyone who stumbles on this PR:
The ND2File.binary_data property returns an nd2.BinaryLayers object representing all of the
binary masks in the nd2 file.
A nd2.BinaryLayers object is a sequence of individual nd2.BinaryLayer
objects (one for each binary layer found in the file). Each BinaryLayer in
the sequence is a named tuple that has, among other things, a name attribute,
and a data attribute that is list of numpy arrays (one for each frame in the
experiment) or None if the binary layer had no data in that frame.
The most common use case will be to cast either the entire BinaryLayers object
or an individual BinaryLayer to a numpy.ndarray:
>>> import nd2
>>> nd2file = nd2.ND2File('path/to/file.nd2')
>>> binary_layers = nd2file.binary_data
# The output array will have shape
# (n_binary_layers, *coord_shape, *frame_shape).
>>> np.asarray(binary_layers)
For example, if the data in the nd2 file has shape (nT, nZ, nC, nY, nX), and
there are 4 binary layers, then the output of np.asarray(nd2file.binary_data) will
have shape (4, nT, nZ, nY, nX). (Note that the nC dimension is not present
in the output array, and the binary layers are always in the first axis).
You can also cast an individual BinaryLayer to a numpy array:
figured out how to decode the binary data in an nd2 file
Info below also present in the readme for anyone who stumbles on this PR:
The
ND2File.binary_dataproperty returns annd2.BinaryLayersobject representing all of the binary masks in the nd2 file.A
nd2.BinaryLayersobject is a sequence of individualnd2.BinaryLayerobjects (one for each binary layer found in the file). EachBinaryLayerin the sequence is a named tuple that has, among other things, anameattribute, and adataattribute that is list of numpy arrays (one for each frame in the experiment) orNoneif the binary layer had no data in that frame.The most common use case will be to cast either the entire
BinaryLayersobject or an individualBinaryLayerto anumpy.ndarray:For example, if the data in the nd2 file has shape
(nT, nZ, nC, nY, nX), and there are 4 binary layers, then the output ofnp.asarray(nd2file.binary_data)will have shape(4, nT, nZ, nY, nX). (Note that thenCdimension is not present in the output array, and the binary layers are always in the first axis).You can also cast an individual
BinaryLayerto a numpy array: