def main(mask, connectivity=8, plot=False):
'''Labels objects in a binary image, i.e. assigns to all pixels of a
connected component an identifier number that is unique for each object
in the image.
Parameters
----------
mask: numpy.ndarray[Union[numpy.bool, numpy.int32]]
binary image that should labeled
connectivity: int, optional
whether a diagonal (``4``) or square (``8``) neighborhood should be
considered (default: ``8``, options: ``{4, 8}``)
plot: bool, optional
whether a plot should be generated (default: ``False``)
Returns
-------
jtmodules.label.Output[Union[numpy.ndarray, str]]
Note
----
If `mask` is not binary, it will be binarized, i.e. pixels will be set to
``True`` if values are greater than zero and ``False`` otherwise.
'''
mask = mask > 0
label_image = label(mask, connectivity)
n = len(np.unique(label_image)[1:])
logger.info('identified %d objects', n)
if plot:
from jtlib import plotting
plots = [
plotting.create_mask_image_plot(mask, 'ul'),
plotting.create_mask_image_plot(label_image, 'ur')
]
figure = plotting.create_figure(plots, title='Labeled image')
else:
figure = str()
return Output(label_image, figure)
def main(mask):
'''Registers objects (connected pixel components) in an image for use by
other (measurement) modules downstream in the pipeline. In case a binary
mask is provided the image is automatically labeled.
Parameters
----------
mask: numpy.ndarray[Union[numpy.bool, numpy.uint16]]
binary or labeled mask
Returns
-------
jtmodules.register_objects.Output
See also
--------
:class:`tmlib.workflow.jterator.handles.SegmentedObjects`
'''
if mask.dtype == 'bool':
label_image = label(mask)
else:
label_image = mask
label_image = label_image.astype(np.int32)
return Output(label_image)
def main(mask):
'''Registers objects (connected pixel components) in an image for use by
other (measurement) modules downstream in the pipeline. In case a binary
mask is provided the image is automatically labeled.
Parameters
----------
mask: numpy.ndarray[Union[numpy.bool, numpy.int32]]
binary or labeled mask
Returns
-------
jtmodules.register_objects.Output
See also
--------
:class:`tmlib.workflow.jterator.handles.SegmentedObjects`
'''
if mask.dtype == 'bool':
label_image = label(mask)
else:
label_image = mask
return Output(label_image)