OMERO ROIs¶
OMERO Python library providing utilities for handling regions of interest.
-
exception
omero_rois.
NoMaskFound
(msg='No mask found')[source]¶ Exception thrown when no foreground pixels were found in a mask
-
exception
omero_rois.
InvalidBinaryImage
(msg='Invalid labels found')[source]¶ Exception thrown when invalid labels are found
-
omero_rois.
mask_from_binary_image
(binim, rgba=None, z=None, c=None, t=None, text=None, raise_on_no_mask=True)[source]¶ Create a mask shape from a binary image (background=0)
Parameters: - binim (numpy.array) – Binary 2D array, must contain values [0, 1] only
- int-4-tuple (rgba) – Optional (red, green, blue, alpha) colour
- z – Optional Z-index for the mask
- c – Optional C-index for the mask
- t – Optional T-index for the mask
- text – Optional text for the mask
- raise_on_no_mask – If True (default) throw an exception if no mask found, otherwise return an empty Mask
Returns: An OMERO mask
Raises: - NoMaskFound – If no labels were found
- InvalidBinaryImage – If the maximum labels is greater than 1
-
omero_rois.
masks_from_label_image
(labelim, rgba=None, z=None, c=None, t=None, text=None, raise_on_no_mask=True)[source]¶ Create mask shapes from a label image (background=0)
Parameters: - labelim (numpy.array) – 2D label array
- int-4-tuple (rgba) – Optional (red, green, blue, alpha) colour
- z – Optional Z-index for the mask
- c – Optional C-index for the mask
- t – Optional T-index for the mask
- text – Optional text for the mask
- raise_on_no_mask – If True (default) throw an exception if no mask found, otherwise return an empty Mask
Returns: A list of OMERO masks in label order ([] if no labels found)