import pathlib
import warnings
[docs]class ROIManagerWarning(UserWarning):
"""Used for unexpected keyword arguments."""
pass
class ROIManager(object):
def __init__(self, identifier=None):
"""Manage regions of interest (ROI) of an image series
Parameters
----------
identifier: str or None
The identifier of the image series.
"""
if not (isinstance(identifier, str) or identifier is None):
raise ValueError("`identifier` must be `None` or a string!")
self.identifier = identifier
self.rois = []
def __len__(self):
return self.rois.__len__()
def add(self, roislice, image_index, roi_index, identifier):
"""Add a ROI to ROIManager
Parameters
----------
roislice: (slice, slice)
Two slices indicating the x- and y-axis limits.
image_index: int
The image index of the image series.
roi_index: int
The ROI index in image `image_index`
identifier: str
The ROI identifier. If `self.identifier` is not contained
within `identifier`, a `ROIManagerWarning` will be issued.
"""
# verify identifier
if not isinstance(identifier, str):
raise ValueError("`identifier` must be a string!")
if self.identifier and self.identifier not in identifier:
msg = "Identifier of ROIManager `{}` ".format(self.identifier) \
+ "does not match that of QPSeries `{}`.".format(identifier)
warnings.warn(msg, ROIManagerWarning)
# verify roislice
if not (isinstance(roislice, (tuple, list))
and len(roislice) == 2
and isinstance(roislice[0], slice)
and isinstance(roislice[1], slice)):
raise ValueError("`roislice` must be a tuple of two slices!")
self.rois.append((identifier, image_index, roi_index, roislice))
def get_from_image_index(self, image_index):
rois = [[r[0], r[3]] for r in self.rois if r[1] == image_index]
return rois
def load(self, path):
"""Load ROIs from a text file"""
path = pathlib.Path(path)
with path.open(mode="r") as fd:
lines = fd.readlines()
# remove empty lines
lines = [ll for ll in lines if ll.strip()]
for ll in lines:
ll = ll.strip().split("\t")
sldata = "".join([c for c in ll[3] if c in ",0123456789"])
sldata = sldata.replace(",,", ",").split(",")
sldata = [int(s) for s in sldata if s]
slice1 = slice(min(sldata[0], sldata[1]),
max(sldata[0], sldata[1]))
slice2 = slice(min(sldata[2], sldata[3]),
max(sldata[2], sldata[3]))
self.add(identifier=ll[0],
image_index=int(ll[1]),
roi_index=int(ll[2]),
roislice=(slice1, slice2)
)
def save(self, path):
"""Save ROIs to a text file (`path` will be overridden)"""
path = pathlib.Path(path)
with path.open(mode="w") as fd:
for roi in self.rois:
roi = [str(r) for r in roi]
fd.write("\t".join(roi) + "\r\n")