def _parse_neo_roi(self, columns):
"""Parses out ROI from OmeroTables columns for 'NEO' datasets."""
log.debug("Parsing %s NEO ROIs..." % (len(columns[0].values)))
image_ids = columns[self.IMAGE_COL].values
rois = list()
# Save our file annotation to the database so we can use an unloaded
# annotation for the saveAndReturnIds that will be triggered below.
self.file_annotation = \
self.update_service.saveAndReturnObject(self.file_annotation)
unloaded_file_annotation = \
FileAnnotationI(self.file_annotation.id.val, False)
batch_no = 1
batches = dict()
for i, image_id in enumerate(image_ids):
unloaded_image = ImageI(image_id, False)
roi = RoiI()
shape = EllipseI()
values = columns[6].values
diameter = rdouble(float(values[i]))
shape.theZ = rint(0)
shape.theT = rint(0)
values = columns[4].values
shape.cx = rdouble(float(values[i]))
values = columns[3].values
shape.cy = rdouble(float(values[i]))
shape.rx = diameter
shape.ry = diameter
roi.addShape(shape)
roi.image = unloaded_image
roi.linkAnnotation(unloaded_file_annotation)
rois.append(roi)
if len(rois) == self.ROI_UPDATE_LIMIT:
self.thread_pool.add_task(
self.update_rois, rois, batches, batch_no)
rois = list()
batch_no += 1
self.thread_pool.add_task(self.update_rois, rois, batches, batch_no)
self.thread_pool.wait_completion()
batch_keys = batches.keys()
batch_keys.sort()
for k in batch_keys:
columns[self.ROI_COL].values += batches[k]
