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add resolve_rois to projectwrapper #92

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add resolve_rois to projectwrapper #92

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55 changes: 54 additions & 1 deletion src/omero_metadata/populate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -302,7 +302,7 @@ def _create_columns(self, klass):
self.DEFAULT_COLUMN_SIZE, list()))
# Ensure ImageColumn is named "Image"
column.name = "Image"
if column.__class__ is RoiColumn and target_class != DatasetI:
if column.__class__ is RoiColumn and target_class != DatasetI and target_class != ProjectI:
append.append(StringColumn(ROI_NAME_COLUMN, '',
self.DEFAULT_COLUMN_SIZE, list()))
# Ensure RoiColumn is named 'Roi'
Expand Down Expand Up @@ -879,6 +879,8 @@ def __init__(self, value_resolver):
self.images_by_name = defaultdict(lambda: dict())
self.datasets_by_id = dict()
self.datasets_by_name = dict()
self.rois_by_id = None
self.shapes_by_id = None
self._load()

def get_image_id_by_name(self, iname, dname=None):
Expand All @@ -887,6 +889,57 @@ def get_image_id_by_name(self, iname, dname=None):
def get_image_name_by_id(self, iid, did=None):
return self.images_by_id[did][iid].name.val

def resolve_roi(self, column, row, value):
# Support Project table with known ROI IDs
if self.rois_by_id is None:
self._load_rois()
try:
return self.rois_by_id[int(value)].id.val
except KeyError:
log.warning('Project is missing ROI: %s' % value)
return -1
except ValueError:
log.warning('Wrong input type for ROI ID: %s' % value)
return -1

def _load_rois(self):
log.debug('Loading ROIs in Project:%d' % self.target_object.id.val)
self.rois_by_id = {}
self.shapes_by_id = {}
query_service = self.client.getSession().getQueryService()
parameters = omero.sys.ParametersI()
parameters.addId(self.target_object.id.val)
data = list()
while True:
parameters.page(len(data), 1000)
rv = unwrap(query_service.projection((
'select distinct i, r, s '
'from Shape s '
'join s.roi as r '
'join r.image as i '
'join i.datasetLinks as dil '
'join dil.parent as d '
'join d.projectLinks as pdl '
'join pdl.parent as p '
'where p.id = :id order by s.id desc'),
parameters, {'omero.group': '-1'}))
if len(rv) == 0:
break
else:
data.extend(rv)
if not data:
raise MetadataError("No ROIs on images in target Project")

for image, roi, shape in data:
# we only care about *IDs* of ROIs and Shapes in the Dataset
rid = roi.id.val
sid = shape.id.val
self.rois_by_id[rid] = roi
self.shapes_by_id[sid] = shape

log.debug('Completed loading ROIs and Shapes in Project: %s'
% self.target_object.id.val)

def resolve_dataset(self, column, row, value):
try:
if column.name.lower() == 'dataset':
Expand Down