def get_rois(self, imageId):
try:
rois = []
roiService = self._connection.getRoiService()
result = roiService.findByImage(long(imageId), None, self._connection.SERVICE_OPTS)
for r in result.rois:
roi = {}
roi['id'] = r.getId().getValue()
# go through all the shapes of the ROI
shapes = []
for s in r.copyShapes():
if s is None: # seems possible in some situations
continue
shapes.append(shapeMarshal(s))
# sort shapes by Z, then T.
shapes.sort(
key=lambda x: "%03d%03d"
% (x.get('theZ', -1), x.get('theT', -1)))
roi['shapes'] = shapes
rois.append(roi)
rois.sort(key=lambda x: x['id'])
return rois
except Exception as e:
print e
return None
def testInsightPolygonMarshal(self):
shape = omero.model.PolygonI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring("points[1,2 2,3 4,5] points1[1,2 2,3 4,5] points2[1,2 2,3 4,5] mask[0,0,0]")
marshaled = shapeMarshal(shape)
self.assertEqual("Polygon", marshaled["type"])
self.assertEqual(self.DEFAULT_ID, marshaled["id"])
self.assertEquals("M 1 2 L 2 3 L 4 5 z", marshaled["points"])
def testOmeXmlPolygonMarshal(self):
shape = omero.model.PolygonI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring("1,2 2,3 4,5")
marshaled = shapeMarshal(shape)
self.assertEqual("Polygon", marshaled["type"])
self.assertEqual(self.DEFAULT_ID, marshaled["id"])
self.assertEquals("M 1 2 L 2 3 L 4 5 z", marshaled["points"])
def testOmeXmlPolyLineFloatMarshal(self):
shape = omero.model.PolylineI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring("1.5,2.5 2,3 4.1,5.1")
marshaled = shapeMarshal(shape)
self.assertEqual("PolyLine", marshaled["type"])
self.assertEqual(self.DEFAULT_ID, marshaled["id"])
self.assertEquals("M 1.5 2.5 L 2 3 L 4.1 5.1", marshaled["points"])
def testOmeXmlPolyLineMarshal(self):
shape = omero.model.PolylineI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring('1,2 2,3 4,5')
marshaled = shapeMarshal(shape)
self.assertEqual('PolyLine', marshaled['type'])
self.assertEqual(self.DEFAULT_ID, marshaled['id'])
self.assertEquals('M 1 2 L 2 3 L 4 5' , marshaled['points'])
def _roi_to_json(roi_object):
return {
'id': roi_object.getId().getValue(),
'shapes': [shapeMarshal(s) for s in roi_object.copyShapes()]
}
def test_point_marshal(self, basic_point):
marshaled = shapeMarshal(basic_point)
self.assert_marshal(marshaled, 'Point')
assert 0.0 == marshaled['x']
assert 0.1 == marshaled['y']
def test_polygon_marshal(self, basic_polygon):
marshaled = shapeMarshal(basic_polygon)
self.assert_marshal(marshaled, 'Polygon')
assert 'M 1 2 L 2 3 L 4 5 z' == marshaled['points']
def test_polyline_marshal(self, basic_polyline):
marshaled = shapeMarshal(basic_polyline)
self.assert_marshal(marshaled, 'PolyLine')
assert 'M 1 2 L 2 3 L 4 5' == marshaled['points']
def testShapeUnrecognisedRoiShapePointsString(self):
shape = omero.model.PolygonI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring('')
marshaled = shapeMarshal(shape)
self.assertEquals(' z', marshaled['points'])
def test_point_marshal(self, basic_point):
marshaled = shapeMarshal(basic_point)
self.assert_marshal(marshaled, "Point")
assert 0.0 == marshaled["x"]
assert 0.1 == marshaled["y"]
def test_polygon_marshal(self, basic_polygon):
marshaled = shapeMarshal(basic_polygon)
self.assert_marshal(marshaled, "Polygon")
assert "M 1 2 L 2 3 L 4 5 z" == marshaled["points"]
def test_polyline_float_marshal(self, float_polyline):
marshaled = shapeMarshal(float_polyline)
self.assert_marshal(marshaled, "PolyLine")
assert "M 1.5 2.5 L 2 3 L 4.1 5.1" == marshaled["points"]
def test_polyline_marshal(self, basic_polyline):
marshaled = shapeMarshal(basic_polyline)
self.assert_marshal(marshaled, "PolyLine")
assert "M 1 2 L 2 3 L 4 5" == marshaled["points"]
def test_arrow_marshal(self, basic_arrow):
marshaled = shapeMarshal(basic_arrow)
self.assert_marshal(marshaled, "Line")
assert marshaled["markerStart"] == "Arrow"
assert marshaled["markerEnd"] == "Arrow"
def testShapeUnrecognisedRoiShapePointsString(self):
shape = omero.model.PolygonI()
shape.id = rlong(self.DEFAULT_ID)
shape.points = rstring("")
marshaled = shapeMarshal(shape)
self.assertEquals(" z", marshaled["points"])
def test_arrow_marshal(self, basic_arrow):
marshaled = shapeMarshal(basic_arrow)
self.assert_marshal(marshaled, 'Line')
assert marshaled['markerStart'] == 'Arrow'
assert marshaled['markerEnd'] == 'Arrow'
def test_ployline_marshal(self, basic_polyline):
marshaled = shapeMarshal(basic_polyline)
self.assert_polyline(marshaled)
assert 'M 1 2 L 2 3 L 4 5' == marshaled['points']
def test_polyline_float_marshal(self, float_polyline):
marshaled = shapeMarshal(float_polyline)
self.assert_marshal(marshaled, 'PolyLine')
assert 'M 1.5 2.5 L 2 3 L 4.1 5.1' == marshaled['points']
def test_polyline_float_marshal(self, float_polyline):
marshaled = shapeMarshal(float_polyline)
self.assert_polyline(marshaled)
assert 'M 1.5 2.5 L 2 3 L 4.1 5.1' == marshaled['points']
def test_unrecognised_roi_shape_points_string(self, empty_polygon):
marshaled = shapeMarshal(empty_polygon)
assert ' z' == marshaled['points']
def test_polygon_marshal(self, basic_polygon):
marshaled = shapeMarshal(basic_polygon)
self.assert_polygon(marshaled)
assert 'M 1 2 L 2 3 L 4 5 z' == marshaled['points']
def _roi_to_json(roi_object):
return {
'id': roi_object.getId().getValue(),
'shapes': [shapeMarshal(s) for s in roi_object.copyShapes()]
}
def test_unrecognised_roi_shape_points_string(self, empty_polygon):
marshaled = shapeMarshal(empty_polygon)
assert ' z' == marshaled['points']