def ellipse():
o = EllipseI()
populate_shape(o)
if SCHEMA_VERSION == "2015-01":
o.cx = rdouble(1.0)
o.cy = rdouble(2.0)
o.rx = rdouble(3.0)
o.ry = rdouble(4.0)
else:
o.x = rdouble(1.0)
o.y = rdouble(2.0)
o.radiusX = rdouble(3.0)
o.radiusY = rdouble(4.0)
o.id = rlong(1L)
return o
def __init__(self, shape = None):
ShapeData.__init__(self);
if(shape==None):
self.setValue(EllipseI());
self.setCx(0);
self.setCy(0);
self.setRx(0);
self.setRy(0);
else:
self.setValue(shape);
def __init__(self, shape=None):
ShapeData.__init__(self)
if(shape is None):
self.setValue(EllipseI())
self.setCx(0)
self.setCy(0)
self.setRx(0)
self.setRy(0)
else:
self.setValue(shape)
def __init__(self, shape=None):
ShapeData.__init__(self)
if (shape is None):
self.setValue(EllipseI())
self.setX(0)
self.setY(0)
self.setRadiusX(0)
self.setRadiusY(0)
else:
self.setValue(shape)
def ellipse():
o = EllipseI()
populate_shape(o)
o.cx = rdouble(1.0)
o.cy = rdouble(2.0)
o.rx = rdouble(3.0)
o.ry = rdouble(4.0)
o.id = rlong(1L)
return o
def shapes(self):
"""Create a bunch of unsaved Shapes."""
rect = RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(20)
rect.width = rdouble(30)
rect.height = rdouble(40)
# Only save theT, not theZ
rect.theT = rint(0)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
# ellipse without saving theZ & theT
ellipse = EllipseI()
ellipse.x = rdouble(33)
ellipse.y = rdouble(44)
ellipse.radiusX = rdouble(55)
ellipse.radiusY = rdouble(66)
ellipse.textValue = rstring("test-Ellipse")
line = LineI()
line.x1 = rdouble(200)
line.x2 = rdouble(300)
line.y1 = rdouble(400)
line.y2 = rdouble(500)
line.textValue = rstring("test-Line")
point = PointI()
point.x = rdouble(1)
point.y = rdouble(1)
point.theZ = rint(1)
point.theT = rint(1)
point.textValue = rstring("test-Point")
polygon = PolygonI()
polygon.theZ = rint(5)
polygon.theT = rint(5)
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 200,200, 250,75"
polygon.points = rstring(points)
mask = MaskI()
mask.setTheC(rint(0))
mask.setTheZ(rint(0))
mask.setTheT(rint(0))
mask.setX(rdouble(100))
mask.setY(rdouble(100))
mask.setWidth(rdouble(500))
mask.setHeight(rdouble(500))
mask.setTextValue(rstring("test-Mask"))
mask.setBytes(None)
return [rect, ellipse, line, point, polygon, mask]
def ellipse_with_annotations():
o = EllipseI()
populate_shape(o)
add_annotations(o)
o.cx = rdouble(1.0)
o.cy = rdouble(2.0)
o.rx = rdouble(3.0)
o.ry = rdouble(4.0)
o.id = rlong(1L)
return o
def ellipse():
o = EllipseI()
populate_shape(o)
o.cx = rdouble(1.0)
o.cy = rdouble(2.0)
o.rx = rdouble(3.0)
o.ry = rdouble(4.0)
o.id = rlong(1L)
return o
def ellipse_with_annotations():
o = EllipseI()
populate_shape(o)
add_annotations(o)
o.cx = rdouble(1.0)
o.cy = rdouble(2.0)
o.rx = rdouble(3.0)
o.ry = rdouble(4.0)
o.id = rlong(1L)
return o
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]
def shapes(self):
"""Create a bunch of unsaved Shapes."""
rect = RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(20)
rect.width = rdouble(30)
rect.height = rdouble(40)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
ellipse = EllipseI()
ellipse.x = rdouble(33)
ellipse.y = rdouble(44)
ellipse.radiusX = rdouble(55)
ellipse.radiusY = rdouble(66)
ellipse.textValue = rstring("test-Ellipse")
line = LineI()
line.x1 = rdouble(20)
line.x2 = rdouble(30)
line.y1 = rdouble(40)
line.y2 = rdouble(50)
line.textValue = rstring("test-Line")
point = PointI()
point.x = rdouble(50)
point.y = rdouble(50)
point.textValue = rstring("test-Point")
polygon = PolygonI()
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 100,100, 150,75"
polygon.points = rstring(points)
polyline = PolylineI()
polyline.points = rstring(points)
return [rect, ellipse, line, point, polygon, polyline]
def createBaseType(self):
return EllipseI()
def createBaseType(self):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
return EllipseI()
def create_omero_shape(shape_type, data, image):
# "line", "path", "polygon", "rectangle", "ellipse"
# NB: assume all points on same plane.
# Use first point to get Z and T index
z_index = get_z(data[0], image)
t_index = get_t(data[0], image)
shape = None
if shape_type == "line":
shape = LineI()
shape.x1 = rdouble(get_x(data[0]))
shape.y1 = rdouble(get_y(data[0]))
shape.x2 = rdouble(get_x(data[1]))
shape.y2 = rdouble(get_y(data[1]))
shape.textValue = rstring("line-from-napari")
elif shape_type == "path" or shape_type == "polygon":
shape = PolylineI() if shape_type == "path" else PolygonI()
# points = "10,20, 50,150, 200,200, 250,75"
points = ["%s,%s" % (get_x(d), get_y(d)) for d in data]
shape.points = rstring(", ".join(points))
shape.textValue = rstring("polyline-from-napari") if shape_type == "path" else rstring("polygon-from-napari")
elif shape_type == "rectangle" or shape_type == "ellipse":
# corners go anti-clockwise starting top-left
x1 = get_x(data[0])
x2 = get_x(data[1])
x3 = get_x(data[2])
x4 = get_x(data[3])
y1 = get_y(data[0])
y2 = get_y(data[1])
y3 = get_y(data[2])
y4 = get_y(data[3])
print(x1,x2)
if shape_type == "rectangle":
# Rectangle not rotated
if x1 == x2:
shape = RectangleI()
# TODO: handle 'updside down' rectangle x3 < x1
shape.x = rdouble(x1)
shape.y = rdouble(y1)
shape.width = rdouble(x3 - x1)
shape.height = rdouble(y2 - y1)
else:
# Rotated Rectangle - save as Polygon
shape = PolygonI()
points = "%s,%s, %s,%s, %s,%s, %s,%s" % (
x1, y1, x2, y2, x3, y3, x4, y4
)
shape.points = rstring(points)
shape.textValue = rstring("rectangle-from-napari")
elif shape_type == "ellipse":
# Ellipse not rotated (ignore floating point rouding)
if int(x1) == int(x2):
shape = EllipseI()
shape.x = rdouble((x1 + x3) / 2)
shape.y = rdouble((y1 + y2) / 2)
shape.radiusX = rdouble(abs(x3 - x1) / 2)
shape.radiusY = rdouble(abs(y2 - y1) / 2)
else:
# TODO: Need to calculate transformation matrix
print("Rotated Ellipse not yet supported!")
shape.textValue = rstring("ellipse-from-napari")
if shape is not None:
shape.theZ = rint(z_index)
shape.theT = rint(t_index)
return shape
def ellipse():
o = EllipseI()
populate_shape(o)
if SCHEMA_VERSION == '2015-01':
o.cx = rdouble(1.0)
o.cy = rdouble(2.0)
o.rx = rdouble(3.0)
o.ry = rdouble(4.0)
else:
o.x = rdouble(1.0)
o.y = rdouble(2.0)
o.radiusX = rdouble(3.0)
o.radiusY = rdouble(4.0)
o.id = rlong(1L)
return o
