def search_cells(self, prediction_mask, img):
if self.edge_only:
if self.return_mask:
cells, prediction_mask = mask_to_cells_edge(
prediction_mask,
img,
self.config,
self.r_min,
self.frame_data,
self.edge_dist,
return_mask=self.return_mask)
else:
cells = mask_to_cells_edge(prediction_mask,
img,
self.config,
self.r_min,
self.frame_data,
self.edge_dist,
return_mask=self.return_mask)
else:
cells = mask_to_cells(prediction_mask, img, self.config,
self.r_min, self.frame_data, self.edge_dist)
return prediction_mask, cells
def segmentation(self, img):
if len(img.shape) == 3:
img = img[:, :, 0]
img = (img - np.mean(img)) / np.std(img).astype(np.float32)
prob_map = self.unet.predict(img[None, :, :, None])[0, :, :, 0]
prediction_mask = prob_map > 0.5
cells = mask_to_cells(prediction_mask, img, self.config, self.r_min, self.frame_data, self.edge_dist)
return prediction_mask, cells, prob_map
def load_polygones(cdb, img_o, ny, nx, points, im, config, r_min, frame_data, edge_dist, irr_th=1.06, sol_th=0.96):
# Loading ellipses/cells from ClickPoints polygon markers.
q_polys = cdb.getPolygons(image=img_o)
mask = np.zeros(img_o.getShape()[0:2], dtype=np.uint8)
for pol in q_polys:
polygon = np.array([pol.points])
if len(polygon[0]) > 5: # Ground Truth may contain accidentally clicked small polygons
path = Path(polygon.squeeze())
grid = path.contains_points(points)
grid = grid.reshape((ny, nx))
mask += grid
cells = mask_to_cells(mask, im, config, r_min, frame_data, edge_dist)
cells_filtered = filter_cells(cells, irr_th, sol_th)
ellipses = np.array(
[[cell["y"], cell["x"], cell["long_axis"], cell["short_axis"], cell["angle"], getStrain(cell)] for cell
in cells])
ellipses_filtered = np.array(
[[cell["y"], cell["x"], cell["long_axis"], cell["short_axis"], cell["angle"], getStrain(cell)] for cell
in cells_filtered])
return mask, ellipses, ellipses_filtered, q_polys
def getMaskEllipse(self, frame):
try:
mask = self.db.getMask(frame=frame).data
im = self.db.getImages(frame=frame)[0]
except AttributeError:
mask_shape = (self.ny, self.nx)
mask = np.zeros(mask_shape, dtype=np.uint8)
img_o = self.db.getImage(frame=frame)
q_polys = self.db.getPolygons(image=img_o)
for pol in q_polys:
if np.shape(pol)[0] != 0:
polygon = np.array([[pol.points]])
if np.sum(
polygon.shape
) > 7: # single point polygon can happen on accident when clicking
path = Path(polygon.squeeze())
grid = path.contains_points(self.points)
grid = grid.reshape(mask_shape)
mask += grid
cells = mask_to_cells(mask, im.data, self.config, self.r_min,
self.frame_data, self.edge_dist)
return mask, cells
