def __get_oriented_image(self, cell, image_stack):
x0 = int(round(cell.x - (self.rescaled_cube_width / 2)))
x1 = int(x0 + self.rescaled_cube_width)
y0 = int(round(cell.y - (self.rescaled_cube_height / 2)))
y1 = int(y0 + self.rescaled_cube_height)
image = image_stack[:, y0:y1, x0:x1]
image = np.moveaxis(image, 0, 2)
if self.augment:
# scale to isotropic, but don't scale back
image = augment(self.augmentation_parameters,
image,
scale_back=False)
pixel_scalings = [
self.cube_height / image.shape[0],
self.cube_width / image.shape[1],
self.cube_depth / image.shape[2],
]
# TODO: ensure this is always the correct size
image = zoom(image, pixel_scalings, order=self.interpolation_order)
return image
def __get_oriented_image(self, image_path):
# if paths are pathlib objs, skimage only reads one plane
image = np.moveaxis(imread(image_path), 0, 2)
if self.augment:
image = augment(self.augmentation_parameters, image)
return image