diff --git a/situr/image/situ_tile.py b/situr/image/situ_tile.py index 9d8e215..60063cb 100644 --- a/situr/image/situ_tile.py +++ b/situr/image/situ_tile.py @@ -1,8 +1,11 @@ +from situr.transformation.round_transformation import RoundTransform import numpy as np from situr.image.situ_image import SituImage from situr.transformation import IdentityRoundTransform +from typing import List + class Tile: ''' @@ -13,7 +16,7 @@ class Tile: X 2048 ''' - def __init__(self, file_list, nucleaus_channel=4): + def __init__(self, file_list: List[List[List[str]]], nucleaus_channel: int = 4): self.images = [] self.round_transformations = [] for situ_image_list in file_list: @@ -33,35 +36,31 @@ class Tile: # TODO: implement pass - def get_image_round(self, round): - return self.images[round] - - def set_round_transformation(self, round, transformation): + def set_round_transformation(self, round, transformation: RoundTransform): self.round_transformations[round] = transformation - def get_round_count(self): + def get_round_count(self) -> int: return len(self.images) - def get_channel_count(self): + def get_channel_count(self) -> int: return self.images[0].get_channel_count() - def get_round(self, round_number): - """This + def get_round(self, round_number: int) -> SituImage: + """This methods returns the round based on round number Args: - round_number (integer): The round number starting with 0 + round_number (int): The round number (starting with index 0) Returns: SituImage: The image corresponding to the requested round number. """ - return self.images[id] + return self.images[round_number] - def to_numpy_array(self): + def to_numpy_array(self) -> np.ndarray: tmp_list = [] for image in self.images: tmp_list.append(image.get_data()) - return np.array(tmp_list) - def get_channel(self, round, channel, focus_level=0): + def get_channel(self, round: int, channel: int, focus_level: int = 0) -> np.ndarray: return self.images[round].get_channel(channel, focus_level=focus_level)