低倍率パッチ切り取り時にずれが生じる問題

 def bb_to_patch(
      self,
      default_level,
      level,
      size,
      stride,
      bb,
      output_main_dir,
      contours_th=0.5,
  ):  # size=(width, height)
    assert isinstance(bb, dict), "bb(bounding-box) must be dict type"
    obj_name = bb['name']

    # bbのx, yをlevel0用に変換（bbはbg_mask_level05における座標のため）
    bx_wsi_0 = bb['x'] * (2 ** default_level)  # bounding-boxの左上x座標(level0)
    by_wsi_0 = bb['y'] * (2 ** default_level) # bounding-boxの左上y座標(level0)

    # bbのw, hを特定のlevel用に変換
    bw_wsi = bb['w'] * (2 ** (default_level - level))  # bounding-boxの横幅(level)
    bh_wsi = bb['h'] * (2 ** (default_level - level))  # bounding-boxの縦幅(level)

    row_max = int((bw_wsi - size[0]) / stride + 1)
    column_max = int((bh_wsi - size[1]) / stride + 1)

    # 細胞領域のマスク画像，背景領域のマスク画像の１ピクセルが特定のレベルのWSIの何ピクセルに相当するか計算
    stride_rate = stride / 2 ** (default_level - level)
    width_rate = size[0] / 2 ** (default_level - level)
    height_rate = size[1] / 2 ** (default_level - level)

    assert self.filename_semantic_mask is not None, "Should set filename_semantic_mask"
    semantic_mask = Image.open(self.filename_semantic_mask)
    semantic_mask_np = np.array(semantic_mask)
    assert self.filename_bg_mask is not None, "Should set filename_bg_mask"
    bg_mask_np = np.array(Image.open(self.filename_bg_mask))

    cnt = 0
    for column in range(column_max):
        for row in range(row_max):
            i = int(bx_wsi_0 + (row * stride * (2 ** level)))
            j = int(by_wsi_0 + (column * stride * (2 ** level)))

            mask_base_idx = {'row': int(bb['x'] + (row * stride_rate)),
                             'col': int(bb['y'] + (column * stride_rate))}

            # width_rate×height_rateの領域(背景領域のマスク画像)の画素値が0の画素数で比較
            if (
                len(
                    np.where(
                        bg_mask_np[
                            mask_base_idx['col']:int(mask_base_idx['col'] + height_rate),
                            mask_base_idx['row']:int(mask_base_idx['row'] + width_rate),
                        ]
                        == 0
                    )[0]
                )
                >= contours_th * height_rate * width_rate
            ):
                # width_rate×height_rateの領域(semanticマスク)の画素値が255以外(背景以外)の画素数で比較
                if (
                    len(
                        np.where(
                            semantic_mask_np[
                                mask_base_idx['col']:int(mask_base_idx['col'] + height_rate),
                                mask_base_idx['row']:int(mask_base_idx['row'] + width_rate),
                            ]
                            != 255
                        )[0]
                    )
                    >= contours_th * height_rate * width_rate
                ):

                    s_p = semantic_mask_np[
                        mask_base_idx['col']:int(mask_base_idx['col'] + height_rate),
                        mask_base_idx['row']:int(mask_base_idx['row'] + width_rate)
                    ]

                    output_dir = self._get_output_dir(
                        s_p, output_main_dir, obj_name)

                    if output_dir is not None:
                        self.read_region((i, j), level, size).save(
                            output_dir
                            + str(level)
                            + "_"
                            + str(cnt).zfill(10)
                            + ".png"
                        )
                        cnt = cnt + 1
KengoAraki / WSI_Predmap

低倍率パッチ切り取り時にずれが生じる問題 #1
