diff --git a/src/cDNA_segmentation.py b/src/cDNA_segmentation.py index 878c56a..4f07e9e 100644 --- a/src/cDNA_segmentation.py +++ b/src/cDNA_segmentation.py @@ -203,27 +203,36 @@ def gridding(gray: np.ndarray) -> tuple: # 第四部分:后处理(参考choice.m, choosemaxobj.m) # ============================================================ -def remove_small_objects(binary: np.ndarray, cell_area: int = 1225, pct: float = 0.02) -> np.ndarray: - """去除面积小于 cell_area*pct 的连通域(pct默认2%)""" - min_size = int(cell_area * pct) +def remove_small_objects(binary: np.ndarray) -> np.ndarray: + """ + 自动去除小连通域。 + + 统计所有连通域的面积中位数,小于中位数 25% 的视为噪声, + 自动剔除,不需要人设定阈值。 + """ labeled, num = ndimage.label(binary) + if num == 0: + return binary + + # 统计每个连通域的面积 + areas = [int(np.sum(labeled == i)) for i in range(1, num + 1)] + median_area = np.median(areas) + min_size = max(1, int(median_area * 0.25)) # 中位数的25%,最少1像素 + result = binary.copy() for i in range(1, num + 1): - if np.sum(labeled == i) < min_size: + if areas[i - 1] < min_size: result[labeled == i] = 0 return result -def keep_largest_object(binary: np.ndarray, cell_area: int = 1225, pct: float = 0.01) -> np.ndarray: - """只保留最大连通域,若最大块面积 < cell_area*pct 则整块抹黑(pct默认1%)""" - min_size = int(cell_area * pct) +def keep_largest_object(binary: np.ndarray) -> np.ndarray: + """每个格子里只保留面积最大的连通域(无需设定阈值)""" labeled, num = ndimage.label(binary) if num == 0: - return binary - areas = [int(np.sum(labeled == i)) for i in range(1, num + 1)] - max_area = max(areas) - if max_area < min_size: return np.zeros_like(binary) + + areas = [int(np.sum(labeled == i)) for i in range(1, num + 1)] max_idx = int(np.argmax(areas)) + 1 return (labeled == max_idx).astype(np.uint8) @@ -375,11 +384,6 @@ def main() -> None: # ---- 步骤3: 全图逐块分割(Otsu + TV去噪) ---- print("\n[步骤3] 全图逐块分割...") - # 计算每个格子的面积,用于自适应后处理阈值 - cell_h = int(np.median(np.diff(y_grid))) if len(y_grid) > 1 else 35 - cell_w = int(np.median(np.diff(x_grid))) if len(x_grid) > 1 else 35 - cell_area = cell_h * cell_w - bw_full = np.zeros_like(gray) if len(x_grid) >= 2 and len(y_grid) >= 2: for i in range(len(y_grid) - 1): @@ -403,12 +407,12 @@ def main() -> None: bw_blk = (blk_denoised > T).astype(np.uint8) except ValueError: bw_blk = np.zeros(blk.shape, dtype=np.uint8) - # 后处理:保留最大连通域(最小面积 = 格子面积的1%) - bw_blk = keep_largest_object(bw_blk, cell_area=cell_area) + # 后处理:保留最大连通域(无需阈值) + bw_blk = keep_largest_object(bw_blk) bw_full[r1:r2, c1:c2] = bw_blk - # 全局去小连通域(最小面积 = 格子面积的2%) - bw_full = remove_small_objects(bw_full, cell_area=cell_area) + # 全局去除小连通域(中位数的25%以下自动判为噪声) + bw_full = remove_small_objects(bw_full) fig_full = plot_full_segmentation(gray, bw_full, "全图逐块Otsu分割结果") fig_full.savefig(os.path.join(OUTPUT_DIR, 'result_full_segmentation.png'), dpi=150, bbox_inches='tight')