在语义分割和实例分割数据集中,标注数据一般给定的是分割图 - mask 或 rle.

从分割标注数据中提取矩形框(bounding boxes)信息.

1. RLE 标注数据

1.1. binary mask to rle

https://www.kaggle.com/paulorzp/run-length-encode-and-decode

import numpy as np 

def rle_encode(binary_mask):
    '''
    binary_mask: numpy array, 1 - mask, 0 - background
    Returns run length as string formated
    '''
    pixels = binary_mask.T.flatten()
    pixels = np.concatenate([[0], pixels, [0]])
    runs = np.where(pixels[1:] != pixels[:-1])[0] + 1
    runs[1::2] -= runs[::2]
    
    return ' '.join(str(x) for x in runs)

1.2. rle to binary mask

def rle_decode(rle_mask, shape=(768, 768)):
    '''
    rle_mask: run-length as string formated (start length)
    shape: (height,width) of array to return 
    Returns numpy array, 1 - mask, 0 - background
    '''
    s = rle_mask.split()
    starts, lengths = [np.asarray(x, dtype=int) for x in (s[0:][::2], s[1:][::2])]
    starts -= 1
    ends = starts + lengths
    binary_mask = np.zeros(shape[0]*shape[1], dtype=np.uint8)
    for lo, hi in zip(starts, ends):
        binary_mask[lo:hi] = 1
        
    return binary_mask.reshape(shape).T  # Needed to align to RLE direction

1.3. rle masks to mask

# 将各个独立的 masks 合并到单个 mask array
def masks_as_image(rle_masks_list, all_masks=None):
    if all_masks is None:
        all_masks = np.zeros((768, 768), dtype = np.int16)
    
    assert isinstance(rle_masks_list, list):
    for rle_mask in rle_masks_list:
        if isinstance(rle_mask, str):
            all_masks += rle_decode(rle_mask)
            
    return np.expand_dims(all_masks, -1)

### 1.4. rle to bounding boxes

RLE 标注数据提取矩形边界框(bounding box) 主要包含如下步骤:

[1] - 采用 masks_as_image 将 RLE mask 转换为 Binary numpy array ;

[2] - 采用 skimage.measure.label 获取 mask 的连通区域(connected regions);

[3] - 采用 skimage.measure.regionprops 度量连通区域的形态学特征(morphological properties) 并得到矩形框(bounding box). 对于每个连通区域的矩形框格式为:(min_row, min_col, max_row, max_col).

如:

from skimage.measure import label as sk_label
from skimage.measure import regionprops as sk_regions

# rle masks.
mask = masks_as_image(rle_masks)
# 
sk_mask = sk_label(mask) 
regions = sk_regions(sk_mask)
for region in regions:
    print('[INFO]bbox: ', region.bbox)
    top, left, bottom, right = region.bbox

注: 这里可能会将互相重叠的主体 masks 误处理为一个,得到错误的矩形框. 可以采用逐个连通区域来处理.

如:

from skimage.measure import regionprops as sk_regions

# rle masks.
for rle_mask in rle_mask:
    binary_mask = rle_decode(rle_mask)

    regions = sk_regions(binary_mask)
    if len(regions) < 1:
        continue
    for region in regions:
        print('[INFO]bbox: ', region.bbox)
        top, left, bottom, right = region.bbox

2. Mask 标注数据

如图:

2.1. cv2.findContours

import numpy as np 
import cv2 # opencv 4.x

def binary_mask_to_box(binary_mask):
    binary_mask = np.array(binary_mask, np.uint8)
    contours,hierarchy = cv2.findContours(
        binary_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
    
    areas = []
    for cnt in contours:
        area = cv2.contourArea(cnt)
        areas.append(area)
    # 取最大面积的连通区域
    idx = areas.index(np.max(areas))
    x, y, w, h = cv2.boundingRect(contours[idx])
    bounding_box = [x, y, x+w, y+h]

    return bounding_box

2.2. skimage.measure.regionprops

如:

# from skimage.measure import label as sk_label
from skimage.measure import regionprops as sk_region

regions = sk_region(binary_mask)
if len(regions) < 1:
    continue
lefts, tops, rights, bottoms = [], [], [], []
for region in regions:
    top, left, bottom, right = region.bbox
    lefts.append(left)
    tops.append(top)
    rights.append(right)
    bottoms.append(bottom)
#
bounding_box = [min(lefts), min(tops), max(rights), max(bottoms)]

2.3. polygon

import numpy as np 
from skimage import measure


def binary_mask_to_polygon(binary_mask, tolerance=0):
    """Converts a binary mask to COCO polygon representation
    Args:
        binary_mask: a 2D binary numpy array where '1's represent the object
        tolerance: Maximum distance from original points of polygon to approximated
            polygonal chain. If tolerance is 0, the original coordinate array is returned.
    """
    polygons = []
    # pad mask to close contours of shapes which start and end at an edge
    padded_binary_mask = np.pad(binary_mask, pad_width=1, mode='constant', constant_values=0)
    contours = measure.find_contours(padded_binary_mask, 0.5)
    contours = np.subtract(contours, 1)
    for contour in contours:
        contour = close_contour(contour)
        contour = measure.approximate_polygon(contour, tolerance)
        if len(contour) < 3:
            continue
        contour = np.flip(contour, axis=1)
        segmentation = contour.ravel().tolist()
        # after padding and subtracting 1 we may get -0.5 points in our segmentation
        segmentation = [0 if i < 0 else i for i in segmentation]
        polygons.append(segmentation)

    return polygons


#
def close_contour(contour):
    if not np.array_equal(contour[0], contour[-1]):
        contour = np.vstack((contour, contour[0]))
    return contour

#
def binary_mask_to_xy(binary_mask):
    polygons = binary_mask_to_polygon(binary_mask, tolerance=2)
    
    #
    xs = []
    ys = []
    for polygon in polygons:
        for tdx in range(0, len(polygon), 2):
            xs.append(polygon[tdx])
            ys.append(polygon[tdx + 1])
    
    return xs, ys

#
xs, ys = binary_mask_to_xy(binary_mask)
if len(xs) < 1 or len(ys) < 1:
    continue
# left, top, right, bottom
bounding_box = [int(min(xs)), int(min(ys)), int(max(xs)), int(max(ys))]

3. 参考

[1] - From masks to bounding boxes - Kaggle

[2] - run-length-encode-and-decode

Last modification:April 9th, 2020 at 11:35 am