overlay.py

#!/usr/bin/env python
# coding: utf-8

###overlay
import cv2
import math
import random
import colorsys
import numpy as np
import itertools
import matplotlib.pyplot as plt
from matplotlib import cm
import os
import scipy.io as io
def get_bounding_box(img):
    """Get bounding box coordinate information."""
    rows = np.any(img, axis=1)
    cols = np.any(img, axis=0)
    rmin, rmax = np.where(rows)[0][[0, -1]]
    cmin, cmax = np.where(cols)[0][[0, -1]]
    # due to python indexing, need to add 1 to max
    # else accessing will be 1px in the box, not out
    rmax += 1
    cmax += 1
    return [rmin, rmax, cmin, cmax]
####
def colorize(ch, vmin, vmax):
    """Will clamp value value outside the provided range to vmax and vmin."""
    cmap = plt.get_cmap("jet")
    ch = np.squeeze(ch.astype("float32"))
    vmin = vmin if vmin is not None else ch.min()
    vmax = vmax if vmax is not None else ch.max()
    ch[ch > vmax] = vmax  # clamp value
    ch[ch < vmin] = vmin
    ch = (ch - vmin) / (vmax - vmin + 1.0e-16)
    # take RGB from RGBA heat map
    ch_cmap = (cmap(ch)[..., :3] * 255).astype("uint8")
    return ch_cmap


####
def random_colors(N, bright=True):
    """Generate random colors.
    
    To get visually distinct colors, generate them in HSV space then
    convert to RGB.
    """
    brightness = 1.0 if bright else 0.7
    hsv = [(i / N, 1, brightness) for i in range(N)]
    colors = list(map(lambda c: colorsys.hsv_to_rgb(*c), hsv))
    random.shuffle(colors)
    return colors


####
def visualize_instances_map(
    input_image, inst_map, type_map=None, type_colour=None, line_thickness=2
):
    """Overlays segmentation results on image as contours.

    Args:
        input_image: input image
        inst_map: instance mask with unique value for every object
        type_map: type mask with unique value for every class
        type_colour: a dict of {type : colour} , `type` is from 0-N
                     and `colour` is a tuple of (R, G, B)
        line_thickness: line thickness of contours

    Returns:
        overlay: output image with segmentation overlay as contours
    """
    overlay = np.copy((input_image).astype(np.uint8))

    inst_list = list(np.unique(inst_map))  # get list of instances
    inst_list.remove(0)  # remove background

    inst_rng_colors = random_colors(len(inst_list))
    inst_rng_colors = np.array(inst_rng_colors) * 255
    inst_rng_colors = inst_rng_colors.astype(np.uint8)

    for inst_idx, inst_id in enumerate(inst_list):
        inst_map_mask = np.array(inst_map == inst_id, np.uint8)  # get single object
        y1, y2, x1, x2 = get_bounding_box(inst_map_mask)
        y1 = y1 - 2 if y1 - 2 >= 0 else y1
        x1 = x1 - 2 if x1 - 2 >= 0 else x1
        x2 = x2 + 2 if x2 + 2 <= inst_map.shape[1] - 1 else x2
        y2 = y2 + 2 if y2 + 2 <= inst_map.shape[0] - 1 else y2
        inst_map_crop = inst_map_mask[y1:y2, x1:x2]
        contours_crop = cv2.findContours(
            inst_map_crop, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE
        )
        # only has 1 instance per map, no need to check #contour detected by opencv
        #print(contours_crop)
        contours_crop = np.squeeze(
            contours_crop[0][0].astype("int32")
        )  # * opencv protocol format may break
        
        if len(contours_crop.shape) == 1:
            contours_crop = contours_crop.reshape(1,-1)
        #print(contours_crop.shape)
        contours_crop += np.asarray([[x1, y1]])  # index correction
        if type_map is not None:
            type_map_crop = type_map[y1:y2, x1:x2]
            type_id = np.unique(type_map_crop).max()  # non-zero
            inst_colour = type_colour[type_id]
        else:
            inst_colour = (inst_rng_colors[inst_idx]).tolist()
        cv2.drawContours(overlay, [contours_crop], -1, inst_colour, line_thickness)
    return overlay


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