Opencv findCountours is not find all contours

edit

i modified /samples/cpp/contours2.cpp

i hope it will be a good start to solve your problem.

try to find a way for better result ( you can filter contours using their roundness ) or wait my update.

#include "opencv2/imgproc.hpp"
#include "opencv2/highgui.hpp"
#include <iostream>

using namespace cv;
using namespace std;

const int w = 500;
int levels = 3;

vector<vector<Point> > contours;
vector<Vec4i> hierarchy;

static void on_trackbar(int, void*)
{
    Mat cnt_img = Mat::zeros(w, w, CV_8UC3);
    int _levels = levels - 3;
    drawContours( cnt_img, contours, _levels <= 0 ? 3 : -1, Scalar(128,255,255),
                  1, LINE_AA, hierarchy, std::abs(_levels) );

    imshow("contours", cnt_img);
}

int main( int, char** argv)
{
    Mat img = imread(argv[1], 0);
    img = img < 170;
    imshow( "image", img );
    //Extract the contours so that
    vector<vector<Point> > contours0;

    findContours( img, contours0, hierarchy, RETR_TREE, CHAIN_APPROX_SIMPLE);

    contours.resize(contours0.size());
    for( size_t k = 0; k < contours0.size(); k++ )
        approxPolyDP(Mat(contours0[k]), contours[k], 3, true);

    namedWindow( "contours", 1 );
    createTrackbar( "levels+3", "contours", &levels, 7, on_trackbar );

    on_trackbar(0,0);
    waitKey();

    return 0;
}

Hello

This solution is not optimal but ... it work in such case:

import numpy as np import cv2 from matplotlib import pyplot as plt

I = cv2.imread('ext_contours.png',cv2.IMREAD_GRAYSCALE)

_,I = cv2.threshold(I,0.,255.,cv2.THRESH_OTSU)
I = cv2.bitwise_not(I)

_,labels,stats,centroid = cv2.connectedComponentsWithStats(I)

result = np.zeros((I.shape[0],I.shape[1],3),np.uint8)

for i in range(0,labels.max()+1):
    mask = cv2.compare(labels,i,cv2.CMP_EQ)

    _,ctrs,_ = cv2.findContours(mask,cv2.RETR_EXTERNAL,cv2.CHAIN_APPROX_SIMPLE)

    result = cv2.drawContours(result,ctrs,-1,(0xFF,0,0))

plt.figure()
plt.imshow(result)    
plt.axis('off')

Hope it helps.