How to go about obtaining coordinates of the pixel from annotated images?

Python
2

You’re right about being wrong.

Look into:
inRange
findContours
moments

An example code is:

	vector<glm::vec3> loop_centres;
	vector<glm::vec3> loop_colours;

	for (size_t i = 0; i < distinct_colours.size(); i++)
	{
		Mat mask;

		inRange(input_light_mat,
			Scalar(static_cast<unsigned char>(distinct_colours[i].r * 255.0f), static_cast<unsigned char>(distinct_colours[i].g * 255.0f), static_cast<unsigned char>(distinct_colours[i].b * 255.0f), 255),
			Scalar(static_cast<unsigned char>(distinct_colours[i].r * 255.0f), static_cast<unsigned char>(distinct_colours[i].g * 255.0f), static_cast<unsigned char>(distinct_colours[i].b * 255.0f), 255),
			mask);

		vector<vector<Point> > loop_contours;
		vector<Vec4i> loop_hierarchy;
		findContours(mask, loop_contours, loop_hierarchy, RETR_LIST, CHAIN_APPROX_NONE);

		for (size_t j = 0; j < loop_contours.size(); j++)
		{
			cv::Moments M = cv::moments(loop_contours[j]);

			if (M.m00 == 0)
				continue;

			cv::Point2f loop_centre(M.m10 / M.m00, M.m01 / M.m00);

			Vec4b pixelValue = input_light_mat.at<Vec4b>(loop_centre.y, loop_centre.x);
			loop_centres.push_back(glm::vec3(loop_centre.x, loop_centre.y, 0));
			loop_colours.push_back(glm::vec3(pixelValue[0] / 255.0f, pixelValue[1] / 255.0f, pixelValue[2] / 255.0f));
		}
	}