demo_trait_extract_parallel_val.py

'''
Name: trait_extract_parallel.py

Version: 1.0

Summary: Extract plant shoot traits (larea, temp_index, max_width, max_height, avg_curv, color_cluster) by paralell processing 
    
Author: suxing liu

Author-email: suxingliu@gmail.com

Created: 2019-04-29

USAGE:

time python3 demo_trait_extract_parallel_val.py -p ~/example/test/ -ft jpg 

time python3 demo_trait_extract_parallel_val.py -p ~/plant-image-analysis/demo_test/16-1_6-25/ -ft jpg

time python3 demo_trait_extract_parallel_val.py -p ~/example/pi_images/22-4_6-27/mask_reverse/ -ft jpg -min 500 -tp ~/example/pi_images/marker_template/16-1_6-23_sticker_match.jpg


'''


# import the necessary packages
import os
import glob
import utils

from collections import Counter

import argparse

from sklearn.cluster import KMeans
from sklearn.cluster import MiniBatchKMeans

from skimage.feature import peak_local_max
from skimage.morphology import medial_axis
from skimage import img_as_float, img_as_ubyte, img_as_bool, img_as_int
from skimage import measure
from skimage.color import rgb2lab, deltaE_cie76
from skimage import morphology
from skimage.segmentation import clear_border, watershed
from skimage.measure import regionprops

from scipy.spatial import distance as dist
from scipy import optimize
from scipy import ndimage
from scipy.interpolate import interp1d

from skan import skeleton_to_csgraph, Skeleton, summarize, draw

import networkx as nx

import imutils

import numpy as np
import argparse
import cv2

import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import matplotlib as mpl
import matplotlib.cm as mtpltcm

import math
import openpyxl
import csv
    
from tabulate import tabulate

import warnings
warnings.filterwarnings("ignore")

import psutil
import concurrent.futures
import multiprocessing
from multiprocessing import Pool
from contextlib import closing

from pathlib import Path 

from matplotlib import collections
from collections import OrderedDict


MBFACTOR = float(1<<20)

# define class for curvature computation
class ComputeCurvature:

    def __init__(self,x,y):
        """ Initialize some variables """
        self.xc = 0  # X-coordinate of circle center
        self.yc = 0  # Y-coordinate of circle center
        self.r = 0   # Radius of the circle
        self.xx = np.array([])  # Data points
        self.yy = np.array([])  # Data points
        self.x = x  # X-coordinate of circle center
        self.y = y  # Y-coordinate of circle center

    def calc_r(self, xc, yc):
        """ calculate the distance of each 2D points from the center (xc, yc) """
        return np.sqrt((self.xx-xc)**2 + (self.yy-yc)**2)

    def f(self, c):
        """ calculate the algebraic distance between the data points and the mean circle centered at c=(xc, yc) """
        ri = self.calc_r(*c)
        return ri - ri.mean()

    def df(self, c):
        """ Jacobian of f_2b
        The axis corresponding to derivatives must be coherent with the col_deriv option of leastsq"""
        xc, yc = c
        df_dc = np.empty((len(c), self.x.size))

        ri = self.calc_r(xc, yc)
        df_dc[0] = (xc - self.x)/ri                   # dR/dxc
        df_dc[1] = (yc - self.y)/ri                   # dR/dyc
        df_dc = df_dc - df_dc.mean(axis=1)[:, np.newaxis]
        return df_dc

    def fit(self, xx, yy):
        self.xx = xx
        self.yy = yy
        center_estimate = np.r_[np.mean(xx), np.mean(yy)]
        center = optimize.leastsq(self.f, center_estimate, Dfun=self.df, col_deriv=True)[0]

        self.xc, self.yc = center
        ri = self.calc_r(*center)
        self.r = ri.mean()

        return 1 / self.r  # Return the curvature



class ColorLabeler:
    def __init__(self):
        # initialize the colors dictionary, containing the color
        # name as the key and the RGB tuple as the value
        colors = OrderedDict({
            "red": (255, 0, 0),
            "green": (0, 255, 0),
            "blue": (0, 0, 255)})
        # allocate memory for the L*a*b* image, then initialize
        # the color names list
        self.lab = np.zeros((len(colors), 1, 3), dtype="uint8")
        self.colorNames = []
        # loop over the colors dictionary
        for (i, (name, rgb)) in enumerate(colors.items()):
            # update the L*a*b* array and the color names list
            self.lab[i] = rgb
            self.colorNames.append(name)
        # convert the L*a*b* array from the RGB color space
        # to L*a*b*
        self.lab = cv2.cvtColor(self.lab, cv2.COLOR_RGB2LAB)


    def label(self, image, c):
        # construct a mask for the contour, then compute the
        # average L*a*b* value for the masked region
        mask = np.zeros(image.shape[:2], dtype="uint8")
        cv2.drawContours(mask, [c], -1, 255, -1)
        mask = cv2.erode(mask, None, iterations=2)
        mean = cv2.mean(image, mask=mask)[:3]
        # initialize the minimum distance found thus far
        minDist = (np.inf, None)
        # loop over the known L*a*b* color values
        for (i, row) in enumerate(self.lab):
            # compute the distance between the current L*a*b*
            # color value and the mean of the image
            d = dist.euclidean(row[0], mean)
            # if the distance is smaller than the current distance,
            # then update the bookkeeping variable
            if d < minDist[0]:
                minDist = (d, i)
        # return the name of the color with the smallest distance
        return self.colorNames[minDist[1]]




# generate foloder to store the output results
def mkdir(path):
    # import module
    import os
 
    # remove space at the beginning
    path=path.strip()
    # remove slash at the end
    path=path.rstrip("\\")
 
    # path exist?   # True  # False
    isExists=os.path.exists(path)
 
    # process
    if not isExists:
        # construct the path and folder
        #print path + ' folder constructed!'
        # make dir
        os.makedirs(path)
        return True
    else:
        # if exists, return 
        #print path+' path exists!'
        return False


# color cluster based object segmentation
def color_cluster_seg(image, args_colorspace, args_channels, args_num_clusters, min_size):
    
    orig_image = image.copy
    
    # Change image color space, if necessary.
    colorSpace = args_colorspace.lower()

    if colorSpace == 'hsv':
        image = cv2.cvtColor(image, cv2.COLOR_BGR2HSV)
        
    elif colorSpace == 'ycrcb' or colorSpace == 'ycc':
        image = cv2.cvtColor(image, cv2.COLOR_BGR2YCrCb)
        
    elif colorSpace == 'lab':
        image = cv2.cvtColor(image, cv2.COLOR_BGR2LAB)
        
    else:
        colorSpace = 'bgr'  # set for file naming purposes

    # Keep only the selected channels for K-means clustering.
    if args_channels != 'all':
        channels = cv2.split(image)
        channelIndices = []
        for char in args_channels:
            channelIndices.append(int(char))
        image = image[:,:,channelIndices]
        if len(image.shape) == 2:
            image.reshape(image.shape[0], image.shape[1], 1)
            
    (width, height, n_channel) = image.shape
    
    
    
    #print("image shape: \n")
    #print(width, height, n_channel)
    
 
    # Flatten the 2D image array into an MxN feature vector, where M is the number of pixels and N is the dimension (number of channels).
    reshaped = image.reshape(image.shape[0] * image.shape[1], image.shape[2])
    

    # Perform K-means clustering.
    if args_num_clusters < 2:
        print('Warning: num-clusters < 2 invalid. Using num-clusters = 2')
    
    #define number of cluster
    numClusters = max(2, args_num_clusters)
    
    # clustering method
    kmeans = KMeans(n_clusters = numClusters, n_init = 40, max_iter = 500).fit(reshaped)
    
    # get lables 
    pred_label = kmeans.labels_
    
    # Reshape result back into a 2D array, where each element represents the corresponding pixel's cluster index (0 to K - 1).
    clustering = np.reshape(np.array(pred_label, dtype=np.uint8), (image.shape[0], image.shape[1]))

    # Sort the cluster labels in order of the frequency with which they occur.
    sortedLabels = sorted([n for n in range(numClusters)],key = lambda x: -np.sum(clustering == x))

    # Initialize K-means grayscale image; set pixel colors based on clustering.
    kmeansImage = np.zeros(image.shape[:2], dtype=np.uint8)
    for i, label in enumerate(sortedLabels):
        kmeansImage[clustering == label] = int(255 / (numClusters - 1)) * i
    
    ret, thresh = cv2.threshold(kmeansImage,0,255,cv2.THRESH_BINARY | cv2.THRESH_OTSU)
    
    #thresh_cleaned = clear_border(thresh)
    
    
    if np.count_nonzero(thresh) > 0:
        
        thresh_cleaned = clear_border(thresh)
        if cv2.countNonZero(thresh_cleaned) == 0:
            thresh_cleaned = thresh
    else:
        thresh_cleaned = thresh
    
    
    thresh_cleaned = thresh

    nb_components, output, stats, centroids = cv2.connectedComponentsWithStats(thresh_cleaned, connectivity = 8)

    # stats[0], centroids[0] are for the background label. ignore
    # cv2.CC_STAT_LEFT, cv2.CC_STAT_TOP, cv2.CC_STAT_WIDTH, cv2.CC_STAT_HEIGHT
    sizes = stats[1:, cv2.CC_STAT_AREA]
    
    Coord_left = stats[1:, cv2.CC_STAT_LEFT]
    
    Coord_top = stats[1:, cv2.CC_STAT_TOP]
    
    Coord_width = stats[1:, cv2.CC_STAT_WIDTH]
    
    Coord_height = stats[1:, cv2.CC_STAT_HEIGHT]
    
    Coord_centroids = centroids
    
    #print("Coord_centroids {}\n".format(centroids[1][1]))
    
    #print("[width, height] {} {}\n".format(width, height))
    
    nb_components = nb_components - 1
    
    #min_size = 2000*1
    
    
    img_thresh = np.zeros([width, height], dtype=np.uint8)
    
    
    #max_label = 1
    #max_size = sizes[1]
    if len(sizes) > 2:
        max_label = 1
        max_size = sizes[1]
    else:
        max_size = width*height*0.1
    

    
    #for every component in the image, keep it only if it's above min_size
    for i in range(0, nb_components):
    
        '''
        #print("{} nb_components found".format(i))
        
        if (sizes[i] >= min_size) and (Coord_left[i] > 1) and (Coord_top[i] > 1) and (Coord_width[i] - Coord_left[i] > 0) and (Coord_height[i] - Coord_top[i] > 0) and (centroids[i][0] - width*0.5 < 10) and ((centroids[i][1] - height*0.5 < 10)) and ((sizes[i] <= max_size)):
            img_thresh[output == i + 1] = 255
            
            print("Foreground center found ")
            
        elif ((Coord_width[i] - Coord_left[i])*0.5 - width < 15) and (centroids[i][0] - width*0.5 < 15) and (centroids[i][1] - height*0.5 < 15) and ((sizes[i] <= max_size)):
            imax = max(enumerate(sizes), key=(lambda x: x[1]))[0] + 1    
            img_thresh[output == imax] = 255
            print("Foreground max found ")
        
        '''
        if (sizes[i] >= min_size):
            
            img_thresh[output == i + 1] = 255
            
            '''
            if len(sizes) > 2:
                max_label = i
                max_size = sizes[i]
                img_thresh[output == max_label] = 255
            else:
                
                img_thresh[output == i + 1] = 255
            '''
    
    '''
    if cv2.countNonZero(clear_border(img_thresh)) == 0:
        
        img_thresh = img_thresh
    else:
        img_thresh = clear_border(img_thresh)
    '''
    #max_label, max_size = max([(i, stats[i, cv2.CC_STAT_AREA]) for i in range(1, nb_components)], key=lambda x: x[1])
    #img_thresh[output == max_label] = 255
    
    #from skimage import img_as_ubyte
    
    #img_thresh = img_as_ubyte(img_thresh)
    
    #print("img_thresh.dtype")
    #print(img_thresh.dtype)
    
    contours, hier = cv2.findContours(img_thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
    
    size_kernel = 10
    
    if len(contours) > 1:
        
        kernel = np.ones((size_kernel,size_kernel), np.uint8)

        dilation = cv2.dilate(img_thresh.copy(), kernel, iterations = 1)
        
        closing = cv2.morphologyEx(dilation, cv2.MORPH_CLOSE, kernel)
        
        img_thresh = closing

    if cv2.countNonZero(img_thresh) == 0:
    
        img_thresh[:] = 0
    
    
    #return img_thresh
    return img_thresh
    
    #return thresh_cleaned
    
# extract medial_axis for binary mask
def medial_axis_image(thresh):
    
    #convert an image from OpenCV to skimage
    thresh_sk = img_as_float(thresh)

    image_bw = img_as_bool((thresh_sk))
    
    image_medial_axis = medial_axis(image_bw)
    
    return image_medial_axis

# extract skeleton for binary mask
def skeleton_bw(thresh):

    # Convert mask to boolean image, rather than 0 and 255 for skimage to use it
    
    #convert an image from OpenCV to skimage
    thresh_sk = img_as_float(thresh)

    image_bw = img_as_bool((thresh_sk))

    #skeleton = morphology.skeletonize(image_bw)
    
    skeleton = morphology.thin(image_bw)

    skeleton_img = skeleton.astype(np.uint8) * 255

    return skeleton_img, skeleton

#watershed based individual leaf segmentation
def watershed_seg(orig, thresh, min_distance_value):
    
    # compute the exact Euclidean distance from every binary
    # pixel to the nearest zero pixel, then find peaks in this
    # distance map
    D = ndimage.distance_transform_edt(thresh)
    
    localMax = peak_local_max(D, indices = False, min_distance = min_distance_value,  labels = thresh)
     
    # perform a connected component analysis on the local peaks,
    # using 8-connectivity, then appy the Watershed algorithm
    markers = ndimage.label(localMax, structure = np.ones((3, 3)))[0]
    
    #print("markers")
    #print(type(markers))
    
    labels = watershed(-D, markers, mask = thresh)
    
    print("[INFO] {} unique segments found\n".format(len(np.unique(labels)) - 1))
    
    return labels


# computation of percentage
def percentage(part, whole):
  
  percentage = "{:.0%}".format(float(part)/float(whole))
  
  return str(percentage)


'''
# extract individual leaf object
def individual_object_seg(orig, labels, save_path, base_name, file_extension):
    
    num_clusters = 5
    
    (width, height, n_channel) = orig.shape
    
    for label in np.unique(labels):
    # if the label is zero, we are examining the 'background'
    # so simply ignore it
        if label == 0:
            continue
     
        # otherwise, allocate memory for the label region and draw
        # it on the mask
        mask = np.zeros((width, height), dtype="uint8")
        mask[labels == label] = 255
        
        # apply individual object mask
        masked = cv2.bitwise_and(orig, orig, mask = mask)
        
        # detect contours in the mask and grab the largest one
        #cnts = cv2.findContours(mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)[-2]
        #contours, hierarchy = cv2.findContours(mask.copy(),cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
        #c = max(contours, key = cv2.contourArea)
        
        #if len(c) >= 5 :
            #label_img = cv2.drawContours(masked, [c], -1, (255, 0, 0), 2)
        
        mkpath_leaf = os.path.dirname(save_path) + '/leaf' + str(label)
        mkdir(mkpath_leaf)
        save_path_leaf = mkpath_leaf + '/'
        
        
        
        #define result path 
        result_img_path = (save_path_leaf + 'leaf_' + str(label) + file_extension)
        cv2.imwrite(result_img_path, masked)
        
        #save color quantization result
        #rgb_colors = color_quantization(image, thresh, save_path, num_clusters)
        rgb_colors, counts = color_region(masked, mask, save_path_leaf, num_clusters)
        
        list_counts = list(counts.values())
        
        #print(type(list_counts))
        
        for value in list_counts:
            
            print(percentage(value, np.sum(list_counts)))
'''

        
        
    
    
        


'''
# watershed segmentation with marker 
def watershed_seg_marker(orig, thresh, min_distance_value, img_marker):
    
    # compute the exact Euclidean distance from every binary
    # pixel to the nearest zero pixel, then find peaks in this
    # distance map
    D = ndimage.distance_transform_edt(thresh)
    
    gray = cv2.cvtColor(img_marker, cv2.COLOR_BGR2GRAY)
    img_marker = cv2.threshold(gray, 128, 255,cv2.THRESH_BINARY | cv2.THRESH_OTSU)[1]
    
    #localMax = peak_local_max(D, indices = False, min_distance = min_distance_value,  labels = thresh)
     
    # perform a connected component analysis on the local peaks,
    # using 8-connectivity, then appy the Watershed algorithm
    markers = ndimage.label(img_marker, structure = np.ones((3, 3)))[0]

    labels = watershed(-D, markers, mask = thresh)

    
    props = regionprops(labels)
    
    areas = [p.area for p in props]
    
    import statistics
    
    
    #outlier_list = outlier_doubleMAD(areas, thresh = 1.0)
    
    #indices = [i for i, x in enumerate(outlier_list) if x]
    
    print(areas)
    print(statistics.mean(areas))
    #
    #print(outlier_list)
    #print(indices)
    
    
    print("[INFO] {} unique segments found\n".format(len(np.unique(labels)) - 1))
    
    return labels
'''

# computation of external traits like contour, convelhull, area, ,max width and height
def comp_external_contour(orig,thresh):
    
    #find contours and get the external one
    contours, hier = cv2.findContours(thresh, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
   
    img_height, img_width, img_channels = orig.shape
   
    index = 1
    
    for c in contours:
        
        #get the bounding rect
        x, y, w, h = cv2.boundingRect(c)
        
        if w>img_width*0.01 and h>img_height*0.01:
            
            trait_img = cv2.drawContours(orig, contours, -1, (255, 255, 0), 1)
    
            # draw a green rectangle to visualize the bounding rect
            roi = orig[y:y+h, x:x+w]
            
            print("ROI {} detected ...\n".format(index))
            #result_file = (save_path +  str(index) + file_extension)
            #cv2.imwrite(result_file, roi)
            
            trait_img = cv2.rectangle(orig, (x, y), (x+w, y+h), (255, 255, 0), 3)
            
            index+= 1

            '''
            #get the min area rect
            rect = cv2.minAreaRect(c)
            box = cv2.boxPoints(rect)
            # convert all coordinates floating point values to int
            box = np.int0(box)
            #draw a red 'nghien' rectangle
            trait_img = cv2.drawContours(orig, [box], 0, (0, 0, 255))
            '''
             # get convex hull
            hull = cv2.convexHull(c)
            # draw it in red color
            trait_img = cv2.drawContours(orig, [hull], -1, (0, 0, 255), 3)
            
            # compute the center of the contour
            M = cv2.moments(c)
            center_X = int(M["m10"] / M["m00"])
            center_Y = int(M["m01"] / M["m00"])
            
            
            '''
            # calculate epsilon base on contour's perimeter
            # contour's perimeter is returned by cv2.arcLength
            epsilon = 0.01 * cv2.arcLength(c, True)
            # get approx polygons
            approx = cv2.approxPolyDP(c, epsilon, True)
            # draw approx polygons
            trait_img = cv2.drawContours(orig, [approx], -1, (0, 255, 0), 1)
         
            # hull is convex shape as a polygon
            hull = cv2.convexHull(c)
            trait_img = cv2.drawContours(orig, [hull], -1, (0, 0, 255))
            '''
            
            '''
            #get the min enclosing circle
            (x, y), radius = cv2.minEnclosingCircle(c)
            # convert all values to int
            center = (int(x), int(y))
            radius = int(radius)
            # and draw the circle in blue
            trait_img = cv2.circle(orig, center, radius, (255, 0, 0), 2)
            '''
            
            area = cv2.contourArea(c)
            print("Leaf area = {0:.2f}... \n".format(area))
            
            
            hull = cv2.convexHull(c)
            hull_area = cv2.contourArea(hull)
            index = float(area)/hull_area
            
            extLeft = tuple(c[c[:,:,0].argmin()][0])
            extRight = tuple(c[c[:,:,0].argmax()][0])
            extTop = tuple(c[c[:,:,1].argmin()][0])
            extBot = tuple(c[c[:,:,1].argmax()][0])
            
            trait_img = cv2.circle(orig, extLeft, 3, (255, 0, 0), -1)
            trait_img = cv2.circle(orig, extRight, 3, (255, 0, 0), -1)
            trait_img = cv2.circle(orig, extTop, 3, (255, 0, 0), -1)
            trait_img = cv2.circle(orig, extBot, 3, (255, 0, 0), -1)
            
            max_width = dist.euclidean(extLeft, extRight)
            max_height = dist.euclidean(extTop, extBot)
            
            if max_width > max_height:
                trait_img = cv2.line(orig, extLeft, extRight, (0,255,0), 2)
            else:
                trait_img = cv2.line(orig, extTop, extBot, (0,255,0), 2)

            print("Width and height are {0:.2f},{1:.2f}... \n".format(w, h))
            
            
            
    return trait_img, area, index, w, h, center_X, center_Y

# scale contour for tracking
def scale_contour(cnt, scale):
    M = cv2.moments(cnt)
    cx = int(M['m10']/M['m00'])
    cy = int(M['m01']/M['m00'])

    cnt_norm = cnt - [cx, cy]
    cnt_scaled = cnt_norm * scale
    cnt_scaled = cnt_scaled + [cx, cy]
    cnt_scaled = cnt_scaled.astype(np.int32)
    
    return cnt_scaled


# individual leaf object segmentation and traits computation
def leaf_traits_computation(orig, labels, center_X, center_Y, save_path, base_name, file_extension):
    
    gray = cv2.cvtColor(orig, cv2.COLOR_BGR2GRAY)
    
    leaf_index_rec = []
    contours_rec = []
    area_rec = []
    curv_rec = []
    temp_index_rec = []
    major_axis_rec = []
    minor_axis_rec = []
    
    color_ratio_rec = []
    
    
    count = 0
    
    num_clusters = 5
    

    # curvature computation
    # loop over the unique labels returned by the Watershed algorithm
    for index, label in enumerate(np.unique(labels), start = 1):
        # if the label is zero, we are examining the 'background'
        # so simply ignore it
        if label == 0:
            continue
     
        # otherwise, allocate memory for the label region and draw
        # it on the mask
        mask = np.zeros(gray.shape, dtype = "uint8")
        mask[labels == label] = 255
        
        
        #get the medial axis of the contour
        image_skeleton, skeleton = skeleton_bw(mask)

        
        
        
        # apply individual object mask
        masked = cv2.bitwise_and(orig, orig, mask = mask)
        
        '''
        
        #individual leaf segmentation and color analysis
        ################################################################################
        mkpath_leaf = os.path.dirname(save_path) + '/leaf' + str(label)
        mkdir(mkpath_leaf)
        save_path_leaf = mkpath_leaf + '/'
        

        #define result path 
        result_img_path = (save_path_leaf + 'leaf_' + str(label) + file_extension)
        cv2.imwrite(result_img_path, masked)
        
        # save _skeleton result
        result_file = (save_path_leaf + 'leaf_skeleton_' + str(label) + file_extension)
        cv2.imwrite(result_file, img_as_ubyte(image_skeleton))
        
        
        #save color quantization result
        #rgb_colors = color_quantization(image, thresh, save_path, num_clusters)
        rgb_colors, counts = color_region(masked, mask, save_path_leaf, num_clusters)
        
        list_counts = list(counts.values())
        
        #print(type(list_counts))
        
        color_ratio = []
        
        for value in list_counts:
            
            #print(percentage(value, np.sum(list_counts)))
            
            color_ratio.append(percentage(value, np.sum(list_counts)))
            
            
        color_ratio_rec.append(color_ratio)
        '''
        
        # detect contours in the mask and grab the largest one
        #cnts = cv2.findContours(mask.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)[-2]
        contours, hierarchy = cv2.findContours(mask.copy(),cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
        c = max(contours, key = cv2.contourArea)
        
        
       
        if len(c) >= 10 :

            contours_rec.append(c)
            area_rec.append(cv2.contourArea(c))

        else:
            # optional to "delete" the small contours
            #label_trait = cv2.drawContours(orig, [c], -1, (0, 0, 255), 2)
            print("lack of enough points to fit ellipse")
    
 
    #sort contours based on its area size
    contours_rec_sorted = [x for _, x in sorted(zip(area_rec, contours_rec), key=lambda pair: pair[0])]
    
    #sort contour area for tracking
    #normalized_area_rec = preprocessing.normalize(sorted(area_rec))
    
    normalized_area_rec = [float(i)/sum(sorted(area_rec)) for i in sorted(area_rec)]
    
    #normalized_area_rec = sorted(area_rec)
    
    
    #cmap = get_cmap(len(contours_rec_sorted)) 
    
    cmap = get_cmap(len(contours_rec_sorted)+1)
    
    
    tracking_backgd = np.zeros(gray.shape, dtype = "uint8")
    #backgd.fill(128)
    
    #backgd = orig
    
    #clean area record list
    area_rec = []
    #individual leaf traits sorting based on area order 
    ################################################################################
    for i in range(len(contours_rec_sorted)):
        
        c = contours_rec_sorted[i]
        
        #assign unique color value in opencv format
        color_rgb = tuple(reversed(cmap(i)[:len(cmap(i))-1]))
        
        color_rgb = tuple([255*x for x in color_rgb])
        
        
        # draw a circle enclosing the object
        ((x, y), r) = cv2.minEnclosingCircle(c)
        #label_trait = cv2.circle(orig, (int(x), int(y)), 3, (0, 255, 0), 2)
        
        #track_trait = cv2.circle(tracking_backgd, (int(x), int(y)), int(normalized_area_rec[i]*200), (255, 255, 255), -1)
        
        #draw filled contour
        #label_trait = cv2.drawContours(orig, [c], -1, color_rgb, -1)
        
        label_trait = cv2.drawContours(orig, [c], -1, color_rgb, 2)
        
        
        
        label_trait = cv2.putText(orig, "#{}".format(i+1), (int(x) - 10, int(y)), cv2.FONT_HERSHEY_SIMPLEX, 0.6, color_rgb, 1)
        #label_trait = cv2.putText(backgd, "#{}".format(i+1), (int(x) - 10, int(y)), cv2.FONT_HERSHEY_SIMPLEX, 0.6, color_rgb, 1)
        
        
        #######################################individual leaf curvature computation
        
        #Get rotated bounding ellipse of contour
        ellipse = cv2.fitEllipse(c)
        
        #get paramters of ellipse
        ((xc,yc), (d1,d2), angle) = ellipse
        
        # draw circle at ellipse center
        #label_trait = cv2.ellipse(orig, ellipse, color_rgb, 2)
        #label_trait = cv2.circle(backgd, (int(xc),int(yc)), 10, color_rgb, -1)
        
        #simplify each leaf as a dot, its size was proportional to leaf area
        #track_trait = cv2.circle(tracking_backgd, (int(xc),int(yc)), int(normalized_area_rec[i]*50), (255, 255, 255), -1)
        #track_trait = cv2.drawContours(tracking_backgd, [scale_contour(c,0.7)], -1, (255, 255, 255), -1)
        
        #draw major radius
        #compute major radius
        rmajor = max(d1,d2)/2
        rminor = min(d1,d2)/2
        
        if angle > 90:
            angle = angle - 90
        else:
            angle = angle + 90
        
        #print(angle)
        
        xtop = xc + math.cos(math.radians(angle))*rmajor
        ytop = yc + math.sin(math.radians(angle))*rmajor
        xbot = xc + math.cos(math.radians(angle+180))*rmajor
        ybot = yc + math.sin(math.radians(angle+180))*rmajor
        
        label_trait = cv2.line(orig, (int(xtop),int(ytop)), (int(xbot),int(ybot)), color_rgb, 1)
                
        #track_trait = cv2.line(tracking_backgd, (int(xtop),int(ytop)), (int(center_X),int(center_Y)), (255, 255, 255), 3)
        
        c_np = np.vstack(c).squeeze()
        
        x = c_np[:,0]
        y = c_np[:,1]
        
        comp_curv = ComputeCurvature(x, y)
        
        curvature = comp_curv.fit(x, y)
        
        #compute temp_index
        temp_index = float(cv2.contourArea(c))/cv2.contourArea(cv2.convexHull(c))
        
        #print("temp_index = {0:.2f}... \n".format(temp_index))
        
        
        #record all traits 
        leaf_index_rec.append(i)
        area_rec.append(cv2.contourArea(c))
        curv_rec.append(curvature)
        
        temp_index_rec.append(temp_index)
        major_axis_rec.append(rmajor)
        minor_axis_rec.append(rminor)
        
    ################################################################################
    
    
    #print('unique labels={0}, len(contours_rec)={1}, len(leaf_index_rec)={2}'.format(np.unique(labels),len(contours_rec),len(leaf_index_rec)))
        
    n_contours = len(contours_rec_sorted)
    
    if n_contours > 0:
        print('average curvature = {0:.2f}\n'.format(sum(curv_rec)/n_contours))
    else:
        n_contours = 1.0
    
    #print(normalized_area_rec)
    #print(area_rec)
    
    #return sum(curv_rec)/n_contours, label_trait, track_trait, leaf_index_rec, contours_rec, area_rec, curv_rec, temp_index_rec, major_axis_rec, minor_axis_rec, color_ratio_rec
    
    return sum(curv_rec)/n_contours, label_trait, leaf_index_rec

# convert RGB value to HEX value
def RGB2HEX(color):
    return "#{:02x}{:02x}{:02x}".format(int(color[0]), int(color[1]), int(color[2]))

'''
def color_quantization(image, mask, save_path, num_clusters):
    
    #grab image width and height
    (h, w) = image.shape[:2]
    
    #change the color storage order
    image = cv2.cvtColor(image, cv2.COLOR_BGR2RGB)
    
    #apply the mask to get the segmentation of plant
    masked_image = cv2.bitwise_and(image, image, mask = mask)
       
    # reshape the image to be a list of pixels
    pixels = masked_image.reshape((masked_image.shape[0] * masked_image.shape[1], 3))
        
    ############################################################
    #Clustering process
    ###############################################################
    # cluster the pixel intensities
    clt = MiniBatchKMeans(n_clusters = num_clusters)
    #clt = KMeans(n_clusters = args["clusters"])
    clt.fit(pixels)

    #assign labels to each cluster 
    labels = clt.fit_predict(pixels)

    #obtain the quantized clusters using each label
    quant = clt.cluster_centers_.astype("uint8")[labels]

    # reshape the feature vectors to images
    quant = quant.reshape((h, w, 3))
    image_rec = pixels.reshape((h, w, 3))
    
    # convert from L*a*b* to RGB
    quant = cv2.cvtColor(quant, cv2.COLOR_RGB2BGR)
    image_rec = cv2.cvtColor(image_rec, cv2.COLOR_RGB2BGR)
    
    # display the images 
    #cv2.imshow("image", np.hstack([image_rec, quant]))
    #cv2.waitKey(0)
    
    #define result path for labeled images
    result_img_path = save_path + 'cluster_out.png'
    
    # save color_quantization results
    cv2.imwrite(result_img_path,quant)

    #Get colors and analze them from masked image
    counts = Counter(labels)
    # sort to ensure correct color percentage
    counts = dict(sorted(counts.items()))
    
    center_colors = clt.cluster_centers_
    
    #print(type(center_colors))

    # We get ordered colors by iterating through the keys
    ordered_colors = [center_colors[i] for i in counts.keys()]
    hex_colors = [RGB2HEX(ordered_colors[i]) for i in counts.keys()]
    rgb_colors = [ordered_colors[i] for i in counts.keys()]
    
    
    #######################################################################################
    threshold = 60
    
    selected_color = rgb2lab(np.uint8(np.asarray([[rgb_colors[0]]])))

    for i in range(num_clusters):
        curr_color = rgb2lab(np.uint8(np.asarray([[rgb_colors[i]]]))) 
        diff = deltaE_cie76(selected_color, curr_color)
        if (diff < threshold):
            print("Color difference value is : {0} \n".format(str(diff)))
    ###########################################################################################
    #print(hex_colors)
    
    index_bkg = [index for index in range(len(hex_colors)) if hex_colors[index] == '#000000']
    
    #print(index_bkg[0])

    #print(counts)
    #remove background color 
    del hex_colors[index_bkg[0]]
    del rgb_colors[index_bkg[0]]
    
    # Using dictionary comprehension to find list 
    # keys having value . 
    delete = [key for key in counts if key == index_bkg[0]] 
  
    # delete the key 
    for key in delete: del counts[key] 
   
    fig = plt.figure(figsize = (6, 6))
    plt.pie(counts.values(), labels = hex_colors, colors = hex_colors)

    #define result path for labeled images
    result_img_path = save_path + 'pie_color.png'
    plt.savefig(result_img_path)
        
    # build a histogram of clusters and then create a figure representing the number of pixels labeled to each color
    hist = utils.centroid_histogram(clt)

    # remove the background color cluster
    clt.cluster_centers_ = np.delete(clt.cluster_centers_, index_bkg[0], axis=0)
    
    #build a histogram of clusters using center lables
    numLabels = utils.plot_centroid_histogram(save_path,clt)

    #create a figure representing the distribution of each color
    bar = utils.plot_colors(hist, clt.cluster_centers_)

    #save a figure of color bar 
    utils.plot_color_bar(save_path, bar)

    return rgb_colors
'''

# get color map for drawing figures
def get_cmap(n, name = 'hsv'):
    '''Returns a function that maps each index in 0, 1, ..., n-1 to a distinct 
    RGB color; the keyword argument name must be a standard mpl colormap name.'''
    return plt.cm.get_cmap(name, n)
    
    
# computation of color distributation 
def color_region(image, mask, save_path, num_clusters):
    
    # read the image
     #grab image width and height
    (h, w) = image.shape[:2]

    #apply the mask to get the segmentation of plant
    masked_image_ori = cv2.bitwise_and(image, image, mask = mask)
    
    #define result path for labeled images
    result_img_path = save_path + 'masked.png'
    cv2.imwrite(result_img_path, masked_image_ori)
    
    # convert to RGB
    image_RGB = cv2.cvtColor(masked_image_ori, cv2.COLOR_BGR2RGB)

    # reshape the image to a 2D array of pixels and 3 color values (RGB)
    pixel_values = image_RGB.reshape((-1, 3))
    
    # convert to float
    pixel_values = np.float32(pixel_values)

    # define stopping criteria
    criteria = (cv2.TERM_CRITERIA_EPS + cv2.TERM_CRITERIA_MAX_ITER, 100, 0.2)

    # number of clusters (K)
    #num_clusters = 5
    compactness, labels, (centers) = cv2.kmeans(pixel_values, num_clusters, None, criteria, 10, cv2.KMEANS_RANDOM_CENTERS)

    # convert back to 8 bit values
    centers = np.uint8(centers)

    # flatten the labels array
    labels_flat = labels.flatten()

    # convert all pixels to the color of the centroids
    segmented_image = centers[labels_flat]

    # reshape back to the original image dimension
    segmented_image = segmented_image.reshape(image_RGB.shape)


    segmented_image_BRG = cv2.cvtColor(segmented_image, cv2.COLOR_RGB2BGR)
    #define result path for labeled images
    result_img_path = save_path + 'clustered.png'
    cv2.imwrite(result_img_path, segmented_image_BRG)


    '''
    fig = plt.figure()
    ax = Axes3D(fig)        
    for label, pix in zip(labels, segmented_image):
        ax.scatter(pix[0], pix[1], pix[2], color = (centers))
            
    result_file = (save_path + base_name + 'color_cluster_distributation.png')
    plt.savefig(result_file)
    '''
    #Show only one chosen cluster 
    #masked_image = np.copy(image)
    masked_image = np.zeros_like(image_RGB)

    # convert to the shape of a vector of pixel values
    masked_image = masked_image.reshape((-1, 3))
    # color (i.e cluster) to render
    #cluster = 2

    cmap = get_cmap(num_clusters+1)
    
    #clrs = sns.color_palette('husl', n_colors = num_clusters)  # a list of RGB tuples

    color_conversion = interp1d([0,1],[0,255])


    for cluster in range(num_clusters):

        print("Processing color cluster {0} ...\n".format(cluster))
        #print(clrs[cluster])
        #print(color_conversion(clrs[cluster]))

        masked_image[labels_flat == cluster] = centers[cluster]

        #print(centers[cluster])

        #convert back to original shape
        masked_image_rp = masked_image.reshape(image_RGB.shape)

        #masked_image_BRG = cv2.cvtColor(masked_image, cv2.COLOR_RGB2BGR)
        #cv2.imwrite('maksed.png', masked_image_BRG)

        gray = cv2.cvtColor(masked_image_rp, cv2.COLOR_BGR2GRAY)

        # threshold the image, then perform a series of erosions +
        # dilations to remove any small regions of noise
        thresh = cv2.threshold(gray, 0, 255, cv2.THRESH_BINARY)[1]

        #thresh_cleaned = clear_border(thresh)

        cnts = cv2.findContours(thresh.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
        cnts = imutils.grab_contours(cnts)
        #c = max(cnts, key=cv2.contourArea)

        '''
        # compute the center of the contour area and draw a circle representing the center
        M = cv2.moments(c)
        cX = int(M["m10"] / M["m00"])
        cY = int(M["m01"] / M["m00"])
        # draw the countour number on the image
        result = cv2.putText(masked_image_rp, "#{}".format(cluster + 1), (cX - 20, cY), cv2.FONT_HERSHEY_SIMPLEX, 1.0, (255, 255, 255), 2)
        '''
        
        
        if not cnts:
            print("findContours is empty")
        else:
            
            # loop over the (unsorted) contours and draw them
            for (i, c) in enumerate(cnts):

                result = cv2.drawContours(masked_image_rp, c, -1, color_conversion(np.random.random(3)), 2)
                #result = cv2.drawContours(masked_image_rp, c, -1, color_conversion(clrs[cluster]), 2)

            #result = result(np.where(result == 0)== 255)
            result[result == 0] = 255


            result_BRG = cv2.cvtColor(result, cv2.COLOR_RGB2BGR)
            result_img_path = save_path + 'result_' + str(cluster) + '.png'
            cv2.imwrite(result_img_path, result_BRG)


    
    counts = Counter(labels_flat)
    # sort to ensure correct color percentage
    counts = dict(sorted(counts.items()))
    
    center_colors = centers

    # We get ordered colors by iterating through the keys
    ordered_colors = [center_colors[i] for i in counts.keys()]
    hex_colors = [RGB2HEX(ordered_colors[i]) for i in counts.keys()]
    rgb_colors = [ordered_colors[i] for i in counts.keys()]

    #print(hex_colors)
    
    index_bkg = [index for index in range(len(hex_colors)) if hex_colors[index] == '#000000']
    
    #print(index_bkg[0])

    #print(counts)
    #remove background color 
    del hex_colors[index_bkg[0]]
    del rgb_colors[index_bkg[0]]
    
    # Using dictionary comprehension to find list 
    # keys having value . 
    delete = [key for key in counts if key == index_bkg[0]] 
  
    # delete the key 
    for key in delete: del counts[key] 
   
    fig = plt.figure(figsize = (6, 6))
    plt.pie(counts.values(), labels = hex_colors, colors = hex_colors)

    #define result path for labeled images
    result_img_path = save_path + 'pie_color.png'
    plt.savefig(result_img_path)

   
    return rgb_colors, counts, hex_colors

# normalize image data
def _normalise_image(image, *, image_cmap=None):
    image = img_as_float(image)
    if image.ndim == 2:
        if image_cmap is None:
            image = gray2rgb(image)
        else:
            image = plt.get_cmap(image_cmap)(image)[..., :3]
    return image


'''
def overlay_skeleton_endpoints(image, stats, *, image_cmap=None, axes=None):

    image = _normalise_image(image, image_cmap=image_cmap)
    summary = stats
    # transforming from row, col to x, y
    #coords_cols = (['image-coord-src-%i' % i for i in [1, 0]] +
    #               ['image-coord-dst-%i' % i for i in [1, 0]])
    
    coords_cols_src = (['image-coord-src-%i' % i for i in [1, 0]])
    coords_cols_dst = (['image-coord-dst-%i' % i for i in [1, 0]])
    
    #coords = summary[coords_cols].values.reshape((-1, 1, 2))
    
    coords_src = summary[coords_cols_src].values
    coords_dst = summary[coords_cols_dst].values

    coords_src_x = [i[0] for i in coords_src]
    coords_src_y = [i[1] for i in coords_src]
    
    coords_dst_x = [i[0] for i in coords_dst]
    coords_dst_y = [i[1] for i in coords_dst]
    
    img_marker = np.zeros_like(image, dtype = np.uint8)
    img_marker.fill(0) # or img[:] = 255
    img_marker[list(map(int, coords_src_y)), list(map(int, coords_src_x))] = 255
    img_marker[list(map(int, coords_dst_y)), list(map(int, coords_dst_x))] = 255
    
    #print("img_marker")
    #print(img_marker.shape)
    
    if axes is None:
        fig, axes = plt.subplots()
    
    axes.axis('off')
    axes.imshow(image)

    axes.scatter(coords_src_x, coords_src_y, c = 'w')
    axes.scatter(coords_dst_x, coords_dst_y, c = 'w')

    return fig, img_marker
    #return coords
'''

def outlier_doubleMAD(data,thresh = 3.5):
    
    """
    FOR ASSYMMETRIC DISTRIBUTION
    Returns : filtered array excluding the outliers

    Parameters : the actual data Points array

    Calculates median to divide data into 2 halves.(skew conditions handled)
    Then those two halves are treated as separate data with calculation same as for symmetric distribution.(first answer) 
    Only difference being , the thresholds are now the median distance of the right and left median with the actual data median
    """
    
    # warning: this function does not check for NAs
    # nor does it address issues when 
    # more than 50% of your data have identical values
    m = np.median(data)
    abs_dev = np.abs(data - m)
    left_mad = np.median(abs_dev[data <= m])
    right_mad = np.median(abs_dev[data >= m])
    data_mad = left_mad * np.ones(len(data))
    data_mad[data > m] = right_mad
    modified_z_score = 0.6745 * abs_dev / data_mad
    modified_z_score[data == m] = 0
    return modified_z_score > thresh



# Convert RGB to LAB color space to access the luminous channel which is independent of colors.
def isbright(image_file):
    
    # Set up threshold value for luminous channel, can be adjusted and generalized 
    thresh = 1.5
    
    # Load image file 
    orig = cv2.imread(image_file)
    
    # Make backup image
    image = orig.copy()
    
    # Get file name
    #abs_path = os.path.abspath(image_file)
    
    #filename, file_extension = os.path.splitext(abs_path)
    #base_name = os.path.splitext(os.path.basename(filename))[0]

    image_file_name = Path(image_file).name
    
    # Convert color space to LAB format and extract L channel
    L, A, B = cv2.split(cv2.cvtColor(image, cv2.COLOR_BGR2LAB))
    
    # Normalize L channel by dividing all pixel values with maximum pixel value
    L = L/np.max(L)
    
    text_bool = "bright" if np.mean(L) < thresh else "dark"
    
    #return image_file_name, np.mean(L), text_bool
    
    print("np.mean(L) < thresh = {}".format(np.mean(L)))
    
    #return np.mean(L) < thresh
    
    return True

# convert from RGB to LAB space
def Lab_distance(image, mask):
    
    # Make backup image
    image_rgb = image.copy()
    
    # apply object mask
    masked_rgb = cv2.bitwise_and(image_rgb, image_rgb, mask = mask)
    
    # Convert color space to LAB space and extract L channel
    L, A, B = cv2.split(cv2.cvtColor(masked_rgb, cv2.COLOR_BGR2LAB))
    
    return masked_rgb, L, A, B
    
#computation of temperature index
def temperature_index(ref_color, rgb_colors):
    
    #print(ref_color)
    
    color_diff = []
    
    for index, value in enumerate(rgb_colors): 
        #print(index, value) 
        curr_color = rgb2lab(np.uint8(np.asarray([[value]])))
        
        #color difference in CIE lab space
        diff = deltaE_cie76(ref_color, curr_color)
        
        color_diff.append(diff)
        
        #print(index, value, diff) 
    
    temp_idex = sum(color_diff) / len(color_diff)/100
    
    print("Color difference are {}: \n".format(temp_idex)) 

    return temp_idex


# computation of all traits 
def extract_traits(image_file):

    #gray = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
        
    abs_path = os.path.abspath(image_file)
    
    filename, file_extension = os.path.splitext(abs_path)
    base_name = os.path.splitext(os.path.basename(filename))[0]

    file_size = os.path.getsize(image_file)/MBFACTOR
    
    image_file_name = Path(image_file).name
   
    #initialize the colormap
    colormap = mpl.cm.jet
    cNorm = mpl.colors.Normalize(vmin=0, vmax=255)
    scalarMap = mtpltcm.ScalarMappable(norm=cNorm, cmap=colormap)
    
    # make the folder to store the results
    #current_path = abs_path + '/'
    
    print("Exacting traits for image : {0}\n".format(str(image_file_name)))
     
    # save folder construction
    if (args['result']):
        save_path = args['result']
    else:
        mkpath = os.path.dirname(abs_path) +'/' + base_name
        mkdir(mkpath)
        save_path = mkpath + '/'
        
        #track_save_path = os.path.dirname(abs_path) + '/trace/'
        #mkdir(track_save_path)

    print ("results_folder: " + save_path)
    
    #print ("track_save_path: " + track_save_path)
    
    #coffient = (87.3536191965406, 69.9979422616578, 116.32627374977, 88.0781733017053, 72.6213559207636, 106.200604960711, 93.3387584464954, 96.1746594499645, 98.9824651280326)
    
    
    if isbright(image_file):
    
        if (file_size > 5.0):
            print("It will take some time due to larger file size {0} MB".format(str(int(file_size))))
        else:
            print("Segmentaing plant object using automatic color clustering method... ")
        
        image = cv2.imread(image_file)
        
        #make backup image
        orig = image.copy()
        
        source_image = cv2.cvtColor(orig, cv2.COLOR_BGR2RGB)
         
        args_colorspace = args['color_space']
        args_channels = args['channels']
        args_num_clusters = args['num_clusters']
        
        
        
        #color clustering based plant object segmentation
        thresh = color_cluster_seg(orig, args_colorspace, args_channels, args_num_clusters, min_size)
        
        if cv2.countNonZero(thresh) == 0:
            
            print ("Segmentaion mask is black \n")
        else:
            print ("Segmentaion mask saved \n")
        
        # save segmentation result
        result_file = (save_path + base_name + '_seg' + file_extension)
        
        #print(filename)
        cv2.imwrite(result_file, thresh)
        
        
        (masked_rgb, L, A, B) = Lab_distance(orig, thresh)
        
        # save Lab result
        result_file = (save_path + base_name + '_L' + file_extension)
        cv2.imwrite(result_file, L)
        
        # save Lab result
        result_file = (save_path + base_name + '_A' + file_extension)
        cv2.imwrite(result_file, A)
        
        # save Lab result
        result_file = (save_path + base_name + '_B' + file_extension)
        cv2.imwrite(result_file, B)
        
        
        num_clusters = 5
        #save color quantization result
        #rgb_colors = color_quantization(image, thresh, save_path, num_clusters)
        
        sticker_thresh = np.zeros([sticker.shape[0], sticker.shape[1]], dtype=np.uint8)
        
        (rgb_colors, counts, hex_colors) = color_region(orig, thresh, save_path, num_clusters)
        
        (rgb_colors_sticker, counts_sticker, hex_colors) = color_region(sticker, sticker_thresh, sticker_path, 2)
        
        ref_color = rgb2lab(np.uint8(np.asarray([[rgb_colors_sticker[0]]])))
        
        ####################################################
        #compute color difference in cie lab space and return difference value
        
        temp_idex = temperature_index(ref_color, rgb_colors)
        
        print("temp_idex : \n",format(temp_idex)) 
        
        '''
        print("Color difference are : ") 
        
        print(selected_color)
        
        color_diff = []
        
        for index, value in enumerate(rgb_colors): 
            #print(index, value) 
            curr_color = rgb2lab(np.uint8(np.asarray([[value]])))
            diff = deltaE_cie76(selected_color, curr_color)
            
            color_diff.append(diff)
            
            #print(index, value, diff) 
        
        temp_idex = sum(color_diff) / len(color_diff)
        
        print(temp_idex) 
        '''
        ###############################################
        
     
     
        '''
        #accquire medial axis of segmentation mask
        #image_skeleton = medial_axis_image(thresh)
        
        image_skeleton, skeleton = skeleton_bw(thresh)

        # save _skeleton result
        result_file = (save_path + base_name + '_skeleton' + file_extension)
        cv2.imwrite(result_file, img_as_ubyte(image_skeleton))
        
        ###
        # ['skeleton-id', 'node-id-src', 'node-id-dst', 'branch-distance', 
        #'branch-type', 'mean-pixel-value', 'stdev-pixel-value', 
        #'image-coord-src-0', 'image-coord-src-1', 'image-coord-dst-0', 'image-coord-dst-1', 
        #'coord-src-0', 'coord-src-1', 'coord-dst-0', 'coord-dst-1', 'euclidean-distance']
        ###
        
        #get brach data
        branch_data = summarize(Skeleton(image_skeleton))
        #print(branch_data)
        
        #select end branch
        sub_branch = branch_data.loc[branch_data['branch-type'] == 1]
        
        sub_branch_branch_distance = sub_branch["branch-distance"].tolist()
     
        # remove outliers in branch distance 
        outlier_list = outlier_doubleMAD(sub_branch_branch_distance, thresh = 3.5)
        
        indices = [i for i, x in enumerate(outlier_list) if x]
        
        sub_branch_cleaned = sub_branch.drop(sub_branch.index[indices])

        #print(outlier_list)
        #print(indices)
        #print(sub_branch)
        
        print(sub_branch_cleaned)
        

        
        branch_type_list = sub_branch_cleaned["branch-type"].tolist()
        
        #print(branch_type_list.count(1))
        
        print("[INFO] {} branch end points found\n".format(branch_type_list.count(1)))
        
        #img_hist = branch_data.hist(column = 'branch-distance', by = 'branch-type', bins = 100)
        #result_file = (save_path + base_name + '_hist' + file_extension)
        #plt.savefig(result_file, transparent = True, bbox_inches = 'tight', pad_inches = 0)
        #plt.close()

        
        fig = plt.plot()
        source_image = cv2.cvtColor(orig, cv2.COLOR_BGR2RGB)
        #img_overlay = draw.overlay_euclidean_skeleton_2d(source_image, branch_data, skeleton_color_source = 'branch-distance', skeleton_colormap = 'hsv')
        img_overlay = draw.overlay_euclidean_skeleton_2d(source_image, branch_data, skeleton_color_source = 'branch-type', skeleton_colormap = 'hsv')
        result_file = (save_path + base_name + '_euclidean_graph_overlay' + file_extension)
        plt.savefig(result_file, transparent = True, bbox_inches = 'tight', pad_inches = 0)
        plt.close()
        
        '''
        
        ############################################## leaf number computation
        '''
        if area > 70000:
            min_distance_value = 38
        else:
            min_distance_value = 20
        '''
        
        
        min_distance_value = 7
        
        
        #watershed based leaf area segmentaiton 
        labels = watershed_seg(orig, thresh, min_distance_value)
        
        #n_leaves = int(len(np.unique(labels)))
        
           
        #find external contour 
        (trait_img, area, temp_index, max_width, max_height, center_X, center_Y) = comp_external_contour(image.copy(),thresh)
        # save segmentation result
        result_file = (save_path + base_name + '_excontour' + file_extension)
        #print(filename)
        cv2.imwrite(result_file, trait_img)   
        
        
        
        
        #labels = watershed_seg_marker(orig, thresh, min_distance_value, img_marker)
        
        #individual_object_seg(orig, labels, save_path, base_name, file_extension)

        #save watershed result label image
        #Map component labels to hue val
        label_hue = np.uint8(128*labels/np.max(labels))
        #label_hue[labels == largest_label] = np.uint8(15)
        blank_ch = 255*np.ones_like(label_hue)
        labeled_img = cv2.merge([label_hue, blank_ch, blank_ch])

        # cvt to BGR for display
        labeled_img = cv2.cvtColor(labeled_img, cv2.COLOR_HSV2BGR)

        # set background label to black
        labeled_img[label_hue==0] = 0
        result_file = (save_path + base_name + '_label' + file_extension)
        #plt.imsave(result_file, img_as_float(labels), cmap = "Spectral")
        cv2.imwrite(result_file, labeled_img)
        
        #(avg_curv, label_trait, track_trait, leaf_index_rec, contours_rec, area_rec, curv_rec, temp_index_rec, major_axis_rec, minor_axis_rec, color_ratio_rec) = leaf_traits_computation(orig, labels, center_X, center_Y, save_path, base_name, file_extension)
        
        (avg_curv, label_trait, leaf_index_rec) = leaf_traits_computation(orig, labels, center_X, center_Y, save_path, base_name, file_extension)
        #print(area_rec, curv_rec, color_ratio_rec)
        
        n_leaves = int(len((leaf_index_rec)))
        
        #print('number of leaves{0}'.format(n_leaves))
        
        #save watershed result label image
        result_file = (save_path + base_name + '_leafspec' + file_extension)
        cv2.imwrite(result_file, label_trait)
        
        #save watershed result label image
        #result_file = (track_save_path + base_name + '_trace' + file_extension)
        #cv2.imwrite(result_file, track_trait)
        

    else:
        
        area=temp_index=max_width=max_height=avg_curv=n_leaves=0
        
    #print("[INFO] {} n_leaves found\n".format(len(np.unique(labels)) - 1))
    
    #Path("/tmp/d/a.dat").name
    
    #return image_file_name, area, temp_index, max_width, max_height, avg_curv, n_leaves, leaf_index_rec, area_rec, curv_rec, temp_index_rec, major_axis_rec, minor_axis_rec, color_ratio_rec
    
    return image_file_name, area, temp_index, max_width, max_height, avg_curv, n_leaves
    
    



#main fucntion for parameters and user input
if __name__ == '__main__':
    
    ap = argparse.ArgumentParser()
    ap.add_argument("-p", "--path", required = True,    help="path to image file")
    ap.add_argument("-ft", "--filetype", required=True,    help="Image filetype")
    #load NIR image for temperature estimation
    #ap.add_argument("-np", "--filetype", required=False,    help="NIR Image filetype and name")
    ap.add_argument("-r", "--result", required = False,    help="result path")
    ap.add_argument('-s', '--color-space', type = str, default ='lab', help='Color space to use: BGR (default), HSV, Lab, YCrCb (YCC)')
    ap.add_argument('-c', '--channels', type = str, default='1', help='Channel indices to use for clustering, where 0 is the first channel,' 
                                                                       + ' 1 is the second channel, etc. E.g., if BGR color space is used, "02" ' 
                                                                       + 'selects channels B and R. (default "all")')
    ap.add_argument('-n', '--num-clusters', type = int, default = 2,  help = 'Number of clusters for K-means clustering (default 2, min 2).')
    ap.add_argument('-min', '--min_size', required=False,  type = int, default = 100,  help = 'min size of object to be segmented.')
    ap.add_argument("-tp", "--temp_path", required = False,  help="template image path")
    
    args = vars(ap.parse_args())
    
    
    # setting path to model file
    file_path = args["path"]
    ext = args['filetype']

    #accquire image file list
    filetype = '*.' + ext
    image_file_path = file_path + filetype
    
    #temperature sticker readings
    min_size = args['min_size']
    
    sticker_path = args['temp_path']
    
    # Read the template 
    sticker = cv2.imread(sticker_path, 0) 
    print("sticker was found")
    
    #accquire image file list
    imgList = sorted(glob.glob(image_file_path))

    #print((imgList))
    #global save_path
    
    n_images = len(imgList)
    
    result_list = []
    
    result_list_leaf = []
    
    #loop execute
    for image in imgList:
        
        (filename, area, temp_index, max_width, max_height, avg_curv, n_leaves) = extract_traits(image)
        
        result_list.append([filename, area, temp_index, max_width, max_height, avg_curv, n_leaves])
        
        #for i in range(len(leaf_index_rec)):
            
            #result_list_leaf.append([filename, leaf_index_rec[i], area_rec[i], curv_rec[i], temp_index_rec[i], major_axis_rec[i], minor_axis_rec[i], color_ratio_rec[i][0], color_ratio_rec[i][1], color_ratio_rec[i][2], color_ratio_rec[i][3]])
    '''
    
    #print(result_list)
    
    for image in imgList:
    
        extract_traits(image)
    '''

    '''
    # get cpu number for parallel processing
    agents = psutil.cpu_count()   
    #agents = multiprocessing.cpu_count() 
    #agents = 8
    
    print("Using {0} cores to perfrom parallel processing... \n".format(int(agents)))
    
    # Create a pool of processes. By default, one is created for each CPU in the machine.
    # extract the bouding box for each image in file list
    with closing(Pool(processes = agents)) as pool:
        result_list = pool.map(extract_traits, imgList)
        pool.terminate()
    '''
    
    
    #trait_file = (os.path.dirname(os.path.abspath(file_path)) + '/' + 'trait.xlsx')
    
    print("Summary: {0} plant images were processed...\n".format(n_images))
    
    #output in command window in a sum table
 
    table = tabulate(result_list, headers = ['filename', 'area', 'temp_index', 'max_width', 'max_height' ,'avg_curv', 'n_leaves'], tablefmt = 'orgtbl')

    print(table + "\n")
    
    
    '''
    print("Summary: Leaf specific traits...\n")
    
    #output in command window in a sum table
 
    table = tabulate(result_list_leaf, headers = ['filename', 'leaf_index', 'area', 'curvature', 'temp', 'major_axis', 'minor_axis', 'cluster 1', 'cluster 2', 'cluster 3', 'cluster 4'], tablefmt = 'orgtbl')

    print(table + "\n")
    '''
    
    
    if (args['result']):

        trait_file = (args['result'] + 'trait.xlsx')
        trait_file_csv = (args['result'] + 'trait.csv')
    else:
        trait_file = (file_path + 'trait.xlsx')
        trait_file_csv = (file_path + 'trait.csv')
    
    
    if os.path.isfile(trait_file):
        # update values
        #Open an xlsx for reading
        wb = openpyxl.load_workbook(trait_file)

        #Get the current Active Sheet
        sheet = wb.active
        
        sheet.delete_rows(2, sheet.max_row+1) # for entire sheet

    else:
        # Keep presets
        wb = openpyxl.Workbook()
        sheet = wb.active
        
        #sheet_leaf = wb.create_sheet()

        sheet.cell(row = 1, column = 1).value = 'filename'
        sheet.cell(row = 1, column = 2).value = 'leaf_area'
        sheet.cell(row = 1, column = 3).value = 'temp_index'
        sheet.cell(row = 1, column = 4).value = 'max_width'
        sheet.cell(row = 1, column = 5).value = 'max_height'
        sheet.cell(row = 1, column = 6).value = 'curvature'
        sheet.cell(row = 1, column = 7).value = 'number_leaf'
        
        '''
        sheet_leaf.cell(row = 1, column = 1).value = 'filename'
        sheet_leaf.cell(row = 1, column = 2).value = 'leaf_index'
        sheet_leaf.cell(row = 1, column = 3).value = 'area'
        sheet_leaf.cell(row = 1, column = 4).value = 'curvature'
        sheet_leaf.cell(row = 1, column = 5).value = 'temp_index'
        sheet_leaf.cell(row = 1, column = 6).value = 'major_axis'
        sheet_leaf.cell(row = 1, column = 7).value = 'minor_axis'
        sheet_leaf.cell(row = 1, column = 8).value = 'color distribution cluster 1'
        sheet_leaf.cell(row = 1, column = 9).value = 'color distribution cluster 2'
        sheet_leaf.cell(row = 1, column = 10).value = 'color distribution cluster 3'
        sheet_leaf.cell(row = 1, column = 11).value = 'color distribution cluster 4'
        '''
        
    for row in result_list:
        sheet.append(row)
   
    #for row in result_list_leaf:
        #sheet_leaf.append(row)
        
    #for row in result_list_leaf:
        #sheet_leaf.append(row)
    
    #save the csv file
    wb.save(trait_file)
    
    
    
    '''
    wb = openpyxl.load_workbook(trait_file)
    sh = wb.active # was .get_active_sheet()
    with open(trait_file_csv, 'w', newline = "") as f:
        c = csv.writer(f)
        for r in sh.rows: # generator; was sh.rows
            c.writerow([cell.value for cell in r])
    '''