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

# # Doing Measures on Images

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# import smilPython 
import smilPython as sp
# functions using matplotlib to display images on jupyter notebooks
from smilPlot import *

import numpy as np


# ## Let's begin
# 

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# Load an image
imIn = sp.Image("http://smil.cmm.mines-paristech.fr/images/DNA_small.png")
#imIn.show()
 
imThr = sp.Image(imIn)
sp.threshold(imIn, imThr)
 
imLbl = sp.Image(imIn, "UINT16")
sp.label(imThr, imLbl)

smilPlot([imIn, imLbl], label = [False, True])


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# Bounding boxes
bboxes = sp.measBoundBoxes(imLbl)
imRec = sp.Image(imIn)
#sp.drawRectangles(imRec, bboxes)
imIn.getViewer().drawOverlay(imRec)

# Blobs measures
blobs = sp.computeBlobs(imLbl)
# areas
areas = sp.measAreas(blobs) # equivalent but faster than measAreas(imLbl)
# barycenters
barys = sp.measBarycenters(imLbl, blobs)
# volume of blobs in imIn
vols  = sp.measVolumes(imIn, blobs)

# Print results
print("{0:5s}  {1:6s}  {2:8s}  {3:s}".format("Label", " Area", " Volume", " Barycenter (x,y)"))
for lbl in blobs.keys():
  print("{0:5d}  {1:6.1f}  {2:8.1f}  ( {3:8.3f} {4:8.3f} )".
        format(lbl, areas[lbl], vols[lbl], barys[lbl][0], barys[lbl][1]))


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