#!/usr/bin/env python

'''
Usage:
measure_sepal.py filename outputdir

- filename = path and name of the stack file containing the object (background=0)
the object is supposed already oriented as follows:
- output = output directory
---------------------------------------------------------------------------------
- CM in the middle of the image
- first principal axis along y
- second principal axis along x

Output:

measured data is written into the file output.csv
flat projections are written in the output directory

'''

from sys import argv
import os
import numpy as np
from scipy.ndimage.morphology import binary_closing, binary_opening

from titk_tools.io import imread, imsave
from bib_sepals import *


print('============== measure_sepal.py =================')

filename = argv[1]
outdir = argv[2]

outputfile=outdir+"/"+outdir+".csv"

outputdir=outdir+"/sections/"
projectiondir=outdir+"/projections"

print(argv)

imname = filename.split('/')[-1]
imnameroot = imname.split('.')[0]

projected2Dimage=projectiondir+"/"+imnameroot+"2D.png"
#projected2Dimage_hight=outdir+"/hight_"+imnameroot+"2D.png"

os.system("mkdir -p "+outputdir)

outname = outputfile.split('/')[-1]
outroot = outname.split('.')[0]

print("----------------------")
print("reading the file ", filename)
print("----------------------")
sepale=imread(filename)
voxelsize = sepale.voxelsize
print("voxelsize=",voxelsize)
s = sepale.shape
print("shape=",s)

print("Projecting on 2D...")

def project2D(im3):
	s2=(s[1],s[0])
	im2=np.zeros(s2, dtype='uint8')
	for i in range(s[0]):
		im2[:,i]=np.array([max(im3[i,j,:]) for j in range(s[1])])
	return im2

def project2D_hightmap(im3):
	s2=(s[1],s[0])
	im2=np.zeros(s2, dtype='uint8')
	for i in range(s[0]):
		im2[:,i]=np.array([list(im3[i,j,:]).index(max(im3[i,j,:])) for j in range(s[1])])
	return im2


sepale2D=project2D(sepale)
imsave2D(projected2Dimage, sepale2D)

'''
sepale2D=project2D_hightmap(sepale)
imsave2D(projected2Dimage_hight, sepale2D)
'''

print('Extracting principal section curves...')

# longitudinal section
x_section = sepale[int(s[0]/2), :, :]
xup_filename = outputdir+imnameroot+'_section_xup.txt'
xdown_filename = outputdir+imnameroot+'_section_xdown.txt'
x_filename = outputdir+imnameroot+'_section_x.txt'
x_pixelsize = (voxelsize[1],voxelsize[2])
xup, xdown = extract_curves(x_section)

write_curve(xup, x_pixelsize, xup_filename)


# transversal section
y_section = sepale[:,int(s[1]/2), :]
yup_filename = outputdir+imnameroot+'_section_yup.txt'
ydown_filename = outputdir+imnameroot+'_section_ydown.txt'
y_filename = outputdir+imnameroot+'_section_y.txt'
y_pixelsize = (voxelsize[0],voxelsize[2])
yup, ydown = extract_curves(y_section)

write_curve(yup, y_pixelsize, yup_filename)


# 
# ----------------------------------------
print('Analyzing principal section curves...')

if not(os.path.isfile(outputfile)):
	FILE = open(outputfile,"w")
	FILE.write('Sepal;CurvedLength;FlatLength;LHeight;LR;LR21;LR22;LR41;LR423;LR44;CurvedWidth;FlatWidth;THeight;TR;TR21;TR22;TR41;TR423;TR44\n')
	FILE.close()

FILE = open(outputfile,"a")
FILE.write(imnameroot+';')

outfile=outroot+'_up_longitudinal.csv'
graph_name= outputdir+imnameroot+'_up_longitudinal.png'
length_x, flatlength_x, height_x, R, R21, R22, R41, R423, R44=analyze_curve1(imnameroot, xup, x_pixelsize, outfile, graph_name)
os.system("rm "+outfile)

FILE.write(str(length_x)+';'+str(flatlength_x)+';'+str(height_x)+';'+str(R)+';'+str(R21)+';'+str(R22)+';'+str(R41)+';'+str(R423)+';'+str(R44)+';')

outfile=outroot+'_up_transversal.csv'
graph_name= outputdir+imnameroot+'_up_transversal.png'
length_y, flatlength_y, height_y, R, R21, R22, R41, R423, R44=analyze_curve1(imnameroot, yup, y_pixelsize, outfile, graph_name)
os.system("rm "+outfile)

FILE.write(str(length_y)+';'+str(flatlength_y)+';'+str(height_y)+';'+str(R)+';'+str(R21)+';'+str(R22)+';'+str(R41)+';'+str(R423)+';'+str(R44)+'\n')