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Guillaume Perréal authored4b985330
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# -*- coding: utf-8 -*-
"""
Created on Wed Sep 11 19:09:06 2019
@author: german.martinez-carvajal
"""
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 11 18:25:20 2019
@author: german.martinez-carvajal
"""
import tifffile
from os import chdir
import numpy as np
import pandas as pd
import multiprocessing as mp
def computations(label):
pore = (image == label)
v = np.count_nonzero(pore)
coords = np.where(image == label) # z, y, x
x0 = np.min(coords[2])
y0 = np.min(coords[1])
z0 = np.min(coords[0])
xf = np.max(coords[2])
yf = np.max(coords[1])
zf = np.max(coords[0])
delta_x = xf - x0
delta_y = yf - y0
delta_z = zf - z0
connected = int(z0 == 0)
return(np.array([label,v,x0,y0,z0,xf,yf,zf, delta_x, delta_y, delta_z, connected]))
def statistics(path_read, file, paht_save, sample_name, n_p):
# reading
chdir(path_read)
print("reading...", path_read, file)
global image
image = tifffile.imread(file)
# counting number of pores
print("extracting labels...")
labels = np.unique(image)
labels = labels[labels !=0]
print("{} labels were found !".format(len(labels)))
# number of pores
num_pores = len(labels)
print('computing ...')
# 12 columns : label,v,x0,y0,z0,xf,yf,zf, delta_x, delta_y, delta_z, connected
my_statistics = np.zeros((num_pores, 12) ,dtype = int)
# Step 1: Init multiprocessing.Pool
if n_p == None:
pool = mp.Pool(mp.cpu_count())
else:
assert n_p < mp.cpu_count()
pool = mp.Pool(n_p)
# Step 2: `pool.apply` the `howmany_within_range()`
my_statistics = pool.map(computations, [label for label in labels])
# Step 3: Don't forget to close
pool.close()
frame = pd.DataFrame(data=my_statistics, # values
index = range(num_pores), # 1st column as index
columns=["label","v (vox)","x0","y0","z0","xf","yf","zf", "delta_x", "delta_y", "delta_z", "connected to top ?"] )
chdir(path_save)
frame.to_csv("statistics_CR_yes_paralelized_{}.csv".format(sample_name) ,sep = ';')
print('finished treating sample {}'.format(sample_name))
path_read = '/home/german.martinez-carvajal/Desktop/These/Connecting_CR/test'
path_save = path_read
file = 'small_top.tif'
sample_name = "small_top"
statistics(path_read, file, path_save, sample_name, n_p = None)