CopySampleImages.py

#! /home/spl/ml/sitk/bin/python

import os
import shutil
import glob
import sys
from pathlib import Path
import re

if len(sys.argv) == 1:
    masterdir = Path.cwd()
else:
    masterdir = Path(sys.argv[1])

sampledir = os.path.join(masterdir,'sampleImg')

if not os.path.exists(sampledir):
    os.mkdir(sampledir)
else:
    shutil.rmtree(sampledir)
    os.mkdir(sampledir)

failed = [] # use this one to output a list of failed registration

for folder in os.listdir(masterdir):

    if 'tibia' in folder.lower():     #if 'week' in folder.lower():
        images = [image for image in sorted(glob.glob(os.path.join(masterdir,folder,'*'))) 
                    if re.search(r"(00\d{3,6}).(tif|bmp|png)$",image)]
        try:
            distal=images[0]  #420
            midline = images[int(len(images)*0.7)]
            proximal=images[-75]
            sampleimg = [proximal,distal,midline]
            for img in sampleimg:
                shutil.copyfile(img,os.path.join(sampledir,os.path.basename(img)))
        except IndexError:
            print('No files for {}'.format(folder))
            failed.append(folder)  #
            continue





print('Done!') #