image_preprocessing_benedict.py

from ThreeDLabeler import preprocessing as pp
import os
import numpy as np
import nibabel as nib

BASE_DIR = ('/mnt/Storage2/Hallgrimsson/Automated_Phenotyping/Global/' +
            'ALL_MICE/Source/')
TAG_DIR = ("/mnt/Storage2/Hallgrimsson/Automated_Phenotyping/Global/ALL_MICE" +
           '/Source/txt')

MNC_DIR = ("/mnt/Storage2/Hallgrimsson/Automated_Phenotyping/Global/ALL_MICE" +
           '/Source/MNC')


tag_files = os.listdir(TAG_DIR)
mnc_files = os.listdir(MNC_DIR)


mnc_files = [i for i in mnc_files if '.mnc' in i]  # necessary for removing png
tag_files = [i for i in tag_files if '.tag' in i]


mnc_num = [i.split('_to_Global')[0] for i in mnc_files]
tag_num = [i.split('_landmar')[0] for i in tag_files]

mnc_num = np.array(mnc_num)
mnc_files = np.array(mnc_files)
tag_num = np.array(tag_num)
tag_files = np.array(tag_files)

diff_files = np.setdiff1d(tag_num, mnc_num)

assert diff_files.shape == (1,)  # to make sure there aren't more than one.

tag_files = np.delete(tag_files, np.where(tag_num == diff_files[0]))
tag_num = np.delete(tag_num, np.where(tag_num == diff_files[0]))

assert np.alltrue(tag_num == mnc_num)

pp.package_to_npy(BASE_DIR, mnc_files[:3],
                  tag_files[:3],
                  mnc_num[:3],
                  mnc_sub_folder='MNC/',
                  tag_sub_folder='txt/',
                  output_path='/home/kail/NewSkulls')


img = nib.load(MNC_DIR+'/'+mnc_files[0])

tag1 = pp.tag_parser(TAG_DIR+'/'+tag_files[0])

test = pp.Image(img.get_data(), tag1)

test.cube().scale