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main_align_2_views.py
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main_align_2_views.py
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#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 9 15:03:04 2018
@author: felix
"""
if __name__=="__main__":
import numpy as np
import Utility_Functions.file_io as fio
import Utility_Functions.stack as stack
from Visualisation.grid_img import viz_grid
import pylab as plt
import Registration.registration_new as registration
from skimage.exposure import rescale_intensity
import Unzipping.unzip as uzip
import scipy.io as spio
import os
dataset_folder = '../../Data/Holly/czifile_test_tiff'
out_view_aligned_folder = os.path.join(dataset_folder, 'view_aligned-t'); fio.mkdir(out_view_aligned_folder)
"""
Load dataset and pair up data.
"""
dataset_files = fio.load_dataset(dataset_folder, ext='.tif', split_key='_',split_position=3) # load in the just aligned files.
view_pair_files = fio.pair_views(dataset_files, ext='.tif', split_key='_',split_position=3, view_by=2)
"""
Do Sift3D registration to align the sequence of paired views.
"""
processfiles = np.hstack(view_pair_files)
reg_config = {'downsample': 8.,
# 'lib_path': '../Pipeline/SIFT3D/build/lib/wrappers/matlab/',
'lib_path': '/home/felix/Documents/Software/SIFT3D/build/lib/wrappers/matlab',
'mode':1,
'return_img':0}
# register views: mode=1
tforms = registration.register3D_SIFT_wrapper(processfiles, dataset_folder, out_view_aligned_folder, reg_config)