B6_dapi_template/automatic_segmentation_program/runner.py

from pathlib import Path
from pprint import pprint
import argparse
import sys
import os
import numpy as np
import scipy.stats
import nibabel as nib
from nipype.interfaces import ants
import registration
import tools
import preprocess

from PIL import Image, ImageSequence
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)

def find_optimal_index(slice_path, template_path, approx, temporary_directory, dist = 2):

    weights = []
    for i in range(approx-dist,approx+dist+1):
        print(f'Slice index: {i}')
        _slice = nib.load(str(slice_path))
        template_slice_loc = str(temporary_directory / f't_slice{i}.nii')
        registered_loc = str(temporary_directory / f'reg_slice{i}.nii')
        transform_prefix = str(temporary_directory / f'{i}-')

        tools.save_slice(str(template_path), template_slice_loc, i, np.eye(4), _slice.header)
        registration.rigid_registration(template_slice_loc, str(slice_path), registered_loc, transform_prefix)

        template_data = nib.load(str(template_slice_loc)).get_fdata()
        registered_data = nib.load(registered_loc).get_fdata()
        registered_data = tools.resize_im(registered_data, template_data)
        nib.save(nib.Nifti1Image(registered_data, np.eye(4)), registered_loc)

        mutualinfo = tools.mutual_info_mask(template_data, registered_data)
        norm_factor = scipy.stats.norm.pdf(i-approx+dist, dist, dist*10) / scipy.stats.norm.pdf(dist, dist, dist*10)
        dice_coef = tools.dice_coef(template_data, registered_data)
        weights.append((i, norm_factor * (0.7 * mutualinfo + 0.3 * dice_coef)))

    pprint(weights)
    optimal = max(weights, key=lambda a: a[1])
    print(optimal[0])
    return optimal[0]

def apply_transform(segmentation, fixed, index, out_dir, temporary_directory):

    seg_slice_loc = out_dir / "segment_slice.nii" 
    tools.save_slice(str(segmentation), str(seg_slice_loc), index, np.eye(4), nib.load(str(fixed)).header)
    post_transform_loc = out_dir / f'Segmentation.nii'

    template_slice_loc = str(temporary_directory / f't_slice{index}.nii')
    registration.full_registration(str(template_slice_loc), str(fixed),
                                   str(Path(out_dir, f'{fixed.stem}_template.nii')), str(out_dir / f'TemplateSlice_'))
                                                             
    transform = [str(out_dir / f"TemplateSlice_InverseComposite.h5")]
    reverse_transform = ants.ApplyTransforms(
            input_image=str(seg_slice_loc),
            reference_image=str(fixed),
            transforms=transform,
            invert_transform_flags=[False],
            interpolation='MultiLabel',
            dimension=2,
            output_image=str(post_transform_loc))
    reverse_transform.run()

    return post_transform_loc

def generate_segmentation(slice_path, segment_path, template_path, approx_index, dapi, output_directory):     
    tools.create_dir(output_directory)

    if slice_path.endswith('.tiff') or slice_path.endswith('.tif'):
        Image.MAX_IMAGE_PIXELS = None
        tif_path = preprocess.tiff_to_nii(slice_path, output_directory)
        slice_path = tif_path[0]
    elif not slice_path.endswith(".nii"):
        print('Selected slice file was neither a nifti or a TIFF file. Please check slice file format')
        sys.exit(2)
        
    out_subdir = Path(output_directory) / Path(slice_path).stem.replace(' ', '_').replace(',','_').replace('.','')
    tools.create_dir(out_subdir)
    temporary_directory = Path(out_subdir) / 'tmp'
    tools.create_dir(temporary_directory)
    channel_paths = preprocess.split_nii_channels(slice_path, out_subdir, True, dapi-1)
    optimal_index = find_optimal_index(channel_paths[dapi-1], template_path, approx_index, temporary_directory)
    seg_loc = apply_transform(segment_path, channel_paths[dapi-1], optimal_index, out_subdir, temporary_directory)
    
    tools.remove_dir(temporary_directory)
    os.remove(Path(out_subdir) / 'segment_slice.nii')
    os.rename(Path(out_subdir) / 'TemplateSlice_Composite.h5', Path(out_subdir) / 'Transformation_Composite.h5')
    os.rename(Path(out_subdir) / 'TemplateSlice_InverseComposite.h5', Path(out_subdir) / 'Transformation_InverseComposite.h5')
    
    return seg_loc

if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("sliceloc", metavar="Slice Location", help="Location of preprocessed slice")
    parser.add_argument("segloc", metavar="Segmentation Location", help="Location of segmentation")
    parser.add_argument("tloc", metavar="Template Location", help="Location of template file")
    parser.add_argument("--approx", type = int, default=-1, help="Approximate index of slice relative to template file")
    parser.add_argument("bregma", metavar = 'Bregma index', type = float, help="Approx bregma coordinates")
    parser.add_argument("out", metavar = 'Output directory', default="output", help="Output directory")
    parser.add_argument("--dapi", type=int, default=0, help="DAPI channel number, default is last channel")

    args = parser.parse_args()
    if args.approx == -1 and not args.bregma:
        print("Error: Please specify an approximate location in the template, or a bregma coordinate of the slice")
        sys.exit(2)
    if args.bregma:
        args.approx = tools.bregma_to_slice_index(args.bregma)
    generate_segmentation(args.sliceloc, args.segloc, args.tloc, args.approx, args.dapi, args.out)