B6_dapi_template/auto_seg.py

# System imports
from pathlib import Path
from pprint import pprint
import argparse
import sys
# 3rd Party imports
import numpy as np
import scipy.stats
import nibabel as nib
from nipype.interfaces import ants
# Local source tree imports
import registration
import tools
import preprocess as pre

TEMP_DIR = Path('temp')
OUTPUT_DIR = Path('output')
IMG_DIR = Path('Images')


def find_optimal_index(slice_path, template_path, approx, dist=3):
    """
    Finds the most appropriate index in template path to register the slice file to.
    :param approx: Approximate index of slice relative to template file
    :param dist: maximum distance of slices away from approximate to index to check
    :return: index of slice in template which has highest metric - combined mutual information and dice coefficient.
    """
    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(TEMP_DIR/f't_slice{i}.nii')
        registered_loc = str(TEMP_DIR/ f'reg_slice{i}.nii')
        transform_prefix = str(TEMP_DIR/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_data()
        registered_data = nib.load(registered_loc).get_data()
        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*2) / scipy.stats.norm.pdf(dist, dist, dist*2)
        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])
    return optimal[0]


def apply_transform(segmentation, fixed, index, out_dir):
    """
    Full transforms the slice->template slice, and then applies the reverse transform to the segmentation slice, to get
    a segmentation of the slice.
    :return: Location of the segmentation slice registered to the slice
    """
    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'{seg_slice_loc.stem}_t.nii'

    template_slice_loc = str(TEMP_DIR / f't_slice{index}.nii')

    registration.full_registration(str(template_slice_loc), str(fixed),
                                   str(Path(out_dir, f'{fixed.stem}_t.nii')), str(out_dir / f'Final-'))
    transform = [str(out_dir / f"Final-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):
    """
    Provided path to slice, segmentation, template and an approximate index, will apply multiple registrations to create
    an automatic segmentation of the slice
    :param dapi: index of DAPI modality channel
    :return: Location of the segmentation slice registered to the slice
    """
    out_subdir = Path(OUT_DIR) / Path(slice_path).stem.replace(' ', '').replace(',', '').replace('.', '')
    tools.create_dir(TEMP_DIR)
    tools.create_dir(out_subdir)

    channel_paths = pre.split_nii_channels(slice_path, out_subdir, False, dapi-1)

    optimal_index = find_optimal_index(channel_paths[dapi-1], template_path, approx_index)

    seg_loc = apply_transform(segment_path, channel_paths[dapi-1], optimal_index, out_subdir)
    tools.remove_dir(TEMP_DIR)
    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", type=float, help="Approx bregma coordinates")
    parser.add_argument("--out", 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()
    OUT_DIR = Path(args.out)
    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)