annotate projective_transformation_points.py @ 7:499ad4d9aa13 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/projective_transformation_points/ commit c045f067a57e8308308cf6329060c7ccd3fc372f

"""
Copyright 2019-2022 Biomedical Computer Vision Group, Heidelberg University.

Distributed under the MIT license.
See file LICENSE for detail or copy at https://opensource.org/licenses/MIT

"""

import argparse

import numpy as np
import pandas as pd
from scipy.ndimage import map_coordinates
from skimage.transform import ProjectiveTransform


def _stackcopy(a, b):
    if a.ndim == 3:
        a[:] = b[:, :, np.newaxis]
    else:
        a[:] = b


def warp_img_coords_batch(coord_map, shape, dtype=np.float64, batch_size=1000000):
    rows, cols = shape[0], shape[1]
    coords_shape = [len(shape), rows, cols]
    if len(shape) == 3:
        coords_shape.append(shape[2])
    coords = np.empty(coords_shape, dtype=dtype)

    tf_coords = np.indices((cols, rows), dtype=dtype).reshape(2, -1).T

    for i in range(0, (tf_coords.shape[0] // batch_size + 1)):
        tf_coords[batch_size * i:batch_size * (i + 1)] = coord_map(tf_coords[batch_size * i:batch_size * (i + 1)])
    tf_coords = tf_coords.T.reshape((-1, cols, rows)).swapaxes(1, 2)

    _stackcopy(coords[1, ...], tf_coords[0, ...])
    _stackcopy(coords[0, ...], tf_coords[1, ...])
    if len(shape) == 3:
        coords[2, ...] = range(shape[2])

    return coords


def warp_coords_batch(coord_map, coords, dtype=np.float64, batch_size=1000000):
    tf_coords = coords.astype(np.float32)[:, ::-1]

    for i in range(0, (tf_coords.shape[0] // batch_size) + 1):
        tf_coords[batch_size * i:batch_size * (i + 1)] = coord_map(tf_coords[batch_size * i:batch_size * (i + 1)])

    return tf_coords[:, ::-1]


def transform(fn_roi_coords, fn_warp_matrix, fn_out):
    data = pd.read_csv(fn_roi_coords, delimiter="\t")
    all_data = np.array(data)

    nrows, ncols = all_data.shape[0:2]
    roi_coords = all_data.take([0, 1], axis=1).astype('int64')

    tol = 10
    moving = np.zeros(np.max(roi_coords, axis=0) + tol, dtype=np.uint32)
    idx_roi_coords = (roi_coords[:, 0] - 1) * moving.shape[1] + roi_coords[:, 1] - 1
    moving.flat[idx_roi_coords] = np.transpose(np.arange(nrows) + 1)

    trans_matrix = np.array(pd.read_csv(fn_warp_matrix, delimiter="\t", header=None))
    transP = ProjectiveTransform(matrix=trans_matrix)
    roi_coords_warped_direct = warp_coords_batch(transP, roi_coords)
    shape_fixed = np.round(np.max(roi_coords_warped_direct, axis=0)).astype(roi_coords.dtype) + tol

    transI = ProjectiveTransform(matrix=np.linalg.inv(trans_matrix))
    img_coords_warped = warp_img_coords_batch(transI, shape_fixed)

    moving_warped = map_coordinates(moving, img_coords_warped, order=0, mode='constant', cval=0)
    idx_roi_coords_warped = np.where(moving_warped > 0)
    roi_annots_warped = moving_warped.compress((moving_warped > 0).flat)

    df = pd.DataFrame()
    col_names = data.columns.tolist()
    df['x'] = idx_roi_coords_warped[0] + 1
    df['y'] = idx_roi_coords_warped[1] + 1
    if ncols > 2:
        for i in range(2, ncols):
            df[col_names[i]] = all_data[:, i].take(roi_annots_warped - 1)
    df.to_csv(fn_out, index=False, sep="\t")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Transform ROIs defined by pixel (point) coordinates")
    parser.add_argument("coords", help="Path to the TSV file of the coordinates (and labels) to be transformed")
    parser.add_argument("tmat", help="Path to the TSV file of the transformation matrix")
    parser.add_argument("out", help="Path to the TSV file of the transformed coordinates (and labels)")
    args = parser.parse_args()
    transform(args.coords, args.tmat, args.out)