annotate spot_detection_2d.py @ 4:14f9986800fa draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf

"""
Copyright 2021-2022 Biomedical Computer Vision Group, Heidelberg University.
Author: Qi Gao ([e-mail])

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

"""

import argparse

import imageio
import numpy as np
import pandas as pd
from skimage.feature import peak_local_max
from skimage.filters import gaussian, laplace


def getbr(xy, img, nb, firstn):
    ndata = xy.shape[0]
    br = np.empty((ndata, 1))
    for j in range(ndata):
        br[j] = np.NaN
        if not np.isnan(xy[j, 0]):
            timg = img[xy[j, 1] - nb - 1:xy[j, 1] + nb, xy[j, 0] - nb - 1:xy[j, 0] + nb]
            br[j] = np.mean(np.sort(timg, axis=None)[-firstn:])
    return br


def spot_detection(fn_in, fn_out, frame_1st=1, frame_end=0,
                   typ_filter='Gauss', ssig=1, th=10,
                   typ_br='smoothed', bd=10):
    ims_ori = imageio.mimread(fn_in, format='TIFF')
    ims_smd = np.zeros((len(ims_ori), ims_ori[0].shape[0], ims_ori[0].shape[1]), dtype='float64')
    if frame_end == 0 or frame_end > len(ims_ori):
        frame_end = len(ims_ori)

    for i in range(frame_1st - 1, frame_end):
        ims_smd[i, :, :] = gaussian(ims_ori[i].astype('float64'), sigma=ssig)
    ims_smd_max = np.max(ims_smd)

    txyb_all = np.array([]).reshape(0, 4)
    for i in range(frame_1st - 1, frame_end):
        tmp = np.copy(ims_smd[i, :, :])
        if typ_filter == 'LoG':
            tmp = laplace(tmp)

        tmp[tmp < th * ims_smd_max / 100] = 0
        coords = peak_local_max(tmp, min_distance=1)
        idx_to_del = np.where((coords[:, 0] <= bd) | (coords[:, 0] >= tmp.shape[0] - bd) |
                              (coords[:, 1] <= bd) | (coords[:, 1] >= tmp.shape[1] - bd))
        coords = np.delete(coords, idx_to_del[0], axis=0)
        xys = coords[:, ::-1]

        if typ_br == 'smoothed':
            intens = getbr(xys, ims_smd[i, :, :], 0, 1)
        elif typ_br == 'robust':
            intens = getbr(xys, ims_ori[i], 1, 4)
        else:
            intens = getbr(xys, ims_ori[i], 0, 1)

        txyb = np.concatenate(((i + 1) * np.ones((xys.shape[0], 1)), xys, intens), axis=1)
        txyb_all = np.concatenate((txyb_all, txyb), axis=0)

    df = pd.DataFrame()
    df['FRAME'] = txyb_all[:, 0].astype(int)
    df['POS_X'] = txyb_all[:, 1].astype(int)
    df['POS_Y'] = txyb_all[:, 2].astype(int)
    df['INTENSITY'] = txyb_all[:, 3]
    df.to_csv(fn_out, index=False, float_format='%.2f', sep="\t")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Spot detection")
    parser.add_argument("fn_in", help="Name of input image sequence (stack)")
    parser.add_argument("fn_out", help="Name of output file to save the coordinates and intensities of detected spots")
    parser.add_argument("frame_1st", type=int, help="Index for the starting frame to detect spots (1 for first frame of the stack)")
    parser.add_argument("frame_end", type=int, help="Index for the last frame to detect spots (0 for the last frame of the stack)")
    parser.add_argument("filter", help="Detection filter")
    parser.add_argument("ssig", type=float, help="Sigma of the Gaussian for noise suppression")
    parser.add_argument("thres", type=float, help="Percentage of the global maximal for thresholding candidate spots")
    parser.add_argument("typ_intens", help="smoothed or robust (for measuring the intensities of spots)")
    parser.add_argument("bndy", type=int, help="Number of pixels (Spots close to image boundaries will be ignored)")
    args = parser.parse_args()
    spot_detection(args.fn_in, args.fn_out,
                   frame_1st=args.frame_1st, frame_end=args.frame_end,
                   typ_filter=args.filter, ssig=args.ssig, th=args.thres,
                   typ_br=args.typ_intens, bd=args.bndy)