Mercurial > repos > imgteam > points_association_nn

annotate points_association_nn.py @ 0:04e692ee53a8 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
author imgteam
date Thu, 22 Jul 2021 22:29:47 +0000
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children b30aa285ac0a
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04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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1 """
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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2 Copyright 2021 Biomedical Computer Vision Group, Heidelberg University.
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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3 Author: Qi Gao (qi.gao@bioquant.uni-heidelberg.de)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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4
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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5 Distributed under the MIT license.
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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6 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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7
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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8 """
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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10 import argparse
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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12 import numpy as np
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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13 import openpyxl # noqa: F401
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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14 import pandas as pd
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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15 import skimage.util
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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18 def disk_mask(imsz, ir, ic, nbpx):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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19 ys, xs = np.ogrid[-nbpx:nbpx + 1, -nbpx:nbpx + 1]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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20 se = xs ** 2 + ys ** 2 <= nbpx ** 2
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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21 mask = np.zeros(imsz, dtype=int)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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22 if ir - nbpx < 0 or ic - nbpx < 0 or ir + nbpx + 1 > imsz[0] or ic + nbpx + 1 > imsz[1]:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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23 mask = skimage.util.pad(mask, nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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24 mask[ir:ir + 2 * nbpx + 1, ic:ic + 2 * nbpx + 1] = se
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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25 mask = skimage.util.crop(mask, nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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26 else:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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27 mask[ir - nbpx:ir + nbpx + 1, ic - nbpx:ic + nbpx + 1] = se
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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28 return mask
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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31 def find_nn(cim, icy, icx, nim, nbpx):
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32 mask = disk_mask(cim.shape, icy, icx, nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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33 iys_nim, ixs_nim = np.where(nim * mask)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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34 if iys_nim.size == 0:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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35 return np.NaN, np.NaN
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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36
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37 d2 = (icy - iys_nim) ** 2 + (icx - ixs_nim) ** 2
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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38 I1 = np.argsort(d2)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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39 iy_nim = iys_nim[I1[0]]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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40 ix_nim = ixs_nim[I1[0]]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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41
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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42 mask = disk_mask(cim.shape, iy_nim, ix_nim, nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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43 iys_cim, ixs_cim = np.where(cim * mask)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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44 d2 = (iy_nim - iys_cim) ** 2 + (ix_nim - ixs_cim) ** 2
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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45 I2 = np.argsort(d2)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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46 if not iys_cim[I2[0]] == icy or not ixs_cim[I2[0]] == icx:
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47 return np.NaN, np.NaN
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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48
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49 return iy_nim, ix_nim
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50
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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51
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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52 def points_linking(fn_in, fn_out, nbpx=6, th=25, minlen=50):
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53 data = pd.read_csv(fn_in, delimiter="\t")
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54 all_data = np.array(data)
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55 assert all_data.shape[1] in [3, 4], 'unknow collum(s) in input data!'
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56
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57 coords = all_data[:, :3].astype('int64')
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58
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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59 frame_1st = np.min(coords[:, 0])
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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60 frame_end = np.max(coords[:, 0])
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61 assert set([i for i in range(frame_1st, frame_end + 1)]).issubset(set(coords[:, 0].tolist())), "spots missing at some time point!"
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62
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63 nSlices = frame_end
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64 stack_h = np.max(coords[:, 2]) + nbpx
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65 stack_w = np.max(coords[:, 1]) + nbpx
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66 stack = np.zeros((stack_h, stack_w, nSlices), dtype='int8')
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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67 stack_r = np.zeros((stack_h, stack_w, nSlices), dtype='float64')
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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68
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69 for i in range(all_data.shape[0]):
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70 iyxz = tuple(coords[i, ::-1] - 1)
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71 stack[iyxz] = 1
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72 stack_r[iyxz] = all_data[i, -1]
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73
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74 tracks_all = np.array([], dtype=float).reshape(0, nSlices, 4)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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75 maxv = np.max(stack_r)
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76 br_max = maxv
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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77 idx_max = np.argmax(stack_r)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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78 while 1:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
79 iyxz = np.unravel_index(idx_max, stack.shape)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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80
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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81 spot_br = np.empty((nSlices, 1))
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
82 track = np.empty((nSlices, 3))
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
83 for i in range(nSlices):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
84 spot_br[i] = np.NaN
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
85 track[i, :] = np.array((np.NaN, np.NaN, np.NaN))
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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86
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
87 spot_br[iyxz[2]] = maxv
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
88 track[iyxz[2], :] = np.array(iyxz[::-1]) + 1
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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89
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
90 # forward
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
91 icy = iyxz[0]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
92 icx = iyxz[1]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
93 for inz in range(iyxz[2] + 1, nSlices):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
94 iny, inx = find_nn(stack[:, :, inz - 1], icy, icx, stack[:, :, inz], nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
95 if np.isnan(iny) and not inz == nSlices - 1:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
96 iny, inx = find_nn(stack[:, :, inz - 1], icy, icx, stack[:, :, inz + 1], nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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97 if np.isnan(iny):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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98 break
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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99 else:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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100 iny = icy
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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101 inx = icx
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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102 stack[iny, inx, inz] = 1
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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103 stack_r[iny, inx, inz] = stack_r[iny, inx, inz - 1]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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104 elif np.isnan(iny) and inz == nSlices - 1:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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105 break
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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106
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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107 track[inz, :] = np.array((inz, inx, iny)) + 1
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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108 spot_br[inz] = stack_r[iny, inx, inz]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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109 icy = iny
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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110 icx = inx
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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111
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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112 # backward
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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113 icy = iyxz[0]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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114 icx = iyxz[1]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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115 for inz in range(iyxz[2] - 1, -1, -1):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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116 iny, inx = find_nn(stack[:, :, inz + 1], icy, icx, stack[:, :, inz], nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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117 if np.isnan(iny) and not inz == 0:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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118 iny, inx = find_nn(stack[:, :, inz + 1], icy, icx, stack[:, :, inz - 1], nbpx)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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119 if np.isnan(iny):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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120 break
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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121 else:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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122 iny = icy
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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123 inx = icx
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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124 stack[iny, inx, inz] = 1
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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125 stack_r[iny, inx, inz] = stack_r[iny, inx, inz + 1]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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126 elif np.isnan(iny) and inz == 0:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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127 break
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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128
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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129 track[inz, :] = np.array((inz, inx, iny)) + 1
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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130 spot_br[inz] = stack_r[iny, inx, inz]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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131 icy = iny
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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132 icx = inx
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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133
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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134 for iz in range(nSlices):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
135 if not np.isnan(track[iz, 0]):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
136 stack[track[iz, 2].astype(int) - 1, track[iz, 1].astype(int) - 1, iz] = 0
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
137 stack_r[track[iz, 2].astype(int) - 1, track[iz, 1].astype(int) - 1, iz] = 0
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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138
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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139 # discard short trajectories
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
140 if np.count_nonzero(~np.isnan(spot_br)) > minlen * (frame_end - frame_1st) / 100:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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141 tmp = np.concatenate((track, spot_br), axis=1)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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142 tracks_all = np.concatenate((tracks_all, tmp.reshape(1, -1, 4)), axis=0)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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143
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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144 maxv = np.max(stack_r)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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145 idx_max = np.argmax(stack_r)
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
146 if maxv < th * br_max / 100:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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147 break
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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148
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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149 with pd.ExcelWriter(fn_out, engine="openpyxl") as writer:
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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150 for i in range(tracks_all.shape[0]):
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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151 df = pd.DataFrame()
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
152 df['FRAME'] = tracks_all[i, :, 0]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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153 df['POS_X'] = tracks_all[i, :, 1]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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diff changeset
154 df['POS_Y'] = tracks_all[i, :, 2]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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155 df['INTENSITY'] = tracks_all[i, :, 3]
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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156 df.to_excel(writer, sheet_name='spot%s' % (i + 1), index=False, float_format='%.2f')
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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157 writer.save()
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158
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159
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160 if __name__ == "__main__":
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161 parser = argparse.ArgumentParser(description="Association of points in consecutive frames using the nearest neighbor algorithm")
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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162 parser.add_argument("fn_in", help="Name of input file (tsv tabular)")
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163 parser.add_argument("fn_out", help="Name of output file (xlsx)")
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164 parser.add_argument("nbpx", type=int, help="Neighborhood size in pixel")
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165 parser.add_argument("thres", type=float, help="Percentage of the global maximal intensity for thresholding some event")
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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166 parser.add_argument("minlen", type=float, help="Minimum length of tracks (percentage of senquence length)")
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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167 args = parser.parse_args()
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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168 points_linking(args.fn_in, args.fn_out, args.nbpx, args.thres, args.minlen)