Mercurial > repos > imgteam > points_association_nn

annotate points_association_nn.py @ 2:b30aa285ac0a draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
author imgteam
date Sun, 25 Jul 2021 20:10:46 +0000
parents 04e692ee53a8
children
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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 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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14 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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17 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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18 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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19 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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20 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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21 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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22 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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23 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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24 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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25 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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26 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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27 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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30 def find_nn(cim, icy, icx, 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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31 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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32 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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33 if iys_nim.size == 0:
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34 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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35
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 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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37 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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38 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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39 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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40
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 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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42 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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43 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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44 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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45 if not iys_cim[I2[0]] == icy or not ixs_cim[I2[0]] == 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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46 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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47
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48 return iy_nim, ix_nim
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49
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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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 def points_linking(fn_in, fn_out, nbpx=6, th=25, minlen=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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52 data = pd.read_csv(fn_in, delimiter="\t")
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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53 all_data = np.array(data)
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54 assert all_data.shape[1] in [3, 4], 'unknow collum(s) in input data!'
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55
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56 coords = all_data[:, :3].astype('int64')
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57
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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58 frame_1st = np.min(coords[:, 0])
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59 frame_end = np.max(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 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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61
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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62 nSlices = frame_end
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63 stack_h = np.max(coords[:, 2]) + nbpx
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64 stack_w = np.max(coords[:, 1]) + nbpx
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65 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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66 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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67
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68 for i in range(all_data.shape[0]):
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69 iyxz = tuple(coords[i, ::-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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70 stack[iyxz] = 1
2
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71 if all_data.shape[1] == 4:
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72 stack_r[iyxz] = all_data[i, -1]
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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73 else:
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74 stack_r[iyxz] = 1
0
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75
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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76 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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77 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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78 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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79 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"
imgteam
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diff changeset
80 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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81 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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82
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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83 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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84 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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85 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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86 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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87 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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88
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 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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90 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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91
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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92 # 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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93 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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94 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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95 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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96 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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97 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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98 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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99 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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100 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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101 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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102 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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103 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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104 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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105 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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106 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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107 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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108
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 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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110 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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111 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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112 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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113
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 # 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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115 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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116 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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117 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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118 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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119 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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120 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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121 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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122 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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123 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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124 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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125 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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126 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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127 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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128 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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129 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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130
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 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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132 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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133 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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134 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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135
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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136 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
137 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
138 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
139 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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140
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 # discard short trajectories
2
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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142 if np.count_nonzero(~np.isnan(spot_br)) > np.max((1, minlen * (frame_end - frame_1st) / 100)):
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 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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144 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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145
04e692ee53a8 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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146 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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147 idx_max = np.argmax(stack_r)
2
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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148 if maxv < th * br_max / 100 or maxv == 0:
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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149 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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150
2
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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diff changeset
151 with pd.ExcelWriter(fn_out) as writer:
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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152 if tracks_all.shape[0] == 0:
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 = pd.DataFrame()
2
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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diff changeset
154 df['No tracks found'] = np.NaN
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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diff changeset
155 df.to_excel(writer, index=False, float_format='%.2f')
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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diff changeset
156 else:
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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157 for i in range(tracks_all.shape[0]):
b30aa285ac0a "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit bf6e2870c94ed4ceb8bce4003813fe11724f5ca2"
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158 df = pd.DataFrame()
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159 df['FRAME'] = tracks_all[i, :, 0]
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160 df['POS_X'] = tracks_all[i, :, 1]
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161 df['POS_Y'] = tracks_all[i, :, 2]
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162 if all_data.shape[1] == 4:
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163 df['INTENSITY'] = tracks_all[i, :, 3]
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164 df.to_excel(writer, sheet_name='spot%s' % (i + 1), index=False, float_format='%.2f')
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165 writer.save()
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166
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167
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168 if __name__ == "__main__":
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169 parser = argparse.ArgumentParser(description="Association of points in consecutive frames using the nearest neighbor algorithm")
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170 parser.add_argument("fn_in", help="Coordinates (and intensities) of input points (tsv tabular)")
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171 parser.add_argument("fn_out", help="Name of output file (xlsx)")
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172 parser.add_argument("nbpx", type=int, help="Neighborhood size (in pixel) for associating points")
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173 parser.add_argument("thres", type=float, help="Tracks with all intensities lower than certain percentage (%) of the global maximal intensity will be discarded")
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174 parser.add_argument("minlen", type=float, help="Minimum length of tracks (percentage of senquence length)")
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175 args = parser.parse_args()
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176 points_linking(args.fn_in, args.fn_out, args.nbpx, args.thres, args.minlen)