Mercurial > repos > imgteam > points_association_nn
annotate points_association_nn.py @ 0:04e692ee53a8 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
author | imgteam |
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date | Thu, 22 Jul 2021 22:29:47 +0000 |
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children | b30aa285ac0a |
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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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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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9 |
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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11 |
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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16 |
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 |
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"
imgteam
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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"
imgteam
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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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29 |
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 |
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): |
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 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 |
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 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: |
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 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 |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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49 return iy_nim, ix_nim |
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 |
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): |
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 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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54 all_data = np.array(data) |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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55 assert all_data.shape[1] in [3, 4], 'unknow collum(s) in input data!' |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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56 |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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57 coords = all_data[:, :3].astype('int64') |
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 |
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]) |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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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!" |
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 |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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63 nSlices = frame_end |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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64 stack_h = np.max(coords[:, 2]) + 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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65 stack_w = np.max(coords[:, 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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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 |
04e692ee53a8
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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69 for i in range(all_data.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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70 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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71 stack[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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72 stack_r[iyxz] = all_data[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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73 |
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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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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) |
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 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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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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82 track = np.empty((nSlices, 3)) |
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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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83 for i in range(nSlices): |
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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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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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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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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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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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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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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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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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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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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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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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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 |
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"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 |
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"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 |
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"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: |
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"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: |
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"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 |
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"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: |
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"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 |
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"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 |
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"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 |
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"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): |
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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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135 if not np.isnan(track[iz, 0]): |
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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points_association_nn/ commit db4c2a87a21f32e5d12d11e68f32773bfc06fcfd"
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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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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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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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146 if maxv < th * br_max / 100: |
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147 break |
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148 |
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149 with pd.ExcelWriter(fn_out, engine="openpyxl") as writer: |
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150 for i in range(tracks_all.shape[0]): |
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151 df = pd.DataFrame() |
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152 df['FRAME'] = tracks_all[i, :, 0] |
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153 df['POS_X'] = tracks_all[i, :, 1] |
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154 df['POS_Y'] = tracks_all[i, :, 2] |
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155 df['INTENSITY'] = tracks_all[i, :, 3] |
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156 df.to_excel(writer, sheet_name='spot%s' % (i + 1), index=False, float_format='%.2f') |
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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") |
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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") |
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166 parser.add_argument("minlen", type=float, help="Minimum length of tracks (percentage of senquence length)") |
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167 args = parser.parse_args() |
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168 points_linking(args.fn_in, args.fn_out, args.nbpx, args.thres, args.minlen) |