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annotate points2label.py @ 2:714a57d6f3a1 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
author imgteam
date Fri, 27 Sep 2024 17:41:06 +0000
parents 3fa3c8e41364
children 2ae122d5d85a
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07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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diff changeset
1 import argparse
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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2 import os
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07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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3 import warnings
07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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5 import giatools.pandas
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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6 import numpy as np
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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7 import pandas as pd
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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8 import scipy.ndimage as ndi
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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9 import skimage.io
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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10 import skimage.segmentation
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07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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13 def rasterize(point_file, out_file, shape, has_header=False, swap_xy=False, bg_value=0, fg_value=None):
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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15 img = np.full(shape, dtype=np.uint16, fill_value=bg_value)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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16 if os.path.exists(point_file) and os.path.getsize(point_file) > 0:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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18 # Read the tabular file with information from the header
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07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 if has_header:
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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20 df = pd.read_csv(point_file, delimiter='\t')
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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22 pos_x_column = giatools.pandas.find_column(df, ['pos_x', 'POS_X'])
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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23 pos_y_column = giatools.pandas.find_column(df, ['pos_y', 'POS_Y'])
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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24 pos_x_list = df[pos_x_column].round().astype(int)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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25 pos_y_list = df[pos_y_column].round().astype(int)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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26 assert len(pos_x_list) == len(pos_y_list)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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28 try:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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29 radius_column = giatools.pandas.find_column(df, ['radius', 'RADIUS'])
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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30 radius_list = df[radius_column]
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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31 assert len(pos_x_list) == len(radius_list)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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32 except KeyError:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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33 radius_list = [0] * len(pos_x_list)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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34
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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35 try:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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36 label_column = giatools.pandas.find_column(df, ['label', 'LABEL'])
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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37 label_list = df[label_column]
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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38 assert len(pos_x_list) == len(label_list)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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39 except KeyError:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
imgteam
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40 label_list = list(range(1, len(pos_x_list) + 1))
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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42 # Read the tabular file without header
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07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43 else:
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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44 df = pd.read_csv(point_file, header=None, delimiter='\t')
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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45 pos_x_list = df[0].round().astype(int)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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46 pos_y_list = df[1].round().astype(int)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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47 assert len(pos_x_list) == len(pos_y_list)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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48 radius_list = [0] * len(pos_x_list)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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49 label_list = list(range(1, len(pos_x_list) + 1))
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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50
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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51 # Optionally swap the coordinates
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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52 if swap_xy:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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53 pos_x_list, pos_y_list = pos_y_list, pos_x_list
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54
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55 # Perform the rasterization
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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56 for y, x, radius, label in zip(pos_y_list, pos_x_list, radius_list, label_list):
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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57 if fg_value is not None:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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58 label = fg_value
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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59
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60 if y < 0 or x < 0 or y >= shape[0] or x >= shape[1]:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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61 raise IndexError(f'The point x={x}, y={y} exceeds the bounds of the image (width: {shape[1]}, height: {shape[0]})')
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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62
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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63 # Rasterize circle and distribute overlapping image area
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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64 if radius > 0:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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65 mask = np.ones(shape, dtype=bool)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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66 mask[y, x] = False
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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67 mask = (ndi.distance_transform_edt(mask) <= radius)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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68
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69 # Compute the overlap (pretend there is none if the rasterization is binary)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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70 if fg_value is None:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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71 overlap = np.logical_and(img > 0, mask)
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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72 else:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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73 overlap = np.zeros(shape, dtype=bool)
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74
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714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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75 # Rasterize the part of the circle which is disjoint from other foreground.
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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76 #
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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77 # In the current implementation, the result depends on the order of the rasterized circles if somewhere
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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78 # more than two circles overlap. This is probably negligable for most applications. To achieve results
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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79 # that are invariant to the order, first all circles would need to be rasterized independently, and
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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80 # then blended together. This, however, would either strongly increase the memory consumption, or
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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81 # require a more complex implementation which exploits the sparsity of the rasterized masks.
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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82 #
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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83 disjoint_mask = np.logical_xor(mask, overlap)
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84 if disjoint_mask.any():
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85 img[disjoint_mask] = label
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86
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87 # Distribute the remaining part of the circle
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88 if overlap.any():
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89 dist = ndi.distance_transform_edt(overlap)
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90 foreground = (img > 0)
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91 img[overlap] = 0
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92 img = skimage.segmentation.watershed(dist, img, mask=foreground)
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93
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94 # Rasterize point (there is no overlapping area to be distributed)
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95 else:
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96 img[y, x] = label
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97
0
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98 else:
2
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99 raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error?
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100
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101 with warnings.catch_warnings():
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102 warnings.simplefilter("ignore")
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103 skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension
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104
0
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105
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106 if __name__ == "__main__":
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107 parser = argparse.ArgumentParser()
2
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108 parser.add_argument('point_file', type=argparse.FileType('r'), help='point file')
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109 parser.add_argument('out_file', type=str, help='out file (TIFF)')
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110 parser.add_argument('shapex', type=int, help='shapex')
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111 parser.add_argument('shapey', type=int, help='shapey')
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112 parser.add_argument('--has_header', dest='has_header', default=False, help='set True if point file has header')
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113 parser.add_argument('--swap_xy', dest='swap_xy', default=False, help='Swap X and Y coordinates')
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114 parser.add_argument('--binary', dest='binary', default=False, help='Produce binary image')
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115
0
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116 args = parser.parse_args()
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117
2
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118 rasterize(
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119 args.point_file.name,
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120 args.out_file,
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121 (args.shapey, args.shapex),
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122 has_header=args.has_header,
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123 swap_xy=args.swap_xy,
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124 fg_value=0xffff if args.binary else None,
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125 )