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annotate points2label.py @ 4:64c155acb864 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
author imgteam
date Mon, 12 May 2025 14:01:09 +0000
parents 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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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
imgteam
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2 import json
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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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3 import os
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07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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4 import warnings
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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5 from typing import (
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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6 Dict,
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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7 List,
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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8 Tuple,
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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9 Union,
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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10 )
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07d362a8af11 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11
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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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12 import giatools.pandas
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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13 import numpy as np
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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14 import numpy.typing as npt
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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 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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16 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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17 import skimage.io
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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18 import skimage.segmentation
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19
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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21 def is_rectangular(points: Union[List[Tuple[float, float]], npt.NDArray]) -> bool:
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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22 points = np.asarray(points)
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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24 # Rectangle must have 5 points, where first and last are identical
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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25 if len(points) != 5 or not (points[0] == points[-1]).all():
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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26 return False
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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28 # Check that all edges align with the axes
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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29 edges = points[1:] - points[:-1]
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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30 if any((edge == 0).sum() != 1 for edge in edges):
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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31 return False
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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33 # All checks have passed, the geometry is rectangular
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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34 return True
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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37 def geojson_to_tabular(geojson: Dict):
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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38 rows = []
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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39 labels = []
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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40 for feature in geojson['features']:
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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41 assert feature['geometry']['type'].lower() == 'polygon', (
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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42 f'Unsupported geometry type: "{feature["geometry"]["type"]}"'
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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43 )
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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44 coords = feature['geometry']['coordinates'][0]
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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45
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46 # Properties and name (label) are optional
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47 try:
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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48 label = feature['properties']['name']
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49 except KeyError:
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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50 label = max(labels, default=0) + 1
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51 labels.append(label)
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52
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53 # Read geometry
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54 xs = [pt[0] for pt in coords]
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55 ys = [pt[1] for pt in coords]
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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56
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57 x = min(xs)
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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58 y = min(ys)
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59
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60 width = max(xs) + 1 - x
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61 height = max(ys) + 1 - y
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62
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63 # Validate geometry (must be rectangular)
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64 assert is_rectangular(list(zip(xs, ys)))
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65
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66 # Append the rectangle
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67 rows.append({
64c155acb864 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 9a40a5d1e1008c26cc327c6d163df2a1af22a1a0
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68 'pos_x': x,
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69 'pos_y': y,
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70 'width': width,
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71 'height': height,
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72 'label': label,
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73 })
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74 df = pd.DataFrame(rows)
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75 point_file = './point_file.tabular'
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76 df.to_csv(point_file, sep='\t', index=False)
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77 return point_file
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79
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80 def rasterize(point_file, out_file, shape, has_header=False, swap_xy=False, bg_value=0, fg_value=None):
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81
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82 img = np.full(shape, dtype=np.uint16, fill_value=bg_value)
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83 if os.path.exists(point_file) and os.path.getsize(point_file) > 0:
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84
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85 # Read the tabular file with information from the header
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86 if has_header:
2
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87 df = pd.read_csv(point_file, delimiter='\t')
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88
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89 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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90 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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91 pos_x_list = df[pos_x_column].round().astype(int)
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92 pos_y_list = df[pos_y_column].round().astype(int)
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93 assert len(pos_x_list) == len(pos_y_list)
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94
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95 try:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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96 radius_column = giatools.pandas.find_column(df, ['radius', 'RADIUS'])
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97 radius_list = df[radius_column]
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98 assert len(pos_x_list) == len(radius_list)
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99 except KeyError:
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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100 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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101
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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102 try:
3
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103 width_column = giatools.pandas.find_column(df, ['width', 'WIDTH'])
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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104 height_column = giatools.pandas.find_column(df, ['height', 'HEIGHT'])
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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105 width_list = df[width_column]
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106 height_list = df[height_column]
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107 assert len(pos_x_list) == len(width_list)
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108 assert len(pos_x_list) == len(height_list)
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109 except KeyError:
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110 width_list = [0] * len(pos_x_list)
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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111 height_list = [0] * len(pos_x_list)
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112
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113 try:
2
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114 label_column = giatools.pandas.find_column(df, ['label', 'LABEL'])
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115 label_list = df[label_column]
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116 assert len(pos_x_list) == len(label_list)
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117 except KeyError:
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118 label_list = list(range(1, len(pos_x_list) + 1))
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119
714a57d6f3a1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
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120 # Read the tabular file without header
0
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121 else:
2
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122 df = pd.read_csv(point_file, header=None, delimiter='\t')
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123 pos_x_list = df[0].round().astype(int)
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124 pos_y_list = df[1].round().astype(int)
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125 assert len(pos_x_list) == len(pos_y_list)
3
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126 radius_list, width_list, height_list = [[0] * len(pos_x_list)] * 3
2
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127 label_list = list(range(1, len(pos_x_list) + 1))
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128
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129 # Optionally swap the coordinates
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130 if swap_xy:
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131 pos_x_list, pos_y_list = pos_y_list, pos_x_list
0
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132
2
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133 # Perform the rasterization
3
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134 for y, x, radius, width, height, label in zip(
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135 pos_y_list, pos_x_list, radius_list, width_list, height_list, label_list,
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136 ):
2
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137 if fg_value is not None:
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138 label = fg_value
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139
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140 if y < 0 or x < 0 or y >= shape[0] or x >= shape[1]:
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141 raise IndexError(f'The point x={x}, y={y} exceeds the bounds of the image (width: {shape[1]}, height: {shape[0]})')
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142
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143 # Rasterize circle and distribute overlapping image area
3
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144 # Rasterize primitive geometry
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145 if radius > 0 or (width > 0 and height > 0):
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146
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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147 # Rasterize circle
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148 if radius > 0:
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149 mask = np.ones(shape, dtype=bool)
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150 mask[y, x] = False
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151 mask = (ndi.distance_transform_edt(mask) <= radius)
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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152 else:
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153 mask = np.zeros(shape, dtype=bool)
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154
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155 # Rasterize rectangle
2ae122d5d85a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 78614a9010c2ca0e1fa5973639c05ab74bcdb148
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156 if width > 0 and height > 0:
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157 mask[
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158 y:min(shape[0], y + width),
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159 x:min(shape[1], x + height)
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160 ] = True
2
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161
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162 # Compute the overlap (pretend there is none if the rasterization is binary)
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163 if fg_value is None:
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164 overlap = np.logical_and(img > 0, mask)
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165 else:
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166 overlap = np.zeros(shape, dtype=bool)
0
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167
2
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168 # Rasterize the part of the circle which is disjoint from other foreground.
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169 #
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170 # In the current implementation, the result depends on the order of the rasterized circles if somewhere
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171 # more than two circles overlap. This is probably negligable for most applications. To achieve results
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172 # that are invariant to the order, first all circles would need to be rasterized independently, and
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173 # then blended together. This, however, would either strongly increase the memory consumption, or
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174 # require a more complex implementation which exploits the sparsity of the rasterized masks.
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175 #
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176 disjoint_mask = np.logical_xor(mask, overlap)
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177 if disjoint_mask.any():
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178 img[disjoint_mask] = label
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179
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180 # Distribute the remaining part of the circle
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181 if overlap.any():
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182 dist = ndi.distance_transform_edt(overlap)
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183 foreground = (img > 0)
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184 img[overlap] = 0
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185 img = skimage.segmentation.watershed(dist, img, mask=foreground)
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186
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187 # Rasterize point (there is no overlapping area to be distributed)
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188 else:
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189 img[y, x] = label
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190
0
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191 else:
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192 raise Exception('{} is empty or does not exist.'.format(point_file)) # appropriate built-in error?
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193
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194 with warnings.catch_warnings():
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195 warnings.simplefilter("ignore")
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196 skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension
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197
0
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198
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199 if __name__ == '__main__':
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200 parser = argparse.ArgumentParser()
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201 parser.add_argument('in_file', type=argparse.FileType('r'), help='Input point file or GeoJSON file')
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202 parser.add_argument('out_file', type=str, help='out file (TIFF)')
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203 parser.add_argument('shapex', type=int, help='shapex')
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204 parser.add_argument('shapey', type=int, help='shapey')
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205 parser.add_argument('--has_header', dest='has_header', default=False, help='set True if point file has header')
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206 parser.add_argument('--swap_xy', dest='swap_xy', default=False, help='Swap X and Y coordinates')
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207 parser.add_argument('--binary', dest='binary', default=False, help='Produce binary image')
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208
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209 args = parser.parse_args()
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210
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211 point_file = args.in_file.name
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212 has_header = args.has_header
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213
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214 try:
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215 with open(args.in_file.name, 'r') as f:
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216 content = json.load(f)
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217 if isinstance(content, dict) and content.get('type') == 'FeatureCollection' and isinstance(content.get('features'), list):
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218 point_file = geojson_to_tabular(content)
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219 has_header = True # header included in the converted file
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220 else:
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221 raise ValueError('Input is a JSON file but not a valid GeoJSON file')
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222 except json.JSONDecodeError:
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223 print('Input is not a valid JSON file. Assuming it a tabular file.')
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224
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225 rasterize(
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226 point_file,
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227 args.out_file,
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228 (args.shapey, args.shapex),
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229 has_header=has_header,
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230 swap_xy=args.swap_xy,
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231 fg_value=0xffff if args.binary else None,
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232 )