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annotate points2binaryimage.py @ 5:5411384e5e1d draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 6fc9ab8db9ef72ac7ded30d7373768feeae9390d
author imgteam
date Fri, 27 Sep 2024 17:41:14 +0000
parents 4c0f16fb9f8d
children
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dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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diff changeset
1 import argparse
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 import os
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 import warnings
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4 from typing import List
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5
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6 import numpy as np
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 import pandas as pd
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8 import scipy.ndimage as ndi
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9 import skimage.io
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12 def find_column(df: pd.DataFrame, candidates: List[str]) -> str:
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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13 """
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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14 Returns the column name present in `df` and the list of `candidates`.
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16 Raises:
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17 KeyError: If there is no candidate column name present in `df`, or more than one.
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18 """
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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19 intersection = frozenset(df.columns) & frozenset(candidates)
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20 if len(intersection) == 0:
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21 raise KeyError(f'No such column: {", ".join(candidates)}')
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22 elif len(intersection) > 1:
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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23 raise KeyError(f'The column names {", ".join(intersection)} are ambiguous')
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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24 else:
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25 return next(iter(intersection))
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28 def points2binaryimage(point_file, out_file, shape, has_header=False, swap_xy=False, bg_value=0, fg_value=0xffff):
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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30 img = np.full(shape, dtype=np.uint16, fill_value=bg_value)
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31 if os.path.exists(point_file) and os.path.getsize(point_file) > 0:
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32
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33 # Read the tabular file with information from the header
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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34 if has_header:
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35 df = pd.read_csv(point_file, delimiter='\t')
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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36 pos_x_column = find_column(df, ['pos_x', 'POS_X'])
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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37 pos_y_column = find_column(df, ['pos_y', 'POS_Y'])
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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38 pos_x_list = df[pos_x_column].round().astype(int)
4c0f16fb9f8d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit a3c77a79db469c9ad18b666f2c64d6e8f573945f
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39 pos_y_list = df[pos_y_column].round().astype(int)
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40 assert len(pos_x_list) == len(pos_y_list)
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41 try:
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42 radius_column = find_column(df, ['radius', 'RADIUS'])
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43 radius_list = df[radius_column]
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44 except KeyError:
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45 radius_list = [0] * len(pos_x_list)
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46
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47 # Read the tabular file without header
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48 else:
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49 df = pd.read_csv(point_file, header=None, delimiter='\t')
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50 pos_x_list = df[0].round().astype(int)
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51 pos_y_list = df[1].round().astype(int)
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52 assert len(pos_x_list) == len(pos_y_list)
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53 radius_list = [0] * len(pos_x_list)
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54
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55 # Optionally swap the coordinates
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56 if swap_xy:
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57 pos_x_list, pos_y_list = pos_y_list, pos_x_list
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59 # Perform the rasterization
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60 for y, x, radius in zip(pos_y_list, pos_x_list, radius_list):
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61
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62 if y < 0 or x < 0 or y >= shape[0] or x >= shape[1]:
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63 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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64
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65 if radius > 0:
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66 mask = np.ones(shape, dtype=bool)
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67 mask[y, x] = False
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68 mask = (ndi.distance_transform_edt(mask) <= radius)
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69 img[mask] = fg_value
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70 else:
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71 img[y, x] = fg_value
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72
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73 else:
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74 raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error?
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76 with warnings.catch_warnings():
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77 warnings.simplefilter("ignore")
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78 skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension
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81 if __name__ == "__main__":
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82 parser = argparse.ArgumentParser()
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83 parser.add_argument('point_file', type=argparse.FileType('r'), help='point file')
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84 parser.add_argument('out_file', type=str, help='out file (TIFF)')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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85 parser.add_argument('shapex', type=int, help='shapex')
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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86 parser.add_argument('shapey', type=int, help='shapey')
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87 parser.add_argument('--has_header', dest='has_header', default=False, help='set True if point file has header')
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88 parser.add_argument('--swap_xy', dest='swap_xy', default=False, help='Swap X and Y coordinates')
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89
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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90 args = parser.parse_args()
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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91
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92 # TOOL
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93 points2binaryimage(args.point_file.name, args.out_file, (args.shapey, args.shapex), has_header=args.has_header, swap_xy=args.swap_xy)