Mercurial > repos > imgteam > spot_detection_2d

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
author imgteam
date Wed, 25 Sep 2024 08:19:22 +0000
parents a58d8f8149e1
children
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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1 """
2
a58d8f8149e1 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 927b78d47c31714776ccdf3d16f26c3779298abb"
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2 Copyright 2021-2022 Biomedical Computer Vision Group, Heidelberg University.
4
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
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3 Authors:
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
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4 - Qi Gao (qi.gao@bioquant.uni-heidelberg.de)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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5 - Leonid Kostrykin (leonid.kostrykin@bioquant.uni-heidelberg.de)
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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7 Distributed under the MIT license.
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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8 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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9 """
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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11 import argparse
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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12
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d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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13 import giatools.io
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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14 import numpy as np
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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15 import pandas as pd
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d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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16 import scipy.ndimage as ndi
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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17 from numpy.typing import NDArray
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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18 from skimage.feature import blob_dog, blob_doh, blob_log
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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20 blob_filters = {
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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21 'dog': blob_dog,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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22 'doh': blob_doh,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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23 'log': blob_log,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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24 }
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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26
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d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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27 def mean_intensity(img: NDArray, y: int, x: int, radius: int) -> float:
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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28 assert img.ndim == 2
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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29 assert radius >= 0
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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30 if radius == 0:
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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31 return float(img[y, x])
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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32 else:
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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33 mask = np.ones(img.shape, bool)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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34 mask[y, x] = False
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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35 mask = (ndi.distance_transform_edt(mask) <= radius)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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36 return img[mask].mean()
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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38
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39 def spot_detection(
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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40 fn_in: str,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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41 fn_out: str,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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42 frame_1st: int,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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43 frame_end: int,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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44 filter_type: str,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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45 min_scale: float,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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46 max_scale: float,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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47 abs_threshold: float,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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48 rel_threshold: float,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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49 boundary: int,
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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50 ) -> None:
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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51
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d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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52 # Load the single-channel 2-D input image (or stack thereof)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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53 stack = giatools.io.imread(fn_in)
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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54
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d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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55 # Normalize input image so that it is a stack of images (possibly a stack of a single image)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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56 assert stack.ndim in (2, 3)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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57 if stack.ndim == 2:
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58 stack = stack.reshape(1, *stack.shape)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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59
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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60 # Slice the stack
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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61 assert frame_1st >= 1
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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62 assert frame_end >= 0
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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63 stack = stack[frame_1st - 1:]
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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64 if frame_end > 0:
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65 stack = stack[:-frame_end]
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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66
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67 # Select the blob detection filter
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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68 assert filter_type.lower() in blob_filters.keys()
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69 blob_filter = blob_filters[filter_type.lower()]
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70
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71 # Perform blob detection on each image of the stack
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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72 detections = list()
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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73 for img_idx, img in enumerate(stack):
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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74 blobs = blob_filter(img, threshold=abs_threshold, threshold_rel=rel_threshold, min_sigma=min_scale, max_sigma=max_scale)
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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75 for blob in blobs:
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76 y, x, scale = blob
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77
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78 # Skip the detection if it is too close to the boundary of the image
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79 if y < boundary or x < boundary or y >= img.shape[0] - boundary or x >= img.shape[1] - boundary:
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80 continue
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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81
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82 # Add the detection to the list of detections
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83 radius = scale * np.sqrt(2) * 2
d77f71572fc4 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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84 intensity = mean_intensity(img, round(y), round(x), round(radius))
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85 detections.append(
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86 {
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87 'frame': img_idx + 1,
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88 'pos_x': round(x),
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89 'pos_y': round(y),
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90 'scale': scale,
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91 'radius': radius,
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92 'intensity': intensity,
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93 }
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94 )
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95
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96 # Build and save dataframe
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97 df = pd.DataFrame.from_dict(detections)
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98 df.to_csv(fn_out, index=False, float_format='%.2f', sep="\t")
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99
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100
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101 if __name__ == "__main__":
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102
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103 parser = argparse.ArgumentParser(description="Spot detection")
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104
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105 parser.add_argument("fn_in", help="Name of input image or image stack.")
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106 parser.add_argument("fn_out", help="Name of output file to write the detections into.")
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107 parser.add_argument("frame_1st", type=int, help="Index for the starting frame to detect spots (1 for first frame of the stack).")
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108 parser.add_argument("frame_end", type=int, help="Index for the last frame to detect spots (0 for the last frame of the stack).")
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109 parser.add_argument("filter_type", help="Detection filter")
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110 parser.add_argument("min_scale", type=float, help="The minimum scale to consider for multi-scale detection.")
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111 parser.add_argument("max_scale", type=float, help="The maximum scale to consider for multi-scale detection.")
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112 parser.add_argument("abs_threshold", type=float, help=(
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113 "Filter responses below this threshold will be ignored. Only filter responses above this thresholding will be considered as blobs. "
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114 "This threshold is ignored if the relative threshold (below) corresponds to a higher response.")
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115 )
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116 parser.add_argument("rel_threshold", type=float, help=(
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117 "Same as the absolute threshold (above), but as a fraction of the overall maximal filter response of an image. "
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118 "This threshold is ignored if it corresponds to a response below the absolute threshold.")
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119 )
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120 parser.add_argument("boundary", type=int, help="Width of image boundaries (in pixel) where spots will be ignored.")
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121
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122 args = parser.parse_args()
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123 spot_detection(args.fn_in, args.fn_out,
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124 frame_1st=args.frame_1st, frame_end=args.frame_end,
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125 filter_type=args.filter_type,
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126 min_scale=args.min_scale, max_scale=args.max_scale,
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127 abs_threshold=args.abs_threshold, rel_threshold=args.rel_threshold,
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128 boundary=args.boundary)