Mercurial > repos > imgteam > spot_detection_2d

annotate spot_detection_2d.py @ 5:e8c9e104e109 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 08:19:30 +0000
parents 4645b356bf3b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
1 """
2
4645b356bf3b "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 927b78d47c31714776ccdf3d16f26c3779298abb"
imgteam
parents: 1
diff changeset
2 Copyright 2021-2022 Biomedical Computer Vision Group, Heidelberg University.
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
3 Authors:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
4 - Qi Gao (qi.gao@bioquant.uni-heidelberg.de)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
5 - Leonid Kostrykin (leonid.kostrykin@bioquant.uni-heidelberg.de)
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
6
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
7 Distributed under the MIT license.
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
8 See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
9 """
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
10
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
11 import argparse
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
12
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
13 import giatools.io
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
14 import numpy as np
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
15 import pandas as pd
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
16 import scipy.ndimage as ndi
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
17 from numpy.typing import NDArray
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
18 from skimage.feature import blob_dog, blob_doh, blob_log
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
19
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
20 blob_filters = {
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
21 'dog': blob_dog,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
22 'doh': blob_doh,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
23 'log': blob_log,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
24 }
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
25
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
26
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
27 def mean_intensity(img: NDArray, y: int, x: int, radius: int) -> float:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
28 assert img.ndim == 2
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
29 assert radius >= 0
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
30 if radius == 0:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
31 return float(img[y, x])
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
32 else:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
33 mask = np.ones(img.shape, bool)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
34 mask[y, x] = False
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
35 mask = (ndi.distance_transform_edt(mask) <= radius)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
36 return img[mask].mean()
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
37
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
38
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
39 def spot_detection(
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
40 fn_in: str,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
41 fn_out: str,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
42 frame_1st: int,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
43 frame_end: int,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
44 filter_type: str,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
45 min_scale: float,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
46 max_scale: float,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
47 abs_threshold: float,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
48 rel_threshold: float,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
49 boundary: int,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
50 ) -> None:
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
51
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
52 # Load the single-channel 2-D input image (or stack thereof)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
53 stack = giatools.io.imread(fn_in)
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
54
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
55 # Normalize input image so that it is a stack of images (possibly a stack of a single image)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
56 assert stack.ndim in (2, 3)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
57 if stack.ndim == 2:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
58 stack = stack.reshape(1, *stack.shape)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
59
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
60 # Slice the stack
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
61 assert frame_1st >= 1
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
62 assert frame_end >= 0
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
63 stack = stack[frame_1st - 1:]
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
64 if frame_end > 0:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
65 stack = stack[:-frame_end]
1
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
imgteam
parents: 0
diff changeset
66
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
67 # Select the blob detection filter
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
68 assert filter_type.lower() in blob_filters.keys()
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
69 blob_filter = blob_filters[filter_type.lower()]
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
70
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
71 # Perform blob detection on each image of the stack
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
72 detections = list()
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
73 for img_idx, img in enumerate(stack):
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
74 blobs = blob_filter(img, threshold=abs_threshold, threshold_rel=rel_threshold, min_sigma=min_scale, max_sigma=max_scale)
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
75 for blob in blobs:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
76 y, x, scale = blob
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
77
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
78 # Skip the detection if it is too close to the boundary of the image
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
79 if y < boundary or x < boundary or y >= img.shape[0] - boundary or x >= img.shape[1] - boundary:
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
80 continue
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
81
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
82 # Add the detection to the list of detections
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
83 radius = scale * np.sqrt(2) * 2
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
84 intensity = mean_intensity(img, round(y), round(x), round(radius))
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
85 detections.append(
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
86 {
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
87 'frame': img_idx + 1,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
88 'pos_x': round(x),
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
89 'pos_y': round(y),
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
90 'scale': scale,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
91 'radius': radius,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
92 'intensity': intensity,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
93 }
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
94 )
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
95
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
96 # Build and save dataframe
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
97 df = pd.DataFrame.from_dict(detections)
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
98 df.to_csv(fn_out, index=False, float_format='%.2f', sep="\t")
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
99
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
100
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
101 if __name__ == "__main__":
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
102
1
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
imgteam
parents: 0
diff changeset
103 parser = argparse.ArgumentParser(description="Spot detection")
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
104
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
105 parser.add_argument("fn_in", help="Name of input image or image stack.")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
106 parser.add_argument("fn_out", help="Name of output file to write the detections into.")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
107 parser.add_argument("frame_1st", type=int, help="Index for the starting frame to detect spots (1 for first frame of the stack).")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
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).")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
109 parser.add_argument("filter_type", help="Detection filter")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
110 parser.add_argument("min_scale", type=float, help="The minimum scale to consider for multi-scale detection.")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
111 parser.add_argument("max_scale", type=float, help="The maximum scale to consider for multi-scale detection.")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
112 parser.add_argument("abs_threshold", type=float, help=(
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
113 "Filter responses below this threshold will be ignored. Only filter responses above this thresholding will be considered as blobs. "
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
114 "This threshold is ignored if the relative threshold (below) corresponds to a higher response.")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
115 )
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
116 parser.add_argument("rel_threshold", type=float, help=(
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
117 "Same as the absolute threshold (above), but as a fraction of the overall maximal filter response of an image. "
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
118 "This threshold is ignored if it corresponds to a response below the absolute threshold.")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
119 )
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
120 parser.add_argument("boundary", type=int, help="Width of image boundaries (in pixel) where spots will be ignored.")
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
121
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
imgteam
parents:
diff changeset
122 args = parser.parse_args()
1
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
imgteam
parents: 0
diff changeset
123 spot_detection(args.fn_in, args.fn_out,
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
imgteam
parents: 0
diff changeset
124 frame_1st=args.frame_1st, frame_end=args.frame_end,
5
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
125 filter_type=args.filter_type,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
126 min_scale=args.min_scale, max_scale=args.max_scale,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
127 abs_threshold=args.abs_threshold, rel_threshold=args.rel_threshold,
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
imgteam
parents: 2
diff changeset
128 boundary=args.boundary)