Project

General

Profile

MSI-Ptolemy API information for developers » History » Version 5

Anchi Cheng, 03/15/2022 05:33 PM

1 1 Anchi Cheng
h1. MSI-Ptolemy API information for developers
2
3 5 Anchi Cheng
h2. Square_Targeting node:
4 1 Anchi Cheng
5
The square finding should operate on each gr image tile at its saved mrc dimension.
6
7 4 Anchi Cheng
h3.  Shell script to call and specified in Blobs settings.
8 3 Anchi Cheng
9
The script should accept the same parameters and give json output as [[Setup_Ptolemy_CLI_shell_script]]
10
11 4 Anchi Cheng
h3. Output json file is a list of square blob founds by the algorithm.  For each item, it requires the following key, value pairs.
12 1 Anchi Cheng
13
h3. area: integer
14
15 2 Anchi Cheng
> number of pixels the square opening on the gr tile image.
16 1 Anchi Cheng
17 2 Anchi Cheng
h3. center: [float, float]
18 1 Anchi Cheng
19 2 Anchi Cheng
> The coordinate of the square opening center [col, row] with [0,0] at the start of the data block in the mrc image.
20 1 Anchi Cheng
21 2 Anchi Cheng
h3. score: float
22 1 Anchi Cheng
23 2 Anchi Cheng
> The score of the blob as goodness of the blob as a good square. The higher the number the better.
24 1 Anchi Cheng
25 2 Anchi Cheng
h3. brightness: float
26 1 Anchi Cheng
27 2 Anchi Cheng
> Mean intensity value or equivalent in the square blob.  This is saved as a part of statistics but not used for filtering.
28
29
h3. vertices: [[float, float], [float, float], [float, float], .....]
30
31
> convex-hull vertices used by leginon to determine if a cursor position is within the square blob. Same coordinate system as centers.
32
33
h2. Example json:
34
35
<pre>
36
[{"vertices": [[600.4, 304.7], [502.5, 334.8], [532.7, 432.7], [630.5, 402.6]], "center": [566, 368], "area": 10488.9, "brightness": 194.2, "score": 0.3902},
37 1 Anchi Cheng
 {"vertices": [[464.1, 568.5], [370.0, 597.5], [399.2, 692.5], [493.3, 663.5]], "center": [431, 630], "area": 9785.5, "brightness": 193.7, "score": 0.2530}]
38 5 Anchi Cheng
</pre>
39
40
h2. Exposure_Targeting node:
41
42
The hole finding should operate on each hl image at its saved mrc dimension.
43
44
h3.  Shell script to call and specified in Hole settings.
45
46
The script should accept the same parameters and give json output as [[Setup_Ptolemy_CLI_shell_script]]
47
48
h3. Output json file is a list of target blob founds by the algorithm.  For each item, it requires the following key, value pairs.
49
50
h3. center: [float, float]
51
52
> The coordinate of the hole center [col, row] with [0,0] at the start of the data block in the mrc image.
53
54
h3. score: float
55
56
> The score of the blob as goodness of the hole as a good hole. The higher the number the better.  The key does not need to be "score".  If you need it in a different name, just change leginon settings to match.
57
58
h2. Example json:
59
60
<pre>
61
[{"center": [566, 368], "score": 0.3902},
62
 {"center": [431, 630], "score": 0.2530}]
63 2 Anchi Cheng
</pre>