MSI-Ptolemy API information for developers » History » Version 8
Anchi Cheng, 07/18/2022 03:29 PM
1 | 1 | Anchi Cheng | h1. MSI-Ptolemy API information for developers |
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3 | 8 | Anchi Cheng | h2. Square_Targeting node (MosaicScoreTargetFinder class): |
4 | 1 | Anchi Cheng | |
5 | The square finding should operate on each gr image tile at its saved mrc dimension. |
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7 | 4 | Anchi Cheng | h3. Shell script to call and specified in Blobs settings. |
8 | 3 | Anchi Cheng | |
9 | 7 | Anchi Cheng | The script should accept the same parameters and give json output as [[Setup_Ptolemy_CLI_shell_script]] for square targeting |
10 | 3 | Anchi Cheng | |
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. |
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13 | h3. area: integer |
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15 | 2 | Anchi Cheng | > number of pixels the square opening on the gr tile image. |
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17 | 2 | Anchi Cheng | h3. center: [float, float] |
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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. |
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21 | 2 | Anchi Cheng | h3. score: float |
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23 | 2 | Anchi Cheng | > The score of the blob as goodness of the blob as a good square. The higher the number the better. |
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25 | 2 | Anchi Cheng | h3. brightness: float |
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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. |
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29 | h3. vertices: [[float, float], [float, float], [float, float], .....] |
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31 | > convex-hull vertices used by leginon to determine if a cursor position is within the square blob. Same coordinate system as centers. |
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33 | h2. Example json: |
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35 | <pre> |
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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}, |
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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> |
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40 | 8 | Anchi Cheng | h2. Exposure_Targeting node (ScoreTargetFinder class): |
41 | 5 | Anchi Cheng | |
42 | The hole finding should operate on each hl image at its saved mrc dimension. |
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44 | h3. Shell script to call and specified in Hole settings. |
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46 | 6 | Anchi Cheng | The script should accept the same parameters and give json output as [[Setup_Ptolemy_CLI_for_exposure_targeting]] |
47 | 5 | Anchi Cheng | |
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. |
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50 | h3. center: [float, float] |
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52 | > The coordinate of the hole center [col, row] with [0,0] at the start of the data block in the mrc image. |
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54 | h3. score: float |
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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. |
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58 | h2. Example json: |
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60 | <pre> |
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61 | [{"center": [566, 368], "score": 0.3902}, |
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62 | {"center": [431, 630], "score": 0.2530}] |
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63 | 2 | Anchi Cheng | </pre> |