MSI-Ptolemy API information for developers¶

Square_Targeting node (MosaicScoreTargetFinder class):¶

The square finding should operate on each gr image tile at its saved mrc dimension.

Shell script to call and specified in Blobs settings.¶

The script should accept the same parameters and give json output as Setup_Ptolemy_CLI_shell_script for square targeting

Output json file is a list of square blob founds by the algorithm. For each item, it requires the following key, value pairs.¶

area: integer¶

number of pixels the square opening on the gr tile image.

center: [float, float]¶

The coordinate of the square opening center [col, row] with [0,0] at the start of the data block in the mrc image.

score: float¶

The score of the blob as goodness of the blob as a good square. The higher the number the better.

brightness: float¶

Mean intensity value or equivalent in the square blob. This is saved as a part of statistics but not used for filtering.

vertices: [[float, float], [float, float], [float, float], .....]¶

convex-hull vertices used by leginon to determine if a cursor position is within the square blob. Same coordinate system as centers.

Example json:¶

[{"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},
 {"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}]

Exposure_Targeting node (ScoreTargetFinder class):¶

The hole finding should operate on each hl image at its saved mrc dimension.

Shell script to call and specified in Hole settings.¶

The script should accept the same parameters and give json output as Setup_Ptolemy_CLI_for_exposure_targeting

Output json file is a list of target blob founds by the algorithm. For each item, it requires the following key, value pairs.¶

center: [float, float]¶

The coordinate of the hole center [col, row] with [0,0] at the start of the data block in the mrc image.

score: float¶

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.

Example json:¶

[{"center": [566, 368], "score": 0.3902},
 {"center": [431, 630], "score": 0.2530}]