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MSI-Ptolemy API information for developers » History » Revision 4

Revision 3 (Anchi Cheng, 03/15/2022 05:19 PM) → Revision 4/8 (Anchi Cheng, 03/15/2022 05:20 PM)

h1. MSI-Ptolemy API information for developers 

 h2. Square_Finding node: 

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

 h3.    # 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]] 

 h3. # Output json file is a list of square blob founds by the algorithm.    For each item, it requires the following key, value pairs. 

 h3. area: integer 

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

 h3. 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. 

 h3. score: float 

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

 h3. brightness: float 

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

 h3. 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. 

 h2. Example json: 

 <pre> 
 [{"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}] 
 </pre>