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Bug #13569

closed

Grid images with no squares found result in Ptolemy error and an empty file

Added by William Rice about 2 years ago. Updated about 2 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
-
Target version:
Appion/Leginon 3.6
Start date:
10/03/2022
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.6
Show in known bugs:
No
Workaround:

Description

  • Ptolemy crashes with the following error if it finds no squares in a LM image, script lowmag_cli.py
    /data/cryoem/cryoemdata/leginon/22sep30c/rawdata/22sep30c_p5b12g4_00032gr.mrc
Traceback (most recent call last):
  File "/home/svc_cryoem/packages/ptolemy/lowmag_cli.py", line 92, in <module>
    main()
  File "/home/svc_cryoem/packages/ptolemy/lowmag_cli.py", line 46, in main
    ex.get_crops(cropper)
  File "/home/svc_cryoem/packages/ptolemy/ptolemy/images.py", line 71, in get_crops
    crops = CropSet(crops, self.boxes, self.rotated_boxes)
  File "/home/svc_cryoem/packages/ptolemy/ptolemy/CropSet.py", line 13, in __init__
    self.center_coords = PointSet2D.concatenate([PointSet2D([int(np.mean(box.y))], [int(np.mean(box.x))]) for box in boxes])
  File "/home/svc_cryoem/packages/ptolemy/ptolemy/PointSet.py", line 93, in concatenate
    new = np.concatenate([ps.as_matrix_y() for ps in list_of_pointsets], axis=0)
  File "<__array_function__ internals>", line 5, in concatenate
ValueError: need at least one array to concatenate
  • it produces an empty output file which then causes problems in the external hole finder in Leginon:
    Exception in thread data binder handler thread:
Traceback (most recent call last):
  File "/usr/lib64/python2.7/threading.py", line 812, in __bootstrap_inner
    self.run()
  File "/usr/lib64/python2.7/threading.py", line 765, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/usr/lib/python2.7/site-packages/leginon/databinder.py", line 131, in handleData
    method(args)
  File "/usr/lib/python2.7/site-packages/leginon/mosaictargetfinder.py", line 201, in handleTargetListDone
    self.autoTargetFinder()
  File "/usr/lib/python2.7/site-packages/leginon/mosaictargetfinder.py", line 241, in autoTargetFinder
    blobs = self.findSquareBlobs()
  File "/usr/lib/python2.7/site-packages/leginon/mosaicexternalfinder.py", line 469, in findSquareBlobs
    self.loadBlobs(label, outpath)
  File "/usr/lib/python2.7/site-packages/leginon/mosaicexternalfinder.py", line 190, in loadBlobs
    line = f.readlines()[0]
IndexError: list index out of range
  • This results in Leginon needing the user to press the square finding button to get a list of squares, and the list is randomly incomplete
  • I added an exception to the Leginon code, in that if the readlines call fails, it returns an empty set of points, which lets Leginon handle an empty file
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