Appion

When working with the automasker and manual masker, the donedict is not updated with completed entries.

Beginning with a dataset, we run the automasker (using em_hole_finder) then assess the results in the Appion viewer.

After completing this, we typically would launch a manual masking with the automasking run set as the run to be assessed.

While launching, the software seems to load properly and detect the presence of a mask and whether or not the image has been kept or rejected, but does not write these out to the donedict. As a result, it iterates through the entire set of images each time it loads (very time intensive), and sometimes exits before presenting the GUI.

We have moved to only using the manual masker and skipping the automask step. We have not run into any problems when using manual masker without assessing an automasker run.