Tristan Bepler

It seems like the fix to get rid of this warning is to copy the micrograph numpy array after parsing the raw mrc file content. Currently, the parsing code operates...

Copying the array should remove the warning, but it isn't necessary, because we don't write the array in place.

In addition to what Alex said about RELION wrappers already in the works, I am happy to accept pull requests implementing most of these features as long as they do...

Yes, `topaz extract` drops the directory and strips the file extension when creating the image name for consistency with `topaz train` and to make associating the particles with different versions...

@PiotrDra This sounds like a python version problem. The f'...' syntax requires python 3.6 or newer. Can you check that your topaz install is using python 3?

As a workaround, running extract on each of the directories individually should solve this problem.

Extract can also be run once per micrograph, e.g. ``` for micrograph.mrc in set_of_micrographs; topaz extract micrograph.mrc ... ``` This also allows writing one output file per micrograph.

commit 752c140a709c745dabdcc2232b6e9444a11e1ef1 adds support for writing extracted coordinates as one file per micrograph and also adds support for piping the micrograph paths to topaz.

At which stage? Topaz train accepts micrographs listed in an image list file. For downstream steps that expect micrographs to be listed on the command line (i.e. topaz extract), bash...

I'll add passing micrograph inputs through a file to the list for extra features to add in the future. If this is something you're interested in working on, I'd be...