crystfel's Introduction

CrystFEL

This is a personal unofficial repository of CrystFEL for processing serial crystallography dataset. The official CrystFEL website is http://www.desy.de/~twhite/crystfel/ and the repository is https://stash.desy.de/projects/CRYS/repos/crystfel/browse.

As of 2016, most features have been merged to the official repository, except for hdfsee improvements. Thus, I do not update this repository very often.

Warning!

I am testing various ideas on this repository. Some are not stable yet and NOT recommended for production work. Use at your own risk!

Added Features

multievent branch

This is personal "master" branch where developments take place. "master" branch tracks the official repository. hdfsee and multiple-lattice branches have been merged here.

More updates in the stream viewer (hdfsee)
- Resizable columns
- Sortable rows
- Support multi-event HDF files

experimental branch

Highly premature, experimental codes. Do NOT use this branch!

get_rms
calculate RMS between observed spot positions and predicted positions.
export_to_pickle
convert a stream file to pickle files cctbx.xfel can read.
very buggy, not working well.
dump_unmerged
dump unmerged (but indices converted to be in the ASU) intensities from a stream file for statistical inspection.

hdfsee improvements

Should be stable enough for general use. Merged to multievent branch.

Load stream file directly into hdfsee
Show spots and (multiple) lattices simultaneously
Show resolution and Miller index to the status bar by clicking
Scrollbar in hdfsee -> merged to the official distribution
Export to ADSC format. -> merged to the official distribution
This is useful for manual inspection of indexing in iMOSFLM. Since the original pixel doesn't have one-to-one correspondence in the output image, this is not perfectly accurate.

multiple-lattice indexing

This feature has been merged into the multievent branch. Seems stable but please carefully examine if it improves the result.

Multiple lattice indexing by calling external indexer(s) many times.
Sending prior-cell information to MOSFLM.
Prior-cell algorithm will be available in the next version of MOSFLM.
Hitrate calculator based on Poisson distribution in doc/hitrate.html

scaling

All features have been merged to the official distirubtion. Thus this branch was deleted.

Calculate CC between reference and each frame
Frame rejection based on CC
Output CC and scale factor from process_hkl to be plotted in R

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crystfel's Issues

indexamajig exits with status 0 when it fails to read files

I was trying to run a build of CrystFEL which was compiled against HDF5 1.8, and it was failing to open the virtual datasets. However, the exit code of indexamajig was 0, which conventionally indicates that a program has run successfully.

I'm guessing that this is because the worker processes try and fail to open the files, but the main controller process restarts fails workers and continues trying to process even though they never work. I can see this makes sense in general - we've noticed that processing often times out on a small number of frames, and it's clearly useful to continue working after those. But it seems unfortunate that it can completely fail to process and still exit as if it had succeeded.

Possible ideas:

The controller could try to open files & datasets before calling the workers, so it fails fast if that doesn't work. But that might not be practical if you have thousands of files with one image each.
Exit with an error code if 0 images are processed
Have a configurable threshold to return an error if e.g. < 95% of specified images are successfully processed.

Add -multi- flag to index modes

Event coordinate is slightly offset in hdfsee

In y direction
Seems binning dependent

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