Age | Commit message (Collapse) | Author | |
---|---|---|---|
2018-06-10 | indexamajig: Estimate resolution based on peaks only | Thomas White | |
2018-05-30 | Whitespace fussiness | Thomas White | |
2018-05-30 | Use only one min-snr option | Thomas White | |
2018-05-30 | Changed parameter window-radius -> local-bg-radius | Yaroslav Gevorkov | |
2018-05-30 | Changed sig_fac to min_snr | Yaroslav Gevorkov | |
2018-05-24 | Generalise peakfinder9 error messages, and fail if not compiled in | Thomas White | |
2018-05-24 | Update authorship and copyright dates | Thomas White | |
2018-05-24 | Formatting | Thomas White | |
2018-05-24 | Add "peakfinder9" | Yaroslav Gevorkov | |
2018-04-20 | Set default bandwidth very small | Thomas White | |
This seems to have been reducing data quality by overpredicting. | |||
2018-02-27 | New partiality model from Ginn et al. | Thomas White | |
2018-02-27 | Formatting | Thomas White | |
2018-02-27 | indexamajig: Add --overpredict | Thomas White | |
2017-06-27 | indexamajig: Add --no-non-hits-in-stream | Thomas White | |
2017-06-21 | indexamajig: Add --min-peaks (basic hitfinder functionality) | Thomas White | |
2017-05-02 | Initial CBF stuff | Thomas White | |
2017-03-31 | Offset peak locations from HDF5 or CXI files by 0.5,0.5 | Thomas White | |
CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry. In contrast, Cheetah considers the peak locations to be pixel indices in the data array. Therefore, a half-pixel offset is needed when importing the peak lists. For users who need the old behaviour, this commit adds a new option indexamajig --no-half-pixel-shift to deactivate this offset. | |||
2017-03-24 | Merge branch 'valerio/peakfinder8' | Thomas White | |
2017-03-13 | Added saturated peak management to peakfinder8 | Valerio Mariani | |
2017-03-10 | Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementation | Valerio Mariani | |
2017-03-08 | Allow indexing system to store its own data, independently of indexing methods | Thomas White | |
Previously, the indexing system passed all the information on to the indexing engines and then forgot about it. That made it difficult to do things like check the indexing solution after prediction refinement, because the target unit cell was unavailable. Now, the indexing system itself can keep some information. Of course, that information includes the private pointers for the indexing engines themselves. I took the opportunity to streamline things a little bit. The caller can now set up the indexing system in one step, without having to separately parse the names of the indexing methods. The caller no longer has to keep track of a separate array of methods, instead just one structure which contains everything. | |||
2017-02-02 | indexamajig: Add ping mechanism to avoid timing out when trying lots of indexers | Thomas White | |
2016-03-01 | indexamajig: Wall clock profiling | Thomas White | |
2016-01-29 | Perform prediction refinement straight after indexing | Thomas White | |
This allows indexing to be attempted again (either a new method or with "retry") if the prediction refinement fails, increasing overall indexing rate. Side-effect: there are some hoops which would need to be jumped through to store the profile radius before refinement and hence enable scripts/plot-predict-refine to work. For now, we'll ignore this as it's clear that the prediction refinement is working. | |||
2015-12-18 | Saturation map fixes | Thomas White | |
2015-10-05 | process_image(): Remove image->data | Thomas White | |
2015-07-13 | Re-work im-sandbox | Thomas White | |
... it certainly needed it. | |||
2015-07-09 | indexamajig: Fix noise filter backup/restore | Thomas White | |
2015-06-18 | Replace semaphore with a mutex | Thomas White | |
A mutex (in a shared memory segment) is the correct synchronisation primitive here. I had confused myself... | |||
2015-06-17 | Use a POSIX semaphore for synchronising terminal access during indexing | Thomas White | |
Nice side-effect: indexamajig -j and --int-diag can now be used together | |||
2015-04-28 | Remove unnecessary rejection tests | Thomas White | |
2015-04-20 | Tweak rejection | Thomas White | |
2015-04-20 | Add a simple rejection criterion to the prediction refinement | Thomas White | |
2015-04-20 | indexamajig: Reset indexing method if all crystals fail integration | Thomas White | |
2015-04-20 | indexamajig: Add --no-refine | Thomas White | |
2015-04-20 | Refine detector position in prediction refinement | Thomas White | |
2015-04-20 | refine_{radius,prediction}: unite common code (pair_peaks), avoid ↵ | Thomas White | |
preliminary integration round | |||
2015-04-20 | Remove debugging statements | Thomas White | |
2015-04-20 | Record profile radius before and after refinement | Thomas White | |
2015-04-20 | Throw out crystals which could not be refined | Thomas White | |
2015-04-20 | Tweak weightings and cutoffs | Thomas White | |
2015-04-20 | Add prediction refinement | Thomas White | |
2015-04-01 | Initialise indexed_by to INDEXING_NONE | Thomas White | |
Not entirely sure how this was missed for so long. | |||
2015-02-20 | indexamajig: Show event ID if there are implausible reflections | Thomas White | |
2015-02-20 | indexamajig: Take a copy of the geometry structure | Thomas White | |
There are already things which alter this structure during processing, and probably more to come. Taking a copy avoids problems down the line and fixes a serious bug when using coffset and a fixed clen. | |||
2015-02-18 | Fix profile radius determination | Thomas White | |
2015-02-16 | indexamajig: --peaks=cxi instead of --peaks=hdf5 --cxi-hdf5-peaks | Thomas White | |
2015-02-12 | Increase max radius to 0.02e9 m^-1 | Thomas White | |
2015-02-12 | indexamajig: Add --fix-{profile-radius,bandwidth,divergence} | Thomas White | |
2015-02-12 | Improved determination of profile radius | Thomas White | |