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2019-07-24indexamajig: Free spectrum if it was generated for this imageThomas White
2019-07-24indexamajig: Set Gaussian spectrum if one is not providedThomas White
2019-03-15Add a couple more set_last_task callsThomas White
2019-03-14indexamajig: Add --no-image-dataThomas White
2019-03-14Tweak ZMQ messagesThomas White
2019-03-14More ZMQ/MsgPack logic fixesThomas White
2019-03-14Fix variable initialisation and decision about data sourceThomas White
2019-03-14Connect up hooks for unpacking MsgPack dataThomas White
2019-03-14Don't always dereference filename_p_eThomas White
2019-03-14ZMQ connection and setup stuffThomas White
2019-03-07indexamajig: Status message improvementsThomas White
1. Show the number of hits 2. Keep producing updates while the last patterns are being processed 3. Don't duplicate the code for displaying the status messages
2019-03-06indexamajig: Rename --min-gradient to --min-squared-gradientThomas White
The eventual aim of this is to deprecate the "--min-gradient" option, resolving the long-standing confusion about whether this option is the gradient or the squared gradient.
2018-12-03indexamajig: Add --wait-for-fileThomas White
2018-11-15indexamajig: Name and shame slow processing stagesThomas White
2018-09-27Write in stream whether crystal was selected as a "hit" or notThomas White
2018-09-10indexamajig: read pink beam spectrum from fileAlexandra Tolstikova
2018-07-27indexamajig: Complain if profile radius determination failsThomas White
2018-06-10indexamajig: Estimate resolution based on peaks onlyThomas White
2018-05-30Whitespace fussinessThomas White
2018-05-30Use only one min-snr optionThomas White
2018-05-30Changed parameter window-radius -> local-bg-radiusYaroslav Gevorkov
2018-05-30Changed sig_fac to min_snrYaroslav Gevorkov
2018-05-24Generalise peakfinder9 error messages, and fail if not compiled inThomas White
2018-05-24Update authorship and copyright datesThomas White
2018-05-24FormattingThomas White
2018-05-24Add "peakfinder9"Yaroslav Gevorkov
2018-04-20Set default bandwidth very smallThomas White
This seems to have been reducing data quality by overpredicting.
2018-02-27New partiality model from Ginn et al.Thomas White
2018-02-27FormattingThomas White
2018-02-27indexamajig: Add --overpredictThomas White
2017-06-27indexamajig: Add --no-non-hits-in-streamThomas White
2017-06-21indexamajig: Add --min-peaks (basic hitfinder functionality)Thomas White
2017-05-02Initial CBF stuffThomas White
2017-03-31Offset peak locations from HDF5 or CXI files by 0.5,0.5Thomas 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.
2017-03-24Merge branch 'valerio/peakfinder8'Thomas White
2017-03-13Added saturated peak management to peakfinder8Valerio Mariani
2017-03-10Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementationValerio Mariani
2017-03-08Allow indexing system to store its own data, independently of indexing methodsThomas 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.
2017-02-02indexamajig: Add ping mechanism to avoid timing out when trying lots of indexersThomas White
2016-03-01indexamajig: Wall clock profilingThomas White
2016-01-29Perform prediction refinement straight after indexingThomas 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.
2015-12-18Saturation map fixesThomas White
2015-10-05process_image(): Remove image->dataThomas White
2015-07-13Re-work im-sandboxThomas White
... it certainly needed it.
2015-07-09indexamajig: Fix noise filter backup/restoreThomas White
2015-06-18Replace semaphore with a mutexThomas White
A mutex (in a shared memory segment) is the correct synchronisation primitive here. I had confused myself...
2015-06-17Use a POSIX semaphore for synchronising terminal access during indexingThomas White
Nice side-effect: indexamajig -j and --int-diag can now be used together
2015-04-28Remove unnecessary rejection testsThomas White
2015-04-20Tweak rejectionThomas White
2015-04-20Add a simple rejection criterion to the prediction refinementThomas White
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