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path: root/libcrystfel/src/peaks.c
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2019-07-19peakFinder9: remove references to image.num_peaks etcThomas White
2019-05-14Remove image.num_peaks and num_saturated_peaksThomas White
These values were inconsistently set by different parts of the code, e.g. different peak search methods. num_saturated_peaks was even set during final integration. Now, the peak count is taken from the ImageFeatureList, so it's authoritative.
2019-05-14Add documentation for search_peaks_peakfinder8Thomas White
2019-05-07Update all source code comments to Doxygen formatThomas White
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.
2018-06-10indexamajig: Estimate resolution based on peaks onlyThomas White
2018-05-30Changed sig_fac to min_snrYaroslav Gevorkov
2018-05-24Generalise peakfinder9 error messages, and fail if not compiled inThomas White
2018-05-24Move FDIP includes to top, and remove unnecessary onesThomas White
2018-05-24Update authorship and copyright datesThomas White
2018-05-24FormattingThomas White
2018-05-24Add "peakfinder9"Yaroslav Gevorkov
2017-03-13Added saturated peak management to peakfinder8Valerio Mariani
2017-03-10Peakfinder8 in CrystFEL. Same results as Anton's Cheetah implementationValerio Mariani
2016-10-14validate_peaks(): Remove drifting and proximity checks, and use original ↵Thomas White
coordinates We trust the HDF5 peaks, even if we can't see a peak there. That means we can't reliably take a centroid and "improve" the coordinates. In some cases, the centroiding procedure seems to be making the peak coordinates worse than they were originally. Now, the only remaining checks are: 1. Is the peak in a bad region of the detector? 2. Is it saturated? (but --use-saturated is the default) 3. If --check-hdf5-snr, is it above the minimum SNR?
2016-07-01No more slab-relative coordinates in libcrystfelThomas White
2016-05-19integrate_peak(): Trap if pk_total=0Thomas White
2016-04-01Add adu_per_photon (distinct from adu_per_eV)Thomas White
2016-01-30Revert "Allow peak check to pass just by accounting for more than 5 peaks"Thomas White
This reverts commit 693aae4d2219632d15174fe4c4f9d0526d6166c4. Reverting because this allows a very large number (~100% "indexing rate") of false solutions to get through simply by slackening the peak detection parameters. Since we know that "-multi" indexing doesn't work well at the moment, let's fix this properly later.
2016-01-06search_peaks_in_panel(): Fix iteration bounds (again)Thomas White
2015-12-18Allow peak check to pass just by accounting for more than 5 peaksThomas White
The "old" criterion is still allowed for a pass, but would filter out multi-lattice hits.
2015-12-17Clean up unused codeThomas White
2015-11-06Fix iteration bounds for peak searchThomas White
It was out by one because of some leftover characters from the previous version.
2015-10-06FussinessThomas White
2015-10-05search_peaks() / integrate_peak(): Remove image->dataThomas White
2014-09-22Beam file removal, part IThomas White
2014-09-02integrate_peak(): Revert use of image->dpThomas White
2014-08-13Remove old bad region tests and use dp instead of data for integration of peaksThomas White
2014-08-13Respect all bad pixels during peak detectionThomas White
Not just no_index panels and bad regions
2014-08-13Remove integrate_peak() from the APIThomas White
Good riddance. One of my least favourite routines.
2014-08-11Take overlaps into account during integrationThomas White
2014-07-24Fixes closest feature detection bugValerio Mariani
2014-03-28validate_peaks(): Count saturated peaks only if they are being rejectedThomas White
2014-03-28integrate_peak(): Useful return codesThomas White
2014-03-26indexamajig: Don't check SNR with --peaks=hdf5 unless given --check-hdf5-snrThomas White
2013-08-20Re-order peak testsThomas White
The old version led to a curious situation where the number of saturated peaks could be much greater than the number of peaks, even without --no-use-saturated.
2013-06-28Don't check max_adu during gradient search if --use-saturated is givenThomas White
2013-06-26Track number of rejected saturated peaksThomas White
2013-05-27Initial integration stuffThomas White
2013-04-24Add docs/stream-format.txt and clarify count of saturated reflectionsThomas White
2013-04-16Restore immediate rejection of pixels above max_aduThomas White
2013-04-16Remove "use_saturated" argument to integrate_peak()Thomas White
There are no side-effects to setting it either way, and the caller can just set saturated=NULL or ignore the result.
2013-02-09Add '--res-cutoff'Thomas White
2013-02-08Saturation counting fixesThomas White
2013-02-08Count saturated peaks and record in the fileThomas White
2013-02-05Fixes for indexing pipelineThomas White
2013-02-04Indexing stuffThomas White
2013-01-30Peak integration changesThomas White
2013-01-04integrate_peak(): check that 'saturated' isn't NULL before usingThomas White
Fixes a segfault
2012-12-03Treat SNR=nan (=0/0) as below any SNR thresholdThomas White
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