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path: root/libcrystfel/src/peaks.c
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2021-04-27Rename libcrystfel's config.h to libcrystfel-config.hThomas White
This removes the big potential for confusion, which has happened several times (see e.g. 095cbebaf6). It also fixes in-tree builds with CMake (but seriously, always use out-of-tree builds). Fixes #2.
2021-03-11detgeom_transform_coords: Take an additional detector shiftThomas White
This allows the refined detector position to be used in a lot of places.
2021-03-05Mass update of copyright dates in source code commentsThomas White
2020-07-30Eliminate duplicate symbolsThomas White
This makes searching easier, and also permits Meson's unity build mode.
2020-07-29Expose a couple more functions for easier testingThomas White
2020-07-29Convert a few more bits and pieces to detgeomThomas White
2020-07-29Convert make_BgMask to detgeomThomas White
2020-07-29Convert estimate_peak_resolution to detgeomThomas White
2020-07-29Split off parse_peaksearch()Thomas White
2020-07-29Add str_peaksearch()Thomas White
Will be needed for passing peak search parameters to indexamajig from GUI
2020-07-29Convert peak detection to use detgeomThomas White
2020-07-29Remove badrow cullingThomas White
Very old, not used at all, and better solved by masking bad regions.
2020-07-29ImageFeatureList: Store panel number, not pointerThomas White
This makes the conversion to DataTemplate/detgeom MUCH easier.
2020-01-10Mass update of copyright datesThomas White
2019-11-13Fix peak check logic for multiple crystalsThomas White
It seems that the code wasn't properly updated when multi-crystal indexing was introducted. This "continue" statement didn't do anything.
2019-09-06Use new peak check only when doing multi-lattice indexingThomas White
2019-09-06New check for indexing solutions (copied across from pinkIndexer)Thomas White
2019-08-26Fix resolution estimationThomas White
Didn't work when the number of peaks was very low.
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
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