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path: root/libcrystfel/src/integration.c
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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.
2019-05-07Update all source code comments to Doxygen formatThomas White
2018-05-17Merge branch 'tom/cmake'Thomas White
2018-03-22Test for CursesThomas White
2018-02-27indexamajig: Add --overpredictThomas White
2018-02-27New partiality model from Ginn et al.Thomas White
2018-02-27Separate partiality calculation from predictionThomas White
2016-07-01No more slab-relative coordinates in libcrystfelThomas White
2016-04-01Add adu_per_photon (distinct from adu_per_eV)Thomas White
2015-12-10Fix integration tests for new saturation mapThomas White
2015-12-05Add option for per-pixel saturation valuesThomas White
2015-11-17Add a warningThomas White
2015-11-17Make gradient background fitting optionalThomas White
2015-11-10Remove old codeThomas White
2015-11-10Fix hardcoded maximum gradient for integrationThomas White
2015-06-26Plug some more leaksThomas 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
2015-04-28Reject boxes with very large gradients during rings integrationThomas White
2015-04-20Make panel assignments invariant during prediction- and post-refinementThomas White
Reflections appearing and disappearing are problematic when trying to do a least-squares refinement. Therefore, assume that reflections stay on panel and keep them under consideration even if their partialities go to zero (i.e. they drift off Bragg). This should stabilise both refinements, and simplifies quite a lot of code. Collateral "damage": the old "select_intersection()" is now gone.
2015-03-13Move solve_svd() to utilsThomas White
2015-02-12prof2d: Fix number of reference profilesThomas White
Thanks again to Takanori Nakane for spotting this
2015-02-12Show warning if CrystFEL was compiled without ncursesThomas White
2014-11-28Remove twod_mapping functionValerio Mariani
2014-11-28indexamajig: Report implausibly negative reflections only after final ↵Thomas White
integration
2014-11-27Fix pre-merging Poisson error calculation for low photon countsThomas White
2014-11-26Do not predict reflections beyond the resolution limit in the first placeThomas White
This is significantly faster than predicting to the edge then applying the resolution cutoff. With the "new" way of estimating the resolution limit, there's no need to integrate first.
2014-11-26Show panel name and correct coordinates in int-diagThomas White
2014-11-09Record number of implausibly negative reflections in streamThomas White
2014-11-02Report filename on terminal if it has implausibly negative reflectionsThomas White
2014-10-23Fix a load of memory leaksThomas White
2014-09-25Remove "sphere", "thin" and "gaussian" partiality models, add "scgaussian"Thomas White
2014-09-05Pass the partiality model through correctlyThomas White
2014-08-14Apply overlap mask to BM_IG pixels as wellThomas White
... because everything except BM_BH is used for centering.
2014-08-14Factorise reflection prediction and do it before creating the maskThomas White
2014-08-13Fix handling of overlapping reflectionsThomas White
2014-08-12Clean up a compiler warning when compiling without cursesThomas White
2014-08-11Take overlaps into account during integrationThomas White
2014-07-24Suspend indexing statistics while --int-diag is displayingThomas White
2014-06-25Pass the partiality model down from the API levelThomas White
2014-04-09Avoid breaking API with integrate_all()Thomas White
2014-04-08indexamajig: Add --push-resThomas White
2014-04-08Remove unused variableThomas White
2014-04-01Fix resolution cutoff so that it (apparently) worksThomas White
2014-03-28Require at least two bright pixels in integration box before moving centreThomas White
2014-03-21FormattingThomas White
2014-03-03Remove silly testThomas White
2014-03-03Test for brightest pixel after checking for closer reciprocal lattice pointThomas White
2014-03-03Include background and peak height in streamThomas White
2014-02-13Fix previous commitThomas White
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