Age | Commit message (Collapse) | Author | |
---|---|---|---|
2021-10-13 | Remove NCurses dependency | Thomas White | |
It's only used once, to get background colours for 'indexamajig --int-diag', itself a rarely used feature. The dependency itself seems to cause problems for some people, particularly those not using system libraries for everything. So I think it's better just to remove it, and use ANSI escape codes directly. | |||
2021-09-07 | check_box: Fix type used for sizeof | Thomas White | |
2021-08-13 | Increase threshold for integration warning | Thomas White | |
The warning about "XXX reflections couldn't be integrated" is tiresome - it appears for practically every indexed pattern because there are always some reflections that fall in bad regions or at panel edges. This suppresses the warning unless the number of integration failures is more than a quarter of the total number of reflections. | |||
2021-07-21 | Reduce variable scope where possible | Thomas White | |
2021-07-21 | Make sure that memory gets freed on realloc failure | Thomas White | |
2021-07-21 | Add missing cleanup on error paths | Thomas White | |
2021-05-17 | Resolve FIXMEs and TODOs | Thomas White | |
Prompted by the article linked below, for each FIXME/TODO I've either referenced an issue in the tracker, or removed it if it's not worth fixing. https://schleiss.io/plotting-source-code-todos-for-open-source-projects | |||
2021-04-27 | Rename libcrystfel's config.h to libcrystfel-config.h | Thomas 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. | |||
2021-03-26 | Add str_integration_method | Thomas White | |
2021-03-11 | detgeom_transform_coords: Take an additional detector shift | Thomas White | |
This allows the refined detector position to be used in a lot of places. | |||
2021-03-05 | Mass update of copyright dates in source code comments | Thomas White | |
2021-01-08 | Remove "Bragg proximity check" during integration | Thomas White | |
This test is meant to avoid integrating overlapping spots. It does a very bad job of this, because it doesn't take into account whether the neighbouring reflection is actually excited, or even allowed by the lattice. It's even worse when we think about wide bandwidth. | |||
2021-01-07 | Formatting fussiness | Thomas White | |
2020-12-07 | Get rid of ImageFeature->rx,ry,rz | Thomas White | |
These needed to be kept up to date with a call to map_all_peaks every time anything changed - wavelength, detector position etc. Not doing so has already led to bugs in another branch, and probably already causes problems on this branch. This patch eliminates the rx,ry,rz completely. Anyone who needs reciprocal space coordinates for a peak is now responsible for calling detgeom_transform_coords themselves. | |||
2020-07-30 | Eliminate duplicate symbols | Thomas White | |
This makes searching easier, and also permits Meson's unity build mode. | |||
2020-07-29 | Expose a couple more functions for easier testing | Thomas White | |
2020-07-29 | Add low-level integration API (for better testing) | Thomas White | |
2020-07-29 | Convert more bits to detgeom | Thomas White | |
2020-07-29 | Convert make_BgMask to detgeom | Thomas White | |
2020-07-29 | Convert prediction and integration to detgeom | Thomas White | |
2020-03-09 | integrate_rings_once: Handle case where reflection is negative by < 1 photon | Thomas White | |
2020-01-10 | Mass update of copyright dates | Thomas White | |
2019-09-23 | Get rid of "rescut" integration flag | Thomas White | |
Its behaviour is 100% covered by the push-res parameter, which can be set to infinity for no cutoff. | |||
2019-09-17 | Add warning if reflections could not be integrated (e.g. due to overlap) | Thomas White | |
2019-05-14 | Remove image.num_peaks and num_saturated_peaks | Thomas 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. | |||
2019-05-07 | Update all source code comments to Doxygen format | Thomas White | |
2018-05-17 | Merge branch 'tom/cmake' | Thomas White | |
2018-03-22 | Test for Curses | Thomas White | |
2018-02-27 | indexamajig: Add --overpredict | Thomas White | |
2018-02-27 | New partiality model from Ginn et al. | Thomas White | |
2018-02-27 | Separate partiality calculation from prediction | Thomas White | |
2016-07-01 | No more slab-relative coordinates in libcrystfel | Thomas White | |
2016-04-01 | Add adu_per_photon (distinct from adu_per_eV) | Thomas White | |
2015-12-10 | Fix integration tests for new saturation map | Thomas White | |
2015-12-05 | Add option for per-pixel saturation values | Thomas White | |
2015-11-17 | Add a warning | Thomas White | |
2015-11-17 | Make gradient background fitting optional | Thomas White | |
2015-11-10 | Remove old code | Thomas White | |
2015-11-10 | Fix hardcoded maximum gradient for integration | Thomas White | |
2015-06-26 | Plug some more leaks | 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 | Reject boxes with very large gradients during rings integration | Thomas White | |
2015-04-20 | Make panel assignments invariant during prediction- and post-refinement | Thomas 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. | |||
2015-03-13 | Move solve_svd() to utils | Thomas White | |
2015-02-12 | prof2d: Fix number of reference profiles | Thomas White | |
Thanks again to Takanori Nakane for spotting this | |||
2015-02-12 | Show warning if CrystFEL was compiled without ncurses | Thomas White | |
2014-11-28 | Remove twod_mapping function | Valerio Mariani | |
2014-11-28 | indexamajig: Report implausibly negative reflections only after final ↵ | Thomas White | |
integration | |||
2014-11-27 | Fix pre-merging Poisson error calculation for low photon counts | Thomas White | |