Age | Commit message (Collapse) | Author | |
---|---|---|---|
2021-03-31 | FromFile indexer, stream2sol.py: Handle spaces in filename | Thomas White | |
2021-03-31 | indexamajig: Handle spaces in filename when retrieving ID from queue | Thomas White | |
2021-03-31 | FromFile indexer, stream2sol.py: Add/update copyright comments | Thomas White | |
2021-03-31 | stream2sol.py: Remove --include-pars | Thomas White | |
These are now obsolete, and the distributed version of CrystFEL will choke on them. | |||
2021-03-31 | stream2sol.py: Remove unused definitions | Thomas White | |
2021-03-31 | stream2sol.py: Add lattice type, centering and unique axis | Thomas White | |
2021-03-31 | stream2sol.py: Strip trailing whitespace | Thomas White | |
2021-03-31 | stream2sol.py: Initial import | Thomas White | |
2021-03-30 | GUI: Fail more gracefully if image file is not present | Thomas White | |
With the new header cache, it's possible to operate completely from the stream. | |||
2021-03-30 | Add header caching layer | Thomas White | |
This simultaneously implements --copy-header/--copy-hdf5-field and gives access to metadata (e.g. detector position or wavelength) when loading from a stream with header-specified values. | |||
2021-03-29 | Add documentation for --harvest-file | Thomas White | |
2021-03-29 | indexamajig: Don't write harvest file if serial start is >1 | Thomas White | |
This will avoid multiple indexamajig processes from overwriting the others' files when running a batch job. | |||
2021-03-26 | partialator: Add missing comma in JSON | Thomas White | |
2021-03-26 | GUI: Tell indexamajig and partialator to write parameter harvest files | Thomas White | |
2021-03-26 | GUI: Add missing model parameter for merging | Thomas White | |
Whoops. | |||
2021-03-26 | partialator: Add --harvest-file | Thomas White | |
2021-03-26 | indexamajig: Add --harvest-file | Thomas White | |
2021-03-26 | Add str_integration_method | Thomas White | |
2021-03-26 | Rearrange 'struct index_args' and remove unused elements | Thomas White | |
"cmfilter" and "integrate_saturated" were unused. | |||
2021-03-25 | indexamajig: Add --camera-length-estimate | Thomas White | |
Unfortunately, PinkIndexer needs the real camera length for its centre refinement. Giving a fake value and scaling the resulting shift does not work - the indexing rate drops with even a small error. Ideally, this would work in the same way as --wavelength-estimate, by using a static value from the geometry file if it's given. However, this is rather complicated to implement because of the way all the units stuff is implemented. Therefore, this is left as an improvement for the future. | |||
2021-03-25 | Add detgeom_mean_camera_length | Thomas White | |
2021-03-25 | PinkIndexer: fix conversion of detector shift | Thomas White | |
2021-03-25 | Fussiness | Thomas White | |
The FIXMEs have both already been fixed. | |||
2021-03-25 | Avoid updating detector geometry structure during prediction refinement | Thomas White | |
This makes the behaviour consistent with the prediction itself, and removes another bit of mutable state. | |||
2021-03-23 | Use crystal's detector shift during prediction | Thomas White | |
Previously, this was handled by updating the detector, but this could easily lead to strange double accounting. | |||
2021-03-23 | Don't automatically set --no-refine --no-check-peaks with PinkIndexer | Thomas White | |
See c876486b for rationale. | |||
2021-03-23 | CMake: ensure RPATH is always set for libcrystfel | Thomas White | |
This helps with finding dependencies installed in non-system locations. | |||
2021-03-23 | CMake: formatting, use pkg_check_modules instead of pkg_search_module | Thomas White | |
2021-03-22 | Allow HDF5 path substitution when there are too many placeholder values | Thomas White | |
This allows, for example, masks which have fewer % signs in their HDF5 locations than the main data. | |||
2021-03-22 | FromFile indexer: Fix prototype | Thomas White | |
2021-03-19 | Merge branch 'tom/fromfile' | Thomas White | |
2021-03-19 | Update AUTHORS and README.md | Thomas White | |
2021-03-19 | FromFile indexer: add copyright notice | Thomas White | |
There is presumably an MPSD that also needs to be added. | |||
2021-03-19 | FromFile indexer: Take account of working directory | Thomas White | |
2021-03-19 | FromFile indexer: New parser and simplification of code | Thomas White | |
Significant change: the solution file must now come with the lattice type, centering and (if applicable) unique axis information at the end of each line, e.g. 'cI' (cubic I), 'mAb' (monoclinic A, unique axis b). | |||
2021-03-19 | Fix mode of uthash.h | Thomas White | |
2021-03-19 | FromFile indexer: Option processing | Thomas White | |
This give FromFile its own private command-lien option processing, like the other indexers. It removes the ability to auto-generate the solution filename, but I don't think there's a way to do that without breaking abstractions. | |||
2021-03-17 | CrystFELImageView: Fix zoom limits | Thomas White | |
2021-03-17 | GUI: Show beam centre more clearly, and optionally | Thomas White | |
2021-03-17 | Add missing conversion to pixels for detector_shift_{x,y} | Thomas White | |
2021-03-17 | Factorise panel in create_detgeom | Thomas White | |
2021-03-16 | CrystFELImageView: Avoid crash when scrolling after image load failure | Thomas White | |
2021-03-16 | Add CONTRIBUTING.md | Thomas White | |
2021-03-16 | get_hkl: Fix logic for loading unit cell | Thomas White | |
2021-03-16 | get_hkl: Add options to export to MTZ and XDS | Thomas White | |
2021-03-16 | Move MTZ and XDS export to libcrystfel | Thomas White | |
2021-03-15 | GUI: Add interface for --fix-profile-radius and --fix-divergence | Thomas White | |
2021-03-12 | FromFile indexer: Add skeleton cleanup procedure | Thomas White | |
2021-03-12 | Remove .gitignore | Thomas White | |
2021-03-12 | FromFile indexer: Update for new event ID in image structure | Thomas White | |