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2021-07-15GUI: Run all jobs with same CWD as GUI itselfThomas White
This requires changing all the paths to relative ones. Previously, the jobs ran with their CWDs set to the corresponding "result" folder. The trouble is, this breaks everything that uses a relative location: image filenames, mask/satmap files referenced by the geometry, etc. Note that this change also means that the temporary folders ("indexamajig.XXX") are now produced in the top-level working directory. Eventually, a GUI option should be added to allow these folders to be put somewhere better (i.e. somewhere fast). Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/44
2021-07-15CrystFELIndexingOpts: Add tooltips for PinkIndexer optionsThomas White
2021-07-15Fix an incorrect error messageThomas White
2021-07-14GUI: Add PinkIndexer options to command lineThomas White
2021-07-14Remove non-API headers from installation listThomas White
Just like the individual indexing methods, these aren't part of the API. peakfinder8.h was there twice, for some reason.
2021-07-14GUI: Get/set PinkIndexer optionsThomas White
2021-07-14GUI: Add PinkIndexer options to 'struct index_params'Thomas White
2021-07-14CrystFELIndexingOpts: Add PinkIndexer optionsThomas White
2021-07-14PinkIndexer: replace long formula with modulus()Thomas White
2021-07-14Add get_combo_idThomas White
2021-07-14GUI: Add placeholders for advanced indexer optionsThomas White
2021-07-14Make all the indexer-specific option structures non-opaqueThomas White
Making them opaque seemed like a nice idea, because all the indexers could take care of their own command-line arguments. However, it doesn't work at all when indexing is run via the API.
2021-07-13GUI: Reject infinite resolution limits for FoMThomas White
2021-07-12GUI: Add Tools->Jump to frameThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/41
2021-07-12GUI: Update the "About" boxThomas White
2021-07-12GUI: Add --wavelength-estimate and --camera-length-estimateThomas White
Only when using PinkIndexer. Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/25
2021-07-09pattern_sim: Fix typo in --helpThomas White
2021-07-08Revert "Bump stream version to 2.4"Thomas White
Rationale: Although the format has technically changed, CrystFEL 0.9.1 and older do not read the "hdf5/" lines anyway. The new "header" lines are just noise, as far as they are concerned. However, increasing the version number causes older CrystFEL versions to reject streams written by newer CrystFEL versions. This is inconvenient, but will be a particular problem since CrystFEL 0.10.0 will most likely be released without a working "geoptimiser". We therefore need to be able to use older CrystFEL versions for refining geometry. Older versions are perfectly capable of reading newer streams. In general, the semantics of stream version numbers are a bit messed up, and we need to work out what they really mean. This reverts commit fdce01adf9fc5950904b644ea755760cb32ec5b2.
2021-07-07Bump stream version to 2.4Thomas White
The format for storing headers has changed from hdf5/location to header/type/location.
2021-07-07Interpret old-style stream header records as floating pointThomas White
The old way of recording metadata in the stream unfortunately doesn't include any information about the data type. Most of the time, floating point is what's intended. Older CrystFEL doesn't know about integer headers at all, but there might be string values if --copy-hdf5-field was used. By interpreting "hdf5/something = val" as floating-point, most things will work, e.g. camera length from HDF5 header enabling stream to be loaded without access to the image data. Anything that can't be interpreted as floating-point will be noisily ignored when loading the stream.
2021-07-07speed.rst: Update formatting and contentThomas White
2021-07-06online.rst: Fix a typoThomas White
2021-07-06SLURM: Show the real error message if job can't be submittedThomas White
2021-07-05Add article about speedThomas White
2021-07-05indexamajig(1): Clarify --min-peaks default valueThomas White
2021-07-01Meson: FussinessThomas White
2021-07-01CMake: Remove vestigial lineThomas White
2021-06-28Update INSTALL.mdThomas White
Better understanding of the fPIC problem.
2021-06-25Meson: Fix build without DoxygenThomas White
2021-06-25Meson: Remove fallback HDF5 search, and add required minimum versionThomas White
Meson's internal HDF5 search should work in all cases since 0.50.0, subject to issues documented in INSTALL.md.
2021-06-25Update INSTALL.mdThomas White
2021-06-23GUI: Avoid writing '(null)' to project fileThomas White
The problem is, '(null)' is not NULL.
2021-06-23CrystFELSymmetrySelector: Set have_pg when PG is set via APIThomas White
2021-06-23GUI: Swap Close/Calculate buttons in FoM windowThomas White
This makes it consistent with all the other windows.
2021-06-23GUI: Fix a tooltipThomas White
2021-06-23Tweak INSTALL.mdThomas White
2021-06-22GUI: Fix paths to streams for merging and ambigatorThomas White
They need to be prefixed with "../" because they are in a different folder.
2021-06-22CrystFELImageView: Adjust threshold for showing box centresThomas White
I find that starting to show centres at a higher magnification level makes it easier to distinguish the centre markers from bright pixels.
2021-06-22GUI: Remove old debugging watchpointThomas White
2021-06-22CrystFELImageView: Rearrange reflection coloursThomas White
Smaller numbers of crystals are more common, so it's better for the second crystal to be something very distinct from the peak search colour.
2021-06-22Update INSTALL.mdThomas White
2021-06-22Add string terminator for fixed-length HDF5 strings from arraysThomas White
2021-06-21Restore HDF5 string handlingThomas White
Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/36
2021-06-21image_cache_header_str: Reject strings containing newlinesThomas White
2021-06-21INSTALL.md: Mention CentOSThomas White
2021-06-21Move installation documentation to INSTALL.mdThomas White
2021-06-17GUI: Add a tooltipThomas White
2021-06-17CMake: Use ZMQ_LDFLAGS instead of ZMQ_LIBRARIESThomas White
2021-06-16GUI: Warn if chunk can't be loaded from streamThomas White
2021-06-16stream_read_chunk: Bail out if detgeom can't be createdThomas White
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