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2021-01-07Formatting fussinessThomas White
2021-01-06partialator: Reject crystals with obviously too large profile radiiThomas White
The criterion for "too large" is 20% of the 1/d value for the lowest reflection which is not systematically absent according to the centering. A profile radius larger than the 1/d value for a reflection will crash the xsphere partiality model, and some visualisation shows that this is a clearly non-physical situation. The profile radius shouldn't be anywhere near the inter-Bragg spacing for reasonable data. However, feedback shows that this is happening quite often in real data, probably due to bad indexing.
2021-01-05Remove unused structure memberThomas White
2020-12-18Add peak_list_type in geometry fileThomas White
2020-12-16Add flag_{lessthan,morethan,equal} in geometry fileThomas White
This makes handling Pilatus/Eiger files, as well as many others, much easier.
2020-12-14Meson: Add GSL to libcrystfel's declare_dependency()Thomas White
2020-12-07Get rid of ImageFeature->rx,ry,rzThomas 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.
2020-10-27Add a new StreamFlag for generating the detgeom structureThomas White
This is a hack, and should be replaced by something which gets the metadata from the stream rather than hitting the read image file every time.
2020-10-27image_set_zero_{data,mask}: Speed up creation of blank arraysThomas White
2020-10-27Fix a possibly overrun stringThomas White
2020-10-26Label all uses of cell tolerancesThomas White
I'm sick of fixing this same issue over and over again. New rule: any code handling unit cell tolerances MUST be labelled with details of units.
2020-10-22image_expand_frames: When files are not HDF5, just return null eventsThomas White
2020-10-22compare_cell_parameters: Accept R/P pair as equivalentThomas White
See 0f18ff76a3d1f5979db for some discussion.
2020-10-15Shuffle default order of indexing methodsThomas White
2020-10-15Add TakeTwo to the list of indexers automatically usedThomas White
2020-10-15TakeTwo: Limit number of seeds to 10, and reduce MAX_OBS_VECTORS to 300Thomas White
This gives a huge speed improvement, without sacrificing very much in indexing rate.
2020-10-07Revert "Move asdf out of set of indexers used by default"Thomas White
This reverts commit 62183aacf906f4aff771295aa378cff039dd50ff. The apparent slowness was due to a bug introduced in August 2019. See 2a8f415df845064186baa833f9fe1ad91c0f5753.
2020-10-07asdf: Fix incorrect units conversion for cell volumeThomas White
2020-10-07Formatting fussinessThomas White
2020-10-07Improve indexer speed profilingThomas White
2020-10-07FussinessThomas White
Commented out debug message is no longer relevant
2020-10-07TakeTwo: Set tp->optsThomas White
2020-10-07TakeTwo: Fix get_chiral_holohedry for "hexagonal H"Thomas White
Fixes CRYS-240
2020-10-06Move asdf out of set of indexers used by defaultThomas White
Sadly, it has the same fatal flaw as TakeTwo: taking forever on a minority of patterns.
2020-10-01asdf: Replace weird loop syntaxThomas White
2020-09-30image_expand_frames: Report non-existent file properlyThomas White
2020-09-25stream_make_index: s/Indexing/Scanning/Thomas White
Because it sounds strange and confusing to index the indexing results.
2020-09-24Fix old warning messageThomas White
2020-09-24Apply default unit scale factor only when value is from headersThomas White
Ugh.
2020-09-17CMake: Change LIBRARIES to LDFLAGSThomas White
Necessary after conversion to pkg-config search, to make sure that custom paths get used.
2020-09-17Add missing includeThomas White
2020-09-17Ensure that fs dimension has higher index than ssThomas White
Reading from HDF5 cannot rearrange dimensions, only select a chunk. Therefore, the layout in memory needs to match the file.
2020-09-16image_hdf5_read: Don't call image_freeThomas White
You didn't allocate it, so you don't free it.
2020-09-16Fix incorrect logic in HDF5 expansionThomas White
2020-09-11xgandalf: Remove C99-style 'for' declarationsThomas White
2020-09-10CMake: Don't compile image-msgpack.c if library is not foundThomas White
2020-09-09get_matrix_name: Improve string handlingThomas White
2020-09-09Add optional measurement of time spent in indexersThomas White
2020-09-08Remove "Command line:" in streamThomas White
This wasn't present in the old version, and it was missing a space anyway.
2020-09-08Un-export image_read_image_dataThomas White
Not needed since f5b3c4db36fa.
2020-09-07Catch another "NULL" event -> //Thomas White
2020-09-04stream_read_chunk: Set image->spectrumThomas White
2020-09-04stream_make_index: Don't require an event ID for every chunkThomas White
Event ID is not written if not needed
2020-09-04make_key: Handle NULL eventThomas White
2020-09-04New API for random access to streamThomas White
2020-09-02Get rid of STREAM_IMAGE_DATAThomas White
No longer needed, and didn't fit very well in the first place.
2020-08-27TakeTwo: Remove internal declarationsThomas White
2020-08-27Fix indentationThomas White
2020-08-27Only compile image-msgpack.c if MessagePack is foundThomas White
2020-08-25Factor out convert_intThomas White
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