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2021-04-21Remove index_args->max_n_peaksThomas White
It's not used anywhere.
2021-04-15Separate ZMQ from MessagePack, switch to pub/sub socketThomas White
Indexamajig uses only ZMQ, to receive streaming data, while libcrystfel uses only msgpack to implement another type of image format. The two of these are eventually tied together in process_image, which does this: if ( have_zmq_data ) interpret_zmq_data_as_msgpack; - however, they would be easy to split up if we wanted to do something else (CBF data over ZMQ, anyone?). This commit also switches the ZMQ connector to use a pub/sub socket instead of a request/reply one. This matches changes in OnDA. At the moment, the MessagePack image reader simply dumps the object to disk.
2021-03-26Rearrange 'struct index_args' and remove unused elementsThomas White
"cmfilter" and "integrate_saturated" were unused.
2021-03-25indexamajig: Add --camera-length-estimateThomas 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.
2021-03-11indexamajig: Add --max-indexer-threadsThomas White
This is a more general replacement for --pinkIndexer-thread-count.
2021-03-11indexamajig: Add --wavelength-estimateThomas White
This is a more sensible non-indexer-specific and non-Xray-specific replacement for --pinkIndexer-override-photon-energy
2021-03-05Mass update of copyright dates in source code commentsThomas White
2020-07-31Move spectrum loading out of indexamajig/process_imageThomas White
2020-07-29Add --no-image-data and --no-mask-dataThomas White
2020-07-29Convert indexamajig to new Stream APIThomas White
2020-07-29Get rid of imagefile_field_list and stuff_from_streamThomas White
The only place this is used is in geoptimiser, to get the average_camera_length, itself a very bad solution.
2020-07-29Port indexamajig to new API, part IThomas White
2020-07-29Add DataTemplate to iargsThomas White
2020-07-29Peak search stuffThomas White
2020-01-10Mass update of copyright datesThomas White
2019-09-23Merge branch 'tom/pinkindexer'Thomas White
2019-09-23indexamajig: Move 'profile' flag out of iargsThomas White
2019-09-20Delegate option processing for indexing methodsThomas White
Involves switching from getopt_long to argp. A big improvement!
2019-09-12indexamajig: Get rid of --fix-bandwidth / use bandwidth from geometry fileThomas White
2019-09-12Fix header include pathThomas White
2019-09-12WhitespaceThomas White
2019-09-12Add pinkIndexer interfaceYaroslav Gevorkov
2019-09-10indexamajig: Add --peaks=noneThomas White
2019-08-16indexamajig: Accept six values for unit cell toleranceThomas White
2019-07-17Merge branch 'tom/zmq'Thomas White
2019-05-29Use Spectrum API for simulationThomas White
2019-03-14indexamajig: Add --no-image-dataThomas White
2019-03-14Compile cleanly without Msgpack or ZMQThomas White
2019-03-14Connect up hooks for unpacking MsgPack dataThomas White
2019-03-14ZMQ connection and setup stuffThomas White
2019-03-06indexamajig: Rename --min-gradient to --min-squared-gradientThomas White
The eventual aim of this is to deprecate the "--min-gradient" option, resolving the long-standing confusion about whether this option is the gradient or the squared gradient.
2018-12-03indexamajig: Add --wait-for-fileThomas White
2018-11-15indexamajig: Name and shame slow processing stagesThomas White
2018-09-10Fussiness / formattingThomas White
2018-09-10indexamajig: read pink beam spectrum from fileAlexandra Tolstikova
2018-06-18Add interface to XGANDALF indexerYaroslav Gevorkov
2018-05-30Use only one min-snr optionThomas White
2018-05-30Changed parameter window-radius -> local-bg-radiusYaroslav Gevorkov
2018-05-30Changed sig_fac to min_snrYaroslav Gevorkov
2018-05-24Update authorship and copyright datesThomas White
2018-05-24Add "peakfinder9"Yaroslav Gevorkov
2018-02-27indexamajig: Add --overpredictThomas White
2017-10-12indexamajig: Simplify Felix optionsThomas White
2017-07-06indexamajig: Add TakeTwo-specific optionsThomas White
2017-06-27indexamajig: Add --no-non-hits-in-streamThomas White
2017-06-21indexamajig: Add --min-peaks (basic hitfinder functionality)Thomas White
2017-05-02Skeleton image file APIThomas White
2017-03-31Offset peak locations from HDF5 or CXI files by 0.5,0.5Thomas White
CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry. In contrast, Cheetah considers the peak locations to be pixel indices in the data array. Therefore, a half-pixel offset is needed when importing the peak lists. For users who need the old behaviour, this commit adds a new option indexamajig --no-half-pixel-shift to deactivate this offset.
2017-03-24Merge branch 'valerio/peakfinder8'Thomas White
2017-03-11Removed unused iargValerio Mariani
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