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Author	SHA1	Message	Date
leonarski_f	527d239d53	JFJOchReader: Add ReadAllSpots option to handle reading just spot finding result	2026-06-02 09:39:26 +02:00
leonarski_f	55b65381db	jfjoch_viewer: Pan with right click + center 000 button	2026-06-01 13:28:16 +02:00
leonarski_f	60d0daabc2	jfjoch_viewer: Orthoscopic perspective to better see grid pattern	2026-06-01 13:22:19 +02:00
leonarski_f	bf94864af8	jfjoch_viewer: Work in progress reciprocal space viewer	2026-06-01 13:18:41 +02:00
leonarski_f	a2fd0a433f	jfjoch_viewer: Work in progress on reciprocal space viewer	2026-06-01 11:00:46 +02:00
leonarski_f	baeef1960e	JFJochViewerReciprocalSpaceWindow: OpenGL version, seems to work well	2026-05-31 19:59:13 +02:00
leonarski_f	b66fa9e5c6	JFJochViewerReciprocalSpaceWindow: Works, but is very slow	2026-05-31 19:48:21 +02:00
leonarski_f	487ee4d25b	jfjoch_viewer: Reciprocal space viewer, first edition	2026-05-30 13:13:53 +02:00
leonarski_f	7d1fa6401c	jfjoch_viewer: Cleaning user mask not dependent on selected ROI	2026-05-30 08:47:52 +02:00
leonarski_f	2251a44b1b	jfjoch_process: Works (more or less)	2026-05-29 20:27:13 +02:00
leonarski_f	33e9a368f6	jfjoch_tests: Fix lattice test with VDS HDF5	2026-05-29 19:50:50 +02:00
leonarski_f	6c8b2d4ddd	jfjoch_process: Enable two-pass algorithm	2026-05-29 17:22:53 +02:00
leonarski_f	40ae325995	IndexAndRefine: Dedicated function to add image to rotation indexer	2026-05-29 16:56:18 +02:00
leonarski_f	caa38a9732	RotationIndexerCounter: Implement rotation indexing counting logic	2026-05-29 16:54:00 +02:00
leonarski_f	7b20eedcbd	RotationIndexer: Remove logic controlling image accumulation	2026-05-29 16:27:22 +02:00
leonarski_f	e3924a08dd	RotationIndexer: Add GetAccumulatedImages() - though not sure if really useful	2026-05-29 16:09:35 +02:00
leonarski_f	0e4d80acd6	RotationIndexer: Add limit on spot count per image (not global), to enable fair-share of images + limit maximum number of images (there is no real benefit of going above 100 images in this model)	2026-05-29 15:24:23 +02:00
leonarski_f	4674aff202	jfjoch_test: Fix JFJochReader_NiggliClass_VDS	2026-05-29 15:03:58 +02:00
leonarski_f	4b609a6e06	RotationIndexer: Separate ProcessImage and GetLattice	2026-05-29 14:58:53 +02:00
leonarski_f	a6f61b0d8a	CMake: In debug mode JFJochVersion needs to be explicitly PIC to link with the plugin	2026-05-29 14:20:10 +02:00
leonarski_f	07d7174eff	XtalOptimizer: Accept std::vector<std::vector<SpotToSave>> for spots input, to distinguish spots between different images	2026-05-29 14:19:47 +02:00
leonarski_f	8660558341	JFJochHDF5Reader: Use lattice, and not Niggli class, to decode symmetry (if symmetry is imposed, then lattice search returns niggli class 0	2026-05-29 12:23:26 +02:00
leonarski_f	b44b0a56fb	RotationIndexer: For fixed space group, set explicitly lattice type and centering for refinement	2026-05-29 12:01:58 +02:00
leonarski_f	56764a948b	JFJochHDF5Reader: Read spots for one image	2026-05-28 22:04:17 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56 1.0.0-rc.146	2026-05-28 18:48:35 +02:00
leonarski_f	75f1c5f954	SHIM library improvements from the HDF Group	2026-05-08 11:39:51 +02:00
leonarski_f	caef26873e	v1.0.0-rc.145 (#55) ... This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144. * **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future. * XDS plugin: Improve performance of VDS reading. * jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD. * jfjoch_writer: Clean-up of HDF5 routines to better handle issues. Reviewed-on: #55 1.0.0-rc.145	2026-05-06 21:50:02 +02:00
leonarski_f	7d34e8a049	v1.0.0-rc.144 (#54) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Improve performance of preview JPEG image generator at receiver startup (saving about 150 ms on measurement start for 16M) Reviewed-on: #54 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.144	2026-05-01 17:06:36 +02:00
leonarski_f	6e0bb971ac	v1.0.0-rc.143 (#53) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. jfjoch_broker: Avoid copying gain calibration together with DiffractionExperiment Reviewed-on: #53 1.0.0-rc.143	2026-04-30 22:16:50 +02:00
leonarski_f	87fde1b32e	v1.0.0-rc.142 (#52) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Support for newer CUDA architectures (notably Blackwell); minimum CUDA version 12.8 * Minor changes to jfjoch_process, jfjoch_fpga_test and jfjoch_lite_perf_test to make them more consistent Reviewed-on: #52 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 16:47:53 +02:00
leonarski_f	d760b12a18	v1.0.0-rc.141 (#51) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Azimuthal integration mapping is generated with parallel computations, significantly reducing setup times * frontend: Fix selection of FFTW in indexing settings Reviewed-on: #51 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 13:04:54 +02:00
leonarski_f	239a441ee6	v1.0.0-rc.140 (#50) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: For DECTRIS detectors, ZeroMQ link is persistent, to save time for establishing new connection * jfjoch_broker: Minor bug fixes for rare conditions Reviewed-on: #50	2026-04-29 21:40:22 +02:00
leonarski_f	4878318c27	v1.0.0-rc.139 (#49) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start` * jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start' * jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time * jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received * jfjoch_broker: Use nanoseconds internally for frame/image/readout time * jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished) * jfojch_broker: Improve profiling of different data analysis steps * jfjoch_broker: Record integration reflection count * jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds) * jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked * jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets **Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time. Reviewed-on: #49 1.0.0-rc.139	2026-04-29 09:50:50 +02:00
leonarski_f	230480e390	v1.0.0-rc.138 (#48) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. jfjoch_broker: Cleanup DECTRIS start-up code to enable a shorter start time jfjoch_broker: Allow for asynchronous start to allow overlapping detector configuration with other beamline preparations jfjoch_broker: Goniometer axis name is converted to lowercase jfjoch_broker: Fix bug, where wrong HTTP error codes were returned jfjoch_broker: Improve sigma estimation during merging (K. Takaba) --------- Co-authored-by: takaba_k <kiyofumi.takaba@psi.ch> Reviewed-on: #48 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.138	2026-04-27 19:56:14 +02:00
leonarski_f	c981e1b91c	v1.0.0-rc.137 (#46) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Better track time for each operation in the processing stack * jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress) * jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress) * jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0) Reviewed-on: #46 1.0.0-rc.137	2026-04-25 19:59:21 +02:00
leonarski_f	c1c170112c	v1.0.0-rc.136 (#45) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Improve logic regarding indexing architecture and thread pools (work in progress). Reviewed-on: #45 1.0.0-rc.136	2026-04-20 11:54:33 +02:00
leonarski_f	bb9f5c715f	v1.0.0-rc.135 (#44) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4) * jfjoch_viewer: Improve image render performance Reviewed-on: #44 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.135	2026-04-16 11:59:59 +02:00
leonarski_f	4a852b4d6b	v1.0.0-rc.134 (#43) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Add better locking for detector object - should help, when detector initialization takes too long * jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata * XDS plugin: Add generation of Jungfraujoch plugin for XDS * CI: Add tests with XDS and DIALS (`xia2.ssx`) Reviewed-on: #43 1.0.0-rc.134	2026-04-09 13:30:47 +02:00
leonarski_f	81bd9a06a1	CI pipeline upgrade (#42) ... Updates to CI pipeline * New docker image for Ubuntu 22.04 with CMake 3.26 * New docker image for Rocky 9 with DIALS 3.27 * New automated test to check for DIALS processing with xia2.ssx Reviewed-on: #42	2026-03-28 20:06:23 +01:00
leonarski_f	6133da1377	v1.0.0-rc.133 ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Use httplib for HTTP server instead of Pistache * jfjoch_broker: Drop OpenSSL support * jfjoch_broker: Base work for multi-lattice support in the future * Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib) Reviewed-on: #41 1.0.0-rc.133	2026-03-26 20:50:33 +01:00
leonarski_f	2ab9deb20b	v1.0.0-rc.123 (#40) ... Documentation update Reviewed-on: #40 1.0.0-rc.132	2026-03-12 12:17:11 +01:00
leonarski_f	166fcdb68f	v1.0.0-rc.131 (#39) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS) * jfjoch_viewer: Fix calibration (pedestal) images being open flipped * jfjoch_process: Add space group detection (EXPERIMENTAL) Reviewed-on: #39 1.0.0-rc.131	2026-03-07 11:34:04 +01:00
leonarski_f	928789a67c	v1.0.0-rc.130 (#37) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Rotation indexer has two retries if failes * jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot) * jfjoch_broker: Integration calculates background mask based on R2 radius * jfjoch_process: HDF5 files are not saved by default Reviewed-on: #37 1.0.0-rc.130	2026-03-06 14:38:56 +01:00
leonarski_f	64002f1e29	v1.0.0-rc.129 (#36) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files) * jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction * jfjoch_broker: Image pusher statistics are accessible via the REST interface * jfjoch_writer: Supports TCP image socket and for these auto-forking option Reviewed-on: #36 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.129	2026-03-05 22:13:12 +01:00
leonarski_f	3036b1d37f	v1.0.0-rc.128 (#35) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Handle properly reuse of image buffer locations * jfjoch_broker: Fix bug in counting idle slots * jfjoch_broker: Force obtuse angle for monoclinic cells * jfjoch_process: Change scaling refinement tolerance Reviewed-on: #35 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.128	2026-03-03 22:24:44 +01:00
leonarski_f	f3e0a15d26	v1.0.0-rc.127 (#34) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Default EIGER readout time is 20 microseconds * jfjoch_broker: Multiple improvements regarding performance * jfjoch_broker: Image buffer allows to track frames in preparation and sending * jfjoch_broker: Dedicated thread for ZeroMQ transmission to better utilize the image buffer * jfjoch_broker: Experimental implementation of transmission with raw TCP/IP sockets * jfjoch_writer: Fixes regarding properly closing files in long data collections * jfjoch_process: Scale & merge has been significantly improved, but it is not yet integrated into mainstream code Reviewed-on: #34 1.0.0-rc.127	2026-03-02 15:57:12 +01:00
leonarski_f	32b681e591	v1.0.0-rc.126 (#33) ... This is an UNSTABLE release. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug for monoclinic space groups being wrongly refined when beta is much different from 90 deg. Reviewed-on: #33 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.126	2026-02-19 07:01:38 +01:00
leonarski_f	1ab257af6c	v1.0.0-rc.125 (#32) ... This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Improve logic on switching on/off spot finding * jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 * jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) * jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis * jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection * jfjoch_writer: Save more information about each reflection Reviewed-on: #32 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.125	2026-02-18 16:17:21 +01:00
leonarski_f	07fe4dd3bb	v1.0.0-rc.124 (#31) ... This is an UNSTABLE release. This version significantly rewrites code to predict reflection position and integrate them, especially in case of rotation crystallography. If things go wrong with analysis, it is better to revert to 1.0.0-rc.123. * jfjoch_broker: Improve refection position prediction and Bragg integration code. * jfjoch_broker: Align with XDS way of calculating Lorentz correction and general notation. * jfjoch_writer: Fix saving mosaicity properly in HDF5 file. * jfjoch_viewer: Introduce high-dynamic range mode for images * jfjoch_viewer: Ctrl+mouse wheel has exponential change in foreground (+/-15%) * jfjoch_viewer: Zoom-in numbers have better readability Reviewed-on: #31 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.124	2026-02-01 13:29:33 +01:00
leonarski_f	1c4dfd03e2	v1.0.0-rc.123 (#30) ... This is an UNSTABLE release. * jfjoch_broker: Use newer version of Google Ceres for (potential) CUDA 13 compatibility * jfjoch_broker: Improve performance of generating preview images, especially for large detectors (9M-16M) * jfjoch_viewer: Improve performance of displaying images, especially for large detectors (9M-16M) * jfjoch_viewer: Add more color schemes for better image readability * HDF5: Common mutex for reading and writing HDF5 if both operations were to happen in the same executable * HDF5: suppress warning if path (upstream group) doesn't exists when checking if leaf exists Reviewed-on: #30 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch> 1.0.0-rc.123	2026-01-30 13:43:09 +01:00