v1.0.0-rc.125 #32

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leonarski_f merged 81 commits from 2601-completness into main 2026-02-18 16:17:21 +01:00

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leonarski_f commented 2026-02-18 16:16:55 +01:00

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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

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

leonarski_f added 81 commits 2026-02-18 16:16:55 +01:00

jfjoch_writer: Save partiality 88701b31db

BraggPrediction: Add partiality calculation 7edad6b7c1

BraggPrediction: Fix for GPU code 60e03bfda6

XtalOptimizer: Fix rotation angles (Claude Opus suggestion :) ) f388922515

AnalyzeIndexing: Log-likelihood approach for mosaicity calculation (like XDS) fed8fd0f57

BraggPredictionRot: Getting it (slowly) right with XDS implementation e0b7594429

jfjoch_tests: Add more tests 787e781eb2

RotationSpotAccumulator: Add (Claude 4.5 Opus) 392af14013

RotationSpotAccumulator: Works, but super slow 1f6477e34f

RotationSpotAccumulator: Should be a bit faster ecc924fe4a

DiffractionGeometry: Store rotation matrix a40e4118e6

SpotToSave: Include phi angle of the spot f9cc99f3c0

XtalOptimizer: Use rotation angle from spot (so it should work for centroid angles) e2ab97c09b

XtalOptimizer: Fix test to include phi angle ae4c28f127

XtalOptimizer: Fix test to include phi angle cb7e7ad576

DiffractionSpot: Consistent definition of rotation angle aac982a239

IndexAndRefine: Simple optimization was not good enough - using a non-linear solver leads to considerably better predictions. 4edebe888e

IndexAndRefine: Fix wrong include file b7a3fb09ef

Reflection: Add delta_phi 70343ec058

JFJochHDF5Reader: Read delta phi 666b52ffc1

Reflection: Save zeta e15944ab56

BraggPredictionRot: Fix partiality 7177d0fed0

ScaleAndMerge: Add rotation partiality model fb493e8ac2

ScaleAndMerge: Further improvement 068ea2eea7

IndexAndRefine: Save all reflections...to integrate scale and merge d6265fe589

ScaleAndMerge: Merge intensities taken from scaling - variances taken directly from least-squares (with some magic from Opus 4.6, which I don't yet understand) 7f1f28f8d3

jfjoch_process: Include scaling - to be tested 6e28ad3523

jfjoch_process: Add French-Wilson (completely written by Opus 4.6...need to understand it properly first :) ) 69ebbed8fb

jfjoch_process: Fix 58f29409e6

CCP4: Add library to save MTZs d4d1f6cd9c

Revert "CCP4: Add library to save MTZs" ... f49cb3a6f0

This reverts commit d4d1f6cd9c.

jfjoch_process: minor fixes to input parameters c40a0332e7

ScaleAndMerge: Fix partiality model 684c3df204

ScaleAndMerge: Fix symbol names k --> g, remove setting first image scale factor to 1 (it is too weak), remove radians e0fd62df2b

BraggPredictionRotGPU: Save delta_phi in degrees, not radians 14402f8175

BraggPredictionGPU: Fix 247ed0e1eb

Ceres: Build with C++ threads 44802ddac4

ScaleAndMerge: Print full report (for now) and use max number of threads 45e4a642f9

ScaleAndMerge: Add log-scaling residual 86afb7697e

ScaleAndMerge: Add option to turn off per image mosaicity 217e86c23b

jfjoch_process: More options de8e8d3a64

jfjoch_process: Fixes 161df2f5a1

jfjoch_process: More fixes 34b24133c7

jfjoch_process: More fixes fd8e263934

ScaleAndMerge: Add AI generated sigmas 1dedd3de33

jfjoch_process: Save reflections as mmCIF (experimental) 38199c480f

ScaleAndMerge: sigma calculation included 0ae85a63f9

ScaleAndMerge: Intensities come from merging 936b63a7a9

WriteMmcif: Fix synchrotron site parameters 8325d87982

RotationParameters: More flexibility on moving average size f0e17fde60

ScaleAndMerge: Minor fixes 832bbe4d89

jfjoch_process: Reformat 1295ee9f85

jfjoch_viewer: Display partiality and reverse LP correction 411276415e

BraggIntegrate2D: Lorentz-Polarization correction is not directly applied 175e938616

jfjoch_process: Don't write header row for hkl file c7bf8c4d13

AzimuthalIntegration: Clear naming for polarization factor 981c8ce0d4

BraggIntegrate2D: Fix polarization correction division c4d4b5d570

jfjoch_process: Write amplitudes at the end into hkl file in addition to mmCIF file (to be improved later) f3e8379a55

jfjoch_process: Add anomalous mode 957980307f

CBOR: Add scale factors (work in progress) 21059d1662

ScaleAndMerge: Remove GoF, refactor merging part 329be6eb33

MXAnalysisAfterFPGA: Add state management to handle disabling functionality properly 30791b1da0

Docs: Add jumbo frames f7f13c45e8

Reflection: slightly reduce struct size be5dff5370

ScaleAndMerge: Add statistics 0ed72eb2ea

ScaleAndMerge: Add statistics 091b3808a4

CBOR: Fix serialization of h,k,l 09b74e78e3

Remove RotationScanAccumulator 0599f1e918

CMake: All packages are named jfjoch, irrespective of slsdet version (for now) 87c8a2e93b

Gitea: Add Rocky9 with SLS9 8759d1f8db

CMake: More options for Ceres backends (to be determined how useful later) ca778992b0

Definitions: Increase MAX_SPOT_COUNT to 64*1024 08f98dab3c

IndexingSettings: FFT should handle cells up to 500.0 A 682ce5e418

jfjoch_process: Remove comment about polarization factor b77ba44de1

BraggPrediction: Zeta set to 1.0 for stills, otherwise merging gets weird b2dda42db9

OpenAPI: Use generator 7.20.0 838b225a44

VERSION: 1.0.0-rc.125 b38d14a34e

Frontend: Update JavaScript 5e535b9d56

Frontend: Disable quick integration switch when not using spot finding 5ed25b887b

CHANGELOG: 1.0.0-rc.125 0adf7f2247

Frontend: updates + fixes cec57aec50

leonarski_f merged commit 1ab257af6c into main 2026-02-18 16:17:21 +01:00

leonarski_f referenced this issue from a commit 2026-02-18 16:17:21 +01:00

v1.0.0-rc.125 (#32)

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appleb_m (appleb_m) buntschu_d (buntschu_d) duan_j (duan_j) glettig_w (glettig_w) gotthard_g (gotthard_g) leonarski_f (leonarski_f) perl_d (perl_d) takaba_k (takaba_k)

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Reference: mx/Jungfraujoch#32