v1.0.0-rc.124 #31

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leonarski_f merged 96 commits from 2601-1.0.0-rc.124 into main 2026-02-01 13:29:33 +01:00

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leonarski_f commented 2026-01-31 09:25:09 +01:00

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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

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

leonarski_f added 81 commits 2026-01-31 09:25:09 +01:00

BraggIntegrate2D: predictions are calculated externally (to make it easier to make a more general 3D routine) 665f7e147c

IndexAndRefine: split into three functions 71ea7a659c

BraggPrediction: Split into a separate directory 752a3323e6

IndexAndRefine: Integration operates in place (prelude to general 3D routine) + fix a bit sorting 6bee563356

Cmake: Add missing subdirectory 734506ec6a

BraggPrediction: Fix to path 7162db87bd

BraggIntegrate2D: fix missing break in switch statement a23fe329aa

AnalyzeIndexing: Handle ice rings in counting percentage of indexed spots d5ba5fc3c4

Indexing: use squared norm to avoid sqrt() in checking indexing solution quality 58cd091273

Indexing: fix indexing tolerance square data type 88dba761e4

Indexing: Fixes to better handling ice ring spots a71e1f16e7

IndexAndRefine: Fix wrong vector being used for predicted reflections e27c09833e

BraggIntegrate2D: Take const vector of predictions and return new vector 319aa0265a

Reflection: Add partiality for prediction (set to one at the moment) b3446736bd

BraggPrediction: Work in progress 20224a01c3

BraggPredictionRotation: Work in progress 2ba69d37c5

BraggPrediction: Work in progress 84237d0e38

AnalyzeIndexing: Move mosaicity to a dedicated function + for rotation indexing always consider as indexed 2971b20b87

BraggIntegrate: Add Lorentz factor (1/sin(2*theta)) for rotation measurment 25f068e111

ScaleAndMerge: Add (very much work in progress) 1926431f7c

BraggIntegrate2D: Fix missing return statement c2559ed510

BraggPredictionRotation: Guard for negative rotation direction 68e99afc9e

BraggPrediction: Minor improvements - predict from -max_hkl to +max_hkl (incl. +max_hkl); small fixed in notation fae05a5cfe

BraggPredictionRotation: Minor fixes to improve readability ffb4fa3b29

jfjoch_process: First iteration 80f893de3b

jfjoch_process: Handle pixel mask correctly in jfjoch_process 36b32c31db

jfjoch_process: Overwrite output files e96b04eb3a

DiffractionExperiment: Add option to check if rotation indexing is enabled (goniometer present + rotation indexing) af2ec340db

jfjoch_process: Clean previous image information (to be optimized) + option to run rotation indexing 05da6bc2dd

MXAnalysis: Generate rotation prediction properly 1353748a2e

IndexAndRefine: Use "standard predictor", just with rotated axis 69cd7b551d

jfjoch_process: Use single IndexAndRefine instance af81601103

RotationIndexer: Remove SetLattice() - not sure why it was necessary in the first place 71f85b294d

IndexAndRefine: Generate predictions based on refined geometry 0a19acb900

CreateBraggPrediction: No rotation for now a31065f6ae

jfjoch_process: Add compression 2de263c3f5

jfjoch_process: A bit more options 05bb18f6f7

XtalOptimizer: Use robust loss function (Cauchy) for least squares 11b1857a35

RotationIndexer: Refine detector angles 30783d4849

jfjoch_process: Add resolution 8c4282b9e6

jfjoch_test: Adjust expected precision - changed way of calculating residual - will work worse on "ideal" data, but should be more outlier safe. To be seen. 0b9463cb0d

IndexAndRefine: Stabilize profile radius and mosaicity, by using moving average 9c5a3f5c12

BraggPredictionRotation: Work in progress 7a1355df23

IndexAndRefine: Minor change in sign...tbd how it should go 3e721dc476

IndexAndRefine: Fix using lattice at zero deg for refinement 7da28b5c9a

jfjoch_extract_hkl: Simple summation of reflections for rotation scan f14eca977d

jfjoch_extract_hkl: Work in progress (early) 2000affffa

jfjoch_extract_hkl: Work in progress -- CC calculation 0e4e5dc8f1

CBOR/HDF5: Save Lorentz-Polarization correction for reflections 4a6085c721

BraggIntegrate: Lorentz-Polarization correction consistent (roughly) with XDS c0fa5c9467

jfjoch_extract_hkl: Work in progress 6f653866e3

hkl_key: Dedicated header 8c7bf61fa7

BraggPrediction: Rotation settings removed from BraggPredictionSettings d3f311dc97

BraggPredictionRotation: New implementation - looks OK, but accuracy is terrible (+/- 10 images wrong) 45ca48cc01

jfjoch_extract_hkl: Fix key 06e50b85a3

XtalOptimizer: Bring back standard loss function for least squares af3fea3e66

BraggPredictionRot: Work in progress bb87ed2df4

Remove BraggPredictionRotGPU from CMake for now 7693b95008

GoniometerAxis: Transformation is based on angle, not image number b7b38b8e7d

IndexAndRefine: Work in progress to understand why rotation indexing doesn't work 626f7abc30

XtalOptimizer: Option to refine unit cell 52c3c3f91a

IndexAndRefine: Don't refine unit cell when optimizing rotation result d1a114aa51

XtalOptimizer: Remove Cauchy leftovers 475ba92d01

XtalOptimizer: Include explicit rotation axis a4ac885d1c

XtalOptimizer: Refine rotation axis 5d7bc6339a

XtalOptimizer: Work in progress to find out what is wrong with rotation axis a3ea378494

IndexAndRefine: Use optimized goniometer axis b9f05b7bc4

SimpleRotXtalOptimizer: Work in progress 52339a7f85

IndexAndRefine: Use small angle approximation for optimizing rotation data a5e582574e

jfjoch_writer: Save mosaicity properly b338f8ea99

AnalyzeIndexing: Fix mosaicity calculation e0355f356f

jfjoch_viewer: Display mosaicity in dataset info 1e507c678d

IndexAndRefine: Use rotation method prediction for reflections e0ddbfa644

BraggPredictionFactory: Fix CUDA includes 297e210d88

Remove BraggPredictionRotation b33cc2a54d

BraggPredictionRotGPU: Fix systematic absences a8ef78fe9f

jfjoch_extract_hkl: print RPL c75507aced

BraggPrediction: Set Lorentz-polarization correction properly 0956e59b9c

BraggPrediction: Set Lorentz-polarization correction properly f5bd76db05

CHANGELOG 6db9a8b2eb

VERSION: 1.0.0-rc.124 89713b6689

leonarski_f added 2 commits 2026-01-31 16:17:53 +01:00

jfjoch_viewer: Changing foreground from mouse wheel deactivates auto-contrast 0c71e9406b

jfjoch_viewer: Pressing "A" sets auto contrast 0a6ade81fa

leonarski_f added 6 commits 2026-01-31 23:35:50 +01:00

jfjoch_viewer: Single green color map fd512fa941

ColorScale: Reduce LUT size to 512 (so it fits L1 cache) f4564e3727

jfjoch_viewer: Clicking A sets auto mode f05cd92a6e

SliderPlusBox: Can change slider max value bbcd29cba9

jfjoch_viewer: Max value for foreground slider is auto updated a523969a9f

jfjoch_viewer: Improve HDR mode 9aaa70c5b6

leonarski_f added 6 commits 2026-02-01 11:19:14 +01:00

jfjoch_viewer: HDR mode uses max value of the image, without robust cut 876c315212

jfjoch_viewer: Fix auto-contrast information lost after reanalyzing image f5bdc41098

jfjoch_viewer: Improve in displaying overlay numbers bf89bd09c0

jfjoch_viewer: Fixes to HDR/auto-contrast logic 6c9d4ebc74

jfjoch_viewer: Ctrl+wheel makes expontential change in foreground 9e8f8d6f9e

CHANGELOG 6191640ccf

leonarski_f added 1 commit 2026-02-01 11:54:15 +01:00

jfjoch_viewer: Use multiple threads to color images 5e17a8f61c

leonarski_f merged commit 07fe4dd3bb into main 2026-02-01 13:29:33 +01:00

leonarski_f referenced this issue from a commit 2026-02-01 13:29:35 +01:00

v1.0.0-rc.124 (#31)

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Reference: mx/Jungfraujoch#31