From d8839183f4b5df3dd6252b0b53bd602baaae59af Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Thu, 5 Mar 2026 19:06:18 +0100 Subject: [PATCH] Docs: update --- docs/CPU_DATA_ANALYSIS.md | 23 +++++++---------------- 1 file changed, 7 insertions(+), 16 deletions(-) diff --git a/docs/CPU_DATA_ANALYSIS.md b/docs/CPU_DATA_ANALYSIS.md index 6b2e9afb..11964973 100644 --- a/docs/CPU_DATA_ANALYSIS.md +++ b/docs/CPU_DATA_ANALYSIS.md @@ -1,6 +1,6 @@ # CPU-side crystallographic data analysis (Jungfraujoch) -This document describes the crystallographic algorithms implemented in Jungfraujoch for **CPU**- and **GPU**-side real‑time and near‑real‑time data analysis. It is written for crystallographers and follows established concepts from **XDS** and **CrystFEL**. Implementation details (GPU kernels, data structures, threading) are intentionally minimized in favour of the underlying crystallographic models and numerical procedures. +This document describes the crystallographic algorithms implemented in Jungfraujoch for **CPU**- and **GPU**-side real‑time and near‑real‑time data analysis. **Scope.** The pipeline covered here comprises: @@ -15,17 +15,16 @@ This document describes the crystallographic algorithms implemented in Jungfrauj 9. scaling and merging, 10. auxiliary statistics (Wilson plot, ⟨I/σ(I)⟩, French–Wilson). -## References (to be cited) +## References -The methods are closely aligned with: +The methods are inspired by solutions implemented in: - W. Kabsch, “XDS”, *Acta Cryst.* **D66** (2010), 125–132 and related XDS papers (rotation geometry, partiality, scaling concepts). - W. Kabsch, “Integration, scaling, space-group assignment and post-refinement”, *Acta Cryst.* **D66** (2010), 133–144 (mosaicity/partiality likelihood treatment; notation such as ζ and rotation factors). -- T. A. White *et al.*, CrystFEL method papers (spot finding, three‑ring integration, serial/still diffraction processing concepts). - -(Exact bibliographic details and DOIs should be inserted in the Sphinx bibliography; the above is the intended citation set.) - ---- +- T. A. White et al., CrystFEL method papers (spot finding, three‑ring integration, serial/still diffraction processing concepts). +- J. Kieffer & J. P. Wright, "PyFAI: a Python library for high performance azimuthal integration on GPU", *Powder Diffraction* **28** (2013), S339-S350 (detector geometry definition, azimuthal integration) +- H. Powell, "The Rossmann Fourier autoindexing algorithm in MOSFLM", *Acta Cryst.* **D55** (1999), 1690-1695 (FFT indexing) +(list is not exhaustive) ## 1. Geometry, reciprocal-space mapping, and basic quantities @@ -616,11 +615,3 @@ Numerical quadrature over a scaled intensity variable is used to compute posteri - **Rotation vs still modes** differ substantially in prediction and scaling because partiality is angle-driven in rotation data and excitation-error-driven in still data. --- - -## 14. Suggested citation wording (Acta Cryst. D style) - -When describing the methods in manuscripts, we recommend phrasing along the lines of: - -> “Real-time data reduction in Jungfraujoch follows established strategies from XDS (Kabsch, 2010a,b) and CrystFEL (White et al.), including strong-pixel spot finding, lattice determination by FFT-based periodicity detection, non-linear refinement of experimental geometry and crystal parameters, and summation integration using a three‑ring background estimator. For rotation datasets, predictions and scaling employ XDS-like quantities such as \(\zeta\) and error-function partiality.” - -(Replace with exact reference list entries as appropriate.) \ No newline at end of file