leonarski_fandClaude Opus 5
6468dd13be
--azint-only and --scale are replaced by --mode mx|azint|scale|calibration, with mx the default. The old flags are removed rather than aliased. Calibration mode fits the detector geometry - PONI x/y, the two tilts and the distance - to a calibrant's powder rings and writes a pyFAI .poni alongside a report of how far each parameter moved from the header. Bragg data constrain the beam centre worst, because it is gauge-coupled to the crystal orientation; a powder ring has no orientation to couple to. --calibrant takes lab6, agbh, ceo2, si or ice. A calibrant is a list of ring positions rather than a unit cell, because hexagonal ice is P6_3/mmc: rings enumerated from its cell would include systematically absent ones. So the crystalline standards generate their rings from a cell and ice carries the measured list, and RingsFromAzimuthalProfile, GuessGeometry and OptimizeGeometry all take ring q. The calibrant table is shared with the viewer's powder panel, which previously carried its own copy. --calibration picks how the rings are measured: rings (default) sums the (q x azimuth) profile over every processed image and fits the arcs in it; spots pools the found spots and fits those. Both use the whole run, with -s/-e/-t selecting images. rings defaults --azim-phi-bins to 32, since a profile with one azimuthal bin has averaged the ring over every direction and cannot locate it. Two fixes this exposed: The extraction window is capped at half the gap to the neighbouring ring. The background under a peak is taken from the ends of its window, so a window wider than half that gap measures the next ring's flank as this ring's background - and hexagonal ice has three rings within 0.06 1/A. Ice calibration was 3.5 px out before this and 0.29 px after; LaB6 is unaffected. RingOptimizer holds rot1/rot2 fixed when only one ring is present. A tilt and a centre offset both move a ring as cos(phi) and are separated only by the tilt's amplitude growing as the ring radius squared, so on a single ring they are exactly degenerate. Measured. LaB6 at five distances: the fitted direct beam is within 0.36 px of an independent implementation out to 300 mm, and D = -0.046 + 1.000788 dtz with an rms of 0.011 mm. At 500 mm one ring is fully on the detector and a second only clips the corners, which is not enough to constrain a tilt - restricting the q range to the resolved ring recovers 0.06 px. Ice: 5.53 -> 0.29 px on one crystal and 4.71 -> 0.80 px on another, against XDS's refined direct beam. On an ice-free crystal the fit is worse than the header, which is the correct outcome. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2.8 KiB
Tools
Besides the main services (jfjoch_broker,
jfjoch_writer, jfjoch_viewer), the repository ships a
number of command-line tools. Each prints its own usage when run with -h or without arguments.
Data analysis
rugnux
Offline CLI tool that runs the full crystallographic analysis pipeline (spot finding, indexing,
integration, scaling/merging) on a stored HDF5 dataset, producing a _process.h5 file and, when
merging, reflection files. Merging is on by default (--no-merge disables it). --mode picks what a
run does: mx (the above, the default), azint (only azimuthal integration, no spot
finding/indexing), scale (re-scale/merge the already-integrated reflections in a _process.h5
without re-integrating) or calibration (detector geometry from a calibrant's powder rings, written
as a .poni file). See rugnux.
jfjoch_extract_hkl
Extracts reflections (HKL list) from a Jungfraujoch master file; can sum the same HKL across
neighbouring images and compare against an XDS INTEGRATE.HKL reference.
FPGA / PCIe card management
jfjoch_pcie_status
Prints detailed status information about the card. Safe to run during data collection:
./jfjoch_pcie_status /dev/jfjoch0
jfjoch_pcie_net_cfg
Reads and modifies the network configuration of the card's interfaces:
jfjoch_pcie_net_cfg <device name>
Read configuration for all network interfaces of a device
jfjoch_pcie_net_cfg <device name> <if number>|fgen
Read configuration for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen ipv4 <IPv4 address>
Set IPv4 address for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen direct 0|1
Set direct mode for a particular network interface / internal frame generator
jfjoch_pcie_net_cfg <device name> <if number>|fgen clear
Clear Ethernet counters for a particular network interface / internal frame generator
jfjoch_pcie_clear_net_counters
Resets the card's Ethernet, UDP and ICMP packet counters (which otherwise run from power-on):
./jfjoch_pcie_clear_net_counters /dev/jfjoch0
Testing, benchmarking and simulation
jfjoch_udp_simulator
UDP packet simulator used to test the Jungfraujoch FPGA receiver.
jfjoch_fpga_test
Exercises and benchmarks the FPGA data path and receiver. With -H it runs the high-level
synthesis C model on the CPU, so no FPGA device is required.
jfjoch_lite_perf_test
Performance test of the lite (CPU/GPU) analysis path — indexing, integration and optional file writing.
jfjoch_hdf5_test
Tests single-threaded HDF5 writer performance.
jfjoch_simplon_test
Minimal test client for a DECTRIS SIMPLON detector API.