Opening a sweep parses the header of every file to get its start angle, and one
header is two dozen std::regex searches: measured at 0.33 ms on a 16 Mpx sweep
and 1.0 ms on one with a longer header, so a 7200-frame sweep spent 7.2 s on one
thread before it read an image. The files are independent, so the scan is shared
out over up to eight of them.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Slurp() returned a fresh std::vector per call, so every frame allocated the
whole compressed file - 18 MB on a 16 Mpx detector - and value-initialised it
before the read overwrote every byte. Measured on one such frame that is 9.2 ms
against 5.4 ms into a buffer that is already there.
ReadInto() now takes the scratch, and the raw image carries it, so a worker
reading a sweep reads every file into the same bytes. Slurp() fills a buffer
instead of returning one, which is also what makes the resize cost nothing when
the next file is the same size as the last.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
GetRawImage() allocated a fresh JFJochReaderRawImage per frame, and on a
miniCBF sweep its buffer holds the whole decoded image: 72.6 MB on a 4150 x
4371 detector. That is over glibc's 32 MB mmap ceiling, so the block is mmapped
and munmapped every image and the decoder faults in 17 700 untouched pages as it
writes them. Measured on one 18.1 Mpx frame, decoding into a fresh buffer takes
61 ms against 16 ms into one that has been written before - the allocation costs
nearly three times what the decode does, and the per-image loop pays it twice
per sweep.
ReadRawImage() fills a raw image the caller owns, so a worker declares one
outside its loop and keeps the pages. GetRawImage() stays as the allocating
wrapper for the single-image callers. The two loops that hand the image to the
process-file writer keep a shared_ptr and recycle it only while the writer
thread is not still reading the previous frame's pixels.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands.
* `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion.
* Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants.
* `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing.
* A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed.
* `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing.
* Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences.
* The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to.
* The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after.
* The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution.
* `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have.
* Twinning is no longer reported when the L-test contradicts it.
* The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's.
* `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots.
* The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area.
Reviewed-on: #76
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_fandClaude Opus 5