Jungfraujoch/docs/RUGNUX_FORMATS.md

What Rugnux reads

Which data rugnux opens, before anything is typed. The short answer: an HDF5 master (NXmx or DECTRIS, from any facility), a PILATUS miniCBF sweep, a marCCD sweep or an SMV sweep (ADSC or Rigaku d*TREK) — nothing else is read, so any other format has to be converted to one of these first.

Input is files, never a directory: an HDF5 master file, or one frame of a PILATUS miniCBF, marCCD or SMV sweep. For rotation data one input is one sweep of one crystal — Rugnux does not combine sweeps or crystals in a run; process each sweep to its own _unmerged.mtz and merge them downstream (see Taking the data onward).

Stills are given as all the files of the dataset, which the shell expands from a glob and which are read in the order given: rugnux run1_master.h5 run2_master.h5 (or rugnux *_master.h5) for several Jungfraujoch/NXmx collections of one setup, rugnux run*.h5 for SACLA, rugnux *.cxi for a Cheetah CXI set and rugnux *.xtc for LCLS streams. Several files must all be of one format; a directory is refused.

• HDF5 master (NXmx-based) — a file written by jfjoch_writer, a DECTRIS EIGER master, or an NXmx master written by another facility's toolchain. Lengths are taken in the unit the file declares, the image size from the image array's own shape, and each data file's images at the path the master's own link names, so masters that state single values as one-element arrays, compose their images as a virtual dataset over the master itself, or keep them somewhere other than /entry/data/data all open. Where the NXmx spellings are absent the pre-NXmx ones are tried, so a DECTRIS firmware 1.x master opens too — including its goniometer, which used to be missed and the sweep read as stills. Images may be bitshuffle+LZ4/Zstd or the HDF Group's plain LZ4 (filter 32004); any other filter is named in the error.
• PILATUS miniCBF sweep — one frame per file, read natively with no conversion and no libcbf. Name any frame of the sweep and the whole sweep is processed: the frames are the ones matching that frame's template (prefix plus digit count), so a directory holding two sweeps is not spliced into one crystal. The geometry, the rotation axis and the detector mounting come from the header, including the imgCIF axis table where the header carries one (see Detector geometry). A raw CBF carries no analysis results, so --mode scale — which re-scales the reflections stored in a _process.h5 — does not accept one. Gzipped frames (.cbf.gz) are read directly, with no decompression step: EMBL Hamburg's beamlines write that form by default, and expanding a sweep first would double the disk it needs. The two forms count as separate sweeps.
• marCCD sweep — what Rayonix MX-series and mar Mosaic detectors write, and what a decade of deposited CCD data is archived as: an uncompressed TIFF with the instrument header in the gap before the pixels. One frame per file, read natively. Naming a frame selects the sweep exactly as for miniCBF, under either naming scheme these detectors use — a numbered stem (xtal_1_00042.mccd) or the frame number as the file extension (D1.042). The distance, beam centre, pixel size, wavelength and the circle that turned come from the header; the rotation axis' direction does not, because the format has nowhere to state it, so the run settles its sign from the data as it does for a miniCBF that carries no axis table. A CCD frame marks no untrusted pixels, so the sweep starts with nothing masked. Like a raw CBF, it carries no analysis results and --mode scale does not accept one.
• SMV sweep — what ADSC Quantum detectors wrote and what Rayonix and others still write, so most archived CCD data from the 2000s is in this form: an ASCII KEY=value; block between braces, then the pixels. One frame per file, read natively, the sweep selected exactly as above. The beam centre it states is in millimetres and is converted here; its convention varies between writers, and a file that states it transposed indexes nothing until the run's own beam-centre measurement replaces it, which it does automatically. The saturation value is read where the header states one (CCD_IMAGE_SATURATION or SATURATED_VALUE); where it does not, overloads are judged on the 16-bit container alone and the reader says so once per sweep. Rigaku d*TREK headers — what Saturn CCDs on rotating-anode home sources write, recognised by their DETECTOR_NAMES key — are read in their own vocabulary: the pixel size and the point of normal incidence from the spatial-distortion record, the image directions from the detector and distortion vectors (so a mirrored or turned image keeps its hand), the distance and the detector circles, including a swung 2θ arm, from the detector goniometer, the spindle and its angles from the rotation record, and the wavelength from the scan record. Pixel values above 32767 are the format's encoded overflows and are expanded with the header's compression ratio.

Support for the two CCD formats — marCCD and SMV — is very limited and provided as-is; they are read so that a CCD sweep does not need a conversion step to be processed. Only the header fields named above are read, and the headers vary by site and vintage, so no promise is made that every writer's dialect opens. The HDF5 and miniCBF paths are the maintained ones.

Serial XFEL inputs

Stills from the XFEL serial-crystallography pipelines are read straight from the files those pipelines write, without a geometry file. Each reader takes from the file what it states; what the file does not state is either measured by rugnux or given on the command line. Every run is read at one wavelength (the mean of the per-shot photon energies where the file states them), the beam centre is measured (the file's centre, the background-isotropy measurement and the point-symmetry capture are indexed on a sample of frames and the best is kept), and a SACLA or CXI file that states no gain is converted to photons with the gain its background shows (--gain overrides; XTC frames stay in detector units unless --gain is given). The saturation level is read off the frames where the file states none.

Format	Read from the file	Measured by rugnux	Given on the command line
Cheetah HDF5 with per-shot groups and a panel table (/tag-N/data, sensors stacked in one frame, their placement in /metadata - as SACLA writes for the MPCCD)	the sensors' positions and in-plane angles, pixel size, nominal camera length and pixel mask (/metadata); each shot's photon energy	beam centre, gain, saturation; with a cell, the camera length (the stated one is nominal) and each sensor's placement	nothing; --detector-distance to give the camera length
Cheetah CXI, single-panel detector (/entry_1/data_1/data, square frames, e.g. a Rayonix at PAL-XFEL)	pixel size, photon energy per shot, camera length, mask_shared	beam centre, gain, saturation	--detector-distance where the stated camera length is wrong
LCLS-I XTC, Rayonix (Camera::FrameV1 events; one or more streams)	photon energy per event (electron-beam record), pixel size (Rayonix model and binning), the camera's pixel offset	beam centre, saturation	--detector-distance (not recorded in XTC); --pixel-size/--wavelength only where the XTC lacks them

The SACLA sensor positions in /metadata are the detector's nominal metrology, a few pixels from a per-beamtime refined geometry; the stills geometry refinement places each sensor as a module (see Module geometry).

What is refused, with a message rather than a wrong answer:

• a Cheetah CXI file of a tiled detector (CSPAD, AGIPD, ePix, JUNGFRAU, MPCCD stored as a slab of panels): the file does not say where the panels lie;
• multi-panel XTC (CSPAD, ePix, JUNGFRAU at LCLS), stored raw with per-module calibration, and an XTC stream holding images of the same size from two cameras;
• unconverted detector data in general (raw ADC values with gain stages and pedestals);
• per-shot wavelengths: they are averaged, never followed shot by shot;
• files of one run that store their frames differently (size, type, compression) or place the sensors differently.

Damaged or compressed XTC images are left out, and so is a last event that a partly downloaded stream ends inside. An XFEL dataset that has already been assembled into single images in an NXmx master opens like any other HDF5 input.

--crystfel-geometry <file> places the panels of an HDF5/CXI input by a CrystFEL geometry file. Only the module geometry is taken from it (panel pixel ranges, fast/slow directions, corners, pixel size, per-panel coffset, the frames' data path) and, optionally, the camera length; everything else it may hold (gain, masks, bad regions, photon energy, value flags) is ignored, with a note in the log. DIALS .expt files are not read.

A mask array the data files do not hold themselves - e.g. a per-run pixel mask beside the frames - is given with --mask-good [<file>:]<dataset>[@<bits>] (a pixel is usable only where the array is non-zero, or has all of <bits>) or --mask-bad [<file>:]<dataset>[@<bits>] (unusable where non-zero, or where it has any of <bits>, e.g. @0xfeff), in the frames' own layout, as stored. Without <file> the dataset is read from each data file - a per-frame mask stored beside the frames. Both may be given more than once, and add to the masks the data files state (the CXI mask_shared and per-shot mask, the /metadata/pixelmask of a panel-table file). A gain the background shows at or below one detector unit per photon is not applied: such frames stay in detector units.

Module geometry

A detector of several modules is described module by module: where each module's pixels are in the image rugnux reads, and where they really are on the detector plane. The modules come from an explicit geometry, never from the image:

• an NXmx file with one NXdetector_module group per module (/entry/instrument/detector/module_0, module_1, ...: what a run writes as <prefix>_modules.h5; the masters Jungfraujoch writes still state the image as one module);
• the panels the XFEL readers know (the SACLA sensors from /metadata, the panels of a --crystfel-geometry file); each panel is put on the image whole, at a whole pixel, and its fraction of a pixel and small turn are its placement;
• --module-geometry <file>: an NXmx file with such groups (what a run writes as <prefix>_modules.h5) or a CrystFEL geometry file whose panels are laid on the image (fs = column, ss = row, corners relative to the beam). It replaces the input's own modules - the way to give the module layout of a master written before the modules were recorded.

Spots are mapped from the image onto the plane, and predictions from the plane back onto the image for integration, so the image itself is never re-assembled. With a cell given, the stills geometry refinement places each module with enough spots on its frames' lattices as a rigid block (shift and in-plane turn, --refine-modules, on by default) where that predicts held-out spots better; modules move only relative to one another, the beam centre, distance and crystal orientations carrying what all of them share. The placement is used from there on for the panels of a foreign multi-panel detector (the sensors of a panel-table file, the panels of a --crystfel-geometry file); for a JUNGFRAU (an NXmx master) it is measured and reported only. Either way it is written to <prefix>_modules.h5, which a later run reads back with --module-geometry.

Spots are always found by rugnux itself, including for the two-pass rotation first pass — the spot lists a dataset may already carry were found online, at the acquisition's threshold and with its ice-band spots already discarded, so reusing them would hide the spot-finding settings from the lattice search.