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](RUGNUX_INTEGRATION.md#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`](JFJOCH_WRITER.md), 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](DETECTOR_GEOMETRY.md)). 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 read at the gain its background shows. Where the pixel values resolve
single photons (a JUNGFRAU file in keV, an AGIPD file) the gain is the spacing of their photon peaks, so a
baseline the file left in does not hide it, and the detector is a photon counter: its frames are counted in
whole photons as they are read. Otherwise (a CCD, an MPCCD, a Rayonix) the gain is the background's
variance per unit mean and the frames are analysed in the units they are stored in: the gain enters only
where a photon count is assumed (the spot finder's threshold, the background clip, the integrated
intensities' variances, which come out in photons). `--gain` gives the value; the background still says
which of the two the detector is. Float frames analysed in their own units are rounded to whole ones.
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; with a cell, the camera length | `--detector-distance` to hold a camera length |
| **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; with a cell, the distance | `--detector-distance` without a cell (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](#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. Taken
from it are the module geometry (panel pixel ranges, fast/slow directions, corners, pixel size,
per-panel `coffset`, the frames' data path), optionally the camera length, and the pixels to leave out:
the mask arrays (`mask`, `mask_file`, `mask_good`, `mask_bad`, or up to eight as `maskN_data`,
`maskN_file`, `maskN_goodbits`, `maskN_badbits`; a panel may state its own), the bad regions (`bad*`,
a box in the laboratory plane or a pixel range on a panel), `mask_edge_pixels` and `no_index`. A mask
dataset with one plane per frame, or with `%` in its path, is applied frame by frame. A relative
`mask_file` is looked for in the working directory, as CrystFEL does, and then beside the geometry file.
Where the geometry names mask arrays, the data file's own (the CXI `mask_shared` and per-shot mask, a
panel table's `/metadata/pixelmask`) are not taken: the geometry says which bits matter. Everything else
it may hold (gain, saturation, 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 or the geometry file state (the CXI `mask_shared` and per-shot mask,
the `/metadata/pixelmask` of a panel-table file, a `--crystfel-geometry` file's masks). A gain the background shows at or below one detector unit
per photon is taken as one.

### 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.