docs: bring the stills geometry and live merge pages in step with rc183

- Stills geometry refinement is on by default for all stills and, without a
  reference cell, anchors on the cell the sampled frames index to; the
  distance is then a hypothesis too (CPU_DATA_ANALYSIS_IMAGE 1.4, overview,
  the -C row of the model/reference table).
- The live serial merge is made in the consensus cell of the frames indexed
  by the first merge, not the dataset settings' cell (JFJOCH_BROKER).
- The CCD inactive-area mask, and the beam-stop finder reading those pixels
  as data, described in CPU_DATA_ANALYSIS_IMAGE 1.6.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UqXYdL4qBGYRiSXSGXfCLu

docs/CPU_DATA_ANALYSIS_IMAGE.md

@@ -294,8 +294,8 @@ sample of frames spread over the run, and three centres are tried: the file's, t
 measurement above, and the point-symmetry capture (a second estimator, because the background one is
 biased where a shadow - a sample-delivery tape, say - covers part of the scattering). Each re-indexes the
 same spots and is scored by how many land on their frame's lattice; the file's centre is kept unless
-another puts at least 1/0.9 as many there. Where a reference cell is given, the detector distance is a
-hypothesis too. The spots of the sample are found without resolution limits (a d-spacing depends on the
+another puts at least 1/0.9 as many there. Where a reference cell is given, or the stills geometry
+refinement has fitted one de novo (below), the detector distance is a hypothesis too. The spots of the sample are found without resolution limits (a d-spacing depends on the
 distance being checked) and spots piled up at one radius - a powder ring - are left out. A scan over
 30-3000 mm in 2.5 % steps at every centre candidate finds the peaks, the strongest are looked at more
 closely and a finer step about the best decides against the file's distance, which is kept unless the best
@@ -304,8 +304,11 @@ The range is in millimetres, not in multiples of the file's value, so a stated c
 nominal or wrong does not limit where the search looks, and an input that states no distance (an XTC) is
 searched too. A distance given with `--detector-distance` is held: it is neither searched nor refined.
 Without a cell nothing is searched in distance: on its own a wrong distance indexes as a wrong cell, not
-as fewer indexed spots. The stills geometry refinement, `--refine-geometry`, then bundle-adjusts the
-centre and the distance together with the cell over strongly indexed frames (§7.7); it is on by default where a reference cell is given.
+as fewer indexed spots. The stills geometry refinement, `--refine-geometry`, bundle-adjusts the
+centre and the distance together with the cell over strongly indexed frames (§7.7); it is on by default for
+all stills. Without a reference cell it anchors on the cell most of the sampled frames index to de novo
+(the frames on it are the ones fitted), and that cell serves the geometry steps only: the run itself is
+still indexed de novo.
 
 **What ends up in the output.** The report's `BEAM_CENTRE` (the PONI) and `DIRECT_BEAM` are the
 geometry the result was integrated at, and so is `JFJOCH_DATASET_SETTINGS`; `POSTREFINE_BEAM_CENTRE`
@@ -447,6 +450,17 @@ value on most frames (already invalid on every frame, but not in the static mask
 them. A CCD (no sensor depth: read with an offset, not Poisson) is left alone. One log line says how
 many pixels were masked and why.
 
+**Outside a CCD's active area.** An input in detector units whose background shows no photon peaks (a
+CCD, an image plate or another integrating detector read through an amplifier) has read noise on every
+live pixel, so no live pixel reads the same value on all 16 frames the detector gain is
+measured on. A pixel that does lies outside the active area - the corners of a round CCD, a border or seam
+the detector's corrections leave at zero - and is masked as dead (bit 1) before the run starts. A test that
+compares a pixel with its own resolution ring cannot see such an area: beyond the circle of
+a round CCD the whole ring reads zero. It is not made where the pixels that do vary read zero on 1 % or
+more of their readings (counted photons, or a file cut at a threshold), since a pixel at zero on every
+frame may then simply have had nothing to record. The beam-stop finder (§1.5) reads these pixels as the
+input has them, because a CCD reads the deep shadow of a beam stop at one value too.
+
 ### 1.7 The saturation level
 
 A detector that saturates clips every value beyond its ceiling down to it, so on a frame's bright tail -

docs/JFJOCH_BROKER.md

@@ -283,8 +283,9 @@ mask in use. Where the start message cannot be sent after the pre-pass (no write
 cannot be set up, the collection ends with that error, reported by `/status` and `/wait_till_done`, and the
 next `/start` runs as usual.
 
-The indexed frames are also merged, as `rugnux --mode scale` merges stills, in memory - in the cell of the
-dataset settings (else the consensus cell of the frames indexed by then) and their space group (else P1).
+The indexed frames are also merged, as `rugnux --mode scale` merges stills, in memory - in the consensus cell
+of the frames indexed by the first merge (the cell of the dataset settings only picks the frames that are
+merged) and the space group of the dataset settings (else P1).
 At half and at three quarters of the images the frames so far are merged beside the analysis, on 8 threads, and
 the result is reported as a provisional step note: crystals, resolution, CC1/2, R_split, completeness and
 ⟨I/σ⟩. The first of these merges scales and post-refines every crystal so far and decides the indexing

docs/RUGNUX_MODEL_AND_REFERENCE.md

@@ -58,7 +58,7 @@ the rest walks through a run step by step.
 | `--reference-column <label>` | An MTZ column label | Which column of the reference is read | Through `-z` only |
 | `--free-flags <file>` | Merged data carrying an R-free set: an MTZ, or a structure-factor mmCIF - typically the deposited reflections of the `--model` | Its R-free set and nothing else: the model is validated and refined against it, on the model's axes, where the merge matches the file's intensities (`R_FREE_FLAGS= FILE`) | The free flags only |
 | `-S, --space-group` | A space group | Fixes it: no space-group search | **Yes**: the group is yours (a fitting model may still relabel its hand) |
-| `-C, --unit-cell` | A cell | Indexing looks for this cell (within tolerance); the FFT search range is widened to cover it; on stills it turns on the shared-geometry refinement and, with `-S` and `--model`, the per-image use of the model | **Yes**: the cell, and the axis order the files are written in |
+| `-C, --unit-cell` | A cell | Indexing looks for this cell (within tolerance); the FFT search range is widened to cover it; on stills the shared-geometry refinement anchors on it (without it, on the cell the frames index to) and, with `-S` and `--model`, the per-image use of the model | **Yes**: the cell, and the axis order the files are written in |
 | `--force-rotation-lattice` | Nine numbers: a lattice | Skips the first-pass indexing and uses this lattice | **Yes**: the lattice |
 | `--report-resolution <dmin>[,<dmax>]` | Another program's resolution range | A second statistics table at that range (`REFRES_*`) | No — report only |
 

docs/RUGNUX_OVERVIEW.md

@@ -100,8 +100,8 @@ the merge is written in. Either way a crystal whose own refined cell already tel
 keeps its indexing ([Advanced ▸ the indexing ambiguity](RUGNUX_ADVANCED.md#the-indexing-ambiguity)). The input may be
 several files given together - Jungfraujoch masters, or the files an XFEL pipeline writes, read without
 a geometry file ([Serial XFEL inputs](RUGNUX_FORMATS.md#serial-xfel-inputs)). Before the images are
-processed the beam centre is decided on a sample of frames, the file's against the measured ones, and a
-given unit cell also decides the detector distance there; the cell is a starting point the frames
+processed the beam centre is decided on a sample of frames, the file's against the measured ones, and the
+detector distance is refined there too, on a given unit cell or, without one, on the cell the frames index to; the cell is a starting point the frames
 refine, and only the frames of its crystal form are merged. With a cell, the geometry refinement places
 each detector module as well ([§1.4](CPU_DATA_ANALYSIS_IMAGE.md#14-the-beam-centre),
 [§7.7](CPU_DATA_ANALYSIS_INDEXING.md#77-stills-a-given-cell-and-the-detector-modules)). The report adds