diff --git a/docs/CPU_DATA_ANALYSIS_IMAGE.md b/docs/CPU_DATA_ANALYSIS_IMAGE.md index 32f37ce5e..40d55dfb2 100644 --- a/docs/CPU_DATA_ANALYSIS_IMAGE.md +++ b/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 - diff --git a/docs/JFJOCH_BROKER.md b/docs/JFJOCH_BROKER.md index a7a9c143c..7ea6040e2 100644 --- a/docs/JFJOCH_BROKER.md +++ b/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 diff --git a/docs/RUGNUX_MODEL_AND_REFERENCE.md b/docs/RUGNUX_MODEL_AND_REFERENCE.md index af0f8ea70..7b7dbb471 100644 --- a/docs/RUGNUX_MODEL_AND_REFERENCE.md +++ b/docs/RUGNUX_MODEL_AND_REFERENCE.md @@ -58,7 +58,7 @@ the rest walks through a run step by step. | `--reference-column