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* `rugnux --model` reports CC(model, data) - the correlation of the merged intensities with the placed, scaled model - by resolution shell, on the same shells as CC1/2, with the reflection count and a significance for each. * `rugnux --model` fits the model's scale, anisotropic B and bulk-solvent parameters on the working reflections only, so the R-free it reports is measured against a model no free reflection helped scale. * The bulk-solvent parameters of `rugnux --model` are searched over their physically meaningful range instead of being fitted without bounds, so a model is never scaled with a solvent term that has silently switched itself off. * The rigid-body placement of `rugnux --model` uses the same bounded bulk solvent as the reported fit, so a model is no longer placed against a target carrying a solvent term with no physical meaning. * `rugnux --model` puts the model into the data's own description of the lattice before placing it, so a model whose cell is written on other axes - I-centred where the run indexed C-centred, a different unique axis, a permuted orthorhombic cell - is placed rather than scored where it was read; `MODEL_CHANGE_OF_BASIS=` and `MODEL_SETTING_AS_READ=` report it when it happens. * The rugnux results report opens with a summary - `VERDICT=` (`OK`, `WARNINGS`, `UNUSABLE`, `FAILED`), `VERDICT_TEXT=`, `PATHOLOGY_FLAGS=` with one closed-vocabulary code per condition that warned, and the `WARNING:` lines, which used to close the file - and the sections after it are renumbered 1-5 with no gaps. * `rugnux --developer` writes the full results report - the pipeline-internal keys and the long explanations the default report now leaves out - and `--finalist-ledger` adds the evidence for every space group the search considered, not only the one it adopted. * The results report warns when the merged data carry no usable signal and when too little of reciprocal space was measured inside the fitted resolution, and omits `FITTED_RESOLUTION` where the CC1/2 curve it is fitted on never falls off. * rugnux detects translational pseudo-symmetry and reports it under the `PSEUDO_TRANSLATION` flag as `TNCS_DETECTED=` and the `TNCS_*` keys - a translation the merged data are exactly invariant under is reported as `UNDECLARED_LATTICE_TRANSLATION=` under `LATTICE_TRANSLATION` instead - and a detected pseudo-translation can no longer buy a false screw axis in the space-group search or hide a twin from the L-test (`L_TEST_VS_TNCS=`). * The space-group search determines glide planes from zonal systematic absences, so a non-Sohncke space group such as P 2_1/c or Pbca is named where the run previously stopped at its Sohncke subgroup; `SOHNCKE_SPACE_GROUP=` carries the best Sohncke group beside it on every run that searched, and a centre of symmetry is never claimed. * Where the cell metric carries more rotational symmetry than the Bravais class the indexer named, the extra rotations are put to the intensities and the space-group search is asked again on the metric's own cell - adopted only where the intensities confirm the higher symmetry - so a lattice that is nearly but not exactly hexagonal, or whose reduction landed in a sub-cell, still reaches its true point group. * Systematic-absence calls rest on the evidence rather than on counts: a screw axis whose absent class the data show extinct is no longer refused because a handful of reflections in it read as present, and `SPACE_GROUP_ALTERNATIVES=` no longer drops a candidate that differs only on a zone the sweep never measured. * A reference correlation measured on too few reflections is refused instead of scored zero, so a run given a reference MTZ is no longer reindexed on an operator that mapped almost everything outside the reference's coverage. * A frame counts as indexed from 6 spots on its lattice rather than 9, so a weakly diffracting crystal whose frames cannot carry 9 is no longer refused the lattice it fits; `--min-indexed-spots` overrides it. * `-C` accepts a known cell in any equivalent description - conventional or primitive, centred or not - instead of only the reduced primitive form, so a centred cell given the way it is published no longer makes the run report that it found no lattice. * Each reflection is corrected for the sensor's quantum efficiency at the angle it meets the detector (attenuation lengths from the NIST tables, which also fixes the spot-width parallax term on CdTe) and for the attenuation of the flight path between the sample and its pixel; `--flight-path air|helium|vacuum` declares the medium - default air, since no file states it - and the report says what was assumed and what it was worth. The unmerged MTZ records the factors in new `QE` and `FLIGHT` columns beside `LP`, so raw counts are `I / LP * QE * FLIGHT`, and `_process.h5` in new optional `qe` and `flight` datasets. * Rotation geometry post-refinement fits the crystal and the detector at once, against the observed spot positions and the observed rocking angles together, so the refined distance depends far less on how wrong the file's distance was. * A coarsely sliced sweep integrates correctly: partials are joined into one rocking event by angle rather than by frame count, so two crossings of the Ewald sphere are no longer summed into one full, and at 0.5 degrees per image or coarser the per-frame geometry refinement accepts a spot whose miss the exposure's own rotation accounts for. * `rugnux --mode scale` reports the detector tilt and direct beam of the geometry it re-scaled at, instead of zeros that read as a flat detector, and no longer warns that no image was indexed on a run whose lattice came from its input file. * Every rotation run that determined a space group and merged reports what the mounting cost: `SPINDLE_LOST_UNIQUE_FRACTION=` is the fraction (0-1) of unique reflections the mounting made unmeasurable under the measured point group, also written to the master as `/entry/MX/spindleLostUniqueFraction` and what the mounting warning fires on; `SPINDLE_SYMMETRY_AXIS_ANGLE_DEG=` / `SPINDLE_SYMMETRY_AXIS_ORDER=` describe the mounting in the `--developer` report. * Stills and grid scans carry a per-image `spindle_blind_fraction` - how much of a rotation sweep's blind cone this orientation would make unrecoverable, 0.5 and above calling for a second orientation - through the CBOR stream, HDF5 (`/entry/MX/spindleBlindFraction`), the plot and scan-result APIs, and the viewer and frontend plots; an absent value means the frame could not be assessed and is not a 0. * The results report's `REPORT_VERSION` is 7. Reviewed-on: #77 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
135 lines
7.4 KiB
TypeScript
135 lines
7.4 KiB
TypeScript
import {memo, useState} from 'react';
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import Paper from '@mui/material/Paper';
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import {Box, Checkbox, FormControlLabel, Grid} from "@mui/material";
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import DataProcessingPlot from "./DataProcessingPlot";
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import Toolbar from "@mui/material/Toolbar";
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import MenuItem from "@mui/material/MenuItem";
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import FormControl from "@mui/material/FormControl";
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import Select, {SelectChangeEvent} from "@mui/material/Select";
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import {azint_unit, plot_type} from "../client";
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type MyProps = {
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type: plot_type,
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height: number
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}
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function DataProcessingPlots({type: initialType, height}: MyProps) {
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const [type, setType] = useState<plot_type>(initialType);
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const [binning, setBinning] = useState("0");
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const [tab, setTab] = useState<String>(initialType);
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const [angleUnits, setAngleUnits] = useState(true);
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const [azintUnit, setAzintUnit] = useState<azint_unit>(azint_unit.Q_RECIP_A);
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const plotTypeChange = (event : SelectChangeEvent<String>) => {
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let val = String(event.target.value).toString();
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setTab(val);
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setType(val as plot_type);
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};
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const handleChange = (event : SelectChangeEvent<String>) => {
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setBinning(String(event.target.value).toString());
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};
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return <Paper style={{textAlign: 'center'}} sx={{ height: height, width: "100%" }}>
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<Toolbar>
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<Grid container sx={{ minWidth: 500 }} >
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<FormControl variant="standard" sx={{ m: 1, minWidth: 500 }}>
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<Select
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value={tab}
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onChange={plotTypeChange}
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label="Plot category"
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sx={{fontWeight: "bold"}}
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>
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<MenuItem value={plot_type.INDEXING_RATE}>Indexing rate</MenuItem>
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<MenuItem value={plot_type.INDEXING_UNIT_CELL_LENGTH}>Indexing unit cell (length)</MenuItem>
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<MenuItem value={plot_type.INDEXING_UNIT_CELL_ANGLE}>Indexing unit cell (angle)</MenuItem>
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<MenuItem value={plot_type.SPOT_COUNT}>Spot count</MenuItem>
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<MenuItem value={plot_type.SPOT_COUNT_LOW_RES}>Spot count low res.</MenuItem>
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<MenuItem value={plot_type.SPOT_COUNT_INDEXED}>Spot count indexed</MenuItem>
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<MenuItem value={plot_type.SPOT_COUNT_ICE}>Spot count ice ring</MenuItem>
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<MenuItem value={plot_type.ICE_RING_SCORE}>Ice ring score</MenuItem>
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<MenuItem value={plot_type.AZINT}>Azimuthal integration profile</MenuItem>
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<MenuItem value={plot_type.AZINT_1D}>Azimuthal integration profile (1D)</MenuItem>
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<MenuItem value={plot_type.BKG_ESTIMATE}>Background estimate</MenuItem>
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<MenuItem value={plot_type.SPINDLE_BLIND_FRACTION}>Spindle blind fraction</MenuItem>
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<MenuItem value={plot_type.RESOLUTION_ESTIMATE}>Diffraction resolution estimate</MenuItem>
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<MenuItem value={plot_type.ROI_SUM}>ROI area sum</MenuItem>
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<MenuItem value={plot_type.ROI_MEAN}>ROI area mean</MenuItem>
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<MenuItem value={plot_type.ROI_WEIGHTED_X}>ROI area weighted X position</MenuItem>
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<MenuItem value={plot_type.ROI_WEIGHTED_Y}>ROI area weighted Y position</MenuItem>
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<MenuItem value={plot_type.ROI_MAX_COUNT}>ROI area max count</MenuItem>
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<MenuItem value={plot_type.ERROR_PIXELS}>Error pixels</MenuItem>
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<MenuItem value={plot_type.SATURATED_PIXELS}>Saturated pixels</MenuItem>
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<MenuItem value={plot_type.STRONG_PIXELS}>Strong pixels (for spot finding)</MenuItem>
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<MenuItem value={plot_type.MAX_PIXEL_VALUE}>Maximum pixel value (excl. overloads)</MenuItem>
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<MenuItem value={plot_type.PROFILE_RADIUS}>Profile radius</MenuItem>
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<MenuItem value={plot_type.B_FACTOR}>Wilson B-factor</MenuItem>
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<MenuItem value={plot_type.BEAM_CENTER_X}>Beam center X (post-indexing geometry refinement)</MenuItem>
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<MenuItem value={plot_type.BEAM_CENTER_Y}>Beam center Y (post-indexing geometry refinement)</MenuItem>
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<MenuItem value={plot_type.INDEXING_LATTICE_COUNT}>Indexed lattice count</MenuItem>
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<MenuItem value={plot_type.INTEGRATED_REFLECTIONS}>Integrated reflections</MenuItem>
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<MenuItem value={plot_type.IMAGE_COLLECTION_EFFICIENCY}>Image collection efficiency</MenuItem>
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<MenuItem value={plot_type.COMPRESSION_RATIO}>Compression ratio</MenuItem>
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<MenuItem value={plot_type.PROCESSING_TIME}> Processing time</MenuItem>
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<MenuItem value={plot_type.RECEIVER_DELAY}>Receiver delay (internal debugging)</MenuItem>
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<MenuItem value={plot_type.RECEIVER_FREE_SEND_BUF}>Receiver free send buffers (internal debugging)</MenuItem>
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</Select>
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</FormControl>
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</Grid>
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<Grid container justifyContent="flex-end">
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<FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
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<FormControlLabel
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control={
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<Checkbox
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checked={angleUnits}
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onChange={(e) => setAngleUnits(e.target.checked)}
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/>
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}
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label="X-axis exp. units"
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/></FormControl>
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<FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
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<FormControlLabel
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control={
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<Checkbox
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checked={azintUnit == azint_unit.TWO_THETA_DEG}
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onChange={(e) => setAzintUnit(
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e.target.checked ? azint_unit.TWO_THETA_DEG : azint_unit.Q_RECIP_A
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)}
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/>
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}
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label="2θ (az. int.)"
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/>
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</FormControl>
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<FormControl variant="standard" sx={{ m: 1, minWidth: 120 }}>
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<Select
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value={binning}
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onChange={handleChange}
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label="Binning"
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>
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<MenuItem value={0}>
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<em>Auto binning</em>
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</MenuItem>
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<MenuItem value={1}>1 image</MenuItem>
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<MenuItem value={10}>10 images</MenuItem>
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<MenuItem value={100}>100 images</MenuItem>
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<MenuItem value={500}>500 images</MenuItem>
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<MenuItem value={1000}>1000 images</MenuItem>
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<MenuItem value={5000}>5000 images</MenuItem>
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<MenuItem value={10000}>10000 images</MenuItem>
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</Select>
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</FormControl>
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</Grid>
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</Toolbar>
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<Box sx={{width:"95%", height: height - 150}} >
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<DataProcessingPlot type={type} binning={Number(binning)} angle={angleUnits}
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azint={azintUnit}/>
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</Box>
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</Paper>
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}
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export default memo(DataProcessingPlots);
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