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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
136 lines
5.9 KiB
TypeScript
136 lines
5.9 KiB
TypeScript
import {memo} from 'react';
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import AppBar from '@mui/material/AppBar';
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import Toolbar from '@mui/material/Toolbar';
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import Typography from '@mui/material/Typography';
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import IconButton from '@mui/material/IconButton';
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import Box from '@mui/material/Box';
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import Stack from '@mui/material/Stack';
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import {indigo, deepOrange} from '@mui/material/colors';
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import MenuIcon from '@mui/icons-material/Menu';
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import {broker_status} from "../client";
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import ButtonWithSnackbar from "./ButtonWithSnackbar";
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type MyProps = {
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s?: broker_status;
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onMenuClick?: () => void;
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}
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// A tight, strong palette: lime = good/running, coral = working/alarm (deeper = worse),
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// light-blue (sidebar) = neutral/idle-connection. Measuring and Pedestal are handled separately.
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const STATE_STYLE: Record<string, { fill: string; text: string }> = {
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Idle: { fill: "secondary.main", text: "rgba(0,0,0,.87)" }, // lime + black text
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Busy: { fill: deepOrange[300], text: "rgba(0,0,0,.87)" }, // light coral
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Error: { fill: deepOrange[700], text: "#fff" }, // deep coral
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Inactive: { fill: indigo[100], text: "rgba(0,0,0,.87)" }, // sidebar light blue
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};
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// Fixed width so the pill fits the longest label ("Calibration · 100 %") and never
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// resizes as the state changes.
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const pillSx = {
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position: "relative", width: 200, height: 36, borderRadius: 999, overflow: "hidden",
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display: "inline-flex", alignItems: "center", justifyContent: "center", flexShrink: 0,
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} as const;
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const pillLabelSx = { position: "relative", fontWeight: 600, fontSize: "0.95rem", whiteSpace: "nowrap" } as const;
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// Three action-button tiers so exactly one button reads as "click me now":
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// hot = lime — the action to take right now
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// active = blue-on-blue (no frame), white text — available, secondary emphasis
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// off = faint ghost — not relevant in this state
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const activeColdSx = { bgcolor: "primary.dark", color: "#fff",
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"&:hover": { bgcolor: "primary.dark", filter: "brightness(1.12)" } };
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const offSx = { bgcolor: "rgba(255,255,255,.10)", color: "rgba(255,255,255,.6)", boxShadow: "none",
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"&:hover": { bgcolor: "rgba(255,255,255,.18)" } };
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const TIER = {
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hot: { color: "secondary", variant: "contained" },
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active: { color: "primary", variant: "contained", sx: activeColdSx },
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off: { color: "inherit", variant: "contained", sx: offSx },
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} as const;
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type Tier = keyof typeof TIER;
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function StatusChip({s}: {s?: broker_status}) {
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if (s === undefined)
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return (
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<Box sx={{...pillSx, border: "1px solid rgba(255,255,255,.6)"}}>
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<Typography component="span" sx={{...pillLabelSx, color: "#fff"}}>Not connected</Typography>
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</Box>
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);
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// Measuring and Pedestal both fill a light-blue (sidebar) track to the progress
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// fraction, with black text legible over both track and fill. Measuring fills lime;
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// Pedestal fills coral (matching its flat-pill colour elsewhere). The "Pedestal"
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// state is shown as "Calibration" — the internal name is kept only for back-compat.
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if (s.state === "Measuring" || s.state === "Pedestal") {
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const pct = Math.max(0, Math.min(100, (s.progress ?? 0) * 100.0));
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const fill = s.state === "Measuring" ? "secondary.main" : deepOrange[300];
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const label = s.state === "Measuring" ? "Measuring" : "Calibration";
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return (
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<Box sx={{...pillSx, bgcolor: indigo[100]}}>
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<Box sx={{position: "absolute", left: 0, top: 0, bottom: 0, width: `${pct}%`,
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bgcolor: fill, transition: "width .4s ease"}}/>
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<Typography component="span" sx={{...pillLabelSx, color: "rgba(0,0,0,.87)"}}>
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{label} · {pct.toFixed(0)} %
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</Typography>
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</Box>
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);
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}
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const style = STATE_STYLE[s.state] ?? { fill: "grey.500", text: "#fff" };
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return (
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<Box sx={{...pillSx, bgcolor: style.fill}}>
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<Typography component="span" sx={{...pillLabelSx, color: style.text}}>{s.state.toString()}</Typography>
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</Box>
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);
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}
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function StatusBar({s, onMenuClick}: MyProps) {
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// Pick each button's tier from the current state, so the one action that makes
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// sense right now is lime and the rest recede.
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const st = s?.state;
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const cancelTier: Tier = (st === 'Measuring' || st === 'Pedestal') ? 'hot'
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: (st === 'Busy' || st === 'Error') ? 'active' : 'off';
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const initTier: Tier = (s === undefined || st === 'Inactive') ? 'hot'
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: (st === 'Idle') ? 'active' : 'off';
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const pedestalActive = st === 'Idle';
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return <AppBar sx={{zIndex: (theme) => theme.zIndex.drawer + 1}}>
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<Toolbar>
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{onMenuClick && (
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<IconButton color="inherit" edge="start" onClick={onMenuClick} sx={{mr: 2}}>
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<MenuIcon/>
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</IconButton>
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)}
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<Typography variant="h6" component="div" noWrap
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sx={{flexGrow: 0.5, fontWeight: 500, letterSpacing: '.02em'}}>
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Jungfraujoch
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</Typography>
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<Box sx={{flexGrow: 2.0, display: 'flex', justifyContent: 'center'}}>
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<StatusChip s={s}/>
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</Box>
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<Box sx={{flexGrow: 2.0}}/>
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<Stack direction="row" spacing={1}>
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<ButtonWithSnackbar
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text={"Cancel"}
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path={"/cancel"}
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{...TIER[cancelTier]}
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/>
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<ButtonWithSnackbar
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text={"Calibrate"}
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path={"/pedestal"}
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disabled={!pedestalActive}
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{...(pedestalActive ? TIER.active : TIER.off)}
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/>
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<ButtonWithSnackbar
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text={"Initialize"}
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path={"/initialize"}
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{...TIER[initTier]}
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/>
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</Stack>
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</Toolbar>
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</AppBar>
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}
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export default memo(StatusBar);
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