v1.0.0-rc.160 (#70)

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: #70

Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

frontend/src/client/types.gen.ts

@@ -99,11 +99,13 @@ export type indexing_algorithm = typeof indexing_algorithm[keyof typeof indexing
  * Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
  * BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
  * OrientationOnly - This option is refining only orientation of the lattice.
+ * Flex - Tries all per-image refinements and keeps whichever indexes the most spots, letting the pipeline decide (the rugnux flex mode).
  *
  */
 export const geom_refinement_algorithm = {
     BEAM_CENTER: 'BeamCenter',
     ORIENTATION_ONLY: 'OrientationOnly',
+    FLEX: 'Flex',
     NONE: 'None'
 } as const;
 
@@ -111,6 +113,7 @@ export const geom_refinement_algorithm = {
  * Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
  * BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
  * OrientationOnly - This option is refining only orientation of the lattice.
+ * Flex - Tries all per-image refinements and keeps whichever indexes the most spots, letting the pipeline decide (the rugnux flex mode).
  *
  */
 export type geom_refinement_algorithm = typeof geom_refinement_algorithm[keyof typeof geom_refinement_algorithm];
@@ -411,8 +414,8 @@ export type unit_cell = {
  * NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
  * NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling
  * NXmxIntegrated - single HDF5 per dataset
- * CBF - CBF format (limited metadata)
- * TIFF - TIFF format (no metadata)
+ * CBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
+ * TIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
  *
  */
 export const file_writer_format = {
@@ -431,8 +434,8 @@ export const file_writer_format = {
  * NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
  * NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling
  * NXmxIntegrated - single HDF5 per dataset
- * CBF - CBF format (limited metadata)
- * TIFF - TIFF format (no metadata)
+ * CBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
+ * TIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
  *
  */
 export type file_writer_format = typeof file_writer_format[keyof typeof file_writer_format];

frontend/src/client/zod.gen.ts

@@ -49,11 +49,13 @@ export const zIndexingAlgorithm = z.enum([
  * Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.
  * BeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).
  * OrientationOnly - This option is refining only orientation of the lattice.
+ * Flex - Tries all per-image refinements and keeps whichever indexes the most spots, letting the pipeline decide (the rugnux flex mode).
  *
  */
 export const zGeomRefinementAlgorithm = z.enum([
     'BeamCenter',
     'OrientationOnly',
+    'Flex',
     'None'
 ]);
 
@@ -178,8 +180,8 @@ export const zDatasetSettings = z.object({
  * NXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia
  * NXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling
  * NXmxIntegrated - single HDF5 per dataset
- * CBF - CBF format (limited metadata)
- * TIFF - TIFF format (no metadata)
+ * CBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
+ * TIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.
  *
  */
 export const zFileWriterFormat = z.enum([

frontend/src/components/AzIntSettings.tsx

@@ -56,6 +56,7 @@ function AzIntSettings({s: serverS}: MyProps) {
                     min={1e-5}
                     units={"A-1"}
                     float={true}
+                    decimals={5}
                     counter={downloadCounter}
                     callback={(val: number, err: boolean) => {
                         setS(prev => ({...prev, q_spacing: val}));
@@ -71,6 +72,7 @@ function AzIntSettings({s: serverS}: MyProps) {
                     max={10.0}
                     units={"A-1"}
                     float={true}
+                    decimals={5}
                     counter={downloadCounter}
                     callback={(val: number, err: boolean) => {
                         setS(prev => ({...prev, low_q_recipA: val}));
@@ -86,6 +88,7 @@ function AzIntSettings({s: serverS}: MyProps) {
                     max={10.0}
                     units={"A-1"}
                     float={true}
+                    decimals={5}
                     counter={downloadCounter}
                     callback={(val: number, err: boolean) => {
                         setS(prev => ({...prev, high_q_recipA: val}));

frontend/src/components/FileWriterSettings.tsx

@@ -75,8 +75,6 @@ function FileWriterSettings({s: serverS}: MyProps) {
                     <MenuItem value={file_writer_format.N_XMX_VDS}>NXmx HDF5 master file with virtual datasets</MenuItem>
                     <MenuItem value={file_writer_format.N_XMX_INTEGRATED}>Single HDF5 file with data and metadata</MenuItem>
                     <MenuItem value={file_writer_format.N_XMX_ONLY_DATA}>No NXmx HDF5 master file (only data files)</MenuItem>
-                    <MenuItem value={file_writer_format.CBF}>miniCBF (only data files; limited metadata)</MenuItem>
-                    <MenuItem value={file_writer_format.TIFF}>TIFF (only data files; no metadata)</MenuItem>
                     <MenuItem value={file_writer_format.NO_FILE_WRITTEN}>No files saved</MenuItem>
                 </Select>
             </FormControl>

frontend/src/components/IndexingSettings.tsx

@@ -155,6 +155,7 @@ function IndexingSettings({s: serverS, status}: MyProps) {
                     <MenuItem value={geom_refinement_algorithm.NONE}>No refinement</MenuItem>
                     <MenuItem value={geom_refinement_algorithm.ORIENTATION_ONLY}>Lattice orientation</MenuItem>
                     <MenuItem value={geom_refinement_algorithm.BEAM_CENTER}>Beam center, lattice orientation and dimensions</MenuItem>
+                    <MenuItem value={geom_refinement_algorithm.FLEX}>Flex (best per-image refinement)</MenuItem>
                 </Select>
             </FormControl>
             <FormControlLabel

frontend/src/components/NumberTextField.tsx

@@ -17,7 +17,8 @@ type MyProps = {
     units?: string,
     disabled?: boolean,
     fullWidth?: boolean,
-    float?: boolean
+    float?: boolean,
+    decimals?: number
 }
 
 function unitsNode(str: string | undefined): ReactNode | null {
@@ -33,7 +34,7 @@ function unitsNode(str: string | undefined): ReactNode | null {
         return <InputAdornment position="end">{str}</InputAdornment>;
 }
 
-function NumberTextField({start_val, default: defaultValue, label, callback, counter, min, max, sx, units, disabled, float}: MyProps) {
+function NumberTextField({start_val, default: defaultValue, label, callback, counter, min, max, sx, units, disabled, float, decimals = 3}: MyProps) {
     const [text, setText] = useState(".");
     const [err, setErr] = useState(true);
     const [val, setVal] = useState(0);
@@ -51,7 +52,7 @@ function NumberTextField({start_val, default: defaultValue, label, callback, cou
         if (float !== true)
             v = Math.round(v);
         else
-            v = Math.round(v * 1000.0) / 1000.0
+            v = Number(v.toFixed(decimals));
 
         setErr(false);
         setVal(v);

frontend/src/version.ts

@@ -1 +1 @@
-export const JFJOCH_VERSION : string = "1.0.0-rc.159";
+export const JFJOCH_VERSION : string = "1.0.0-rc.160";