Rugnux report: warn only where the evidence supports the claim
Report-layer fixes from the warnings audit of the rc173 full battery. Processing is unchanged (merged MTZ/HKL bit-identical on the sets checked). - SUPERCELL_POSSIBLE stays a key and a summary line; a warning only where the rocking part reaches 20% (sub-cells that refine normally rocked at 2.1-16.2%, the accepted doubled cells at 4.2% and 29.1%). The summary says where further lattice domains may put spots on the half-integer nodes. - LATTICE_TRANSLATION only where the Patterson at the vector reaches 90% of the origin (UNDECLARED_LATTICE_TRANSLATION_PCT, new); the two admitted vectors on the battery read 79% and 85% on crystals refining in the deposited cell, and are now reported as a very strong pseudo-translation. PSEUDO_TRANSLATION warns from a 20% peak (xtriage convention; detected peaks were 8.1% on one set, 24.8-63.2% on the rest). - <|L|> outside 0.375-0.55 (on the adopted or the pre-search merge) is TWINNING_VERDICT= NOT_READABLE with no warning, instead of a twin or SYMMETRY_SUSPECT reading. - NO_LATTICE no longer fires on a rotation run that indexed the sweep with no frame indexed on its own; INDEXING_RATE is --developer on rotation. - A rotation run that finds no lattice writes a report (VERDICT= FAILED, NO_LATTICE) before exiting 1, instead of an input-parameter error and no report (NoLatticeFound). - Powder and Ice summary lines, ICE_* keys, and a POWDER_RINGS flag from a 0.5 spot fraction. - SWEEP_GAPS warns only where the degraded ranges cover 10% of the sweep (77 -> 48 sets). - A single rotation sweep no longer carries an INDEXING_AMBIGUITY warning (one orientation matrix, consistent hand); INDEXING_AMBIGUITY_OPERATORS and an Indexing choice line instead. - A DOMAIN more than 10 deg away is a second crystal; the MULTIPLE_LATTICES sum is documented. - Mosaicity line and docs name XDS's suggested REFLECTING_RANGE_E.S.D. as the comparable number (0.90x median over 34 in-house sets; per-image SIGMAR runs ~1.35x higher). - HARMONIC_CONTAMINATION, SCALING_NOT_CONVERGED, POWDER_RINGS in the documented vocabulary. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
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@@ -33,6 +33,15 @@
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* Rugnux reports further lattices found in the spots the main lattice leaves over on rotation data - split-crystal and twin domains, a crystal that changes along the sweep, a related or an unrelated cell (`EXTRA_LATTICE_*` keys, a `Multiple lattices` summary line) - and warns (`MULTIPLE_LATTICES`) where domains of the crystal hold at least 10 % of the spot intensity; processing is unchanged.
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* Rugnux reports the mosaicity the merge used (`MOSAICITY_DEG=` with `MOSAICITY_DEG_P10=`/`_P90=` over the frames, and a summary line), as XDS's sigma_M (`REFLECTING_RANGE_E.S.D.`).
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* `rugnux --polarization` is documented as the polarization degree (XDS `FRACTION_OF_POLARIZATION` = (1 + p)/2); the default 0.99 suits undulators.
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* Rugnux warns about a possible supercell (`SUPERCELL_POSSIBLE`) only where the half-integer class rocks at 20 % or more; weaker cases are stated on the summary's `Supercell` line.
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* Rugnux warns about an undeclared lattice translation only where the Patterson reaches 90 % of the origin there (`UNDECLARED_LATTICE_TRANSLATION_PCT=`), and about a pseudo-translation only from a 20 % peak.
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* Rugnux reports `TWINNING_VERDICT= NOT_READABLE`, without a warning, where <|L|> lies outside its physical range (below 0.375 or above 0.55).
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* Rugnux no longer reports `NO_LATTICE` on a rotation run that indexed the sweep although no single frame indexed on its own; `INDEXING_RATE=` is a `--developer` key on rotation runs.
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* Rugnux writes a report with `VERDICT= FAILED` and `NO_LATTICE` when a rotation run finds no crystal lattice, instead of stopping with an input-parameter error and no report.
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* Rugnux adds `Powder` and `Ice` summary lines and `ICE_*` keys, and warns (`POWDER_RINGS`) where powder rings hold at least half of the spots.
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* Rugnux warns about degraded sweep ranges (`SWEEP_GAPS`) only where together they cover at least 10 % of the sweep.
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* Rugnux no longer warns about an indexing ambiguity on a rotation sweep, which is indexed consistently; it reports the operators (`INDEXING_AMBIGUITY_OPERATORS=`, an `Indexing choice` summary line).
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* Rugnux calls a further lattice more than 10° from the main one a second crystal rather than a split crystal.
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### 1.0.0-rc.172
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+78
-18
@@ -138,7 +138,8 @@ report used to have no evaluative line anywhere until its last section: a run th
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and a run that produced a textbook data set read identically for their first three hundred lines.
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- **`VERDICT=`** is a closed vocabulary — `OK`, `WARNINGS`, `UNUSABLE`, `FAILED`. `FAILED` means no
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lattice was determined or the run was cancelled; `UNUSABLE` means the data merged but carry no
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lattice was determined or the run was cancelled (a sample with no crystal in the beam ends here, with
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`NO_LATTICE`, and the run exits with status 1); `UNUSABLE` means the data merged but carry no
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usable signal; `WARNINGS` means something else needs attention; `OK` means nothing did. It is
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decided from the warnings the rest of the report produced, so it introduces no new analysis and
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cannot disagree with the sections below it.
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@@ -148,9 +149,20 @@ and a run that produced a textbook data set read identically for their first thr
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`SYMMETRY_AMBIGUITY`, `CENTERING_UNTESTED`, `UNUSABLE_MERGE`, `LOW_COMPLETENESS`, `SWEEP_GAPS`,
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`GONIO_SCALE`, `SPINDLE_CAP`, `ANISOTROPY`, `TWINNING`, `PSEUDO_TRANSLATION`,
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`LATTICE_TRANSLATION`, `MODEL_HAND`, `MODEL_NOT_VALIDATED`, `REFERENCE_MISMATCH`, `CANCELLED`, `RESOLUTION_FIT`,
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`FLIGHT_PATH`, `GEOMETRY_NOT_CONVERGED`, `SUPERCELL_POSSIBLE`, `MULTIPLE_LATTICES`. `NONE` when nothing fired. A code appears if and only if its
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`FLIGHT_PATH`, `GEOMETRY_NOT_CONVERGED`, `SCALING_NOT_CONVERGED`, `HARMONIC_CONTAMINATION`,
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`SUPERCELL_POSSIBLE`, `MULTIPLE_LATTICES`, `POWDER_RINGS`. `NONE` when nothing fired. A code appears if and only if its
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warning fired, so the flags and the `WARNING:` lines are two renderings of one list — the closed
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type for machinery, the open sentence for a person.
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- Below them, one line each, the facts a reader needs before reading further: space group, cell,
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mosaicity, the powder and ice rings, multiple lattices, resolution, completeness, signal, anomalous
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signal, anisotropy, pseudo-symmetry, twinning, supercell, radiation damage and the sweep. A line
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states a finding that is not a condition too - weak powder rings, a possible supercell no stronger than
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correct cells show, an arbitrary indexing choice (`Indexing choice`, a rotation sweep whose cell
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admits alternative indexing: one sweep is indexed consistently, so it matters only against other data;
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the operators are **`INDEXING_AMBIGUITY_OPERATORS=`** in section 2). On serial stills the same ambiguity
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mixes the hands in the merge, and is an `INDEXING_AMBIGUITY` warning. `INDEXING_RATE=` - the share of
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frames the per-image indexer took - is a stills measure: a rotation run indexes the sweep as a whole, so
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there it is written only with `--developer`, and `NO_LATTICE` rests on whether the sweep was indexed.
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- **`WARNING_COUNT=`** and the **`WARNING:`** lines follow, in the same section. They are what they
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always were; they have moved from the bottom of the file to the top.
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@@ -283,6 +295,10 @@ experiment was useless". It is reported beside `ROTATION_REJECTED_DEG` on purpos
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*frames* moves when the same experiment is re-sliced, and a percentage of the *rotation* does not.
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The prose headline above the table states both.
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A `SWEEP_GAPS` warning is given, one per range, only where the degraded ranges together cover at least
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10 % of the sweep's rotation; below that they are in the table and the summary's `Sweep` line, and the
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warning lines in `--developer`. One or two frames rejected on a long sweep do not change what the data are.
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`SWEEP_QUALITY_STATUS` distinguishes **`COMPUTED`** (the diagnostic ran; a count of 0 means the sweep
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was clean throughout) from **`NOT_COMPUTED`** (it did not run — no scaling and merging, or stills
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data). A consumer must not read a missing table or a zero count as "clean" without checking it.
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@@ -419,7 +435,27 @@ can be asked to trust on such a pattern; it is absent where they stay separable
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which is the ordinary case. `POWDER_EXCLUDED_FROM_INDEXING` says whether the run needed them
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left out to index at all (with `POWDER_INDEXING_D_MIN` the resolution the retried first pass used).
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Rings are detected far more often than they are excluded: exclusion happens only where a first pass
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found no usable lattice. The measurement is described in
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found no usable lattice. The summary's `Powder` line states the rings on every run that found a lattice;
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a warning under the `POWDER_RINGS` flag is given only where they hold at least half the spots
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(`POWDER_SPOT_FRACTION=` 0.5 or more) - where the contaminant diffracts more than the crystal.
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Hexagonal ice is also measured by the merge itself, which leaves reflections on the ice rings out of
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scaling (and keeps them in the merge) where it finds ice:
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```
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ICE_RINGS_DETECTED= TRUE
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ICE_RING_SCORE= 2.69
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ICE_SPOT_RATIO= 1.08
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ICE_REFLECTIONS_ON_RINGS_PCT= 25.7
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```
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**`ICE_RING_SCORE=`** is the strongest ice ring over the smooth radial background (fine-grained ice
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that makes a smooth ring), **`ICE_SPOT_RATIO=`** the pile-up of found spots on the ring positions
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against the ice-free flanks beside them (ice in large crystallites); 1 is no ice on either.
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**`ICE_RINGS_DETECTED=`** is `TRUE` where either passes its gate (1.5 and 2.0), and
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**`ICE_REFLECTIONS_ON_RINGS_PCT=`** is then the share of the integrated reflections set aside from
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scaling. The summary has an `Ice` line. Ice handling is automatic and costs the merge nothing, so it is
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not a warning. The measurement is described in
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[CPU/GPU data analysis ▸ Resolution and ice-ring handling](CPU_DATA_ANALYSIS_IMAGE.md#33-resolution-and-ice-ring-handling).
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## Index-2 superstructure
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@@ -441,14 +477,17 @@ and rocks is a superstructure whose reflections this run did not integrate; **`S
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is the Niggli-reduced cell the lattice would double to, to give with `-C` to process on it. One that is
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occupied but hardly rocks is diffuse or disordered intensity rather than Bragg reflections.
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**`SUPERCELL_POSSIBLE=`** is `TRUE`, with a warning under the `SUPERCELL_POSSIBLE` flag, where the
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class is measured (`SUPERCELL_I_OVER_SIGMA=` at least 0.5) and part of it rocks like Bragg reflections
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(`SUPERCELL_ROCK_PCT=` at least 2 %, three standard errors clear of zero). It is advice to check, not a
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finding: the same numbers come from a real doubled cell and from a correct cell with weak ordered
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intensity between its reflections, and which of the two a structure is decided by refinement. Process
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both settings - the run's cell, and `SUPERCELL_DOUBLED_CELL=` given with `-C` - and compare them there. The
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summary at the top of the report carries the same advice on its `Supercell` line, beside
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pseudo-symmetry and twinning.
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**`SUPERCELL_POSSIBLE=`** is `TRUE` where the class is measured (`SUPERCELL_I_OVER_SIGMA=` at least
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0.5) and part of it rocks like Bragg reflections (`SUPERCELL_ROCK_PCT=` at least 2 %, three standard
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errors clear of zero). It is advice to check, not a finding: the same numbers come from a real doubled
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cell and from a correct cell with weak ordered intensity between its reflections - or with further
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lattice domains whose spots land on the half-integer positions - and which of the two a structure is
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decided by refinement. Process both settings - the run's cell, and `SUPERCELL_DOUBLED_CELL=` given with
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`-C` - and compare them there. The summary at the top of the report carries that advice on its
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`Supercell` line, and says so where further lattice domains were found. A warning under the
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`SUPERCELL_POSSIBLE` flag is given only where the rocking part reaches 20 %: on a battery of rotation
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data sets, correct sub-cells rocked at 2-16 %, and a real doubled cell can read anywhere in that range
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too, so below 20 % nothing measured here tells the two apart.
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## Further lattices
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@@ -467,7 +506,7 @@ non-ice spots of those frames and of their summed intensity; **`EXTRA_LATTICE_CO
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lattices listed. For each, numbered from 1 in the order found:
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- **`EXTRA_LATTICE_<n>_KIND=`** — `DOMAIN`: the same cell, misoriented, over the whole sweep (a split
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crystal); `TWIN_DOMAIN`: the same, turned by 180° (within 3°) — a non-merohedral twin domain;
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crystal; more than 10° from the main lattice, the report calls it a second crystal); `TWIN_DOMAIN`: the same, turned by 180° (within 3°) — a non-merohedral twin domain;
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`SEGMENTED`: the same cell, with at least 60 % of its spots in 2 of 8 equal blocks of the sweep — the
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crystal in the beam changes along the rotation; `RELATED_CELL`: a cell whose volume is 1 to 8 times,
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or a 1/2 to 1/8 of, the main one's — a question about the main cell (see the supercell keys above and
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@@ -487,8 +526,8 @@ lattices listed. For each, numbered from 1 in the order found:
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**`EXTRA_LATTICE_INTENSITY_PCT=`** sums the intensity share of the domains (`DOMAIN`, `TWIN_DOMAIN`, `SEGMENTED`);
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a `RELATED_CELL` or `FOREIGN` lattice is listed but not counted, since it is as often a wrong main lattice or tNCS
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as a second crystal,
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and **`MULTIPLE_LATTICES=`** is `TRUE`, with a warning under the `MULTIPLE_LATTICES` flag, where that is
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at least 10 %. It is information, not a failure: a split crystal whose second domain is half as strong
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and **`MULTIPLE_LATTICES=`** is `TRUE`, with a warning under the `MULTIPLE_LATTICES` flag, where that
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sum is at least 10 % - the domains together, not the strongest alone. It is information, not a failure: a split crystal whose second domain is half as strong
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as the main one can still give data as good as XDS's, since the domains' reflections are only a problem
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where they overlap the main lattice's. Look at the crystal, and at the result. The summary at the top of
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the report has a `Multiple lattices` line, `none found` where nothing was listed.
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@@ -498,7 +537,10 @@ the report has a `Multiple lattices` line, `none found` where nothing was listed
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**`MOSAICITY_DEG=`** (section 2, and a `Mosaicity` line in the summary) is the mosaic spread the merge
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computed partiality from, on rotation data: Kabsch's σ_M, the standard deviation (not the FWHM) of a
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reflection's rocking curve in degrees, in the same partiality model as XDS - so it is the number to set
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beside XDS's `REFLECTING_RANGE_E.S.D.`. It is fitted on every frame by maximum likelihood from the
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beside XDS's `REFLECTING_RANGE_E.S.D.`: the value under *SUGGESTED VALUES FOR INPUT PARAMETERS* at the
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end of `INTEGRATE.LP`, which `CORRECT.LP` repeats. On in-house rotation data it reads 0.90× that value
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(median over 34 data sets). XDS's per-image `SIGMAR` column and the per-block *CRYSTAL MOSAICITY* in
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`INTEGRATE.LP` are a different number - they run about 1.35× higher - and are not the comparison. It is fitted on every frame by maximum likelihood from the
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rocking offsets of that frame's 250 strongest indexed spots, with the energy bandwidth taken out where
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the beam has one (XDS keeps it in), and smoothed in frame order; the value is the median over the frames,
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with **`MOSAICITY_DEG_P10=`** and **`MOSAICITY_DEG_P90=`** for its spread. The per-frame values are the
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@@ -518,6 +560,11 @@ all, `INCONCLUSIVE` means the Patterson was measured but too few acentric reflec
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whether the vector it names modulates the intensities. Neither is a statement that the crystal has no
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pseudo-symmetry.
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A warning under the `PSEUDO_TRANSLATION` flag is given where `TNCS_DETECTED= TRUE` and the Patterson
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peak is at least 20 % of the origin - the height at which phenix.xtriage, too, calls a
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pseudo-translation one molecular replacement must be told about. A detection below that is significant
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for these data but its modulation is small; the summary calls it weak.
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`TRUE` requires **both** of two tests, because either alone over-calls by about a factor of two:
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- **`TNCS_PATTERSON_PEAK_PCT=`** — the largest off-origin peak of the native Patterson, as a
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@@ -541,9 +588,13 @@ smaller cell would contradict it. Only `TNCS_SUBLATTICE= NEAR_EXTINCT_CLASS` —
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almost gone — says the reported cell may be a supercell.
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**`UNDECLARED_LATTICE_TRANSLATION=`** is a different finding, and is reported instead of a
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pseudo-symmetry rather than as one. The merged data are *exactly* invariant under the translation, and
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a translation the data are exactly invariant under is a lattice vector by definition — so the centring
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or the cell is wrong, not the packing. It is what a centred lattice merged in P1 looks like, which
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pseudo-symmetry rather than as one: a translation at which the Patterson reaches at least 75 % of the
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origin, **`UNDECLARED_LATTICE_TRANSLATION_PCT=`**. Near 100 % the merged data are invariant under it, and
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a translation the data are invariant under is a lattice vector by definition — so the centring or the
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cell is wrong, not the packing; an undeclared centring reads 83-102 %. A warning under the
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`LATTICE_TRANSLATION` flag is given from 90 %. Between 75 and 90 % it is a pseudo-translation so strong it
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is nearly a lattice translation: the warning is then under `PSEUDO_TRANSLATION`, since molecular
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replacement needs it declared unless refinement shows the cell to be a supercell. It is what a centred lattice merged in P1 looks like, which
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`--mode scale` on a file with no space group produces by design. The pseudo-symmetry search continues
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underneath it, so a real pseudo-translation sitting under an undeclared centring is still found.
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@@ -555,6 +606,15 @@ that do preserve the class (`REPAIRED`), and where no step does, `UNREADABLE` sa
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dropped from the twin verdict **in both directions**: it can no longer indicate a twin, and it can no
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longer be read as proof that there is none. The second moment then decides alone.
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**`TWINNING_VERDICT=`** is `NO_INDICATION`, `INDICATED` (⟨|L|⟩ below 0.44, the phenix.xtriage convention,
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or the second moment low, in a Laue class that admits a twin law), `SYMMETRY_SUSPECT` (the same low
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reading in a holohedral class, where no twin law exists and a false adopted operator gives the same
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distribution) or `NOT_READABLE`. ⟨|L|⟩ has a physical range: 0.5 untwinned, 0.375 a perfect twin,
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whatever the law. Where it reads below 0.375, or above 0.55 (on this merge or on the one before the
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space-group search), no twin fraction explains it - the statistic is distorted, by tNCS, anisotropy,
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overlapping reflections of a very long cell, or too few reflections - and the verdict is
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`NOT_READABLE`, with no warning: it says nothing about twinning, nor about the space group.
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## Diffraction anisotropy
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Section 4 also reports how much the fall-off with resolution depends on **direction**, and whether that is
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@@ -370,6 +370,7 @@ TranslationalNCSResult AnalyzeTranslationalNCS(const std::vector<MergedReflectio
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if (result.peak_percent < kLatticeTranslationPct || !std::isfinite(height))
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break;
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result.undeclared_lattice_translations.push_back(frac);
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result.undeclared_lattice_translation_pct.push_back(100.0 * height / origin);
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equivalents.push_back(Vec3{frac[0], frac[1], frac[2]});
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build_near_mask();
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}
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@@ -752,12 +753,15 @@ std::string TranslationalNCSToText(const TranslationalNCSResult &result) {
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return os.str();
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}
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os << std::fixed;
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for (const auto &t : result.undeclared_lattice_translations)
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os << " The data are invariant under (" << std::setprecision(3) << t[0] << ", " << t[1]
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<< ", " << t[2] << ") - the Patterson is as high there as at the origin, so that is a\n"
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<< " LATTICE translation, not a pseudo-symmetry, and the space group in use does not\n"
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<< " declare it. Either the lattice is centred and the merge is not, or the cell is a\n"
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<< " supercell. Excluded, and the search continued past it.\n";
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for (size_t i = 0; i < result.undeclared_lattice_translations.size(); ++i) {
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const auto &t = result.undeclared_lattice_translations[i];
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os << " The Patterson at (" << std::setprecision(3) << t[0] << ", " << t[1] << ", " << t[2]
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<< ") is " << std::setprecision(0) << result.undeclared_lattice_translation_pct[i]
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<< "% of the origin: nearly every reflection is invariant under it,\n"
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<< " so it is a LATTICE translation the space group in use does not declare (a centred\n"
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<< " lattice merged without its centring, or a supercell) - or, short of ~90%, a\n"
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<< " pseudo-translation so strong it is nearly one. Excluded, and the search continued past it.\n";
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}
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os << " Native Patterson off-origin peak " << std::setprecision(1) << result.peak_percent
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<< "% of the origin";
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if (result.vector_length_A > 0.0)
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@@ -72,6 +72,10 @@ struct TranslationalNCSResult {
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// exclusion and the search continues past them, so a real pseudo-translation sitting underneath
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// one is still found.
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std::vector<std::array<double, 3>> undeclared_lattice_translations;
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// The Patterson at each of them, % of the origin (the same order). At least the 75% that admits a
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// vector here; an undeclared centring reads 83-102%, and a very strong pseudo-translation can
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// reach the lower part of that band too.
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std::vector<double> undeclared_lattice_translation_pct;
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// ---- (b) modulation depth -----------------------------------------------------------------
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// False when the Patterson was measured but the modulation test could not run (too few acentric
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@@ -48,6 +48,7 @@ namespace PathologyCode {
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constexpr const char *MULTIPLE_LATTICES = "MULTIPLE_LATTICES"; // a second lattice carries much of the spot intensity
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constexpr const char *GEOMETRY_NOT_CONVERGED = "GEOMETRY_NOT_CONVERGED"; // the geometry walk ran out of rounds
|
||||
constexpr const char *SCALING_NOT_CONVERGED = "SCALING_NOT_CONVERGED"; // the per-frame scales hit their cap still moving
|
||||
constexpr const char *POWDER_RINGS = "POWDER_RINGS"; // most of the spots are on powder rings
|
||||
}
|
||||
|
||||
// A closed type plus an open description. The type is what machinery switches on; the text is what a
|
||||
|
||||
+244
-48
@@ -37,6 +37,9 @@ namespace {
|
||||
// 14: R_MODEL / R_MODEL_SHELL_SCALED / MODEL_RADIAL_MISFIT in section 5 - R over all the
|
||||
// reflections, with and without one free scale per shell, and the size of that rescale.
|
||||
// R_WORK and R_FREE are unchanged and still describe the model the maps were made from.
|
||||
// 15: TWINNING_VERDICT gains NOT_READABLE (<|L|> outside its physical range); ICE_* keys,
|
||||
// UNDECLARED_LATTICE_TRANSLATION_PCT and INDEXING_AMBIGUITY_OPERATORS; INDEXING_RATE is a
|
||||
// --developer key on rotation runs; the POWDER_RINGS flag.
|
||||
// 8: every line that is not `KEY= value` and not blank starts with `#`, warnings included
|
||||
// (`# WARNING:`); the header gains RUGNUX_DOWNLOAD and BUILD_CXX_FLAGS, and RUGNUX_GIT is
|
||||
// the full build-time hash.
|
||||
@@ -59,6 +62,65 @@ namespace {
|
||||
return sc.i_over_sigma >= 0.5 && sc.rock_pct >= 2.0 && sc.rock_pct > 3.0 * sc.rock_se_pct;
|
||||
}
|
||||
|
||||
// ...and a warning only where the rocking part is larger than any correct sub-cell showed. On the
|
||||
// rc173 battery SUPERCELL_POSSIBLE named 15 rotation sets: 13 refine normally in the sub-cell and
|
||||
// rock at 2.1-16.2%, where twin or split domains often put spots on the half-integer nodes; the
|
||||
// two accepted doubled cells rock at 4.2% and 29.1%. Nothing measured here separates the first of
|
||||
// those from the sub-cells, so it stays a summary line; only a rocking part no sub-cell reached
|
||||
// is a condition.
|
||||
constexpr double SUPERCELL_WARNING_ROCK_PCT = 20.0;
|
||||
|
||||
// A translation the Patterson puts at this share of the origin is a lattice translation. The
|
||||
// analysis admits a vector from 75%, and an undeclared centring reads 83-102% (TranslationalNCS.cpp);
|
||||
// on the rc173 battery the only two admitted vectors read 79% and 85%, on crystals that refine
|
||||
// normally in the cell as it stands. Below this it is reported as a pseudo-translation so strong it
|
||||
// is nearly a lattice translation, and refinement is what tells the two apart.
|
||||
constexpr double LATTICE_TRANSLATION_WARNING_PCT = 90.0;
|
||||
|
||||
// A pseudo-translation below this Patterson peak is real where TNCS_DETECTED says so, but not what
|
||||
// a molecular-replacement program has to be told about: its intensity modulation is small. The
|
||||
// convention phenix.xtriage uses (a peak above 20% of the origin). On the rc173 battery the
|
||||
// detected peaks are 8.1% on one set and 24.8-63.2% on the other 21.
|
||||
constexpr double PSEUDO_TRANSLATION_WARNING_PCT = 20.0;
|
||||
|
||||
// The physical range of <|L|>: 0.5 untwinned, 0.375 a perfect twin, whatever the twin law. A
|
||||
// reading outside it is not a twin fraction - tNCS, anisotropy, overlapping reflections of a long
|
||||
// cell or too few reflections distort the statistic. Above 0.5 the battery reads up to 0.54 on
|
||||
// pseudo-centred crystals, so the upper bound leaves that room.
|
||||
bool LTestOutsidePhysicalRange(double mean_abs_l) {
|
||||
return mean_abs_l < 0.375 || mean_abs_l > 0.55;
|
||||
}
|
||||
|
||||
// Powder rings holding at least this share of the pre-scan's spots are a condition; fewer are
|
||||
// stated in the summary only. POWDER_RINGS_DETECTED is TRUE on 63 of the rc173 battery's 235 sets,
|
||||
// 35 of them at 0.2 or more and 13 at 0.5 or more - where the rings hold more spots than the crystal.
|
||||
constexpr double POWDER_WARNING_SPOT_FRACTION = 0.5;
|
||||
|
||||
// Degraded ranges that together cover less than this share of the sweep are listed in the table and
|
||||
// the summary but not warned about: one or two frames rejected, or a short weak stretch, does not
|
||||
// change what the data are. On the rc173 battery the warning fired on 77 of 235 sets; this keeps 48.
|
||||
constexpr double SWEEP_GAPS_WARNING_FRACTION = 0.10;
|
||||
|
||||
// Whether <|L|> - on the merge reported, or on the one the space-group search was given - reads
|
||||
// outside its physical range. Then no twin verdict is read from it, in either direction.
|
||||
bool TwinStatisticsAbnormal(const ProcessResult &r) {
|
||||
const auto abnormal = [](const TwinningAnalysisResult &t) {
|
||||
return t.l_test_pairs > 0 && !t.l_test_contaminated_by_tncs && LTestOutsidePhysicalRange(t.mean_abs_l);
|
||||
};
|
||||
return abnormal(r.twinning) || (r.pre_promotion_twinning && abnormal(*r.pre_promotion_twinning));
|
||||
}
|
||||
|
||||
std::string TwinVerdict(const ProcessResult &r) {
|
||||
if (!TwinStatisticsAbnormal(r))
|
||||
return TwinningVerdictLine(r.twinning);
|
||||
std::string l = fmt::format("<|L|> {:.3f}", r.twinning.mean_abs_l);
|
||||
if (r.pre_promotion_twinning)
|
||||
l += fmt::format(", {:.3f} before the space-group search", r.pre_promotion_twinning->mean_abs_l);
|
||||
return fmt::format("not readable ({}: outside the 0.375-0.5 any twin fraction gives, so the "
|
||||
"intensity statistics are distorted - by tNCS, anisotropy, overlapping reflections "
|
||||
"of a long cell or too few reflections - and say nothing about twinning)", l);
|
||||
}
|
||||
|
||||
// Domains of the crystal itself - misoriented, turned by 180 deg, or holding a segment of the sweep -
|
||||
// that together hold at least this share of the non-ice spot intensity are worth the user's look. A
|
||||
// related cell is a question about the crystal's own cell (left to the supercell keys), and an
|
||||
@@ -82,7 +144,10 @@ namespace {
|
||||
std::string LeftoverLatticeLine(const LeftoverLattice &l) {
|
||||
switch (l.kind) {
|
||||
case LeftoverLatticeKind::Domain:
|
||||
return fmt::format("split crystal, {:.1f} deg from the main lattice", l.misorientation_deg);
|
||||
// A few degrees is one crystal split in two; tens of degrees is a second crystal.
|
||||
return fmt::format("{}, {:.1f} deg from the main lattice",
|
||||
l.misorientation_deg > 10.0 ? "second crystal" : "split crystal",
|
||||
l.misorientation_deg);
|
||||
case LeftoverLatticeKind::TwinDomain:
|
||||
return fmt::format("non-merohedral twin domain, {:.1f} deg from the main lattice",
|
||||
l.misorientation_deg);
|
||||
@@ -535,9 +600,14 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
{
|
||||
ReportSection s;
|
||||
s.title = "2. CRYSTAL";
|
||||
// The share of frames the per-image indexer took. A stills measure: a rotation run indexes the
|
||||
// sweep as a whole and integrates every frame on that lattice, so on sparse frames it can read
|
||||
// 0 while the whole sweep merges.
|
||||
if (result.indexing_rate.has_value())
|
||||
Add(s, KeyReal("INDEXING_RATE", *result.indexing_rate, "{:.4f}"));
|
||||
Add(s, KeyReal("INDEXING_RATE", *result.indexing_rate, "{:.4f}", rotation));
|
||||
Add(s, KeyBool("LATTICE_FOUND", result.consensus_cell.has_value()));
|
||||
if (!result.indexing_ambiguity_operators.empty())
|
||||
Add(s, KeyText("INDEXING_AMBIGUITY_OPERATORS", result.indexing_ambiguity_operators));
|
||||
if (result.consensus_cell.has_value())
|
||||
Add(s, KeyText("UNIT_CELL_CONSTANTS", CellString(*result.consensus_cell)));
|
||||
// Kabsch's sigma_M, the Gaussian e.s.d. of the rocking width in degrees - XDS's
|
||||
@@ -572,7 +642,8 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
result.space_group_search->sohncke_space_group->xhm()));
|
||||
// This fired on every --mode scale run, falsely: that path never fills indexing_rate, because
|
||||
// the lattice comes from the input file, and a missing optional read as a measured zero.
|
||||
if (result.indexing_rate.has_value() && *result.indexing_rate <= 0.0f)
|
||||
// ...and a rotation run can index the sweep with no single frame indexing on its own.
|
||||
if (result.indexing_rate.has_value() && *result.indexing_rate <= 0.0f && !result.rotation_lattice_found)
|
||||
Warn(doc, PathologyCode::NO_LATTICE,
|
||||
"No image indexed - no crystal lattice was determined from this dataset");
|
||||
|
||||
@@ -1157,7 +1228,7 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
Add(s, KeyText("SUPERCELL_DOUBLED_CELL", CellString(sc.doubled_cell)));
|
||||
const bool possible = SupercellPossible(sc);
|
||||
Add(s, KeyBool("SUPERCELL_POSSIBLE", possible));
|
||||
if (possible)
|
||||
if (possible && sc.rock_pct >= SUPERCELL_WARNING_ROCK_PCT)
|
||||
Warn(doc, PathologyCode::SUPERCELL_POSSIBLE,
|
||||
fmt::format("Half-integer reflections of parity {} {} {} carry Bragg-like intensity ({:.0f}% "
|
||||
"of the lattice's, rocking part {:.1f}%): the true cell may be twice as large. "
|
||||
@@ -1175,7 +1246,10 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
" empty. One that is occupied and rocks is an index-2 superstructure the lattice does not\n"
|
||||
" index: its reflections are not integrated. To process on the doubled lattice, give\n"
|
||||
" SUPERCELL_DOUBLED_CELL with -C. An occupied class that does not rock is diffuse or\n"
|
||||
" disordered intensity rather than Bragg reflections."));
|
||||
" disordered intensity rather than Bragg reflections. SUPERCELL_POSSIBLE is TRUE where\n"
|
||||
" the class is measured and rocks; it is a warning only where the rocking part reaches\n"
|
||||
" 20%, since correct cells with weak ordered intensity, or with further lattice domains\n"
|
||||
" whose spots land on the half-integer positions, read up to about 16%."));
|
||||
Add(s, Blank());
|
||||
}
|
||||
|
||||
@@ -1212,8 +1286,8 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
if (CountsAsDomain(l) && (!strongest || l.intensity_pct > strongest->intensity_pct))
|
||||
strongest = &l;
|
||||
Warn(doc, PathologyCode::MULTIPLE_LATTICES,
|
||||
fmt::format("Further domains of the crystal carry {:.0f}% of the spot intensity against {:.0f}% on the "
|
||||
"main one (the strongest: {}); only the main lattice is integrated. This does "
|
||||
fmt::format("Further lattices of the same cell carry {:.0f}% of the spot intensity together, against "
|
||||
"{:.0f}% on the main one (the strongest: {}); only the main lattice is integrated. This does "
|
||||
"not by itself make the data worse - check the crystal, and the result",
|
||||
second, c.primary_intensity_pct, LeftoverLatticeLine(*strongest)));
|
||||
}
|
||||
@@ -1223,12 +1297,15 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
" times; a lattice is listed when the leftover spots sit on it far more often than at a\n"
|
||||
" displaced spindle angle (Z >= 5). Percentages are of the non-ice spots of the spread and\n"
|
||||
" validation frames and of their summed intensity. KIND: DOMAIN - the same cell misoriented,\n"
|
||||
" over the whole sweep (a split crystal); TWIN_DOMAIN - the same, turned by 180 deg (a\n"
|
||||
" over the whole sweep (a split crystal; more than 10 deg away, a second crystal); TWIN_DOMAIN -\n"
|
||||
" the same, turned by 180 deg (a\n"
|
||||
" non-merohedral twin); SEGMENTED - the same cell, but SWEEP_CONCENTRATION >= 0.6 of its\n"
|
||||
" spots fall in 2 of 8 blocks of the sweep (the crystal in the beam changes); RELATED_CELL -\n"
|
||||
" a cell an integer multiple or fraction of the main one's volume, a question about the\n"
|
||||
" main cell (see SUPERCELL_* and the harmonic above); FOREIGN - an unrelated cell (a second\n"
|
||||
" crystal, or a wrong main lattice). Only the main lattice is integrated."));
|
||||
" crystal, or a wrong main lattice). MULTIPLE_LATTICES is TRUE where DOMAIN, TWIN_DOMAIN\n"
|
||||
" and SEGMENTED lattices together (EXTRA_LATTICE_INTENSITY_PCT) hold 10% or more of the\n"
|
||||
" intensity. Only the main lattice is integrated."));
|
||||
Add(s, Blank());
|
||||
}
|
||||
|
||||
@@ -1256,6 +1333,12 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
{"TRUE", "FALSE"}));
|
||||
if (result.powder_indexing_d_min_A)
|
||||
Add(s, KeyReal("POWDER_INDEXING_D_MIN", *result.powder_indexing_d_min_A, "{:.2f}"));
|
||||
if (pw.spot_fraction >= POWDER_WARNING_SPOT_FRACTION)
|
||||
Warn(doc, PathologyCode::POWDER_RINGS, fmt::format(
|
||||
"Powder rings hold {:.0f}% of the spots found ({} rings): a crystalline phase other "
|
||||
"than the crystal diffracts more than the crystal does. Reflections of the crystal "
|
||||
"that fall on a ring carry its intensity too",
|
||||
100.0f * pw.spot_fraction, pw.rings_q_recipA.size()));
|
||||
Add(s, Blank());
|
||||
Add(s, Prose(fmt::format(
|
||||
" Powder contamination: {} rings, holding {:.0f}% of the spots the pre-scan found\n"
|
||||
@@ -1271,6 +1354,27 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
Add(s, Blank());
|
||||
}
|
||||
|
||||
// ---- hexagonal ice, as the merge's ice-ring handling measured it
|
||||
if (result.ice_ring_score || result.ice_spot_ratio) {
|
||||
Add(s, KeyBool("ICE_RINGS_DETECTED", result.ice_rings_detected));
|
||||
if (result.ice_ring_score)
|
||||
Add(s, KeyReal("ICE_RING_SCORE", *result.ice_ring_score, "{:.2f}"));
|
||||
if (result.ice_spot_ratio)
|
||||
Add(s, KeyReal("ICE_SPOT_RATIO", *result.ice_spot_ratio, "{:.2f}"));
|
||||
if (result.ice_rings_detected)
|
||||
Add(s, KeyReal("ICE_REFLECTIONS_ON_RINGS_PCT", 100.0 * result.ice_flagged_fraction, "{:.1f}"));
|
||||
Add(s, Blank());
|
||||
Add(s, Prose(result.ice_rings_detected
|
||||
? fmt::format(" Ice rings: DETECTED. The {:.1f}% of the integrated reflections that lie on the\n"
|
||||
" hexagonal-ice rings were left out of scaling and kept in the merge.",
|
||||
100.0 * result.ice_flagged_fraction)
|
||||
: std::string(" Ice rings: none detected, so no reflection was set aside for them.")));
|
||||
Add(s, Prose(" ICE_RING_SCORE is the strongest ice ring over the smooth radial background (smooth\n"
|
||||
" ice), ICE_SPOT_RATIO the pile-up of found spots on the ring positions against the\n"
|
||||
" flanks beside them (ice in large crystallites); 1 is no ice on either.", true));
|
||||
Add(s, Blank());
|
||||
}
|
||||
|
||||
// ---- translational pseudo-symmetry
|
||||
// Printed immediately before the twinning block, and in the same section, because the two
|
||||
// interact: a pseudo-translation that is not a half-integer vector biases <|L|> upwards and
|
||||
@@ -1297,9 +1401,20 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
// A different finding from a pseudo-symmetry, and reported as one: the data are
|
||||
// EXACTLY invariant under these, so the centring or the cell is wrong rather than the
|
||||
// molecules being packed unusually.
|
||||
for (const auto &v : t.undeclared_lattice_translations)
|
||||
for (size_t i = 0; i < t.undeclared_lattice_translations.size(); ++i) {
|
||||
const auto &v = t.undeclared_lattice_translations[i];
|
||||
Add(s, KeyText("UNDECLARED_LATTICE_TRANSLATION",
|
||||
fmt::format("{:.3f} {:.3f} {:.3f}", v[0], v[1], v[2])));
|
||||
if (i < t.undeclared_lattice_translation_pct.size())
|
||||
Add(s, KeyReal("UNDECLARED_LATTICE_TRANSLATION_PCT", t.undeclared_lattice_translation_pct[i],
|
||||
"{:.1f}"));
|
||||
}
|
||||
// The first one, at the height it was found at: a lattice translation where the Patterson
|
||||
// there is close to the origin's, a very strong pseudo-translation below that.
|
||||
const bool undeclared = !t.undeclared_lattice_translations.empty();
|
||||
const double undeclared_pct = t.undeclared_lattice_translation_pct.empty()
|
||||
? 100.0 : t.undeclared_lattice_translation_pct.front();
|
||||
const bool lattice_translation = undeclared && undeclared_pct >= LATTICE_TRANSLATION_WARNING_PCT;
|
||||
Add(s, KeyReal("TNCS_PATTERSON_PEAK_PCT", t.peak_percent, "{:.1f}"));
|
||||
Add(s, KeyReal("TNCS_PATTERSON_PEAK_Z", t.peak_z, "{:.1f}"));
|
||||
Add(s, KeyText("TNCS_PATTERSON_NULL_PCT",
|
||||
@@ -1353,15 +1468,31 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
" The reported cell is therefore a supercell candidate rather than a settled result,\n"
|
||||
" and the rival hypothesis is a cell with this translation as a lattice vector."));
|
||||
|
||||
if (!t.undeclared_lattice_translations.empty()) {
|
||||
if (lattice_translation) {
|
||||
const auto &v = t.undeclared_lattice_translations.front();
|
||||
Add(s, ProseDefaultOnly(fmt::format(
|
||||
"\n The merged data are EXACTLY invariant under ({:.3f}, {:.3f}, {:.3f}), which the space\n"
|
||||
" group in use does not declare. A translation the data are exactly invariant under is a\n"
|
||||
" lattice vector by definition, so it is the centring or the cell that is wrong, not the\n"
|
||||
" packing. The pseudo-symmetry search continues underneath it, so the numbers above still\n"
|
||||
" describe the crystal and not the missing centring.", v[0], v[1], v[2])));
|
||||
"\n The merged data are invariant under ({:.3f}, {:.3f}, {:.3f}) - the Patterson there is\n"
|
||||
" {:.0f}% of the origin - which the space group in use does not declare. A translation the\n"
|
||||
" data are invariant under is a lattice vector by definition, so it is the centring or the\n"
|
||||
" cell that is wrong, not the packing. The pseudo-symmetry search continues underneath it,\n"
|
||||
" so the numbers above still describe the crystal and not the missing centring.",
|
||||
v[0], v[1], v[2], undeclared_pct)));
|
||||
} else if (undeclared) {
|
||||
const auto &v = t.undeclared_lattice_translations.front();
|
||||
Add(s, ProseDefaultOnly(fmt::format(
|
||||
"\n The Patterson at ({:.3f}, {:.3f}, {:.3f}) is {:.0f}% of the origin: short of the ~100%\n"
|
||||
" of a lattice translation, far above the ordinary pseudo-translation, so the class it\n"
|
||||
" suppresses is nearly empty over 20-5 A. Either the cell is a supercell of one with this\n"
|
||||
" vector as a lattice translation, or the crystal has a very strong pseudo-translation,\n"
|
||||
" which molecular replacement needs declared; refinement in this cell tells them apart.\n"
|
||||
" The pseudo-symmetry numbers above were measured underneath it.",
|
||||
v[0], v[1], v[2], undeclared_pct)));
|
||||
}
|
||||
if (t.detected && t.peak_percent < PSEUDO_TRANSLATION_WARNING_PCT)
|
||||
Add(s, ProseDefaultOnly(fmt::format(
|
||||
"\n The peak is significant but weak: below the {:.0f}% of the origin at which a\n"
|
||||
" pseudo-translation is conventionally declared to molecular replacement.",
|
||||
PSEUDO_TRANSLATION_WARNING_PCT)));
|
||||
|
||||
Add(s, Prose("\n" + TranslationalNCSToText(t), true));
|
||||
if (t.modulation_measured && !t.detected)
|
||||
@@ -1373,21 +1504,29 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
" intensities. Either test alone over-calls by about a factor of two on a corpus of merged\n"
|
||||
" datasets.", true));
|
||||
|
||||
if (t.detected)
|
||||
if (t.detected && t.peak_percent >= PSEUDO_TRANSLATION_WARNING_PCT)
|
||||
Warn(doc, PathologyCode::PSEUDO_TRANSLATION, fmt::format(
|
||||
"Translational pseudo-symmetry: Patterson off-origin peak {:.1f}% of the origin at "
|
||||
"({:.3f}, {:.3f}, {:.3f}), {:.1f} A - the molecular-replacement program needs the "
|
||||
"vector declared, or it will be searching against a modulation it does not model",
|
||||
t.peak_percent, t.vector_frac[0], t.vector_frac[1], t.vector_frac[2],
|
||||
t.vector_length_A));
|
||||
if (!t.undeclared_lattice_translations.empty())
|
||||
if (lattice_translation)
|
||||
Warn(doc, PathologyCode::LATTICE_TRANSLATION, fmt::format(
|
||||
"The merged data are exactly invariant under the translation ({:.3f}, {:.3f}, {:.3f}), "
|
||||
"which the space group in use does not declare - the lattice centring or the unit cell "
|
||||
"is wrong",
|
||||
"The merged data are invariant under the translation ({:.3f}, {:.3f}, {:.3f}) - the "
|
||||
"Patterson there is {:.0f}% of the origin - which the space group in use does not "
|
||||
"declare: the lattice centring or the unit cell is wrong",
|
||||
t.undeclared_lattice_translations[0][0],
|
||||
t.undeclared_lattice_translations[0][1],
|
||||
t.undeclared_lattice_translations[0][2]));
|
||||
t.undeclared_lattice_translations[0][2], undeclared_pct));
|
||||
else if (undeclared)
|
||||
Warn(doc, PathologyCode::PSEUDO_TRANSLATION, fmt::format(
|
||||
"Very strong translational pseudo-symmetry: the Patterson at ({:.3f}, {:.3f}, {:.3f}) is "
|
||||
"{:.0f}% of the origin - the molecular-replacement program needs the vector declared, "
|
||||
"unless refinement shows the cell to be a supercell with this vector as a lattice translation",
|
||||
t.undeclared_lattice_translations[0][0],
|
||||
t.undeclared_lattice_translations[0][1],
|
||||
t.undeclared_lattice_translations[0][2], undeclared_pct));
|
||||
if (t.detected && t.near_extinct_class)
|
||||
Warn(doc, PathologyCode::LATTICE_TRANSLATION, fmt::format(
|
||||
"The pseudo-translation at {:.1f} A suppresses its phase class almost completely, so the "
|
||||
@@ -1413,11 +1552,15 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
// One verdict, in the words every other place uses (TwinningVerdictLine): INDICATED is a twin
|
||||
// in a class that admits one; SYMMETRY_SUSPECT is the same low reading in a holohedral class,
|
||||
// where it says an adopted operator averages unequal intensities.
|
||||
// NOT_READABLE where <|L|> reads outside the range any twin fraction gives: then neither
|
||||
// twinning nor a false operator is read from it.
|
||||
const bool abnormal = TwinStatisticsAbnormal(result);
|
||||
Add(s, KeyEnum("TWINNING_VERDICT",
|
||||
tw.adopted_operators_suspect ? "SYMMETRY_SUSPECT"
|
||||
abnormal ? "NOT_READABLE"
|
||||
: tw.adopted_operators_suspect ? "SYMMETRY_SUSPECT"
|
||||
: tw.twinning_suspected ? "INDICATED"
|
||||
: "NO_INDICATION",
|
||||
{"NO_INDICATION", "INDICATED", "SYMMETRY_SUSPECT"}));
|
||||
{"NO_INDICATION", "INDICATED", "SYMMETRY_SUSPECT", "NOT_READABLE"}));
|
||||
// The fraction comes from the statistic that carries the verdict, and the key beside it says
|
||||
// which. None is quoted where it cannot be measured: merged under a false operator, or from a
|
||||
// second moment a pseudo-translation inflates.
|
||||
@@ -1441,8 +1584,8 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
{"UNAFFECTED", "REPAIRED", "UNREADABLE", "NOT_MEASURED"}));
|
||||
}
|
||||
Add(s, Blank());
|
||||
Add(s, Prose(" Twinning: " + TwinningVerdictLine(tw) + "."));
|
||||
if (tw.adopted_operators_suspect)
|
||||
Add(s, Prose(" Twinning: " + TwinVerdict(result) + "."));
|
||||
if (!abnormal && tw.adopted_operators_suspect)
|
||||
Add(s, Prose(fmt::format(
|
||||
" The Laue class is holohedral, so no twin law exists within it - but merging under a\n"
|
||||
" false operator gives exactly this distribution, whatever the twin fraction. {} Either\n"
|
||||
@@ -1451,7 +1594,7 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
tw.laue_class_was_chosen_by_promotion
|
||||
? "The class was chosen by the space-group search, so that promotion is suspect."
|
||||
: "The space group in use is higher than these intensities support.")));
|
||||
else if (tw.twinning_suspected)
|
||||
else if (!abnormal && tw.twinning_suspected)
|
||||
Add(s, Prose(" Refinement against these data needs a twin law."));
|
||||
else if (tw.l_test_contaminated_by_tncs)
|
||||
// <|L|> is the number this sentence would otherwise rest on, and on this crystal it is
|
||||
@@ -1497,14 +1640,14 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
tz.control.mean_abs_e2_minus_1, tz.control.standard_error)));
|
||||
Add(s, Prose("\n" + TwinImmuneZonesToText(tz)));
|
||||
}
|
||||
if (tw.adopted_operators_suspect)
|
||||
if (!abnormal && tw.adopted_operators_suspect)
|
||||
Warn(doc, PathologyCode::TWINNING, fmt::format(
|
||||
"An adopted symmetry operator relates unequal intensities (<|L|> = {:.3f} in a holohedral "
|
||||
"Laue class, where a genuine operator reads about 0.5 and a false one 0.375): the "
|
||||
"space group may be too high, or the crystal is a twin whose law the point group "
|
||||
"absorbed - refine in a subgroup",
|
||||
tw.mean_abs_l));
|
||||
else if (tw.twinning_suspected)
|
||||
else if (!abnormal && tw.twinning_suspected)
|
||||
Warn(doc, PathologyCode::TWINNING, fmt::format(
|
||||
"Twinning is indicated ({}) - refinement against the merged data needs a twin law",
|
||||
TwinningVerdictLine(tw)));
|
||||
@@ -1533,6 +1676,12 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
// ---- sweep quality
|
||||
{
|
||||
const auto &sq = result.merge_statistics.sweep_quality;
|
||||
// Whether the degraded ranges together are a condition of the data set, or a few frames the
|
||||
// table and the summary line account for.
|
||||
double degraded_deg = 0.0;
|
||||
for (const auto &r : sq.ranges)
|
||||
degraded_deg += r.rotation_deg;
|
||||
const bool material = degraded_deg >= SWEEP_GAPS_WARNING_FRACTION * sq.sweep_deg;
|
||||
const int n_sweep_frames = sq.frames_merged + sq.frames_downgraded + sq.frames_rejected;
|
||||
auto pct = [&](int n) { return n_sweep_frames > 0 ? 100.0 * n / n_sweep_frames : 0.0; };
|
||||
// A delta-CC1/2 or its standard error that could not be measured prints as a dash - a
|
||||
@@ -1648,7 +1797,7 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
"Frames {}-{} {} ({:.1f} deg, scale {:.2f} and CC {:.2f} of the run, {:.0f}% scaled){}",
|
||||
r.first_image, r.last_image, SweepQualityReasonText(r.reason),
|
||||
r.rotation_deg, r.mean_relative_scale, r.mean_relative_cc,
|
||||
100.0 * r.indexed_fraction, cost));
|
||||
100.0 * r.indexed_fraction, cost), !material);
|
||||
}
|
||||
Add(s, std::move(e));
|
||||
}
|
||||
@@ -2052,7 +2201,9 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
|
||||
const auto &o = result.merge_statistics.overall;
|
||||
const std::string group = result.space_group ? result.space_group->xhm() : std::string("P 1");
|
||||
if (no_lattice)
|
||||
if (no_lattice && result.images_processed == 0)
|
||||
doc.verdict_text = "No crystal lattice was found in these frames; nothing was integrated or merged.";
|
||||
else if (no_lattice)
|
||||
doc.verdict_text = fmt::format(
|
||||
"No crystal lattice was determined from {} images; nothing was integrated or merged.",
|
||||
result.images_processed);
|
||||
@@ -2108,9 +2259,26 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
if (result.consensus_cell)
|
||||
row("Unit cell", CellString(*result.consensus_cell));
|
||||
if (std::isfinite(result.mosaicity_deg))
|
||||
row("Mosaicity", fmt::format("{:.3f} deg (sigma_M as XDS; {:.3f}-{:.3f} over 80% of the frames)",
|
||||
row("Mosaicity", fmt::format("{:.3f} deg (sigma_M, comparable with XDS's REFLECTING_RANGE_E.S.D.; "
|
||||
"{:.3f}-{:.3f} over 80% of the frames)",
|
||||
result.mosaicity_deg, result.mosaicity_deg_p10,
|
||||
result.mosaicity_deg_p90));
|
||||
if (!result.indexing_ambiguity_operators.empty())
|
||||
row("Indexing choice", fmt::format("alternative indexing {} - one sweep is indexed consistently, "
|
||||
"so it matters only against other data: index against those "
|
||||
"with -z or --model", result.indexing_ambiguity_operators));
|
||||
if (!result.powder.rings_q_recipA.empty() || result.consensus_cell) {
|
||||
const auto &pw = result.powder;
|
||||
row("Powder", pw.rings_q_recipA.empty() ? std::string("no rings detected")
|
||||
: fmt::format("{} rings holding {:.0f}% of the spots found{}", pw.rings_q_recipA.size(),
|
||||
100.0f * pw.spot_fraction,
|
||||
result.powder_excluded_from_indexing ? "; left out of indexing" : ""));
|
||||
}
|
||||
if (result.ice_ring_score || result.ice_spot_ratio)
|
||||
row("Ice", result.ice_rings_detected
|
||||
? fmt::format("rings DETECTED: the {:.1f}% of the reflections on them were left out of "
|
||||
"scaling, kept in the merge", 100.0 * result.ice_flagged_fraction)
|
||||
: std::string("no rings detected"));
|
||||
if (result.harmonic.detected)
|
||||
row("Beam", fmt::format("higher harmonic INDICATED ({:.0f} % of the unindexed spots "
|
||||
"are lattice points at lambda/3)", result.harmonic.fraction));
|
||||
@@ -2175,23 +2343,51 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
|
||||
: fmt::format("{}: deltaB {:.1f} A^2", sev, an.delta_b));
|
||||
}
|
||||
}
|
||||
if (result.tncs.measurable)
|
||||
row("Pseudo-symmetry", result.tncs.detected
|
||||
? fmt::format("INDICATED (Patterson peak {:.1f}% of origin, {:.1f} A)",
|
||||
result.tncs.peak_percent, result.tncs.vector_length_A)
|
||||
: std::string("no indication"));
|
||||
if (result.tncs.measurable) {
|
||||
const auto &t = result.tncs;
|
||||
std::string ps;
|
||||
if (!t.undeclared_lattice_translations.empty()) {
|
||||
const auto &v = t.undeclared_lattice_translations.front();
|
||||
const double pct = t.undeclared_lattice_translation_pct.empty()
|
||||
? 100.0 : t.undeclared_lattice_translation_pct.front();
|
||||
ps = fmt::format("{} ({:.3f} {:.3f} {:.3f}, Patterson {:.0f}% of origin)",
|
||||
pct >= LATTICE_TRANSLATION_WARNING_PCT
|
||||
? "undeclared LATTICE translation"
|
||||
: "VERY STRONG, nearly a lattice translation",
|
||||
v[0], v[1], v[2], pct);
|
||||
}
|
||||
if (t.detected)
|
||||
ps += (ps.empty() ? "" : "; ") + fmt::format(
|
||||
"{} (Patterson peak {:.1f}% of origin, {:.1f} A)",
|
||||
t.peak_percent >= PSEUDO_TRANSLATION_WARNING_PCT
|
||||
? "INDICATED" : "weak - below the 20% that matters for molecular replacement",
|
||||
t.peak_percent, t.vector_length_A);
|
||||
row("Pseudo-symmetry", ps.empty() ? std::string("no indication") : ps);
|
||||
}
|
||||
if (result.twinning.l_test_pairs > 0)
|
||||
row("Twinning", TwinningVerdictLine(result.twinning));
|
||||
if (result.supercell)
|
||||
row("Supercell", SupercellPossible(*result.supercell)
|
||||
? fmt::format("POSSIBLE - class {} {} {} rocks like Bragg reflections ({:.1f}%); "
|
||||
"process also with -C \"{:.2f},{:.2f},{:.2f},{:.2f},{:.2f},{:.2f}\" "
|
||||
"and compare", result.supercell->h, result.supercell->k,
|
||||
result.supercell->l, result.supercell->rock_pct,
|
||||
result.supercell->doubled_cell.a, result.supercell->doubled_cell.b,
|
||||
result.supercell->doubled_cell.c, result.supercell->doubled_cell.alpha,
|
||||
result.supercell->doubled_cell.beta, result.supercell->doubled_cell.gamma)
|
||||
: std::string("no indication"));
|
||||
row("Twinning", TwinVerdict(result));
|
||||
if (result.supercell) {
|
||||
const auto &sc = *result.supercell;
|
||||
const std::string doubled = fmt::format(
|
||||
"process also with -C \"{:.2f},{:.2f},{:.2f},{:.2f},{:.2f},{:.2f}\" and compare",
|
||||
sc.doubled_cell.a, sc.doubled_cell.b, sc.doubled_cell.c,
|
||||
sc.doubled_cell.alpha, sc.doubled_cell.beta, sc.doubled_cell.gamma);
|
||||
// Spots of further domains of the crystal can land on the half-integer positions.
|
||||
const bool domains = result.leftover_lattices && DomainIntensityPct(*result.leftover_lattices) >= 5.0;
|
||||
if (!SupercellPossible(sc))
|
||||
row("Supercell", "no indication");
|
||||
else if (sc.rock_pct >= SUPERCELL_WARNING_ROCK_PCT)
|
||||
row("Supercell", fmt::format("POSSIBLE - class {} {} {} rocks like Bragg reflections "
|
||||
"({:.1f}%); {}", sc.h, sc.k, sc.l, sc.rock_pct, doubled));
|
||||
else
|
||||
row("Supercell", fmt::format("weak Bragg-like intensity in class {} {} {} (rocking part "
|
||||
"{:.1f}%) - as correct cells with weak ordered intensity "
|
||||
"show{}; to test a doubled cell, {}", sc.h, sc.k, sc.l,
|
||||
sc.rock_pct,
|
||||
domains ? ", and the further lattice domains found may put "
|
||||
"spots there" : "",
|
||||
doubled));
|
||||
}
|
||||
const double db = result.merge_statistics.radiation_damage_delta_b;
|
||||
if (std::isfinite(db))
|
||||
row("Radiation damage", fmt::format("relative B {:+.2f} A^2 over the sweep", db));
|
||||
|
||||
+21
-10
@@ -4717,8 +4717,7 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
|
||||
"data - free the resource it needs (a GPU shared with "
|
||||
"another process is the usual cause) and run again.",
|
||||
*best.indexer_error));
|
||||
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
||||
std::string("Two-pass rotation indexing found no lattice.") + next_steps);
|
||||
throw NoLatticeFound(std::string("Two-pass rotation indexing found no lattice.") + next_steps);
|
||||
}
|
||||
// Short-axis hypothesis - the small-molecule case.
|
||||
//
|
||||
@@ -4980,8 +4979,7 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
|
||||
// reflection by the small angle the constraint snapped away - and without the cell in
|
||||
// the message there is nothing to see that from.
|
||||
const auto &c = best.result->search_result.conventional.GetUnitCell();
|
||||
throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
|
||||
fmt::format("Two-pass rotation indexing found only a lattice that "
|
||||
throw NoLatticeFound(fmt::format("Two-pass rotation indexing found only a lattice that "
|
||||
"takes {:.1f}% of the validation spots against the "
|
||||
"{:.1f}% a wrong spindle angle takes - it is not this "
|
||||
"crystal's lattice. It was {}-centred {}, "
|
||||
@@ -5790,6 +5788,8 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
|
||||
const bool ice_present = (!ice_score.has_value() || *ice_score >= ice_min_score)
|
||||
|| (ice_min_spot_ratio > 0.0f && ice_spot_ratio.has_value()
|
||||
&& *ice_spot_ratio >= ice_min_spot_ratio);
|
||||
result.ice_ring_score = ice_score;
|
||||
result.ice_spot_ratio = ice_spot_ratio;
|
||||
if (experiment_.IsDetectIceRings() && !ice_present) {
|
||||
logger.Info("Ice-ring handling: measured ice score {:.2f} < {:.2f} and spot ratio {:.2f} < "
|
||||
"{:.2f}, no ice detected - ice-ring handling skipped entirely",
|
||||
@@ -5805,6 +5805,8 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
|
||||
++flagged;
|
||||
}
|
||||
}
|
||||
result.ice_rings_detected = true;
|
||||
result.ice_flagged_fraction = total > 0 ? static_cast<double>(flagged) / total : 0.0;
|
||||
logger.Info("Ice-ring handling: ice score {:.2f} (gate {:.2f}), spot ratio {:.2f} (gate "
|
||||
"{:.2f}); flagged {} of {} reflections on ice rings (half-width {:.3f} A^-1); "
|
||||
"excluded from scaling, kept for merging",
|
||||
@@ -7940,14 +7942,21 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
|
||||
// been fitted (validation step below), so the warning stands here exactly as in a run
|
||||
// without a model, and is withdrawn there if the model's indexing probe decided it.
|
||||
// On serial stills with -C and -S the model is already in `ambiguity_reference`.
|
||||
if (!ambiguity_reference) {
|
||||
if (!ambiguity_reference && experiment_.IsRotationIndexing()) {
|
||||
// One sweep has one orientation matrix, so every frame is in the same hand and the
|
||||
// merge mixes nothing. The hand is arbitrary, which matters only against other
|
||||
// data: the report states it, and it is not a condition of this data set.
|
||||
logger.Info("Indexing ambiguity: this cell / space group admits alternative indexing "
|
||||
"(reindex operator(s): {}); one sweep is indexed in one hand, arbitrary "
|
||||
"against other data sets", laws);
|
||||
result.indexing_ambiguity_operators = laws;
|
||||
} else if (!ambiguity_reference) {
|
||||
const std::string msg = fmt::format(
|
||||
"Indexing ambiguity: this cell / space group admits alternative indexing "
|
||||
"(reindex operator(s): {}). {} are indexed in one hand at random, and rugnux can only "
|
||||
"break this against an external reference. WITHOUT one the merge mixes the hands and "
|
||||
"CC1/2 is degraded; a reference MTZ (-z) or a model ({}) resolves it.",
|
||||
laws, experiment_.IsRotationIndexing() ? "Lattices" : "Serial-stills crystals",
|
||||
experiment_.IsRotationIndexing() ? "--model" : "--model, which needs -C and -S here");
|
||||
"(reindex operator(s): {}). Serial-stills crystals are indexed in one hand at random, "
|
||||
"and rugnux can only break this against an external reference. WITHOUT one the merge "
|
||||
"mixes the hands and CC1/2 is degraded; a reference MTZ (-z) or a model (--model, "
|
||||
"which needs -C and -S here) resolves it.", laws);
|
||||
logger.Warning("{}", msg);
|
||||
ambiguity_warning_text = " !! " + msg + "\n\n";
|
||||
stats_text << ambiguity_warning_text;
|
||||
@@ -8212,6 +8221,8 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
|
||||
"Model validation did not run: " + validation.failure_reason});
|
||||
// The ambiguity warning above was issued before the model was read; take it back only
|
||||
// where the model actually settled the indexing.
|
||||
if (validation.indexing_decided)
|
||||
result.indexing_ambiguity_operators.clear();
|
||||
if (validation.indexing_decided && !ambiguity_warning_text.empty()) {
|
||||
std::erase_if(result.warnings, [](const ReportWarning &w) {
|
||||
return w.code == PathologyCode::INDEXING_AMBIGUITY;
|
||||
|
||||
@@ -14,6 +14,7 @@
|
||||
#include "../common/DiffractionExperiment.h"
|
||||
#include "../common/PixelMask.h"
|
||||
#include "../common/CrystalLattice.h"
|
||||
#include "../common/JFJochException.h"
|
||||
#include "../common/Reflection.h" // MergedReflection
|
||||
#include "../common/JFJochMessages.h" // DataMessage
|
||||
#include "../common/JFJochReceiverPlots.h" // MeanProcessingTime
|
||||
@@ -230,6 +231,16 @@ RotationScaleWalk WalkRotationScale(double first_fit,
|
||||
const std::function<std::optional<double>(float)> &refit_at,
|
||||
int max_rounds);
|
||||
|
||||
// The first pass found no lattice of the crystal in the frames - what a sample with no crystal in the
|
||||
// beam ends in. A statement about the data, not an error in the input: the CLI writes a report with
|
||||
// a FAILED verdict for it. `reason` is the explanation without the exception category.
|
||||
class NoLatticeFound : public JFJochException {
|
||||
public:
|
||||
std::string reason;
|
||||
explicit NoLatticeFound(const std::string &r)
|
||||
: JFJochException(JFJochExceptionCategory::InputParameterInvalid, r), reason(r) {}
|
||||
};
|
||||
|
||||
struct ProcessResult {
|
||||
bool cancelled = false;
|
||||
uint64_t images_processed = 0;
|
||||
@@ -412,6 +423,18 @@ struct ProcessResult {
|
||||
// the indexing spot list at where it did.
|
||||
bool powder_excluded_from_indexing = false;
|
||||
std::optional<float> powder_indexing_d_min_A;
|
||||
// Hexagonal ice, as the merge's ice-ring handling measured it: the ring score on the radial
|
||||
// profile and the spot pile-up on the ring positions (1 = no ice on either), whether either
|
||||
// passed its gate, and the share of the integrated reflections then flagged as on a ring (left
|
||||
// out of scaling, kept in the merge). Report only; unset where the merge did not run.
|
||||
std::optional<float> ice_ring_score;
|
||||
std::optional<float> ice_spot_ratio;
|
||||
bool ice_rings_detected = false;
|
||||
double ice_flagged_fraction = 0.0;
|
||||
// The reindex operators a rotation run's cell and space group admit (" ; "-joined), where no
|
||||
// reference or model fixed the choice. Within one sweep the choice is arbitrary but consistent;
|
||||
// it matters only against other data. Empty where there is none, or where it was resolved.
|
||||
std::string indexing_ambiguity_operators;
|
||||
|
||||
// The same analysis measured BEFORE the space group was decided, on the subgroup merge the search
|
||||
// was given. It is the only twinning number a promotion cannot contaminate: once a higher Laue
|
||||
@@ -732,6 +755,8 @@ public:
|
||||
|
||||
// Runs the configured workflow to completion or until Cancel(). Throws on setup failure.
|
||||
ProcessResult Run(RugnuxObserver *observer = nullptr);
|
||||
// The pre-scan's powder measurement, for a report on a run that ended without a result.
|
||||
const PowderRings &GetPowderRings() const { return powder_; }
|
||||
|
||||
// Request cancellation; safe to call from any thread (the worker loop checks between images).
|
||||
void Cancel() { cancelled_ = true; }
|
||||
|
||||
+19
-1
@@ -2794,6 +2794,23 @@ static int RunRugnux(int argc, char **argv) {
|
||||
ProcessResult result;
|
||||
try {
|
||||
result = process.Run();
|
||||
} catch (const NoLatticeFound &e) {
|
||||
// No crystal in these frames is a result, and the report says so - VERDICT= FAILED with
|
||||
// NO_LATTICE - before the run exits as failed.
|
||||
logger.Error("No crystal lattice found: {}", e.reason);
|
||||
ProcessResult failed;
|
||||
failed.warnings.push_back({PathologyCode::NO_LATTICE, "No crystal lattice was found: " + e.reason});
|
||||
failed.powder = process.GetPowderRings();
|
||||
failed.used_beam_x_pxl = experiment.GetBeamX_pxl();
|
||||
failed.used_beam_y_pxl = experiment.GetBeamY_pxl();
|
||||
failed.used_distance_mm = experiment.GetDetectorDistance_mm();
|
||||
const auto direct = experiment.GetDiffractionGeometry().GetDirectBeam_pxl();
|
||||
failed.used_direct_beam_x_pxl = direct.first;
|
||||
failed.used_direct_beam_y_pxl = direct.second;
|
||||
provenance.wall_time_s = std::chrono::duration<double>(
|
||||
std::chrono::steady_clock::now() - invocation_start).count();
|
||||
WriteResultReport(output_prefix, input_file, experiment, failed, logger, provenance);
|
||||
exit(EXIT_FAILURE);
|
||||
} catch (const std::exception &e) {
|
||||
logger.Error("Processing failed: {}", e.what());
|
||||
exit(EXIT_FAILURE);
|
||||
@@ -2834,7 +2851,8 @@ static int RunRugnux(int argc, char **argv) {
|
||||
// Only when something actually indexed: with a zero indexing rate the cell is whatever the lattice
|
||||
// search happened to return and no reflection was measured on it, so printing it as the run's answer
|
||||
// states a result the data do not support.
|
||||
const bool anything_indexed = result.indexing_rate.value_or(0.0f) > 0.0f;
|
||||
// A rotation run can index the sweep as a whole with no frame indexing on its own.
|
||||
const bool anything_indexed = result.indexing_rate.value_or(0.0f) > 0.0f || result.rotation_lattice_found;
|
||||
if (result.space_group.has_value() && anything_indexed) {
|
||||
std::string line = fmt::format("Space group: {} (No. {})", result.space_group->short_name(),
|
||||
result.space_group->number);
|
||||
|
||||
@@ -816,11 +816,31 @@ TEST_CASE("ResultReport_TranslationalNCS", "[Diagnostics]") {
|
||||
result.tncs.detected = false;
|
||||
result.tncs.near_extinct_class = false;
|
||||
result.tncs.undeclared_lattice_translations.push_back({0.5, 0.5, 0.0});
|
||||
result.tncs.undeclared_lattice_translation_pct.push_back(98.0);
|
||||
const auto lat = RenderResultReport("prefix", "in.h5", x, result);
|
||||
CHECK(lat.find("\nTNCS_DETECTED= FALSE\n") != std::string::npos);
|
||||
CHECK(lat.find("\nUNDECLARED_LATTICE_TRANSLATION= 0.500 0.500 0.000\n") != std::string::npos);
|
||||
CHECK(lat.find("\nUNDECLARED_LATTICE_TRANSLATION_PCT= 98.0\n") != std::string::npos);
|
||||
CHECK(lat.find("\nPATHOLOGY_FLAGS= LATTICE_TRANSLATION\n") != std::string::npos);
|
||||
CHECK(lat.find("\nTNCS_SUBLATTICE=") == std::string::npos);
|
||||
|
||||
// Admitted at 75% but short of a lattice translation's height: the claim is a very strong
|
||||
// pseudo-translation, which is what molecular replacement has to be told.
|
||||
result.tncs.undeclared_lattice_translation_pct = {80.0};
|
||||
const auto strong = RenderResultReport("prefix", "in.h5", x, result);
|
||||
CHECK(strong.find("\nPATHOLOGY_FLAGS= PSEUDO_TRANSLATION\n") != std::string::npos);
|
||||
CHECK(strong.find("VERY STRONG, nearly a lattice translation") != std::string::npos);
|
||||
CHECK(strong.find("invariant under the translation") == std::string::npos);
|
||||
|
||||
// Significant, but a peak this weak is not one molecular replacement needs declared.
|
||||
result.tncs.undeclared_lattice_translations.clear();
|
||||
result.tncs.undeclared_lattice_translation_pct.clear();
|
||||
result.tncs.detected = true;
|
||||
result.tncs.peak_percent = 8.1;
|
||||
const auto weak = RenderResultReport("prefix", "in.h5", x, result);
|
||||
CHECK(weak.find("\nTNCS_DETECTED= TRUE\n") != std::string::npos);
|
||||
CHECK(weak.find("PSEUDO_TRANSLATION") == std::string::npos);
|
||||
CHECK(weak.find("weak - below the 20% that matters for molecular replacement") != std::string::npos);
|
||||
}
|
||||
|
||||
TEST_CASE("ResultReport_GeometryNotConverged", "[Diagnostics]") {
|
||||
@@ -961,3 +981,178 @@ TEST_CASE("ResultReport_Mosaicity", "[Diagnostics]") {
|
||||
CHECK(text.find("MOSAICITY_DEG_P90= 0.105") != std::string::npos);
|
||||
CHECK(text.find("Mosaicity 0.091 deg") != std::string::npos);
|
||||
}
|
||||
|
||||
TEST_CASE("ResultReport_SupercellDemoted", "[Diagnostics]") {
|
||||
DiffractionExperiment x(DetJF(1));
|
||||
ProcessResult result;
|
||||
result.consensus_cell = UnitCell{.a = 50.0f, .b = 60.0f, .c = 70.0f,
|
||||
.alpha = 90.0f, .beta = 90.0f, .gamma = 90.0f};
|
||||
result.has_merge_statistics = true;
|
||||
ProcessResult::SupercellClass sc;
|
||||
sc.h = 0; sc.k = 0; sc.l = 1;
|
||||
sc.occupancy_pct = 18.0;
|
||||
sc.rock_pct = 5.0;
|
||||
sc.rock_se_pct = 0.4;
|
||||
sc.i_over_sigma = 1.2;
|
||||
sc.doubled_cell = UnitCell{.a = 50.0f, .b = 60.0f, .c = 140.0f, .alpha = 90.0f, .beta = 90.0f, .gamma = 90.0f};
|
||||
result.supercell = sc;
|
||||
|
||||
// Possible, as correct sub-cells also read: stated, not warned about.
|
||||
auto text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("\nSUPERCELL_POSSIBLE= TRUE\n") != std::string::npos);
|
||||
CHECK(text.find("\nPATHOLOGY_FLAGS= NONE\n") != std::string::npos);
|
||||
CHECK(text.find("weak Bragg-like intensity in class 0 0 1") != std::string::npos);
|
||||
CHECK(text.find("may put spots there") == std::string::npos);
|
||||
|
||||
// Further domains of the crystal can put spots on the half-integer nodes, and the line says so.
|
||||
LeftoverLatticeCensus census;
|
||||
census.primary_intensity_pct = 70.0;
|
||||
census.lattices.push_back(LeftoverLattice{.kind = LeftoverLatticeKind::TwinDomain, .cell = *result.consensus_cell,
|
||||
.volume_ratio = 1.0, .misorientation_deg = 179.5, .z = 50.0,
|
||||
.spots_pct = 8.0, .intensity_pct = 7.0, .sweep_concentration = 0.3});
|
||||
result.leftover_lattices = census;
|
||||
text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("the further lattice domains found may put spots there") != std::string::npos);
|
||||
|
||||
// A rocking part no correct sub-cell reached is a condition.
|
||||
result.supercell->rock_pct = 29.0;
|
||||
text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("\nPATHOLOGY_FLAGS= SUPERCELL_POSSIBLE\n") != std::string::npos);
|
||||
CHECK(text.find("POSSIBLE - class 0 0 1 rocks like Bragg reflections (29.0%)") != std::string::npos);
|
||||
}
|
||||
|
||||
TEST_CASE("ResultReport_TwinningOutsidePhysicalRange", "[Diagnostics]") {
|
||||
DiffractionExperiment x(DetJF(1));
|
||||
ProcessResult result;
|
||||
result.consensus_cell = UnitCell{.a = 70.0f, .b = 70.0f, .c = 70.0f,
|
||||
.alpha = 90.0f, .beta = 90.0f, .gamma = 90.0f};
|
||||
result.has_merge_statistics = true;
|
||||
result.twinning.l_test_pairs = 5000;
|
||||
result.twinning.mean_abs_l = 0.355;
|
||||
result.twinning.second_moment = 1.60;
|
||||
result.twinning.twinning_suspected = true;
|
||||
result.twinning.adopted_operators_suspect = true;
|
||||
|
||||
// Below the 0.375 of a perfect twin: no twin fraction can give it, so neither a twin nor a false
|
||||
// operator is read from it.
|
||||
auto text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("\nTWINNING_VERDICT= NOT_READABLE\n") != std::string::npos);
|
||||
CHECK(text.find("TWINNING ") == std::string::npos);
|
||||
CHECK(text.find("\nPATHOLOGY_FLAGS= NONE\n") != std::string::npos);
|
||||
CHECK(text.find("Twinning not readable (<|L|> 0.355") != std::string::npos);
|
||||
CHECK(text.find("SYMMETRY SUSPECT") == std::string::npos);
|
||||
|
||||
// Inside the range on the adopted merge but far above 0.5 on the merge before the search: the
|
||||
// statistic is distorted on these data, and the low adopted reading is not evidence either.
|
||||
result.twinning.mean_abs_l = 0.395;
|
||||
TwinningAnalysisResult pre;
|
||||
pre.l_test_pairs = 5000;
|
||||
pre.mean_abs_l = 0.590;
|
||||
result.pre_promotion_twinning = pre;
|
||||
text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("\nTWINNING_VERDICT= NOT_READABLE\n") != std::string::npos);
|
||||
CHECK(text.find("0.590 before the space-group search") != std::string::npos);
|
||||
|
||||
// An ordinary reading keeps its verdict.
|
||||
result.pre_promotion_twinning.reset();
|
||||
result.twinning.adopted_operators_suspect = false;
|
||||
result.twinning.mean_abs_l = 0.419;
|
||||
text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("\nTWINNING_VERDICT= INDICATED\n") != std::string::npos);
|
||||
CHECK(text.find("\nPATHOLOGY_FLAGS= TWINNING\n") != std::string::npos);
|
||||
}
|
||||
|
||||
TEST_CASE("ResultReport_RotationLatticeWithoutIndexedFrames", "[Diagnostics]") {
|
||||
DiffractionExperiment x(DetJF(1));
|
||||
// A rotation run that indexed the sweep as a whole while no frame indexed on its own.
|
||||
ProcessResult result;
|
||||
result.images_processed = 1800;
|
||||
result.indexing_rate = 0.0f;
|
||||
result.rotation_lattice_found = true;
|
||||
result.consensus_cell = UnitCell{.a = 50.0f, .b = 60.0f, .c = 70.0f,
|
||||
.alpha = 90.0f, .beta = 100.0f, .gamma = 90.0f};
|
||||
const auto text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("NO_LATTICE") == std::string::npos);
|
||||
CHECK(text.find("No image indexed") == std::string::npos);
|
||||
CHECK(text.find("\nLATTICE_FOUND= TRUE\n") != std::string::npos);
|
||||
|
||||
// The no-crystal exit: the CLI hands over only the reason. The verdict has no image count to quote.
|
||||
ProcessResult none;
|
||||
none.warnings.push_back({PathologyCode::NO_LATTICE, "No crystal lattice was found: none"});
|
||||
const auto failed = RenderResultReport("p", "in.h5", x, none);
|
||||
CHECK(failed.find("\nVERDICT= FAILED\n") != std::string::npos);
|
||||
CHECK(failed.find("\nPATHOLOGY_FLAGS= NO_LATTICE\n") != std::string::npos);
|
||||
CHECK(failed.find("No crystal lattice was found in these frames") != std::string::npos);
|
||||
CHECK(failed.find("UNIT_CELL_CONSTANTS=") == std::string::npos);
|
||||
CHECK(failed.find("SPACE_GROUP_NUMBER=") == std::string::npos);
|
||||
}
|
||||
|
||||
TEST_CASE("ResultReport_PowderAndIce", "[Diagnostics]") {
|
||||
DiffractionExperiment x(DetJF(1));
|
||||
ProcessResult result;
|
||||
result.consensus_cell = UnitCell{.a = 79.0f, .b = 79.0f, .c = 38.0f,
|
||||
.alpha = 90.0f, .beta = 90.0f, .gamma = 90.0f};
|
||||
result.has_merge_statistics = true;
|
||||
|
||||
auto text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("Powder no rings detected") != std::string::npos);
|
||||
CHECK(text.find("ICE_RINGS_DETECTED") == std::string::npos);
|
||||
|
||||
result.powder.rings_q_recipA = {1.61f, 1.71f, 1.82f};
|
||||
result.powder.spot_fraction = 0.20f;
|
||||
result.ice_ring_score = 2.69f;
|
||||
result.ice_spot_ratio = 1.08f;
|
||||
result.ice_rings_detected = true;
|
||||
result.ice_flagged_fraction = 0.257;
|
||||
text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("Powder 3 rings holding 20% of the spots found") != std::string::npos);
|
||||
CHECK(text.find("\nICE_RINGS_DETECTED= TRUE\n") != std::string::npos);
|
||||
CHECK(text.find("\nICE_REFLECTIONS_ON_RINGS_PCT= 25.7\n") != std::string::npos);
|
||||
CHECK(text.find("Ice rings DETECTED: the 25.7% of the reflections") != std::string::npos);
|
||||
CHECK(text.find("POWDER_RINGS ") == std::string::npos);
|
||||
CHECK(text.find("\nPATHOLOGY_FLAGS= NONE\n") != std::string::npos);
|
||||
|
||||
// Most of the spots on rings is a condition.
|
||||
result.powder.spot_fraction = 0.74f;
|
||||
text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("\nPATHOLOGY_FLAGS= POWDER_RINGS\n") != std::string::npos);
|
||||
}
|
||||
|
||||
TEST_CASE("ResultReport_SweepGapsMaterial", "[Diagnostics]") {
|
||||
DiffractionExperiment x(DetJF(1));
|
||||
ProcessResult result;
|
||||
result.consensus_cell = UnitCell{.a = 79.0f, .b = 79.0f, .c = 38.0f,
|
||||
.alpha = 90.0f, .beta = 90.0f, .gamma = 90.0f};
|
||||
result.has_merge_statistics = true;
|
||||
result.merge_statistics.sweep_quality = TestSweepQuality();
|
||||
// Two frames of a long sweep: in the table and the summary, not a condition of the data set.
|
||||
result.merge_statistics.sweep_quality.sweep_deg = 360.0f;
|
||||
result.merge_statistics.sweep_quality.ranges.resize(1);
|
||||
result.merge_statistics.sweep_quality.ranges[0].rotation_deg = 1.0f;
|
||||
auto text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("SWEEP_GAPS") == std::string::npos);
|
||||
CHECK(text.find("Frames 100-149") == std::string::npos);
|
||||
RunProvenance dev;
|
||||
dev.developer = true;
|
||||
CHECK(RenderResultReport("p", "in.h5", x, result, dev).find("Frames 100-149") != std::string::npos);
|
||||
|
||||
result.merge_statistics.sweep_quality.ranges[0].rotation_deg = 40.0f;
|
||||
text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("\nPATHOLOGY_FLAGS= SWEEP_GAPS\n") != std::string::npos);
|
||||
}
|
||||
|
||||
TEST_CASE("ResultReport_SecondCrystal", "[Diagnostics]") {
|
||||
DiffractionExperiment x(DetJF(1));
|
||||
ProcessResult result;
|
||||
result.consensus_cell = UnitCell{.a = 79.0f, .b = 79.0f, .c = 38.0f,
|
||||
.alpha = 90.0f, .beta = 90.0f, .gamma = 90.0f};
|
||||
LeftoverLatticeCensus census;
|
||||
census.primary_intensity_pct = 80.0;
|
||||
census.lattices.push_back(LeftoverLattice{.kind = LeftoverLatticeKind::Domain, .cell = *result.consensus_cell,
|
||||
.volume_ratio = 1.0, .misorientation_deg = 38.9, .z = 50.0,
|
||||
.spots_pct = 12.0, .intensity_pct = 14.0, .sweep_concentration = 0.3});
|
||||
result.leftover_lattices = census;
|
||||
const auto text = RenderResultReport("p", "in.h5", x, result);
|
||||
CHECK(text.find("second crystal, 38.9 deg from the main lattice") != std::string::npos);
|
||||
CHECK(text.find("split crystal, ") == std::string::npos);
|
||||
}
|
||||
Reference in new issue
Block a user