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Jungfraujoch/viewer/widgets/JFJochViewerSettingsDock.h
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leonarski_fandClaude Opus 5 16bf3408f0 Address code-review findings; make detection limits detector-driven
One changeset, developed together in response to a review of this branch, so the
files carry several of the changes at once. Full test suite passes (733 cases).

Spot finding
- Split ImageSpotFinder into Detect() (flag strong pixels - the expensive
  per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with
  Run() = both. The per-image min-pix escalation now detects ONCE and repeats
  only the cheap extraction, instead of re-running the whole finder four times
  per frame as it did on the default path. It also keeps the winning attempt's
  spot list rather than re-extracting it, so the frame that is integrated is
  exactly the frame that was scored - which a GPU re-extract could not guarantee
  (float atomic ordering).
- spot_finding_time_s no longer swallows indexing time, and indexing_time_s now
  sums every escalation call instead of reporting only the last.

Detection limits follow the detector
- The azimuthal-integration upper q and the spot-finding high-resolution limit
  are now std::optional, in the C++ structs AND in the OpenAPI schema, and
  resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_
  recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a
  pixel outside that q range could never be strong - the integration range
  silently bounded what detection could see, regardless of the requested
  resolution limit. Regenerated the C++ and TypeScript clients; the viewer and
  the web frontend each gained a "to detector edge" switch.

Detection defaults are now per workflow (measured, not assumed)
- Stills: adaptive detection, min-pix chosen per image, no resolution clipping.
- Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit.
  On a 33-crystal rotation battery, adaptive detection helped four hard crystals
  but deterministically broke three (a lost space group, a halved indexing rate,
  a collapsed merge), and the detector-edge limit cost indexing on a strong
  rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and
  --no-adaptive-spots is new.

Indexer seed escalation
- Stop escalating once a seed's lattice explains >= 90% of the seed spots.
  Previously any frame with >= 80 spots always paid three indexer calls, online
  broker included.

Merge-consistency filter
- --min-image-cc gated on a per-image CC computed BEFORE the stills partiality
  post-refinement and never refreshed; the refiner now recomputes it, so the
  reported CC describes the data that are actually merged.
- Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the
  merge, the error model and MergeStats can no longer disagree about which
  images are in (the --scale path merged unfiltered while its statistics were
  filtered).

Per-image B-factor refinement (-B) removed
- Measured on four serial-stills datasets: it is a no-op where the per-image fit
  is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas
  +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on
  14-25% of images). It had also been silently DISCARDED since the partiality
  post-refinement landed - reported but not applied. Rather than fix and keep a
  knob with no demonstrated benefit, the flag and the whole image_scale_b_factor
  chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and
  read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs.
  ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS.
  (The Wilson per-image b_factor is a different quantity and stays.)

Stills partiality width now fits both of its components
- sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d*
  with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2
  on d*^2. The angular-only width is fitted over a d*^2-dense population, so it
  was pinned by the high-resolution edge and collapsed at low d*: median
  partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55%
  of them under the merge's partiality floor, and the survivors divided by those
  values - which inflated the merged low-resolution intensity scale 3.6x
  (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x,
  no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and
  R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining
  R-free are all blind to that ramp, which is why it survived earlier validation;
  the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged).

Removed dead code from add-then-remove churn
- Prediction-time "still partiality" (unreachable: no setter), the phantom
  IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the
  constant it always was), StillsPartialityRefine's caller-less Settings
  constructor and its reference to a long-gone env var, ProcessImage's unread
  bool return, an unused include, and a dead viewer overlay hook.

Also
- Viewer: the magnifier compared a QImage with itself, so its scene rect was set
  once ever and it could not pan into a larger dataset; the hover tail timer
  could fire after leaveEvent and resurrect the resolution readout outside the
  image.
- update_version.sh regenerated the frontend lock file BEFORE bumping the
  version (every release shipped an off-by-one lock), and did git rm/git add on
  a path that has not existed since the client moved to src/client - with no
  set -e, both failed silently.
- fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a
  redirect, not a test, so dkms add never ran.
- Unit tests for the adaptive-threshold host functions, which had none.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-07-27 09:07:00 +02:00

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// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <QWidget>
#include <memory>
#include "../../common/DiffractionExperiment.h"
#include "../../common/IndexingSettings.h"
#include "../../common/AzimuthalIntegrationSettings.h"
#include "../../common/BraggIntegrationSettings.h"
#include "../../common/ScalingSettings.h"
#include "../../image_analysis/spot_finding/SpotFindingSettings.h"
#include "../../reader/JFJochReaderDataset.h"
#include "../../reader/JFJochReaderImage.h"
#include "../ReferenceMtzInfo.h"
class QStackedWidget;
class QCheckBox;
class QComboBox;
class QLabel;
class QPushButton;
class SliderPlusBox;
class NumberLineEdit;
class PowderCalibrationWidget;
// The single, always-visible settings panel: an MX / AzInt toggle picks the page, and the panel is
// the one place all processing settings live (there is no separate window, so no synchronisation).
// "Analyze image" / "Analyze dataset" sit on top; the MX/AzInt choice decides what a dataset run does.
// Edits feed straight back into the running analysis via the worker.
class JFJochViewerSettingsDock : public QWidget {
Q_OBJECT
public:
JFJochViewerSettingsDock(const SpotFindingSettings &spot, const IndexingSettings &indexing,
const AzimuthalIntegrationSettings &azint, const BraggIntegrationSettings &bragg,
const ScalingSettings &scaling, QWidget *parent = nullptr);
public slots:
void datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset);
void loadImage(std::shared_ptr<const JFJochReaderImage> image);
void referenceLoaded(ReferenceMtzInfo info); // worker reports a (un)loaded reference MTZ
// Dataset re-processing reads a stored HDF5 file, so it is unavailable on a live HTTP stream:
// grey out "Analyze dataset" while connected rather than failing with a dialog afterwards.
void setHttpConnection(bool connected, QString addr);
signals:
void spotFindingChanged(const SpotFindingSettings &spot, const IndexingSettings &indexing, int64_t max_spots);
void azintChanged(const AzimuthalIntegrationSettings &settings);
void braggChanged(BraggIntegrationSettings settings);
void scalingChanged(ScalingSettings settings);
void experimentChanged(const DiffractionExperiment &experiment);
void findBeamCenter(const UnitCell &calibrant, bool guess);
void ringsFromCalibration(QVector<float> rings);
void referenceSelected(QString path, QString column); // user picked a reference MTZ / column
void reanalyzeImage(bool armed); // "Analyze image" toggle
void analyzeDataset(bool azint); // "Analyze dataset"; azint = AzInt page selected
private:
SpotFindingSettings spot_;
IndexingSettings indexing_;
AzimuthalIntegrationSettings azint_;
BraggIntegrationSettings bragg_;
ScalingSettings scaling_;
DiffractionExperiment experiment_;
bool have_experiment_ = false; // geometry edits only take effect once a dataset is loaded
int64_t max_spots_ = 1000;
// Min-pix is kept as the pair the UI shows - the fixed value AND whether to choose it per image -
// because spot_.min_pix_per_spot can only hold one of the two (unset = per image). SyncMinPix()
// turns the pair into that field, and per-image only ever applies to stills.
bool adaptive_min_pix_ = false;
int64_t min_pix_value_ = 2;
bool azint_mode_ = false; // false = MX page, true = AzInt page (drives "Analyze dataset")
// "Analyze dataset" hero button, disabled while a live HTTP source is connected.
QPushButton *analyzeDatasetBtn_ = nullptr;
// Indexing-algorithm combo + the description line under it (kept so the Auto resolution refreshes).
QComboBox *algo_ = nullptr;
QLabel *algoDesc_ = nullptr;
// "Process as stills" — kept so datasetLoaded can enable it only when the dataset has a goniometer
// (a rotation dataset); it drives indexing/scaling mode via ApplyProcessingMode().
QCheckBox *stills_ = nullptr;
// Geometry fields (shared by both MX and AzInt, since both need the same geometry)
NumberLineEdit *energy_ = nullptr;
NumberLineEdit *distance_ = nullptr;
NumberLineEdit *beamX_ = nullptr;
NumberLineEdit *beamY_ = nullptr;
NumberLineEdit *rot1_ = nullptr; // detector tilt (PONI rot1), deg
NumberLineEdit *rot2_ = nullptr; // detector tilt (PONI rot2), deg
// Crystal fields
QCheckBox *cellKnown_ = nullptr;
NumberLineEdit *cellA_ = nullptr, *cellB_ = nullptr, *cellC_ = nullptr;
NumberLineEdit *cellAlpha_ = nullptr, *cellBeta_ = nullptr, *cellGamma_ = nullptr;
NumberLineEdit *spaceGroup_ = nullptr;
QLabel *spaceGroupName_ = nullptr; // resolved HermannMauguin symbol
// Reference dataset (MTZ) for scaling / CCref. The chosen file is remembered so a
// column change re-loads the same file; the worker owns the reflections, this just drives it.
QPushButton *refButton_ = nullptr;
QComboBox *refColumn_ = nullptr;
QLabel *refSummary_ = nullptr;
QLabel *refWarning_ = nullptr;
QString refPath_;
PowderCalibrationWidget *powder_ = nullptr;
QWidget *BuildGeometrySection();
QWidget *BuildMXPage();
QWidget *BuildBraggSection();
QWidget *BuildScalingSection();
QWidget *BuildReferenceSection();
QWidget *BuildAzIntPage();
void SyncMinPix();
void EmitSpotFinding();
void EmitExperiment();
void ApplyProcessingMode(); // "Process as stills" -> indexing + scaling rotation/stills mode
void UpdateAlgorithmDescription();
void RefreshGeometryFields();
void UpdateSpaceGroupName();
};