leonarski_fandClaude Opus 4.8
786af96b3b
Space-group search (image_analysis/scale_merge/SearchSpaceGroup): - Two-stage POINTLESS-style determination. Stage A scores each distinct rotation operator once (was once per candidate space group, ~34x faster on lysozyme: ~26s -> <1s) and picks the largest point group all of whose operators confirm. Stage B picks the maximal space group whose predicted absences are confirmed weak, fixing the prototype's default to the symmorphic group (it returned P422 instead of P4(3)2(1)2). Enantiomorphic / origin-ambiguous pairs (P4(1) vs P4(3), I222 vs I2(1)2(1)2(1)) are reported as indistinguishable. - Constrain candidates to subgroups of the lattice (metric) holohedry and weigh centering only P-vs-metric, fed from rotation indexing's LatticeSearch result. Integration / pipeline: - With no user-fixed space group, predict in P (IndexAndRefine) so the centering-absent reflections are integrated and the search can confirm/deny centering (catching pseudo-centering / a missed superstructure) instead of trusting the metric; a user-fixed group still rejects absences in integration. - JFJochProcess: scale+merge in P1 -> determine the space group -> set it and re-scale+merge in it (statistics then come out in the right symmetry) -> write it to /entry/sample/space_group_number (new EndMessage.space_group_number, preferred by NXmx::Sample). jfjoch_scale no longer searches; it consumes the file's space group (and no longer clobbers it with an empty -S). Twinning (new image_analysis/scale_merge/TwinningAnalysis): Padilla-Yeates L-test (<|L|>, <L^2>; acentric-only, positive intensities so L is bounded) plus a shell-normalised <I^2>/<I>^2 second moment and a twin-fraction estimate. Reported after the final merge in jfjoch_process and jfjoch_scale, and surfaced in the jfjoch_viewer merge-statistics window with a red outline when twinning is suspected. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
101 lines
4.5 KiB
C++
101 lines
4.5 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <QElapsedTimer>
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#include <QString>
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#include <QWidget>
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#include <vector>
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#include "../JFJochProcessController.h"
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#include "../JFJochImageReadingWorker.h" // ReprocessingInputs
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class QTableWidget;
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class QProgressBar;
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class QStackedWidget;
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class QToolBar;
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class QToolButton;
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// Makes processing a first-class GUI activity: a dockable panel with a table of processing jobs run
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// on the current dataset. A job can be run locally (off the GUI thread, via JFJochProcessController)
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// or its jfjoch_process command line copied for a cluster. A finished local run is registered as a
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// reader snapshot so its results become a selectable view of the dataset. Re-processing reads a
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// stored HDF5 file, so the panel shows an explanatory message while connected to a live HTTP stream.
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class JFJochProcessingJobsWindow : public QWidget {
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Q_OBJECT
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public:
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explicit JFJochProcessingJobsWindow(JFJochImageReadingWorker *worker, QWidget *parent = nullptr);
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signals:
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void registerSnapshot(QString id, QString label, QString master_path);
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void activateSnapshot(QString id);
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void renameRun(QString id, QString label);
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void removeRun(QString id);
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void writeStatusBar(QString message, int timeout_ms = 0);
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// Live per-image results while a job runs, for the dataset-info plots (nullptr clears it).
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void liveDataset(std::shared_ptr<const JFJochReaderDataset> dataset);
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void jobStarted(); // a reprocessing job was launched — reveal the (hidden-by-default) panel
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public slots:
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void onHttpConnectionChanged(bool connected, QString addr);
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void clearJobs(); // reset the table on a new file (re-adds the Original row)
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void setActiveRun(QString active_id); // bold the row of the run currently shown in the plots
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void newJob(bool azint = false); // the panel's "Analyze dataset" action; azint = AzInt page
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private slots:
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void cancelJob();
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void removeResult();
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void viewResults();
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void onPhase(QString phase);
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void onProgress(quint64 done, quint64 total);
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void onFinished(ProcessResult result);
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void onFailed(QString error);
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private:
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struct JobInfo {
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QString id; // stable reader-snapshot key
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QString label; // editable display name (legend / table)
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QString snapshot_path; // empty unless saved
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bool has_result = false;
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// Merge statistics captured when a scaling/merging job finished (drive the analysis window).
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bool has_merge_stats = false;
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MergeStatistics merge_stats;
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double isa = 0.0;
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bool merge_has_reference = false;
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TwinningAnalysisResult twinning; // twinning test of the merged intensities
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QToolButton *graph_btn = nullptr; // per-row "show statistics" button (enabled once stats exist)
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};
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struct JobSpec {
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ProcessMode mode = ProcessMode::FullAnalysis;
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int start_image = 0;
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int end_image = 0; // 0 == to the end
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int threads = 4;
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bool save = true;
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QString prefix;
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bool rotation = false;
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int rotation_images = 30; // images used to find the rotation lattice (first pass)
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bool scaling = false;
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};
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// Returns 0 = cancel, 1 = run locally, 2 = copy command line; fills spec from the dialog.
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int askJob(const ReprocessingInputs &inputs, JobSpec &spec, bool azint);
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ProcessConfig buildConfig(const JobSpec &spec, const ReprocessingInputs &inputs) const;
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void setStatus(int row, const QString &text);
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void addOriginalRow(); // the file's own data as the first, always-present run
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void addRowActions(int row, const QString &id); // per-row graph (stats) + trash (remove) buttons
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void showStats(const QString &id); // open the merge-statistics window for a run
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void removeRunById(const QString &id); // remove a run from the table + reader
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JFJochImageReadingWorker *worker_;
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JFJochProcessController *controller_;
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QToolBar *toolbar_;
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QStackedWidget *stack_; // page 0: jobs table, page 1: HTTP-mode message
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QTableWidget *table_;
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QProgressBar *running_bar_ = nullptr; // lives in the running row's Status cell
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QElapsedTimer job_timer_; // running job wall-clock, for rate + ETA
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int running_row_ = -1;
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int job_counter_ = 0;
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std::vector<JobInfo> jobs_;
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};
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