The rc178 branch continued after #88 was squash-merged; this is its content fromb9ada7914(the tree #88 squashed) to094eee31a, as one change on main. The individual commits stay on the rc178 branch: - still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes - AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets - DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked - tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout - Dense per-pixel maps through the panel table (panel layout stage 1) - Panel id on spots and the panel table in the start message - Viewer and preview show a panel detector as it lies on the detector plane - Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster - Panel layout stage 2: prediction and Bragg integration through the panel table - XTC reader: frames handed up as stored, streams indexed in parallel - XFEL reader: integer frames stay integer, one gain, placement by panel - EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery" - still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed - float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count - CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them - Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table - Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane - still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good - still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file - still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition - stills fixed cost: geometry refinement and pre-scan do the same work in less wall time - stills geometry sample and trial spot finding run as many workers as the image pass - Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame - StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's - MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in) - Stills given a cell: the written cell is the mean over the frames that are merged - Stills: the radial curvature correction decided per run on the same empty apertures - StillsPartialityRefine: measure the run width only on shells with signal - Stills pre-scan: report the paired z of the radial-correction comparison - module placement: the five concurrent fits each keep every thread - still battery: score R-free against the deposited data through the same dimple protocol - still battery: the R-free target is the lower of the deposition's dimple and published values - Stills: background clip follows the radial curve; signal disk from the lattice spacing - Stills keep an overloaded observation as a lower bound instead of dropping it - Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip - battery: R-free against the deposition without refinement only, one protocol for rotation and stills - still battery: EuXFEL sets run on a 2,000-image subset for now - stills geometry refinement: fit the detector distance and the cell together - stills geometry refinement: a distance given with --detector-distance is held in the joint fit - Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count - Metal integration test: the CPU comparison runs on a rotation experiment - Stills: kept overloads go back to the drop where they are not concentrated at low resolution - stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated - battery results: XFEL still battery 20261022-1358 on rc1780cf62452c- 12 sets, cold, R_free unrefined - battery results: still summary gains the resolution of our merge and of the deposition - Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value - Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed - XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock - stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes - rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid - stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree - CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get - broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4) - frontend: Mol* viewer of the placed model and its density on the Rugnux live page - writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does - rugnux live maps: one unit cell centred on the model; the viewer opens on all of it - Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer - Mol* viewer: open with the maps drawn within 10 A of the centre of view - Mol* viewer: aaredb's structure-viewer setup, on a black stage - rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons - Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2) - ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI) - stills tilt decision: the modules stay where the run placed them - still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it - battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC - Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons - BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it - ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization - BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain - ShadowFinder: measure the modulation robustly under a wide one-sided shadow - ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation - ShadowFinder: back to the predicted polarization factor, in the plane the background shows - MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again - battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables - XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel - stills geometry trial: the hypotheses a search asks are indexed side by side - stills tilt decision: the fits start beside the pre-scan and the geometry trial - XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache - XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step - GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block - GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart - docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts - battery: doc_check.py cross-checks the manifests against the dataset pages - stills module placement: the placement fit gets half the threads, each held-out fit an eighth - still battery: the EuXFEL sets run on all their frames, as the published still runs did - battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table - macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
186 lines
8.3 KiB
C++
186 lines
8.3 KiB
C++
// SPDX-FileCopyrightText: 2025 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 <QPainterPath>
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#include "JFJochImage.h"
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#include "../../reader/JFJochReaderImage.h"
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#include "../../common/ROIDefinition.h"
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class ROIAzimuthal;
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class DiffractionGeometry;
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class JFJochDiffractionImage : public JFJochImage {
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Q_OBJECT
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QColor spot_color = Qt::green;
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QColor prediction_color = Qt::darkRed;
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QColor ice_ring_color = Qt::cyan;
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QColor second_lattice_color = QColor(0xFA, 0x72, 0x68); // coral, the viewer "finishing" accent
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// With outlining on, spot markers are drawn twice: a black pen this much wider underneath,
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// then the marker on top. The hues mean something - cyan is the colour of ice, magenta is
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// the one colour no colour map contains - so none of them moves to gain contrast. The casing
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// carries the marker where the colour map's low end is light, the bright core carries it
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// where it is dark, so one mechanism covers both without branching on the colour map. It is
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// opt-in (default off): the doubled stroke makes the markers harder to read for some users.
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// Predictions are left alone: darkRed is already legible on a light map and a black casing
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// does nothing for it on a dark one.
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static constexpr int MARKER_CASING_EXTRA_WIDTH = 4;
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float hover_resolution = NAN;
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// The "d = ... A" readout is painted in drawForeground() in viewport pixels rather than kept
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// as a scene item, so updating it dirties only its own rect. hover_text_rect_ is where it
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// currently sits, in viewport coordinates.
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QRect hover_text_rect_;
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[[nodiscard]] QString HoverResolutionLabel() const;
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// Counts are exact integers: label them from the int32 image rather than from a float copy,
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// which both avoids materialising that copy and cannot round large summed values.
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[[nodiscard]] QString PixelLabel(int x, int y) const override;
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// This is the view that has detector counts, so it is the one that offers an ROI
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[[nodiscard]] bool AllowROI() const override { return true; }
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void drawForeground(QPainter *painter, const QRectF &rect) override;
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// The readout sits at a fixed viewport position, but QGraphicsView scrolls by blitting the
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// viewport, which carries the painted text along with it - so its old and new places both have
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// to be repainted when the view pans.
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void scrollContentsBy(int dx, int dy) override;
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public:
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enum class RingMode {Auto, Estimation, Manual, None, IceRings};
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Q_ENUM(RingMode)
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JFJochDiffractionImage(QWidget *parent = nullptr);
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private:
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void addCustomOverlay() override;
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void LoadImageInternal();
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// Colour straight from the int32 detector image; no float copy of it is ever built
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void ColorRow(size_t y, const PixelColorMap &map, QRgb *out) const override;
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void DrawResolutionRings();
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void DrawROIs();
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void DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color, const DiffractionGeometry &geom);
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void AddROILabel(const std::string &name, const QColor &color, float px, float py);
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// Interactive editing of the selected (named) ROI: move box/circle for now.
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bool roiEditPress(const QPointF &scenePos) override;
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void roiEditMove(const QPointF &scenePos) override;
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void roiEditRelease() override;
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void roiScratchDrawn() override;
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void keyPressEvent(QKeyEvent *event) override; // Delete removes the selected ROI
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[[nodiscard]] ROIDefinition BuildEditedROIDefinition() const; // current ROIs with the edit applied
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[[nodiscard]] ResizeHandle hitTestBoxHandle(const QRectF &r, const QPointF &p, qreal tol) const;
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// Grab points for an azimuthal ROI: inner/outer arc (resize Q/d) and the two phi
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// edges (rotate). The phi handles are only meaningful for a sector (HasPhi()).
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void azimuthalHandles(const ROIAzimuthal &az, const DiffractionGeometry &geom,
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QPointF &inner, QPointF &outer, QPointF &phimin, QPointF &phimax) const;
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QString selected_roi_;
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enum class RoiEdit { None, MoveBox, ResizeBox, MoveCircle, ResizeCircle,
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AzimInner, AzimOuter, RotatePhiMin, RotatePhiMax };
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RoiEdit roi_edit_ = RoiEdit::None;
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ResizeHandle box_handle_ = ResizeHandle::None;
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QString edit_name_;
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QRectF edit_box_;
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QPointF edit_center_;
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double edit_radius_ = 0;
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float edit_d_min_ = 0, edit_d_max_ = 0, edit_phi_min_ = 0, edit_phi_max_ = 0; // azimuthal edit state
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bool edit_has_phi_ = false;
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QPointF move_last_;
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bool live_pending_ = false; // a live edit is being recomputed; throttles emissions
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void DrawSpots();
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void DrawPredictions();
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void DrawBeamCenter();
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void DrawTopPixels();
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void DrawSaturation();
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void DrawResolutionText();
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void DrawCross(float x, float y, float size, float width, float z = 1);
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void UpdateForeground();
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// The foreground the current image suggests: the top of the valid range in HDR mode, the
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// auto-contrast value otherwise. Empty when there is no image to take it from.
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[[nodiscard]] std::optional<float> AutoForegroundValue() const;
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void ResetBackground();
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bool one_shot_auto_ = false; // `A` applied the auto value; pressing it again makes Auto permanent
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void leaveEvent(QEvent *event) override;
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std::shared_ptr<const JFJochReaderImage> image;
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// What is shown: the image itself for a flat detector, else the image gathered onto the detector
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// plane (AssembleToPlane), whose top-left pixel sits at origin_. The scene is the detector plane
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// either way, so spots, predictions, rings and ROIs are drawn where the geometry puts them.
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std::shared_ptr<const std::vector<int32_t>> pixels_;
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// Scene position of a pixel of the stored image (index into image->Image()); empty in a gap.
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[[nodiscard]] std::optional<QPointF> StoredPixelToScene(int64_t index) const;
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int32_t show_highest_pixels = 0;
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QVector<float> res_ring = {};
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// Constant-d contours traced for res_ring, kept across overlay rebuilds; see DrawResolutionRings
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QVector<float> ring_cache_key_ = {};
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QVector<std::pair<float, QPainterPath>> ring_cache_ = {};
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RingMode ring_mode = RingMode::Estimation;
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bool show_spots = false;
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bool show_predictions = false;
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bool show_roi_labels = false;
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bool show_roi_fill = false;
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bool highlight_ice_rings = true;
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bool hide_unindexed_spots = false;
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bool hide_ice_ring_spots = false;
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bool outline_spots = false; // black casing under spot markers, see MARKER_CASING_EXTRA_WIDTH
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void mouseHover(const QPointF &scenePos, Qt::KeyboardModifiers modifiers) override;
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// The magnifier follows the cursor only while Shift is held, and meanwhile a frame here
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// shows the area it covers. magnifier_frame_ is empty while the frame is hidden.
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QSizeF magnifier_field_;
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QRectF magnifier_frame_;
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void SetMagnifierFrame(const QRectF &r);
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signals:
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void magnifierMoved(QPointF scenePos); // in pixels of the shown image, as the magnifier has them
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void pixelsChanged(std::shared_ptr<const std::vector<int32_t>> pixels); // the shown image changed
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void roiGeometryEdited(ROIDefinition rois);
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void roiSelected(QString name); // user picked an ROI by clicking it on the image
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public slots:
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void setSelectedROI(QString name);
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void loadImage(std::shared_ptr<const JFJochReaderImage> image);
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void setAutoForeground(bool input);
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// Apply the auto-contrast value once, leaving Auto as it was; pressing it a second time on the
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// same image switches Auto on for good (which keeps recomputing it on every subsequent image).
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void oneShotAutoForeground();
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void setResolutionRing(QVector<float> v);
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void setResolutionRingMode(RingMode mode);
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void showSpots(bool input);
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void showPredictions(bool input);
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void showROILabels(bool input);
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void showROIFill(bool input);
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void setSpotColor(QColor input);
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void setPredictionColor(QColor input);
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void showHighestPixels(int32_t v);
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void showSaturation(bool input);
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void showBeamStop(bool input);
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void highlightIceRings(bool input);
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void hideUnindexedSpots(bool input);
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void hideIceRingSpots(bool input);
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void outlineSpots(bool input);
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void setHDRMode(bool input);
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void setMagnifierField(QSizeF size);
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void hideMagnifierFrame();
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};
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