Files
Jungfraujoch/viewer/image_viewer/JFJochDiffractionImage.h
T
leonarski_fandClaude Opus 5.5 0a515bb086 rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG
The rc178 branch continued after #88 was squash-merged; this is its content from b9ada7914 (the tree
#88 squashed) to 094eee31a, 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 rc178 0cf62452c - 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
2026-10-23 17:56:42 +02:00

186 lines
8.3 KiB
C++

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#pragma once
#include <QPainterPath>
#include "JFJochImage.h"
#include "../../reader/JFJochReaderImage.h"
#include "../../common/ROIDefinition.h"
class ROIAzimuthal;
class DiffractionGeometry;
class JFJochDiffractionImage : public JFJochImage {
Q_OBJECT
QColor spot_color = Qt::green;
QColor prediction_color = Qt::darkRed;
QColor ice_ring_color = Qt::cyan;
QColor second_lattice_color = QColor(0xFA, 0x72, 0x68); // coral, the viewer "finishing" accent
// With outlining on, spot markers are drawn twice: a black pen this much wider underneath,
// then the marker on top. The hues mean something - cyan is the colour of ice, magenta is
// the one colour no colour map contains - so none of them moves to gain contrast. The casing
// carries the marker where the colour map's low end is light, the bright core carries it
// where it is dark, so one mechanism covers both without branching on the colour map. It is
// opt-in (default off): the doubled stroke makes the markers harder to read for some users.
// Predictions are left alone: darkRed is already legible on a light map and a black casing
// does nothing for it on a dark one.
static constexpr int MARKER_CASING_EXTRA_WIDTH = 4;
float hover_resolution = NAN;
// The "d = ... A" readout is painted in drawForeground() in viewport pixels rather than kept
// as a scene item, so updating it dirties only its own rect. hover_text_rect_ is where it
// currently sits, in viewport coordinates.
QRect hover_text_rect_;
[[nodiscard]] QString HoverResolutionLabel() const;
// Counts are exact integers: label them from the int32 image rather than from a float copy,
// which both avoids materialising that copy and cannot round large summed values.
[[nodiscard]] QString PixelLabel(int x, int y) const override;
// This is the view that has detector counts, so it is the one that offers an ROI
[[nodiscard]] bool AllowROI() const override { return true; }
void drawForeground(QPainter *painter, const QRectF &rect) override;
// The readout sits at a fixed viewport position, but QGraphicsView scrolls by blitting the
// viewport, which carries the painted text along with it - so its old and new places both have
// to be repainted when the view pans.
void scrollContentsBy(int dx, int dy) override;
public:
enum class RingMode {Auto, Estimation, Manual, None, IceRings};
Q_ENUM(RingMode)
JFJochDiffractionImage(QWidget *parent = nullptr);
private:
void addCustomOverlay() override;
void LoadImageInternal();
// Colour straight from the int32 detector image; no float copy of it is ever built
void ColorRow(size_t y, const PixelColorMap &map, QRgb *out) const override;
void DrawResolutionRings();
void DrawROIs();
void DrawAzimuthalROI(const ROIAzimuthal &az, const QColor &color, const DiffractionGeometry &geom);
void AddROILabel(const std::string &name, const QColor &color, float px, float py);
// Interactive editing of the selected (named) ROI: move box/circle for now.
bool roiEditPress(const QPointF &scenePos) override;
void roiEditMove(const QPointF &scenePos) override;
void roiEditRelease() override;
void roiScratchDrawn() override;
void keyPressEvent(QKeyEvent *event) override; // Delete removes the selected ROI
[[nodiscard]] ROIDefinition BuildEditedROIDefinition() const; // current ROIs with the edit applied
[[nodiscard]] ResizeHandle hitTestBoxHandle(const QRectF &r, const QPointF &p, qreal tol) const;
// Grab points for an azimuthal ROI: inner/outer arc (resize Q/d) and the two phi
// edges (rotate). The phi handles are only meaningful for a sector (HasPhi()).
void azimuthalHandles(const ROIAzimuthal &az, const DiffractionGeometry &geom,
QPointF &inner, QPointF &outer, QPointF &phimin, QPointF &phimax) const;
QString selected_roi_;
enum class RoiEdit { None, MoveBox, ResizeBox, MoveCircle, ResizeCircle,
AzimInner, AzimOuter, RotatePhiMin, RotatePhiMax };
RoiEdit roi_edit_ = RoiEdit::None;
ResizeHandle box_handle_ = ResizeHandle::None;
QString edit_name_;
QRectF edit_box_;
QPointF edit_center_;
double edit_radius_ = 0;
float edit_d_min_ = 0, edit_d_max_ = 0, edit_phi_min_ = 0, edit_phi_max_ = 0; // azimuthal edit state
bool edit_has_phi_ = false;
QPointF move_last_;
bool live_pending_ = false; // a live edit is being recomputed; throttles emissions
void DrawSpots();
void DrawPredictions();
void DrawBeamCenter();
void DrawTopPixels();
void DrawSaturation();
void DrawResolutionText();
void DrawCross(float x, float y, float size, float width, float z = 1);
void UpdateForeground();
// The foreground the current image suggests: the top of the valid range in HDR mode, the
// auto-contrast value otherwise. Empty when there is no image to take it from.
[[nodiscard]] std::optional<float> AutoForegroundValue() const;
void ResetBackground();
bool one_shot_auto_ = false; // `A` applied the auto value; pressing it again makes Auto permanent
void leaveEvent(QEvent *event) override;
std::shared_ptr<const JFJochReaderImage> image;
// What is shown: the image itself for a flat detector, else the image gathered onto the detector
// plane (AssembleToPlane), whose top-left pixel sits at origin_. The scene is the detector plane
// either way, so spots, predictions, rings and ROIs are drawn where the geometry puts them.
std::shared_ptr<const std::vector<int32_t>> pixels_;
// Scene position of a pixel of the stored image (index into image->Image()); empty in a gap.
[[nodiscard]] std::optional<QPointF> StoredPixelToScene(int64_t index) const;
int32_t show_highest_pixels = 0;
QVector<float> res_ring = {};
// Constant-d contours traced for res_ring, kept across overlay rebuilds; see DrawResolutionRings
QVector<float> ring_cache_key_ = {};
QVector<std::pair<float, QPainterPath>> ring_cache_ = {};
RingMode ring_mode = RingMode::Estimation;
bool show_spots = false;
bool show_predictions = false;
bool show_roi_labels = false;
bool show_roi_fill = false;
bool highlight_ice_rings = true;
bool hide_unindexed_spots = false;
bool hide_ice_ring_spots = false;
bool outline_spots = false; // black casing under spot markers, see MARKER_CASING_EXTRA_WIDTH
void mouseHover(const QPointF &scenePos, Qt::KeyboardModifiers modifiers) override;
// The magnifier follows the cursor only while Shift is held, and meanwhile a frame here
// shows the area it covers. magnifier_frame_ is empty while the frame is hidden.
QSizeF magnifier_field_;
QRectF magnifier_frame_;
void SetMagnifierFrame(const QRectF &r);
signals:
void magnifierMoved(QPointF scenePos); // in pixels of the shown image, as the magnifier has them
void pixelsChanged(std::shared_ptr<const std::vector<int32_t>> pixels); // the shown image changed
void roiGeometryEdited(ROIDefinition rois);
void roiSelected(QString name); // user picked an ROI by clicking it on the image
public slots:
void setSelectedROI(QString name);
void loadImage(std::shared_ptr<const JFJochReaderImage> image);
void setAutoForeground(bool input);
// Apply the auto-contrast value once, leaving Auto as it was; pressing it a second time on the
// same image switches Auto on for good (which keeps recomputing it on every subsequent image).
void oneShotAutoForeground();
void setResolutionRing(QVector<float> v);
void setResolutionRingMode(RingMode mode);
void showSpots(bool input);
void showPredictions(bool input);
void showROILabels(bool input);
void showROIFill(bool input);
void setSpotColor(QColor input);
void setPredictionColor(QColor input);
void showHighestPixels(int32_t v);
void showSaturation(bool input);
void showBeamStop(bool input);
void highlightIceRings(bool input);
void hideUnindexedSpots(bool input);
void hideIceRingSpots(bool input);
void outlineSpots(bool input);
void setHDRMode(bool input);
void setMagnifierField(QSizeF size);
void hideMagnifierFrame();
};