Files
Jungfraujoch/viewer/image_viewer/JFJochFollowerImage.cpp
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

143 lines
5.1 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochFollowerImage.h"
#include "JFJochImage.h"
#include "../../common/ColorScale.h"
#include <algorithm>
#include <cmath>
#include <QGraphicsScene>
#include <QPainter>
#include <QWheelEvent>
// Same wording as the main view's per-pixel labels
static QString PixelValueText(int32_t value) {
if (value == GAP_PXL_VALUE)
return QStringLiteral("Gap");
if (value == ERROR_PXL_VALUE)
return QStringLiteral("Err");
if (value == BEAM_STOP_PXL_VALUE)
return QStringLiteral("Stop");
if (value == SATURATED_PXL_VALUE)
return QStringLiteral("Sat");
return QString::number(value);
}
JFJochFollowerImage::JFJochFollowerImage(QWidget *parent) : QGraphicsView(parent) {
setScene(new QGraphicsScene(this));
setTransformationAnchor(QGraphicsView::AnchorViewCenter);
setHorizontalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
setVerticalScrollBarPolicy(Qt::ScrollBarAlwaysOff);
setTransform(QTransform::fromScale(zoom_, zoom_));
}
void JFJochFollowerImage::SetFrame(std::shared_ptr<const QImage> frame) {
const bool same_pointer = (frame_ == frame);
frame_ = std::move(frame);
if (!frame_ || frame_->isNull()) {
scene()->clear();
item_ = nullptr;
return;
}
// The producer reuses one buffer, so normally only the pixels changed and the item stays.
if (!item_ || !same_pointer) {
scene()->clear();
item_ = new JFJochImageItem(frame_);
scene()->addItem(item_);
}
// The producer reassigns its buffer in place when the frame size changes, so the pointer says
// nothing about the dimensions - compare against the size we last saw.
if (frame_->size() != frame_size_) {
frame_size_ = frame_->size();
item_->refresh();
scene()->setSceneRect(0, 0, frame_size_.width(), frame_size_.height());
// Until the user has pointed somewhere, show the middle rather than the top-left corner
centerOn(center_set_ ? center_ : scene()->sceneRect().center());
}
viewport()->update();
}
void JFJochFollowerImage::SetPixelValues(std::shared_ptr<const std::vector<int32_t>> pixels) {
values_ = std::move(pixels);
}
void JFJochFollowerImage::CenterAt(QPointF scenePos) {
center_ = scenePos;
center_set_ = true;
if (!frame_ || frame_->isNull())
return;
centerOn(scenePos);
}
void JFJochFollowerImage::SetZoom(double zoom, int label_font_px) {
const QPointF center = mapToScene(viewport()->rect().center());
zoom_ = zoom;
label_font_px_ = label_font_px;
setTransform(QTransform::fromScale(zoom_, zoom_));
centerOn(center);
emit fieldChanged(QSizeF(viewport()->width() / zoom_, viewport()->height() / zoom_));
}
void JFJochFollowerImage::wheelEvent(QWheelEvent *event) {
// Zoom comes in fixed levels; let the wheel scroll the panel the view sits in instead
event->ignore();
}
void JFJochFollowerImage::resizeEvent(QResizeEvent *event) {
QGraphicsView::resizeEvent(event);
if (center_set_)
centerOn(center_);
emit fieldChanged(QSizeF(viewport()->width() / zoom_, viewport()->height() / zoom_));
}
void JFJochFollowerImage::drawForeground(QPainter *painter, const QRectF &rect) {
QGraphicsView::drawForeground(painter, rect);
if (label_font_px_ == 0 || !values_ || !frame_ || frame_->isNull())
return;
const int W = frame_->width();
const int H = frame_->height();
const auto &pixels = *values_;
if (static_cast<int64_t>(pixels.size()) < static_cast<int64_t>(W) * H)
return; // values belong to a different frame
// Clipped to the exposed area, for the same reason as JFJochImage::drawPixelLabels.
const QRectF visible = mapToScene(viewport()->rect()).boundingRect() & rect;
const int x0 = std::max(0, static_cast<int>(std::floor(visible.left())));
const int x1 = std::min(W, static_cast<int>(std::ceil(visible.right())));
const int y0 = std::max(0, static_cast<int>(std::floor(visible.top())));
const int y1 = std::min(H, static_cast<int>(std::ceil(visible.bottom())));
if (x1 <= x0 || y1 <= y0 || (x1 - x0) * (y1 - y0) > kMaxLabels)
return;
// Lay the text out in viewport pixels so it stays a constant, readable size
painter->save();
painter->resetTransform();
QFont font("DejaVu Sans Mono");
font.setStyleHint(QFont::TypeWriter);
font.setPixelSize(label_font_px_);
painter->setFont(font);
for (int y = y0; y < y1; y++) {
for (int x = x0; x < x1; x++) {
const QRect cell = mapFromScene(QRectF(x, y, 1, 1)).boundingRect();
const QRgb c = frame_->pixel(x, y);
const rgb col{.r = static_cast<uint8_t>(qRed(c)),
.g = static_cast<uint8_t>(qGreen(c)),
.b = static_cast<uint8_t>(qBlue(c))};
painter->setPen(luminance(col) > 128.0 ? Qt::black : Qt::white);
painter->drawText(cell, Qt::AlignCenter, PixelValueText(pixels[y * W + x]));
}
}
painter->restore();
}