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