One changeset, developed together in response to a review of this branch, so the files carry several of the changes at once. Full test suite passes (733 cases). Spot finding - Split ImageSpotFinder into Detect() (flag strong pixels - the expensive per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with Run() = both. The per-image min-pix escalation now detects ONCE and repeats only the cheap extraction, instead of re-running the whole finder four times per frame as it did on the default path. It also keeps the winning attempt's spot list rather than re-extracting it, so the frame that is integrated is exactly the frame that was scored - which a GPU re-extract could not guarantee (float atomic ordering). - spot_finding_time_s no longer swallows indexing time, and indexing_time_s now sums every escalation call instead of reporting only the last. Detection limits follow the detector - The azimuthal-integration upper q and the spot-finding high-resolution limit are now std::optional, in the C++ structs AND in the OpenAPI schema, and resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_ recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a pixel outside that q range could never be strong - the integration range silently bounded what detection could see, regardless of the requested resolution limit. Regenerated the C++ and TypeScript clients; the viewer and the web frontend each gained a "to detector edge" switch. Detection defaults are now per workflow (measured, not assumed) - Stills: adaptive detection, min-pix chosen per image, no resolution clipping. - Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit. On a 33-crystal rotation battery, adaptive detection helped four hard crystals but deterministically broke three (a lost space group, a halved indexing rate, a collapsed merge), and the detector-edge limit cost indexing on a strong rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and --no-adaptive-spots is new. Indexer seed escalation - Stop escalating once a seed's lattice explains >= 90% of the seed spots. Previously any frame with >= 80 spots always paid three indexer calls, online broker included. Merge-consistency filter - --min-image-cc gated on a per-image CC computed BEFORE the stills partiality post-refinement and never refreshed; the refiner now recomputes it, so the reported CC describes the data that are actually merged. - Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the merge, the error model and MergeStats can no longer disagree about which images are in (the --scale path merged unfiltered while its statistics were filtered). Per-image B-factor refinement (-B) removed - Measured on four serial-stills datasets: it is a no-op where the per-image fit is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on 14-25% of images). It had also been silently DISCARDED since the partiality post-refinement landed - reported but not applied. Rather than fix and keep a knob with no demonstrated benefit, the flag and the whole image_scale_b_factor chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs. ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS. (The Wilson per-image b_factor is a different quantity and stays.) Stills partiality width now fits both of its components - sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d* with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2 on d*^2. The angular-only width is fitted over a d*^2-dense population, so it was pinned by the high-resolution edge and collapsed at low d*: median partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55% of them under the merge's partiality floor, and the survivors divided by those values - which inflated the merged low-resolution intensity scale 3.6x (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x, no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining R-free are all blind to that ramp, which is why it survived earlier validation; the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged). Removed dead code from add-then-remove churn - Prediction-time "still partiality" (unreachable: no setter), the phantom IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the constant it always was), StillsPartialityRefine's caller-less Settings constructor and its reference to a long-gone env var, ProcessImage's unread bool return, an unused include, and a dead viewer overlay hook. Also - Viewer: the magnifier compared a QImage with itself, so its scene rect was set once ever and it could not pan into a larger dataset; the hover tail timer could fire after leaveEvent and resurrect the resolution readout outside the image. - update_version.sh regenerated the frontend lock file BEFORE bumping the version (every release shipped an off-by-one lock), and did git rm/git add on a path that has not existed since the client moved to src/client - with no set -e, both failed silently. - fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a redirect, not a test, so dkms add never ran. - Unit tests for the adaptive-threshold host functions, which had none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
212 lines
7.6 KiB
C++
212 lines
7.6 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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#include "JFJochViewerImageListWindow.h"
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#include <QVBoxLayout>
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#include <QHeaderView>
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#include <QCloseEvent>
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namespace {
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constexpr int ScaleSortRole = Qt::UserRole + 1;
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constexpr double ScaleNotAvailableSortValue = -1.0e100;
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}
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JFJochViewerImageListWindow::JFJochViewerImageListWindow(QWidget *parent) : JFJochHelperWindow(parent) {
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QWidget *centralWidget = new QWidget(this);
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setCentralWidget(centralWidget);
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QVBoxLayout *layout = new QVBoxLayout(centralWidget);
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tableView = new QTableView(this);
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tableModel = new QStandardItemModel(this);
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setupTableModel();
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proxyModel = new QSortFilterProxyModel(this);
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proxyModel->setSourceModel(tableModel);
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proxyModel->setSortRole(ScaleSortRole);
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tableView->setModel(proxyModel);
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tableView->sortByColumn(0, Qt::AscendingOrder);
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tableView->setEditTriggers(QAbstractItemView::NoEditTriggers);
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tableView->setSortingEnabled(true);
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tableView->verticalHeader()->setVisible(false);
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tableView->horizontalHeader()->setSectionsClickable(true);
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tableView->horizontalHeader()->setSortIndicatorShown(true);
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tableView->setSelectionBehavior(QAbstractItemView::SelectRows);
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tableView->setSelectionMode(QAbstractItemView::SingleSelection);
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tableView->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
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layout->addWidget(tableView);
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setWindowTitle("Image statistics");
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resize(800, 600);
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connect(tableView, &QTableView::doubleClicked, this, &JFJochViewerImageListWindow::onTableRowDoubleClicked);
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}
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void JFJochViewerImageListWindow::setupTableModel()
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{
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tableModel->setColumnCount(8);
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tableModel->setHeaderData(0, Qt::Horizontal, "#");
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tableModel->setHeaderData(1, Qt::Horizontal, "Bkg");
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tableModel->setHeaderData(2, Qt::Horizontal, "Index");
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tableModel->setHeaderData(3, Qt::Horizontal, "Spots");
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tableModel->setHeaderData(4, Qt::Horizontal, "Res. [A]");
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tableModel->setHeaderData(5, Qt::Horizontal, "Max val");
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tableModel->setHeaderData(6, Qt::Horizontal, "Scale factor");
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tableModel->setHeaderData(7, Qt::Horizontal, "Scale CC");
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}
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void JFJochViewerImageListWindow::addDataRow(int imageNumber, double backgroundEstimate,
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const QString& indexingResult,
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int spotCount,
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double resolutionEstimate,
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int64_t max_value,
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double image_scale_factor,
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double image_scale_cc_percent) {
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QList<QStandardItem*> rowItems;
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QStandardItem *imageItem = new QStandardItem();
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imageItem->setData(imageNumber, Qt::DisplayRole);
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imageItem->setData(imageNumber, ScaleSortRole);
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rowItems.append(imageItem);
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QStandardItem *bgItem = new QStandardItem();
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bgItem->setData(backgroundEstimate, Qt::DisplayRole);
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bgItem->setData(backgroundEstimate, ScaleSortRole);
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rowItems.append(bgItem);
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QStandardItem *indexingItem = new QStandardItem(indexingResult);
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if (indexingResult == "Yes")
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indexingItem->setData(1, ScaleSortRole);
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else if (indexingResult == "No")
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indexingItem->setData(0, ScaleSortRole);
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else
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indexingItem->setData(-1, ScaleSortRole);
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rowItems.append(indexingItem);
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QStandardItem *spotItem = new QStandardItem();
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spotItem->setData(spotCount, Qt::DisplayRole);
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spotItem->setData(spotCount, ScaleSortRole);
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rowItems.append(spotItem);
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QStandardItem *resolutionItem = new QStandardItem();
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resolutionItem->setData(QString::number(resolutionEstimate, 'f', 2), Qt::DisplayRole);
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resolutionItem->setData(resolutionEstimate, ScaleSortRole);
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rowItems.append(resolutionItem);
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QStandardItem *maxValueItem = new QStandardItem();
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maxValueItem->setData(static_cast<int32_t>(max_value), Qt::DisplayRole);
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maxValueItem->setData(static_cast<int32_t>(max_value), ScaleSortRole);
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rowItems.append(maxValueItem);
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QStandardItem *scaleFactorItem = new QStandardItem();
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if (std::isfinite(image_scale_factor)) {
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scaleFactorItem->setData(image_scale_factor, Qt::DisplayRole);
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scaleFactorItem->setData(image_scale_factor, ScaleSortRole);
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} else {
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scaleFactorItem->setData("N/A", Qt::DisplayRole);
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scaleFactorItem->setData(ScaleNotAvailableSortValue, ScaleSortRole);
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}
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rowItems.append(scaleFactorItem);
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QStandardItem *scaleCCItem = new QStandardItem();
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if (std::isfinite(image_scale_cc_percent)) {
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scaleCCItem->setData(QString::number(image_scale_cc_percent, 'f', 1) + "%", Qt::DisplayRole);
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scaleCCItem->setData(image_scale_cc_percent, ScaleSortRole);
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} else {
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scaleCCItem->setData("N/A", Qt::DisplayRole);
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scaleCCItem->setData(ScaleNotAvailableSortValue, ScaleSortRole);
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}
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rowItems.append(scaleCCItem);
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tableModel->appendRow(rowItems);
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}
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void JFJochViewerImageListWindow::clearAllData() {
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tableModel->removeRows(0, tableModel->rowCount());
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}
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void JFJochViewerImageListWindow::datasetLoaded(std::shared_ptr<const JFJochReaderDataset> dataset) {
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clearAllData();
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if (!dataset)
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return;
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for (int i = 0; i < dataset->experiment.GetImageNum(); i++) {
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float bkg_estimate = 0;
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if (dataset->bkg_estimate.size() > i)
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bkg_estimate = dataset->bkg_estimate[i];
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int32_t spot_count = 0;
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if (dataset->spot_count.size() > i)
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spot_count = dataset->spot_count[i];
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float res_estimation = 0.0f;
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if (dataset->resolution_estimate.size() > i)
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res_estimation = dataset->resolution_estimate[i];
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QString indexing_result = "N/A";
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if (dataset->indexing_result.size() > i) {
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if (dataset->indexing_result[i] == 0)
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indexing_result = "No";
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else
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indexing_result = "Yes";
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}
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int64_t max_value = 0;
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if (dataset->max_value.size() > i)
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max_value = dataset->max_value[i];
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double image_scale_factor = NAN;
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if (dataset->image_scale_factor.size() > i)
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image_scale_factor = dataset->image_scale_factor[i];
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double image_scale_cc_percent = NAN;
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if (dataset->image_scale_cc.size() > i)
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image_scale_cc_percent = dataset->image_scale_cc[i] * 100.0;
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addDataRow(i + 1,
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bkg_estimate,
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indexing_result,
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spot_count,
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res_estimation,
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max_value,
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image_scale_factor,
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image_scale_cc_percent);
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}
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}
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void JFJochViewerImageListWindow::imageLoaded(std::shared_ptr<const JFJochReaderImage> image) {
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int curr_row = -1;
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if (image)
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curr_row = image->ImageData().number;
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for (int row = 0; row < tableModel->rowCount(); row++) {
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for (int col = 0; col < tableModel->columnCount(); ++col) {
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QStandardItem *item = tableModel->item(row, col);
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if (item) {
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if (row == curr_row)
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item->setBackground(Qt::blue);
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else
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item->setBackground(Qt::white);
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}
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}
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}
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}
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void JFJochViewerImageListWindow::onTableRowDoubleClicked(const QModelIndex &index) {
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if (!index.isValid())
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return;
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QModelIndex sourceIndex = proxyModel->mapToSource(index);
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int imageNumber = tableModel->item(sourceIndex.row(), 0)->data(Qt::DisplayRole).toInt();
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emit imageSelected(imageNumber - 1, 1);
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}
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