leonarski_fandClaude Opus 5
99123f33df
The L-test now divides each intensity by its resolution-shell mean before forming pairs, over the shells whose <I/sigma> reaches 1 (the floor the second moment already used). Two index steps are not the same resolution, and on a small cell with a steep fall-off the raw pairs read <|L|> up to 0.08 high: an untwinned crystal 0.568 and a partial twin 0.427 where phenix.xtriage reads 0.486 and 0.360. Normalised, the four reference merges (6toc, 6iu9, 5j23, a lysozyme) agree with xtriage within 0.02 (0.487, 0.376, 0.374, 0.480). Selection stays by shell, never by the reflection's own I/sigma, which biases <|L|> down. Equal-count shells were tried for the second moment and widen its gap to xtriage, so the shells are kept. The L-test is no longer switched off in holohedral Laue classes. Merging I(h) with I(Th) under a false operator gives (I(h)+I(Th))/2 for every twin fraction, the perfect-twin distribution, so <|L|> < 0.42 there is reported as an adopted operator averaging unequal intensities (promotion suspect, or a twin law absorbed into the point group) - a warning, not a veto. Over 42 holohedral merges of the corpus the genuine ones read 0.436-0.513, the over-promoted H3 twin 0.374, and one ~490 A-axis crystal 0.365. The verdict is one line (TwinningVerdictLine) used by the stats text, the report prose, the summary row, the warning and the viewer; a new TWINNING_VERDICT key names it. The twin fraction comes from the statistic that carries the verdict (the L-test unless the call rests on the second moment alone), is not quoted from a second moment under a detected pseudo-translation, and is not quoted at all on a merge under a suspect operator. The pre-search numbers (measured on the P1 search merge) are user-visible, are measured with that merge's own pseudo-translation declared, and leave out the reflections the lattice centring extinguishes - an R lattice in its hexagonal cell otherwise pairs present with absent reflections (5j23: 0.633 with them, 0.40 without). Report-only: no space-group decision, merge or intensity changes. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
400 lines
18 KiB
C++
400 lines
18 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 "JFJochMergeStatsWindow.h"
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#include <cmath>
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#include <limits>
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#include <QButtonGroup>
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#include <QComboBox>
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#include <QFontDatabase>
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#include <QFrame>
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#include <QHBoxLayout>
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#include <QPlainTextEdit>
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#include <QHeaderView>
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#include <QLabel>
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#include <QStackedWidget>
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#include <QStringList>
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#include <QTableWidget>
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#include <QToolButton>
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#include <QVBoxLayout>
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#include <QtCharts/QChart>
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#include <QtCharts/QChartView>
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#include <QtCharts/QLineSeries>
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#include <QtCharts/QLogValueAxis>
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#include <QtCharts/QScatterSeries>
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#include <QtCharts/QValueAxis>
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#include "../charts/JFJochSimpleChartView.h"
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#include "../widgets/ToolbarIcons.h"
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namespace {
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// Per-shell metric value (NaN -> dropped by the chart). Keep in sync with the combo entries.
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double ShellMetric(const MergeStatisticsShell &s, int metric) {
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switch (metric) {
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case 0: return s.cc_half * 100.0; // CC1/2 (%)
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case 1: return s.r_meas * 100.0; // R-meas (%)
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case 2: return s.mean_i_over_sigma; // <I/sigma>
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case 3: return s.possible_unique_reflections > 0 // Completeness (%)
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? 100.0 * s.unique_reflections / s.possible_unique_reflections : NAN;
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case 4: return s.unique_reflections > 0 // Multiplicity
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? static_cast<double>(s.total_observations) / s.unique_reflections : NAN;
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case 5: return s.cc_ref * 100.0; // CCref (%)
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default: return NAN;
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}
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}
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// A big-number "card" for the hero row: large navy value over a small grey caption.
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QWidget *MakeCard(const QString &value, const QString &caption, QWidget *parent) {
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auto *card = new QFrame(parent);
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card->setFrameShape(QFrame::StyledPanel);
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auto *l = new QVBoxLayout(card);
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l->setContentsMargins(12, 8, 12, 8);
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l->setSpacing(0);
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auto *v = new QLabel(value, card);
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QFont f = v->font();
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f.setPointSizeF(f.pointSizeF() * 2.2);
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f.setBold(true);
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v->setFont(f);
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v->setStyleSheet("color: #1F3A5F;");
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v->setAlignment(Qt::AlignCenter);
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auto *c = new QLabel(caption, card);
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c->setStyleSheet("color: gray;");
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c->setAlignment(Qt::AlignCenter);
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l->addWidget(v);
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l->addWidget(c);
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return card;
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}
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}
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JFJochMergeStatsWindow::JFJochMergeStatsWindow(const QString &title, const MergeStatistics &stats,
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double isa, bool has_reference,
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const TwinningAnalysisResult &twinning,
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const std::optional<gemmi::SpaceGroup> &space_group,
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const std::optional<SearchSpaceGroupResult> &space_group_search,
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const std::vector<std::pair<float, float>> &merged_i_sigma,
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const QString &report,
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QWidget *parent)
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: QWidget(parent, Qt::Window), stats_(stats), has_reference_(has_reference) {
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setWindowTitle("Merge statistics — " + title);
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setAttribute(Qt::WA_DeleteOnClose);
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resize(740, 560);
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auto *layout = new QVBoxLayout(this);
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// --- Hero row: overall numbers ---
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const auto &o = stats_.overall;
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const double completeness = o.possible_unique_reflections > 0
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? 100.0 * o.unique_reflections / o.possible_unique_reflections : NAN;
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const double multiplicity = o.unique_reflections > 0
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? static_cast<double>(o.total_observations) / o.unique_reflections : NAN;
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auto pct = [](double v) { return std::isfinite(v) ? QString::number(v, 'f', 1) + "%" : QStringLiteral("—"); };
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auto num = [](double v, int d) { return std::isfinite(v) ? QString::number(v, 'f', d) : QStringLiteral("—"); };
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auto *hero = new QHBoxLayout();
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// High-resolution limit of the merge (d_min). When no scaling resolution limit is given it is set
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// by the CC1/2 logistic cutoff, so it varies per run - show it first.
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if (o.d_min < o.d_max)
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hero->addWidget(MakeCard(QString::asprintf("%.2f", o.d_min), "Resolution [Å]", this));
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hero->addWidget(MakeCard(num(isa, 1), "ISa", this));
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hero->addWidget(MakeCard(pct(o.cc_half * 100.0), "CC½", this));
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hero->addWidget(MakeCard(pct(o.r_meas * 100.0), "R-meas", this));
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hero->addWidget(MakeCard(pct(completeness), "Completeness", this));
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hero->addWidget(MakeCard(num(multiplicity, 1), "Multiplicity", this));
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// Wilson B describes how fast the intensities fall off with resolution; the radiation-damage
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// Delta-B is how much MORE they fall off by the end of the run than at the start (rotation only).
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if (std::isfinite(stats_.wilson_b))
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hero->addWidget(MakeCard(num(stats_.wilson_b, 1), "Wilson B [Ų]", this));
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if (std::isfinite(stats_.radiation_damage_delta_b)) {
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const double db = stats_.radiation_damage_delta_b;
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hero->addWidget(MakeCard((db > 0 ? "+" : "") + num(db, 1), "ΔB, damage [Ų]", this));
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}
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if (has_reference_)
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hero->addWidget(MakeCard(pct(o.cc_ref * 100.0), "CCref", this));
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if (space_group.has_value())
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hero->addWidget(MakeCard(QString::fromStdString(space_group->short_name()), "Space group", this));
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layout->addLayout(hero);
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// De-novo space-group search: the point group + the ranked candidates it scored (only present when
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// the space group was not fixed by the user). A summary line above a compact table.
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if (space_group_search.has_value() && !space_group_search->candidates.empty()) {
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const auto &sgs = *space_group_search;
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QString summary = "Point group " + QString::fromStdString(sgs.point_group_hm.empty() ? "?" : sgs.point_group_hm);
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if (!sgs.alternatives.empty()) {
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QStringList alts;
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for (const auto &alt : sgs.alternatives)
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alts << QString::fromStdString(alt.short_name());
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summary += " · indistinguishable from these data: " + alts.join(", ");
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}
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auto *sgLabel = new QLabel(summary, this);
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sgLabel->setStyleSheet("color: gray;");
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layout->addWidget(sgLabel);
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auto *sgTable = new QTableWidget(this);
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sgTable->setEditTriggers(QAbstractItemView::NoEditTriggers);
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sgTable->verticalHeader()->setVisible(false);
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const QStringList sgHeaders{"Space group", "Absent", "Viol.", "⟨I/σ⟩ abs", "⟨I/σ⟩ pres", "Consistent"};
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sgTable->setColumnCount(sgHeaders.size());
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sgTable->setHorizontalHeaderLabels(sgHeaders);
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sgTable->setRowCount(static_cast<int>(sgs.candidates.size()));
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for (int i = 0; i < static_cast<int>(sgs.candidates.size()); ++i) {
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const auto &c = sgs.candidates[i];
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int col = 0;
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auto set = [&](const QString &t, bool leftAlign = false) {
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auto *it = new QTableWidgetItem(t);
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it->setTextAlignment((leftAlign ? Qt::AlignLeft : Qt::AlignRight) | Qt::AlignVCenter);
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if (c.selected) { QFont f = it->font(); f.setBold(true); it->setFont(f); }
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sgTable->setItem(i, col++, it);
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};
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set(QString::fromStdString(c.space_group.short_name()) + (c.selected ? " *" : ""), true);
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set(QString::number(c.absent_observed));
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set(QString::number(c.absent_violations));
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set(QString::number(c.absent_mean_i_over_sigma, 'f', 2));
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set(QString::number(c.present_mean_i_over_sigma, 'f', 2));
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set(c.consistent ? QStringLiteral("yes") : QStringLiteral("no"));
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}
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sgTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
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sgTable->setMaximumHeight(160); // a secondary detail — keep the shells plot the focus
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layout->addWidget(sgTable);
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}
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// --- Twinning test (Padilla-Yeates L-test + second moment) ---
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// A red-outlined banner flags suspected twinning; otherwise a quiet grey "all clear".
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if (twinning.l_test_pairs > 0) {
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QString text = QString("Twinning: ⟨|L|⟩ = %1 ⟨I²⟩/⟨I⟩² = %2")
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.arg(twinning.mean_abs_l, 0, 'f', 3)
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.arg(twinning.second_moment, 0, 'f', 2);
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text += " — " + QString::fromStdString(TwinningVerdictLine(twinning));
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auto *banner = new QLabel(text, this);
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banner->setContentsMargins(10, 6, 10, 6);
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if (twinning.twinning_suspected)
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banner->setStyleSheet("color: rgb(160,0,0); border: 1px solid red; border-radius: 4px;");
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else
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banner->setStyleSheet("color: gray;");
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layout->addWidget(banner);
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}
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// --- Controls: plot/table view toggle (icon buttons) + per-resolution metric selector ---
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auto *row = new QHBoxLayout();
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auto *plotBtn = new QToolButton(this);
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plotBtn->setIcon(ToolbarIcons::linePlot());
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plotBtn->setCheckable(true);
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plotBtn->setChecked(true);
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plotBtn->setToolTip("Per-resolution plot");
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plotBtn->setStyleSheet(ToolbarIcons::buttonStyle());
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auto *tableBtn = new QToolButton(this);
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tableBtn->setIcon(ToolbarIcons::table());
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tableBtn->setCheckable(true);
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tableBtn->setToolTip("Per-shell table");
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tableBtn->setStyleSheet(ToolbarIcons::buttonStyle());
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auto *isaBtn = new QToolButton(this);
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isaBtn->setIcon(ToolbarIcons::linePlot());
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isaBtn->setCheckable(true);
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isaBtn->setToolTip("ISa diagnostic: merged I/σ against I");
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isaBtn->setStyleSheet(ToolbarIcons::buttonStyle());
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auto *reportBtn = new QToolButton(this);
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reportBtn->setText("Report");
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reportBtn->setCheckable(true);
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reportBtn->setToolTip("The rugnux result report, as written to <prefix>_report.txt");
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reportBtn->setStyleSheet(ToolbarIcons::buttonStyle());
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auto *viewGroup = new QButtonGroup(this);
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viewGroup->setExclusive(true);
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viewGroup->addButton(plotBtn, 0);
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viewGroup->addButton(tableBtn, 1);
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viewGroup->addButton(isaBtn, 2);
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viewGroup->addButton(reportBtn, 3);
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row->addWidget(plotBtn);
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row->addWidget(tableBtn);
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row->addWidget(isaBtn);
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row->addWidget(reportBtn);
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row->addSpacing(12);
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metricLabel_ = new QLabel("Metric:", this);
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row->addWidget(metricLabel_);
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metric_ = new QComboBox(this);
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metric_->addItem("CC½ (%)", 0);
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metric_->addItem("R-meas (%)", 1);
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metric_->addItem("⟨I/σ⟩", 2);
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metric_->addItem("Completeness (%)", 3);
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metric_->addItem("Multiplicity", 4);
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if (has_reference_)
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metric_->addItem("CCref (%)", 5);
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row->addWidget(metric_);
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row->addStretch();
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layout->addLayout(row);
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// --- Stacked plot / table ---
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stack_ = new QStackedWidget(this);
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chart_ = new JFJochSimpleChartView(this);
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table_ = new QTableWidget(this);
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table_->setEditTriggers(QAbstractItemView::NoEditTriggers);
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table_->verticalHeader()->setVisible(false);
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stack_->addWidget(chart_); // page 0
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stack_->addWidget(table_); // page 1
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isa_page_ = buildIsaDiagnostic(merged_i_sigma, isa);
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if (isa_page_)
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stack_->addWidget(isa_page_); // page 2
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else
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isaBtn->setEnabled(false);
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// The report is prose and fixed-width tables meant to be read as written - a plain text view
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// in a fixed-width font, never wrapped.
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if (!report.isEmpty()) {
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auto *report_view = new QPlainTextEdit(this);
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report_view->setReadOnly(true);
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report_view->setLineWrapMode(QPlainTextEdit::NoWrap);
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report_view->setFont(QFontDatabase::systemFont(QFontDatabase::FixedFont));
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report_view->setPlainText(report);
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report_page_ = report_view;
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stack_->addWidget(report_page_);
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} else {
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reportBtn->setEnabled(false);
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}
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layout->addWidget(stack_, 1);
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connect(metric_, &QComboBox::currentIndexChanged, this, [this](int) { updatePlot(); });
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// Button ids map to page widgets, not stack indices: an absent page (no ISa scatter, no
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// report) would otherwise shift every page behind it.
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connect(viewGroup, &QButtonGroup::idClicked, this, [this](int idx) {
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QWidget *const pages[] = {chart_, table_, isa_page_, report_page_};
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if (idx >= 0 && idx < 4 && pages[idx])
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stack_->setCurrentWidget(pages[idx]);
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metric_->setVisible(idx == 0); // the metric selector + its label only apply to the plot
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metricLabel_->setVisible(idx == 0);
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});
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buildTable();
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updatePlot();
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}
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// Merged I/sigma against I. The error model says sigma -> b*I for strong reflections, so I/sigma
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// flattens off at 1/b = ISa: the plot shows whether the reported number is where the data actually
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// level out. Log intensity axis, because the reflections span several decades and the asymptote lives
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// at the strong end.
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QWidget *JFJochMergeStatsWindow::buildIsaDiagnostic(const std::vector<std::pair<float, float>> &i_sigma,
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double isa) {
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auto *points = new QScatterSeries();
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points->setName("merged reflections");
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points->setMarkerSize(4.0);
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points->setBorderColor(Qt::transparent);
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points->setColor(QColor(0x1F, 0x3A, 0x5F, 0x60));
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double i_lo = std::numeric_limits<double>::max(), i_hi = 0.0, r_hi = 0.0;
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for (const auto &[I, sigma] : i_sigma) {
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if (!(I > 0.0f) || !(sigma > 0.0f))
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continue; // the log axis cannot show a non-positive intensity
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const double ratio = I / sigma;
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points->append(I, ratio);
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i_lo = std::min(i_lo, static_cast<double>(I));
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i_hi = std::max(i_hi, static_cast<double>(I));
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r_hi = std::max(r_hi, ratio);
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}
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if (points->count() < 2 || !(i_hi > i_lo)) {
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delete points;
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return nullptr;
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}
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auto *chart = new QChart();
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chart->legend()->setVisible(false);
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chart->addSeries(points);
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auto *ax = new QLogValueAxis();
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ax->setBase(10.0);
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ax->setTitleText("merged I");
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ax->setRange(i_lo, i_hi);
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auto *ay = new QValueAxis();
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ay->setTitleText("merged I/σ");
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ay->setRange(0.0, std::max(r_hi, std::isfinite(isa) ? isa * 1.2 : 0.0) * 1.05);
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chart->addAxis(ax, Qt::AlignBottom);
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chart->addAxis(ay, Qt::AlignLeft);
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points->attachAxis(ax);
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points->attachAxis(ay);
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if (std::isfinite(isa) && isa > 0.0) {
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auto *line = new QLineSeries();
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line->append(i_lo, isa);
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line->append(i_hi, isa);
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QPen pen(QColor(0xC0, 0x39, 0x2B));
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pen.setStyle(Qt::DashLine);
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pen.setWidth(2);
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line->setPen(pen);
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chart->addSeries(line);
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line->attachAxis(ax);
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line->attachAxis(ay);
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}
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auto *view = new QChartView(chart, this);
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view->setRenderHint(QPainter::Antialiasing);
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view->setToolTip(std::isfinite(isa) && isa > 0.0
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? QString("Dashed line: reported ISa = %1. The strong reflections should level "
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"off there.").arg(isa, 0, 'f', 1)
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: QString("No ISa was determined for this merge."));
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return view;
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}
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void JFJochMergeStatsWindow::updatePlot() {
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const int metric = metric_->currentData().toInt();
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std::vector<float> x, y;
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double dmax = 0.0;
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x.reserve(stats_.shells.size());
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y.reserve(stats_.shells.size());
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for (const auto &s: stats_.shells) {
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x.push_back(s.mean_one_over_d2);
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const double v = ShellMetric(s, metric);
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y.push_back(static_cast<float>(v));
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if (std::isfinite(v))
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dmax = std::max(dmax, v);
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}
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// Absolute y-axis so positions are comparable: CC1/2 + CCref are 0..100, completeness 0..(>=100),
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// multiplicity / R-meas / I-sigma start at 0. It has to be given to UpdateData rather than set
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// on the axis afterwards, or the tick labels still describe the range of the data.
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double ymax = 1.0;
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switch (metric) {
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case 0: case 5: ymax = 100.0; break; // CC1/2, CCref
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case 3: ymax = std::max(100.0, dmax * 1.05); break; // Completeness
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default: ymax = dmax > 0.0 ? dmax * 1.05 : 1.0; break; // R-meas, I/sigma, multiplicity
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}
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chart_->UpdateData(x, y, "Resolution [Å]", metric_->currentText(), true,
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std::make_pair(0.0, ymax));
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}
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void JFJochMergeStatsWindow::buildTable() {
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QStringList headers{"Res. [Å]", "N_obs", "Unique", "Compl. %", "Mult.", "⟨I/σ⟩", "R-meas %", "CC½ %"};
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if (has_reference_)
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headers << "CCref %";
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table_->setColumnCount(headers.size());
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table_->setHorizontalHeaderLabels(headers);
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table_->setRowCount(static_cast<int>(stats_.shells.size()) + 1); // shells + overall
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auto fillRow = [&](int rowIdx, const MergeStatisticsShell &s, const QString &resLabel) {
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int c = 0;
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auto set = [&](const QString &t) {
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auto *it = new QTableWidgetItem(t);
|
||
it->setTextAlignment(Qt::AlignRight | Qt::AlignVCenter); // numbers right-aligned
|
||
table_->setItem(rowIdx, c++, it);
|
||
};
|
||
const double compl_ = s.possible_unique_reflections > 0
|
||
? 100.0 * s.unique_reflections / s.possible_unique_reflections : NAN;
|
||
const double mult = s.unique_reflections > 0
|
||
? static_cast<double>(s.total_observations) / s.unique_reflections : NAN;
|
||
set(resLabel);
|
||
set(QString::number(s.total_observations));
|
||
set(QString::number(s.unique_reflections));
|
||
set(std::isfinite(compl_) ? QString::number(compl_, 'f', 1) : QStringLiteral("—"));
|
||
set(std::isfinite(mult) ? QString::number(mult, 'f', 1) : QStringLiteral("—"));
|
||
set(QString::number(s.mean_i_over_sigma, 'f', 1));
|
||
set(QString::number(s.r_meas * 100.0, 'f', 1));
|
||
set(QString::number(s.cc_half * 100.0, 'f', 1));
|
||
if (has_reference_)
|
||
set(QString::number(s.cc_ref * 100.0, 'f', 1));
|
||
};
|
||
|
||
int rowIdx = 0;
|
||
for (const auto &s: stats_.shells)
|
||
fillRow(rowIdx++, s, QString::number(s.d_min, 'f', 2));
|
||
fillRow(rowIdx, stats_.overall, QStringLiteral("Overall"));
|
||
|
||
// Equal-width columns that fill the table (no super-wide last column).
|
||
table_->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
|
||
}
|