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Jungfraujoch/viewer/widgets/JFJochViewerImageStatistics.cpp
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leonarski_fandClaude Fable 5.1 7f884f67c7 Per-dataset bearer tokens in the broker; viewer token, model option, grid-scan plot, dark theme, tutorial 
jfjoch_broker: /start takes an optional `tokens` list (any number, all equivalent; writeOnly in the
API). While the current dataset has any, the endpoints that expose it - /statistics/data_collection,
/result/scan, /image_buffer/{start.cbor,image.cbor,image.jpeg,image.tiff}, /preview/plot{,.bin} -
answer 401 unless the request carries `Authorization: Bearer <token>`; /statistics keeps serving
the instrument view and only omits its `measurement` block. Enforcement is one pre-routing hook
over a named path set (the same set carries `bearerAuth` in jfjoch_api.yaml); tokens are compared
in constant time and never read back or logged. The tokens are replaced only by an accepted start,
and atomically with clearing the previous run's status, plots and image buffer, in this order:
clear, swap, import the new settings - so no moment serves the old run under the new tokens or the
new run's name under the old ones. Settings are validated on a copy first so a refused start
changes nothing.

jfjoch_viewer: a Token field (password echo) next to the http/https scheme in Open HTTP Connection,
JUNGFRAUJOCH_HTTP_TOKEN, and D-Bus LoadFile(..., token) / SetHttpToken; the dialog overrides the
others, nothing is persisted. A 401 clears the display, stops following and puts a line on the
status bar - no dialog, since a dataset changing hands is the normal cause.

Web frontend: key button in the top bar (token in sessionStorage, applied to the bearerAuth
operations by the generated client, and to the raw preview fetch), a tokens field in the start
form, and a "token required" hint on the plots. Python client: Configuration(access_token=...)
after regeneration.

Viewer: reference dataset accepts a structure-factor mmCIF (already read by content; the dialog
now offers it) and a model file can be chosen next to it (ProcessConfig::model_path, as
rugnux --model); the job also carries the reference's free-R flags, cell and setting, and the
copied command line states -z / --reference-column / --model. A grid scan keeps its own preferred
dataset-info plot and "Spots + background" means the spot count there. Dark theme: the navy hero
buttons, checked segments, warning texts and chart guide lines follow the theme instead of their
light-theme colours.

Docs: SECURITY.md section 3 is now the implemented scheme; a guided tour with four screenshots
in JFJOCH_VIEWER.md; broker, OpenAPI, Python client and frontend pages mention the token.

Tests: BearerTokens unit test and an HTTP round trip over the real broker HTTP layer (jfjoch_test
now compiles JFJochBrokerHttp.cpp and links httplib).

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
2026-09-27 10:30:06 +02:00

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// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochViewerImageStatistics.h"
#include "../ViewerTheme.h"
#include "../../common/time_utc.h"
#include <QFormLayout>
#include <QRegularExpression>
// Two aligned rows - the lengths over their angles, so that alpha sits below a, beta below b,
// gamma below c. Qt's rich text does not inherit a surrounding colour into a table, so the
// colour is applied per cell.
static QString mkUnitCell(const UnitCell &uc, const char *color = nullptr) {
const QString style = color ? QString(" style=\"color: %1;\"").arg(color) : QString();
auto num = [&style](double v) {
// Padded to three integer digits with figure spaces (digit-wide), so the columns hold
// still as values change magnitude; no axis reaches 1000 Å and no angle 1000°.
QString s = QString::number(v, 'f', 1);
while (s.size() < 5)
s.prepend(QChar(0x2007));
return QString("<td align=\"right\"%1><b>%2</b>&nbsp;&nbsp;</td>")
.arg(style).arg(s);
};
auto unit = [&style](const char *u) {
return QString("<td%1>%2</td>").arg(style).arg(u);
};
return "<table cellspacing=\"0\" cellpadding=\"0\"><tr>"
+ num(uc.a) + num(uc.b) + num(uc.c) + unit("Å")
+ "</tr><tr>"
+ num(uc.alpha) + num(uc.beta) + num(uc.gamma) + unit("°")
+ "</tr></table>";
}
static QString mkSourceInstrumentText(const DiffractionExperiment& exp) {
QString src, inst;
const auto &m = exp.GetInstrumentMetadata();
if (!m.GetSourceName().empty()) src = QString::fromStdString(m.GetSourceName());
if (!m.GetInstrumentName().empty()) inst = QString::fromStdString(m.GetInstrumentName());
if (!src.isEmpty() && !inst.isEmpty()) return src + " / " + inst;
if (!src.isEmpty()) return src;
if (!inst.isEmpty()) return inst;
return QString("-");
}
static QString mkSourceInstrumentTooltip(const DiffractionExperiment &exp) {
QStringList tooltips;
if (exp.GetRingCurrent_mA().has_value()) {
tooltips << QString("Ring current: <b>%1</b> mA").arg(exp.GetRingCurrent_mA().value(), 0, 'f', 2);
}
if (exp.GetTotalFlux().has_value()) {
tooltips << QString("Total flux: <b>%1</b> ph/s").arg(exp.GetTotalFlux().value(), 0, 'e', 2);
}
if (exp.GetAttenuatorTransmission().has_value()) {
tooltips << QString("Attenuation: <b>%1</b>").arg(exp.GetAttenuatorTransmission().value(), 0, 'f', 3);
}
return tooltips.join("<br/>");
}
static QString mkSampleText(const DiffractionExperiment& exp) {
const auto& name = exp.GetSampleName();
return name.empty() ? QString("-") : QString::fromStdString(name);
}
static QString mkSampleTooltip(const DiffractionExperiment& exp) {
if (exp.GetSampleTemperature_K().has_value()) {
return QString("Sample temperature: <b>%1</b> K").arg(exp.GetSampleTemperature_K().value(), 0, 'f', 2);
}
return QString();
}
static QString mkSymmetry(const LatticeMessage& sym) {
QString text("Bravais lattice: <b>");
switch (sym.crystal_system) {
case gemmi::CrystalSystem::Triclinic:
text += "a";
break;
case gemmi::CrystalSystem::Monoclinic:
text += "m";
break;
case gemmi::CrystalSystem::Orthorhombic:
text += "o";
break;
case gemmi::CrystalSystem::Tetragonal:
text += "t";
break;
case gemmi::CrystalSystem::Hexagonal:
text += "h";
break;
case gemmi::CrystalSystem::Cubic:
text += "c";
break;
default: ;
}
text += QString(sym.centering) + "</b><br/>";
text += QString("Niggli class <b>%1</b><br/>").arg(sym.niggli_class);
return text;
}
JFJochViewerImageStatistics::JFJochViewerImageStatistics(QWidget *parent) : QWidget(parent) {
QFormLayout* layout = new QFormLayout(this);
// Order: what the dataset is, then how it was collected, then what this image contains.
// A dataset name is long and wraps: keep three lines of room from the start, so the rows below
// do not jump as one dataset's name wraps further than the next one's.
dataset_name = new QLabel(this);
dataset_name->setWordWrap(true);
dataset_name->setAlignment(Qt::AlignTop | Qt::AlignLeft);
dataset_name->setMinimumHeight(3 * fontMetrics().lineSpacing());
auto *dataset_name_label = new QLabel("Dataset:");
dataset_name_label->setAlignment(Qt::AlignTop | Qt::AlignLeft);
layout->addRow(dataset_name_label, dataset_name);
collection_time = new QLabel(this);
collection_time->setWordWrap(true);
layout->addRow(new QLabel("Collection time:"), collection_time);
source_name = new QLabel(this);
layout->addRow("Source / Instrument:", source_name);
sample_name = new QLabel(this);
layout->addRow("Sample:", sample_name);
detector_name = new QLabel(this);
layout->addRow(new QLabel("Detector:"), detector_name);
detector_distance = new QLabel(this);
layout->addRow(new QLabel("Detector distance:"), detector_distance);
beam_center = new QLabel(this);
layout->addRow(new QLabel("Beam center:"), beam_center);
wavelength = new QLabel(this);
layout->addRow(new QLabel("Wavelength:"), wavelength);
exposure_time = new QLabel(this);
layout->addRow(new QLabel("Exposure Time:"), exposure_time);
rotation_angle_label = new QLabel(this);
rotation_angle = new QLabel(this);
layout->addRow(rotation_angle_label, rotation_angle);
// Sample-head angles that do not move during a run (an SLS Smargon writes chi and phi). Both
// labels stay empty for a file that carries none, so the row costs nothing where it means nothing.
smargon_label = new QLabel(this);
smargon_angles = new QLabel(this);
layout->addRow(smargon_label, smargon_angles);
valid_values = new QLabel(this);
layout->addRow(new QLabel("Valid values:"), valid_values);
masked_pixels = new QLabel(this);
layout->addRow(new QLabel("Masked pixels:"), masked_pixels);
spots = new QLabel(this);
layout->addRow(new QLabel("Spots:"), spots);
bkg_estimate = new QLabel(this);
layout->addRow(new QLabel("Background:"), bkg_estimate);
indexed = new QLabel(this);
layout->addRow(new QLabel("Indexing:"), indexed);
multiple_lattices = new QLabel(this);
layout->addRow(multiple_lattices);
res_estimate = new QLabel(this);
layout->addRow(new QLabel("Resolution estimate:"), res_estimate);
profile_radius_label = new QLabel("");
profile_radius = new QLabel(this);
layout->addRow(profile_radius_label, profile_radius);
}
QString TrimZeros(double number, int precision) {
auto s = QString::number(number, 'f', precision);
s.remove(QRegularExpression("\\.?0+$"));
if (s.isEmpty()) s = "0";
return s;
}
template <typename Duration>
QString FormatTime(Duration time, int precision = 6) {
return TrimZeros(std::chrono::duration<float>(time).count(), precision);
}
void JFJochViewerImageStatistics::loadImage(std::shared_ptr<const JFJochReaderImage> image) {
if (!image) {
source_name->setText("");
sample_name->setText("");
dataset_name->setText("");
collection_time->setText("");
detector_name->setText("");
detector_name->setToolTip("");
detector_distance->setText("");
beam_center->setText("");
wavelength->setText("");
wavelength->setToolTip("");
exposure_time->setText("");
exposure_time->setToolTip("");
rotation_angle->setText("");
rotation_angle->setToolTip("");
rotation_angle_label->setText("");
smargon_label->setText("");
smargon_angles->setText("");
valid_values->setText("");
valid_values->setToolTip("");
spots->setText("");
bkg_estimate->setText("");
indexed->setText("");
indexed->setToolTip("");
multiple_lattices->setText("");
profile_radius_label->setText("");
profile_radius->setText("");
profile_radius->setToolTip("");
res_estimate->setText("");
masked_pixels->setText("");
masked_pixels->setToolTip("");
return;
}
QString text;
auto &exp = image->Dataset().experiment;
// Word wrap never breaks inside a word, and a dataset name is one long word. A zero-width space
// is a break opportunity the wrap takes only when it needs one, so marking "/" first, then "_",
// then every few characters of a run with neither, wraps at a path separator where one fits, at
// an underscore next, and mid-name only for a component too long to fit a line at all.
const QChar zwsp(0x200B);
QString path;
int run = 0; // characters since the last break opportunity
for (const QChar c: QString::fromStdString(exp.GetFilePrefix())) {
path.append(c);
if (c == '/' || c == '_') {
path.append(zwsp);
run = 0;
} else if (++run >= 12) {
path.append(zwsp);
run = 0;
}
}
text = QString("<b>%1</b>").arg(path);
dataset_name->setText(text);
const QString collected = QString::fromStdString(utc_to_local_human_readable(image->Dataset().arm_date));
collection_time->setText(collected.isEmpty() ? QString("-") : QString("<b>%1</b>").arg(collected));
detector_distance->setText(QString("<b>%1</b> mm").arg(QString::number(exp.GetDetectorDistance_mm(), 'f', 3)));
beam_center->setText(QString("<b>%1</b> <b>%2</b> pxl")
.arg(QString::number(exp.GetBeamX_pxl(), 'f', 2))
.arg(QString::number(exp.GetBeamY_pxl(), 'f', 2)));
wavelength->setText(QString("<b>%1</b> Å").arg(QString::number(exp.GetWavelength_A(), 'f', 4)));
wavelength->setToolTip(QString("Energy: <b>%1</b> eV")
.arg(QString::number(exp.GetIncidentEnergy_keV() * 1000.0, 'f', 0)));
text = QString("<b>%1</b>").arg(QString::fromStdString(exp.GetDetectorDescription()));
detector_name->setToolTip(QString("Width: <b>%1</b> pxl (<b>%2</b> mm)<br/>Height: <b>%3</b> pxl (<b>%4</b> mm)<br/>Pixel size: <b>%5</b> μm")
.arg(QString::number(exp.GetXPixelsNum()))
.arg(QString::number(exp.GetXPixelsNum() * exp.GetPixelSize_mm(), 'f', 3))
.arg(QString::number(exp.GetYPixelsNum()))
.arg(QString::number(exp.GetYPixelsNum() * exp.GetPixelSize_mm(), 'f', 3))
.arg(QString::number(exp.GetPixelSize_mm() * 1000.0, 'f', 0)));
detector_name->setText(text);
source_name->setText(QString("<b>%1</b>").arg(mkSourceInstrumentText(exp)));
source_name->setToolTip(mkSourceInstrumentTooltip(exp));
sample_name->setText(QString("<b>%1</b>").arg(mkSampleText(exp)));
sample_name->setToolTip(mkSampleTooltip(exp));
if (exp.GetGoniometer()) {
// An axis that is present but does not turn has no wedge to add: state the angle it stands at.
const float wedge = exp.GetGoniometer()->GetWedge_deg();
const QString angle = TrimZeros(exp.GetGoniometer()->GetAngle_deg(image->ImageData().number), 3);
rotation_angle_label->setText("Goniometer angle:");
rotation_angle->setText(wedge == 0.0f
? QString("<b>%1°</b>").arg(angle)
: QString("<b>%1° + %2°</b>").arg(angle).arg(TrimZeros(wedge, 3)));
rotation_angle->setToolTip(QString("Start angle: <b>%1°</b><br/>Increment: <b>%2°</b>")
.arg(TrimZeros(exp.GetGoniometer()->GetStart_deg(), 3))
.arg(TrimZeros(exp.GetGoniometer()->GetIncrement_deg(), 3))
);
} else if (exp.GetGridScan()) {
rotation_angle_label->setText("Grid scan:");
rotation_angle->setText(QString("<b>%1</b> x <b>%2</b> μm")
.arg(QString::number(exp.GetGridScan()->GetGridStepX_um(), 'f', 1))
.arg(QString::number(exp.GetGridScan()->GetGridStepY_um(), 'f', 1)));
rotation_angle->setToolTip(QString("Grid size: <b>%1</b> x <b>%2</b> μm<br/>"
"Grid elements: <b>%3</b> x <b>%4</b>")
.arg(QString::number(exp.GetGridScan()->GetGridSizeX_um()))
.arg(QString::number(exp.GetGridScan()->GetGridSizeY_um()))
.arg(QString::number(exp.GetGridScan()->GetGridSizeX_step()))
.arg(QString::number(exp.GetGridScan()->GetGridSizeY_step())));
} else {
rotation_angle_label->setText("");
rotation_angle->setText(QString(""));
rotation_angle->setToolTip("");
}
if (const auto head = exp.GetDatasetSettings().GetSmargonPosition()) {
// One decimal, and an angle that rounds to zero reads "0.0" - a stage that sits a hundredth
// of a degree below zero should not be reported as "-0.0".
auto head_angle = [](float deg) {
return QString::number(std::abs(deg) < 0.05f ? 0.0f : deg, 'f', 1);
};
smargon_label->setText("Smargon:");
smargon_angles->setText(QString("chi <b>%1</b>° / phi <b>%2</b>°")
.arg(head_angle(head->chi_deg))
.arg(head_angle(head->phi_deg)));
} else {
smargon_label->setText("");
smargon_angles->setText("");
}
exposure_time->setText(QString("<b>%1</b> s").arg(FormatTime(exp.GetImageTime())));
exposure_time->setToolTip(QString("Count time: <b>%1</b> s<br/>").arg(FormatTime(exp.GetImageCountTime())));
text = QString("<b>%1</b>").arg(image->ImageData().spots.size());
spots->setText(text);
if (image->ImageData().spot_count.has_value())
spots->setToolTip(QString("Unfiltered (total): <b>%1</b> <br/>Low resolution: <b>%2</b><br/>Ice ring: <b>%3</b><br/>Indexed <b>%4</b><br/>")
.arg(image->ImageData().spot_count.value())
.arg(image->ImageData().spot_count_low_res.value_or(0))
.arg(image->ImageData().spot_count_ice_rings.value_or(0))
.arg(image->ImageData().spot_count_indexed.value_or(0)));
auto mm = image->ValidMinMax();
if (mm.has_value()) {
text = QString("<b>%1</b> - <b>%2</b>")
.arg(mm->first)
.arg(mm->second);
valid_values->setText(text);
} else {
valid_values->setText("N/A");
}
valid_values->setToolTip(QString("Error pixels: <b>%1</b><br/>Saturated pixels: <b>%2</b>")
.arg(image->ErrorPixels().size()).arg(image->SaturatedPixels().size()));
if (!image->Dataset().bkg_estimate.empty()) {
text = QString("<b>%1</b>").arg(image->ImageData().bkg_estimate.value_or(0));
bkg_estimate->setText(text);
} else {
bkg_estimate->setText("N/A");
}
auto pr = image->ImageData().profile_radius;
auto mos = image->ImageData().mosaicity_deg;
if (mos && std::isfinite(mos.value())) {
text = QString("<b>%1</b>°").arg(QString::number(mos.value(), 'f', 2));
profile_radius_label->setText("Mosaicity:");
profile_radius->setText(text);
if (pr && std::isfinite(pr.value())) {
text = QString("Profile radius <b>%1</b> Å<sup>-1</sup>").arg(QString::number(pr.value(), 'f', 6));
profile_radius->setToolTip(text);
} else
profile_radius->setToolTip("");
} else if (pr && std::isfinite(pr.value())) {
profile_radius_label->setText("Profile radius:");
text = QString("<b>%1</b> Å<sup>-1</sup>").arg(QString::number(pr.value(), 'f', 6));
profile_radius->setText(text);
profile_radius->setToolTip("");
} else {
profile_radius_label->setText("");
profile_radius->setText("");
profile_radius->setToolTip("");
}
auto res = image->ImageData().resolution_estimate;
if (res && std::isfinite(res.value())) {
text = QString("<b>%1</b> Å").arg(QString::number(res.value(), 'f', 2));
res_estimate->setText(text);
} else {
res_estimate->setText("N/A");
}
float total_pixels = image->Dataset().experiment.GetPixelsNum();
if (total_pixels == 0)
total_pixels = 1;
auto mask_stats = image->Dataset().pixel_mask->GetStatistics();
text = QString("<b>%1</b>").arg(mask_stats.total_masked);
masked_pixels->setText(text);
masked_pixels->setToolTip(
QString(
"Error pixels: <b>%1</b> (%2 %)<br/> Noisy pixels: <b>%3</b> (%4 %) <br/> User mask: <b>%5</b> (%6 %)<br/>"
"Chip gaps: <b>%7</b> (%8 %)<br/>"
"Non active area (module gap and fill): <b>%9</b> (%10 %)")
.arg(mask_stats.error_pixel).arg(QString::number(mask_stats.error_pixel / total_pixels * 100.0, 'f', 1))
.arg(mask_stats.noisy_pixel).arg(QString::number(mask_stats.noisy_pixel / total_pixels * 100.0, 'f', 1))
.arg(mask_stats.user_mask).arg(QString::number(mask_stats.user_mask / total_pixels * 100.0, 'f', 1))
.arg(mask_stats.chip_gap_pixel).arg(QString::number(mask_stats.chip_gap_pixel / total_pixels * 100.0, 'f', 1))
.arg(mask_stats.module_gap_pixel).arg(QString::number(mask_stats.module_gap_pixel / total_pixels * 100.0, 'f', 1))
);
if (!image->Dataset().indexing_result.empty()) {
QString tooltip;
auto latt = image->ImageData().indexing_lattice;
if (latt) {
text = mkUnitCell(latt->GetUnitCell(), DarkTheme() ? "violet" : "purple");
auto vec0 = latt->Vec0();
auto vec1 = latt->Vec1();
auto vec2 = latt->Vec2();
tooltip = QString("<b>Lattice vectors (Å):</b><br/>"
"a = (%1, %2, %3)<br/>"
"b = (%4, %5, %6)<br/>"
"c = (%7, %8, %9)")
.arg(vec0.x, 7, 'f', 1)
.arg(vec0.y, 7, 'f', 1)
.arg(vec0.z, 7, 'f', 1)
.arg(vec1.x, 7, 'f', 1)
.arg(vec1.y, 7, 'f', 1)
.arg(vec1.z, 7, 'f', 1)
.arg(vec2.x, 7, 'f', 1)
.arg(vec2.y, 7, 'f', 1)
.arg(vec2.z, 7, 'f', 1);
if (image->ImageData().lattice_type) {
tooltip += QString("<br/><br/>");
tooltip += mkSymmetry(*image->ImageData().lattice_type);
} else if (image->Dataset().experiment.GetSpaceGroupNumber()) {
tooltip += QString("<br/><br/>Space group (user-provided): <b>%1</b>")
.arg(QString::fromStdString(image->Dataset().experiment.GetSpaceGroupName()));
}
} else
// Not indexed is a normal state, not an error - grey, so red keeps meaning trouble.
text = QString("<span style=\"color: gray;\">No lattice</span>");
indexed->setToolTip(tooltip);
indexed->setText(text);
} else {
indexed->setText("N/A");
}
if (image->ImageData().indexing_lattice_count.value_or(0) > 1)
multiple_lattices->setText(QString("<span style=\"color: %1;\"><b>Multiple lattices detected</b></span>")
.arg(AlertTextColor().name()));
else
multiple_lattices->setText("");
}
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