Files
Jungfraujoch/receiver/RugnuxLiveStatus.cpp
T
leonarski_f baec34685d Rugnux live: the uploaded model is refined after placement; refined scores, model, maps and blobs in the status, the viewer and the hero
The live run refines a placed model as `rugnux` does (ProcessConfig::refine), after every decision
and before the end message; a cut before it starts leaves it out, as the model. The writer still
gets the placed model; the refined one stays with the broker.

API (broker/jfjoch_api.yaml):
- rugnux_live_model.refinement (rugnux_live_refinement): performed, reason, on_gpu, seconds, r_work,
  r_free, rmsd_bonds_A, rmsd_angles_deg, blob_count, blobs (at most 50, rugnux_live_blob: kind, x, y,
  z, peak_sigma, volume_A3, nearest_atom, nearest_atom_distance_A)
- rugnux_live_status.refined_model
- /rugnux/model.cif and /rugnux/map.ccp4 take stage=placed|refined, by default the refined model
  where there is one; the anomalous map stays on the placed model's phases (the refined
  coefficients carry none).
Regenerated broker/gen, frontend/src/client, redoc, and the python client docs (which also brings
the hero fields and rugnux_live_model it was missing).

Frontend: the model card keeps its green/red and gets "R-free 0.xx (refined)" as its context line,
"refining..." while the step runs; the model section adds refined R-free and blob tiles; Mol*
shows the refined model and maps, with the blobs as small spheres coloured by reading (switch, off
at first). The Refinement step is in the timeline like any other.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 3b47fb9a53b7dfad1c1ed289e169094c8d3d9d3e)
2026-10-26 01:38:25 +01:00

155 lines
4.9 KiB
C++

// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "RugnuxLiveStatus.h"
double RugnuxLiveStatus::Since(std::chrono::steady_clock::time_point t) const {
return std::chrono::duration<double>(t - start).count();
}
double RugnuxLiveStatus::Now() const {
return Since(std::chrono::steady_clock::now());
}
void RugnuxLiveStatus::CloseStep() {
if (!s.steps.empty() && !s.steps.back().duration_s)
s.steps.back().duration_s = Now() - s.steps.back().started_s;
}
void RugnuxLiveStatus::Start(int64_t images_expected, std::optional<double> expected_collection_s,
std::chrono::steady_clock::time_point start_received) {
std::unique_lock ul(m);
s = RugnuxLiveSnapshot{};
s.state = RugnuxLiveState::Running;
s.images_expected = images_expected;
s.expected_collection_s = expected_collection_s;
start = start_received;
last_image.reset();
}
void RugnuxLiveStatus::ImageReceived(std::chrono::steady_clock::time_point received) {
std::unique_lock ul(m);
++s.images_received;
// Several forward threads report, so the images need not come here in the order they arrived.
const double t = Since(received);
if (!s.start_to_first_image_s || t < s.start_to_first_image_s.value())
s.start_to_first_image_s = t;
if (!last_image || received > last_image.value())
last_image = received;
}
void RugnuxLiveStatus::Step(const std::string &title) {
std::unique_lock ul(m);
CloseStep();
s.steps.push_back(RugnuxLiveStep{.title = title, .started_s = Now()});
s.step_progress.reset();
}
void RugnuxLiveStatus::Note(const std::string &text) {
std::unique_lock ul(m);
if (s.steps.empty())
s.steps.push_back(RugnuxLiveStep{.title = "", .started_s = Now()});
s.steps.back().notes.push_back(text);
}
void RugnuxLiveStatus::Progress(uint64_t done, uint64_t total) {
std::unique_lock ul(m);
if (total > 0)
s.step_progress = static_cast<float>(done) / static_cast<float>(total);
}
void RugnuxLiveStatus::Finish(RugnuxLiveState state, const std::string &message) {
std::unique_lock ul(m);
CloseStep();
s.elapsed_s = Now();
s.state = state;
s.message = message;
s.step_progress.reset();
}
void RugnuxLiveStatus::Result(const std::string &verdict, const std::string &verdict_text,
const std::vector<std::pair<std::string, std::string>> &summary,
const std::vector<std::string> &warnings, bool anomalous_signal) {
std::unique_lock ul(m);
s.verdict = verdict;
s.verdict_text = verdict_text;
s.summary = summary;
s.warnings = warnings;
s.anomalous_signal = anomalous_signal;
}
void RugnuxLiveStatus::Model(const RugnuxLiveModel &model) {
std::unique_lock ul(m);
s.model = model;
}
void RugnuxLiveStatus::Headline(const std::string &space_group, std::optional<double> d_min,
std::optional<double> isa) {
std::unique_lock ul(m);
s.space_group = space_group;
s.d_min = d_min;
s.isa = isa;
}
void RugnuxLiveStatus::Latency(double last_image_to_written_s) {
std::unique_lock ul(m);
s.last_image_to_written_s = last_image_to_written_s;
}
std::optional<std::chrono::steady_clock::time_point> RugnuxLiveStatus::LastImage() {
std::unique_lock ul(m);
if (last_image)
s.last_image_s = Since(last_image.value());
return last_image;
}
void RugnuxLiveStatus::Cut(const std::string &reason) {
std::unique_lock ul(m);
s.cut = reason;
s.cut_s = Now();
}
void RugnuxLiveStatus::Probe(const std::string &text) {
std::unique_lock ul(m);
s.probe = text;
s.probe_s = Now();
}
void RugnuxLiveStatus::Warning(const std::string &text) {
std::unique_lock ul(m);
s.warnings.push_back(text);
}
void RugnuxLiveStatus::Structure(std::shared_ptr<const RugnuxStructure> structure,
std::shared_ptr<const RugnuxStructure> refined_structure) {
std::unique_lock ul(m);
s.structure = std::move(structure);
s.refined_structure = std::move(refined_structure);
}
void RugnuxLiveStatus::Clear() {
std::unique_lock ul(m);
s = RugnuxLiveSnapshot{};
last_image.reset();
}
RugnuxLiveSnapshot RugnuxLiveStatus::Get() const {
std::unique_lock ul(m);
RugnuxLiveSnapshot ret = s;
if (s.state == RugnuxLiveState::Running)
ret.elapsed_s = Now();
// Held since START, reported since the first image - or, before it has come, since now.
const double zero = s.start_to_first_image_s.value_or(s.state == RugnuxLiveState::Running ? ret.elapsed_s : 0.0);
ret.elapsed_s -= zero;
for (auto &step: ret.steps)
step.started_s -= zero;
if (ret.probe_s)
*ret.probe_s -= zero;
if (ret.last_image_s)
*ret.last_image_s -= zero;
if (ret.cut_s)
*ret.cut_s -= zero;
return ret;
}