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v1.0.0-rc.181 (#92)
* Rugnux: Several rotation sweeps of one crystal are merged as one dataset (`rugnux a_master.h5 b_master.h5`), on a common indexing and cell, with a non-isomorphous sweep left out and reported; `--sweeps separate` processes each sweep on its own. Bruker `.sfrm` frames and imgCIF files with a full goniometer axis chain are read.
* Rugnux: More robust rotation processing - a retry with a more sensitive spot finder when no lattice is found, a self-consistent detector distance, long axes and doubled cells tested as hypotheses, a `-C` supercell multiple stepped down, and each ice ring merged, down-weighted or rejected on its own.
* Rugnux: Serial stills are merged with a partiality-aware error model, reported as `ERROR_MODEL_A/B/C` with no ISa or R_merge/R_meas/R_pim; runs without `-S` have an overall intensity scale about 0.86-0.88 times that of earlier versions, with unchanged statistics. A second crystal form is left out of the merge and reported, the indexing ambiguity is resolved more reliably, and `--model` no longer influences processing.
* Rugnux: The reported CC1/2 is the standard unweighted one, which can be lower than before on sweeps with weak frames; ISa comes with a 95% interval (`ISA_LOW`/`ISA_HIGH`).
* Rugnux: Model refinement adds anisotropic/TLS, local NCS and twin refinement where R-free supports them; building waters and relabelling ions is now off by default (`--refine-solvent` turns it on).
* NXmx: A detector of several modules is written as `module_0` ... `module_N` only, so DIALS reads each module as its own panel.
* Other: JPEG previews use a bundled encoder (libjpeg-turbo no longer needed), Rugnux prints how to cite it, and the release archives contain the HTML documentation.

Reviewed-on: #92
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
2026-11-02 12:05:20 +01:00

180 lines
5.9 KiB
C++

// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include "JFJochGridScanImage.h"
#include <QGraphicsItem>
JFJochGridScanImage::JFJochGridScanImage(QWidget *parent) : JFJochImage(parent) {}
void JFJochGridScanImage::clear() {
W = 0;
H = 0;
this->settings = std::nullopt;
if (scene())
scene()->clear();
resetScenePointers();
}
void JFJochGridScanImage::loadData(const std::vector<float> &data, const GridScanSettings &settings, bool in_one_over_d2) {
if (data.empty()) {
clear();
return;
}
this->settings = settings;
W = settings.GetGridSizeX_step();
H = settings.GetGridSizeY_step();
// Draw a cell in the proportion of the area it covers, so a scan with a coarse x step and a
// fine y step looks like the sample region it was taken over, not like a square grid.
pixel_aspect_ = std::fabs(settings.GetGridStepY_um() / settings.GetGridStepX_um());
image_fp = settings.Rearrange(data, NAN);
std::vector<int64_t> indices(image_fp.size());
std::iota(indices.begin(), indices.end(), 0);
image_index = settings.Rearrange(indices, -1);
one_over_d2 = in_one_over_d2;
if (one_over_d2) {
for (int i = 0; i < image_fp.size(); i++)
if (!std::isnan(image_fp[i]))
image_fp[i] = 1.0f / (image_fp[i] * image_fp[i]);
}
float minv = std::numeric_limits<float>::infinity();
float maxv = -std::numeric_limits<float>::infinity();
for (float v : image_fp) {
if (std::isfinite(v)) {
if (v < minv) minv = v;
if (v > maxv) maxv = v;
}
}
if (!std::isfinite(minv) || !std::isfinite(maxv)) {
minv = 0.0f;
maxv = 1.0f;
}
if (!(maxv > minv)) {
maxv = minv + 1.0f;
}
background = minv;
foreground = maxv;
RenderImage();
Redraw();
}
void JFJochGridScanImage::mouseHover(const QPointF &pt, Qt::KeyboardModifiers modifiers) {
// Map mouse position to image pixel if inside bounds
if (W == 0 || H == 0 || image_index.empty())
return;
// Convert view coordinates to image pixel by truncation
int x = static_cast<int>(pt.x());
int y = static_cast<int>(pt.y());
if (x < 0 || x >= W || y < 0 || y >= H)
return;
int idx = y * W + x;
if (idx < 0 || idx >= static_cast<int>(image_index.size()))
return;
int64_t image_id = image_index[idx];
if (image_id >= 0) {
if (modifiers & Qt::ShiftModifier)
emit imageSelected(image_id);
if (one_over_d2) {
if (std::isnan(image_fp[idx]))
emit writeStatusBar(QString("Image %1 x %2 y %3 no resolution estimation")
.arg(image_id)
.arg(x)
.arg(y),
6000);
else
emit writeStatusBar(QString("Image %1 x %2 y %3 d = %4 Å")
.arg(image_id)
.arg(x)
.arg(y)
.arg(QString::number(1 / std::sqrt(image_fp[idx]), 'f', 2)),
6000);
} else {
emit writeStatusBar(QString("Image %1 x %2 y %3 value %4")
.arg(image_id)
.arg(x)
.arg(y)
.arg(QString::number(image_fp[idx], 'f', 3)),
6000);
}
}
}
void JFJochGridScanImage::loadImage(QMouseEvent *event) {
// Map mouse position to image pixel if inside bounds
if (W == 0 || H == 0 || image_index.empty())
return;
const QPointF pt = mapToScene(event->pos());
// Convert view coordinates to image pixel by truncation
int x = static_cast<int>(pt.x());
int y = static_cast<int>(pt.y());
if (x < 0 || x >= W || y < 0 || y >= H)
return;
int idx = y * W + x;
if (idx < 0 || idx >= static_cast<int>(image_index.size()))
return;
int64_t image_id = image_index[idx];
if (image_id >= 0)
emit imageSelected(image_id);
}
void JFJochGridScanImage::mouseDoubleClickEvent(QMouseEvent *event) {
// Map mouse position to image pixel if inside bounds
if (W == 0 || H == 0 || image_index.empty())
return;
const QPointF pt = mapToScene(event->pos());
// Convert view coordinates to image pixel by truncation
int x = static_cast<int>(pt.x());
int y = static_cast<int>(pt.y());
if (x < 0 || x >= W || y < 0 || y >= H)
return;
int idx = y * W + x;
if (idx < 0 || idx >= static_cast<int>(image_index.size()))
return;
int64_t image_id = image_index[idx];
if (image_id >= 0)
emit imageSelected(image_id);
JFJochImage::mouseDoubleClickEvent(event);
}
void JFJochGridScanImage::setImage(int64_t val) {
// The image can lie outside the grid: live, the broker's image and dataset are fetched apart and
// can belong to different collections, and a re-emitted image can meet a newer dataset's grid.
// Such an image has no cell to mark (GetElementPos*_step would throw on the GUI thread).
if (settings && val >= 0 && val < settings->GetNElem()) {
current_image_W = settings->GetElementPosX_step(val);
current_image_H = settings->GetElementPosY_step(val);
} else {
current_image_W = -1;
current_image_H = -1;
}
Redraw();
}
void JFJochGridScanImage::addCustomOverlay() {
if (current_image_W < 0 || current_image_H < 0 || current_image_W >= W || current_image_H >= H)
return;
QPen pen(feature_color, 3);
pen.setCosmetic(true);
auto *rect = scene()->addRect(current_image_W, current_image_H, 1, 1, pen);
addOverlayItem(rect);
}