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Jungfraujoch/tests/ROIMapTest.cpp
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leonarski_fandClaude Opus 5.5 0a515bb086 rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG 
The rc178 branch continued after #88 was squash-merged; this is its content from b9ada7914 (the tree
#88 squashed) to 094eee31a, as one change on main. The individual commits stay on the rc178 branch:

- still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes
- AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets
- DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked
- tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout
- Dense per-pixel maps through the panel table (panel layout stage 1)
- Panel id on spots and the panel table in the start message
- Viewer and preview show a panel detector as it lies on the detector plane
- Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
- Panel layout stage 2: prediction and Bragg integration through the panel table
- XTC reader: frames handed up as stored, streams indexed in parallel
- XFEL reader: integer frames stay integer, one gain, placement by panel
- EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery"
- still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed
- float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count
- CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them
- Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table
- Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane
- still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good
- still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file
- still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition
- stills fixed cost: geometry refinement and pre-scan do the same work in less wall time
- stills geometry sample and trial spot finding run as many workers as the image pass
- Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame
- StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's
- MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in)
- Stills given a cell: the written cell is the mean over the frames that are merged
- Stills: the radial curvature correction decided per run on the same empty apertures
- StillsPartialityRefine: measure the run width only on shells with signal
- Stills pre-scan: report the paired z of the radial-correction comparison
- module placement: the five concurrent fits each keep every thread
- still battery: score R-free against the deposited data through the same dimple protocol
- still battery: the R-free target is the lower of the deposition's dimple and published values
- Stills: background clip follows the radial curve; signal disk from the lattice spacing
- Stills keep an overloaded observation as a lower bound instead of dropping it
- Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip
- battery: R-free against the deposition without refinement only, one protocol for rotation and stills
- still battery: EuXFEL sets run on a 2,000-image subset for now
- stills geometry refinement: fit the detector distance and the cell together
- stills geometry refinement: a distance given with --detector-distance is held in the joint fit
- Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count
- Metal integration test: the CPU comparison runs on a rotation experiment
- Stills: kept overloads go back to the drop where they are not concentrated at low resolution
- stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated
- battery results: XFEL still battery 20261022-1358 on rc178 0cf62452c - 12 sets, cold, R_free unrefined
- battery results: still summary gains the resolution of our merge and of the deposition
- Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value
- Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed
- XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock
- stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes
- rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid
- stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree
- CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get
- broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4)
- frontend: Mol* viewer of the placed model and its density on the Rugnux live page
- writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does
- rugnux live maps: one unit cell centred on the model; the viewer opens on all of it
- Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer
- Mol* viewer: open with the maps drawn within 10 A of the centre of view
- Mol* viewer: aaredb's structure-viewer setup, on a black stage
- rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons
- Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2)
- ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI)
- stills tilt decision: the modules stay where the run placed them
- still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it
- battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC
- Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons
- BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it
- ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization
- BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain
- ShadowFinder: measure the modulation robustly under a wide one-sided shadow
- ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation
- ShadowFinder: back to the predicted polarization factor, in the plane the background shows
- MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again
- battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables
- XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel
- stills geometry trial: the hypotheses a search asks are indexed side by side
- stills tilt decision: the fits start beside the pre-scan and the geometry trial
- XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache
- XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step
- GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block
- GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart
- docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts
- battery: doc_check.py cross-checks the manifests against the dataset pages
- stills module placement: the placement fit gets half the threads, each held-out fit an eighth
- still battery: the EuXFEL sets run on all their frames, as the published still runs did
- battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table
- macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
2026-10-23 17:56:42 +02:00

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// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only
#include <catch2/catch_all.hpp>
#include "../common/ROIMap.h"
#include "../common/DiffractionExperiment.h"
TEST_CASE("ROICircle", "[ROIMap]") {
std::unique_ptr<ROICircle> circle;
REQUIRE_THROWS(circle = std::make_unique<ROICircle>("roi1", 200,200,0));
REQUIRE_THROWS(circle = std::make_unique<ROICircle>("roi1", 200,200,-5.0));
REQUIRE_NOTHROW(circle = std::make_unique<ROICircle>("roi1", 200,220,2));
REQUIRE(circle->GetName() == "roi1");
REQUIRE(circle->GetX() == 200.0f);
REQUIRE(circle->GetY() == 220.0f);
REQUIRE(circle->GetRadius_pxl() == 2.0f);
}
TEST_CASE("ROICircle_MarkROI", "[ROIMap]") {
DiffractionExperiment x(DetJF(1));
ROICircle c1("roi1", 200,220,2);
ROICircle c2("roi1", 200,220,1);
std::vector<uint16_t> mask(x.GetPixelsNum(), 0);
std::vector<float> res(x.GetPixelsNum());
REQUIRE_NOTHROW(c1.MarkROI(mask, 15, x.GetXPixelsNum(), x.GetYPixelsNum(), res));
REQUIRE_NOTHROW(c2.MarkROI(mask, 1, x.GetXPixelsNum(), x.GetYPixelsNum(), res));
REQUIRE (mask[220 * x.GetXPixelsNum() + 200] == ((1<<15) | (1<<1)));
REQUIRE (mask[218 * x.GetXPixelsNum() + 200] == (1<<15));
REQUIRE (mask[220 * x.GetXPixelsNum() + 202] == (1<<15));
REQUIRE (mask[221 * x.GetXPixelsNum() + 201] == (1<<15));
REQUIRE (mask[218 * x.GetXPixelsNum() + 202] == 0);
}
TEST_CASE("ROIBox_SwapX", "[ROIMap]") {
std::unique_ptr<ROIBox> rectangle;
REQUIRE_NOTHROW(rectangle = std::make_unique<ROIBox>("roi1", 200, 199, 199, 221));
REQUIRE(rectangle->GetXMax() == 200);
REQUIRE(rectangle->GetXMin() == 199);
REQUIRE(rectangle->GetYMax() == 221);
REQUIRE(rectangle->GetYMin() == 199);
}
TEST_CASE("ROIBox_SwapY", "[ROIMap]") {
std::unique_ptr<ROIBox> rectangle;
REQUIRE_NOTHROW(rectangle = std::make_unique<ROIBox>("roi1", 200,220,199, 198));
REQUIRE(rectangle->GetXMax() == 220);
REQUIRE(rectangle->GetXMin() == 200);
REQUIRE(rectangle->GetYMax() == 199);
REQUIRE(rectangle->GetYMin() == 198);
}
TEST_CASE("ROIBox_NegativeBounds", "[ROIMap]") {
DiffractionExperiment x(DetJF(1));
std::unique_ptr<ROIBox> rectangle;
REQUIRE_NOTHROW(rectangle = std::make_unique<ROIBox>("roi1", -200,220,220, 221));
REQUIRE(rectangle->GetXMin() == 0);
REQUIRE(rectangle->GetXMax() == 220);
REQUIRE_NOTHROW(rectangle = std::make_unique<ROIBox>("roi1", 200,-220,220, 221));
REQUIRE(rectangle->GetXMin() == 0);
REQUIRE(rectangle->GetXMax() == 200);
REQUIRE_NOTHROW(rectangle = std::make_unique<ROIBox>("roi1", -200,-20,220, 221));
REQUIRE(rectangle->GetXMin() == 0);
REQUIRE(rectangle->GetXMax() == -1);
REQUIRE(rectangle->GetWidth() == 0);
REQUIRE(rectangle->GetArea() == 0);
REQUIRE_NOTHROW(rectangle = std::make_unique<ROIBox>("roi1", 220,221,-200, -20));
REQUIRE(rectangle->GetYMin() == 0);
REQUIRE(rectangle->GetYMax() == -1);
REQUIRE(rectangle->GetHeight() == 0);
REQUIRE(rectangle->GetArea() == 0);
}
TEST_CASE("ROIBox_MarkROI", "[ROIMap]") {
DiffractionExperiment x(DetJF(1));
ROIBox r1("roi1", 198,202,218, 222);
ROIBox r2("roi2", 198,202,222, 250);
std::vector<uint16_t> mask(x.GetPixelsNum(), 0);
std::vector<float> res(x.GetPixelsNum());
REQUIRE_NOTHROW(r1.MarkROI(mask, 12, x.GetXPixelsNum(), x.GetYPixelsNum(), res));
REQUIRE_NOTHROW(r2.MarkROI(mask, 13, x.GetXPixelsNum(), x.GetYPixelsNum(), res));
REQUIRE (mask[220 * x.GetXPixelsNum() + 202] == (1<<12));
REQUIRE (mask[218 * x.GetXPixelsNum() + 198] == (1<<12));
REQUIRE (mask[218 * x.GetXPixelsNum() + 202] == (1<<12));
REQUIRE (mask[218 * x.GetXPixelsNum() + 202] == (1<<12));
REQUIRE (mask[222 * x.GetXPixelsNum() + 201] == ((1<<12) | (1<<13)));
REQUIRE (mask[223 * x.GetXPixelsNum() + 200] == (1<<13));
REQUIRE (mask[218 * x.GetXPixelsNum() + 197] == 0);
REQUIRE (mask[218 * x.GetXPixelsNum() + 203] == 0);
REQUIRE (mask[217 * x.GetXPixelsNum() + 200] == 0);
}
TEST_CASE("ROIBox_MarkROI_OutOfBounds", "[ROIMap]") {
DiffractionExperiment x(DetJF(1));
ROIBox r1("roi1", x.GetXPixelsNum(),x.GetXPixelsNum() + 10,218, 222);
ROIBox r2("roi2", 198,202,x.GetYPixelsNum(), x.GetYPixelsNum() + 10);
std::vector<uint16_t> mask(x.GetPixelsNum() * 4, 0); // Set the array to much more to protect for eventual out-out-bounds access
std::vector<float> res(x.GetPixelsNum());
REQUIRE_NOTHROW(r1.MarkROI(mask, 12, x.GetXPixelsNum(), x.GetYPixelsNum(), res));
REQUIRE_NOTHROW(r2.MarkROI(mask, 13, x.GetXPixelsNum(), x.GetYPixelsNum(), res));
size_t err = 0;
for (const auto &i: mask) {
if (i != 0) err++;
}
REQUIRE(err == 0);
}
TEST_CASE("ROIBox", "[ROIMap]") {
std::unique_ptr<ROIBox> rectangle;
REQUIRE_NOTHROW(rectangle = std::make_unique<ROIBox>("roi1", 198,202,218, 222));
REQUIRE(rectangle->GetName() == "roi1");
REQUIRE(rectangle->GetXMin() == 198);
REQUIRE(rectangle->GetXMax() == 202);
REQUIRE(rectangle->GetYMin() == 218);
REQUIRE(rectangle->GetYMax() == 222);
REQUIRE(rectangle->GetWidth() == 5);
REQUIRE(rectangle->GetHeight() == 5);
REQUIRE(rectangle->GetArea() == 25);
}
TEST_CASE("ROIAzimuthal", "[ROIMap]") {
std::unique_ptr<ROIAzimuthal> roi;
REQUIRE_NOTHROW(roi = std::make_unique<ROIAzimuthal>("roi1", 3.0, 5.0));
REQUIRE(roi->GetDMin_A() == 3.0);
REQUIRE(roi->GetDMax_A() == 5.0);
}
TEST_CASE("ROIAzimuthal_Swap", "[ROIMap]") {
std::unique_ptr<ROIAzimuthal> roi;
REQUIRE_NOTHROW(roi = std::make_unique<ROIAzimuthal>("roi1", 3.0, 2.0));
REQUIRE(roi->GetDMin_A() == 2.0);
REQUIRE(roi->GetDMax_A() == 3.0);
}
TEST_CASE("ROIAzimuthal_neg_resolution", "[ROIMap]") {
std::unique_ptr<ROIAzimuthal> roi;
REQUIRE_THROWS(roi = std::make_unique<ROIAzimuthal>("roi1", -1.0, 5.0));
REQUIRE_THROWS(roi = std::make_unique<ROIAzimuthal>("roi1", 5.0, -5.0));
REQUIRE_THROWS(roi = std::make_unique<ROIAzimuthal>("roi1", 5.0, 0.0));
REQUIRE_THROWS(roi = std::make_unique<ROIAzimuthal>("roi1", 0.0, 5.0));
}
TEST_CASE("ROIAzimuthal_ROImark", "[ROIMap]") {
DiffractionExperiment x(DetJF(1));
std::vector<float> resolution_map(x.GetPixelsNum(), 3.0);
resolution_map[1] = 2.0;
resolution_map[2] = 1.0;
resolution_map[3] = 0.0;
resolution_map[4] = 5.0;
ROIAzimuthal r1("roi1", 2.0, 4.0);
ROIAzimuthal r2("roi2", 3.0, 6.0);
std::vector<uint16_t> mask(x.GetPixelsNum(), 0);
REQUIRE_NOTHROW(r1.MarkROI(mask, 15, x.GetXPixelsNum(), x.GetYPixelsNum(), resolution_map));
REQUIRE_NOTHROW(r2.MarkROI(mask, 1, x.GetXPixelsNum(), x.GetYPixelsNum(), resolution_map));
REQUIRE(mask[0] == ((1<<1) | (1 << 15)));
REQUIRE(mask[1] == (1<<15));
REQUIRE(mask[2] == 0);
REQUIRE(mask[3] == 0);
REQUIRE(mask[4] == (1<<1));
for (int i = 5; i < x.GetPixelsNum(); i++) {
REQUIRE(mask[i] == ((1<<1) | (1 << 15)));
}
}
TEST_CASE("ROIAzimuthal_Phi", "[ROIMap]") {
ROIAzimuthal full("roi1", 2.0, 4.0);
REQUIRE_FALSE(full.HasPhi());
// Full ring: phi is ignored, only d-range matters
REQUIRE(full.CheckROI(0, 0, 3.0, 123.0));
REQUIRE(full.CheckROI(0, 0, 3.0, 0.0));
REQUIRE_FALSE(full.CheckROI(0, 0, 1.0, 123.0));
ROIAzimuthal sector("roi2", 2.0, 4.0, 30.0f, 90.0f);
REQUIRE(sector.HasPhi());
REQUIRE(sector.GetPhiMin_deg() == 30.0f);
REQUIRE(sector.GetPhiMax_deg() == 90.0f);
REQUIRE(sector.CheckROI(0, 0, 3.0, 60.0));
REQUIRE(sector.CheckROI(0, 0, 3.0, 30.0)); // inclusive bounds
REQUIRE(sector.CheckROI(0, 0, 3.0, 90.0));
REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 120.0));
REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 0.0));
REQUIRE_FALSE(sector.CheckROI(0, 0, 1.0, 60.0)); // outside d-range
}
TEST_CASE("ROIAzimuthal_Phi_Wrap", "[ROIMap]") {
// Sector wrapping across 0 deg: 350 .. 10
ROIAzimuthal sector("roi1", 2.0, 4.0, 350.0f, 10.0f);
REQUIRE(sector.HasPhi());
REQUIRE(sector.CheckROI(0, 0, 3.0, 355.0));
REQUIRE(sector.CheckROI(0, 0, 3.0, 5.0));
REQUIRE(sector.CheckROI(0, 0, 3.0, 0.0));
REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 180.0));
REQUIRE_FALSE(sector.CheckROI(0, 0, 3.0, 11.0));
}
TEST_CASE("ROIAzimuthal_Phi_Normalize", "[ROIMap]") {
// Out-of-range inputs are normalized to [0, 360)
ROIAzimuthal sector("roi1", 2.0, 4.0, -30.0f, 400.0f);
REQUIRE(sector.GetPhiMin_deg() == 330.0f);
REQUIRE(sector.GetPhiMax_deg() == 40.0f);
// Default (no phi bounds) and equal bounds are both the full ring
ROIAzimuthal full("roi2", 2.0, 4.0);
REQUIRE_FALSE(full.HasPhi());
ROIAzimuthal equal_bounds("roi3", 2.0, 4.0, 45.0f, 45.0f);
REQUIRE_FALSE(equal_bounds.HasPhi());
}
TEST_CASE("ROIAzimuthal_Phi_MarkROI", "[ROIMap]") {
DiffractionExperiment x(DetJF(1));
std::vector<float> resolution_map(x.GetPixelsNum(), 3.0);
std::vector<float> phi_map(x.GetPixelsNum(), 0.0);
phi_map[0] = 45.0;
phi_map[1] = 200.0;
phi_map[2] = 45.0;
resolution_map[2] = 1.0; // outside d-range
ROIAzimuthal sector("roi1", 2.0, 4.0, 30.0f, 90.0f);
std::vector<uint16_t> mask(x.GetPixelsNum(), 0);
REQUIRE_NOTHROW(sector.MarkROI(mask, 3, x.GetXPixelsNum(), x.GetYPixelsNum(), resolution_map, phi_map));
REQUIRE(mask[0] == (1<<3)); // d in range, phi 45 in [30, 90]
REQUIRE(mask[1] == 0); // phi 200 outside sector
REQUIRE(mask[2] == 0); // d outside range
for (int i = 3; i < x.GetPixelsNum(); i++)
REQUIRE(mask[i] == 0); // phi 0 outside sector
}
TEST_CASE("ROIMap") {
DiffractionExperiment x(DetJF(1));
ROIMap mask;
REQUIRE(mask.empty());
mask.SetROI({
.boxes = {
ROIBox("roi12", 100, 120, 240, 260),
ROIBox("roi11", 200, 220, 240, 260)
},
.circles = {ROICircle("roi7", 300, 400, 5)}
});
REQUIRE(!mask.empty());
mask.SetROI({
.boxes = {ROIBox("roi12", 100, 120, 240, 260)},
.circles = {ROICircle("roi7", 300, 400, 5)}
});
REQUIRE(!mask.empty());
// Check arrays are proper size
REQUIRE(mask.GetROINameMap().size() == 2);
auto map = mask.GetROIMap(x.GetDiffractionGeometry(), x.GetModules(),
x.GetXPixelsNum(),
x.GetYPixelsNum());
REQUIRE(map.size() == x.GetPixelsNum());
auto it1 = mask.GetROINameMap().find("roi12");
REQUIRE(it1 != mask.GetROINameMap().end());
REQUIRE(it1->second == 0);
REQUIRE(map[260 * x.GetXPixelsNum() + 100] == (1<<0));
auto it2 = mask.GetROINameMap().find("roi7");
REQUIRE(it2 != mask.GetROINameMap().end());
REQUIRE(it2->second == 1);
REQUIRE(map[405 * x.GetXPixelsNum() + 300] == (1<<1));
mask.SetROI({});
REQUIRE(mask.empty());
}
TEST_CASE("ROIMap_Empty") {
DiffractionExperiment x(DetJF(1));
REQUIRE(x.ROI().empty());
size_t err = 0;
for (const auto &i: x.ExportROIMap()) {
if (i != 0)
err++;
}
REQUIRE(err == 0);
}
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