Every input is a file named on the command line, read in the order given (a shell glob gives them sorted by name); a directory is refused with the glob form to use instead. - Several Jungfraujoch/NXmx masters of stills are read as one run (JFJochMultiReader): their images one after another, the pixel masks combined, the per-image efficiency placed at each input's images. They must share the detector, wavelength (0.1%), distance (0.1 mm) and beam centre (1 px), since stills geometry refinement refines one geometry for all frames; rotation sweeps are refused. The log gives the indexing rate of each input beside the run's (ProcessResult::image_indexed). - SACLA HDF5 / CXI (JFJochCrystFELReader::ReadFiles, ReadCXI, Open) and XTC (JFJochXTCReader::ReadFiles) take the list of files instead of scanning a directory; CanReadCXI and xtc::CanRead accept only a file; ListFiles and xtc::CollectStreams are gone. - Several inputs must be one format, --mode mx, and stored files (no broker, no --simulate-live); one frame of a CBF/marCCD/SMV sweep still names the whole sweep. Validated: two Jungfraujoch lysozyme stills runs together (49,920 frames, known cell) 57.1% indexed (59.3% / 54.9% per run), 1.22 A, CC1/2 0.986, R_split 8.8%, REFMAC R/R-free 0.253/0.269 against 0.257/0.273 for the earlier hand-built combined master. Rotation: 5reo and lyso_x10sa_90deg_1 unchanged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
106 lines
4.3 KiB
C++
106 lines
4.3 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 <catch2/catch_all.hpp>
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#include "../common/DiffractionExperiment.h"
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#include "../reader/JFJochMultiReader.h"
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namespace {
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// A stills collection of n frames held in memory: frame i answers with one spot at x = tag + i, so
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// which input and which of its frames was read can be told from the spot.
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class FakeStills : public JFJochReader {
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uint64_t n;
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float tag;
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bool LoadImage_i(std::shared_ptr<JFJochReaderDataset> &, DataMessage &, std::vector<uint8_t> &,
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int64_t, bool) override { return false; }
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public:
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FakeStills(uint64_t n_, float tag_, const DiffractionExperiment &x, std::vector<uint32_t> mask,
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std::vector<float> efficiency = {}) : n(n_), tag(tag_) {
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auto d = std::make_shared<JFJochReaderDataset>();
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d->experiment = x;
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d->pixel_mask = std::make_shared<const PixelMask>(mask);
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d->efficiency = std::move(efficiency);
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SetStartMessage(d);
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}
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[[nodiscard]] uint64_t GetNumberOfImages() const override { return n; }
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void Close() override {}
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bool ReadRawImage(int64_t, JFJochReaderRawImage &) override { return true; }
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std::vector<SpotToSave> ReadSpots(int64_t image) const override {
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SpotToSave s;
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s.x = tag + static_cast<float>(image);
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return {s};
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}
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};
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DiffractionExperiment Stills() {
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DiffractionExperiment x(DetJF(1));
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x.BeamX_pxl(500).BeamY_pxl(250).DetectorDistance_mm(100).IncidentEnergy_keV(12.4);
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return x;
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}
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std::vector<uint32_t> EmptyMask(const DiffractionExperiment &x) {
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return std::vector<uint32_t>(x.GetXPixelsNum() * x.GetYPixelsNum(), 0);
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}
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}
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TEST_CASE("JFJochMultiReader_Concatenates", "[JFJochMultiReader][portable]") {
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const auto x = Stills();
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auto mask_a = EmptyMask(x);
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auto mask_b = EmptyMask(x);
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mask_a[3] = 1;
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mask_b[7] = 4;
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std::vector<std::unique_ptr<JFJochReader>> inputs;
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inputs.push_back(std::make_unique<FakeStills>(3, 100.0f, x, mask_a, std::vector<float>{0.5f, 0.5f, 0.5f}));
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inputs.push_back(std::make_unique<FakeStills>(2, 200.0f, x, mask_b));
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JFJochMultiReader reader(std::move(inputs));
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REQUIRE(reader.GetNumberOfImages() == 5);
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REQUIRE(reader.GetNumberOfInputs() == 2);
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CHECK(reader.FirstImage(1) == 3);
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CHECK(reader.ImagesInInput(1) == 2);
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CHECK(reader.ReadSpots(0)[0].x == Catch::Approx(100.0f));
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CHECK(reader.ReadSpots(2)[0].x == Catch::Approx(102.0f));
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CHECK(reader.ReadSpots(3)[0].x == Catch::Approx(200.0f));
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CHECK(reader.ReadSpots(4)[0].x == Catch::Approx(201.0f));
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CHECK_THROWS(reader.ReadSpots(5));
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const auto dataset = reader.GetDataset();
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const auto &mask = dataset->pixel_mask->GetMask();
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CHECK(mask[3] == 1);
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CHECK(mask[7] == 4);
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CHECK(mask[5] == 0);
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// The second input states no efficiency: its frames count as fully collected.
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REQUIRE(dataset->efficiency.size() == 5);
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CHECK(dataset->efficiency[2] == Catch::Approx(0.5f));
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CHECK(dataset->efficiency[3] == Catch::Approx(1.0f));
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}
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TEST_CASE("JFJochMultiReader_RefusesOtherGeometry", "[JFJochMultiReader][portable]") {
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const auto x = Stills();
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auto other = Stills();
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SECTION("distance") { other.DetectorDistance_mm(101); }
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SECTION("beam centre") { other.BeamX_pxl(503); }
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SECTION("wavelength") { other.IncidentEnergy_keV(12.6); }
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std::vector<std::unique_ptr<JFJochReader>> inputs;
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inputs.push_back(std::make_unique<FakeStills>(1, 0.0f, x, EmptyMask(x)));
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inputs.push_back(std::make_unique<FakeStills>(1, 0.0f, other, EmptyMask(other)));
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CHECK_THROWS(JFJochMultiReader(std::move(inputs)));
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}
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TEST_CASE("JFJochMultiReader_RefusesRotation", "[JFJochMultiReader][portable]") {
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const auto x = Stills();
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auto rotation = Stills();
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rotation.Goniometer(GoniometerAxis("omega", 0.0f, 0.1f, Coord(1, 0, 0), {}));
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std::vector<std::unique_ptr<JFJochReader>> inputs;
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inputs.push_back(std::make_unique<FakeStills>(1, 0.0f, x, EmptyMask(x)));
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inputs.push_back(std::make_unique<FakeStills>(1, 0.0f, rotation, EmptyMask(rotation)));
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CHECK_THROWS(JFJochMultiReader(std::move(inputs)));
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}
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