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jfjoch_process: Save reflections as mmCIF (experimental)

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leonarski_f
2026-02-12 18:09:35 +01:00
parent 1dedd3de33
commit 38199c480f
4 changed files with 252 additions and 13 deletions
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tools/jfjoch_process.cpp
+38 -12
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@@ -25,6 +25,7 @@
#include "../receiver/JFJochReceiverPlots.h"
#include "../compression/JFJochCompressor.h"
#include "../image_analysis/scale_merge/FrenchWilson.h"
#include "../image_analysis/WriteMmcif.h" // (actually include at top of file)
void print_usage(Logger &logger) {
logger.Info("Usage ./jfjoch_analysis {<options>} <input.h5>");
@@ -489,19 +490,44 @@ int main(int argc, char **argv) {
auto fw = FrenchWilson(scale_result->merged, fw_opts);
const std::string fw_path = output_prefix + "_amplitudes.hkl";
std::ofstream fw_file(fw_path);
if (!fw_file) {
logger.Error("Cannot open {} for writing", fw_path);
} else {
fw_file << "# h k l F sigmaF I_fw sigmaI\n";
for (const auto& r : fw) {
fw_file << r.h << " " << r.k << " " << r.l << " "
<< r.F << " " << r.sigmaF << " "
<< r.I << " " << r.sigmaI << "\n";
{
MmcifMetadata cif_meta;
// Unit cell — from rotation indexing result or experiment setting
if (rotation_indexer_ret.has_value()) {
cif_meta.unit_cell = rotation_indexer_ret->lattice.GetUnitCell();
} else if (experiment.GetUnitCell().has_value()) {
cif_meta.unit_cell = experiment.GetUnitCell().value();
}
// Space group
if (auto sg = experiment.GetGemmiSpaceGroup(); sg.has_value()) {
cif_meta.space_group_name = sg->hm;
cif_meta.space_group_number = sg->number;
} else if (space_group) {
cif_meta.space_group_name = space_group->hm;
cif_meta.space_group_number = space_group->number;
}
// Detector & experiment info
cif_meta.detector_name = experiment.GetDetectorDescription();
cif_meta.wavelength_A = experiment.GetWavelength_A();
cif_meta.detector_distance_mm = experiment.GetDetectorDistance_mm();
cif_meta.sample_temperature_K = experiment.GetSampleTemperature_K();
cif_meta.sample_name = experiment.GetSampleName();
cif_meta.data_block_name = output_prefix;
cif_meta.beamline = experiment.GetInstrumentName();
cif_meta.source = experiment.GetSourceName();
const std::string cif_path = output_prefix + "_amplitudes.cif";
try {
WriteMmcifReflections(cif_path, fw, cif_meta);
logger.Info("Wrote mmCIF reflections to {}", cif_path);
} catch (const std::exception& e) {
logger.Error("Failed to write mmCIF: {}", e.what());
}
fw_file.close();
logger.Info("French-Wilson: wrote {} amplitudes to {}", fw.size(), fw_path);
}
}
} else {