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jfjoch_process/jfjoch_scale: Improve parameter handling

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This commit is contained in:
leonarski_f
2026-05-20 08:37:19 +02:00
parent 18c0d0cf6f
commit 52281bfd58
2 changed files with 109 additions and 70 deletions
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tools/jfjoch_process.cpp
+20 -15
View File
@@ -32,7 +32,7 @@
#include "../image_analysis/WriteReflections.h"
#include "../image_analysis/UpdateReflectionResolution.h"
void print_usage(Logger &logger) {
void print_usage() {
std::cout << "Usage ./jfjoch_analysis {<options>} <input.h5>" << std::endl;
std::cout << "Options:" << std::endl;
std::cout << " -o, --output-prefix <txt> Output file prefix (default: output)" << std::endl;
@@ -46,30 +46,30 @@ void print_usage(Logger &logger) {
std::cout << " Spot finding" << std::endl;
std::cout << " --spot-sigma <num> Noise sigma level for spot finding (default: 3.0)" << std::endl;
std::cout << " --spot-threshold <num> Photon count threshold for spot finding (default: 10)" << std::endl;
std::cout << " --spot-resolution <num> High resolution limit for spot finding (default: 1.5)" << std::endl;
std::cout << " --spot-high-resolution <num> High resolution limit for spot finding (default: 1.5)" << std::endl;
std::cout << " --max-spots <num> Max spot count (default: 250)" << std::endl;
std::cout << std::endl;
std::cout << " Indexing" << std::endl;
std::cout << " -R, --rotation-indexing[=num] Rotation indexing (optional: min angular range deg)" << std::endl;
std::cout << " -X, --indexing-algorithm <txt> Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
std::cout << " -F, --fft-indexing Use FFT indexing algorithm (shortcut for -X FFT)" << std::endl;
std::cout << " -S, --space-group <num> Space group number - used for both indexing and scaling" << std::endl;
std::cout << " -C, --unit-cell <cell> Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
std::cout << " --no-beam-center-refine No least-square beam center refinement" << std::endl;
std::cout << std::endl;
std::cout << " Scaling and merging" << std::endl;
std::cout << " -M, --scale-merge Scale and merge (refine mosaicity) and write scaled.hkl + image.dat" << std::endl;
std::cout << " -P, --partiality <txt> Partiality refinement fixed|rot|unity (default: fixed)" << std::endl;
std::cout << " -M, --scale-merge Scale and merge (refine mosaicity) and write scaled.hkl + image.dat" << std::endl;
std::cout << " -P, --partiality <txt> Partiality refinement fixed|rot|unity (default: fixed)" << std::endl;
std::cout << " -A, --anomalous Anomalous mode (don't merge Friedel pairs)" << std::endl;
std::cout << " -B, --refine-bfactor Refine per image B-factor" << std::endl;
std::cout << " -w, --wedge[=num] Refine image wedge during scaling with starting wedge value" << std::endl;
std::cout << " --scaling-high-resolution <num> High resolution limit for spot finding (default: no limit)" << std::endl;
std::cout << " --min-partiality <num> Minimum partiality to accept reflection (default: 0.02)" << std::endl;
std::cout << " --min-image-cc <num> Per-image CC limit in percent (default: no limit)" << std::endl;
std::cout << " --scaling-iterations <num> Number of scaling iterations with no reference data (default: 3)" << std::endl;
std::cout << " -z, --reference-mtz <file> Reference MTZ file" << std::endl;
}
}
enum {
OPT_SPOT_SIGMA = 1000,
@@ -79,7 +79,8 @@ enum {
OPT_NO_BEAM_CENTER_REFINE,
OPT_MIN_PARTIALITY,
OPT_MIN_IMAGE_CC,
OPT_SCALING_ITERATIONS
OPT_SCALING_ITERATIONS,
OPT_SCALING_HIGH_RESOLUTION
};
static option long_options[] = {
@@ -88,7 +89,7 @@ static option long_options[] = {
{"threads", required_argument, nullptr, 'N'},
{"start-image", required_argument, nullptr, 's'},
{"end-image", required_argument, nullptr, 'e'},
{"stride", required_argument, nullptr, 't'},
{"stride", required_argument, nullptr, 't'},
{"rotation-indexing", optional_argument, nullptr, 'R'},
{"indexing-algorithm", required_argument, nullptr, 'X'},
{"unit-cell", required_argument, nullptr, 'C'},
@@ -102,12 +103,13 @@ static option long_options[] = {
{"spot-sigma", required_argument, nullptr, OPT_SPOT_SIGMA},
{"spot-threshold", required_argument, nullptr, OPT_SPOT_THRESHOLD},
{"spot-resolution", required_argument, nullptr, OPT_SPOT_RESOLUTION},
{"spot-high-resolution", required_argument, nullptr, OPT_SPOT_RESOLUTION},
{"max-spots", required_argument, nullptr, OPT_MAX_SPOTS},
{"no-beam-center-refine", no_argument, nullptr, OPT_NO_BEAM_CENTER_REFINE},
{"min-partiality", required_argument, nullptr, OPT_MIN_PARTIALITY},
{"min-image-cc", required_argument, nullptr, OPT_MIN_IMAGE_CC},
{"scaling-iterations", required_argument, nullptr, OPT_SCALING_ITERATIONS},
{"scaling-high-resolution", required_argument, nullptr, OPT_SCALING_HIGH_RESOLUTION},
{nullptr, 0, nullptr, 0}
};
@@ -219,7 +221,7 @@ int main(int argc, char **argv) {
std::optional<float> d_min_scale_merge;
if (argc == 1) {
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
@@ -268,7 +270,7 @@ int main(int argc, char **argv) {
indexing_algorithm = IndexingAlgorithmEnum::None;
else {
logger.Error("Invalid indexing algorithm: {}", alg);
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
break;
@@ -279,7 +281,7 @@ int main(int argc, char **argv) {
logger.Error(
"Invalid unit cell. Expected: \"a,b,c,alpha,beta,gamma\" (6 floats, comma-separated, no spaces). Got: {}",
optarg ? optarg : "<null>");
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
fixed_reference_unit_cell = uc;
@@ -317,7 +319,7 @@ int main(int argc, char **argv) {
partiality_model = PartialityModel::Rotation;
else {
logger.Error("Invalid partiality mode: {}", optarg);
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
break;
@@ -350,6 +352,9 @@ int main(int argc, char **argv) {
case OPT_MIN_IMAGE_CC:
min_image_cc = std::stod(optarg);
break;
case OPT_SCALING_HIGH_RESOLUTION:
d_min_scale_merge = atof(optarg);
break;
case OPT_SCALING_ITERATIONS:
scaling_iter = atoi(optarg);
if (scaling_iter <= 0) {
@@ -359,14 +364,14 @@ int main(int argc, char **argv) {
break;
default:
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
}
if (optind != argc - 1) {
logger.Error("Input file not specified");
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
tools/jfjoch_scale.cpp
+89 -55
View File
@@ -11,6 +11,7 @@
#include <chrono>
#include <fstream>
#include <sstream>
#include <getopt.h>
#include "../reader/JFJochHDF5Reader.h"
#include "../common/Logger.h"
@@ -31,27 +32,60 @@
#include "../image_analysis/WriteReflections.h"
#include "../image_analysis/UpdateReflectionResolution.h"
void print_usage(Logger &logger) {
logger.Info("Usage ./jfjoch_analysis {<options>} <input.h5>");
logger.Info("Options:");
logger.Info(" -o<txt> Output file prefix (default: output)");
logger.Info(" -N<num> Number of threads (default: 1)");
logger.Info(" -s<num> Start image number (default: 0)");
logger.Info(" -e<num> End image number (default: all)");
logger.Info(" -v Verbose output");
logger.Info("");
logger.Info(" Scaling and merging");
logger.Info(" -S<num> Space group number");
logger.Info(" -D<num> High resolution limit for scaling/merging (default: 0.0; no limit)");
logger.Info(" -P<txt> Partiality refinement fixed|rot|unity (default: fixed)");
logger.Info(" -A Anomalous mode (don't merge Friedel pairs)");
logger.Info(" -B Refine per image B-factor");
logger.Info(" -w<num> Refine image wedge during scaling with starting wedge value");
logger.Info(" -p<num> Minimum partiality to accept reflection (default: 0.02)");
logger.Info(" -q<num> Per-image CC limit in percent (default: no limit)");
logger.Info(" -i<num> Number of scaling iterations with no reference data (default: 3) ");
void print_usage() {
std::cout << "Usage ./jfjoch_scale {<options>} <input.h5>" << std::endl;
std::cout << "Options:" << std::endl;
std::cout << " -o, --output-prefix <txt> Output file prefix (default: output)" << std::endl;
std::cout << " -N, --threads <num> Number of threads (default: 1)" << std::endl;
std::cout << " -s, --start-image <num> Start image number (default: 0)" << std::endl;
std::cout << " -e, --end-image <num> End image number (default: all)" << std::endl;
std::cout << " -v, --verbose Verbose output" << std::endl;
std::cout << "" << std::endl;
std::cout << " Scaling and merging" << std::endl;
std::cout << " -S, --space-group <num> Space group number" << std::endl;
std::cout <<
" -D, --scaling-high-resolution <num> High resolution limit for scaling/merging (default: 0.0; no limit)"
<< std::endl;
std::cout << " -P, --partiality <txt> Partiality refinement fixed|rot|unity (default: fixed)" <<
std::endl;
std::cout << " -A, --anomalous Anomalous mode (don't merge Friedel pairs)" << std::endl;
std::cout << " -B, --refine-bfactor Refine per image B-factor" << std::endl;
std::cout << " -w, --wedge[=num] Refine image wedge during scaling with starting wedge value"
<< std::endl;
std::cout << " --min-partiality <num> Minimum partiality to accept reflection (default: 0.02)" <<
std::endl;
std::cout << " --min-image-cc <num> Per-image CC limit in percent (default: no limit)" << std::endl;
std::cout << " --scaling-iterations <num> Number of scaling iterations with no reference data (default: 3)"
<< std::endl;
std::cout << " -z, --reference-mtz <file> Reference MTZ file" << std::endl;
}
enum {
OPT_MIN_PARTIALITY = 1000,
OPT_MIN_IMAGE_CC,
OPT_SCALING_ITERATIONS
};
static option long_options[] = {
{"verbose", no_argument, nullptr, 'v'},
{"output-prefix", required_argument, nullptr, 'o'},
{"threads", required_argument, nullptr, 'N'},
{"start-image", required_argument, nullptr, 's'},
{"end-image", required_argument, nullptr, 'e'},
{"reference-mtz", required_argument, nullptr, 'z'},
{"space-group", required_argument, nullptr, 'S'},
{"partiality", required_argument, nullptr, 'P'},
{"anomalous", no_argument, nullptr, 'A'},
{"refine-bfactor", no_argument, nullptr, 'B'},
{"wedge", optional_argument, nullptr, 'w'},
{"scaling-high-resolution", required_argument, nullptr, 'D'},
{"min-partiality", required_argument, nullptr, OPT_MIN_PARTIALITY},
{"min-image-cc", required_argument, nullptr, OPT_MIN_IMAGE_CC},
{"scaling-iterations", required_argument, nullptr, OPT_SCALING_ITERATIONS},
{nullptr, 0, nullptr, 0}
};
int main(int argc, char **argv) {
RegisterHDF5Filter();
@@ -80,18 +114,21 @@ int main(int argc, char **argv) {
std::optional<float> d_min_scale_merge;
if (argc == 1) {
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
int opt;
while ((opt = getopt(argc, argv, "o:z:N:s:e:p:q:Bw::vD:S:A:P:")) != -1) {
int option_index = 0;
const char *short_opts = "vo:N:s:e:z:S:P:ABw::D:p:q:i:";
while ((opt = getopt_long(argc, argv, short_opts, long_options, &option_index)) != -1) {
switch (opt) {
case 'o':
output_prefix = optarg;
break;
case 'z':
ref_mtz = optarg;
case 'v':
verbose = true;
break;
case 'N':
nthreads = atoi(optarg);
@@ -102,33 +139,12 @@ int main(int argc, char **argv) {
case 'e':
end_image = atoi(optarg);
break;
case 'p':
min_partiality = std::stod(optarg);
break;
case 'q':
min_image_cc = std::stod(optarg);
break;
case 'B':
refine_bfactor = true;
break;
case 'w':
refine_wedge = true;
if (optarg)
wedge_for_scaling = std::stod(optarg);
break;
case 'v':
verbose = true;
break;
case 'D':
d_min_scale_merge = atof(optarg);
logger.Info("High resolution limit for scaling/merging set to {:.2f} A", d_min_scale_merge.value());
case 'z':
ref_mtz = optarg;
break;
case 'S':
space_group_number = atoi(optarg);
break;
case 'A':
anomalous_mode = true;
break;
case 'P':
if (strcmp(optarg, "unity") == 0)
partiality_model = PartialityModel::Unity;
@@ -138,26 +154,44 @@ int main(int argc, char **argv) {
partiality_model = PartialityModel::Rotation;
else {
logger.Error("Invalid partiality mode: {}", optarg);
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
break;
case 'i':
case 'A':
anomalous_mode = true;
break;
case 'B':
refine_bfactor = true;
break;
case 'w':
refine_wedge = true;
if (optarg)
wedge_for_scaling = std::stod(optarg);
break;
case 'D':
d_min_scale_merge = atof(optarg);
logger.Info("High resolution limit for scaling/merging set to {:.2f} A", d_min_scale_merge.value());
break;
case OPT_MIN_PARTIALITY:
min_partiality = std::stod(optarg);
break;
case OPT_MIN_IMAGE_CC:
min_image_cc = std::stod(optarg);
break;
case OPT_SCALING_ITERATIONS:
scaling_iter = atoi(optarg);
if (scaling_iter <= 0) {
logger.Error("Invalid scaling iteration count: {}", scaling_iter);
exit(EXIT_FAILURE);
}
break;
default:
print_usage(logger);
exit(EXIT_FAILURE);
}
}
if (optind != argc - 1) {
logger.Error("Input file not specified");
print_usage(logger);
print_usage();
exit(EXIT_FAILURE);
}
@@ -252,7 +286,7 @@ int main(int argc, char **argv) {
auto refl_stats = UpdateReflectionResolution(experiment.GetUnitCell().value(), reflections);
logger.Info("Read {} reflections from {} images", refl_stats.n_reflections, refl_stats.n_images);
std::vector<float> mosaicity(end_image - start_image + 1);
for (int i = 0; i < end_image - start_image + 1; i++) {
mosaicity[i] = dataset->mosaicity_deg[start_image + i];
@@ -270,7 +304,7 @@ int main(int argc, char **argv) {
scale_result = scaling.Scale(reflections, mosaicity, nthreads);
} else {
ScaleOnTheFly scaling(experiment, reference_data);
scale_result = scaling.Scale(reflections,mosaicity, nthreads);
scale_result = scaling.Scale(reflections, mosaicity, nthreads);
}
scale_result.SaveToFile(output_prefix + "_iter" + std::to_string(i) + "_scale.dat");
@@ -292,7 +326,7 @@ int main(int argc, char **argv) {
auto merge_result = MergeAll(experiment, reflections, merge_mask);
auto merge_stats = MergeStats(experiment, merge_result, reflections, experiment.GetUnitCell().value(), merge_mask,
reference_data);
reference_data);
auto merge_end = std::chrono::steady_clock::now();
double merge_time = std::chrono::duration<double>(merge_end - merge_start).count();