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Merge pull request #145 from aglowacki/master
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Changed export roi v9 layout
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Arthur Glowacki authored Sep 14, 2022
2 parents 404e808 + a605c98 commit 3beb9de
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Showing 15 changed files with 807 additions and 99 deletions.
8 changes: 7 additions & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,8 @@ find_package(netCDF CONFIG REQUIRED)
find_package(yaml-cpp CONFIG REQUIRED)

set(EIGEN3_INCLUDES "${PROJECT_SOURCE_DIR}/src/support/eigen-git-mirror" CACHE PATH "Eigen include folder")

# todo
# option(BUILD_WITH_OPENCL "Build with OPENCL support" OFF)
option(BUILD_WITH_PYBIND11 "Build python binding with PyBind11" OFF)
option(BUILD_WITH_ZMQ "Build with ZeroMQ" OFF)
option(BUILD_FOR_PHI "Build for Intel Phi" OFF)
Expand Down Expand Up @@ -468,6 +469,11 @@ IF (BUILD_WITH_TIRPC)
target_link_libraries (xrf_maps LINK_PUBLIC libtirpc.so)
ENDIF()

IF (BUILD_WITH_OPENCL)
find_package(CLBlast CONFIG REQUIRED)
target_link_libraries(xrf_maps PRIVATE clblast)
ENDIF()

#install(TARGETS xrf_maps libxrf_io libxrf_fit
# EXPORT libxrf-export
# LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
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108 changes: 82 additions & 26 deletions src/core/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,9 @@ POSSIBILITY OF SUCH DAMAGE.
#include "core/process_whole.h"
#include <cctype>


#define MAX_DETECTORS 7

// ----------------------------------------------------------------------------

void help()
Expand All @@ -59,6 +62,7 @@ void help()
logit_s<<"Options: \n";
logit_s<<"--nthreads : <int> number of threads to use (default is all system threads) \n";
logit_s<<"--quantify-with : <standard.txt> File to use as quantification standard \n";
logit_s<<"--quantify-fit <routines,>: If you want to perform quantification without having to re-fit all datasets. See --fit for routine options \n";
logit_s<<"--detectors : <int,..> Detectors to process, Defaults to 0,1,2,3 for 4 detector \n";
logit_s<<"--generate-avg-h5 : Generate .h5 file which is the average of all detectors .h50 - h.53 or range specified. \n";
logit_s<<"--add-v9layout : Generate .h5 file which has v9 layout able to open in IDL MAPS software. \n";
Expand All @@ -74,7 +78,8 @@ void help()
" 1 = matrix batch fit\n 2 = batch fit without tails\n 3 = batch fit with tails\n 4 = batch fit with free E, everything else fixed \n";
logit_s<<"--optimize-fit-routine : <general,hybrid> General (default): passes elements amplitudes as fit parameters. Hybrid only passes fit parameters and fits element amplitudes using NNLS\n";
logit_s<<"--optimizer <lmfit, mpfit> : Choose which optimizer to use for --optimize-fit-override-params or matrix fit routine \n";
logit_s<<"--optimize-rois : Looks in 'rois' directory and performs --optimize-fit-override-params on each roi separately. \n";
logit_s<<"--optimizer-fxg-tols <tol_override_val> : Default is LM_FIT = " << DP_LM_USERTOL << " , MP_FIT = " << 1.192e-10 << "\n";
logit_s<<"--optimize-rois : Looks in 'rois' directory and performs --optimize-fit-override-params on each roi separately. Needs to have --quantify-rois <maps_standardinfo.txt> and --quantify-fit <routines,> \n";
logit_s<<"Fitting Routines: \n";
logit_s<< "--fit <routines,> comma seperated \n";
logit_s<<" roi : element energy region of interest \n";
Expand All @@ -97,6 +102,8 @@ void help()
logit_s<<"xrf_maps --fit roi,matrix --dir /data/dataset1 --files scan1.mda,scan2.mda \n";
logit_s<<" Perform roi, matrix, and nnls analysis on the directory /data/dataset1, use maps_standard.txt information for quantification \n";
logit_s<<"xrf_maps --fit roi,matrix,nnls --quantify-with maps_standard.txt --dir /data/dataset1 \n";
logit_s<<" Perform optimization of an integrated roi spectra \n";
logit_s<<"xrf_maps --optimize-rois --quantify-rois maps_standardinfo.txt --quantify-fit roi,matrix,nnls --dir /data/dataset1 \n";
}

// ----------------------------------------------------------------------------
Expand All @@ -115,9 +122,32 @@ void set_optimizer(Command_Line_Parser& clp, data_struct::Analysis_Job<T_real>&
std::string opt = clp.get_option("--optimize-fit-routine");
if (opt == "hybrid")
{
logI << "Using Hybrid optimizer\n";
analysis_job.optimize_fit_routine = OPTIMIZE_FIT_ROUTINE::HYBRID;
}
}

if (clp.option_exists("--optimizer-fxg-tols"))
{
T_real fxg_tol;
if (std::is_same<T_real, float>::value)
{
fxg_tol = std::stof(clp.get_option("--optimizer-fxg-tols"));
}
else if (std::is_same<T_real, double>::value)
{
fxg_tol = std::stod(clp.get_option("--optimizer-fxg-tols"));
}

std::unordered_map<std::string, T_real> opt_map;
opt_map[STR_OPT_FTOL] = fxg_tol;
opt_map[STR_OPT_XTOL] = fxg_tol;
opt_map[STR_OPT_GTOL] = fxg_tol;

logI << "Setting FTOL, XTOL, GTOL to " << fxg_tol << "\n";

analysis_job.optimizer()->set_options(opt_map);
}
}

// ----------------------------------------------------------------------------
Expand Down Expand Up @@ -209,7 +239,7 @@ void set_detectors(Command_Line_Parser& clp, data_struct::Analysis_Job<T_real>&
}
else
{
for (size_t det = 0; det < 7; det++)
for (size_t det = 0; det < MAX_DETECTORS; det++)
{
analysis_job.detector_num_arr.push_back(det);
}
Expand Down Expand Up @@ -316,27 +346,28 @@ int set_dir_and_files(Command_Line_Parser& clp, data_struct::Analysis_Job<T_real
//if they were not then look for them in $dataset_directory/mda
if (dset_file.length() < 1)
{
for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files(dataset_dir, ".hdf5"))
{
analysis_job.dataset_files.push_back(itr);
}
for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files(dataset_dir, ".h5"))
{
analysis_job.dataset_files.push_back(itr);
}
for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files(dataset_dir, ".emd"))
{
analysis_job.dataset_files.push_back(itr);
}
for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files(dataset_dir, ".mda"))
{
analysis_job.dataset_files.push_back(itr);
}
for (auto& itr : io::file::File_Scan::inst()->find_all_dataset_files(dataset_dir + "mda" + DIR_END_CHAR, ".mda"))
std::vector<std::string> search_ext_list;
std::vector<std::string> search_ext_mda_list;

search_ext_list.push_back(".hdf5");
search_ext_list.push_back(".h5");
search_ext_list.push_back(".emd");
search_ext_list.push_back(".mda");

io::file::File_Scan::inst()->find_all_dataset_files_by_list(dataset_dir, search_ext_list, analysis_job.dataset_files);


search_ext_mda_list.push_back(".mda");
search_ext_mda_list.push_back(".mca");
for (int i = 0; i < MAX_DETECTORS; i++)
{
analysis_job.dataset_files.push_back(itr);
std::string mca_str = ".mca" + std::to_string(i);
search_ext_mda_list.push_back(mca_str);
}
// don't want to open h5 avg files for optimize

io::file::File_Scan::inst()->find_all_dataset_files_by_list(dataset_dir + "mda" + DIR_END_CHAR, search_ext_mda_list, analysis_job.dataset_files);

// don't want to open h5 avg files for optimize because we optimize by detector , not avg
for (auto& itr : analysis_job.dataset_files)
{
analysis_job.optimize_dataset_files.push_back(itr);
Expand Down Expand Up @@ -499,16 +530,13 @@ int run_quantification(Command_Line_Parser& clp)

if (analysis_job.quantification_standard_filename.length() > 0)
{
perform_quantification(&analysis_job);
perform_quantification(&analysis_job, true);
}
else
{
logE << "Please specify filename with quantification information (usually maps_standardinfo.txt)\n";
return -1;
}


//iterate_datasets_and_update(analysis_job);
}
else
{
Expand All @@ -524,12 +552,40 @@ int run_optimize_rois(Command_Line_Parser& clp)
{
data_struct::Analysis_Job<double> analysis_job;

// Force perform quantification until we have proper loading quant from hdf5 finished
if (set_general_options(clp, analysis_job) == -1)
{
return -1;
}
set_fit_routines(clp, analysis_job);
/*
if (analysis_job.fitting_routines.size() == 0)
{
logE << "Please specify fit routines with --quantify-fit roi,nnls,matrix \n";
return -1;
}
*/
//Check if we want to quantifiy with a standard
if (clp.option_exists("--quantify-rois"))
{
analysis_job.quantification_standard_filename = clp.get_option("--quantify-rois");
}

optimize_rois(analysis_job);
if (io::file::init_analysis_job_detectors(&analysis_job))
{
io::file::File_Scan::inst()->populate_netcdf_hdf5_files(analysis_job.dataset_directory);

if (analysis_job.quantification_standard_filename.length() > 0)
{
perform_quantification(&analysis_job, false);
}
optimize_rois(analysis_job);
}
else
{
logE << "Error initalizing detectors!\n";
return -1;
}

return 0;
}
Expand Down
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