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Commit b05ae0d

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author
Arthur Glowacki
committed
added ability to load custom polarity pattern for polar xanes scans
1 parent 883cf8c commit b05ae0d

2 files changed

Lines changed: 79 additions & 34 deletions

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‎src/io/file/hdf5_io.h‎

Lines changed: 78 additions & 33 deletions
Original file line numberDiff line numberDiff line change
@@ -1036,7 +1036,7 @@ class DLL_EXPORT HDF5_IO
10361036
//-----------------------------------------------------------------------------
10371037
// load spectra volume as float (T_real) but scan_info as double (T_real2)
10381038
template<typename T_real, typename T_real2>
1039-
bool load_spectra_vol_polar_energy_scan(std::string path, std::string filename, size_t detector_num, data_struct::Spectra_Volume<T_real>* spec_vol, data_struct::Scan_Info<T_real2> &scan_info, bool logerr = true)
1039+
bool load_spectra_vol_polar_energy_scan(std::string path, std::string filename, size_t detector_num, data_struct::Spectra_Volume<T_real>* spec_vol, data_struct::Scan_Info<T_real2> &scan_info, data_struct::Params_Override<T_real>* params_override, bool logerr = true)
10401040
{
10411041
std::stack<std::pair<hid_t, H5_OBJECTS> > close_map;
10421042
hid_t file_id, dset_id, space_id;
@@ -1247,9 +1247,10 @@ class DLL_EXPORT HDF5_IO
12471247
scan_info.meta_info.scan_type = STR_SCAN_TYPE_POLAR_XANES;
12481248
// Take 1 spectra per magnetic polarization, divide them by 2 and store in each row
12491249
scan_info.meta_info.requested_cols = dims3[0] / 2;
1250-
scan_info.meta_info.requested_rows = 2;
1250+
scan_info.meta_info.requested_rows = 2; // two polarities
12511251
scan_info.meta_info.x_axis.resize(scan_info.meta_info.requested_cols);
12521252
scan_info.meta_info.y_axis.resize(scan_info.meta_info.requested_rows);
1253+
scan_info.meta_info.polarity_pattern = params_override->polarity_pattern;
12531254
spec_vol->resize_and_zero(scan_info.meta_info.requested_rows, scan_info.meta_info.requested_cols, dims3[2]);
12541255

12551256
struct data_struct::Scaler_Map<T_real2> energy_map;
@@ -1314,58 +1315,90 @@ class DLL_EXPORT HDF5_IO
13141315
int polarity = 0;
13151316
int idx = 0;
13161317

1317-
if(use_pr1 && (pr1_array.size() != dims3[0]))
1318+
if (params_override != nullptr && params_override->polarity_pattern.size() == 0)
13181319
{
1319-
logE<<str_pr1_path<<" is not the same size as spectra data. Can not load properly.\n";
1320-
_close_h5_objects(close_map);
1321-
return false;
1322-
}
1323-
else if(use_pr1 == false && (pr2_array.size() != dims3[0]))
1324-
{
1325-
logE<<str_pr2_path<<" is not the same size as spectra data. Can not load properly.\n";
1326-
_close_h5_objects(close_map);
1327-
return false;
1320+
if (use_pr1 && (pr1_array.size() != dims3[0]))
1321+
{
1322+
logE << str_pr1_path << " is not the same size as spectra data. Can not load properly.\n";
1323+
_close_h5_objects(close_map);
1324+
return false;
1325+
}
1326+
else if (use_pr1 == false && (pr2_array.size() != dims3[0]))
1327+
{
1328+
logE << str_pr2_path << " is not the same size as spectra data. Can not load properly.\n";
1329+
_close_h5_objects(close_map);
1330+
return false;
1331+
}
13281332
}
1333+
int polarity_str_idx = 0;
1334+
int left_pol_idx = 0;
1335+
int right_pol_idx = 0;
13291336

13301337
for(size_t i = 0; i < dims3[0]; i++)
13311338
{
13321339
offset3[0] = i;
13331340
H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset3, nullptr, count3, nullptr);
13341341

1335-
if(i > 0)
1342+
if (params_override != nullptr && params_override->polarity_pattern.size() > 0)
1343+
{
1344+
if (polarity_str_idx >= params_override->polarity_pattern.size())
1345+
{
1346+
polarity_str_idx = 0;
1347+
}
1348+
if (params_override->polarity_pattern.at(polarity_str_idx) == 'L')
1349+
{
1350+
polarity = 0;
1351+
idx = left_pol_idx;
1352+
left_pol_idx++;
1353+
}
1354+
else if (params_override->polarity_pattern.at(polarity_str_idx) == 'R')
1355+
{
1356+
polarity = 1;
1357+
idx = right_pol_idx;
1358+
right_pol_idx++;
1359+
}
1360+
else
1361+
{
1362+
logW << "Unknown polarity override " << params_override->polarity_pattern[polarity_str_idx] << " in override string : " << params_override->polarity_pattern << "\n";
1363+
}
1364+
}
1365+
else
13361366
{
1337-
if(use_pr1)
1367+
if (i > 0)
13381368
{
1339-
if(pr1_array[i] != pr1_array[i-1])
1369+
if (use_pr1)
13401370
{
1341-
if(polarity == 1)
1342-
{
1343-
polarity = 0;
1344-
idx++;
1345-
}
1346-
else
1371+
if (pr1_array[i] != pr1_array[i - 1])
13471372
{
1348-
polarity = 1;
1373+
if (polarity == 1)
1374+
{
1375+
polarity = 0;
1376+
idx++;
1377+
}
1378+
else
1379+
{
1380+
polarity = 1;
1381+
}
13491382
}
13501383
}
1351-
}
1352-
else
1353-
{
1354-
if(pr2_array[i] != pr2_array[i-1])
1384+
else
13551385
{
1356-
if(polarity == 1)
1386+
if (pr2_array[i] != pr2_array[i - 1])
13571387
{
1358-
polarity = 0;
1388+
if (polarity == 1)
1389+
{
1390+
polarity = 0;
1391+
}
1392+
else
1393+
{
1394+
polarity = 1;
1395+
}
13591396
}
13601397
else
13611398
{
1362-
polarity = 1;
1399+
idx++;
13631400
}
13641401
}
1365-
else
1366-
{
1367-
idx++;
1368-
}
13691402
}
13701403
}
13711404

@@ -8468,6 +8501,18 @@ class DLL_EXPORT HDF5_IO
84688501
}
84698502
}
84708503

8504+
//Save polarity pattern
8505+
if (_open_h5_dataset(STR_POLARITY_PATTERN, filetype, scan_grp_id, 1, count, count, dset_id, dataspace_id))
8506+
{
8507+
char tmp_char[255] = { 0 };
8508+
meta_info->polarity_pattern.copy(tmp_char, 254);
8509+
status = H5Dwrite(dset_id, memtype, memoryspace_id, dataspace_id, H5P_DEFAULT, (void*)tmp_char);
8510+
if (status < 0)
8511+
{
8512+
logE << "failed to write " << STR_POLARITY_PATTERN << "\n";
8513+
}
8514+
}
8515+
84718516
if (_open_h5_dataset(STR_SCAN_TIME_STAMP, filetype, scan_grp_id, 1, count, count, dset_id, dataspace_id))
84728517
{
84738518
char tmp_char[255] = { 0 };

‎src/io/file/hl_file_io.h‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -916,7 +916,7 @@ DLL_EXPORT bool load_spectra_volume(std::string dataset_directory,
916916
{
917917
// try to load polar hdf master file
918918
data_struct::Scan_Info<double> scan_info;
919-
if(true == io::file::HDF5_IO::inst()->load_spectra_vol_polar_energy_scan(dataset_directory, dataset_file, detector_num, spectra_volume, scan_info))
919+
if(true == io::file::HDF5_IO::inst()->load_spectra_vol_polar_energy_scan(dataset_directory, dataset_file, detector_num, spectra_volume, scan_info, params_override))
920920
{
921921
scan_type = STR_SCAN_TYPE_POLAR_XANES;
922922
if(io::file::HDF5_IO::inst()->start_save_seq(true))

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