mx/Jungfraujoch
0
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases 37 Wiki Activity

v1.0.0-rc.72

Browse Source
This commit is contained in:
leonarski_f
2025-09-08 20:28:59 +02:00
parent 6c88c6902e
commit c67337cfe1
275 changed files with 7525 additions and 1039 deletions
Download Patch File Download Diff File Expand all files Collapse all files

50
writer/HDF5DataFilePluginMX.cpp
View File

@@ -4,7 +4,10 @@
#include "HDF5DataFilePluginMX.h"
#define RESERVE_IMAGES 1000
HDF5DataFilePluginMX::HDF5DataFilePluginMX(size_t in_max_spots) : max_spots(in_max_spots) {}
HDF5DataFilePluginMX::HDF5DataFilePluginMX(const StartMessage& msg)
: max_spots(msg.max_spot_count) {
}
void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg) {
bkg_estimate.reserve(RESERVE_IMAGES);
@@ -17,12 +20,18 @@ void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg)
spot_int.reserve(max_spots * RESERVE_IMAGES);
spot_indexed.reserve(max_spots * RESERVE_IMAGES);
spot_ice_ring.reserve(max_spots * RESERVE_IMAGES);
angle_from_ewald_sphere.reserve(max_spots * RESERVE_IMAGES);
spot_h.reserve(max_spots * RESERVE_IMAGES);
spot_k.reserve(max_spots * RESERVE_IMAGES);
spot_l.reserve(max_spots * RESERVE_IMAGES);
spot_dist_ewald.reserve(max_spots * RESERVE_IMAGES);
beam_corr_x.reserve(RESERVE_IMAGES);
beam_corr_y.reserve(RESERVE_IMAGES);
npeaks.reserve(RESERVE_IMAGES);
strong_pixel_count.reserve(RESERVE_IMAGES);
indexed.reserve(RESERVE_IMAGES);
mosaicity.reserve(RESERVE_IMAGES);
profile_radius.reserve(RESERVE_IMAGES);
b_factor.reserve(RESERVE_IMAGES);
indexed_lattice.reserve(9 * RESERVE_IMAGES);
spot_count_rings.reserve(RESERVE_IMAGES);
@@ -44,9 +53,12 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
spot_int.resize(max_spots * (max_image_number + 1));
spot_indexed.resize(max_spots * (max_image_number + 1));
spot_ice_ring.resize(max_spots * (max_image_number + 1));
spot_h.resize(max_spots * (max_image_number + 1));
spot_k.resize(max_spots * (max_image_number + 1));
spot_l.resize(max_spots * (max_image_number + 1));
spot_dist_ewald.resize(max_spots * (max_image_number + 1));
indexed_lattice.resize((max_image_number + 1) * 9);
angle_from_ewald_sphere.resize((max_image_number + 1) * 9);
}
uint32_t spot_cnt = std::min(msg.spots.size(), max_spots);
@@ -57,7 +69,10 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
spot_int[max_spots * image_number + i] = msg.spots[i].intensity;
spot_indexed[max_spots * image_number + i] = msg.spots[i].indexed;
spot_ice_ring[max_spots * image_number + i] = msg.spots[i].ice_ring;
angle_from_ewald_sphere[max_spots * image_number + i] = msg.spots[i].angle_from_ewald_sphere;
spot_h[max_spots * image_number + i] = msg.spots[i].h;
spot_k[max_spots * image_number + i] = msg.spots[i].k;
spot_l[max_spots * image_number + i] = msg.spots[i].l;
spot_dist_ewald[max_spots * image_number + i] = msg.spots[i].dist_ewald_sphere;
}
npeaks[image_number] = spot_cnt;
@@ -67,8 +82,8 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
if (msg.indexing_result.has_value())
indexed[image_number] = msg.indexing_result.value();
if (msg.mosaicity.has_value())
mosaicity[image_number] = msg.mosaicity.value();
if (msg.profile_radius.has_value())
profile_radius[image_number] = msg.profile_radius.value();
if (msg.b_factor.has_value())
b_factor[image_number] = msg.b_factor.value();
@@ -79,6 +94,11 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
if (msg.spot_count_ice_rings)
spot_count_rings[image_number] = msg.spot_count_ice_rings.value();
if (msg.beam_corr_x)
beam_corr_x[image_number] = msg.beam_corr_x.value();
if (msg.beam_corr_y)
beam_corr_y[image_number] = msg.beam_corr_y.value();
if (msg.indexing_lattice) {
auto tmp = msg.indexing_lattice->GetVector();
@@ -96,8 +116,12 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
data_file.SaveVector("/entry/MX/peakTotalIntensity", spot_int, {(hsize_t) (max_image_number + 1), max_spots});
data_file.SaveVector("/entry/MX/peakIndexed", spot_indexed, {(hsize_t) (max_image_number + 1), max_spots});
data_file.SaveVector("/entry/MX/peakIceRingRes", spot_ice_ring, {(hsize_t) (max_image_number + 1), max_spots});
data_file.SaveVector("/entry/MX/peakIndexedAngleFromEwald", angle_from_ewald_sphere, {(hsize_t) (max_image_number + 1), max_spots});
data_file.SaveVector("/entry/MX/nPeaks", npeaks.vec());
data_file.SaveVector("/entry/MX/peakH", spot_h, {(hsize_t) (max_image_number + 1), max_spots});
data_file.SaveVector("/entry/MX/peakK", spot_k, {(hsize_t) (max_image_number + 1), max_spots});
data_file.SaveVector("/entry/MX/peakL", spot_l, {(hsize_t) (max_image_number + 1), max_spots});
data_file.SaveVector("/entry/MX/peakDistEwaldSphere", spot_dist_ewald, {(hsize_t) (max_image_number + 1), max_spots});
}
if (!strong_pixel_count.empty())
@@ -111,10 +135,16 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
data_file.SaveVector("/entry/MX/latticeIndexed", indexed_lattice, {(hsize_t) (max_image_number + 1), 9});
if (!bkg_estimate.empty())
data_file.SaveVector("/entry/MX/bkgEstimate", bkg_estimate.vec());
if (!mosaicity.empty())
data_file.SaveVector("/entry/MX/mosaicity", mosaicity.vec())->Units("deg");
if (!profile_radius.empty())
data_file.SaveVector("/entry/MX/profileRadius", profile_radius.vec())->Units("Angstrom^-1");
if (!b_factor.empty())
data_file.SaveVector("/entry/MX/bFactor", b_factor.vec())->Units("Angstrom^2");
if (!beam_corr_x.empty())
data_file.SaveVector("/entry/MX/beam_corr_x", beam_corr_x.vec())->Units("pixel");
if (!beam_corr_y.empty())
data_file.SaveVector("/entry/MX/beam_corr_y", beam_corr_y.vec())->Units("pixel");
if (!resolution_estimate.empty())
data_file.SaveVector("/entry/MX/resolutionEstimate", resolution_estimate.vec())->Units("Angstrom");
}