v1.0.0-rc.146 (#56)

This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.

jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset.
jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling.
jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file.
jfjoch_scale: Dedicated tool for rescaling/merging existing data.
jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel.

WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being.

Reviewed-on: #56

writer/HDF5DataFilePluginMX.cpp

@@ -94,6 +94,11 @@ void HDF5DataFilePluginMX::OpenFile(HDF5File &data_file, const DataMessage &msg,
     spot_count_indexed.reserve(images_per_file);
     spot_count_low_res.reserve(images_per_file);
     integrated_reflections.reserve(images_per_file);
+
+    image_scale_factor.reserve(images_per_file);
+    image_scale_cc.reserve(images_per_file);
+    image_scale_mosaicity.reserve(images_per_file);
+    image_scale_b_factor.reserve(images_per_file);
 }
 
 void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number) {
@@ -171,6 +176,14 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
             bravais_lattice[image_number] = "";
             niggli_class[image_number] = 0;
         }
+
+        if (!image_scale_factor.empty())
+            image_scale_present = true;
+
+        image_scale_factor[image_number] = msg.image_scale_factor.value_or(NAN);
+        image_scale_cc[image_number] = msg.image_scale_cc.value_or(NAN);
+        image_scale_mosaicity[image_number] = msg.image_scale_mosaicity.value_or(NAN);
+        image_scale_b_factor[image_number] = msg.image_scale_b_factor.value_or(NAN);
     }
 }
 
@@ -225,11 +238,18 @@ void HDF5DataFilePluginMX::WriteFinal(HDF5File &data_file) {
     if (!beam_corr_y.empty())
         data_file.SaveVector("/entry/MX/beam_corr_y", beam_corr_y.vec())->Units("pixel");
     if (!niggli_class.empty())
-        data_file.SaveVector("/entry/MX/niggli_class", niggli_class.vec());
+        data_file.SaveVector("/entry/MX/niggliClass", niggli_class.vec());
     if (!bravais_lattice.empty())
-        data_file.SaveVector("/entry/MX/bravais_lattice", bravais_lattice.vec());
+        data_file.SaveVector("/entry/MX/bravaisLattice", bravais_lattice.vec());
     if (!resolution_estimate.empty())
         data_file.SaveVector("/entry/MX/resolutionEstimate", resolution_estimate.vec())->Units("Angstrom");
     if (!integrated_reflections.empty())
         data_file.SaveVector("/entry/MX/integratedReflections", integrated_reflections.vec());
+
+    if (image_scale_present) {
+        data_file.SaveVector("/entry/MX/imageScaleFactor", image_scale_factor.vec());
+        data_file.SaveVector("/entry/MX/imageScaleCC", image_scale_cc.vec());
+        data_file.SaveVector("/entry/MX/imageScaleMosaicity", image_scale_mosaicity.vec())->Units("deg");
+        data_file.SaveVector("/entry/MX/imageScaleBFactor", image_scale_b_factor.vec())->Units("Angstrom^2");
+    }
 }