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v1.0.0-rc.146 (#56)
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Browse Source 
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
This commit was merged in pull request #56.
This commit is contained in:
leonarski_f
2026-05-28 18:48:35 +02:00
parent 75f1c5f954
commit fc68a9baed
273 changed files with 16303 additions and 2642 deletions
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frame_serialize/CBORStream2Deserializer.cpp
+101 -1
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@@ -228,6 +228,42 @@ namespace {
return {ptr, len};
}
void GetCBORUInt8Array(CborValue &value, std::vector<uint8_t> &v) {
if (GetCBORTag(value) != TagUnsignedInt8Bit)
throw JFJochException(JFJochExceptionCategory::CBORError, "Incorrect array type tag");
auto [ptr, len] = GetCBORByteString(value);
v.resize(len);
memcpy(v.data(), ptr, len);
}
void GetCBORInt32Array(CborValue &value, std::vector<int32_t> &v) {
if (GetCBORTag(value) != TagSignedInt32BitLE)
throw JFJochException(JFJochExceptionCategory::CBORError, "Incorrect array type tag");
auto [ptr, len] = GetCBORByteString(value);
if (len % sizeof(int32_t))
throw JFJochException(JFJochExceptionCategory::CBORError, "Size mismatch");
v.resize(len / sizeof(int32_t));
memcpy(v.data(), ptr, len);
}
void GetCBORInt64Array(CborValue &value, std::vector<int64_t> &v) {
if (GetCBORTag(value) != TagSignedInt64BitLE)
throw JFJochException(JFJochExceptionCategory::CBORError, "Incorrect array type tag");
auto [ptr, len] = GetCBORByteString(value);
if (len % sizeof(int64_t))
throw JFJochException(JFJochExceptionCategory::CBORError, "Size mismatch");
v.resize(len / sizeof(int64_t));
memcpy(v.data(), ptr, len);
}
void GetCBORFloatArray(CborValue &value, std::vector<float> &v) {
if (GetCBORTag(value) != TagFloatLE)
throw JFJochException(JFJochExceptionCategory::CBORError, "Incorrect array type tag");
@@ -455,6 +491,10 @@ namespace {
r.predicted_x = GetCBORFloat(map_value);
else if (key == "y")
r.predicted_y = GetCBORFloat(map_value);
else if (key == "obs_x")
r.observed_x = GetCBORFloat(map_value);
else if (key == "obs_y")
r.observed_y = GetCBORFloat(map_value);
else if (key == "d")
r.d = GetCBORFloat(map_value);
else if (key == "I")
@@ -473,6 +513,8 @@ namespace {
r.partiality = GetCBORFloat(map_value);
else if (key == "zeta")
r.zeta = GetCBORFloat(map_value);
else if (key == "image_scale_corr")
r.image_scale_corr = GetCBORFloat(map_value);
else
cbor_value_advance(&map_value);
}
@@ -691,6 +733,10 @@ namespace {
message.processing_time_s = GetCBORFloat(value);
else if (key == "preprocessing_time")
message.preprocessing_time_s = GetCBORFloat(value);
else if (key == "compression_time")
message.compression_time_s = GetCBORFloat(value);
else if (key == "image_scale_time")
message.image_scale_time_s = GetCBORFloat(value);
else if (key == "azint_time")
message.azint_time_s = GetCBORFloat(value);
else if (key == "profile_radius")
@@ -749,6 +795,14 @@ namespace {
message.beam_corr_x = GetCBORFloat(value);
else if (key == "beam_corr_y")
message.beam_corr_y = GetCBORFloat(value);
else if (key == "image_scale_factor")
message.image_scale_factor = GetCBORFloat(value);
else if (key == "image_scale_cc")
message.image_scale_cc = GetCBORFloat(value);
else if (key == "image_scale_mosaicity")
message.image_scale_mosaicity = GetCBORFloat(value);
else if (key == "image_scale_b_factor")
message.image_scale_b_factor = GetCBORFloat(value);
else if (key == "roi_integrals")
ProcessROIElementMap(message, value);
else {
@@ -1012,6 +1066,8 @@ namespace {
ProcessROIConfig(message, j["roi"]);
if (j.contains("gain_file_names"))
message.gain_file_names = j["gain_file_names"];
if (j.contains("write_images"))
message.write_images = j["write_images"];
if (j.contains("write_master_file"))
message.write_master_file = j["write_master_file"];
if (j.contains("data_reduction_factor_serialmx"))
@@ -1282,8 +1338,52 @@ namespace {
message.bkg_estimate = GetCBORFloat(value);
else if (key == "indexing_rate")
message.indexing_rate = GetCBORFloat(value);
else if (key == "data_collection_efficiency_image")
GetCBORFloatArray(value, message.data_collection_efficiency);
else if (key == "spot_count")
GetCBORInt32Array(value, message.spot_count);
else if (key == "spot_count_ice_ring")
GetCBORInt32Array(value, message.spot_count_ice_ring);
else if (key == "spot_count_low_res")
GetCBORInt32Array(value, message.spot_count_low_res);
else if (key == "spot_count_indexed")
GetCBORInt32Array(value, message.spot_count_indexed);
else if (key == "image_indexed")
GetCBORUInt8Array(value, message.image_indexed);
else if (key == "v_bkg_estimate")
GetCBORFloatArray(value, message.v_bkg_estimate);
else if (key == "profile_radius")
GetCBORFloatArray(value, message.profile_radius);
else if (key == "mosaicity")
GetCBORFloatArray(value, message.mosaicity);
else if (key == "bFactor")
GetCBORFloatArray(value, message.bFactor);
else if (key == "resolution_estimate")
GetCBORFloatArray(value, message.resolution_estimate);
else if (key == "min_viable_pixel_value")
GetCBORInt64Array(value, message.min_viable_pixel_value);
else if (key == "max_viable_pixel_value")
GetCBORInt64Array(value, message.max_viable_pixel_value);
else if (key == "saturated_pixel_count")
GetCBORInt32Array(value, message.saturated_pixel_count);
else if (key == "error_pixel_count")
GetCBORInt32Array(value, message.error_pixel_count);
else if (key == "image_scale_factor")
GetCBORFloatArray(value, message.scale_factor);
GetCBORFloatArray(value, message.image_scale_factor);
else if (key == "image_scale_cc")
GetCBORFloatArray(value, message.image_scale_cc);
else if (key == "image_scale_mosaicity")
GetCBORFloatArray(value, message.image_scale_mosaicity);
else if (key == "image_scale_b_factor")
GetCBORFloatArray(value, message.image_scale_b_factor);
else if (key == "integrated_reflections")
GetCBORInt32Array(value, message.integrated_reflections);
else if (key == "niggli_class")
GetCBORUInt8Array(value, message.niggli_class);
else if (key == "unit_cell")
message.unit_cell = ProcessUnitCellElement(value);
else if (key == "pixel_sum")
GetCBORInt64Array(value, message.pixel_sum);
else if (key == "rotation_lattice") {
std::vector<float> tmp;
GetCBORFloatArray(value, tmp);