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BraggIntegrate2D: Keeps observed x and y positions for reflections
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This commit is contained in:
leonarski_f
2026-05-24 12:38:54 +02:00
parent 752d3e95f1
commit 6621ddb2ef
11 changed files with 50 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files
common/Reflection.h
+2
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@@ -18,6 +18,8 @@ struct Reflection {
float delta_phi_deg; // phi angle from XDS - difference from middle of current frame (NOT an absolute angle)
float predicted_x;
float predicted_y;
float observed_x;
float observed_y;
float d;
float I;
float bkg;
docs/CBOR.md
+4 -2
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@@ -139,8 +139,10 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
| - h | int64 | Miller index | | |
| - k | int64 | Miller index | | |
| - l | int64 | Miller index | | |
| - x | float | position in x (pixels) | | |
| - y | float | position in y (pixels) | | |
| - x | float | prediced position in x (pixels) | | |
| - y | float | predicted position in y (pixels) | | |
| - obs_x | float | observed position in x (pixels) | | |
| - obs_y | float | observed position in y (pixels) | | |
| - d | float | resolution \[Angstrom\] | | |
| - I | float | integrated intensity (photons) | | |
| - bkg | float | mean background value (photons) | | |
frame_serialize/CBORStream2Deserializer.cpp
+4
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@@ -491,6 +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")
frame_serialize/CBORStream2Serializer.cpp
+2
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@@ -255,6 +255,8 @@ inline void CBOR_ENC(CborEncoder &encoder, const Reflection& r) {
CBOR_ENC(mapEncoder, "phi", r.delta_phi_deg);
CBOR_ENC(mapEncoder, "x", r.predicted_x);
CBOR_ENC(mapEncoder, "y", r.predicted_y);
CBOR_ENC(mapEncoder, "obs_x", r.observed_x);
CBOR_ENC(mapEncoder, "obs_y", r.observed_y);
CBOR_ENC(mapEncoder, "d", r.d);
CBOR_ENC(mapEncoder, "I", r.I);
CBOR_ENC(mapEncoder, "bkg", r.bkg);
image_analysis/bragg_integration/BraggIntegrate2D.cpp
+11 -3
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@@ -92,6 +92,9 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
int64_t I_sum = 0;
int64_t I_npixel_inner = 0;
int64_t I_npixel_integrated = 0;
int64_t I_sum_x = 0;
int64_t I_sum_y = 0;
std::vector<T> bkg_values;
bkg_values.reserve(static_cast<size_t>((x1 - x0 + 1) * (y1 - y0 + 1)));
@@ -108,6 +111,8 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
if (dist_sq < r_1_sq) {
I_sum += pixel;
I_sum_x += x * pixel;
I_sum_y += y * pixel;
I_npixel_integrated++;
} else if (dist_sq >= r_2_sq && dist_sq < r_3_sq) {
if (reflection_mask[y * xpixel + x] != 0)
@@ -120,13 +125,16 @@ void IntegrateReflection(Reflection &r, const T *image, const std::vector<uint8_
if ((I_npixel_integrated == I_npixel_inner) && (bkg_values.size() > 5)) {
r.bkg = Median(bkg_values);
r.I = static_cast<float>(I_sum) - static_cast<float>(I_npixel_integrated) * r.bkg;
if (I_sum > 0) {
r.observed_x = static_cast<float>(I_sum_x) / static_cast<float>(I_sum);
r.observed_y = static_cast<float>(I_sum_y) / static_cast<float>(I_sum);
}
// sigma is max of the:
// - 1 (for very small numbers)
// - 1 (for zero photons)
// - Poisson noise (sqrt(I_sum)) (for in between)
// - minimum_sigma_in_regards_to_i of Intensity (for very large numbers)
r.sigma = 1.0;
r.sigma = std::max(r.sigma, r.I * minimum_sigma_in_regards_to_i);
r.sigma = std::max(1.0f, r.I * minimum_sigma_in_regards_to_i);
if (I_sum > 0)
r.sigma = std::max(r.sigma, std::sqrt(static_cast<float>(I_sum)));
r.observed = true;
image_analysis/bragg_prediction/BraggPrediction.cpp
+2
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@@ -127,6 +127,8 @@ int BraggPrediction::Calc(const DiffractionExperiment &experiment, const Crystal
.delta_phi_deg = delta_phi_deg,
.predicted_x = x,
.predicted_y = y,
.observed_x = NAN,
.observed_y = NAN,
.d = d,
.dist_ewald = dist_ewald_sphere,
.rlp = 1.0,
image_analysis/bragg_prediction/BraggPredictionGPU.cu
+2
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@@ -110,6 +110,8 @@ namespace {
out.delta_phi_deg = angle_from_ewald_sphere_deg(C.S0, recip_x, recip_y, recip_z, recip_sq);
out.predicted_x = x;
out.predicted_y = y;
out.observed_x = NAN;
out.observed_y = NAN;
out.d = 1.0f / sqrtf(recip_sq);
out.dist_ewald = dist_ewald;
out.rlp = 1.0f;
image_analysis/bragg_prediction/BraggPredictionRot.cpp
+2
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@@ -137,6 +137,8 @@ int BraggPredictionRot::Calc(const DiffractionExperiment &experiment, const Crys
.delta_phi_deg = phi * 180.0f / static_cast<float>(M_PI),
.predicted_x = x,
.predicted_y = y,
.observed_x = NAN,
.observed_y = NAN,
.d = d,
.dist_ewald = dist_ewald_sphere,
.rlp = lorentz_reciprocal,
image_analysis/bragg_prediction/BraggPredictionRotGPU.cu
+2
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@@ -153,6 +153,8 @@ namespace {
out[count].delta_phi_deg = phi * 180.0 / M_PI;
out[count].predicted_x = x;
out[count].predicted_y = y;
out[count].observed_x = NAN;
out[count].observed_y = NAN;
out[count].d = 1.0f / sqrtf(p0_sq);
out[count].dist_ewald = dist_ewald;
out[count].rlp = lorentz;
reader/JFJochHDF5Reader.cpp
+12 -1
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@@ -140,7 +140,8 @@ bool ReadReflectionsFromGroup(HDF5Object &file,
auto l = file.ReadOptVector<int32_t>(image_group_name + "/l");
auto predicted_x = file.ReadOptVector<float>(image_group_name + "/predicted_x");
auto predicted_y = file.ReadOptVector<float>(image_group_name + "/predicted_y");
auto obs_x = file.ReadOptVector<float>(image_group_name + "/observed_x");
auto obs_y = file.ReadOptVector<float>(image_group_name + "/observed_y");
auto d = file.ReadOptVector<float>(image_group_name + "/d");
auto int_sum = file.ReadOptVector<float>(image_group_name + "/int_sum");
auto int_err = file.ReadOptVector<float>(image_group_name + "/int_err");
@@ -175,6 +176,14 @@ bool ReadReflectionsFromGroup(HDF5Object &file,
if (image_scale_corr.size() > i)
image_scale_corr_val = image_scale_corr[i];
float obs_x_val = NAN;
float obs_y_val = NAN;
if (obs_x.size() > i && obs_y.size() > i) {
obs_x_val = obs_x[i];
obs_y_val = obs_y[i];
}
Reflection r{
.h = h.at(i),
.k = k.at(i),
@@ -182,6 +191,8 @@ bool ReadReflectionsFromGroup(HDF5Object &file,
.delta_phi_deg = delta_phi_val,
.predicted_x = predicted_x.at(i),
.predicted_y = predicted_y.at(i),
.observed_x = obs_x_val,
.observed_y = obs_y_val,
.d = d.at(i),
.I = int_sum.at(i),
.bkg = bkg.at(i),
writer/HDF5DataFilePluginReflection.cpp
+7 -1
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@@ -16,7 +16,7 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
std::vector<int32_t> h, k, l;
std::vector<float> I, sigma, d, lp;
std::vector<float> image, phi, pred_x, pred_y, bkg, partiality, zeta, scale_factor;
std::vector<float> image, phi, pred_x, pred_y, obs_x, obs_y, bkg, partiality, zeta, scale_factor;
h.reserve(msg.reflections.size());
k.reserve(msg.reflections.size());
@@ -26,6 +26,8 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
d.reserve(msg.reflections.size());
pred_x.reserve(msg.reflections.size());
pred_y.reserve(msg.reflections.size());
obs_x.reserve(msg.reflections.size());
obs_y.reserve(msg.reflections.size());
bkg.reserve(msg.reflections.size());
lp.reserve(msg.reflections.size());
partiality.reserve(msg.reflections.size());
@@ -44,6 +46,8 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
d.emplace_back(refl.d);
pred_x.emplace_back(refl.predicted_x);
pred_y.emplace_back(refl.predicted_y);
obs_x.emplace_back(refl.observed_x);
obs_y.emplace_back(refl.observed_y);
bkg.emplace_back(refl.bkg);
lp.emplace_back(1.0/refl.rlp);
partiality.emplace_back(refl.partiality);
@@ -62,6 +66,8 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
image_group.SaveVector("delta_phi", phi);
image_group.SaveVector("predicted_x", pred_x);
image_group.SaveVector("predicted_y", pred_y);
image_group.SaveVector("observed_x", obs_x);
image_group.SaveVector("observed_y", obs_y);
image_group.SaveVector("int_sum", I);
image_group.SaveVector("int_err", sigma);
image_group.SaveVector("background_mean", bkg);