Merge pull request #122 from aglowacki/master

Added dead_time and fix analysis during scan
AdvancedPhotonSource · Oct 8, 2021 · 36226af · 36226af
2 parents ed8b4c8 + be303d0
commit 36226af
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Showing 7 changed files with 125 additions and 1 deletion.
diff --git a/src/core/main.cpp b/src/core/main.cpp
@@ -346,6 +346,10 @@ int main(int argc, char *argv[])
         }
     }
 
+    if (clp.option_exists("--add_background"))
+    {
+        analysis_job.add_background = true;
+    }
 
     //TODO: add --quantify-only option if you already did the fits and just want to add quantification
 
@@ -410,7 +414,8 @@ int main(int argc, char *argv[])
 		//analysis_job.update_scalers || 
 		analysis_job.export_int_fitted_to_csv || 
 		analysis_job.update_us_amps_str.length() > 0 ||
-		analysis_job.update_quant_us_amps_str.length() > 0;
+		analysis_job.update_quant_us_amps_str.length() > 0 ||
+        analysis_job.add_background;
 
     bool update_h5_fit = analysis_job.fitting_routines.size() > 0 ||
 		optimize_fit_override_params ||

diff --git a/src/core/process_whole.cpp b/src/core/process_whole.cpp
@@ -890,6 +890,20 @@ void interate_datasets_and_update(data_struct::Analysis_Job& analysis_job)
             io::generate_h5_averages(analysis_job.dataset_directory, dataset_file, analysis_job.detector_num_arr);
         }
 
+        if (analysis_job.add_background)
+        {
+            data_struct::Detector* detector = analysis_job.get_detector(0);
+
+            if (detector != nullptr)
+            {
+                io::file::HDF5_IO::inst()->add_background(analysis_job.dataset_directory, dataset_file, detector->fit_params_override_dict);
+            }
+            else
+            {
+                logW << "Detector == nullptr for add_background\n";
+            }
+        }
+
         //generate a list of dataset to update
         std::vector<std::string> hdf5_dataset_list;
 

diff --git a/src/data_struct/analysis_job.cpp b/src/data_struct/analysis_job.cpp
@@ -70,6 +70,7 @@ Analysis_Job::Analysis_Job()
     stream_over_network = false;
     //update_scalers = false;
     export_int_fitted_to_csv = false;
+    add_background = false;
     command_line = "";
     theta_pv = "";
     network_source_ip = "";

diff --git a/src/data_struct/analysis_job.h b/src/data_struct/analysis_job.h
@@ -137,6 +137,8 @@ class DLL_EXPORT Analysis_Job
 
     bool export_int_fitted_to_csv;
 
+    bool add_background;
+
 	long long mem_limit;
 
 	std::string update_us_amps_str;

diff --git a/src/io/file/hdf5_io.cpp b/src/io/file/hdf5_io.cpp
@@ -7450,6 +7450,97 @@ bool HDF5_IO::save_scan_scalers_bnl(std::string path,
 
 //-----------------------------------------------------------------------------
 
+bool HDF5_IO::add_background(std::string directory, std::string filename, data_struct::Params_Override& params)
+{
+
+    std::lock_guard<std::mutex> lock(_mutex);
+
+    std::string fullname = directory + DIR_END_CHAR + "img.dat" + DIR_END_CHAR + filename;
+    logI << fullname << "\n";
+    hid_t file_id = H5Fopen(fullname.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
+    if (file_id < 0)
+    {
+        logE << "Could not open file\n";
+        return false;
+    }
+    hid_t mca_arr_id = H5Dopen(file_id, "/MAPS/mca_arr", H5P_DEFAULT);
+    if (mca_arr_id < 0)
+    {
+        H5Fclose(file_id);
+        logW << "Could not open /MAPS/mca_arr\n";
+        return false;
+    }
+
+    hid_t back_arr_id = H5Dopen(file_id, "/MAPS/mca_background", H5P_DEFAULT);
+    if (back_arr_id < 0)
+    {
+        hid_t ocpypl_id = H5Pcreate(H5P_OBJECT_COPY);
+        hid_t status = H5Ocopy(file_id, "/MAPS/mca_arr", file_id, "/MAPS/mca_background", ocpypl_id, H5P_DEFAULT);
+        if (status < 0)
+        {
+            H5Fclose(file_id);
+            logW << "Could not copy /MAPS/mca_arr to /MAPS/mca_background\n";
+            return false;
+        }
+        back_arr_id = H5Dopen(file_id, "/MAPS/mca_background", H5P_DEFAULT);
+        if (back_arr_id < 0)
+        {
+            H5Fclose(file_id);
+            logW << "Could not open mca_background after copy /MAPS/mca_arr to /MAPS/mca_background\n";
+            return false;
+        }
+    }
+
+    hid_t mca_arr_space = H5Dget_space(mca_arr_id);
+
+    int rank = H5Sget_simple_extent_ndims(mca_arr_space);
+
+    hsize_t dims_in[3];
+    hsize_t offset[3] = { 0,0,0 };
+    hsize_t count[3] = { 0,1,1 };
+    int status_n = H5Sget_simple_extent_dims(mca_arr_space, &dims_in[0], NULL);
+    if (status_n < 0)
+    {
+        H5Fclose(file_id);
+        logW << "Can't get dims\n";
+        return false;
+    }
+    count[0] = dims_in[0];
+    hid_t memoryspace_id = H5Screate_simple(1, dims_in, nullptr);
+
+    data_struct::ArrayXr buffer(count[0]);
+    fitting::models::Range energy_range = data_struct::get_energy_range(dims_in[0], &(params.fit_params));
+
+	logI << params.fit_params.value(STR_ENERGY_OFFSET) << " " << params.fit_params.value(STR_ENERGY_SLOPE) << " " << params.fit_params.value(STR_ENERGY_QUADRATIC) << " " << 0.0f << " " << params.fit_params.value(STR_SNIP_WIDTH) << " " << energy_range.min << " " << energy_range.max << "\n ";
+
+    for (hsize_t x = 0; x < dims_in[1]; x++)
+    {
+        logI << fullname << " " <<x<< " " << dims_in[1] <<"\n";
+        for (hsize_t y = 0; y < dims_in[2]; y++)
+        {
+            offset[1] = x;
+            offset[2] = y;
+            H5Sselect_hyperslab(mca_arr_space, H5S_SELECT_SET, offset, nullptr, count, nullptr);
+            hid_t error = H5Dread(mca_arr_id, H5T_NATIVE_REAL, memoryspace_id, mca_arr_space, H5P_DEFAULT, buffer.data());
+            if (error > -1 )
+            {
+                ArrayXr background = data_struct::snip_background((data_struct::Spectra*)&buffer, params.fit_params.value(STR_ENERGY_OFFSET), params.fit_params.value(STR_ENERGY_SLOPE), params.fit_params.value(STR_ENERGY_QUADRATIC), 0.0f, params.fit_params.value(STR_SNIP_WIDTH), energy_range.min, energy_range.max);
+                error = H5Dwrite(back_arr_id, H5T_NATIVE_REAL, memoryspace_id, mca_arr_space, H5P_DEFAULT, background.data());
+                if (error < 0)
+                {
+                    logE << x << " " << y << " bad write\n";
+                }
+            }
+        }
+    }
+    H5Dclose(mca_arr_id);
+    H5Dclose(back_arr_id);
+    H5Fclose(file_id);
+
+}
+
+//-----------------------------------------------------------------------------
+
 bool HDF5_IO::generate_avg(std::string avg_filename, std::vector<std::string> files_to_avg)
 {
     std::lock_guard<std::mutex> lock(_mutex);

diff --git a/src/io/file/hdf5_io.h b/src/io/file/hdf5_io.h
@@ -241,6 +241,8 @@ class DLL_EXPORT HDF5_IO
 
     bool end_save_seq(bool loginfo=true);
 
+    bool add_background(std::string directory, std::string filename, data_struct::Params_Override& params);
+
 private:
 
     HDF5_IO();

diff --git a/src/io/file/mda_io.cpp b/src/io/file/mda_io.cpp
@@ -1236,6 +1236,15 @@ void MDA_IO::_load_extra_pvs_vector()
 			_scan_info.extra_pvs.push_back(e_pv);
 		}
 	}
+	else
+	{
+		data_struct::Extra_PV e_pv;
+		e_pv.name = "NULL";
+		e_pv.description = "NULL";
+		e_pv.unit = "NULL";
+		e_pv.value = "NULL";
+		_scan_info.extra_pvs.push_back(e_pv);
+	}
 
 }