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Add ability to put their own 'add_ref_line.xml' files in their user d…
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…ata directory, to load on application start.
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@wcjohns
wcjohns committed Feb 16, 2024
1 parent b9ca86e commit 6a7f741
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58 changes: 42 additions & 16 deletions data/add_ref_line.xml
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@@ -1,5 +1,47 @@
<?xml version="1.0" encoding="utf-8" ?>

<!-- If you want to define your own reference photopeak lines in InterSpec, you
can copy this file to the applications data directory (See Help -> Data for this
location, but usually on Windows its 'C:\Users\username\AppData\Roaming\InterSpec'
and on macOS '/Users/username/Library/Containers/gov.sandia.macOS.InterSpec/Data/Library/Application Support/sandia.InterSpec')
and then use the examples provided here to define your own source (and delete the rest of the sources defined).
Your custom file will be loaded after this file that comes with InterSpec.
Currently you can define two source type:
1) SourceLines: this is simple energy and branching ratio pairs.
The "Reference Photopeaks" tab will then display
the lines on the spectrum, but you can not associate
a peak with one of these lines (although this may
change in the future).
2) NucMixture: this is a mixture of nuclide, at a specified relative
activities to each other. When the name of the NucMixture
is entered into the "Reference Photopeaks" tab, the lines
of the nuclides will be displayed, and gamma-line associations
with peaks can happen as normal. You can also enter custom
ages into the UI to change the amount of progeny in-growth.
Note that the activity fraction specified, is currently at the
aged time (not at t=0), but this may be refined in the future.
-->

<RefLineDefinitions>
<SourceLines name="HPGe(n,n)">
<!-- Each line consists of two numbers; the energy (in keV) and the relative branching ratio,
separated by a space.
You can optionally add an attribute, "info", which will show up when you mouse-over the
line in InterSpec.
-->
<Line info="...some info...">430 1.0</Line>
<Line>488 1.0</Line>
<Line>562 1.0</Line>
<Line>596 1.0</Line>
<Line>630 1.0</Line>
<Line>691 1.0</Line>
<Line>834 1.0</Line>
<Line>1039.6 1.0</Line>
</SourceLines>

<!-- Nuclide mixtures must be made up of valid nuclides.
-->
<NucMixture name="Pu low burnup" default-age="20y">
<!-- From FRMAC Gamma Spectroscopist Knowledge Guide 2019-08, Michael Enghauser, Table 13-1 -->
<Nuc name="Pu238" act-frac="0.010" />
Expand Down Expand Up @@ -54,20 +96,4 @@
<Nuc name="U235" act-frac="3.592" />
<Nuc name="U234" act-frac="96.373" />
</NucMixture>

<SourceLines name="HPGe(n,n)">
<!-- Each line consists of two numbers; the energy (in keV) and the relative branching ratio,
separated by a space.
You can optionally add an attribute, "info", which will show up when you mouse-over the
line in InterSpec.
-->
<Line info="...some info...">430 1.0</Line>
<Line>488 1.0</Line>
<Line>562 1.0</Line>
<Line>596 1.0</Line>
<Line>630 1.0</Line>
<Line>691 1.0</Line>
<Line>834 1.0</Line>
<Line>1039.6 1.0</Line>
</SourceLines>
</RefLineDefinitions>
253 changes: 134 additions & 119 deletions src/ReferenceLineInfo.cpp
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Expand Up @@ -131,145 +131,159 @@ namespace

sm_have_tried_init = true;

const string data_dir = InterSpec::staticDataDirectory();
const string custom_mix_path = SpecUtils::append_path( data_dir, "add_ref_line.xml" );

try
{
const SandiaDecay::SandiaDecayDataBase *db = DecayDataBaseServer::database();
assert( db );
if( !db )
throw std::logic_error( "invalid SandiaDecayDataBase" );

auto answer = make_shared<map<string,NucMix>>();

std::vector<char> data;
SpecUtils::load_file_data( custom_mix_path.c_str(), data );

rapidxml::xml_document<char> doc;
const int flags = rapidxml::parse_normalize_whitespace | rapidxml::parse_trim_whitespace;
doc.parse<flags>( &data.front() );
auto load_ref_line_file = []( const string filepath, map<string,NucMix> &nuc_mixes, map<string,CustomSrcLines> &custom_lines ){

const XmlNode *ref_lines = doc.first_node( "RefLineDefinitions" );
if( !ref_lines )
throw runtime_error( "No RefLineDefinitions node." );

XML_FOREACH_CHILD( nuc_mix, ref_lines, "NucMixture" )
try
{
const XmlAttribute *mix_name = XML_FIRST_ATTRIB( nuc_mix, "name" );
const XmlAttribute *def_age = XML_FIRST_ATTRIB( nuc_mix, "default-age" );
const SandiaDecay::SandiaDecayDataBase *db = DecayDataBaseServer::database();
assert( db );
if( !db )
throw std::logic_error( "invalid SandiaDecayDataBase" );

string mix_name_str = SpecUtils::xml_value_str( mix_name );
if( mix_name_str.empty() )
throw runtime_error( "No mixture name" );
std::vector<char> data;
SpecUtils::load_file_data( filepath.c_str(), data );

NucMix mix;
mix.m_name = mix_name_str;
mix.m_default_age = 0.0;
mix.m_default_age_str = "";
if( def_age )
{
mix.m_default_age_str = SpecUtils::xml_value_str( def_age );
mix.m_default_age = PhysicalUnits::stringToTimeDuration( mix.m_default_age_str );
}
rapidxml::xml_document<char> doc;
const int flags = rapidxml::parse_normalize_whitespace | rapidxml::parse_trim_whitespace;
doc.parse<flags>( &data.front() );

const XmlNode *ref_lines = doc.first_node( "RefLineDefinitions" );
if( !ref_lines )
throw runtime_error( "No RefLineDefinitions node." );

double act_fraction_sum = 0.0;
XML_FOREACH_CHILD( nuc, nuc_mix, "Nuc" )
XML_FOREACH_CHILD( nuc_mix, ref_lines, "NucMixture" )
{
const XmlAttribute *nuc_name = XML_FIRST_ATTRIB( nuc, "name" );
const XmlAttribute *nuc_act_frac = XML_FIRST_ATTRIB( nuc, "act-frac" );
const XmlAttribute *mix_name = XML_FIRST_ATTRIB( nuc_mix, "name" );
const XmlAttribute *def_age = XML_FIRST_ATTRIB( nuc_mix, "default-age" );

if( !nuc_name || !nuc_name->value_size() )
throw runtime_error( "No nuclide name" );
string mix_name_str = SpecUtils::xml_value_str( mix_name );
if( mix_name_str.empty() )
throw runtime_error( "No mixture name" );

const string nuc_name_str = SpecUtils::xml_value_str( nuc_name );
NucMix mix;
mix.m_name = mix_name_str;
mix.m_default_age = 0.0;
mix.m_default_age_str = "";
if( def_age )
{
mix.m_default_age_str = SpecUtils::xml_value_str( def_age );
mix.m_default_age = PhysicalUnits::stringToTimeDuration( mix.m_default_age_str );
}

if( !nuc_act_frac || !nuc_act_frac->value_size() )
throw runtime_error( "No activity fraction for " + nuc_name_str
+ " in " + mix_name_str );
double act_fraction_sum = 0.0;
XML_FOREACH_CHILD( nuc, nuc_mix, "Nuc" )
{
const XmlAttribute *nuc_name = XML_FIRST_ATTRIB( nuc, "name" );
const XmlAttribute *nuc_act_frac = XML_FIRST_ATTRIB( nuc, "act-frac" );

if( !nuc_name || !nuc_name->value_size() )
throw runtime_error( "No nuclide name" );

const string nuc_name_str = SpecUtils::xml_value_str( nuc_name );

if( !nuc_act_frac || !nuc_act_frac->value_size() )
throw runtime_error( "No activity fraction for " + nuc_name_str
+ " in " + mix_name_str );

NucMixComp comp;
comp.m_age_offset = 0.0;
comp.m_nuclide = db->nuclide( nuc_name_str );
if( !comp.m_nuclide )
throw runtime_error( "Invalid nuclide: " + nuc_name_str );

if( !SpecUtils::parse_double( nuc_act_frac->value(), nuc_act_frac->value_size(),
comp.m_act_fraction )
|| (comp.m_act_fraction < 0.0) )
throw runtime_error( "Invalid activity fraction: " + nuc_name_str );

act_fraction_sum += comp.m_act_fraction;
mix.m_components.push_back( std::move(comp) );
}//XML_FOREACH_CHILD( nuc, nuc_mix, "Nuc" )

NucMixComp comp;
comp.m_age_offset = 0.0;
comp.m_nuclide = db->nuclide( nuc_name_str );
if( !comp.m_nuclide )
throw runtime_error( "Invalid nuclide: " + nuc_name_str );
if( (act_fraction_sum <= 0.0) || IsNan(act_fraction_sum) || IsInf(act_fraction_sum) )
throw runtime_error( "Invalid activity fraction sum" );

if( !SpecUtils::parse_double( nuc_act_frac->value(), nuc_act_frac->value_size(),
comp.m_act_fraction )
|| (comp.m_act_fraction < 0.0) )
throw runtime_error( "Invalid activity fraction: " + nuc_name_str );
for( auto &m : mix.m_components )
m.m_act_fraction /= act_fraction_sum ;

act_fraction_sum += comp.m_act_fraction;
mix.m_components.push_back( std::move(comp) );
}//XML_FOREACH_CHILD( nuc, nuc_mix, "Nuc" )

if( (act_fraction_sum <= 0.0) || IsNan(act_fraction_sum) || IsInf(act_fraction_sum) )
throw runtime_error( "Invalid activity fraction sum" );

for( auto &m : mix.m_components )
m.m_act_fraction /= act_fraction_sum ;

sanitize_label_str( mix_name_str );
(*answer)[mix_name_str] = std::move(mix);
}//XML_FOREACH_CHILD( nuc_mix, ref_lines, "NucMixture" )

sm_nuc_mixes = answer;


auto custom_lines = make_shared<map<string,CustomSrcLines>>();
XML_FOREACH_CHILD( source, ref_lines, "SourceLines" )
{
const XmlAttribute *src_name = XML_FIRST_ATTRIB( source, "name" );
string src_name_str = SpecUtils::xml_value_str( src_name );
SpecUtils::trim( src_name_str );
sanitize_label_str( mix_name_str );
nuc_mixes[mix_name_str] = std::move(mix);
}//XML_FOREACH_CHILD( nuc_mix, ref_lines, "NucMixture" )

if( src_name_str.empty() )
throw runtime_error( "No name specified for a SourceLines element" );

CustomSrcLines src_lines;
src_lines.m_name = src_name_str;
src_lines.m_max_branch_ratio = 0.0;
XML_FOREACH_CHILD( line, source, "Line" )
XML_FOREACH_CHILD( source, ref_lines, "SourceLines" )
{
const XmlAttribute *info = XML_FIRST_ATTRIB( line, "info" );
string info_str = SpecUtils::xml_value_str( info );
SpecUtils::trim( info_str );
const XmlAttribute *src_name = XML_FIRST_ATTRIB( source, "name" );
string src_name_str = SpecUtils::xml_value_str( src_name );
SpecUtils::trim( src_name_str );

const string values_str = SpecUtils::xml_value_str( line );
if( src_name_str.empty() )
throw runtime_error( "No name specified for a SourceLines element" );

vector<float> values;
SpecUtils::split_to_floats( values_str, values );
if( values.size() != 2 )
throw runtime_error( "SourceLines named '" + src_name_str + "' provided "
+ std::to_string(values.size()) + " values (expected two numbers)" );

const float energy = values[0];
const float br = values[1];
CustomSrcLines src_lines;
src_lines.m_name = src_name_str;
src_lines.m_max_branch_ratio = 0.0;
XML_FOREACH_CHILD( line, source, "Line" )
{
const XmlAttribute *info = XML_FIRST_ATTRIB( line, "info" );
string info_str = SpecUtils::xml_value_str( info );
SpecUtils::trim( info_str );

const string values_str = SpecUtils::xml_value_str( line );

vector<float> values;
SpecUtils::split_to_floats( values_str, values );
if( values.size() != 2 )
throw runtime_error( "SourceLines named '" + src_name_str + "' provided "
+ std::to_string(values.size()) + " values (expected two numbers)" );

const float energy = values[0];
const float br = values[1];

if( (energy <= 0.f) || (br < 0.0f) )
throw runtime_error( "SourceLines named '" + src_name_str + "' has a negative value." );

src_lines.m_max_branch_ratio = std::max( src_lines.m_max_branch_ratio, br );

src_lines.m_lines.emplace_back( energy, br, std::move(info_str) );
}//XML_FOREACH_CHILD( line, source, "Line" )

if( (energy <= 0.f) || (br < 0.0f) )
throw runtime_error( "SourceLines named '" + src_name_str + "' has a negative value." );
if( src_lines.m_lines.empty() )
throw runtime_error( "No lines specified for SourceLines named '" + src_name_str + "'" );

src_lines.m_max_branch_ratio = std::max( src_lines.m_max_branch_ratio, br );
if( src_lines.m_max_branch_ratio <= 0.0f )
throw runtime_error( "Lines specified for SourceLines named '" + src_name_str + "' were all zero amplitude." );

src_lines.m_lines.emplace_back( energy, br, std::move(info_str) );
}//XML_FOREACH_CHILD( line, source, "Line" )

if( src_lines.m_lines.empty() )
throw runtime_error( "No lines specified for SourceLines named '" + src_name_str + "'" );

if( src_lines.m_max_branch_ratio <= 0.0f )
throw runtime_error( "Lines specified for SourceLines named '" + src_name_str + "' were all zero amplitude." );

sanitize_label_str( src_name_str );
(*custom_lines)[std::move(src_name_str)] = std::move(src_lines);
}//XML_FOREACH_CHILD( source, ref_lines, "SourceLines" )

sm_custom_lines = custom_lines;
}catch( std::exception &e )
{
cerr << "Failed to load '" << custom_mix_path << "' as custom ref lines: "
<< e.what() << endl;
}//try / catch to load XML data
sanitize_label_str( src_name_str );
custom_lines[std::move(src_name_str)] = std::move(src_lines);
}//XML_FOREACH_CHILD( source, ref_lines, "SourceLines" )
}catch( std::exception &e )
{
cerr << "Failed to load '" << filepath << "' as custom ref lines: "
<< e.what() << endl;
}//try / catch to load XML data
};//auto load_ref_line_file lambda


const string data_dir = InterSpec::staticDataDirectory();
const string add_lines_path = SpecUtils::append_path( data_dir, "add_ref_line.xml" );

auto nuc_mixes = make_shared<map<string,NucMix>>();
auto custom_lines = make_shared<map<string,CustomSrcLines>>();

load_ref_line_file( add_lines_path, *nuc_mixes, *custom_lines );

#if( BUILD_AS_ELECTRON_APP || IOS || ANDROID || BUILD_AS_OSX_APP || BUILD_AS_LOCAL_SERVER || BUILD_AS_WX_WIDGETS_APP || BUILD_AS_UNIT_TEST_SUITE )
const string user_data_dir = InterSpec::writableDataDirectory();
const string custom_lines_path = SpecUtils::append_path( user_data_dir, "add_ref_line.xml" );

// Any duplicate names, will overwrite what comes with InterSpec
if( SpecUtils::is_file( custom_lines_path ) )
load_ref_line_file( custom_lines_path, *nuc_mixes, *custom_lines );
#endif

sm_nuc_mixes = nuc_mixes;
sm_custom_lines = custom_lines;

//const double end_time = SpecUtils::get_wall_time();
//cout << "load_custom_nuc_mixes(): took " << (end_time - start_time) << " s" << endl;
Expand Down Expand Up @@ -2134,6 +2148,7 @@ std::shared_ptr<ReferenceLineInfo> ReferenceLineInfo::generateRefLineInfo( RefLi
{
for( const NucMixComp &comp : nuc_mix->m_components )
{
// TODO: NucMixComp::m_age_offset should be implemented, and used to define the point in time the relative activities are defined for, so when the user ages things, the relative activities of the parent nuclides will be modified
tuple<vector<ReferenceLineInfo::RefLine>,vector<coincidence_info_t>,bool> nuc_line_info
= make_nuc_lines( comp.m_nuclide, age + comp.m_age_offset, input );

Expand Down

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