From 9c205e6311bdbf76262ddd35625278190b3b83aa Mon Sep 17 00:00:00 2001 From: William Johnson Date: Mon, 9 Sep 2024 14:47:06 -0700 Subject: [PATCH] More work on templating batch results. Added HTML report and HTML summary. Renamed or re-defined a lot of the JSON variables, and fixed some bugs with them. Maybe fix a compile issue with tests on Win32. Getting closer to having templating of act/shield fit results good-enough. --- CMakeLists.txt | 20 +- InterSpec/AppUtils.h | 1 + InterSpec/BatchPeak.h | 2 +- InterSpec/GammaInteractionCalc.h | 4 +- .../ShieldSourceFitLog/act_fit.tmplt.html | 513 +++++++++++++++++ .../ShieldSourceFitLog/std_fit_log.tmplt.txt | 6 +- ...ummary.tmplt.txt => std_summary.tmplt.csv} | 1 - src/AppUtils.cpp | 28 + src/BatchActivity.cpp | 523 +++++++++++++----- src/BatchCommandLine.cpp | 35 +- src/DecayChainChart.cpp | 37 +- src/ShowRiidInstrumentsAna.cpp | 11 +- 12 files changed, 973 insertions(+), 208 deletions(-) create mode 100644 InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html rename InterSpec_resources/static_text/ShieldSourceFitLog/{std_summary.tmplt.txt => std_summary.tmplt.csv} (99%) diff --git a/CMakeLists.txt b/CMakeLists.txt index 205d1f47..e458d1db 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -135,6 +135,10 @@ set(MAX_SPECTRUM_MEMMORY_SIZE_MB 256 "Amount of memory to allow spectra to take up before trying to offload them onto disk when not in use" ) +# If we are creating the normal InterSpec executable, and the InterSpec_batch executable, +# we will compile LibInterSpec as a shared library, so both exes can use it; otherwise +# we will create a static library, and statically link it into our final executable. +# (Electron doesnt need a separate exe for batch) if( (USE_BATCH_TOOLS AND NOT BUILD_AS_ELECTRON_APP) OR BUILD_AS_OSX_APP ) set( INTERSPEC_LIB_TYPE SHARED ) else() @@ -142,17 +146,6 @@ else() endif() -if(WIN32) - #0x0601==Win7, 0x0501=WinXP (Wt CMakeLists.txt uses 0x0501x) - #target_compile_definitions( InterSpecLib PUBLIC -D _WIN32_WINNT=0x0601 -D WINVER=0x0601 -D _SCL_SECURE_NO_WARNINGS /bigobj /MP ) - -# set(EXECUTABLE_OUTPUT_PATH . CACHE PATH "Path to executables" FORCE) -# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj /MP /wd4996 /wd4267" ) -else(WIN32) -# set(EXECUTABLE_OUTPUT_PATH bin CACHE PATH "Path to executables" FORCE) -endif(WIN32) - - SET(MYSQL_DATABASE_TO_USE "dev" CACHE STRING "Which mysql database to use (if applicable): dev/qc/prod") @@ -642,11 +635,12 @@ target_compile_options(InterSpecLib PRIVATE >) if(WIN32) #0x0601==Win7, 0x0501=WinXP (Wt CMakeLists.txt uses 0x0501x) - target_compile_definitions( InterSpecLib PUBLIC -D _WIN32_WINNT=0x0601 -D WINVER=0x0601 -D _SCL_SECURE_NO_WARNINGS ) + target_compile_definitions( InterSpecLib PUBLIC -D _WIN32_WINNT=0x0601 -D WINVER=0x0601 -D _SCL_SECURE_NO_WARNINGS /bigobj ) target_compile_definitions( InterSpecLib PRIVATE InterSpec_EXPORTS ) if( USE_BATCH_TOOLS ) - target_compile_options( InterSpecLib PUBLIC /bigobj ) + # We get error compiling multi-processor debug build of shared LibInterSpec, presumably due to some + # file locking issues, so only enable parallel builds for release, if we are building shared LibInterSpec target_compile_options( InterSpecLib PUBLIC $<$:/MP> ) else( USE_BATCH_TOOLS ) add_definitions( /MP ) diff --git a/InterSpec/AppUtils.h b/InterSpec/AppUtils.h index 18fec0ff..9f8a0061 100644 --- a/InterSpec/AppUtils.h +++ b/InterSpec/AppUtils.h @@ -109,6 +109,7 @@ namespace AppUtils const bool include_path ); #endif //#if( !ANDROID && !IOS && !BUILD_FOR_WEB_DEPLOYMENT ) + InterSpec_API std::string file_contents( const std::string &filename ); #ifdef _WIN32 /** Get command line arguments encoded as UTF-8. diff --git a/InterSpec/BatchPeak.h b/InterSpec/BatchPeak.h index d35b18f7..211fa861 100644 --- a/InterSpec/BatchPeak.h +++ b/InterSpec/BatchPeak.h @@ -81,7 +81,7 @@ namespace BatchPeak std::vector report_templates; /** File path to report templates that summarizes all input files. */ - std::string summary_report_template; + std::vector summary_report_templates; };//struct BatchPeakFitOptions diff --git a/InterSpec/GammaInteractionCalc.h b/InterSpec/GammaInteractionCalc.h index a1c891c3..0a81b8cb 100644 --- a/InterSpec/GammaInteractionCalc.h +++ b/InterSpec/GammaInteractionCalc.h @@ -419,7 +419,9 @@ struct PeakResultPlotInfo */ struct PeakDetail { - double energy, decayParticleEnergy, fwhm, counts, countsUncert, cps, cpsUncert; + double energy, decayParticleEnergy, fwhm; + /** counts=peak.peakArea(); countsUncert=peak.peakAreaUncert(); cps=peak.peakArea()/LiveTime*/ + double counts, countsUncert, cps, cpsUncert; double expectedCounts, observedCounts, observedUncert, numSigmaOff; double observedOverExpected, observedOverExpectedUncert; //float modelInto4Pi, modelInto4PiCps; diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html b/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html new file mode 100644 index 00000000..4c888839 --- /dev/null +++ b/InterSpec_resources/static_text/ShieldSourceFitLog/act_fit.tmplt.html @@ -0,0 +1,513 @@ + + + + + + {{ Filename }} Results + + + + + + + + + + + + + + + + + + +

+ Results for {{ Filename }} +

+ +
+
+ +
+ + +
+
    +
  • + {% if exists("background") %} Foreground: {% endif %} + + + + + + + + + + + + + + + + + + + + + {% if foreground.HasNeutrons %} + + + + + + + + + + + {% endif %} + + {% if existsIn(foreground,"SpectrumTitle") %} + + + + + {% endif %} + + + + + + + + + + + + + + + + {% if foreground.HasGps %} + + + {% endif %} + + {% if foreground.HasInstrumentRid %} + + + + + {% endif %} +
    Live Time: + {{ printFixed(foreground.LiveTime_s,3) }} seconds ({{ foreground.LiveTime }}) + Real Time: + {{ printFixed(foreground.RealTime_s,3) }} seconds ({{ foreground.RealTime }}) + Dead Time: + {{ printFixed(foreground.DeadTime_percent,2) }}% +
    Meas. Time: + {% if foreground.StartTimeIsValid %} + {{ foreground.StartTime }} + {% else %} + Not Available + {% endif %} + Gamma Sum: {{ printCompact(foreground.GammaSum,6) }} countsGamma CPS: {{ printCompact(foreground.GammaCps,5) }}
    Neutron Count: foreground.NeutronSum Neut. Live Time: foreground.NeutronLiveTime Neutron CPS: {{ printFixed(foreground.NeutronCps,4) }}
    Title: {{ foreground.SpectrumTitle }}
    Manufacturer: {% if existsIn(foreground,"Manufacturer") %} {{ foreground.Manufacturer }} {% else %} -- {% endif %} Det. Type: {% if existsIn(foreground,"DetectorType") %} {{ foreground.DetectorType }} {% else %} -- {% endif %} Inst. Model: {% if existsIn(foreground,"InstrumentModel") %} {{ foreground.InstrumentModel }} {% else %} -- {% endif %}
    Serial Number: {% if existsIn(foreground,"SerialNumber") %} {{ foreground.SerialNumber }} {% else %} -- {% endif %} lat/lon: {{ printFixed(foreground.Latitude,7) }}{{ printFixed(foreground.Longitude,7) }}
    Inst. RID: {{ foreground.InstrumentRidSummary }}
    +
    • + {% if exists("background") %} +
  • + Background: + + + + + + + + + + + + + + + + + + + + + {% if background.HasNeutrons %} + + + + + + + + + + + {% endif %} + + {% if existsIn(background,"SpectrumTitle") %} + + + + + {% endif %} + + + + + +
    Live Time: + {{ printFixed(background.LiveTime_s,3) }} seconds ({{ background.LiveTime }}) + Real Time: + : {{ printFixed(background.RealTime_s,3) }} seconds ({{ background.RealTime }}) + Dead Time:{{ printFixed(background.DeadTime_percent,2) }}%
    Meas. Time: + {% if background.StartTimeIsValid %} + {{ background.StartTime }} + {% else %} + Not Available + {% endif %} + Gamma Sum: {{ printCompact(background.GammaSum,6) }} countsGamma CPS: {{ printCompact(background.GammaCps,5) }}
    Neutron Count: background.NeutronSum Neut. Live Time: background.NeutronLiveTime Neutron CPS: {{ printFixed(background.NeutronCps,4) }}
    Title: {{ background.SpectrumTitle }}
    Live Time Normalization Factor: {{ background.Normalization }}
    +
    • + {% endif %} + + {% if Detector %} +
  • + Detector: + + + + + {% if Detector.Radius_cm > 0.0 %} + + + {% endif %} + + + {% if FixedGeometryDetector %} + + {% else %} + + + {% endif %} + +
    Name:{{ Detector.Name }}Radius:{{ printFixed(Detector.Radius_cm,1) }}
    + Results given as {{ ActShieldFitSetup.FixedGeometryType }}. + Distance to source center from detector: {{ ActShieldFitSetup.Distance }}
    +
    • + {% endif %} + + {% if NumSources > 0 %} +
  • + {% if ActShieldFitSetup.FitOptions.InterferenceCorrection %}Allowing multiple nuclides being fit for to potentially contribute to the same photopeak{% else %}Not allowing multiple nuclides being fit for to contribute to the same photopeak{% endif %} +
    • + {% endif %} + + {% if ActShieldFitSetup.FitOptions.DecayDuringMeasurement %} +
  • + Branching ratios are being corrected for nuclide decay during measurement. +
    • + {% endif %} + + {% if exists("background") %} +
  • + {% if ActShieldFitSetup.FitOptions.BackgroundPeakSubtract %} + Background peaks are subtracted. + {% else %} + Background peaks are not being subtracted. + {% endif %} +
    • + {% endif %} + +
+
+ +
+Sources: + + + + + {% if AnySourceAgeFit %} + + + {% endif %} + + + + {% if HasTraceSource %} + + + + {% endif %} + + +## for src in Sources + + + + {% if AnySourceAgeFit %} + + + {% endif %} + + + + {% if HasTraceSource %} + + + + {% endif %} + +## endfor + +
NuclideAgeAge UncertAge Fit?ActivityActivity UncertActivity Fit?Trace Src Act.Trace Src Act. UncertIs Trace Src
{{ src.Nuclide }} {{ src.Age }} {% if src.AgeIsFit %} {{ src.AgeUncert }} {% endif %} {{ src.AgeIsFit }} {{ src.Activity }} {% if src.ActivityIsFit %} {{ src.ActivityUncert }} {% endif %} {{ src.ActivityIsFit }} {% if src.IsTraceSource %} {{src.TraceDisplayActivity}} {% endif %} {% if src.IsTraceSource and src.ActivityIsFit %} {{ src.TraceDisplayActivityUncert }} {% endif %} {{ src.IsTraceSource }}
+
+ + +
+ Peaks: + + + + + + + + + + + + + + + + + + +{% if exists("PeaksUsedForActivityFitting") %} +## for peak in PeaksUsedForActivityFitting.Peaks + + + + + + + + + + + + + + +##endfor +{% endif %} + +
Energy (keV)FWHMAreaΔAreaCPSBack. CountsSignal CountsAssigned Nuc.Int. EffDet. EffPred.σ off
{{ printFixed(peak.Energy_keV,2) }}{{ printFixed(peak.FWHM,3) }}{{ printCompact(peak.Counts,5) }}{{ printCompact(peak.CountsUncert,5) }}{{ printFixed(peak.Cps, 3) }} ± {{ printFixed(peak.CpsUncert,3) }} + {% if existsIn(peak,"BackgroundCounts") %} + {{ printCompact(peak.BackgroundCounts, 5) }} + {% endif %} + {{ printCompact(peak.SignalCounts,4) }} ± {{ printCompact(peak.SignalCountsUncert,4) }}{{ peak.AssignedNuclide }} ({{ printFixed(peak.DecayParticleEnergy_keV,1) }}){{ printCompact(peak.DetectorIntrinsicEff,5) }}{{ printCompact(peak.DetectorEff,5) }}{{ printCompact(peak.PredictedCounts,5) }}{{ printFixed(peak.PredictedNumSigmaOff,3) }}
+ + +
+ + +
+(Gamma contribution counts currently not correct!) +
    +## for src in Sources +
  • Peak contributions from {{ src.Nuclide }}: + + + + + + + + + + + + + + + +## for peak in src.PeaksThisNucContributesTo + + + + + + + {% if existsIn(peak,"ThisNucsGammasForPeak") %} +## for src in peak.ThisNucsGammasForPeak + {% if loop.is_first %} + {% else %} + + + + + + {% endif %} + + + + +##endfor + {% else %} + + + + + {% endif %} +##endfor + +
    Energy (keV)Signal CountsΔCountsModel SumNuclideγ Energyγ Counts
    {{ printFixed(peak.Energy_keV,2) }}{{ printCompact(peak.SignalCounts,5) }}{{ printCompact(peak.SignalCountsUncert,5) }}{{ printCompact(peak.PredictedCounts,5) }}
    {{ src.Nuclide }}{{ printFixed(src.Energy_keV,3) }}{{ printCompact(src.CountsContributedToPeak,6) }}
    +
    • +##endfor +
+ + Contributions to peaks from fit model: + + + +
+ + + +
+ + + + + + + + + +
+{% if exists("Shieldings") and existsIn(Shieldings,"Shields") %}
+Shieldings:
+## for shield in Shieldings.Shields
+{% if shield.IsGeneric %}
+    Generic AN={{ shield.AN }}, AD={{ shield.AD }} g/cm3:
+{% else %}
+    {{ shield.Name }}{% if existsIn(shield,"Formula") %}, {{ shield.Formula }},{% endif %} density={{ shield.Density }} g/cm3, {{ Shieldings.Geometry }}: [{% for dimNum in range(Shieldings.NumDimensions) %}{% if dimNum > 1 %}, {% endif %}{{ at(Shieldings.DimensionMeanings,dimNum) }}_thickness={{at(shield.Thicknesses,dimNum)}}{% endfor %}]
+{% endif %}
+{% if exists("PeaksUsedForActivityFitting") %}
+## for peak in PeaksUsedForActivityFitting.Peaks
+        {% if (shield.ShieldingNumber < length(peak.ShieldAttenuations)) and (at(peak.ShieldAttenuations,shield.ShieldingNumber) > 0.0) %}For peak at {{ peak.Energy}} keV, attenuation multiple of {{ at(peak.ShieldAttenuations,shield.ShieldingNumber) }}{% endif %}
+
+##endfor
+{% endif %}
+
+##endfor
+{% endif %}
+
+
+## for src in Sources
+{{ src.Nuclide }} fit activity {{ src.Activity }}{% if src.ActivityIsFit %} with uncertainty {{ src.ActivityUncert }} ({{ src.ActivityUncertPercent }}) {% endif %} at {% if src.AgeIsFit %}assumed {% else %}fit {% endif %} age {{ src.Age }}
+## endfor
+Geometry: {% if FixedGeometryDetector %}Fixed geometry, {{ ActShieldFitSetup.FixedGeometryType }}.{% else %}{{ ActShieldFitSetup.Geometry }}{% endif %}
+{% if exists("Shieldings") %}
+Shieldings:
+{% if exists("Shieldings") and existsIn(Shieldings,"Shields") %}
+## for shield in Shieldings.Shields
+{% if shield.IsGeneric %}
+    Generic shielding AN={{ shield.AN }}, AD={{ shield.AD }} g/cm3
+{% else %}
+    {{ shield.Name }} has density {{ shield.Density }} g/cm3 and dimensions {% for i in range(shield.NumDimensions) %} {{ at(Shieldings.DimensionMeanings,i) }}: {{ at(shield.Thicknesses, i) }}{% if at(shield.DimensionIsFit, i) %} (+-{{ at(shield.ThicknessesUncerts,i) }}) {% endif %} {% endfor %}
+{% endif %}
+##endfor
+{% else %}
+    None
+{% endif %}
+{% endif %}
+
+ +
+
    +
  • There were {{ NumDof }} parameters fit for
    • +
  • It took {{ NumberFcnCalls }} solution trials to reach chi2={{ printCompact(FitChi2,5) }} with an estimated distance to minumum of {{ printCompact(EstimatedDistanceToMinimum,5) }}
    • +
  • Exemplar File: {{ ExemplarFile }}{% if exists("ExemplarSampleNumbers") %}, exemplar samples: {{ ExemplarSampleNumbers }}{% endif %}
    • +
  • Analysis Performed at: {{ AnalysisTime }}, + from CWD={{CurrentWorkingDirectory}}, + with InterSpec compiled {{ InterSpecCompileDateIso }}{% if exists("InterSpecExecutablePath") %}, + and executable at {{ InterSpecExecutablePath }} + {% endif %} +
    • +
+
+ + + + diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt b/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt index 00bfe689..4d90785e 100644 --- a/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt +++ b/InterSpec_resources/static_text/ShieldSourceFitLog/std_fit_log.tmplt.txt @@ -13,15 +13,15 @@ Sources: Peak attributed to {{ peak.DecayParticleEnergy }} keV received {{ gamma.CpsContributedToPeak }} from {{ gamma.Energy }} keV line{% if existsIn(gamma,"DecayCorrection") %} (decay correction {{ gamma.DecayCorrection }}){% endif %}, which has I={{ gamma.BranchingRatio }} ##endfor ##endfor -## endfor +##endfor {% if exists("Shieldings") and existsIn(Shieldings,"Shields") %} Shieldings: ## for shield in Shieldings.Shields {% if shield.IsGeneric %} - Generic AN={{ shield.AN }}, AD={{ shield.AD }} g/cm3: + Generic AN={{ shield.AN }}, AD={{ shield.AD }} g/cm2: {% else %} - {{ shield.Name }}{% if existsIn(shield,"Formula") %}, {{ shield.Formula }},{% endif %} density={{ shield.Density }} g/cm3, {{ Shieldings.Geometry }}: [{% for dimNum in range(Shieldings.NumDimensions) %}{% if dimNum > 1 %}, {% endif %}{{ at(Shieldings.DimensionMeanings,dimNum) }}_thickness={{at(shield.Thicknesses,dimNum)}}{% endfor %}] + {{ shield.Name }}{% if existsIn(shield,"Formula") %}, {{ shield.Formula }},{% endif %} density={{ shield.Density_gPerCm3 }} g/cm3, {{ Shieldings.Geometry }}: [{% for dimNum in range(Shieldings.NumDimensions) %}{% if dimNum > 1 %}, {% endif %}{{ at(Shieldings.DimensionMeanings,dimNum) }}_thickness={{at(shield.Thicknesses,dimNum)}}{% endfor %}] {% endif %} {% if exists("PeaksUsedForActivityFitting") %} ## for peak in PeaksUsedForActivityFitting.Peaks diff --git a/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.txt b/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.csv similarity index 99% rename from InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.txt rename to InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.csv index 0f78e579..846e2452 100644 --- a/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.txt +++ b/InterSpec_resources/static_text/ShieldSourceFitLog/std_summary.tmplt.csv @@ -13,6 +13,5 @@ Filename, Nuclide, Activity, ActivityUncertainty, ActivityUncertainty (%), Nucli ## for file in Files ## for src in file.Sources {{ file.Filename }},{{ src.Nuclide }}, {{ src.Activity }}, {% if src.ActivityIsFit %}{{ src.ActivityUncert }}{% endif %}, {% if src.ActivityIsFit %}{{ src.ActivityUncertPercent }}%{% endif %}, {{ src.Age }}, {% if src.AgeIsFit %}{{ src.AgeUncert }}{% endif %} - ## endfor ## endfor diff --git a/src/AppUtils.cpp b/src/AppUtils.cpp index 38057769..93bde4a4 100644 --- a/src/AppUtils.cpp +++ b/src/AppUtils.cpp @@ -375,6 +375,34 @@ bool locate_file( string &filename, const bool is_dir, }//bool locate_file( ... ) #endif //#if( !ANDROID && !IOS && !BUILD_FOR_WEB_DEPLOYMENT ) + +std::string file_contents( const std::string &filename ) +{ + //Copied from SpecUtils::load_file_data( const char * const filename, std::vector &data ); +#ifdef _WIN32 + const std::wstring wfilename = SpecUtils::convert_from_utf8_to_utf16(filename); + basic_ifstream stream(wfilename.c_str(), ios::binary); +#else + basic_ifstream stream(filename.c_str(), ios::binary); +#endif + + if (!stream) + throw runtime_error(string("cannot open file ") + filename); + stream.unsetf(ios::skipws); + + // Determine stream size + stream.seekg(0, ios::end); + size_t size = static_cast( stream.tellg() ); + stream.seekg(0); + + string data; + data.resize( size ); + stream.read(&data.front(), static_cast(size)); + + return data; +}//std::string file_contents( const std::string &filename ) + + #ifdef _WIN32 /** Get command line arguments encoded as UTF-8. This function just leaks the memory diff --git a/src/BatchActivity.cpp b/src/BatchActivity.cpp index cc3c17fa..37febad0 100644 --- a/src/BatchActivity.cpp +++ b/src/BatchActivity.cpp @@ -55,6 +55,7 @@ #include "InterSpec/DecayDataBaseServer.h" #include "InterSpec/DetectorPeakResponse.h" #include "InterSpec/GammaInteractionCalc.h" +#include "InterSpec/ShowRiidInstrumentsAna.h" using namespace std; @@ -380,58 +381,54 @@ void add_basic_peak_info( const GammaInteractionCalc::PeakDetail &peak, nlohmann char buffer[64] = { '\0' }; snprintf( buffer, sizeof(buffer), "%.2f", peak.energy ); peak_json["Energy"] = string(buffer); - peak_json["EnergyKeV"] = peak.energy; + peak_json["Energy_keV"] = peak.energy; snprintf( buffer, sizeof(buffer), "%.3f", peak.decayParticleEnergy ); peak_json["DecayParticleEnergy"] = string(buffer); + peak_json["DecayParticleEnergy_keV"] = peak.decayParticleEnergy; peak_json["AssignedNuclide"] = peak.assignedNuclide; - peak_json["FWHM"] = SpecUtils::printCompact(peak.fwhm, 4); + peak_json["FWHM"] = peak.fwhm; - snprintf( buffer, sizeof(buffer), "%.2f", peak.counts ); - peak_json["Counts"] = string(buffer); + + peak_json["Counts"] = peak.counts; peak_json["CountsStr"] = SpecUtils::printCompact(peak.counts, 4); - snprintf( buffer, sizeof(buffer), "%.2f", peak.countsUncert ); - peak_json["CountsUncert"] = string(buffer); + peak_json["CountsUncert"] = peak.countsUncert; peak_json["CountsUncertStr"] = SpecUtils::printCompact(peak.countsUncert, 4); - peak_json["Cps"] = SpecUtils::printCompact(peak.cps, 4); - peak_json["CpsUncert"] = SpecUtils::printCompact(peak.cpsUncert, 4); + peak_json["Cps"] = peak.cps; + peak_json["CpsStr"] = SpecUtils::printCompact(peak.cps,4); + peak_json["CpsUncert"] = peak.cpsUncert; peak_json["ShieldAttenuations"] = peak.m_attenuations; if( peak.backgroundCounts > 0.0 ) { - snprintf( buffer, sizeof(buffer), "%.2f", peak.backgroundCounts ); - peak_json["BackgroundCounts"] = string(buffer); + peak_json["BackgroundCounts"] = peak.backgroundCounts; peak_json["BackgroundCountsStr"] = SpecUtils::printCompact(peak.backgroundCounts, 4); if( peak.backgroundCountsUncert > 0.0 ) { - snprintf( buffer, sizeof(buffer), "%.2f", peak.backgroundCountsUncert ); - peak_json["BackgroundCountsUncert"] = string(buffer); + peak_json["BackgroundCountsUncert"] = peak.backgroundCountsUncert; peak_json["BackgroundCountsUncertStr"] = SpecUtils::printCompact(peak.backgroundCountsUncert, 4); } }//if( peak.backgroundCounts > 0.0 ) - snprintf( buffer, sizeof(buffer), "%.2f", peak.observedCounts ); - peak_json["SignalCounts"] = string(buffer); + peak_json["SignalCounts"] = peak.observedCounts; peak_json["SignalCountsStr"] = SpecUtils::printCompact(peak.observedCounts, 4); - snprintf( buffer, sizeof(buffer), "%.2f", peak.observedUncert ); - peak_json["SignalCountsUncert"] = string(buffer); + peak_json["SignalCountsUncert"] = peak.observedUncert; peak_json["SignalCountsUncertStr"] = SpecUtils::printCompact(peak.observedUncert, 4); - snprintf( buffer, sizeof(buffer), "%.2f", peak.expectedCounts ); - peak_json["PredictedCounts"] = string(buffer); - peak_json["PredictedNumSigmaOff"] = SpecUtils::printCompact(peak.numSigmaOff, 4); + peak_json["PredictedCounts"] = peak.expectedCounts; + peak_json["PredictedNumSigmaOff"] = peak.numSigmaOff; - peak_json["ObservedOverPredicted"] = SpecUtils::printCompact(peak.observedOverExpected, 5); - peak_json["ObservedOverPredictedUncert"] = SpecUtils::printCompact(peak.observedOverExpectedUncert, 5); + peak_json["ObservedOverPredicted"] = peak.observedOverExpected; + peak_json["ObservedOverPredictedUncert"] = peak.observedOverExpectedUncert; - peak_json["DetectorSolidAngleFraction"] = SpecUtils::printCompact(peak.detSolidAngle, 5); - peak_json["DetectorIntrinsicEff"] = SpecUtils::printCompact(peak.detIntrinsicEff, 5); - peak_json["DetectorEff"] = SpecUtils::printCompact(peak.detEff, 5); + peak_json["DetectorSolidAngleFraction"] = peak.detSolidAngle; + peak_json["DetectorIntrinsicEff"] = peak.detIntrinsicEff; + peak_json["DetectorEff"] = peak.detEff; }//add_basic_peak_info( const PeakDetail &peak, nlohmann::basic_json<> &peak_json ) -void add_gamma_info_for_peak( const GammaInteractionCalc::PeakDetail::PeakSrc &ps, +void add_gamma_info_for_peak( const GammaInteractionCalc::PeakDetail::PeakSrc &ps, const GammaInteractionCalc::SourceDetails * const src, const std::shared_ptr &drf, const bool useBq, @@ -444,22 +441,22 @@ void add_gamma_info_for_peak( const GammaInteractionCalc::PeakDetail::PeakSrc &p gamma_json["Nuclide"] = ps.nuclide ? ps.nuclide->symbol : string("null"); gamma_json["Energy"] = string(buffer); - gamma_json["EnergyKeV"] = ps.energy; + gamma_json["Energy_keV"] = ps.energy; - gamma_json["BranchingRatio"] = SpecUtils::printCompact( ps.br, 5 ); - gamma_json["BranchingRatioFloat"] = ps.br; + gamma_json["BranchingRatio"] = ps.br; + gamma_json["BranchingRatioStr"] = SpecUtils::printCompact( ps.br, 5 ); - gamma_json["CpsContributedToPeak"] = SpecUtils::printCompact( ps.cps, 5 ); - gamma_json["CpsContributedToPeakFloat"] = ps.cps; + gamma_json["CpsContributedToPeak"] = ps.cps; + gamma_json["CpsContributedToPeakStr"] = SpecUtils::printCompact( ps.cps, 5 ); - gamma_json["CountsContributedToPeak"] = SpecUtils::printCompact( ps.counts, 5 ); - gamma_json["CountsContributedToPeakFloat"] = ps.counts; + gamma_json["CountsContributedToPeak"] = ps.counts; + gamma_json["CountsContributedToPeakStr"] = SpecUtils::printCompact( ps.counts, 5 ); gamma_json["HasDecayCorrection"] = (ps.decayCorrection > 0.0); if( ps.decayCorrection > 0.0 ) { - gamma_json["DecayCorrection"] = SpecUtils::printCompact(ps.decayCorrection, 4); - gamma_json["DecayCorrectionFloat"] = ps.decayCorrection; + gamma_json["DecayCorrection"] = ps.decayCorrection; + gamma_json["DecayCorrectionStr"] = SpecUtils::printCompact(ps.decayCorrection, 4); } // The other information in `PeakDetail::PeakSrc` should be repeat of @@ -583,13 +580,19 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul if( !results.errormsgs.empty() ) data["ErrorMessages"] = results.errormsgs; - + int num_sources = 0; + bool hasAnyTraceSrc = false, hasAnyVolumetricSrc = false, hasFitAnyAge = false; if( results.source_calc_details ) { for( const GammaInteractionCalc::SourceDetails &src : *results.source_calc_details ) { data["Sources"].push_back( {} ); auto &src_json = data["Sources"].back(); + + ++num_sources; + hasAnyTraceSrc |= src.isTraceSource; + hasAnyVolumetricSrc |= src.isSelfAttenSource; + hasFitAnyAge |= src.ageIsFit; add_basic_src_details( src, drf, useBq, src_json ); @@ -629,14 +632,24 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul }//for( loop over results.source_calc_details ) }//if( results.source_calc_details ) + data["NumSources"] = num_sources; + + data["HasTraceSource"] = hasAnyTraceSrc; + data["HasSelfAttenSource"] = hasAnyVolumetricSrc; + data["HasVolumetricSource"] = (hasAnyTraceSrc || hasAnyVolumetricSrc); + data["AnySourceAgeFit"] = hasFitAnyAge; - if( results.shield_calc_details ) + auto &shieldings_json = data["Shieldings"]; + shieldings_json["Geometry"] = GammaInteractionCalc::to_str(results.geometry); + + bool fitAnyShielding = false; + if( !results.shield_calc_details ) + { + shieldings_json["NumberShieldings"] = 0; + }else { const vector &shield_details = *results.shield_calc_details; - auto &shieldings_json = data["Shieldings"]; - - shieldings_json["Geometry"] = GammaInteractionCalc::to_str(results.geometry); shieldings_json["NumberShieldings"] = static_cast( shield_details.size() ); switch( results.geometry ) { @@ -675,8 +688,8 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul { shield_json["Formula"] = shield.m_chemical_formula; const double density = shield.m_density * PhysicalUnits::cm3 / PhysicalUnits::g; - shield_json["Density"] = SpecUtils::printCompact(density, 5); - shield_json["DensityFloat"] = density; + shield_json["Density_gPerCm3"] = density; + shield_json["DensityStr"] = SpecUtils::printCompact(density, 5) + " g/cm3"; } if( shield.m_an > 0 ) @@ -690,6 +703,8 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul const bool fitAD = shield.m_fit_dimension[1]; shield_json["FitAN"] = fitAn; shield_json["FitAD"] = fitAD; + fitAnyShielding |= fitAn; + fitAnyShielding |= fitAD; } const vector fit_dim( shield.m_fit_dimension, shield.m_fit_dimension + shield.m_num_dimensions ); @@ -737,6 +752,7 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul for( unsigned int dim = 0; dim < shield.m_num_dimensions; ++dim ) { + fitAnyShielding |= fit_dim[dim]; thicknesses[dim] = outer_dims[dim] - inner_dims[dim]; thicknesses_strs[dim] = PhysicalUnits::printToBestLengthUnits( thicknesses[dim], 5 ); inner_dims_strs[dim] = PhysicalUnits::printToBestLengthUnits( inner_dims[dim], 5 ); @@ -799,12 +815,12 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul assert( comp.m_nuclide ); self_atten_json["Nuclide"] = comp.m_nuclide ? comp.m_nuclide->symbol : string("null"); self_atten_json["IsFittingMassFraction"] = comp.m_is_fit; - self_atten_json["MassFraction"] = SpecUtils::printCompact(comp.m_mass_frac, 5); - self_atten_json["MassFractionFloat"] = comp.m_mass_frac; + self_atten_json["MassFraction"] = comp.m_mass_frac; + self_atten_json["MassFractionStr"] = SpecUtils::printCompact(comp.m_mass_frac, 5); if( comp.m_is_fit ) { - self_atten_json["MassFractionUncert"] = SpecUtils::printCompact(comp.m_mass_frac_uncert, 5); - self_atten_json["MassFractionUncertFloat"] = comp.m_mass_frac_uncert; + self_atten_json["MassFractionUncert"] = comp.m_mass_frac_uncert; + self_atten_json["MassFractionUncertStr"] = SpecUtils::printCompact(comp.m_mass_frac_uncert, 5); } assert( results.source_calc_details ); @@ -855,6 +871,8 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul }//for( const GammaInteractionCalc::ShieldingDetails &shield : *results.shield_calc_details ) }//if( results.shield_calc_details ) + data["AnyShieldingFit"] = fitAnyShielding; + // Add Peak Details to JSON if( results.peak_calc_details ) @@ -888,28 +906,28 @@ void shield_src_fit_results_to_json( const ShieldingSourceFitCalc::ModelFitResul add_basic_src_details( *pos, drf, useBq, src_json ); - peak_json["HasDecayCorrection"] = (pksrc.decayCorrection > 0.0); + src_json["HasDecayCorrection"] = (pksrc.decayCorrection > 0.0); if( pksrc.decayCorrection > 0.0 ) { - peak_json["DecayCorrection"] = SpecUtils::printCompact(pksrc.decayCorrection, 4); - peak_json["DecayCorrectionFloat"] = pksrc.decayCorrection; + peak_json["DecayCorrection"] = pksrc.decayCorrection; + peak_json["DecayCorrectionStr"] = SpecUtils::printCompact(pksrc.decayCorrection, 4); } char buffer[64] = { '\0' }; snprintf( buffer, sizeof(buffer), "%.2f", pksrc.energy ); - peak_json["Energy"] = string(buffer); - peak_json["EnergyKeV"] = pksrc.energy; + src_json["Energy"] = string(buffer); + src_json["Energy_keV"] = pksrc.energy; - peak_json["Cps"] = SpecUtils::printCompact(pksrc.cps, 4); - peak_json["CpsFloat"] = pksrc.cps; + src_json["Cps"] = pksrc.cps; + src_json["CpsStr"] = SpecUtils::printCompact(pksrc.cps, 4); - peak_json["BranchingRatio"] = SpecUtils::printCompact( pksrc.br, 5 ); - peak_json["BranchingRatioFloat"] = pksrc.br; + src_json["BranchingRatio"] = pksrc.br; + src_json["BranchingRatioStr"] = SpecUtils::printCompact( pksrc.br, 5 ); snprintf( buffer, sizeof(buffer), "%.2f", pksrc.counts ); - peak_json["Counts"] = string(buffer); - peak_json["CountsFloat"] = pksrc.counts; + src_json["Counts"] = pksrc.counts; + src_json["CountsStr"] = string(buffer); }//for( const GammaInteractionCalc::PeakDetail::PeakSrc &pksrc : peak.m_sources ) // We could loop over the volumetric sources, and add info, but... @@ -1004,14 +1022,13 @@ void fit_activities_in_files( const std::string &exemplar_filename, // Load report templates, and setup inja::environment //InterSpec::setStaticDataDirectory( SpecUtils::append_path(datadir,"data") ); - string default_tmplt_dir = InterSpec::staticDataDirectory(); - assert( !default_tmplt_dir.empty() ); - if( default_tmplt_dir.empty() ) - default_tmplt_dir = "./data"; - default_tmplt_dir = SpecUtils::append_path( default_tmplt_dir, ".." ); //Also see: `WServer::instance()->appRoot()`, which isnt valid right now - default_tmplt_dir = SpecUtils::append_path( default_tmplt_dir, "InterSpec_resources" ); - default_tmplt_dir = SpecUtils::append_path( default_tmplt_dir, "static_text" ); - default_tmplt_dir = SpecUtils::append_path( default_tmplt_dir, "ShieldSourceFitLog" ); + assert( !InterSpec::staticDataDirectory().empty() ); + const string static_data_dir = InterSpec::staticDataDirectory().empty() ? string("./data") + : InterSpec::staticDataDirectory(); + //Also see: `WServer::instance()->appRoot()`, which isnt valid right now + const string app_root = SpecUtils::append_path( static_data_dir, ".." ); + const string docroot = SpecUtils::append_path( app_root, "InterSpec_resources" ); + const string static_txt = SpecUtils::append_path( docroot, "static_text" ); // inja assumes trailing path separator, for its template path #if( defined(_WIN32) ) @@ -1019,10 +1036,7 @@ void fit_activities_in_files( const std::string &exemplar_filename, #else const char path_sep = '/'; #endif - - if( !default_tmplt_dir.empty() && (default_tmplt_dir.back() != path_sep) ) - default_tmplt_dir += path_sep; - + const string default_tmplt_dir = SpecUtils::append_path( static_txt, "ShieldSourceFitLog" ) + path_sep; string tmplt_dir; @@ -1040,6 +1054,17 @@ void fit_activities_in_files( const std::string &exemplar_filename, throw runtime_error( string("Template include directory, '") + tmplt_dir + "', doesnt look to be a valid directory - not performing analysis." ); +#if( SpecUtils_ENABLE_D3_CHART ) + const string d3_js = AppUtils::file_contents( SpecUtils::append_path( docroot, "d3.v3.min.js") ); + + const string sc_js_fn = SpecUtils::is_file( SpecUtils::append_path( docroot, "SpectrumChartD3.min.js") ) + ? "SpectrumChartD3.min.js" : "SpectrumChartD3.js"; + const string sc_css_fn = SpecUtils::is_file( SpecUtils::append_path( docroot, "SpectrumChartD3.min.css") ) + ? "SpectrumChartD3.min.css" : "SpectrumChartD3.css"; + + const string sc_js = AppUtils::file_contents( SpecUtils::append_path( docroot, sc_js_fn ) ); + const string sc_css = AppUtils::file_contents( SpecUtils::append_path( docroot, sc_css_fn ) ); +#endif // SpecUtils_ENABLE_D3_CHART inja::Environment env{ tmplt_dir }; env.set_trim_blocks( true ); // remove the first newline after a block @@ -1054,37 +1079,76 @@ void fit_activities_in_files( const std::string &exemplar_filename, #endif // Add some callbacks incase people want more control over the precision of their printouts - env.add_callback( "printFixed", 2, []( inja::Arguments& args ) -> std::string { - const double val = args.at(0)->get(); - const int numDecimal = std::max( 0, args.at(1)->get() ); - - char buffer[64] = { '\0' }; - snprintf( buffer, sizeof(buffer), "%.*f", numDecimal, val ); - - return std::string(buffer); - } ); + const auto printFixed = []( inja::Arguments& args ) -> std::string { + try + { + const double val = args.at(0)->get(); + const int numDecimal = std::max( 0, args.at(1)->get() ); + + char buffer[64] = { '\0' }; + snprintf( buffer, sizeof(buffer), "%.*f", numDecimal, val ); + + return std::string(buffer); + }catch( inja::InjaError &e ) + { + const string msg = "Error converting 'printFixed' argument to number.\n" + "line " + std::to_string(e.location.line) + ", column " + std::to_string(e.location.column) + + "): " + e.message + "."; + + cerr << msg << endl; + throw; + } + }; + env.add_callback( "printFixed", 2, printFixed ); - env.add_callback( "printCompact", 2, []( inja::Arguments& args ) -> std::string { - const double val = args.at(0)->get(); - const int numSigFig = args.at(1)->get(); - if( numSigFig <= 1 ) - throw runtime_error( "printCompact: you must print at least one significant figures" ); - - return SpecUtils::printCompact( val, static_cast(numSigFig) ); - } ); + const auto printCompact = []( inja::Arguments& args ) -> std::string { + try + { + const double val = args.at(0)->get(); + const int numSigFig = args.at(1)->get(); + if( numSigFig <= 1 ) + throw runtime_error( "printCompact: you must print at least one significant figures" ); + + return SpecUtils::printCompact( val, static_cast(numSigFig) ); + }catch( inja::InjaError &e ) + { + const string msg = "Error converting 'printCompact' argument to number.\n" + "line " + std::to_string(e.location.line) + ", column " + std::to_string(e.location.column) + + "): " + e.message + "."; + + cerr << msg << endl; + throw; + } + return ""; + }; + + env.add_callback( "printCompact", 2, printCompact ); try { // If we're using a custom include path, opening templates from the default template location // is problematic, so we'll just create a new `inja::Environment` to open the default // templates, and then add them to `env` - not really tested yet. - const string def_tmplt = SpecUtils::append_path( default_tmplt_dir, "std_fit_log.tmplt.txt" ); inja::Environment sub_env; - inja::Template tmplt = sub_env.parse_template( def_tmplt ); - env.include_template( "default-act-fit-results", tmplt ); - - //TODO: Work on other templates we can include + sub_env.add_callback( "printFixed", 2, printFixed ); + sub_env.add_callback( "printCompact", 2, printCompact ); + + const string def_txt_tmplt = SpecUtils::append_path( default_tmplt_dir, "std_fit_log.tmplt.txt" ); + inja::Template txt_tmplt = sub_env.parse_template( def_txt_tmplt ); + env.include_template( "default-act-fit-txt-results", txt_tmplt ); + + const string def_html_tmplt = SpecUtils::append_path( default_tmplt_dir, "act_fit.tmplt.html" ); + inja::Template html_tmplt = sub_env.parse_template( def_html_tmplt ); + env.include_template( "default-act-fit-html-results", html_tmplt ); + + const string def_csv_summary_tmplt = SpecUtils::append_path( default_tmplt_dir, "std_summary.tmplt.csv" ); + inja::Template csv_sum_tmplt = sub_env.parse_template( def_csv_summary_tmplt ); + env.include_template( "default-act-fit-csv-summary", csv_sum_tmplt ); + + const string def_html_summary_tmplt = SpecUtils::append_path( default_tmplt_dir, "std_summary.tmplt.html" ); + inja::Template html_sum_tmplt = sub_env.parse_template( def_html_summary_tmplt ); + env.include_template( "default-act-fit-html-summary", html_sum_tmplt ); }catch( std::exception &e ) { cerr << "Error loading default template: " << e.what() << endl; @@ -1098,8 +1162,23 @@ void fit_activities_in_files( const std::string &exemplar_filename, if( !file_ext.empty() ) outname = outname.substr(0, outname.size() - file_ext.size()); - string tmplt_name = tmplt; + string tmplt_name = SpecUtils::filename( tmplt ); string tmplt_ext = SpecUtils::file_extension(tmplt_name); + if( SpecUtils::iequals_ascii(tmplt_name, "csv") ) + { + tmplt_name = "act_fit"; + tmplt_ext = ".csv"; + }else if( SpecUtils::iequals_ascii(tmplt_name, "txt") + || SpecUtils::iequals_ascii(tmplt_name, "text") ) + { + tmplt_name = "act_fit"; + tmplt_ext = ".txt"; + }else if( SpecUtils::iequals_ascii(tmplt_name, "html") ) + { + tmplt_name = "act_fit"; + tmplt_ext = ".html"; + } + size_t pos = SpecUtils::ifind_substr_ascii(tmplt_name, "tmplt"); if( pos == string::npos ) pos = SpecUtils::ifind_substr_ascii(tmplt_name, "template"); @@ -1125,6 +1204,12 @@ void fit_activities_in_files( const std::string &exemplar_filename, bool set_setup_info_to_summary_json = false; nlohmann::json summary_json; +#if( SpecUtils_ENABLE_D3_CHART ) + summary_json["D3_JS"] = d3_js; + summary_json["SpectrumChart_JS"] = sc_js; + summary_json["SpectrumChart_CSS"] = sc_css; +#endif // SpecUtils_ENABLE_D3_CHART + add_exe_info_to_json( summary_json ); summary_json["ExemplarFile"] = exemplar_filename; @@ -1173,9 +1258,14 @@ void fit_activities_in_files( const std::string &exemplar_filename, // log file, and then upgrade from this to hit HTML with the charts and peak fits and stuff. nlohmann::json data; + data["ExemplarFile"] = exemplar_filename; + if( !exemplar_sample_nums.empty() ) + data["ExemplarSampleNumbers"] = vector{begin(exemplar_sample_nums), end(exemplar_sample_nums)}; + auto add_hist_to_json = []( nlohmann::json &data, const bool is_background, const shared_ptr &spec_ptr, + const shared_ptr &spec_file, const std::set &sample_numbers, const string &filename, const shared_ptr &peak_fit ){ @@ -1227,22 +1317,128 @@ void fit_activities_in_files( const std::string &exemplar_filename, } const char * const label = is_background ? "background" : "foreground"; - data[label] = { - { "LiveTime_s", lt }, - { "LiveTime", lt_str }, - { "RealTime_s", rt }, - { "RealTime", rt_str }, - { "LowerSpectrumEnergy", spec.gamma_channel_lower(0) }, - { "UpperSpectrumEnergy", spec.gamma_channel_upper(spec.num_gamma_channels() - 1) }, - { "NumberChannels", (int)spec.num_gamma_channels() }, - { "GammaSum", spec.gamma_count_sum() }, - { "ContainedNeutrons", spec.contained_neutron() }, - { "NeutronSum", spec.neutron_counts_sum() }, - { "SampleNumbers", sample_nums }, - //detector names? - { "Filename", filename }, - { "spectrum", spectrum_json } - }; + auto &spec_obj = data[label]; + + spec_obj["LiveTime"] = lt_str; + spec_obj["RealTime"] = rt_str; + spec_obj["LiveTime_s"] = lt; + spec_obj["RealTime_s"] = rt; + spec_obj["DeadTime"] = PhysicalUnits::printToBestTimeUnits(rt - lt); + spec_obj["DeadTime_s"] = (rt - lt)/PhysicalUnits::second; + spec_obj["DeadTime_percent"] = 100.0*(rt - lt) / rt; + spec_obj["StartTime"] = SpecUtils::to_extended_iso_string( spec.start_time() ); + spec_obj["StartTime_iso"] = SpecUtils::to_iso_string( spec.start_time() ); + spec_obj["StartTime_vax"] = SpecUtils::to_vax_string( spec.start_time() ); + spec_obj["StartTimeIsValid"] = !SpecUtils::is_special( spec.start_time() ); + spec_obj["LowerSpectrumEnergy"] = spec.gamma_channel_lower(0); + spec_obj["UpperSpectrumEnergy"] = spec.gamma_channel_upper(spec.num_gamma_channels() - 1); + spec_obj["NumberChannels"] = (int)spec.num_gamma_channels(); + spec_obj["GammaSum"] = spec.gamma_count_sum(); + spec_obj["GammaCps"] = (spec.live_time() > 0.0) ? (spec.gamma_count_sum() / spec.live_time()) : -1.0; + spec_obj["SampleNumbers"] = sample_nums; + //detector names? + spec_obj["Filename"] = filename; + spec_obj["spectrum"] = spectrum_json; + spec_obj["HasGps"] = spec.has_gps_info(); + if( spec.has_gps_info() ) + { + spec_obj["Longitude"] = spec.longitude(); + spec_obj["Latitude"] = spec.latitude(); + } + spec_obj["HasNeutrons"] = spec.contained_neutron(); + if( spec.contained_neutron() ) + { + spec_obj["NeutronCounts"] = spec.neutron_counts_sum(); + spec_obj["NeutronLiveTime"] = spec.neutron_live_time(); + spec_obj["NeutronCps"] = spec.neutron_counts_sum() / spec.neutron_live_time(); + } + + if( !spec.title().empty() ) + spec_obj["SpectrumTitle"] = spec.title(); + + //The measured ambient radiation dose equivalent rate value, in microsieverts per hour (μSv/h). + if( spec.dose_rate() >= 0.0 ) + spec_obj["DoseRate_uSvPerHour"] = spec.dose_rate(); + + //The measured radiation exposure rate value, in milliroentgen per hour (mR/h). + if( spec.exposure_rate() >= 0.0 ) + spec_obj["ExposureRate_mRPerHour"] = spec.exposure_rate(); + + if( !spec.detector_type().empty() ) + spec_obj["DetectorTypeDesc"] = spec.detector_type(); + + if( !spec.detector_name().empty() ) + spec_obj["DetectorName"] = spec.detector_name(); + + //SourceType source_type() const; + + if( !spec.remarks().empty() ) + spec_obj["SpectrumRemarks"] = spec.remarks(); + + if( !spec.parse_warnings().empty() ) + spec_obj["SpectrumParseWarnings"] = spec.parse_warnings(); + + spec_obj["IsDerivedData"] = (spec.derived_data_properties() != 0); + + spec_obj["DerivedIoiSum"] = static_cast(spec.derived_data_properties() + & static_cast(SpecUtils::Measurement::DerivedDataProperties::ItemOfInterestSum)); + spec_obj["DerivedUsedForRidAnalysis"] = static_cast(spec.derived_data_properties() + & static_cast(SpecUtils::Measurement::DerivedDataProperties::UsedForAnalysis)); + spec_obj["DerivedProcessedFurther"] = static_cast(spec.derived_data_properties() + & static_cast(SpecUtils::Measurement::DerivedDataProperties::ProcessedFurther)); + spec_obj["DerivedBackgroundSub"] = static_cast(spec.derived_data_properties() + & static_cast(SpecUtils::Measurement::DerivedDataProperties::BackgroundSubtracted)); + spec_obj["DerivedIsBackground"] = static_cast(spec.derived_data_properties() + & static_cast(SpecUtils::Measurement::DerivedDataProperties::IsBackground)); + + auto cal = spec.energy_calibration(); + auto &cal_obj = spec_obj["EnergyCal"]; + + cal_obj["NumChannels"] = cal ? static_cast(cal->num_channels()) : 0; + const SpecUtils::EnergyCalType cal_type = cal ? cal->type() : SpecUtils::EnergyCalType::InvalidEquationType; + switch( cal_type ) + { + case SpecUtils::EnergyCalType::Polynomial: + case SpecUtils::EnergyCalType::UnspecifiedUsingDefaultPolynomial: + cal_obj["Type"] = "Polynomial"; + cal_obj["Coefficients"] = vector{ begin(cal->coefficients()), end(cal->coefficients()) }; + break; + + case SpecUtils::EnergyCalType::FullRangeFraction: + cal_obj["Type"] = "FullRangeFraction"; + cal_obj["Coefficients"] = vector{ begin(cal->coefficients()), end(cal->coefficients()) }; + break; + case SpecUtils::EnergyCalType::LowerChannelEdge: + cal_obj["Type"] = "LowerChannelEdge"; + break; + case SpecUtils::EnergyCalType::InvalidEquationType: + cal_obj["Type"] = "Invalid"; + break; + }//switch( cal->type() ) + + if( cal && !cal->deviation_pairs().empty() ) + { + vector> pairs; + for( const pair &p : cal->deviation_pairs() ) + pairs.push_back( { static_cast(p.first), static_cast(p.second) } ); + cal_obj["DeviationPairs"] = pairs; + }//if( dev pairs ) + + if( spec_file ) + { + spec_obj["InstrumentModel"] = spec_file->instrument_model(); + spec_obj["SerialNumber"] = spec_file->instrument_id(); + spec_obj["Manufacturer"] = spec_file->manufacturer(); + spec_obj["InstrumentType"] = spec_file->instrument_type(); + spec_obj["DetectorType"] = SpecUtils::detectorTypeToString( spec_file->detector_type() ); + spec_obj["NumberRecordsInFile"] = static_cast( spec_file->num_measurements() ); + spec_obj["RemarksInFile"] = spec_file->remarks(); + spec_obj["ParseWarningsForFile"] = spec_file->parse_warnings(); + + spec_obj["HasInstrumentRid"] = !!spec_file->detectors_analysis(); + if( spec_file->detectors_analysis() ) + spec_obj["InstrumentRidSummary"] = riidAnaSummary( spec_file ); + }//if( spec_file ) };//add_hist_to_json(...) auto add_peak_fit_options_to_json = []( nlohmann::json &data, const BatchPeak::BatchPeakFitOptions &options ){ @@ -1266,13 +1462,14 @@ void fit_activities_in_files( const std::string &exemplar_filename, options_obj["ReportTemplateIncludeDir"] = options.template_include_dir; options_obj["ReportTemplates"] = options.report_templates; - options_obj["ReportSummaryTemplate"] = options.summary_report_template; + options_obj["ReportSummaryTemplates"] = options.summary_report_templates; }; if( fit_results.m_foreground ) { add_hist_to_json( data, false, fit_results.m_foreground, + fit_results.m_foreground_file, fit_results.m_foreground_sample_numbers, fit_results.m_filename, fit_results.m_peak_fit_results ); }//if( fit_results.m_foreground ) @@ -1281,10 +1478,18 @@ void fit_activities_in_files( const std::string &exemplar_filename, { string filename = fit_results.m_background_file ? fit_results.m_background_file->filename() : string(); + + // We'll only add background file info, if different than foreground file + shared_ptr back_file = (fit_results.m_background_file != fit_results.m_foreground_file) + ? fit_results.m_background_file : nullptr; + add_hist_to_json( data, true, fit_results.m_background, + back_file, fit_results.m_background_sample_numbers, filename, fit_results.m_background_peak_fit_results ); - } + + data["background"]["Normalization"] = fit_results.m_foreground->live_time() / fit_results.m_background->live_time(); + }//if( fit_results.m_background ) add_peak_fit_options_to_json( data, fit_results.m_options ); @@ -1305,15 +1510,25 @@ void fit_activities_in_files( const std::string &exemplar_filename, //std::cout << std::setw(4) << data << std::endl; +#if( SpecUtils_ENABLE_D3_CHART ) + data["D3_JS"] = d3_js; + data["SpectrumChart_JS"] = sc_js; + data["SpectrumChart_CSS"] = sc_css; +#endif // SpecUtils_ENABLE_D3_CHART + + for( string tmplt : options.report_templates ) { try { string rpt; - if( SpecUtils::iequals_ascii(tmplt, "default" ) ) + if( SpecUtils::iequals_ascii(tmplt, "txt" ) ) { - rpt = env.render("{% include \"default-act-fit-results\" %}", data); + rpt = env.render("{% include \"default-act-fit-txt-results\" %}", data); + }else if( SpecUtils::iequals_ascii(tmplt, "html" ) ) + { + rpt = env.render("{% include \"default-act-fit-html-results\" %}", data); }else { const bool is_in_inc = SpecUtils::is_file( SpecUtils::append_path(tmplt_dir, tmplt) ); @@ -1344,13 +1559,15 @@ void fit_activities_in_files( const std::string &exemplar_filename, } inja::Environment sub_env; + sub_env.add_callback( "printFixed", 2, printFixed ); + sub_env.add_callback( "printCompact", 2, printCompact ); injatmplt = sub_env.parse_template( tmplt ); }// rpt = env.render( injatmplt, data ); }//if( default report format ) / else - if( options.to_stdout ) + if( options.to_stdout && !SpecUtils::iequals_ascii(tmplt, "html" ) ) cout << "\n\n" << rpt << endl << endl; if( !options.output_dir.empty() ) @@ -1391,9 +1608,6 @@ void fit_activities_in_files( const std::string &exemplar_filename, }//for( const string &tmplt : options.report_templates ) - - - assert( fit_results.m_peak_fit_results && fit_results.m_peak_fit_results->measurement ); if( options.write_n42_with_results && fit_results.m_peak_fit_results @@ -1500,52 +1714,67 @@ void fit_activities_in_files( const std::string &exemplar_filename, } }//for( const string filename : files ) - if( !options.summary_report_template.empty() - && !SpecUtils::iequals_ascii( options.summary_report_template, "none" ) ) + for( const string &summary_tmplt : options.summary_report_templates ) { try { - string summary_tmplt = options.summary_report_template; - - if( SpecUtils::iequals_ascii( summary_tmplt, "default" ) ) - summary_tmplt = "std_summary.tmplt.txt"; - - inja::Template injatmplt; - - const string inc_dir_summary_tmplt = SpecUtils::append_path(tmplt_dir, summary_tmplt); - bool is_file = SpecUtils::is_file( inc_dir_summary_tmplt ); - if( is_file ) + string rpt; + if( SpecUtils::iequals_ascii(summary_tmplt, "csv" ) ) + { + rpt = env.render( "{% include \"default-act-fit-csv-summary\" %}", summary_json ); + }else if( SpecUtils::iequals_ascii(summary_tmplt, "html" ) ) { - injatmplt = env.parse_template( summary_tmplt ); + rpt = env.render( "{% include \"default-act-fit-html-summary\" %}", summary_json ); }else { - string found_path = summary_tmplt; - is_file = SpecUtils::is_file( found_path ); - if( !is_file ) + inja::Template injatmplt; + + const string inc_dir_summary_tmplt = SpecUtils::append_path(tmplt_dir, summary_tmplt); + bool is_file = SpecUtils::is_file( inc_dir_summary_tmplt ); + if( is_file ) { - found_path = SpecUtils::append_path(default_tmplt_dir, summary_tmplt); + injatmplt = env.parse_template( summary_tmplt ); + }else + { + string found_path = summary_tmplt; is_file = SpecUtils::is_file( found_path ); - } - - if( !is_file ) - throw runtime_error( "Failed to find file '" + summary_tmplt + "'." - " Please specify full path to file, or use the" - " 'report-template-include-dir' option to specify" - " directory where the report is located." ); + if( !is_file ) + { + found_path = SpecUtils::append_path(default_tmplt_dir, summary_tmplt); + is_file = SpecUtils::is_file( found_path ); + } + + if( !is_file ) + throw runtime_error( "Failed to find file '" + summary_tmplt + "'." + " Please specify full path to file, or use the" + " 'report-template-include-dir' option to specify" + " directory where the report is located." ); + + inja::Environment sub_env; + sub_env.add_callback( "printFixed", 2, printFixed ); + sub_env.add_callback( "printCompact", 2, printCompact ); + injatmplt = sub_env.parse_template( found_path ); + }//if( is_file ) / else - inja::Environment sub_env; - injatmplt = sub_env.parse_template( found_path ); - } - - const string rpt = env.render( injatmplt, summary_json ); + rpt = env.render( injatmplt, summary_json ); + }//if( CSV ) else if ( HTML ) else - if( options.to_stdout ) + if( options.to_stdout && !SpecUtils::iequals_ascii(summary_tmplt, "html" ) ) cout << "\n\n" << rpt << endl << endl; if( !options.output_dir.empty() ) { - const string out_file = output_filename( "", summary_tmplt ); + string outbase = ""; + if( SpecUtils::iequals_ascii(summary_tmplt, "txt") + || SpecUtils::iequals_ascii(summary_tmplt, "text") + || SpecUtils::iequals_ascii(summary_tmplt, "csv") + || SpecUtils::iequals_ascii(summary_tmplt, "html") ) + { + outbase = "summary"; + } + + const string out_file = output_filename( outbase, summary_tmplt ); if( SpecUtils::is_file(out_file) && !options.overwrite_output_files ) { @@ -1569,7 +1798,7 @@ void fit_activities_in_files( const std::string &exemplar_filename, { const string msg = "Error templating summary output (" + e.type + ": line " + std::to_string(e.location.line) + ", column " + std::to_string(e.location.column) - + " of '" + options.summary_report_template + "'): " + e.message + "."; + + " of '" + summary_tmplt + "'): " + e.message + "."; cerr << msg << endl; warnings.push_back( msg ); diff --git a/src/BatchCommandLine.cpp b/src/BatchCommandLine.cpp index 0bb49cab..7ab675da 100644 --- a/src/BatchCommandLine.cpp +++ b/src/BatchCommandLine.cpp @@ -147,8 +147,8 @@ int run_batch_command( int argc, char **argv ) bool output_stdout, refit_energy_cal, use_exemplar_energy_cal, write_n42_with_results; bool show_nonfit_peaks, overwrite_output_files, create_csv_output; - vector input_files, report_templates; - string exemplar_path, output_path, exemplar_samples, background_sub_file, background_samples, summary_report_template, template_include_dir; + vector input_files, report_templates, summary_report_templates; + string exemplar_path, output_path, exemplar_samples, background_sub_file, background_samples, template_include_dir; po::options_description peak_cl_desc("Allowed batch peak-fit, and activity-fit options", term_width, min_description_length); peak_cl_desc.add_options() @@ -202,11 +202,11 @@ int run_batch_command( int argc, char **argv ) ) ("file-report-template", po::value>(&report_templates)->multitoken(), "One or more spectrum report template files - for each input file, a report will be produced with each template specified." - " You can also specify \"default\", or \"none\"." + " You can also specify \"default\" (=txt+html), \"txt\", \"html\", or \"none\"." ) - ("summary-report-template", po::value(&summary_report_template)->default_value("default"), - "The template file used to provide a summary of all input files." - " You can also specify \"default\", or \"none\"." + ("summary-report-template", po::value>(&summary_report_templates)->multitoken(), + "One or more template files used to provide a summary of all input files." + " You can also specify \"default\" (=csv+html), \"csv\", \"html\", or \"none\"." ) ("report-template-include-dir", po::value(&template_include_dir)->default_value("default"), "A directory containing report templates; specifying this allows templates to include other templates." @@ -320,11 +320,28 @@ int run_batch_command( int argc, char **argv ) if( report_templates.empty() && (output_stdout || !output_path.empty()) ) report_templates.push_back( "default" ); + if( summary_report_templates.empty() && (output_stdout || !output_path.empty()) ) + summary_report_templates.push_back( "default" ); + + auto set_def = []( vector &args, const vector def_args ){ + const auto eq = []( const string &v ){ return SpecUtils::iequals_ascii(v, "default" ); }; + const size_t num_defaults = std::count_if( begin(args), end(args), eq); + args.erase( std::remove_if( begin(args), end(args), eq), end(args) ); + if( num_defaults ) + args.insert( end(args), begin(def_args), end(def_args) ); + + const auto want_none = [](const string &v){ return SpecUtils::iequals_ascii(v, "none"); }; + if( std::count_if( begin(args), end(args), want_none) ) + args.clear(); + }; + + set_def( report_templates, {"txt", "html"} ); + set_def( summary_report_templates, {"csv", "html"} ); + if( contain_not_none && templates_contain_none ) throw runtime_error( "You can not specify to use no report templates, and also specify to use other templates." ); - if( output_path.empty() && !output_stdout - && (contain_not_none || !SpecUtils::iequals_ascii(summary_report_template, "none")) ) + if( output_path.empty() && !summary_report_templates.empty() ) throw runtime_error( "You must provide an output directory if specifying to use any templates for results." ); BatchActivity::BatchActivityFitOptions options; //derived from BatchPeak::BatchPeakFitOptions @@ -340,7 +357,7 @@ int run_batch_command( int argc, char **argv ) options.background_subtract_samples = background_sample_nums; options.use_bq = use_bq; options.report_templates = report_templates; - options.summary_report_template = summary_report_template; + options.summary_report_templates = summary_report_templates; options.template_include_dir = template_include_dir; if( batch_peak_fit ) diff --git a/src/DecayChainChart.cpp b/src/DecayChainChart.cpp index 05c64e40..f7b8ae4a 100644 --- a/src/DecayChainChart.cpp +++ b/src/DecayChainChart.cpp @@ -59,6 +59,7 @@ #include "SandiaDecay/SandiaDecay.h" +#include "InterSpec/AppUtils.h" #include "InterSpec/AuxWindow.h" #include "InterSpec/InterSpec.h" #include "InterSpec/ColorTheme.h" @@ -136,32 +137,6 @@ namespace }//decay_particle_info(...) - std::string file_contents( const string &filename ) - { - //Copied from SpecUtils::load_file_data( const char * const filename, std::vector &data ); -#ifdef _WIN32 - const std::wstring wfilename = SpecUtils::convert_from_utf8_to_utf16(filename); - basic_ifstream stream(wfilename.c_str(), ios::binary); -#else - basic_ifstream stream(filename.c_str(), ios::binary); -#endif - - if (!stream) - throw runtime_error(string("cannot open file ") + filename); - stream.unsetf(ios::skipws); - - // Determine stream size - stream.seekg(0, ios::end); - size_t size = static_cast( stream.tellg() ); - stream.seekg(0); - - string data; - data.resize( size ); - stream.read(&data.front(), static_cast(size)); - - return data; - }//std::string file_contents( const std::string &filename, std::vector &data ) - class DecayChainHtmlResource : public Wt::WResource { @@ -238,17 +213,17 @@ class DecayChainHtmlResource : public Wt::WResource const string docroot = SpecUtils::append_path( m_app->docRoot(), "InterSpec_resources" ); - string htmls = file_contents( SpecUtils::append_path( docroot, "DecayChartStandalone.tmplt.html") ); + string htmls = AppUtils::file_contents( SpecUtils::append_path( docroot, "DecayChartStandalone.tmplt.html") ); //#if( SpecUtils_D3_SUPPORT_FILE_STATIC ) // const string d3_js = (const char *)D3SpectrumExport::d3_js(); //#else - // const string d3_js = file_contents( D3SpectrumExport::d3_js_filename() ); + // const string d3_js = AppUtils::file_contents( D3SpectrumExport::d3_js_filename() ); //#endif - const string d3_js = file_contents( SpecUtils::append_path( docroot, "d3.v3.min.js") ); - const string dcc_js = file_contents( SpecUtils::append_path( docroot, "DecayChainChart.js") ); - const string dcc_css = file_contents( SpecUtils::append_path( docroot, "DecayChainChart.css") ); + const string d3_js = AppUtils::file_contents( SpecUtils::append_path( docroot, "d3.v3.min.js") ); + const string dcc_js = AppUtils::file_contents( SpecUtils::append_path( docroot, "DecayChainChart.js") ); + const string dcc_css = AppUtils::file_contents( SpecUtils::append_path( docroot, "DecayChainChart.css") ); js << "/* ------ Begin d3.v3.js ------ */\n" diff --git a/src/ShowRiidInstrumentsAna.cpp b/src/ShowRiidInstrumentsAna.cpp index d6ee8691..c6e0e0b5 100644 --- a/src/ShowRiidInstrumentsAna.cpp +++ b/src/ShowRiidInstrumentsAna.cpp @@ -377,8 +377,15 @@ std::string riidAnaSummary( const std::shared_ptr &spec ) if( summary.empty() && ana->results_.empty() ) { - InterSpec::instance()->useMessageResourceBundle( "ShowRiidInstrumentsAna" ); - summary = WString::tr("srria-no-nucs").toUTF8(); + InterSpec *viewer = InterSpec::instance(); + if( viewer ) + { + viewer->useMessageResourceBundle( "ShowRiidInstrumentsAna" ); + summary = WString::tr("srria-no-nucs").toUTF8(); + }else + { + summary = "No nuclides identified."; + } } return Wt::Utils::htmlEncode( WString::fromUTF8(summary),0).toUTF8();