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log_file.cpp
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//
// log_file.cpp
// SLiM
//
// Created by Ben Haller on 11/2/20.
// Copyright (c) 2020-2025 Philipp Messer. All rights reserved.
// A product of the Messer Lab, http://messerlab.org/slim/
//
// This file is part of SLiM.
//
// SLiM is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
//
// SLiM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along with SLiM. If not, see <http://www.gnu.org/licenses/>.
#include "log_file.h"
#include <utility>
#include <algorithm>
#include <vector>
#include <iomanip>
#include "slim_globals.h"
#include "community.h"
#include "species.h"
#include "subpopulation.h"
//
// LogFile
//
#pragma mark -
#pragma mark LogFile
#pragma mark -
LogFile::LogFile(Community &p_community) : community_(p_community)
{
}
LogFile::~LogFile(void)
{
}
void LogFile::Raise_UsesStringKeys(void) const
{
EIDOS_TERMINATION << "ERROR (LogFile::Raise_UsesStringKeys): cannot use an integer key with the target LogFile object; LogFile always uses string keys." << EidosTerminate(nullptr);
}
void LogFile::ConfigureFile(const std::string &p_filePath, std::vector<const std::string *> &p_initialContents, bool p_append, bool p_compress, const std::string &p_sep)
{
user_file_path_ = p_filePath;
// correct the user-visible path to end in ".gz" if it doesn't already
if (p_compress && !Eidos_string_hasSuffix(user_file_path_, ".gz"))
user_file_path_.append(".gz");
// Resolve a ~ at the start of the path, and get a canonical absolute path
resolved_file_path_ = Eidos_AbsolutePath(user_file_path_);
compress_ = p_compress;
sep_ = p_sep;
// We always open the file for writing (or appending) synchronously and write out the initial contents, if any
Eidos_WriteToFile(resolved_file_path_, p_initialContents, p_append, p_compress, EidosFileFlush::kForceFlush);
}
void LogFile::SetLogInterval(bool p_autologging_enabled, int64_t p_logInterval)
{
if (p_autologging_enabled && (p_logInterval < 1))
EIDOS_TERMINATION << "ERROR (LogFile::SetLogInterval): the log interval must be >= 1 (or NULL, to disable automatic logging)." << EidosTerminate();
autologging_enabled_ = p_autologging_enabled;
log_interval_ = p_autologging_enabled ? p_logInterval : 0;
autolog_start_ = community_.Tick();
}
void LogFile::SetFlushInterval(bool p_explicit_flushing, int64_t p_flushInterval)
{
if (p_explicit_flushing && (p_flushInterval < 1))
EIDOS_TERMINATION << "ERROR (LogFile::SetFlushInterval): the flush interval must be >= 1 (or NULL, to request the default flushing behavior)." << EidosTerminate();
explicit_flushing_ = p_explicit_flushing;
flush_interval_ = p_flushInterval;
}
EidosValue_SP LogFile::_GeneratedValue_Cycle(const LogFileGeneratorInfo &p_generator_info)
{
const std::vector<Species *> &all_species = community_.AllSpecies();
Species *species = all_species[p_generator_info.objectid_];
slim_tick_t cycle = species->Cycle();
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int(cycle));
}
EidosValue_SP LogFile::_GeneratedValue_CycleStage(const LogFileGeneratorInfo &p_generator_info)
{
#pragma unused(p_generator_info)
SLiMCycleStage cycle_stage = community_.CycleStage();
std::string stage_string = StringForSLiMCycleStage(cycle_stage);
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_String(stage_string));
}
EidosValue_SP LogFile::_GeneratedValue_PopulationSexRatio(const LogFileGeneratorInfo &p_generator_info)
{
const std::vector<Species *> &all_species = community_.AllSpecies();
Species *species = all_species[p_generator_info.objectid_];
if (species->SexEnabled())
{
slim_popsize_t total_individuals = 0, total_males = 0;
for (auto &subpop_iter : species->population_.subpops_)
{
Subpopulation *subpop = subpop_iter.second;
slim_popsize_t subpop_size = subpop->parent_subpop_size_;
slim_popsize_t first_male_index = subpop->parent_first_male_index_;
total_individuals += subpop_size;
total_males += (subpop_size - first_male_index);
}
double sex_ratio = (total_individuals == 0) ? 0.0 : (total_males / (double)total_individuals);
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float(sex_ratio));
}
else
{
// no dictionary entry, which will produce NULL
return gStaticEidosValueNULL;
}
}
EidosValue_SP LogFile::_GeneratedValue_PopulationSize(const LogFileGeneratorInfo &p_generator_info)
{
#pragma unused(p_generator_info)
const std::vector<Species *> &all_species = community_.AllSpecies();
Species *species = all_species[p_generator_info.objectid_];
slim_popsize_t total_individuals = 0;
for (auto &subpop_iter : species->population_.subpops_)
total_individuals += (subpop_iter.second)->parent_subpop_size_;
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int(total_individuals));
}
EidosValue_SP LogFile::_GeneratedValue_SubpopulationSexRatio(const LogFileGeneratorInfo &p_generator_info)
{
Subpopulation *subpop = community_.SubpopulationWithID(p_generator_info.objectid_);
if (subpop && subpop->species_.SexEnabled())
{
slim_popsize_t subpop_size = subpop->parent_subpop_size_;
slim_popsize_t first_male_index = subpop->parent_first_male_index_;
double sex_ratio = (subpop_size == 0) ? 0.0 : ((subpop_size - first_male_index) / (double)subpop_size);
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float(sex_ratio));
}
else
{
// no dictionary entry, which will produce NULL
return gStaticEidosValueNULL;
}
}
EidosValue_SP LogFile::_GeneratedValue_SubpopulationSize(const LogFileGeneratorInfo &p_generator_info)
{
Subpopulation *subpop = community_.SubpopulationWithID(p_generator_info.objectid_);
if (subpop)
{
slim_popsize_t subpop_size = subpop->parent_subpop_size_;
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int(subpop_size));
}
else
{
// no dictionary entry, which will produce NULL
return gStaticEidosValueNULL;
}
}
EidosValue_SP LogFile::_GeneratedValue_Tick(const LogFileGeneratorInfo &p_generator_info)
{
#pragma unused(p_generator_info)
slim_tick_t tick = community_.Tick();
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int(tick));
}
EidosValue_SP LogFile::_GeneratedValue_CustomScript(const LogFileGeneratorInfo &p_generator_info)
{
// See, e.g., Subpopulation::ApplyFitnessEffectCallbacks() for comments on running scripts
THREAD_SAFETY_IN_ACTIVE_PARALLEL("LogFile::_GeneratedValue_CustomScript(): running Eidos lambda");
EidosScript *generator_script = p_generator_info.script_;
EidosErrorContext error_context_save = gEidosErrorContext;
gEidosErrorContext = EidosErrorContext{{-1, -1, -1, -1}, generator_script};
EidosValue_SP result_SP;
try
{
EidosSymbolTable callback_symbols(EidosSymbolTableType::kContextConstantsTable, &community_.SymbolTable());
EidosSymbolTable client_symbols(EidosSymbolTableType::kLocalVariablesTable, &callback_symbols);
EidosFunctionMap &function_map = community_.FunctionMap();
EidosInterpreter interpreter(*generator_script, client_symbols, function_map, &community_, SLIM_OUTSTREAM, SLIM_ERRSTREAM);
callback_symbols.InitializeConstantSymbolEntry(gID_context, p_generator_info.context_);
result_SP = interpreter.EvaluateInterpreterBlock(false, true); // do not print output, return the last statement value
if (result_SP->Type() == EidosValueType::kValueObject)
EIDOS_TERMINATION << "ERROR (LogFile::_GeneratedValue_CustomScript): a LogFile generator script for addCustomColumn() may not return type object." << EidosTerminate(nullptr);
if ((result_SP->Type() != EidosValueType::kValueNULL) && (result_SP->Count() != 1))
EIDOS_TERMINATION << "ERROR (LogFile::_GeneratedValue_CustomScript): a LogFile generator script for addCustomColumn() must return a singleton value, or NULL." << EidosTerminate(nullptr);
}
catch (...)
{
if (gEidosTerminateThrows)
{
// In some cases, such as if the error occurred in a derived user-defined function, we can
// actually get a user script error context at this point, and don't need to intervene.
if (!gEidosErrorContext.currentScript || (gEidosErrorContext.currentScript->UserScriptUTF16Offset() == -1))
{
gEidosErrorContext = error_context_save;
TranslateErrorContextToUserScript("_GeneratedValue_CustomScript()");
}
}
throw;
}
gEidosErrorContext = error_context_save;
return result_SP;
}
void LogFile::_GeneratedValues_CustomMeanAndSD(const LogFileGeneratorInfo &p_generator_info, EidosValue_SP *p_generated_value_1, EidosValue_SP *p_generated_value_2)
{
// See, e.g., Subpopulation::ApplyFitnessEffectCallbacks() for comments on running scripts
THREAD_SAFETY_IN_ACTIVE_PARALLEL("LogFile::_GeneratedValues_CustomMeanAndSD(): running Eidos lambda");
EidosScript *generator_script = p_generator_info.script_;
EidosErrorContext error_context_save = gEidosErrorContext;
gEidosErrorContext = EidosErrorContext{{-1, -1, -1, -1}, generator_script};
EidosValue_SP result_SP;
try
{
EidosSymbolTable callback_symbols(EidosSymbolTableType::kContextConstantsTable, &community_.SymbolTable());
EidosSymbolTable client_symbols(EidosSymbolTableType::kLocalVariablesTable, &callback_symbols);
EidosFunctionMap &function_map = community_.FunctionMap();
EidosInterpreter interpreter(*generator_script, client_symbols, function_map, nullptr, SLIM_OUTSTREAM, SLIM_ERRSTREAM);
callback_symbols.InitializeConstantSymbolEntry(gID_context, p_generator_info.context_);
result_SP = interpreter.EvaluateInterpreterBlock(false, true); // do not print output, return the last statement value
if ((result_SP->Type() != EidosValueType::kValueInt) && (result_SP->Type() != EidosValueType::kValueFloat) && (result_SP->Type() != EidosValueType::kValueNULL))
EIDOS_TERMINATION << "ERROR (LogFile::_GeneratedValues_CustomMeanAndSD): a LogFile generator script for addMeanSDColumns() must return a vector of type integer or float, or NULL." << EidosTerminate(nullptr);
if (result_SP->Count() == 0)
{
// A zero-length result vector, including NULL, will write out NA for mean and sd
*p_generated_value_1 = gStaticEidosValueNULL;
*p_generated_value_2 = gStaticEidosValueNULL;
}
else
{
// A non-zero result vector gets evaluated for its mean and sd (sd==NA if length 1)
// We just use eidos_functions here, since it does exactly what we want anyway
std::vector<EidosValue_SP> argument_vec;
argument_vec.emplace_back(result_SP);
if (result_SP->Count() == 1)
{
*p_generated_value_1 = Eidos_ExecuteFunction_mean(argument_vec, interpreter);
*p_generated_value_2 = gStaticEidosValueNULL;
}
else
{
*p_generated_value_1 = Eidos_ExecuteFunction_mean(argument_vec, interpreter);
*p_generated_value_2 = Eidos_ExecuteFunction_sd(argument_vec, interpreter);
}
}
}
catch (...)
{
if (gEidosTerminateThrows)
{
// In some cases, such as if the error occurred in a derived user-defined function, we can
// actually get a user script error context at this point, and don't need to intervene.
if (!gEidosErrorContext.currentScript || (gEidosErrorContext.currentScript->UserScriptUTF16Offset() == -1))
{
gEidosErrorContext = error_context_save;
TranslateErrorContextToUserScript("_GeneratedValues_CustomMeanAndSD()");
}
}
throw;
}
gEidosErrorContext = error_context_save;
}
void LogFile::_OutputValue(std::ostringstream &p_out, EidosValue *p_value)
{
EidosValueType type = p_value->Type();
if (type == EidosValueType::kValueNULL)
{
// NULL gets logged as NA; mixes paradigms a bit, but seems useful
p_out << "NA";
}
else
{
// Use EidosValue to write the value. However, we want to control the precision of float output.
// Note that this is not thread-safe.
int old_precision = gEidosFloatOutputPrecision;
gEidosFloatOutputPrecision = float_precision_;
p_out << *p_value; // FIXME this doesn't handle string quoting well at present
gEidosFloatOutputPrecision = old_precision;
}
}
void LogFile::AppendNewRow(void)
{
THREAD_SAFETY_IN_ACTIVE_PARALLEL("LogFile::AppendNewRow(): filesystem write");
// Guarantee that we are in the parent generation for all generators, so they don't need to worry
const std::vector<Species *> &all_species = community_.AllSpecies();
for (Species *species : all_species)
if (species->population_.child_generation_valid_)
EIDOS_TERMINATION << "ERROR (LogFile::AppendNewRow): (internal error) generating logfile entry with child generation active!" << EidosTerminate();
std::vector<const std::string *> line_vec;
std::string header_line;
std::string row_line;
// Gather all generators into our Dictionary
RemoveAllKeys();
// Generate the header row if needed
if (!header_logged_)
{
std::ostringstream ss;
bool first_column = true;
#ifdef SLIMGUI
std::vector<std::string> gui_line;
#endif
for (const std::string &column_name : column_names_)
{
if (!first_column)
ss << sep_;
first_column = false;
ss << column_name;
#ifdef SLIMGUI
std::ostringstream gui_ss;
gui_ss << column_name;
gui_line.emplace_back(gui_ss.str());
#endif
}
header_line = ss.str();
line_vec.emplace_back(&header_line);
#ifdef SLIMGUI
emitted_lines_.emplace_back(std::move(gui_line));
#endif
// Having emitted the header line, we lock ourselves to prevent inconsistencies in the emitted table
header_logged_ = true;
}
// Generate the text of the row from the Dictionary entries
{
std::ostringstream ss;
int column_index = 0;
#ifdef SLIMGUI
std::vector<std::string> gui_line;
#endif
for (const LogFileGeneratorInfo &generator : generator_info_)
{
EidosValue_SP generated_value;
switch (generator.type_)
{
case LogFileGeneratorType::kGenerator_Cycle:
generated_value = _GeneratedValue_Cycle(generator);
break;
case LogFileGeneratorType::kGenerator_CycleStage:
generated_value = _GeneratedValue_CycleStage(generator);
break;
case LogFileGeneratorType::kGenerator_PopulationSexRatio:
generated_value = _GeneratedValue_PopulationSexRatio(generator);
break;
case LogFileGeneratorType::kGenerator_PopulationSize:
generated_value = _GeneratedValue_PopulationSize(generator);
break;
case LogFileGeneratorType::kGenerator_SubpopulationSexRatio:
generated_value = _GeneratedValue_SubpopulationSexRatio(generator);
break;
case LogFileGeneratorType::kGenerator_SubpopulationSize:
generated_value = _GeneratedValue_SubpopulationSize(generator);
break;
case LogFileGeneratorType::kGenerator_Tick:
generated_value = _GeneratedValue_Tick(generator);
break;
case LogFileGeneratorType::kGenerator_CustomScript:
generated_value = _GeneratedValue_CustomScript(generator);
break;
case LogFileGeneratorType::kGenerator_CustomMeanAndSD:
{
// This requires special-casing because it generates two columns
EidosValue_SP generated_value_1, generated_value_2;
_GeneratedValues_CustomMeanAndSD(generator, &generated_value_1, &generated_value_2);
// emit generated_value_1
if (column_index != 0)
ss << sep_;
_OutputValue(ss, generated_value_1.get());
#ifdef SLIMGUI
std::ostringstream gui_ss;
_OutputValue(gui_ss, generated_value_1.get());
gui_line.emplace_back(gui_ss.str());
#endif
if (generated_value_1->Type() != EidosValueType::kValueNULL)
SetKeyValue_StringKeys(column_names_[column_index], std::move(generated_value_1));
column_index++;
// let the code below emit generated_value_2
generated_value = generated_value_2;
break;
}
case LogFileGeneratorType::kGenerator_SuppliedColumn:
generated_value = supplied_values_.GetValueForKey_StringKeys(column_names_[column_index]);
break;
}
// Emit the generated value and add it to our Dictionary state
if (column_index != 0)
ss << sep_;
_OutputValue(ss, generated_value.get());
#ifdef SLIMGUI
std::ostringstream gui_ss;
_OutputValue(gui_ss, generated_value.get());
gui_line.emplace_back(gui_ss.str());
#endif
if (generated_value->Type() != EidosValueType::kValueNULL)
SetKeyValue_StringKeys(column_names_[column_index], std::move(generated_value));
column_index++;
}
row_line = ss.str();
line_vec.emplace_back(&row_line);
#ifdef SLIMGUI
emitted_lines_.emplace_back(std::move(gui_line));
#endif
}
supplied_values_.RemoveAllKeys();
ContentsChanged("LogFile::AppendNewRow()");
// Write out the row
EidosFileFlush flush = EidosFileFlush::kDefaultFlush;
if (explicit_flushing_)
{
unflushed_row_count_++;
if (unflushed_row_count_ >= flush_interval_)
{
flush = EidosFileFlush::kForceFlush;
unflushed_row_count_ = 0;
}
else
{
flush = EidosFileFlush::kNoFlush;
}
}
Eidos_WriteToFile(resolved_file_path_, line_vec, true, compress_, flush);
}
void LogFile::TickEndCallout(void)
{
if (autologging_enabled_)
{
slim_tick_t tick = community_.Tick();
if ((tick - autolog_start_) % log_interval_ == 0)
AppendNewRow();
}
}
std::vector<std::string> LogFile::SortedKeys_StringKeys(void) const
{
// We want to return the column names in order, so we have to override EidosDictionaryUnretained here
// Our column_names_ vector should correspond to EidosDictionaryUnretained's state, just with a fixed order
std::vector<std::string> string_keys;
if (header_logged_)
{
for (const std::string &column_name : column_names_)
string_keys.push_back(column_name);
}
return string_keys;
}
const EidosClass *LogFile::Class(void) const
{
return gSLiM_LogFile_Class;
}
void LogFile::Print(std::ostream &p_ostream) const
{
p_ostream << Class()->ClassNameForDisplay() << "<" << user_file_path_ << ">";
}
EidosValue_SP LogFile::GetProperty(EidosGlobalStringID p_property_id)
{
// All of our strings are in the global registry, so we can require a successful lookup
switch (p_property_id)
{
// constants
//case gEidosID_allKeys: // not technically overridden here, but we override AllKeys() to provide new behavior
case gEidosID_filePath:
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_String(user_file_path_));
case gID_logInterval:
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int(log_interval_));
// variables
case gID_precision:
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int(float_precision_));
case gID_tag:
{
slim_usertag_t tag_value = tag_value_;
if (tag_value == SLIM_TAG_UNSET_VALUE)
EIDOS_TERMINATION << "ERROR (LogFile::GetProperty): property tag accessed on simulation object before being set." << EidosTerminate();
return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int(tag_value));
}
// all others, including gID_none
default:
return super::GetProperty(p_property_id);
}
}
void LogFile::SetProperty(EidosGlobalStringID p_property_id, const EidosValue &p_value)
{
// All of our strings are in the global registry, so we can require a successful lookup
switch (p_property_id)
{
case gID_precision:
{
int64_t value = p_value.IntAtIndex_NOCAST(0, nullptr);
if ((value < 1) || (value > 22))
EIDOS_TERMINATION << "ERROR (LogFile::SetProperty): property precision must be in [1,22]." << EidosTerminate();
float_precision_ = (int)value;
return;
}
case gID_tag:
{
slim_usertag_t value = SLiMCastToUsertagTypeOrRaise(p_value.IntAtIndex_NOCAST(0, nullptr));
tag_value_ = value;
return;
}
default:
{
return super::SetProperty(p_property_id, p_value);
}
}
}
EidosValue_SP LogFile::ExecuteInstanceMethod(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
switch (p_method_id)
{
// our own methods
case gID_addCustomColumn: return ExecuteMethod_addCustomColumn(p_method_id, p_arguments, p_interpreter);
case gID_addCycle: return ExecuteMethod_addCycle(p_method_id, p_arguments, p_interpreter);
case gID_addCycleStage: return ExecuteMethod_addCycleStage(p_method_id, p_arguments, p_interpreter);
case gID_addMeanSDColumns: return ExecuteMethod_addMeanSDColumns(p_method_id, p_arguments, p_interpreter);
case gID_addPopulationSexRatio: return ExecuteMethod_addPopulationSexRatio(p_method_id, p_arguments, p_interpreter);
case gID_addPopulationSize: return ExecuteMethod_addPopulationSize(p_method_id, p_arguments, p_interpreter);
case gID_addSubpopulationSexRatio: return ExecuteMethod_addSubpopulationSexRatio(p_method_id, p_arguments, p_interpreter);
case gID_addSubpopulationSize: return ExecuteMethod_addSubpopulationSize(p_method_id, p_arguments, p_interpreter);
case gID_addSuppliedColumn: return ExecuteMethod_addSuppliedColumn(p_method_id, p_arguments, p_interpreter);
case gID_addTick: return ExecuteMethod_addTick(p_method_id, p_arguments, p_interpreter);
case gID_flush: return ExecuteMethod_flush(p_method_id, p_arguments, p_interpreter);
case gID_logRow: return ExecuteMethod_logRow(p_method_id, p_arguments, p_interpreter);
case gID_setLogInterval: return ExecuteMethod_setLogInterval(p_method_id, p_arguments, p_interpreter);
case gID_setFilePath: return ExecuteMethod_setFilePath(p_method_id, p_arguments, p_interpreter);
case gID_setSuppliedValue: return ExecuteMethod_setSuppliedValue(p_method_id, p_arguments, p_interpreter);
case gID_willAutolog: return ExecuteMethod_willAutolog(p_method_id, p_arguments, p_interpreter);
// overrides from Dictionary
case gEidosID_addKeysAndValuesFrom: return ExecuteMethod_addKeysAndValuesFrom(p_method_id, p_arguments, p_interpreter);
case gEidosID_appendKeysAndValuesFrom: return ExecuteMethod_appendKeysAndValuesFrom(p_method_id, p_arguments, p_interpreter);
case gEidosID_clearKeysAndValues: return ExecuteMethod_clearKeysAndValues(p_method_id, p_arguments, p_interpreter);
case gEidosID_setValue: return ExecuteMethod_setValue(p_method_id, p_arguments, p_interpreter);
default: return super::ExecuteInstanceMethod(p_method_id, p_arguments, p_interpreter);
}
}
void LogFile::RaiseForLockedHeader(const std::string &p_caller_name)
{
EIDOS_TERMINATION << "ERROR (" << p_caller_name << "): this LogFile has already emitted its header line, so new data generators cannot be added." << EidosTerminate(nullptr);
}
// ********************* - (void)addCustomColumn(string$ columnName, string$ source, [* context = NULL])
EidosValue_SP LogFile::ExecuteMethod_addCustomColumn(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addCustomColumn");
EidosValue_String *columnName_value = (EidosValue_String *)p_arguments[0].get();
EidosValue_String *source_value = (EidosValue_String *)p_arguments[1].get();
EidosValue_SP context_value = p_arguments[2];
const std::string &column_name = columnName_value->StringRefAtIndex_NOCAST(0, nullptr);
const std::string &source = source_value->StringRefAtIndex_NOCAST(0, nullptr);
// See, e.g., Subpopulation::ApplyFitnessEffectCallbacks() for comments on parsing/running script blocks
EidosErrorContext error_context_save = gEidosErrorContext;
EidosScript *source_script = new EidosScript(source);
gEidosErrorContext = EidosErrorContext{{-1, -1, -1, -1}, source_script};
try {
source_script->Tokenize();
source_script->ParseInterpreterBlockToAST(false);
}
catch (...)
{
if (gEidosTerminateThrows)
{
gEidosErrorContext = error_context_save;
TranslateErrorContextToUserScript("ExecuteMethod_addCustomColumn()");
}
delete source_script;
source_script = nullptr;
EIDOS_TERMINATION << "ERROR (LogFile::ExecuteMethod_addCustomColumn): tokenize/parse error in script for addCustomColumn()." << EidosTerminate();
}
gEidosErrorContext = error_context_save;
// Check contextValue for validity and make a copy of it. Copying is needed to
// ensure that the value is not changed underneath us externally, for example
// by a for loop; see https://github.com/MesserLab/SLiM/issues/496.
if (context_value->Type() == EidosValueType::kValueObject)
{
EidosValue_Object *context_object = (EidosValue_Object *)context_value.get();
if (!context_object->Class()->UsesRetainRelease())
EIDOS_TERMINATION << "ERROR (LogFile::ExecuteMethod_addCustomColumn): the context parameter to addCustomColumn() cannot be an object of a class that is not under retain-release, since the lifetime of such objects cannot be guaranteed. See the documentation for addCustomColumn() for discussion of this limitation." << EidosTerminate();
}
context_value = context_value->CopyValues();
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_CustomScript, source_script, -1, std::move(context_value));
column_names_.emplace_back(column_name);
return gStaticEidosValueVOID;
}
// ********************* - (void)addCycle([No<Species>$ species])
EidosValue_SP LogFile::ExecuteMethod_addCycle(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addCycle");
// Figure out the species to log; if species is NULL, check for a singleton species to default to
EidosValue *species_value = p_arguments[0].get();
Species *species = SLiM_ExtractSpeciesFromEidosValue_No(species_value, 0, &SLiM_GetCommunityFromInterpreter(p_interpreter), "addCycle()");
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_Cycle, nullptr, species->species_id_, EidosValue_SP());
// column name is "cycle" in single-species models; append the species name in multispecies models
std::string col_name = "cycle";
if (community_.is_explicit_species_)
{
col_name.append("_");
col_name.append(species->name_);
}
column_names_.emplace_back(col_name);
return gStaticEidosValueVOID;
}
// ********************* - (void)addCycleStage()
EidosValue_SP LogFile::ExecuteMethod_addCycleStage(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addCycleStage");
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_CycleStage, nullptr, -1, EidosValue_SP());
column_names_.emplace_back("cycle_stage");
return gStaticEidosValueVOID;
}
// ********************* - (void)addMeanSDColumns(string$ columnName, string$ source, [* context = NULL])
EidosValue_SP LogFile::ExecuteMethod_addMeanSDColumns(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addMeanSDColumns");
EidosValue_String *columnName_value = (EidosValue_String *)p_arguments[0].get();
EidosValue_String *source_value = (EidosValue_String *)p_arguments[1].get();
EidosValue_SP context_value = p_arguments[2];
const std::string &column_name = columnName_value->StringRefAtIndex_NOCAST(0, nullptr);
const std::string &source = source_value->StringRefAtIndex_NOCAST(0, nullptr);
EidosErrorContext error_context_save = gEidosErrorContext;
EidosScript *source_script = new EidosScript(source);
gEidosErrorContext = EidosErrorContext{{-1, -1, -1, -1}, source_script};
try {
source_script->Tokenize();
source_script->ParseInterpreterBlockToAST(false);
}
catch (...)
{
if (gEidosTerminateThrows)
{
gEidosErrorContext = error_context_save;
TranslateErrorContextToUserScript("ExecuteMethod_addMeanSDColumns()");
}
delete source_script;
source_script = nullptr;
EIDOS_TERMINATION << "ERROR (LogFile::ExecuteMethod_addMeanSDColumns): tokenize/parse error in script for addMeanSDColumns()." << EidosTerminate();
}
gEidosErrorContext = error_context_save;
// Check contextValue for validity and make a copy of it. Copying is needed to
// ensure that the value is not changed underneath us externally, for example
// by a for loop; see https://github.com/MesserLab/SLiM/issues/496.
if (context_value->Type() == EidosValueType::kValueObject)
{
EidosValue_Object *context_object = (EidosValue_Object *)context_value.get();
if (!context_object->Class()->UsesRetainRelease())
EIDOS_TERMINATION << "ERROR (LogFile::ExecuteMethod_addMeanSDColumns): the context parameter to addMeanSDColumns() cannot be an object of a class that is not under retain-release, since the lifetime of such objects cannot be guaranteed. See the documentation for addCustomColumn() for discussion of this limitation." << EidosTerminate();
}
context_value = context_value->CopyValues();
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_CustomMeanAndSD, source_script, -1, std::move(context_value));
column_names_.emplace_back(column_name + "_mean");
column_names_.emplace_back(column_name + "_sd");
return gStaticEidosValueVOID;
}
// ********************* - (void)addPopulationSexRatio([No<Species>$ species])
EidosValue_SP LogFile::ExecuteMethod_addPopulationSexRatio(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addPopulationSexRatio");
// Figure out the species to log; if species is NULL, check for a singleton species to default to
EidosValue *species_value = p_arguments[0].get();
Species *species = SLiM_ExtractSpeciesFromEidosValue_No(species_value, 0, &SLiM_GetCommunityFromInterpreter(p_interpreter), "addPopulationSexRatio()");
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_PopulationSexRatio, nullptr, species->species_id_, EidosValue_SP());
// column name is "sex_ratio" in single-species models; append the species name in multispecies models
std::string col_name = "sex_ratio";
if (community_.is_explicit_species_)
{
col_name.append("_");
col_name.append(species->name_);
}
column_names_.emplace_back(col_name);
return gStaticEidosValueVOID;
}
// ********************* - (void)addPopulationSize([No<Species>$ species])
EidosValue_SP LogFile::ExecuteMethod_addPopulationSize(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addPopulationSize");
// Figure out the species to log; if species is NULL, check for a singleton species to default to
EidosValue *species_value = p_arguments[0].get();
Species *species = SLiM_ExtractSpeciesFromEidosValue_No(species_value, 0, &SLiM_GetCommunityFromInterpreter(p_interpreter), "addPopulationSize()");
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_PopulationSize, nullptr, species->species_id_, EidosValue_SP());
// column name is "num_individuals" in single-species models; append the species name in multispecies models
std::string col_name = "num_individuals";
if (community_.is_explicit_species_)
{
col_name.append("_");
col_name.append(species->name_);
}
column_names_.emplace_back(col_name);
return gStaticEidosValueVOID;
}
// ********************* - (void)addSubpopulationSexRatio(io<Subpopulation>$ subpop)
EidosValue_SP LogFile::ExecuteMethod_addSubpopulationSexRatio(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addSubpopulationSexRatio");
// Extract the subpopulation id; we allow reference to nonexistent subpopulations, which is unusual, so there's no function to use
EidosValue *subpop_value = p_arguments[0].get();
slim_objectid_t subpop_id;
if (subpop_value->Type() == EidosValueType::kValueInt)
{
subpop_id = SLiMCastToObjectidTypeOrRaise(subpop_value->IntAtIndex_NOCAST(0, nullptr));
}
else
{
Subpopulation *subpop = (Subpopulation *)(subpop_value->ObjectElementAtIndex_NOCAST(0, nullptr));
subpop_id = subpop->subpopulation_id_;
}
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_SubpopulationSexRatio, nullptr, subpop_id, EidosValue_SP());
column_names_.emplace_back(SLiMEidosScript::IDStringWithPrefix('p', subpop_id) + "_sex_ratio");
return gStaticEidosValueVOID;
}
// ********************* - (void)addSubpopulationSize(io<Subpopulation>$ subpop)
EidosValue_SP LogFile::ExecuteMethod_addSubpopulationSize(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addSubpopulationSize");
// Extract the subpopulation id; we allow reference to nonexistent subpopulations, which is unusual, so there's no function to use
EidosValue *subpop_value = p_arguments[0].get();
slim_objectid_t subpop_id;
if (subpop_value->Type() == EidosValueType::kValueInt)
{
subpop_id = SLiMCastToObjectidTypeOrRaise(subpop_value->IntAtIndex_NOCAST(0, nullptr));
}
else
{
Subpopulation *subpop = (Subpopulation *)(subpop_value->ObjectElementAtIndex_NOCAST(0, nullptr));
subpop_id = subpop->subpopulation_id_;
}
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_SubpopulationSize, nullptr, subpop_id, EidosValue_SP());
column_names_.emplace_back(SLiMEidosScript::IDStringWithPrefix('p', subpop_id) + "_num_individuals");
return gStaticEidosValueVOID;
}
// ********************* - (void)addSuppliedColumn(string$ columnName)
EidosValue_SP LogFile::ExecuteMethod_addSuppliedColumn(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addSuppliedColumn");
EidosValue_String *columnName_value = (EidosValue_String *)p_arguments[0].get();
const std::string &column_name = columnName_value->StringRefAtIndex_NOCAST(0, nullptr);
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_SuppliedColumn, nullptr, -1, EidosValue_SP());
column_names_.emplace_back(column_name);
return gStaticEidosValueVOID;
}
// ********************* - (void)addTick()
EidosValue_SP LogFile::ExecuteMethod_addTick(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
if (header_logged_)
RaiseForLockedHeader("LogFile::ExecuteMethod_addTick");
generator_info_.emplace_back(LogFileGeneratorType::kGenerator_Tick, nullptr, -1, EidosValue_SP());
column_names_.emplace_back("tick");
return gStaticEidosValueVOID;
}
// ********************* - (void)flush(void)
EidosValue_SP LogFile::ExecuteMethod_flush(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
Eidos_FlushFile(resolved_file_path_);
unflushed_row_count_ = 0;
return gStaticEidosValueVOID;
}
// ********************* - (void)logRow(void)
EidosValue_SP LogFile::ExecuteMethod_logRow(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_arguments, p_interpreter)
AppendNewRow();
return gStaticEidosValueVOID;
}
// ********************* - (void)setLogInterval([Ni$ logInterval = NULL])
EidosValue_SP LogFile::ExecuteMethod_setLogInterval(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_interpreter)
EidosValue *logInterval_value = p_arguments[0].get();
bool autologging = false;
int64_t logInterval = 0;
if (logInterval_value->Type() == EidosValueType::kValueNULL)
{
// NULL turns off autologging
autologging = false;
logInterval = 0;
}
else
{
autologging = true;
logInterval = logInterval_value->IntAtIndex_NOCAST(0, nullptr);
}
SetLogInterval(autologging, logInterval);
return gStaticEidosValueVOID;
}
// ********************* - (void)setFilePath(string$ filePath, [Ns initialContents = NULL], [logical$ append = F], [Nl$ compress = NULL], [Ns$ sep = NULL])
EidosValue_SP LogFile::ExecuteMethod_setFilePath(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
{
#pragma unused (p_method_id, p_interpreter)
EidosValue_String *filePath_value = (EidosValue_String *)p_arguments[0].get();
EidosValue *initialContents_value = p_arguments[1].get();
EidosValue *append_value = p_arguments[2].get();
EidosValue *compress_value = p_arguments[3].get();
EidosValue_String *sep_value = (EidosValue_String *)p_arguments[4].get();
// Note that the parameters and their interpretation is different from Community::ExecuteMethod_createLogFile();
// in particular, NULL here means "keep the existing value"
const std::string &filePath = filePath_value->StringRefAtIndex_NOCAST(0, nullptr);
std::vector<const std::string *> initialContents;
bool append = append_value->LogicalAtIndex_NOCAST(0, nullptr);