/*
* Production: Input Statement
* FIRST set: { KW_T (only INPUT) }
*/
void input_statement(void) {
match(KW_T, INPUT);
match(LPR_T, NO_ATTR);
variable_list();
match(RPR_T,NO_ATTR);
match(EOS_T,NO_ATTR);
gen_incode("PLATY: INPUT statement parsed");
}
/** Compiles a grammar to the output file. */
void compile(ast::grammar& g) {
//print pre-amble
out << "#pragma once" << std::endl
<< std::endl
<< "/* THE FOLLOWING HAS BEEN AUTOMATICALLY GENERATED BY THE EGG PARSER GENERATOR." << std::endl
<< " * DO NOT EDIT. */" << std::endl
<< std::endl
;
//print pre-code
if ( ! g.pre.empty() ) {
out << "// {%" << std::endl
<< g.pre << std::endl
<< "// %}" << std::endl
<< std::endl
;
}
//get needed includes
out << "#include <string>" << std::endl
<< "#include \"parse.hpp\"" << std::endl
<< std::endl
;
//setup parser namespace
out << "namespace " << name << " {" << std::endl
<< std::endl
;
//pre-declare matchers
for (auto it = g.rs.begin(); it != g.rs.end(); ++it) {
ast::grammar_rule& r = **it;
out << "\tparse::result<" << r.type << "> " << r.name << "(parse::state&);" << std::endl;
}
out << std::endl;
//generate matching functions
vars = variable_list(g);
for (auto it = g.rs.begin(); it != g.rs.end(); ++it) {
ast::grammar_rule& r = **it;
compile(r);
}
//close parser namespace
out << "} /* namespace " << name << " */" << std::endl
<< std::endl
;
//print post-code
if ( ! g.post.empty() ) {
out << "// {%" << std::endl
<< g.post << std::endl
<< "// %}" << std::endl
<< std::endl
;
}
}
/* FIRST(output list)={variable identifier,STR_T,e}
<output list> ->
<variable list> | STR_T | e
Author: Kyle Hinskens */
void output_list(void) {
switch(lookahead_token.code) {
case STR_T:
match(STR_T, NO_ATTR);
gen_incode("Output list (string literal) parsed");
break;
case AVID_T:
case SVID_T:
variable_list();
break;
default:
gen_incode("Output list (empty) parsed");
break;
}
}
/*
* Production: Optional Variable List
* FIRST set: { AVID_T, SVID_T, STR_T, e }
*/
void opt_variable_list(void) {
switch (lookahead.code) {
case AVID_T:
case SVID_T:
variable_list();
return;
case STR_T:
match(STR_T, NO_ATTR);
gen_incode("PLATY: Output list (string literal) parsed");
return;
default:
gen_incode("PLATY: Output list (empty) parsed");
}
}
int cnt(void)
{
std::shared_ptr<group_connectometry_analysis> database(new group_connectometry_analysis);
std::cout << "reading connectometry db" <<std::endl;
if(!database->load_database(po.get("source").c_str()))
{
std::cout << "invalid database format" << std::endl;
return 1;
}
std::shared_ptr<group_connectometry> vbc(new group_connectometry(0,database,po.get("source").c_str(),false));
vbc->setAttribute(Qt::WA_DeleteOnClose);
vbc->show();
//vbc->hide();
if(!po.has("demo"))
{
std::cout << "please assign demographic file" << std::endl;
return 1;
}
std::string error_msg;
if(!vbc->load_demographic_file(po.get("demo").c_str(),error_msg))
{
std::cout << error_msg << std::endl;
return 1;
}
if(po.has("missing_value"))
{
vbc->ui->missing_data_checked->setChecked(true);
vbc->ui->missing_value->setValue(po.get("missing_value",9999));
std::cout << "missing value=" << vbc->ui->missing_value->value() << std::endl;
}
if(!po.has("voi") || !po.has("variable_list"))
{
std::cout << "please assign --voi and --variable_list" << std::endl;
return 1;
}
{
std::string var_text = po.get("variable_list");
std::replace(var_text.begin(),var_text.end(),',',' ');
std::istringstream var_in(var_text);
std::vector<int> variable_list(
(std::istream_iterator<int>(var_in)),
(std::istream_iterator<int>()));
for(int i = 0;i < vbc->ui->variable_list->count();++i)
vbc->ui->variable_list->item(i)->setCheckState(Qt::Unchecked);
std::cout << "variables=";
int voi_index = po.get("voi",0);
int voi_sel = -1;
std::string voi_text;
for(int i = 0;i < variable_list.size();++i)
{
int index = variable_list[i];
if(index >= vbc->ui->variable_list->count())
{
std::cout << "Invalid number in the variable_list:" << index << std::endl;
return 1;
}
if(index == voi_index)
{
voi_sel = vbc->ui->variable_list->count();
voi_text = vbc->ui->variable_list->item(index)->text().toStdString();
}
vbc->ui->variable_list->item(index)->setCheckState(Qt::Checked);
if(i)
std::cout << ",";
std::cout << vbc->ui->variable_list->item(index)->text().toStdString();
}
std::cout << std::endl;
if(voi_sel == -1)
{
std::cout << "variable of interest is not included in the variable list" << std::endl;
return 1;
}
vbc->on_variable_list_clicked(QModelIndex());
vbc->ui->foi->update();
vbc->ui->foi->setCurrentText(voi_text.c_str());
std::cout << "study variable=" << vbc->ui->foi->currentText().toStdString() << std::endl;
}
vbc->ui->threshold->setValue(po.get("t_threshold",float(vbc->ui->threshold->value())));
std::cout << "t_threshold=" << vbc->ui->threshold->value() << std::endl;
vbc->ui->seed_count->setValue(po.get("seed_count",10000));
std::cout << "seed_count=" << vbc->ui->seed_count->value() << std::endl;
vbc->ui->permutation_count->setValue(po.get("permutation",int(2000)));
std::cout << "permutation=" << vbc->ui->permutation_count->value() << std::endl;
vbc->ui->multithread->setValue(po.get("thread_count",int(std::thread::hardware_concurrency())));
std::cout << "thread=" << vbc->ui->multithread->value() << std::endl;
vbc->ui->track_trimming->setValue(po.get("trim",1));
std::cout << "trim=" << vbc->ui->track_trimming->value() << std::endl;
if(po.get("normalized_qa",int(0)))
{
std::cout << "normalized qa" << std::endl;
vbc->ui->normalize_qa->setChecked(true);
}
if(po.has("fdr_threshold"))
{
vbc->ui->rb_fdr->setChecked(true);
vbc->ui->fdr_threshold->setValue(po.get("fdr_threshold",0.05f));
std::cout << "fdr_threshold=" << vbc->ui->fdr_threshold->value() << std::endl;
}
else
{
vbc->ui->rb_length->setChecked(true);
vbc->ui->length_threshold->setValue(po.get("length_threshold",int(40)));
std::cout << "length_threshold=" << vbc->ui->length_threshold->value() << std::endl;
}
// check rois
{
const int total_count = 18;
char roi_names[total_count][5] = {"roi","roi2","roi3","roi4","roi5","roa","roa2","roa3","roa4","roa5","end","end2","seed","ter","ter2","ter3","ter4","ter5"};
unsigned char type[total_count] = {0,0,0,0,0,1,1,1,1,1,2,2,3,4,4,4,4,4};
for(int index = 0;index < total_count;++index)
if (po.has(roi_names[index]))
{
ROIRegion roi(vbc->vbc->handle);
if(!load_region(vbc->vbc->handle,roi,po.get(roi_names[index])))
return 1;
vbc->add_new_roi(po.get(roi_names[index]).c_str(),
po.get(roi_names[index]).c_str(),
roi.get_region_voxels_raw(),type[index]);
std::cout << roi_names[index] << "=" << po.get(roi_names[index]) << std::endl;
vbc->ui->roi_user_defined->setChecked(true);
vbc->ui->roi_whole_brain->setChecked(false);
}
}
vbc->on_run_clicked();
std::cout << vbc->vbc->report << std::endl;
std::cout << "running connectometry" << std::endl;
vbc->vbc->wait();
std::cout << "output results" << std::endl;
vbc->calculate_FDR();
std::cout << "close GUI" << std::endl;
vbc->close();
vbc.reset();
return 0;
}
int move_resolved(mixed item, mixed dest) {
move_object(item, dest);
if (!objectp(item)) { item = find_object(item); }
if (!objectp(dest)) { dest = find_object(dest); }
return (item && dest && (environment(item) == dest));
}
/**
* Return an object's capabilities map.
*
* @param ob the object to query
* @return a mapping of all the object's capabilities
*/
mapping query_capabilities(object ob) {
mapping result = ([ ]);
mixed *vars = variable_list(ob, RETURN_FUNCTION_NAME
| RETURN_VARIABLE_VALUE);
int i = 0;
while ((i = member(vars, CAPABILITIES_VAR_STR, i)) != -1) {
mixed val = vars[++i];
if (mappingp(val)) {
result += val;
}
i++;
}
return result;
}
/**
* Allows you to target an object for the efun binary_message().
*
* @param who the object to receive message
