/**
* Run the database seeds.
*
* @return void
*/
public function run()
{
Eloquent::unguard();
$algorithmsXmls = File::allFiles(public_path() . '/algorithms');
foreach ($algorithmsXmls as $algorithmsXml) {
$dom = new DomDocument();
$dom->load($algorithmsXml);
$root = $dom->documentElement;
$modality = Modality::whereName($root->getAttribute('modality'))->first();
if (empty($modality)) {
throw new Exception("Could not find modality! ({$algorithmsXml})");
}
$protocolName = $root->getAttribute('protocol');
$protocol = Protocol::whereName($protocolName)->whereModalityId($modality->Id)->first();
if (empty($protocol)) {
\Log::warning("Could not find protocol! ({$algorithmsXml})");
continue;
}
$arguments = [];
$parameters = [];
$description = "";
foreach ($root->childNodes as $node) {
if (get_class($node) == 'DOMText') {
continue;
}
switch ($node->nodeName) {
case 'arguments':
foreach ($node->childNodes as $argument) {
if (get_class($argument) == 'DOMText') {
continue;
}
$arguments[] = ['Name' => $argument->getAttribute('name')];
}
break;
case 'parameters':
foreach ($node->childNodes as $parameter) {
if (get_class($parameter) == 'DOMText') {
continue;
}
$parameters[] = ['Name' => $parameter->getAttribute('name'), 'Type' => $parameter->getAttribute('type'), 'Value' => $parameter->hasAttribute('value') ? $parameter->getAttribute('value') : null];
}
break;
case 'description':
$description = $node->textContent;
break;
default:
throw new Exception("Unrecognized entry in algorithm XML - {$node->nodeName}! ({$algorithmsXml})");
}
}
$algorithm = new Algorithm();
$algorithm->content = $description;
$resultName = $root->getAttribute('result');
$resultType = $root->getAttribute('type');
$result = Parameter::whereName($resultName)->first();
if (empty($result)) {
$result = Parameter::create(['Name' => $resultName, 'Type' => $resultType]);
}
$algorithm->result()->associate($result);
$algorithm->protocol()->associate($protocol);
$algorithm->save();
foreach ($arguments as $argument) {
$algorithm->arguments()->attach(Argument::create($argument));
}
foreach ($parameters as $parameter) {
$algorithm->attribute($parameter);
}
}
}
public function makeSimulation($caption, $patient, $organ, $model, $protocol, $parameterData, $regionData, $needles)
{
$numerical_model = NumericalModel::whereName($model)->first();
$protocol = Protocol::whereName($protocol)->whereModalityId($numerical_model->Modality_Id)->first();
$context = Context::byNameFamily($organ, 'organ');
$combinations = $numerical_model->Combinations()->whereProtocolId($protocol->Id)->where(Context::$idField, "=", $context->Id);
$combination = $combinations->first();
$simulation = Simulation::create(['Combination_Id' => $combination->Combination_Id, 'Patient_Id' => $patient->Id ?: '00000000-0000-0000-0000-000000000000', 'Caption' => 'Sample Simulation for ' . $caption, 'SegmentationType' => 0, 'Progress' => '0', 'State' => 0, 'Color' => 0, 'Active' => 0]);
/*
foreach ($regionData as $name => $locations)
{
$region = Region::whereName($name)->first();
foreach ($locations as $location)
$simulation->regions()->attach($region, ['Location' => $location]);
}
*/
$simulation->save();
$simulationNeedles = [];
$needleData = [];
$needleUserParameters = new Collection();
$n = 0;
foreach ($needles as $needleConfig) {
$n++;
$needle = Needle::whereManufacturer($needleConfig["Manufacturer"])->whereName($needleConfig["Name"])->first();
$needleUserParameters[$needle->Id] = new Collection();
$simulationNeedle = SimulationNeedle::create(['Needle_Id' => $needle->Id, 'Simulation_Id' => $simulation->Id, 'Target_Id' => $this->makePointSet($needleConfig["Parameters"]["NEEDLE_TIP_LOCATION"])->Id, 'Entry_Id' => $this->makePointSet($needleConfig["Parameters"]["NEEDLE_ENTRY_LOCATION"])->Id]);
$simulationNeedleId = $simulationNeedle->Id;
foreach ($needleConfig["Parameters"] as $paramName => $paramValue) {
$parameter = Parameter::whereName($paramName)->first();
$parameter->Value = $paramValue;
$needleUserParameters[$needle->Id][$paramName] = $parameter;
}
$simulationNeedles[] = $needle;
}
$parameters = new Collection();
foreach ($parameterData as $parameterName => $value) {
$parameter = Parameter::whereName($parameterName)->first();
$parameter->Value = $value;
$parameters[$parameter->Name] = $parameter;
}
$incompatibilities = [];
$userRequiredParameters = [];
list($parameters, $needleParameters) = $combination->compileParameters($parameters, $simulationNeedles, $needleUserParameters, $incompatibilities, $userRequiredParameters);
if (count($incompatibilities)) {
var_dump($incompatibilities);
var_dump($userRequiredParameters);
}
foreach ($parameters as $parameterName => $parameter) {
$simulation->Parameters()->attach($parameter, ['ValueSet' => $parameter->Value]);
}
$simulation->SimulationNeedles->each(function ($simulationNeedle) use($needleParameters) {
if (array_key_exists($simulationNeedle->Needle_Id, $needleParameters)) {
$needleParameters[$simulationNeedle->Needle_Id]->each(function ($p) use($simulationNeedle) {
$simulationNeedle->Parameters()->attach($p);
});
}
});
$this->r++;
print "Simulation #{$this->r}: " . $simulation->Combination->asString . " [ " . strtoupper($simulation->Id) . " ]\n";
}