/**
* Run the database seeds.
*
* @return void
*/
public function run()
{
Eloquent::unguard();
if (!Config::get('gosmart.integrated_patient_database')) {
\Log::warning("Can only seed simulations if a patient database is available");
return;
}
$this->clean();
//$this->deepClean();
$organs = ['liver', 'kidney'];
foreach ($organs as $organ) {
$referenceSimulation[$organ] = [];
$sim = Simulation::join('ItemSet_Patient AS IS_P', 'IS_P.Id', '=', 'Simulation.Patient_Id')->join('ItemSet AS IS', 'IS.Id', '=', 'IS_P.Id')->join('Simulation_Needle AS SN', 'SN.Simulation_Id', '=', 'Simulation.Id')->where('IS_P.OrganType', '=', ContextEnum::value($organ))->where('IS.IsDeleted', '=', 'FALSE')->select('Simulation.*')->first();
if ($sim) {
$referenceSimulation[$organ]["patient"] = DB::table('ItemSet_Patient')->whereId($sim->Patient_Id)->first();
$referenceNeedle = $sim->SimulationNeedles->first();
$referenceSimulation[$organ]["target"] = $referenceNeedle->Target;
$referenceSimulation[$organ]["entry"] = $referenceNeedle->Entry;
} else {
$referenceSimulation[$organ]["patient"] = NULL;
$referenceSimulation[$organ]["target"] = PointSet::fromArray([0, 0, 0]);
$referenceSimulation[$organ]["entry"] = PointSet::fromArray([1, 1, 1]);
}
}
foreach (['5cm', '4cm', '3cm', '2cm'] as $length) {
$this->makeSimulation("{$length} RITA RFA", $referenceSimulation["liver"]["patient"], 'liver', 'NUMA RFA Basic SIF', "RITA Starburst {$length} Protocol", [], ['organ' => ["organ.vtp"], 'vessels' => ["vessels1.vtp"], 'tumour' => ["tumour.vtp"]], [["Manufacturer" => "RITA", "Name" => "Starburst MRI", "Parameters" => ['NEEDLE_TIP_LOCATION' => $referenceSimulation["liver"]["target"]->asString, 'NEEDLE_ENTRY_LOCATION' => $referenceSimulation["liver"]["entry"]->asString]]]);
}
$this->makeSimulation('Cryoablation', $referenceSimulation["kidney"]["patient"], 'kidney', 'NUMA Cryoablation Basic SIF', 'Empty', ['SETTING_FINAL_TIMESTEP' => '300'], ['organ' => ["organ.vtp"], 'vessels' => ["vessels1.vtp"], 'tumour' => ["tumour.vtp"]], [["Manufacturer" => "Galil Medical", "Name" => "IceROD", "Parameters" => ['NEEDLE_TIP_LOCATION' => $referenceSimulation["kidney"]["target"]->asString, 'NEEDLE_ENTRY_LOCATION' => $referenceSimulation["kidney"]["entry"]->asString]]]);
$needleDeltas = [[10, 8, -5], [10, 8, 5], [10, -8, -5], [10, -8, 5], [10, 5, 0], [10, -5, 0]];
$ireTipCentre = $referenceSimulation["liver"]["target"]->asArray;
$ireEntryCentre = $referenceSimulation["liver"]["entry"]->asArray;
$parallel = array_map(function ($c) use($ireTipCentre, $ireEntryCentre) {
return $ireTipCentre[$c] - $ireEntryCentre[$c];
}, [0, 1, 2]);
$norm = sqrt($parallel[0] * $parallel[0] + $parallel[1] * $parallel[1] + $parallel[2] * $parallel[2]);
$parallel = array_map(function ($c) use($norm) {
return $c / $norm;
}, $parallel);
$randVec = [0, 1.2384717624, 3.42878E-6];
$perp1 = crossProduct($parallel, $randVec);
$perp2 = crossProduct($parallel, $perp1);
//$parallel = [1, 0, 0];
//$perp1 = [0, 1, 0];
//$perp2 = [0, 0, 1];
$ireNeedles = [];
foreach ($needleDeltas as $needleDelta) {
$needleOffset = array_map(function ($c) use($needleDelta, $parallel, $perp1, $perp2) {
return $needleDelta[0] * $parallel[$c] + $needleDelta[1] * $perp1[$c] + $needleDelta[2] * $perp2[$c];
}, [0, 1, 2]);
$needleTip = array_map(function ($p) {
return $p[0] + $p[1];
}, array_map(null, $ireTipCentre, $needleOffset));
$ireNeedle = ["Manufacturer" => "Angiodynamics", "Name" => "Basic", "Parameters" => ['NEEDLE_TIP_LOCATION' => json_encode($needleTip), 'NEEDLE_ENTRY_LOCATION' => json_encode(array_map(function ($p) {
return $p[0] + $p[1];
}, array_map(null, $ireEntryCentre, $needleOffset)))]];
$ireNeedles[] = $ireNeedle;
}
$this->makeSimulation('IRE', $referenceSimulation["liver"]["patient"], 'liver', 'NUMA IRE 3D SIF', 'Empty', ['CONSTANT_IRE_POTENTIAL_DIFFERENCES' => "[1300, 1500, 1300, 1900, 1300, 1300, 1300, 1900, 1300]"], ['organ' => ["organ.vtp"], 'vessels' => ["vessels1.vtp"], 'tumour' => ["tumour.vtp"]], $ireNeedles);
$this->makeSimulation('Amica MWA', $referenceSimulation["kidney"]["patient"], 'kidney', 'NUMA MWA Nonlinear SIF', 'Generic modifiable power', [], ['organ' => ["organ.vtp"], 'vessels' => ["vessels1.vtp"], 'tumour' => ["tumour.vtp"]], [["Manufacturer" => "HS", "Name" => "APK11150T19V5", "Parameters" => ['NEEDLE_TIP_LOCATION' => $referenceSimulation["kidney"]["target"]->asString, 'NEEDLE_ENTRY_LOCATION' => $referenceSimulation["kidney"]["entry"]->asString]]]);
}
public static function fromXml($xml)
{
$xpath = new DOMXpath($xml);
$simulation = new static();
$simulationNode = $xpath->query('//simulationDefinition/simulation')->item(0);
$simulation->Id = strtoupper($simulationNode->getAttribute('id'));
$simulationAttributes = ['Caption', 'SegmentationType', 'Progress', 'State', 'Color', 'Active'];
foreach ($simulationAttributes as $simulationAttribute) {
$simulation->{$simulationAttribute} = $simulationNode->getAttribute(strtolower($simulationAttribute));
}
//if (Simulation::find($simulation->Id))
// return [false, "Simulation with this ID already exists"];
$simulationNeedle = [];
$combination = Combination::find($xpath->query('//simulationDefinition/combination/@id')->item(0)->value);
if (!$combination) {
throw new Exception("Cannot find combination (you may be able to work around this manually from the XML)");
}
$patient = DB::table('ItemSet_Patient')->where('Id', '=', $xpath->query('//simulationDefinition/simulation/patient/@id')->item(0)->value)->get();
if (empty($patient)) {
throw new Exception("Patient no longer exists");
}
$patient = $patient[0];
$simulation->Combination_Id = $combination->Combination_Id;
$simulation->Patient_Id = $patient->Id;
$simulation->Id = null;
$simulation->save();
$parameterNodes = $xpath->query('//simulationDefinition/parameters/parameter');
$parameters = [];
foreach ($parameterNodes as $parameterNode) {
$parameter = Parameter::whereName($parameterNode->getAttribute("name"))->first();
$simulation->Parameters()->attach($parameter, ["ValueSet" => $parameterNode->getAttribute("value")]);
}
$needleNodes = $xpath->query('//simulationDefinition/numericalModel/needles/needle');
foreach ($needleNodes as $needleNode) {
$needle = Needle::find($needleNode->getAttribute("id"));
if (!$needle) {
throw new Exception("Needle not found");
}
$simulationNeedle = new SimulationNeedle();
$simulationNeedle->Needle_Id = $needle->Id;
$simulationNeedle->Simulation_Id = $simulation->Id;
$simulationNeedle->save();
$parameterNodes = $xpath->query('//simulationDefinition/numericalModel/needles/needle/parameters/parameter');
$parameters = [];
foreach ($parameterNodes as $parameterNode) {
$parameter = Parameter::whereName($parameterNode->getAttribute("name"))->first();
switch ($parameter->Name) {
case "NEEDLE_TIP_LOCATION":
$target = PointSet::fromArray(json_decode($parameterNode->getAttribute("value")));
$target->save();
$simulationNeedle->Target_Id = $target->Id;
break;
case "NEEDLE_ENTRY_LOCATION":
$entry = PointSet::fromArray(json_decode($parameterNode->getAttribute("value")));
$entry->save();
$simulationNeedle->Entry_Id = $entry->Id;
break;
default:
$simulationNeedle->Parameters()->attach($parameter, ["ValueSet" => $parameterNode->getAttribute("value")]);
}
}
$simulationNeedle->save();
}
//foreach ($parameters as $sP)
//{
// $sP->Simulation_Id = $simulation->Id;
// $sP->save();
//}
$simulation->save();
return $simulation;
}
