public function xml($parent, $suppliedRegions, &$incompatibilities, $needles = [], $needleUserData = [], $backup = false) { foreach ($this->results as $result) { $resultNode = new DOMNode("result"); $resultNode->setAttribute('name', $this->result->name); $parent->appendChild($resultNode); } $regions = []; $regionsNode = new DOMElement("regions"); $parent->appendChild($regionsNode); foreach ($this->Regions as $region) { $entries = $suppliedRegions->filter(function ($r) use($region) { return in_array($r->SegmentationType, $region->SegmentationTypes); }); $entries->each(function ($e) { $e->Location = strtolower($e->FileId) . '/' . $e->FileName . '.' . $e->Extension; }); $suppliedCount = $entries->count(); $pivot = $region->pivot; if (Config::get('gosmart.check_regions') !== false) { if ($pivot->Maximum !== null && $suppliedCount > $pivot->Maximum) { $incompatibilities[] = "Too many region entries for {$region->Name} (max {$pivot->Maximum}, provided {$suppliedCount})"; } if ($pivot->Minimum !== null && $suppliedCount < $pivot->Minimum) { $incompatibilities[] = "Too few region entries for {$region->Name} (min {$pivot->Minimum}, provided {$suppliedCount})"; } } else { if ($pivot->Minimum) { for ($k = 0; $k < $pivot->Minimum - $entries->count(); $k++) { $entry = clone $region; $entries[] = $entry; $entry->Location = $region->Name . '.vtp'; } } } $k = 0; foreach ($entries as $entry) { $regionNode = new DOMElement("region"); $regionsNode->appendChild($regionNode); $regionNode->setAttribute('id', $region->Name . '-' . $k); $regionNode->setAttribute('name', $region->Name); $regionNode->setAttribute('format', $region->Format); $regionNode->setAttribute('input', $entry->Location); $regionNode->setAttribute('groups', $region->Groups); /* groups should be a JSON array */ $k += 1; } $suppliedRegions = $suppliedRegions->reject(function ($r) use($region) { return $r->SegmentationType == $region->SegmentationType; }); } //if (count($suppliedRegions)) // $incompatibilities[] = "Unknown regions for model $this->Name : " . implode(', ', $suppliedRegions->lists('Name')); $needlesNode = new DOMElement("needles"); $parent->appendChild($needlesNode); $i = 1; foreach ($needles as $simulationNeedle) { $needle = $simulationNeedle->Needle; if ($simulationNeedle->Index) { $needleIx = 'needle' . $simulationNeedle->Index; } else { $needleIx = 'needle' . $i; } $i += 1; $needleNode = new DOMElement("needle"); $needlesNode->appendChild($needleNode); $needleNode->setAttribute("index", $needleIx); if ($backup) { $needleNode->setAttribute("id", $needle->Id); $needleNode->setAttribute("name", $needle->Name); } /* isset checks value whether NULL */ if (isset($needleUserData[$needleIx]) && isset($needleUserData[$needleIx]['class'])) { $needleNode->setAttribute("class", $needleUserData[$needleIx]['class']); } else { if (!empty($needle->Class)) { $needleNode->setAttribute("class", $needle->Class); } else { $incompatibilities[] = "Needle class is not given for " . $needleIx; } } if (isset($needleUserData[$needleIx]) && isset($needleUserData[$needleIx]['file'])) { $needleNode->setAttribute("file", $needleUserData[$needleIx]['file']); } else { if (!empty($needle->Geometry)) { $needleNode->setAttribute("file", $needle->Geometry); } else { $incompatibilities[] = "Needle file is not given for " . $needleIx; } } $parametersNode = new DOMElement("parameters"); $needleNode->appendChild($parametersNode); $tipParameter = Parameter::whereName("NEEDLE_TIP_LOCATION")->first(); $tipParameter->Value = json_encode($simulationNeedle->Target->asArray); $entryParameter = Parameter::whereName("NEEDLE_ENTRY_LOCATION")->first(); $entryParameter->Value = json_encode($simulationNeedle->Entry->asArray); $tipParameter->xml($parametersNode, $backup); $entryParameter->xml($parametersNode, $backup); $simulationNeedle->Parameters->each(function ($parameter) use($parametersNode, $backup) { $parameter->xml($parametersNode, $backup); }); } $definition = new DOMElement("definition"); $definitionText = new DOMText($this->Definition); $parent->appendChild($definition); $definition->setAttribute('family', $this->Family); $definition->appendChild($definitionText); }
/** * 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 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 $simulation; }
public function makeSimulation($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"; }
/** * Update the specified resource in storage. * * @param int $id * @return Response */ public function update($id) { $simulation = Simulation::find($id); if (Input::has('caption')) { $simulation->Caption = Input::get('caption'); } $simulation->save(); if (Input::has('Combination_Id')) { $simulation->Combination_Id = Input::get('Combination_Id'); $simulation->save(); $this->rebuild($simulation->Id); } foreach ($simulation->Parameters as $parameter) { if (Input::has('parameters-' . $parameter->Id)) { $parameter->pivot->ValueSet = Input::get('parameters-' . $parameter->Id); $parameter->pivot->save(); } } if (Input::get('new-parameter-name') && Input::get('new-parameter-value') != '') { $parameter = Parameter::whereName(Input::get('new-parameter-name'))->first(); if ($parameter) { $simulation->Parameters()->attach($parameter, ["ValueSet" => Input::get('new-parameter-value')]); $simulation->save(); } } foreach ($simulation->SimulationNeedles as $simulationNeedle) { foreach ($simulationNeedle->Parameters as $parameter) { if (Input::has('needle-parameters-' . $simulationNeedle->Id . '-' . $parameter->Id)) { $parameter->pivot->ValueSet = Input::get('needle-parameters-' . $simulationNeedle->Id . '-' . $parameter->Id); $parameter->pivot->save(); } } $newparameterprefix = 'needle-' . $simulationNeedle->Id . '-new-parameter-'; if (Input::get($newparameterprefix . 'name') && Input::get($newparameterprefix . 'value') != '') { $parameter = Parameter::whereName(Input::get($newparameterprefix . 'name'))->first(); if ($parameter) { $simulationNeedle->Parameters()->attach($parameter, ["ValueSet" => Input::get($newparameterprefix . 'value')]); $simulationNeedle->save(); } } } if (Input::get('removing')) { if (Input::get('simulation-needle-id')) { $simulationNeedle = SimulationNeedle::find(Input::get('simulation-needle-id')); $simulationNeedle->delete(); } if (Input::get('region-remove-id')) { $region = Region::find(Input::get('region-remove-id')); if (Input::get('region-remove-location')) { $simulation->Regions()->newPivotStatementForId($region->Id)->where('Location', '=', Input::get('region-remove-location'))->delete(); } else { $simulation->Regions()->newPivotStatementForId($region->Id)->whereNull('Location')->delete(); } } } else { if (Input::get('needle-id')) { $needle = Needle::find(Input::get('needle-id')); $simulationNeedle = new SimulationNeedle(); $simulationNeedle->Simulation_Id = $simulation->Id; $simulationNeedle->Needle_Id = $needle->Id; $target = json_decode(Input::get('needle-target')); $simulationNeedle->Target_Id = PointSet::create(['X' => $target[0], 'Y' => $target[1], 'Z' => $target[2]])->Id; $entry = json_decode(Input::get('needle-entry')); $simulationNeedle->Entry_Id = PointSet::create(['X' => $entry[0], 'Y' => $entry[1], 'Z' => $entry[2]])->Id; $simulationNeedle->save(); } if (Input::get('region-id')) { $region = Region::find(Input::get('region-id')); $simulation->Regions()->attach($region, ['Location' => Input::get('region-location')]); $simulation->save(); } } return Redirect::route('simulation.edit', $id); }
public function attribute($data, $context = null, $overwrite = true, $overwrite_parameter = false) { $name = $data['Name']; if (!$this->Id) { throw new InvalidArgumentException("Cowardly refusing to create an empty (universal) attribute"); } /* Convention over configuration */ $id_name = train_case(get_class($this)) . '_Id'; if ($id_name == 'Context_Id') { $id_name = Context::$idField; } $parameterClause = ParameterAttribution::where($id_name, '=', $this->Id); $activeFields = [snake_case(get_class($this))]; if ($context !== null) { $activeFields[] = 'context'; $parameterClause = $parameterClause->where(Context::$idContext, '=', $context->Id); } $parameterAttributions = $parameterClause->whereHas('parameter', function ($q) use($name) { $q->where('Name', '=', $name); })->get()->filter(function ($pa) use($activeFields) { return empty(array_diff(array_values($pa->activeFields()), array_values($activeFields))); }); $parameterAttribution = $parameterAttributions->first(); $parameterAttributions->each(function ($pa) { $pa->delete(); }); if (array_key_exists('Value', $data)) { $value = $data['Value']; unset($data['Value']); } else { $value = null; } if (array_key_exists('Widget', $data)) { $widget = $data['Widget']; unset($data['Widget']); } else { $widget = null; } if (array_key_exists('Units', $data)) { $units = $data['Units']; unset($data['Units']); } else { $units = null; } if (array_key_exists('Editable', $data)) { $editable = $data['Editable']; unset($data['Editable']); } else { $editable = 2; } if ($parameterAttribution) { $parameter = $parameterAttribution->parameter; if ($overwrite) { $parameterAttribution->Value = $value; $parameterAttribution->Editable = $editable; $parameterAttribution->Widget = $widget; $parameterAttribution->Units = $units; $parameterAttribution->save(); } else { $value = $parameterAttribution->Value; $editable = $parameterAttribution->Editable; $widget = $parameterAttribution->Widget; $units = $parameterAttribution->Units; } } else { $parameter = Parameter::whereName($data['Name'])->first(); if (empty($parameter)) { $parameter = Parameter::create($data); } else { $parameter->update(array_filter($data)); } /* Convention over configuration */ $id_name = train_case(get_class($this)) . '_Id'; if ($id_name == 'Context_Id') { $id_name = Context::$idField; } $type = array_key_exists('Type', $data) ? $data['Type'] : $parameter->Type; $widget = isset($widget) ? $widget : $parameter->Widget; $units = isset($units) ? $units : $parameter->Units; $attribution = [$id_name => $this->Id, 'Parameter_Id' => $parameter->Id, 'Value' => $value, 'Format' => $type, 'Editable' => $editable, 'Widget' => $widget, 'Units' => $units]; if ($context !== null) { $attribution[Context::$idContext] = $context->Id; } $parameterAttribution = ParameterAttribution::create($attribution); } if ($parameter->Widget === null && $parameter->Units === null || $overwrite_parameter) { $parameter->Widget = $widget; $parameter->Units = $units; } $parameter->Value = $value; $parameter->Editable = $editable; $parameter->Widget = $widget; $parameter->Units = $units; $parameterAttribution->save(); return $parameter; }
/** * Run the database seeds. * * @return void */ public function run() { Eloquent::unguard(); $parameterFields = ['name', 'type', 'widget', 'description', 'units', 'priority', 'restriction']; $attributionFields = ['Name', 'Type', 'Widget', 'Units']; $constantsXmls = File::allFiles(public_path() . '/constants'); foreach ($constantsXmls as $constantsXml) { $dom = new DomDocument(); $dom->load($constantsXml); $root = $dom->documentElement; $class = $root->getAttribute('class'); $name = $root->getAttribute('name'); //FIXME: Not very safe! if (Config::get('gosmart.context_as_enum') && $class == 'Context') { if ($root->hasAttribute('family')) { $family = $root->getAttribute('family'); } else { $family = 'organ'; } $target = Context::byNameFamily($name, $family); } else { $object = new $class(); $objectQuery = $object->whereName($name); if ($root->hasAttribute('family')) { $objectQuery = $objectQuery->whereFamily($root->getAttribute('family')); } $target = $objectQuery->first(); } if (empty($target)) { throw new Exception("Did not find object {$name} ({$class}) for {$constantsXml}"); } foreach ($root->childNodes as $constant) { if (get_class($constant) == 'DOMText') { continue; } if (!$constant->hasAttribute('name')) { throw new Exception("Constant missing name! ({$constantsXml})"); } $present = array_filter($parameterFields, [$constant, 'hasAttribute']); $parameterData = []; array_map(function ($a) use(&$parameterData, $constant) { $parameterData[train_case($a)] = $constant->getAttribute($a); }, $present); if (!$constant->hasAttribute('description')) { $parameterData['Description'] = $parameterData['Name']; } $parameterData['Name'] = preg_replace('/[ -]/', '_', $parameterData['Name']); $parameterData['Name'] = strtoupper($constant->nodeName) . '_' . strtoupper(preg_replace('/[[:^word:]]/', '', $parameterData['Name'])); if (!$constant->hasAttribute('type')) { $parameterData['Type'] = 'float'; } $parameter = Parameter::whereName($parameterData['Name'])->first(); if (empty($parameter)) { $parameter = Parameter::create($parameterData); } else { $parameter->fill($parameterData)->save(); } $id_name = train_case($class) . '_Id'; if ($id_name == "Context_Id") { $id_name = Context::$idField; } $attributionData = array_intersect_key($parameterData, array_flip($attributionFields)); if ($constant->hasAttribute('context')) { //$attributionData[Context::$idField] = Context::byNameFamily($constant->getAttribute('context'), $constant->getAttribute('contextFamily') ?: 'organ')->first()->id; $context = Context::byNameFamily($constant->getAttribute('context'), $constant->getAttribute('contextFamily') ?: 'organ')->first(); } else { $context = null; } if ($constant->hasAttribute('value')) { $attributionData['Value'] = $constant->getAttribute('value'); } else { $attributionData['Value'] = null; } $attribution = $target->attribute($attributionData, $context); } } }