Skip to content

Commit

Permalink
Add CouchDB_Import_EEG.php
Browse files Browse the repository at this point in the history
  • Loading branch information
@jeffersoncasimir
jeffersoncasimir committed Oct 1, 2024
1 parent dfa2ce3 commit 9159906
Show file tree
Hide file tree
Showing 2 changed files with 666 additions and 0 deletions.
333 changes: 333 additions & 0 deletions tools/CouchDB_EEG_Importer.php
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,333 @@
<?php
require_once __DIR__ . "/../../vendor/autoload.php";
require_once __DIR__ . '/../../tools/generic_includes.php';
require_once __DIR__ . "/../modules/electrophysiology_browser/php/models/electrophysiofile.class.inc";

use LORIS\electrophysiology_browser\Models\ElectrophysioFile;

/**
* Wrapper around CouchDB EEG functions
*
* @category Main
* @package Loris
* @author Loris Team <loris-dev@bic.mni.mcgill.ca>
* @license Loris license
* @link https://www.github.com/aces/Loris/
*/
class CouchDBEEGImporter
{
var $SQLDB; // reference to the database handler, store here instead
// of using Database::singleton in case it's a mreock.
var $CouchDB; // reference to the CouchDB database handler

// this is just in an instance variable to make
// the code a little more readable.
private $Dictionary = array();

/**
* Constructor for CouchDBMRIImporter
*/
function __construct()
{
$factory = \NDB_Factory::singleton();
$config = \NDB_Config::singleton();
$couchConfig = $config->getSetting('CouchDB');
$this->SQLDB = $factory->Database();
$this->CouchDB = $factory->couchDB(
$couchConfig['dbName'],
$couchConfig['hostname'],
intval($couchConfig['port']),
$couchConfig['admin'],
$couchConfig['adminpass']
);
}

/**
* Runs the script
*
* @return void
*/
function run()
{
$this->updateDataDict();
$CandidateData = $this->getCandidateData();
$results = $this->updateCandidateDocs($CandidateData);
$this->createRunLog($results);
}

/**
* Add data dictionary in DQT
*
*
* @return void
*/
function updateDataDict()
{

$this->Dictionary = array();

$eeg_array = [
'Acquisition_Time' => 'Acquisition Time',
'FilePaths' => 'Paths of all session recordings',
'age_at_scan' => 'Subject\'s age at scan',
'CapManufacturer' => 'Cap Manufacturer',
'CapManufacturersModelName' => 'Manufacturer Cap Model Name',
'EEGChannelCount' => 'EEG Channel Count',
'EOGChannelCount' => 'EOG Channel Count',
'ECGChannelCount' => 'ECG Channel Count',
'EMGChannelCount' => 'EMG Channel Count',
'EEGReference' => 'EEG Reference',
'EEGGround' => 'EEG Ground',
'EEGPlacementScheme' => 'EEG Placement Scheme',
'HardwareFilters' => 'Hardware Filters',
'InstitutionName' => 'Institution Name',
'InstitutionAddress' => 'Institution Address',
'MiscChannelCount' => 'Misc Channel Count',
'Manufacturer' => 'Manufacturer',
'ManufacturerModelName' => 'Manufacturer Model Name',
'PowerLineFrequency' => 'Power Line Frequency',
'RecordingType' => 'Recording Type',
'RecordingDuration' => 'Recording Duration',
'SamplingFrequency' => 'Sampling Frequency',
'SoftwareFilters' => 'Software Filters',
'SoftwareVersions' => 'Software Version',
'TriggerChannelCount' => 'Trigger Channel Count',
'TaskDescription' => 'Task Description',
'TaskName' => 'Task Name',
'OutputType' => 'Output type - raw or derived',
'HEDTags' => 'HED Tags - Unique List',
'HEDTagsShortForm' => 'HED Tags - Short Form',
];

foreach ($eeg_array as $field => $desc) {
$this->Dictionary[$field] = array(
'Type' => "varchar(255)",
'Description' => $desc
);
}

$this->CouchDB->replaceDoc(
"DataDictionary:eeg_data",
array(
'Meta' => array('DataDict' => true),
'DataDictionary' => array('eeg_data' => $this->Dictionary)
)
);
}


/**
* Get Candidate Data
*
* @return array
*/
public function getCandidateData(): array
{
$query = "SELECT
psc.Name AS Site,
c.PSCID AS PSCID,
c.CandID AS DCCID,
Project.Name AS Project,
s.Visit_label AS Visit_Label,
MIN(pf.AcquisitionTime) AS Acquisition_Time,
MIN(pf.InsertTime) AS Insert_Time,
GROUP_CONCAT(DISTINCT pot.OutputTypeName) AS OutputType,
s.ID AS SessionID,
s.CenterID AS CenterID,
s.ProjectID AS ProjectID,
GROUP_CONCAT(DISTINCT pf.FilePath) AS FilePaths,
GROUP_CONCAT(DISTINCT pef.EventFileID) AS EventFileID
FROM physiological_file pf
LEFT JOIN session s ON (s.ID=pf.SessionID)
LEFT JOIN candidate c USING (CandID)
LEFT JOIN psc ON (s.CenterID=psc.CenterID)
LEFT JOIN Project ON (s.ProjectID=Project.ProjectID)
LEFT JOIN physiological_event_file pef
USING (PhysiologicalFileID)
LEFT JOIN physiological_output_type pot
USING (PhysiologicalOutputTypeID)
WHERE c.Active='Y'
AND s.Active='Y'
AND pf.FileType IN (
SELECT type FROM ImagingFileTypes WHERE Description LIKE '%(EEG)'
)
GROUP BY SessionID";


$CandidateData = $this->SQLDB->pselect($query, array());
foreach ($CandidateData as &$row) {
$sessionID = $row['SessionID'];
$eeg_header_results = $this->_addEEGHeaderInfo($sessionID);
$row = array_merge($row, $eeg_header_results);
}
return $CandidateData;
}

/**
* Add EEG header information
*
* @param int $sessionID Session ID
*
* @return array Array of EEG header info
*/
function _addEEGHeaderInfo(int $sessionID): array
{
$records = $this->SQLDB->pselect(
"SELECT
Name,
GROUP_CONCAT(DISTINCT Value SEPARATOR ',\n') AS Value
FROM physiological_parameter_file
JOIN parameter_type USING (ParameterTypeID)
LEFT JOIN physiological_file USING (PhysiologicalFileID)
WHERE Name IN (
'age_at_scan',
'CapManufacturer',
'CapManufacturersModelName',
'ECGChannelCount',
'EEGChannelCount',
'EEGGround',
'EEGPlacementScheme',
'EEGReference',
'EMGChannelCount',
'EOGChannelCount',
'HardwareFilters',
'InstitutionAddress',
'InstitutionName',
'Manufacturer',
'ManufacturersModelName',
'MiscChannelCount',
'PowerLineFrequency',
'RecordingDuration',
'RecordingType',
'SamplingFrequency',
'SoftwareFilters',
'SoftwareVersions',
'TaskDescription',
'TaskName',
'TriggerChannelCount'
)
AND SessionID=:sid
GROUP BY Name",
['sid' => $sessionID]
);

$header = [];
foreach ($records as $index => $record) {
$header[$record['Name']] = $record['Value'];
}

$hed_tags = $this->SQLDB->pselect(
"WITH DatasetTags AS (
SELECT DISTINCT HEDTagID
FROM bids_event_dataset_mapping
WHERE ProjectID = (
SELECT ProjectID
FROM session
WHERE ID = :sid
)
), EventRelTags AS (
SELECT DISTINCT ptehr.HEDTagID
FROM physiological_task_event_hed_rel AS ptehr
JOIN physiological_task_event AS pte ON ptehr.PhysiologicalTaskEventID = pte.PhysiologicalTaskEventID
JOIN physiological_file AS pf ON pte.PhysiologicalFileID = pf.PhysiologicalFileID
WHERE pf.SessionID = :sid
)
SELECT
GROUP_CONCAT(DISTINCT hed_schema_nodes.Name) AS Name,
GROUP_CONCAT(DISTINCT hed_schema_nodes.LongName) AS LongName
FROM hed_schema_nodes
WHERE hed_schema_nodes.ID IN (
SELECT HEDTagID FROM DatasetTags
UNION
SELECT HEDTagID FROM EventRelTags
);",
['sid' => $sessionID]
);

if (count($hed_tags) > 0) {
$header['HEDTags'] = $hed_tags[0]['LongName'];
$header['HEDTagsShortForm'] = $hed_tags[0]['Name'];
}

return $header;
}

/**
* Updates DQT with the new data
*
* @param array $data Candidate data to be updated
*
* @return void
*/
function updateCandidateDocs($data)
{
$results = [
'new' => 0,
'modified' => 0,
'unchanged' => 0,
];

foreach ($data as $index => $candidateRecord) {
$doc = $candidateRecord;
$identifier = [
$candidateRecord['PSCID'],
$candidateRecord['Visit_Label']
];
$docid = 'EEG_Files:' . join('_', $identifier);
unset($doc['PSCID']);
unset($doc['Visit_Label']);
unset($doc['SessionID']);

$success = $this->CouchDB->replaceDoc(
$docid,
array(
'Meta' => array(
'DocType' => 'eeg_data',
'identifier' => $identifier,
),
'data' => $doc,
)
);
print $docid . ": " . $success . "\n";

if (!isset($results[$success])) {
$results[$success] = 0;
}

$results[$success] += 1;
}

return $results;
}

/**
* Creates run log
*
* @param array $results The results of running the query
*
* @return void
*/
function createRunLog($results)
{
$now = date("c");
$id = $this->CouchDB->createDoc(
[
'Meta' => ['DocType' => 'RunLog'],
'RunInfo' => [
'Script' => 'EEG Data Importer',
'Time' => "$now",
'DocsCreated' => $results['new'],
'DocsModified' => $results['modified'],
'DocsUnchanged' => $results['unchanged'],
],
]
);
print "Created run log with id $id\n";
}
}

// Don't run if we're doing the unit tests; the unit test will call run.
if(!class_exists('UnitTestCase')) {
$Runner = new CouchDBEEGImporter();
$Runner->run();
}
Loading

0 comments on commit 9159906

Please sign in to comment.