AnonymiseVFCommand::actiontransformFmes PHP Method

    public function actiontransformFmes($fmesDir, $outputDir, $realPidFile, $anonPidFile)
    {
        foreach (array($fmesDir, $realPidFile, $anonPidFile) as $file) {
            if (!file_exists($file)) {
                echo $file . ' does not exist' . PHP_EOL;
                exit(1);
            }
        }
        $realPids = file_get_contents($realPidFile);
        $anonPids = file_get_contents($anonPidFile);
        $rPids = explode(PHP_EOL, $realPids);
        $aPids = explode(PHP_EOL, $anonPids);
        // make sure PID count is equal:
        if (count($rPids) != count($aPids)) {
            echo 'Error: PID counts do not match; file contents must match 1-1' . PHP_EOL;
            exit(1);
        }
        // check all real patients exist:
        foreach ($aPids as $pid) {
            if ($pid) {
                if (count(Patient::model()->find("hos_num='" . $pid . "'")) < 1) {
                    echo 'Failed to find anonymous patient ' . $pid . PHP_EOL;
                    exit(1);
                }
            }
        }
        // now check that all 'real' patients are listed in the files:
        $entries = array();
        // build up an array of matches we've encountered so far, and if it's
        // been matched before, ignore it.
        $smgr = Yii::app()->service;
        $fhirMarshal = Yii::app()->fhirMarshal;
        if ($entry = glob($fmesDir . '/*.fmes')) {
            foreach ($entry as $file) {
                $field = file_get_contents($file);
                $fieldObject = $fhirMarshal->parseXml($field);
                $match = $this->getHosNum($file, $field);
                if (!in_array($match, $entries)) {
                    // only add it if it's in the list of real patient IDs:
                    if (in_array($match, $rPids)) {
                        array_push($entries, $match);
                    }
                }
            }
        }
        // now create new FMES files
        // need to go through each one, pairing anonymised IDs with real ones,
        // replacing the real ID with the anonymised ID; note that we also
        // need to swap out the image and do some redaction:
        if ($entry = glob($fmesDir . '/*.fmes')) {
            foreach ($entry as $file) {
                $field = file_get_contents($file);
                $fieldObject = $fhirMarshal->parseXml($field);
                // swap out hos nums:
                $match = $this->getHosNum($file, $field);
                if (in_array($match, $rPids)) {
                    $index = array_search($match, $rPids);
                    $anonPid = $aPids[$index];
                    unset($fieldObject->patient_id);
                    $fieldObject->patient_id = '__OE_PATIENT_ID_' . $anonPid . '__';
                    echo 'replacing ' . $match . ' with ' . $anonPid . PHP_EOL;
                } else {
                    // not interested, move on:
                    continue;
                }
                // now swap out the actual image. This is slightly involved -
                // we need to write the image to temporary file, perform
                // image operations on it to anonymise PID, DoB etc.,
                // step 1: extract image:
                $image = base64_decode($fieldObject->image_scan_data);
                unset($fieldObject->image_scan_data);
                // now redact it - we need to perform imagemagick operations:
                $img = 'img.gif';
                file_put_contents($img, $image);
                $image = new Imagick($img);
                $this->fillImage($image);
                $image->writeImage($img);
                $contents = file_get_contents($img);
                $fieldObject->image_scan_data = base64_encode($contents);
                $doc = new DOMDocument();
                file_put_contents($outputDir . '/' . basename($file), $fhirMarshal->renderXml($fieldObject));
                echo 'Successfully written ' . $file . PHP_EOL;
            }
        }
    }