sted_parameters.php

<?php
// This file is part of the Huygens Remote Manager
// Copyright and license notice: see license.txt

use hrm\DatabaseConnection;
use hrm\Nav;
use hrm\param\base\Parameter;
use hrm\param\ImageFileFormat;
use hrm\param\Sted3D;
use hrm\param\StedDepletionMode;
use hrm\param\StedImmunity;
use hrm\param\StedSaturationFactor;
use hrm\param\StedWavelength;

require_once dirname(__FILE__) . '/inc/bootstrap.php';

/* *****************************************************************************
 *
 * START SESSION, CHECK LOGIN STATE, INITIALIZE WHAT NEEDED
 *
 **************************************************************************** */

session_start();

if (!isset($_SESSION['user']) || !$_SESSION['user']->isLoggedIn()) {
    header("Location: " . "login.php");
    exit();
}
$message = "";

$chanCnt = $_SESSION['setting']->numberOfChannels();

/* *****************************************************************************
 *
 * SET THE CONFIDENCES FOR THE RELEVANT PARAMETERS
 *
 **************************************************************************** */

$fileFormat = $_SESSION['setting']->parameter("ImageFileFormat");
$parameterNames = $_SESSION['setting']->stedParameterNames();
$db = DatabaseConnection::get();
foreach ($parameterNames as $name) {
    $parameter = $_SESSION['setting']->parameter($name);
    /** @var ImageFileFormat $fileFormat */
    $confidenceLevel =
        $db->getParameterConfidenceLevel($fileFormat->value(), $name);
    /** @var Parameter $parameter */
    $parameter->setConfidenceLevel($confidenceLevel);
    $_SESSION['setting']->set($parameter);
}


/* *****************************************************************************
 *
 * MANAGE THE STED DEPLETION MODE
 *
 **************************************************************************** */

/** @var StedDepletionMode $stedDeplParam */
$stedDeplParam = $_SESSION['setting']->parameter("StedDepletionMode");
$stedDepl = $stedDeplParam->value();
for ($i = 0; $i < $chanCnt; $i++) {
    $stedDeplKey = "StedDepl{$i}";
    if (isset($_POST[$stedDeplKey])) {
        $stedDepl[$i] = $_POST[$stedDeplKey];
    }
}
$stedDeplParam->setValue($stedDepl);
$_SESSION['setting']->set($stedDeplParam);

/* *****************************************************************************
 *
 * MANAGE THE STED SATURATION FACTOR
 *
 **************************************************************************** */

/** @var StedSaturationFactor $stedSatFactParam */
$stedSatFactParam = $_SESSION['setting']->parameter("StedSaturationFactor");
$stedSatFactParam->setNumberOfChannels($chanCnt);
$stedSatFact = $stedSatFactParam->value();

for ($i = 0; $i < $chanCnt; $i++) {
    $stedSatFactKey = "StedSaturationFactor{$i}";
    if (isset($_POST[$stedSatFactKey])) {
        $stedSatFact[$i] = $_POST[$stedSatFactKey];
    }
}

$stedSatFactParam->setValue($stedSatFact);
$stedSatFactParam->setNumberOfChannels($chanCnt);

$_SESSION['setting']->set($stedSatFactParam);

/* *****************************************************************************
 *
 * MANAGE THE STED DEPLETION WAVELENGTH
 *
 **************************************************************************** */

/** @var StedWavelength $stedLambdaParam */
$stedLambdaParam = $_SESSION['setting']->parameter("StedWavelength");
$stedLambdaParam->setNumberOfChannels($chanCnt);
$stedLambda = $stedLambdaParam->value();

for ($i = 0; $i < $chanCnt; $i++) {
    $stedLambdaKey = "StedWavelength{$i}";
    if (isset($_POST[$stedLambdaKey])) {
        $stedLambda[$i] = $_POST[$stedLambdaKey];
    }
}
$stedLambdaParam->setValue($stedLambda);
$stedLambdaParam->setNumberOfChannels($chanCnt);

$_SESSION['setting']->set($stedLambdaParam);

/* *****************************************************************************
 *
 * MANAGE THE STED IMMUNITY FRACTION
 *
 **************************************************************************** */

/** @var StedImmunity $stedImmunityParam */
$stedImmunityParam = $_SESSION['setting']->parameter("StedImmunity");
$stedImmunityParam->setNumberOfChannels($chanCnt);
$stedImmunity = $stedImmunityParam->value();

for ($i = 0; $i < $chanCnt; $i++) {
    $stedImmunityKey = "StedImmunity{$i}";
    if (isset($_POST[$stedImmunityKey])) {
        $stedImmunity[$i] = $_POST[$stedImmunityKey];
    }
}
$stedImmunityParam->setValue($stedImmunity);
$stedImmunityParam->setNumberOfChannels($chanCnt);

$_SESSION['setting']->set($stedImmunityParam);

/* *****************************************************************************
 *
 * MANAGE THE STED 3D FACTOR
 *
 **************************************************************************** */

if ($_SESSION['setting']->isSted3D()) {
    /** @var Sted3D $sted3DParam */
    $sted3DParam = $_SESSION['setting']->parameter("Sted3D");
    $sted3DParam->setNumberOfChannels($chanCnt);
    $sted3D = $sted3DParam->value();

    for ($i = 0; $i < $chanCnt; $i++) {
        $sted3DKey = "Sted3D{$i}";
        if (isset($_POST[$sted3DKey])) {
            $sted3D[$i] = $_POST[$sted3DKey];
        }
    }
    $sted3DParam->setValue($sted3D);
    $sted3DParam->setNumberOfChannels($chanCnt);

    $_SESSION['setting']->set($sted3DParam);
}

/* *****************************************************************************
 *
 * WHICH IS THE NEXT PAGE?
 *
 **************************************************************************** */

// Here we try to figure out whether we have to continue after this page or not.
// If the user chose to use a measured PSF or if there is a refractive index
// mismatch, there will be more pages after this. Otherwise, we save the
// settings to the database and go back to select_parameter_settings.php.
// Besides the destination page, also the control buttons will need to be
// adapted.

$saveToDB = false;

$PSF = $_SESSION['setting']->parameter('PointSpreadFunction')->value();

if ($PSF == 'measured') {
    $pageToGo = 'select_psf.php';
    // Make sure to turn off the correction
    $_SESSION['setting']->parameter(
        'AberrationCorrectionNecessary')->setValue('0');
} else {
    // Get the refractive indices: if they are not set, the floatval conversion
    // will change them into 0s
    $sampleRI = floatval($_SESSION['setting']->parameter(
        'SampleMedium')->translatedValue());
    $objectiveRI = floatval($_SESSION['setting']->parameter(
        'ObjectiveType')->translatedValue());

    // Calculate the deviation
    if (($sampleRI == 0) || ($objectiveRI == 0)) {
        // If at least one of the refractive indices is not known, we cannot
        // calculate whether an aberration correction is necessary and we leave
        // the decision to the user in the aberration_correction.php page.
        $pageToGo = 'aberration_correction.php';
        $_SESSION['setting']->parameter(
            'AberrationCorrectionNecessary')->setValue('1');
    } else {
        // If we know both the refractive indices we can calculate the deviation
        // and skip the aberration correction page in case the deviation is smaller
        // than 1%.
        $deviation = abs($sampleRI - $objectiveRI) / $objectiveRI;

        // Do we need to go to the aberration correction page?
        if ($deviation < 0.01) {
            // We can save the parameters
            $saveToDB = true;
            $pageToGo = 'select_parameter_settings.php';
            // Make sure to turn off the correction
            $_SESSION['setting']->parameter(
                'AberrationCorrectionNecessary')->setValue('0');
        } else {
            $pageToGo = 'aberration_correction.php';
            $_SESSION['setting']->parameter(
                'AberrationCorrectionNecessary')->setValue('1');
        }
    }
}


/* *****************************************************************************
 *
 * PROCESS THE POSTED PARAMETERS
 *
 **************************************************************************** */

if ($_SESSION['setting']->checkPostedStedParameters($_POST)) {
    if ($saveToDB) {
        $saved = $_SESSION['setting']->save();
        $message = $_SESSION['setting']->message();
        if ($saved) {
            header("Location: " . $pageToGo);
            exit();
        }
    }
    header("Location: " . $pageToGo);
    exit();
} else {
    $message = $_SESSION['setting']->message();
}


/* *****************************************************************************
 *
 * CREATE THE PAGE
 *
 **************************************************************************** */

// Javascript includes
$script = array("settings.js", "quickhelp/help.js",
    "quickhelp/stedParameters.js");
include("header.inc.php");
?>

<!--
   Tooltips
 -->
<span class="toolTip" id="ttSpanBack">
        Go back to previous page.
    </span>
<span class="toolTip" id="ttSpanCancel">
        Abort editing and go back to the image parameters selection page.
        All changes will be lost!
    </span>
<span class="toolTip" id="ttSpanForward">
        Continue to next page.
    </span>
<span class="toolTip" id="ttSpanSave">
        Save and return to the image parameters selection page.
    </span>

<div id="nav">
    <div id="navleft">
        <ul>
            <?php
            echo(Nav::linkWikiPage('STED'));
            ?>
            <li> [ <?php echo $_SESSION['setting']->name(); ?> ]</li>
        </ul>
    </div>
    <div id="navright">
        <ul>
            <?php
            echo(Nav::textUser($_SESSION['user']->name()));
            ?>
        </ul>
    </div>
    <div class="clear"></div>
</div>


<div id="content">

    <h3>STED Parameters </h3>

    <form method="post" action="" id="select">

        <h4>How did you set up the STED system?</h4>


        <?php
        /***************************************************************************
         *
         * StedDeplMode
         ***************************************************************************/

        /** @var StedDepletionMode $parameterStedDeplMode */
        $parameterStedDeplMode = $_SESSION['setting']->parameter("StedDepletionMode");
        ?>

        <fieldset class="setting <?php
        echo $parameterStedDeplMode->confidenceLevel(); ?>"
                  onmouseover="changeQuickHelp( 'deplMode' );">

            <legend>
                <a href="javascript:openWindow(
                       'http://www.svi.nl/HuygensRemoteManagerHelpSTED')">
                    <img src="images/help.png" alt="?"/>
                </a>
                STED Depletion Mode
            </legend>

            <p class="message_confidence_<?php echo $parameterStedDeplMode->confidenceLevel(); ?>"></p>

            <div class="StedDeplModeValues">
                <table class="StedDeplModeValues">

                    <?php
                    $possibleValues = $parameterStedDeplMode->possibleValues();

                    /* Make sure the Confocal option is the last one. */
                    for ($i = 0; $i < count($possibleValues); $i++) {
                        $arrValue = array_shift($possibleValues);
                        array_push($possibleValues, $arrValue);
                        if (strstr($arrValue, "Confocal")) {
                            break;
                        }
                    }

                    /* Loop on rows. */

                    for ($chan = 0; $chan < $chanCnt; $chan++) {
                        ?>
                        <tr>
                            <td>Ch<?php echo $chan; ?>:</td>

                            <td>
                                <select
                                    name="StedDepletionMode<?php echo $chan; ?>"
                                    title="STED depletion mode for channel <?php echo $chan; ?>"
                                    onclick="changeStedEntryProperties(this,<?php echo $chan; ?>)"
                                    onchange="changeStedEntryProperties(this,<?php echo $chan; ?>)">

                                    <?php
                                    /* Loop for select options. */

                                    foreach ($possibleValues as $possibleValue) {
                                        $translatedValue =
                                            $parameterStedDeplMode->translatedValueFor($possibleValue);

                                        if ($translatedValue == $stedDepl[$chan]) {
                                            $selected = " selected=\"selected\"";
                                        } else {
                                            $selected = "";
                                        }
                                        ?>
                                        <option
                                            value=<?php echo $translatedValue;
                                        echo $selected; ?>>
                                            <?php echo $possibleValue; ?>
                                        </option>
                                        <?php
                                    }                    /* End of loop for select options. */
                                    ?>
                                </select>
                            </td>

                        </tr>
                        <?php
                    }                        /* End of loop on rows. */
                    ?>

                </table> <!-- StedDeplModeValues -->
            </div> <!-- StedDeplModeValues -->

        </fieldset>


        <?php
        /***************************************************************************
         *
         * StedSatFact
         ***************************************************************************/

        /** @var StedSaturationFactor $parameterStedSatFact */
        $parameterStedSatFact = $_SESSION['setting']->parameter("StedSaturationFactor");
        ?>

        <fieldset class="setting <?php
        echo $parameterStedSatFact->confidenceLevel(); ?>"
                  onmouseover="changeQuickHelp( 'satFact' );">

            <legend>
                <a href="javascript:openWindow(
                       'http://www.svi.nl/HuygensRemoteManagerHelpSTED')">
                    <img src="images/help.png" alt="?"/>
                </a>
                STED Saturation Factor
            </legend>

            <p class="message_confidence_<?php echo $parameterStedSatFact->confidenceLevel(); ?>"></p>

            <div class="multichannel">
                <?php

                for ($i = 0; $i < $chanCnt; $i++) {

                    /* Add a line break after a number of entries. */
                    if ($_SESSION['setting']->numberOfChannels() == 4) {
                        if ($i == 2) {
                            echo "<br />";
                        }
                    } else {
                        if ($i == 3) {
                            echo "<br />";
                        }
                    }

                    ?>
                    <span class="nowrap">
        Ch<?php echo $i ?>:&nbsp;&nbsp;&nbsp;
        <span class="multichannel">
            <input name="StedSaturationFactor<?php echo $i ?>"
                   id="StedSaturationFactor<?php echo $i ?>"
                   title="STED saturation factor for channel <?php echo $chan; ?>"
                   type="text"
                   size="6"
                   value="<?php
                   if ($i <= sizeof($stedSatFact)) {
                       echo $stedSatFact[$i];
                   } ?>"
                   class="multichannelinput"/>
        </span>&nbsp;
    </span>
                    <?php
                }
                ?>

        </fieldset>

        <?php
        /***************************************************************************
         *
         * StedLambda
         ***************************************************************************/

        /** @var StedWavelength $parameterStedLambda */
        $parameterStedLambda = $_SESSION['setting']->parameter("StedWavelength");
        ?>

        <fieldset class="setting <?php
        echo $parameterStedLambda->confidenceLevel(); ?>"
                  onmouseover="changeQuickHelp( 'lambda' );">

            <legend>
                <a href="javascript:openWindow(
                       'http://www.svi.nl/HuygensRemoteManagerHelpSTED')">
                    <img src="images/help.png" alt="?"/>
                </a>
                STED Wavelength (nm)
            </legend>

            <p class="message_confidence_<?php echo $parameterStedLambda->confidenceLevel(); ?>"></p>

            <div class="multichannel">
                <?php

                for ($i = 0; $i < $chanCnt; $i++) {

                    /* Add a line break after a number of entries. */
                    if ($_SESSION['setting']->numberOfChannels() == 4) {
                        if ($i == 2) {
                            echo "<br />";
                        }
                    } else {
                        if ($i == 3) {
                            echo "<br />";
                        }
                    }

                    ?>
                    <span class="nowrap">
        Ch<?php echo $i ?>:&nbsp;&nbsp;&nbsp;
        <span class="multichannel">
            <input name="StedWavelength<?php echo $i ?>"
                   id="StedWavelength<?php echo $i ?>"
                   title="STED wavelength for channel <?php echo $chan; ?>"
                   type="text"
                   size="6"
                   value="<?php
                   if ($i <= sizeof($stedLambda)) {
                       echo $stedLambda[$i];
                   } ?>"
                   class="multichannelinput"/>
        </span>&nbsp;
    </span>
                    <?php
                }
                ?>

        </fieldset>


        <?php
        /***************************************************************************
         *
         * StedImmunity
         ***************************************************************************/

        /** @var StedImmunity $parameterStedImmunity */
        $parameterStedImmunity = $_SESSION['setting']->parameter("StedImmunity");
        ?>

        <fieldset class="setting <?php
        echo $parameterStedImmunity->confidenceLevel(); ?>"
                  onmouseover="changeQuickHelp( 'immunity' );">

            <legend>
                <a href="javascript:openWindow(
                       'http://www.svi.nl/HuygensRemoteManagerHelpSTED')">
                    <img src="images/help.png" alt="?"/>
                </a>
                STED Immunity Fraction (%)
            </legend>

            <p class="message_confidence_<?php echo $parameterStedImmunity->confidenceLevel(); ?>"></p>

            <div class="multichannel">
                <?php

                for ($i = 0; $i < $chanCnt; $i++) {

                    /* Add a line break after a number of entries. */
                    if ($_SESSION['setting']->numberOfChannels() == 4) {
                        if ($i == 2) {
                            echo "<br />";
                        }
                    } else {
                        if ($i == 3) {
                            echo "<br />";
                        }
                    }

                    ?>
                    <span class="nowrap">
        Ch<?php echo $i ?>:&nbsp;&nbsp;&nbsp;
        <span class="multichannel">
            <input name="StedImmunity<?php echo $i ?>"
                   id="StedImmunity<?php echo $i ?>"
                   title="STED immunity for channel <?php echo $chan; ?>"
                   type="text"
                   size="6"
                   value="<?php
                   if ($i <= sizeof($stedImmunity)) {
                       echo $stedImmunity[$i];
                   } ?>"
                   class="multichannelinput"/>
        </span>&nbsp;
    </span>
                    <?php
                }
                ?>

        </fieldset>


        <?php
        /***************************************************************************
         *
         * Sted3D
         ***************************************************************************/

        if ($_SESSION['setting']->isSted3D()) {
            /** @var Sted3D $parameterSted3D */
            $parameterSted3D = $_SESSION['setting']->parameter("Sted3D");
            ?>

            <fieldset class="setting <?php
            echo $parameterSted3D->confidenceLevel(); ?>"
                      onmouseover="changeQuickHelp( '3d' );">

                <legend>
                    <a href="javascript:openWindow(
                       'http://www.svi.nl/HuygensRemoteManagerHelpSTED')">
                        <img src="images/help.png" alt="?"/>
                    </a>
                    STED 3D (%)
                </legend>

                <p class="message_confidence_<?php echo $parameterSted3D->confidenceLevel(); ?>"></p>

                <div class="multichannel">
                    <?php

                    for ($i = 0; $i < $chanCnt; $i++) {

                        /* Add a line break after a number of entries. */
                        if ($_SESSION['setting']->numberOfChannels() == 4) {
                            if ($i == 2) {
                                echo "<br />";
                            }
                        } else {
                            if ($i == 3) {
                                echo "<br />";
                            }
                        }

                        ?>
                        <span class="nowrap">
        Ch<?php echo $i ?>:&nbsp;&nbsp;&nbsp;
        <span class="multichannel">
            <input name="Sted3D<?php echo $i ?>"
                   id="Sted3D<?php echo $i ?>"
                   title="STED 3D (%) for channel <?php echo $chan; ?>"
                   type="text"
                   size="6"
                   value="<?php
                   if ($i <= sizeof($sted3D)) {
                       echo $sted3D[$i];
                   } ?>"
                   class="multichannelinput"/>
        </span>&nbsp;
    </span>
                        <?php
                    }
                    ?>

            </fieldset>
            <?php
        }
        ?>

        <?php
        /****************************************************************************
         *
         * End of Parameters
         ****************************************************************************/
        ?>

        <div><input name="OK" type="hidden"/></div>

        <div id="controls"
             onmouseover="changeQuickHelp( 'default' )">
            <input type="button" value="" class="icon previous"
                   onmouseover="TagToTip('ttSpanBack' )"
                   onmouseout="UnTip()"
                   onclick="document.location.href='capturing_parameter.php'"/>
            <input type="button" value="" class="icon up"
                   onmouseover="TagToTip('ttSpanCancel' )"
                   onmouseout="UnTip()"
                   onclick="document.location.href='select_parameter_settings.php'"/>
            <?php
            if ($pageToGo != "select_parameter_settings.php") {
                ?>
                <input type="submit" value="" class="icon next"
                       onmouseover="TagToTip('ttSpanForward' )"
                       onmouseout="UnTip()"
                       onclick="process()"/>
                <?php
            } else {
                ?>
                <input type="submit" value="" class="icon save"
                       onmouseover="TagToTip('ttSpanSave' )"
                       onmouseout="UnTip()"
                       onclick="process()"/>
                <?php
            }
            ?>
        </div>
    </form>

</div> <!-- content -->


<div id="rightpanel"
     onmouseover="changeQuickHelp( 'default' );">

    <div id="info">

        <h3>Quick help</h3>

        <div id="contextHelp"
             onmouseover="changeQuickHelp( 'default' )">
        </div>

        <?php
        if (!$_SESSION["user"]->isAdmin()) {
            ?>

            <div class="requirements">
                Parameter requirements<br/>adapted for <b>
                    <?php
                    $fileFormat = $_SESSION['setting']->parameter("ImageFileFormat");
                    echo $fileFormat->value();
                    ?>
                </b> files
            </div>

            <?php
        }
        ?>

    </div>

    <div id="message">
        <?php

        echo "<p>$message</p>";

        ?>
    </div>

</div> <!-- rightpanel -->

<script type="text/javascript">
    setStedEntryProperties(<?php echo $chanCnt; ?>);
</script>

<?php
include("footer.inc.php");
?>