coloc_analysis.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\setting\AnalysisSetting;
use hrm\Util;

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();
}

if ($_SESSION['user']->isAdmin()) {
    $db = DatabaseConnection::get();
    $maxChanCnt = $db->getMaxChanCnt();
    $_SESSION['analysis_setting']->setNumberOfChannels($maxChanCnt);
} else {
    $_SESSION['analysis_setting']->setNumberOfChannels(
        $_SESSION['setting']->numberOfChannels());
}

if (!isset($_SESSION['analysis_setting'])) {
    $_SESSION['analysis_setting'] = new AnalysisSetting();
}
$message = "";


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

if ($_SESSION['analysis_setting']->checkPostedAnalysisParameters($_POST)) {
    $saved = $_SESSION['analysis_setting']->save();
    if ($saved) {
        header("Location: " . "select_analysis_settings.php");
        exit();
    } else {
        $message = $_SESSION['analysis_setting']->message();
    }
} else {
    $message = $_SESSION['analysis_setting']->message();
}


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

// Javascript includes
$script = array("settings.js", "quickhelp/help.js", "quickhelp/colocHelp.js");

include("header.inc.php");

?>

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


<div id="content">

    <h3>Analysis - Colocalization</h3>

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

        <?php

        /*
              COLOCALIZATION
        */
        
        ?>
        
        <fieldset class="setting"
                  onmouseover="changeQuickHelp( 'perform' );">

            <legend>
                <a href="javascript:openWindow(
                    'http://www.svi.nl/ColocalizationBasics')">
                    <img src="images/help.png" alt="?"/>
                </a>
                Would you like to perform Colocalization Analysis?
            </legend>
            <select id="ColocAnalysis"
                    title="Perform coloc analysis?"
                    name="ColocAnalysis"
                    class="selection"
                    onchange="switchColocMode();">

                <?php

                /*
                      COLOCALIZATION ANALYSIS
                */
                $parameterPerformColocAnalysis =
                    $_SESSION['analysis_setting']->parameter("ColocAnalysis");
                $possibleValues = $parameterPerformColocAnalysis->possibleValues();
                $selectedMode = $parameterPerformColocAnalysis->value();

                foreach ($possibleValues as $possibleValue) {
                    $translation =
                        $parameterPerformColocAnalysis->translatedValueFor($possibleValue);
                    if ($possibleValue == $selectedMode) {
                        $option = "selected=\"selected\"";
                    } else {
                        $option = "";
                    }
                    ?>
                    <option <?php echo $option ?>
                        value="<?php echo $possibleValue ?>">
                        <?php echo $translation ?>
                    </option>
                    <?php
                }
                ?>

            </select>
        </fieldset>


        <?php

        /*
              COLOCALIZATION CHANNELS
        */

        $visibility = " style=\"display: none\"";
        if ($parameterPerformColocAnalysis->value() == 1)
            $visibility = " style=\"display: block\"";

        ?>


        <div id="ColocChannelSelectionDiv"<?php echo $visibility ?>>
            <fieldset class="setting"
                      onmouseover="changeQuickHelp( 'channels' );">

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

                <?php
                $parameterColocChannel =
                    $_SESSION['analysis_setting']->parameter("ColocChannel");

                $selectedValues = $parameterColocChannel->value();

                for ($chan = 0;
                     $chan < $_SESSION['analysis_setting']->numberOfChannels();
                     $chan++) {
                    if (true == Util::isValueInArray($selectedValues, $chan)) {
                        $checked = "checked";
                    } else {
                        $checked = "";
                    }

                    ?>
                    Ch. <?php echo $chan; ?>: <input type="checkbox"
                                                     title="Coloc channel <?php echo $chan; ?>"
                                                     name="ColocChannel[]"
                                                     value=<?php echo $chan;
                                                     if ($checked) {
                                                     ?> checked=<?php echo $checked;
                    } ?>
                    />
                <?php } ?>
            </fieldset>
        </div> <!-- ColocChannelSelectionDiv -->


        <?php
        /*
              COLOCALIZATION COEFFICIENTS
        */
        ?>

        <div id="ColocCoefficientSelectionDiv"<?php echo $visibility ?>>
            <fieldset class="setting"
                      onmouseover="changeQuickHelp( 'coeff' );">

                <legend>
                    <a href="javascript:openWindow(
                       'http://www.svi.nl/ColocalizationCoefficientsInBrief')">
                        <img src="images/help.png" alt="?"/>
                    </a>
                    Colocalization coefficients
                </legend>
                <table>
                    <?php
                    $parameterColocCoefficient =
                        $_SESSION['analysis_setting']->parameter("ColocCoefficient");

                    /* Which coloc coefficients should be displayed as choice? */
                    $possibleValues = $parameterColocCoefficient->possibleValues();

                    /* Were there coloc coefficients selected previously? */
                    $selectedValues = $parameterColocCoefficient->value();

                    /* The coefficients will be split into two columns. */
                    $cellCnt = 0;

                    foreach ($possibleValues as $possibleValue) {

                        if (in_array($possibleValue, $selectedValues)) {
                            $checked = "checked";
                        } else {
                            $checked = "";
                        }

                        if (($cellCnt % 3) == 0) {
                            echo "<tr>";
                        }
                        $translation =
                            $parameterColocCoefficient->translatedValueFor($possibleValue);
                        ?>
                        <td class="text">
                            <?php echo $translation; ?>
                        </td>
                        <td class="check">
                            <input type="checkbox"
                                   title="Coloc coefficient <?php echo $possibleValue; ?>"
                                   name="ColocCoefficient[]" value=
                                   <?php echo $possibleValue;
                                   if ($checked) {
                                   ?> checked=<?php echo $checked;
                            } ?>
                            /></td>
                        <?php
                        if ((($cellCnt + 1) % 3) == 0) {
                            echo "</tr>";
                        }
                        $cellCnt++;

                    }
                    ?>
                </table>
            </fieldset>
        </div> <!-- ColocCoefficientSelectionDiv -->


        <?php
        /*
              COLOCALIZATION THRESHOLD
        */
        ?>
        <div id="ColocThresholdSelectionDiv"<?php echo $visibility ?>>
            <fieldset class="setting"
                      onmouseover="changeQuickHelp( 'threshold' );">
                <legend>
                    <a href="javascript:openWindow(
                       'http://www.svi.nl/ColocalizationBasics')">
                        <img src="images/help.png" alt="?"/>
                    </a>
                    Threshold
                </legend>

                <?php
                $parameterColocThresh =
                    $_SESSION['analysis_setting']->parameter("ColocThreshold");
                $colocThreshold = $parameterColocThresh->internalValue();

                $flag = "";
                if ($colocThreshold[0] == "" || $colocThreshold[0] == "auto") {
                    $flag = " checked=\"checked\"";
                }
                ?>
                <p>
                    <input type="radio"
                           id="ColocThresholdAuto"
                           title="Coloc threshold auto"
                           name="ColocThresholdMode"
                           value="auto"<?php echo $flag ?> />
                    Automatic estimation
                </p>
                <?php

                $flag = "";
                if ($colocThreshold[0] != "" && $colocThreshold[0] != "auto") {
                    $flag = " checked=\"checked\"";
                }

                ?>

                <input type="radio"
                       id="ColocThresholdManual"
                       title="Coloc threshold manual"
                       name="ColocThresholdMode"
                       value="manual"<?php echo $flag ?> />
                Percentage of the intensity range (%):

                <div class="multichannel">
                    <?php
                    for ($chan = 0;
                         $chan < $_SESSION['analysis_setting']->numberOfChannels();
                         $chan++) {
                        $threshold = "";
                        if ($colocThreshold[0] != "auto") {
                            $threshold = $colocThreshold[$chan];
                        }

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

                        ?>
                        <span class="nowrap">Ch<?php echo $chan ?>:
        &nbsp;&nbsp;&nbsp;
        <span class="multichannel">
        <input id="ColocThreshold<?php echo $chan ?>"
               title="Coloc threshold channel <?php echo $chan ?>""
        name="ColocThreshold<?php echo $chan ?>"
        type="text"
        size="8"
        value="<?php echo $threshold ?>"
        class="multichannelinput"
        onclick="document.forms[0].ColocThresholdManual.checked=true"/>
        </span>&nbsp;
        </span>

                        <?php
                    }
                    ?>
                </div><!--multichannel-->

            </fieldset>
        </div> <!--ColocThresholdSelectionDiv-->


        <?php
        /*
              COLOCALIZATION MAPS
        */
        ?>

        <div id="ColocMapSelectionDiv"<?php echo $visibility ?>>
            <fieldset class="setting"
                      onmouseover="changeQuickHelp( 'maps' );">

                <legend>
                    <a href="javascript:openWindow(
                       'http://www.svi.nl/ColocalizationMap')">
                        <img src="images/help.png" alt="?"/>
                    </a>
                    Colocalization maps
                </legend>


                <?php
                $parameterColocMap =
                    $_SESSION['analysis_setting']->parameter("ColocMap");


                $possibleValues = $parameterColocMap->possibleValues();

                foreach ($possibleValues as $possibleValue) {
                    $translation =
                        $parameterColocMap->translatedValueFor($possibleValue);

                    $flag = "";
                    if ($possibleValue == $parameterColocMap->value()) {
                        $flag = "checked=\"checked\" ";
                    }

                    ?>
                    <input type="radio"
                           name="ColocMap"
                           title="Coloc map <?php echo $possibleValue ?>"
                           value="<?php echo $possibleValue ?>"
                        <?php echo $flag ?>/>
                    <?php echo $translation ?>
                    <?php
                }
                ?>

            </fieldset>
        </div> <!-- ColocMapSelectionDiv -->


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

        <div id="controls"
             onmouseover="changeQuickHelp( 'default' );">
            <input type="button" value="" class="icon up"
                   id="controls_cancel"
                   onclick="document.location.href='select_analysis_settings.php'"/>
            <input type="submit" value="" class="icon save"
                   id="controls_save"
                   onclick="process()"/>
        </div>

    </form>


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


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

    <div id="info">

        <h3>Quick help</h3>

        <div id="contextHelp">
            <p>On this page you can specify whether you would like to perform
                colocalization analysis on the deconvolved images.</p>
            <p>You can select the channels to be taken into account for
                colocalization analysis, as well as the colocalization
                coefficients and maps.</p>
        </div>

    </div>

    <div id="message">
        <?php

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

        ?>
    </div>

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


<?php

/*
 * Tooltips.
 *
 * Define $tooltips array with object id as key and tooltip string as value.
 */
$tooltips = array(
    "controls_cancel" => "Abort editing and go back to the processing parameters selection page. All changes will be lost!",
    "controls_save" => "Save and return to the processing parameters selection page.",
);

include("footer.inc.php");

?>