estimate_snr_from_image.php

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

use hrm\HuygensTools;
use hrm\Nav;
use hrm\Util;

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

// Two private functions, for the two tasks of this script:

// This configures and shows the file browser module inc/FileBrowser.php.
// The Signal-to-noise estimator works only on raw images, so the listed
// directory is the source ('src') one.
function showFileBrowser()
{

    //$browse_folder can be 'src' or 'dest'.
    $browse_folder = "src";
    $page_title = "Estimate SNR from a raw image";
    $explanation_text = "Please choose an image and click on the calculator " .
        "button to estimate the SNR.";
    $form_title = "Available images";
    $top_nav_left = Nav::linkWikiPage('HuygensRemoteManagerHelpSnrEstimator');
    $top_nav_right = "";
    $multiple_files = false;
    // Number of displayed files.
    $size = 15;
    $type = "";
    $useTemplateData = 0;
    if ($_SESSION['user']->isAdmin()) {
        // The administrator can edit templates without adding a task, so no
        // image type is predefined in this case...
        $restrictFileType = false;
        $expandSubImages = true;
    } else {
        // Users can only estimate the SNR inside the workflow of a task
        // creation, so a selected file type is known at this point. Show files
        // of the same type as in the current task:
        $restrictFileType = true;
        $fileFormat = $_SESSION['setting']->parameter("ImageFileFormat");
        $type = $fileFormat->value();
        // To (re)generate the thumbnails, use data from the current template
        // for colors (wavelengths).
        $useTemplateData = 1;
    }
    $file_buttons = array();
    $file_buttons[] = "update";

    $additionalHTMLElements = "
             <!-- SNR estimation algorithm -->
             <fieldset class=\"setting\" >

                 <legend>
                     <a href=\"javascript:openWindow(
                       'http://www.svi.nl/HuygensRemoteManagerHelpSNREstimationAlgorithm')\">
                       <img src=\"images/help.png\" alt=\"?\" /></a>
                       SNR estimation algorithm
                 </legend>

                 <select name=\"SNREstimationAlgorithm\" class=\"selection\" >
                 ";

    $algorithm = "";
    if (isset($_POST["SNREstimationAlgorithm"])) {
        $algorithm = $_POST["SNREstimationAlgorithm"];
    }

    $selected = "";
    if ($algorithm == "new") {
        $selected = "selected=\"selected\"";
    }

    $additionalHTMLElements .= "
        <option value=\"new\" $selected>Auto</option>";

    $selected = "";
    if ($algorithm == "old") {
        $selected = "selected=\"selected\"";
    }

    $additionalHTMLElements .= "
        <option value=\"old\" $selected>Legacy</option>";

    $additionalHTMLElements .= "
          </select>
        </fieldset>
        <p>&nbsp;</p>";

    $control_buttons = "
        <input type=\"button\" value=\"\" class=\"icon up\"
        onmouseover=\"Tip('Go back without estimating the SNR.')\"
        onmouseout=\"UnTip()\"
        onclick=\"document.location.href='task_parameter.php'\" />";

    $control_buttons .= "
        <input name=\"estimate\" type=\"submit\" value=\"\" class=\"icon calc\"
        onmouseover=\"Tip('Estimate SNR from a selected image.' )\"
        onmouseout=\"UnTip()\"
        onclick=\"setActionToCalcSNR();\" />";

    $info = '
            <h3>Quick help</h3>

            <p>Select a raw image to estimate the Signal-to-Noise Ratio (SNR).
               You can then use the estimated SNR values in the Restoration
               Settings to deconvolve similar images, acquired under similar
               conditions.</p>

            <p>You have a choice of two SNR estimation algorithms. Please click
               on the corresponding help button for additional information.</p>';

    if ($type != "") {
        $info .= "<p>Only images of type <b>$type</b>, as set in the image selection
        filter, are shown.</p>";
    }

    $info .= '<p>Please notice that undersampled or clipped images will provide
            wrong estimations, as well as wrong deconvolution results!</p>
            <p>An SNR value must be set per image channel: please select an
               image that is representative of the datasets you will deconvolve,
               as each channel may have a different noise level.</p>
            <p>Please mind that, in this context, the SNR
               is not a property of the images but a parameter
               for the deconvolution that you can tune, to adapt the result to
               the experimental needs.
               The estimated value is just a reasonable initial parameter.</p>
            <p>Click <b>Help</b> on the top menu for more details.</p>
               ';

    include("./inc/FileBrowser.php");
}


// This function does the main job.
// When a file name is posted, this function processes it by sending it to
// Huygens in the background and showing the result images with the different
// SNR estimations. The best value is shown, but other more pessimistic and
// optimistic values are also included for the user to visually verify the
// validity of the estimate.
function estimateSnrFromFile($file)
{

    include("header.inc.php");

    $top_nav_left = Nav::linkWikiPage('HuygensRemoteManagerHelpSnrEstimator');
    $top_nav_right = "";

    // Noise estimations can be done only in raw images.

    $psrc = $_SESSION['fileserver']->sourceFolder();
    $basename = basename($psrc . "/" . $file);
    $psrc = dirname($psrc . "/" . $file);
    $subDir = dirname($file);
    if ($subDir != ".") {
        $subDir .= "/";
    } else {
        $subDir = "";
    }
    $pdest = $psrc . "/hrm_previews";

    $series = "auto";
    $extra = "";

    if (!$_SESSION['user']->isAdmin()) {

        // This is only for when template parameters are available, in a
        // 'add task' workflow. Admin can't see specific colors, just whatever
        // comes from the image.

        $nchan = $_SESSION['setting']->NumberOfChannels();
        $lmbV = "\"";
        $lambda = $_SESSION['setting']->parameter("EmissionWavelength");
        $l = $lambda->value();
        for ($i = 0; $i < $nchan; $i++) {
            $lmbV .= " " . $l[$i];
        }
        $lmbV .= "\"";

        $xy = $_SESSION['setting']->parameter("CCDCaptorSizeX");
        $z = $_SESSION['setting']->parameter("ZStepSize");
        $xy_s = $xy->value() / 1000.0;
        $z_s = $z->value() / 1000.0;
        $extra = " -emission $lmbV -sampling \"$xy_s $xy_s $z_s\"";

        // Set the -series auto | off option depending on the file type.
        $series = "off";
        if (isset($_SESSION['autoseries']) && $_SESSION['autoseries'] == "TRUE") {
            $series = "auto";
        }

        /** @var \hrm\param\ImageFileFormat $formatParam */
        $formatParam = $_SESSION['setting']->parameter('ImageFileFormat');
        $format = $formatParam->value();
        if ($format == "tiff" || $format == "tiff-single") {
            // Olympus FluoView, or single XY plane: always
            $series = "off";
        }
    }


    // Build the call to HuCore to estimate the SNR value with one of the
    // two algorithms
    if (isset($_POST['SNREstimationAlgorithm'])) {
        $algorithm = $_POST['SNREstimationAlgorithm'];
    } else {
        $algorithm = "old";
    }

    $opt = "-basename \"$basename\" -src \"$psrc\" -dest \"$pdest\" " .
        "-returnImages \"0.5 0.71 1 1.71 \" -snrVersion \"$algorithm\" " .
        "-series $series $extra";

    // Build a label to be shown at the SNR results page .
    if ($algorithm == "old") {
        $algLabel = "Legacy";
    } else {
        $algLabel = "Auto";
    }

    // When no particular SNR estimation image is shown (in a small portion of
    // the image), the image preview goes back to the whole image.
    $defaultView = $_SESSION['fileserver']->imgPreview($file, "src",
        "preview_xy", false);


    ?>


    <div id="content">
        <div id="output">
            <h3><img alt="SNR" src="./images/results_title.png"
                     width="40"/>&nbsp;&nbsp;Estimating SNR
            </h3>
            <fieldset>
                <center>
                    Processing file<br/><?php echo $file; ?>...<br/>
                    <b>Please wait</b>
                    <img src="images/spin.gif">
                </center>
            </fieldset>
        </div>
        <div id="controls"
             class=""
             onmouseover="smoothChangeDivCond('general', 'thumb',
                 '<?php echo Util::escapeJavaScript($defaultView); ?>', 200);">
        </div>
    </div> <!-- content -->

    <div id="rightpanel"
         onmouseover="smoothChangeDivCond('general','thumb',
             '<?php echo Util::escapeJavaScript($defaultView); ?>', 200);">
        <div id="info">
            <?php // echo $defaultView;  ?>
        </div>

        <div id="message">
        </div> <!-- message -->

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

    <!-- Post-processing output: -->
    <div id="tmp">
        <?php

        ob_flush();
        flush();

        // Launch Huygens Core in the background to do the calculations. It will
        // write the JPEG images in a predefined location for this script to
        // display them.

        $estimation = HuygensTools::askHuCore("estimateSnrFromImage", $opt);

        // If estimation failed, we interrupt.
        if ($estimation == null) {
            exit("Error estimating SNR value!");
        }

        // No line-breaks in the output, it is going to be escaped for JavaScript.
        $output =
            "<h3><img alt=\"SNR\" src=\"./images/results_title.png\" " .
            "width=\"40\"/>&nbsp;&nbsp;SNR estimation (" . $algLabel . ")</h3>" .
            "<fieldset>" .
            "<table>";

        $chanCnt = $estimation['channelCnt'];


        $msgSNR = "<p>Suggested SNR values per channel:</p><p>";
        $msgBG = "<p>Estimated background per channel:</p><p>";
        $msgClip = "";

        // Keep the results in an easy place to access them later
        $calculatedSNRValues = array();

        for ($ch = 0; $ch < $chanCnt; $ch++) {
            $output .= "<tr><td>" .
                "<table>" .
                "<tr><td colspan=\"1\">" .
                "<b><hr>Channel $ch</b></td></tr><tr>";

            $chKey = "Ch_$ch,";
            $estSNR = $estimation[$chKey . 'estSNR'];
            $calculatedSNRValues[$ch] = $estSNR;
            $msgSNR .= "Ch $ch: <strong>$estSNR</strong><br />";
            $estBG = $estimation[$chKey . 'estBG'];
            $msgBG .= "Ch $ch: $estBG<br />";
            $estClipFactor = $estimation[$chKey . 'estClipFactor'];

            if ($estClipFactor > 0.0005) {
                if ($chanCnt > 1) {
                    if ($msgClip == "") {
                        $msgClip = "<p>The following channels contain <b>clipped" .
                            " voxels</b>. This affects the SNR estimations and the " .
                            "quality of the deconvolution.</p><p>";
                    }
                    $msgClip .= "Ch $ch: ~" . ($estClipFactor * 100) .
                        "% clipped voxels<br>";
                } else {
                    $msgClip = "<p>The image contains about " .
                        ($estClipFactor * 100) . "% of <b>clipped" .
                        " voxels</b>. This affects the SNR estimation and the " .
                        "quality of the deconvolution.";
                }
            }

            $simVals = explode(" ", $estimation[$chKey . 'simulationList']);
            $simImg = explode(" ", $estimation[$chKey . 'simulationImages']);
            $simZoom = explode(" ", $estimation[$chKey . 'simulationZoom']);
            $bestColumn = array_search($estSNR, $simVals);
            $preload = "if (document.images) {\n";

            $i = 0;
            foreach ($simVals as $snr) {
                $output .= "<td>";

                $tmbFile = urlencode($subDir . $simImg[$i]);
                $zoomFile = urlencode($subDir . $simZoom[$i]);
                if ($snr == 0) {
                    $tag = "Original reference data";
                } else {
                    $tag = "SNR $snr";
                    if ($snr == $estSNR) {
                        $tag = "<b>$tag</b> (Suggested value)";
                    } else if ($snr < $estSNR) {
                        $tag = "$tag (Pessimistic estimate)";
                    } else {
                        $tag = "$tag (Optimistic estimate)";
                    }
                }
                $zoomImg = Util::escapeJavaScript(
                    "<p><b>Portion of channel $ch:</b></p>" .
                    "<p>$tag</p><img src=\"file_management.php?getThumbnail=" .
                    $zoomFile . "&amp;dir=src\" alt=\"SNR $snr\" id=\"ithumb\"" .
                    " />");

                $preload .= ' pic' . $i . '= new Image(200,200); ' . "\n" .
                    'pic' . $i . '.src="file_management.php?getThumbnail=' .
                    $tmbFile . '&dir=src"; ' . "\n";

                if ($snr == 0) {
                    for ($j = 1; $j < $bestColumn; $j++) {
                        // Align the original with the best SNR result
                        $output .= "</td><td>";
                    }
                    $output .= "<img src=\"file_management.php?getThumbnail=" .
                        $tmbFile . "&amp;dir=src\" alt=\"SNR $snr\" " .
                        "onmouseover=\"Tip('$tag'); " .
                        "changeDiv('thumb','$zoomImg', 300); " .
                        "window.divCondition = 'zoom';\"  " .
                        "onmouseout=\"UnTip()\"/>";
                    $output .= "<br /><small>Original</small>";
                } else {
                    $output .= "<img src=\"file_management.php?getThumbnail=" .
                        $tmbFile . "&amp;dir=src\" alt=\"SNR $snr\" " .
                        "onmouseover=\"Tip('Simulation for $tag'); " .
                        "changeDiv('thumb','$zoomImg', 300); " .
                        "window.divCondition = 'zoom';\" " .
                        "onmouseout=\"UnTip()\"/>";
                    if ($snr == $estSNR) {
                        $output .= "<br /><small><b>SNR ~ $snr</b></small>";
                    } else {
                        $output .= "<br /><small>$snr</small>";
                    }
                }

                if ($snr == 0) {
                    $output .= "</td></tr><tr>";
                } else {
                    $output .= "</td>";
                }
                $i++;
            }
            $output .= "</tr></table></td></tr>";
        }

        $msgSNR .= "</p>";
        $msgBG .= "</p>";
        $msgClip .= "</p>";

        # Do not report the $msgBG, not to confuse the users.

        $message = "<h3>Estimation results</h3>" . $msgClip . $msgSNR;

        if (isset($estimation['error'])) {
            foreach ($estimation['error'] as $line) {
                $message .= $line;
            }
        }
        $message .= "<div id=\"thumb\">" . $defaultView . "</div>";
        $output .= "</table></fieldset>";
        $preload .= "} ";


        ?>

        <?php
        // Now create the buttons

        // Navigations buttons are shown after the image is processed. No
        // line-breaks in this declarations, as this is going to be escaped for
        // JavaScript.

        // We put the buttons in a form since we want to submit
        $buttons = "<form method=\"post\" action=\"\" id=\"store\">";

        // We put the 'controls' div around the buttons
        $buttons .= "<div>";

        // We store the calculated values in hidden controls
        $buttons .= "<input type=\"hidden\" name=\"store\" value=\"store\" />";
        for ($i = 0; $i < count($calculatedSNRValues); $i++) {
            $buttons .= "<input type=\"hidden\" " .
                "name=\"Channel$i\" id=\"btn-channel'.($i+1).'\" value=\"$calculatedSNRValues[$i]\" />";
        }

        $buttons .= "<input type=\"button\" value=\"\" class=\"icon previous\" " .
            "onmouseover=\"Tip('Try again on another image.' )\" " .
            "onmouseout=\"UnTip()\" " .
            "onclick=\"document.location.href='estimate_snr_from_image.php'\" />";

        $buttons .= "<input type=\"button\" value=\"\" class=\"icon up\" " .
            "onmouseover=\"Tip('Discard the calculated values and " .
            "return to the restoration parameters page.' )\" " .
            "onmouseout=\"UnTip()\" " .
            "onclick=\"document.location.href='task_parameter.php'\" />";

        $buttons .= "<input type=\"submit\" name=\"store\" class=\"icon next\" " .
            "onmouseover=\"Tip('Accept the calculated values and " .
            "return to the restoration parameters page.' )\" " .
            "onmouseout=\"UnTip()\" value=\"\" /></div>";

        $buttons .= "</div>";

        $buttons .= "</form>";

        ?>
    </div>
    <script type="text/javascript">
        window.divCondition = 'general';
        <?php
        // Preloading code doesn't seem to help (at least if it doesn't go in
        // the head of the document;
        // echo $preload;
        ?>

        // Show the results with a nice JavaScript smooth transition.
        smoothChangeDiv('info',
            '<?php echo Util::escapeJavaScript($message); ?>', 1300);
        smoothChangeDiv('output',
            '<?php echo Util::escapeJavaScript($output); ?>', 1000);
        smoothChangeDiv('controls',
            '<?php echo Util::escapeJavaScript($buttons); ?>', 1500);
        changeDiv('tmp', '');

        function getScrollTop() {
            if (typeof window.pageYOffset !== 'undefined') {
                // Most browsers
                return window.pageYOffset;
            }

            var d = document.documentElement;
            if (d.clientHeight) {
                // IE in standards mode
                return d.scrollTop;
            }

            // IE in quirks mode
            return document.body.scrollTop;
        }
        window.onscroll = function () {
            var box = document.getElementById('thumb'),
                scroll = getScrollTop();

            var basketEl = document.getElementById('basket');
            console.log(basketEl.clientHeight);
            if (scroll <= 200) {
                box.style.top = "0px";
            }
            else if (scroll > basketEl.clientHeight) {

            } else {
                box.style.top = (scroll - 200) + "px";
            }
        };

    </script>

    <?php
}


// This is the starting point of this script.


session_start();

if (isset($_GET['home'])) {
    header("Location: " . "home.php");
    exit();
}

// Keep track of where we are coming from
$_SESSION['filemanager_referer'] = $_SERVER['HTTP_REFERER'];
$_SESSION['referer'] = $_SERVER['HTTP_REFERER'];

// Ask the user to login if necessary.
if (!isset($_SESSION['user']) || !$_SESSION['user']->isLoggedIn()) {
    header("Location: " . "login.php");
    exit();
}

// If the $_SESSION['SNR_Calculated'] flag is set we unset it, to make sure
// that it is there only when 'storing' and going back to
// 'parameter_'task_parameter.php'
if (isset($_SESSION['SNR_Calculated'])) {
    unset($_SESSION['SNR_Calculated']);
}

// Depending on the user actions (or lack thereof) we either display or refresh
// the file browser, or we estimate the SNR from the selected image
if (isset($_POST['estimate']) && isset($_POST['userfiles'])) {

    // Estimate the SNR from the selected file
    $task = "calculate";
    $file = $_POST['userfiles'][0];
    estimateSnrFromFile($file);

} elseif (isset($_POST['store'])) {

    // Collect the calculated SNR values
    $found = true;
    $ch = 0;
    $estSNR = array();
    if (isset($_POST['Channel0'])) {
        $estSNR[0] = $_POST['Channel0'];
        while (1) {
            $ch++;
            $chName = "Channel$ch";
            if (isset($_POST[$chName])) {
                $estSNR[$ch] = $_POST[$chName];
            } else {
                break;
            }
        }
    }

    // Now store the calculated values in the Parameter and back into the session
    /** @var \hrm\param\SignalNoiseRatio $snrParam */
    $snrParam = $_SESSION['task_setting']->parameter('SignalNoiseRatio');
    $snrParam->setValue($estSNR);
    $_SESSION['task_setting']->set($snrParam);

    // Inform task_parameter.php that we do not want the values to be
    // recovered from SessionStorage
    $_SESSION['SNR_Calculated'] = 'true';

    // And now go back to task_parameter.php
    header("Location: " . "task_parameter.php");
    exit();

} else {

    // Just show (or refresh) the file browser with the file list
    showFileBrowser();

}

include("footer.inc.php");

?>