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calculate_bp_pinhole.php
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calculate_bp_pinhole.php
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<?php
// This file is part of the Huygens Remote Manager
// Copyright and license notice: see license.txt
use hrm\Nav;
require_once dirname(__FILE__) . '/inc/bootstrap.php';
session_start();
if (!isset ($_SESSION['user']) || !$_SESSION['user']->isLoggedIn()) {
header("Location: " . "login.php");
exit ();
}
$params = array("d", "na", "wl", "mo", "msys");
$reportparams = array("micro", "d", "na", "wl", "mo", "msys", "c");
// What follows is a mini-database of microscope models with the necessary known
// parameters.
// Developers adding a new microscope model should see the usage of these
// parameters at
// https://svi.nl/index.php?edit=ReportOtherMicroscope
// It is not easy because originally this was not to be included in HRM but
// online on the SVI server. Popular demand convinced us to include it embedded
// in HRM but without much time to make this more programmer-friendly.
// Still it is easier than it looks, so please just read the linked
// instructions.
// Or even better, just report the new model to SVI and we will include online
// and in HRM, for the benefit of all users:
// https://svi.nl/ReportOtherMicroscope
$microscopes = array(
"Biorad MRC 500, 600 and 1024" =>
array("micro=Biorad_MRC_500_600_1024¶m=Pinhole+diameter+(mm)&a=1&b=0&na=0&wl=0&msys=53.2&c=0.5&u=-3&cmsys=1&extra1=1.25&txt1=Fluorescence+attachment&extra2=1.25&txt2=DIC+attachment", "https://svi.nl/BioradMRC_500_600_1024"),
"Biorad Radiance" =>
array("micro=Biorad_Radiance¶m=Pinhole+diameter+(mm)&a=1&b=0&na=0&wl=0&msys=73.2&c=0.5&u=-3&cmsys=1&extra1=1.25&txt1=Fluorescence+attachment&extra2=1.25&txt2=DIC+attachment", "https://svi.nl/Biorad_Radiance"),
"Leica confocal TCS 4d (parameter P_8)" =>
array
("micro=Leica_TCS4d_P8¶m=Reported+parameter+(P_8)&a=2.39216&b=20&na=0&wl=0&msys=4.5&c=0.56419&u=-6",
"https://svi.nl/LeicaConfocal_TCS4d_SP1_NT"),
"Leica confocals TCS 4d, SP1 and NT (Airy disk units)" =>
array
("micro=Leica_TCS4d_SP1_NT_Airy_units¶m=Number+of+Airy+disks&msys=0&mo=0&c=0.56419&a=0&b=0&u=0&wl=580",
"https://svi.nl/LeicaConfocal_TCS4d_SP1_NT"),
"Leica confocal SP2" =>
array("micro=Leica_TCS_SP2_Airy_units¶m=Number+of+Airy+disks&msys=0&mo=0&c=0.56419&a=0&b=0&u=0&wl=580", "https://svi.nl/LeicaConfocal_TCS_SP2"),
"Leica confocal SP5" =>
array("micro=Leica_TCS_SP5_Airy_units¶m=Number+of+Airy+disks&msys=0&mo=0&c=0.56419&a=0&b=0&u=0&wl=580", "https://svi.nl/LeicaConfocal_TCS_SP5"),
"Leica confocal SP8" =>
array("micro=Leica_TCS_SP8_Airy_units¶m=Number+of+Airy+disks&msys=0&mo=0&c=0.56419&a=0&b=0&u=0&wl=580", "https://svi.nl/LeicaConfocal_TCS_SP8"),
"Nikon TE2000-E with the C1 scanning head" =>
array("micro=Nikon_TE2000E_C1¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1&c=0.5&u=-6&extra1=1.5&txt1=Optional+1.5x+magnification",
"https://svi.nl/Nikon_TE2000E_C1"),
"Nikon TE2000-E with the C2 scanning head" =>
array("micro=Nikon_TE2000E_C2¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1&c=0.5&u=-6&extra1=1.5&txt1=Optional+1.5x+magnification",
"https://svi.nl/Nikon_TE2000E_C2"),
"Nikon A1, A1 Plus, A1HD25, A1RHD25, AX, AXR" =>
array("micro=Nikon_A_Series¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1&c=0.456&u=-6", "https://svi.nl/Nikon_A_Series"),
"Olympus FV10i" =>
array("micro=Olympus_FV10i¶m=Pinhole+side+(microns)&a=1&b=0&na=0&wl=0&msys=3.8&c=0.399&u=-6", "https://svi.nl/Olympus_FV10i"),
"Olympus FV300 and FVX" =>
array("micro=Olympus_FV300¶m=Reported+pinhole+parameter&table=1&a=1&b=0&na=0&wl=0&msys=3.426&c=0.5&u=-6", "https://svi.nl/Olympus_FV300"),
"Olympus FV500" =>
array("micro=Olympus_FV500¶m=Pinhole+side+(microns)&a=1&b=0&na=0&wl=0&msys=3.8&c=0.5641896&u=-6", "https://svi.nl/Olympus_FV500"),
"Olympus FV1000" =>
array("micro=Olympus_FV1000¶m=Pinhole+side+(microns)&a=1&b=0&na=0&wl=0&msys=3.82&c=0.5641896&u=-6", "https://svi.nl/Olympus_FV1000"),
"Olympus FV3000" =>
array("micro=Olympus_FV3000¶m=Pinhole+side+(microns)&a=1&b=0&na=0&wl=0&msys=7.6&c=0.5641896&u=-6", "https://svi.nl/Olympus_FV3000"),
"Yokogawa spinning disk - pinhole RADIUS - all CSU models" =>
array("micro=Yokogawa_spinning_disk&d=50&a=1&b=0&na=0&wl=0&msys=1&c=0.5&u=-6",
"https://svi.nl/YokogawaDisk"),
"Yokogawa spinning disk - pinhole DISTANCE - CSU-10, CSU-22, CSU-X1" =>
array("micro=Yokogawa_disk_(pinhole_distance)&d=253&a=1&b=0&na=0&wl=0&msys=1&c=1&u=-6&ru=-6&rtag=pinhole+distance",
"https://svi.nl/BackProjectedPinholeDistance"),
"Yokogawa spinning disk - pinhole DISTANCE - CSU-W1" =>
array("micro=Yokogawa_disk_(pinhole_distance)&d=253&a=1&b=0&na=0&wl=0&msys=0.5065&c=1&u=-6&ru=-6&rtag=pinhole+distance",
"https://svi.nl/BackProjectedPinholeDistance"),
"Visitech Infinity spinning disk - pinhole RADIUS" =>
array("micro=Visitech_spinning_disk&d=50&a=1&b=0&na=0&wl=0&msys=1&c=0.5&u=-6",
"https://svi.nl/Visitech_Infinity"),
"Visitech Infinity spinning disk - pinhole DISTANCE" =>
array("micro=Visitech_disk_(pinhole_distance)&d=253&a=1&b=0&na=0&wl=0&msys=1&c=1&u=-6&ru=-6&rtag=pinhole+distance",
"https://svi.nl/BackProjectedPinholeDistance"),
"Zeiss LSM410 inverted" =>
array("micro=Zeiss_LSM410_inverted_P8¶m=Reported+parameter+(P_8)&a=3.92157&b=0&na=0&wl=0&msys=2.23&c=0.56419&u=-6",
"https://svi.nl/Zeiss_LSM410_inverted"),
"Zeiss LSM510" =>
array("micro=Zeiss_LSM510¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=3.33&c=0.5&u=-6", "https://svi.nl/Zeiss_LSM510"),
"Zeiss LSM700" =>
array("micro=Zeiss_LSM700¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1.53&c=0.564&u=-6", "https://svi.nl/Zeiss_LSM700"),
"Zeiss LSM710" =>
array("micro=Zeiss_LSM710¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1.9048&c=0.564&u=-6", "https://svi.nl/Zeiss_LSM710"),
"Zeiss LSM780" =>
array("micro=Zeiss_780¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1.9048&c=0.564&u=-6", "https://svi.nl/Zeiss_LSM780"),
"Zeiss LSM800" =>
array("micro=Zeiss_800¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1.53&c=0.564&u=-6", "https://svi.nl/Zeiss_LSM800"),
"Zeiss LSM880" =>
array("micro=Zeiss_800¶m=Pinhole+diameter+(microns)&a=1&b=0&na=0&wl=0&msys=1.9048&c=0.564&u=-6", "https://svi.nl/Zeiss_LSM880"),
"Not listed" =>
array("micro=Not_listed_microscope¶m=Pinhole+physical+diameter+(microns)&a=1&b=0&na=0&wl=0&u=-6", "https://svi.nl/ReportOtherMicroscope")
);
function globalize_vars($var_string, $type)
{
global ${$type};
if ($var_string && $type) {
$var_name = trim(strtok($var_string, ","));
global ${$var_name};
if (!isset(${$var_name}) && isset(${$type}["$var_name"]))
${$var_name} = ${$type}["$var_name"];
#echo $var_name, $$var_name, " ";
while ($var_name) {
$var_name = trim(strtok(","));
global ${$var_name};
if (!isset(${$var_name}) && isset(${$type}["$var_name"]))
${$var_name} = ${$type}["$var_name"];
}
}
}
// Parameters passed by _GET or _POST that are dumped in global variables:
$post_string = "param, micro, d, a, b, c, u, wl, na, mo, msys, task, ref, " .
"cmsys, extra1, extra2, table, txt1, txt2, checked1, checked2, " .
"help, ru, rtag";
globalize_vars($post_string, "_POST");
globalize_vars($post_string, "_GET");
if (!isset($ref) || $ref == "")
$ref = "capturing_parameter.php";
if (!isset($ru) || $ru == "") $ru = "-9";
// Units of the input parameter
switch ($u) {
case 0:
$units = "(m)";
break;
case -3:
$units = "(mm)";
break;
case -6:
$units = "(µm)";
break;
case -9:
$units = "(nm)";
break;
default:
$units = "";
break;
}
// Units of the reported parameter
switch ($ru) {
case 0:
$runits = "(m)";
break;
case -3:
$runits = "(mm)";
break;
case -6:
$runits = "(µm)";
break;
case -9:
$runits = "(nm)";
break;
default:
$runits = "";
break;
}
if (!isset($rtag) || $rtag == "") {
$rtag = "pinhole radius";
}
if ($param == "") $param = "Reported parameter $units";
$Label = array("micro" => "Microscope model",
"d" => $param,
"wl" => "Wavelength (nm)",
"na" => "Lens numerical aperture",
"mo" => "Objective magnification",
"msys" => "Internal system magnification",
"c" => "Shape factor"
);
$Default = array("micro" => "Not specified",
"d" => "",
"wl" => "590",
"na" => "1.3",
"mo" => "100",
"msys" => "1",
"c" => "0.5"
);
function field($p)
{
global $Label, $WikiURL, $WikiArticle;
#$string = " <a target=\"SviWiki\" href=\"".$WikiURL.$WikiArticle[$param]."\">";
$string = $Label[$p];
#$string .= "</a> ";
return $string;
}
function fieldEntry($p)
{
global $Details, $Default;
global ${$p};
if (isset($$p)) $val = $$p;
else $val = $Default[$p];
$string = field($p);
$string .= "<input type=\"text\" " .
"name=\"$p\" size=\"5\" value=\"" .
$val . "\">";
#$string .= "<td>".$Details[$param]."</td>";
return $string;
}
# --
function start() {
global $microscopes, $na;
echo "<h4>Please choose a microscope from the following list:</h4>";
echo "\n<ul>";
$script = $_SERVER['PHP_SELF'];
foreach ($microscopes as $m => $data) {
$extra = "";
// If na is not defined in the model parameters take the one reported
// from HRM.
if (!strstr($data[0], "na=") && isset($na) && $na != "") {
$extra = "&na=$na";
}
echo "\n<li><a href=\"$script?$data[0]&help=$data[1]&task=form$extra\">$m</a></li>";
}
echo "\n</ul>";
echo "<div id=\"controls\">
<input type=\"button\" value=\"\" class=\"icon up\"
onmouseover=\"Tip('Go back without calculating the ' +
'backprojected pinhole radius for your microscope.')\"
onmouseout=\"UnTip()\"
onclick=\"document.location.href='capturing_parameter.php'\" /></div>";
echo "\n</div> <!-- content -->\n";
?>
<div id="rightpanel">
<div id="info">
<h3>Quick help</h3>
<?php
echo "<p>The following forms will assist you in calculating the " .
"(circular-equivalent) backprojected pinhole radius expressed in " .
"nanometers, that you can enter directly in the HRM settings.</p>";
echo "<p>Please mind that there is one special entry to calculate ";
echo "pinhole distances in spinning disks.</p>";
echo "<p>Click <b>Help</b> on the top menu for more details.</p>";
echo "<p>Start by selecting your microscope model from the list on the
left, or click on cancel at the bottom to go back.</p>";
echo "</div>";
echo "</div>";
}
function form($error = false, $imglink = "") {
global $params, $reportparams, $ref, $help, $rtag, $ru;
global $a, $b, $c, $d, $u, $param, $wl, $na, $mo, $msys, $micro, $units;
global $cmsys, $table, $extra1, $txt1, $extra2, $txt2, $checked1, $checked2;
// Initialize message
$message = "";
if ($error) print $error . "<br><br>";
print "\n<h3>" . str_replace("_", " ", $micro) . "</h3>";
print "\n<form action=\"calculate_bp_pinhole.php\" method=\"post\"" .
" id=\"select\">";
print "\n<fieldset class=\"setting\">";
print "\nEnter the parameters as reported by your microscope:";
print "\n<INPUT TYPE=\"hidden\" name=\"task\" value=\"calc\">";
print "\n<INPUT TYPE=\"hidden\" name=\"ref\" value=\""
. $ref . "\">";
print "\n<INPUT TYPE=\"hidden\" name=\"param\" value=\""
. $param . "\">";
#print "\n<INPUT TYPE=\"hidden\" name=\"micro\" value=\""
#.$micro."\">";
print "\n<INPUT TYPE=\"hidden\" name=\"a\" value=\""
. $a . "\">";
print "\n<INPUT TYPE=\"hidden\" name=\"b\" value=\""
. $b . "\">";
# print "\n<INPUT TYPE=\"hidden\" name=\"c\" value=\""
#.$c."\">";
print "\n<INPUT TYPE=\"hidden\" name=\"u\" value=\""
. $u . "\">";
print "\n<INPUT TYPE=\"hidden\" name=\"ru\" value=\""
. $ru . "\">";
print "\n<INPUT TYPE=\"hidden\" name=\"rtag\" value=\""
. $rtag . "\">";
print "\n<INPUT TYPE=\"hidden\" name=\"table\" value=\""
. $table . "\">";
print "\n<br><br>";
$afterTable = "";
foreach ($reportparams as $entry) {
if (!isset($$entry) && $$entry !== "" && $$entry !== 0
|| ($entry == "msys" && $cmsys == 1)
) {
print fieldEntry($entry) . "<br>\n";
} else
$afterTable .= "\n<INPUT TYPE=\"hidden\" name=\"" . $entry .
"\" value=\"" . $$entry . "\">";
}
if (isset($extra1) && isset($txt1)) {
print (urldecode($txt1));
print ("\n<input type=\"checkbox\" name=\"extra1\" value=\"$extra1\"" .
" $checked1><br>"); #checked
}
if (isset($extra2) && isset($txt2)) {
print (urldecode($txt2));
print ("\n<input type=\"checkbox\" name=\"extra2\" value=\"$extra2\"" .
" $checked2><br>"); #checked
}
print "<div><input name=\"OK\" type=\"hidden\" /></div>";
print "\n$afterTable";
?>
</fieldset>
<div id="controls">
<input type="button" value="" class="icon previous"
onmouseover="Tip('Go back to the microscope list.' )"
onmouseout="UnTip()"
onclick="document.location.href='<?php echo $_SERVER['PHP_SELF']; ?>'"/>
<input type="submit" value="" class="icon calc"
onmouseover="Tip('Calculate the backprojected pinhole ' +
'radius or distance from the entered parameters.' )"
onmouseout="UnTip()"
onclick="process()"/>
</div>
</form>
</div> <!-- content -->
<div id="rightpanel">
<div id="info">
<h3>Quick help</h3>
<p>
Enter or confirm the requested values and press the calculator
button to calculate the
<a href="javascript:openWindow('
https://svi.nl/BackProjected')">
back projected
</a>
pinhole radius.
Press the back button to go back to the list of microscopes.
</p>
<p>
Read more about the
<a href="javascript:openWindow('<?php echo $help; ?>')">
<?php echo $micro; ?></a> model.
</p>
</div>
<div id="message">
<?php
echo "<p>$message</p>";
?>
</div>
</div> <!-- rightpanel -->
<?php
} # END form
# --
function serve()
{
global $a, $b, $c, $d, $u, $param, $wl, $na, $mo, $msys, $micro;
global $extra1, $extra2, $table, $ru, $runits, $rtag;
global $ref, $params, $Label, $Default, $reportparams;
$warning = NULL;
$out = "";
$error = "";
foreach ($params as $entry) {
# $out .= $entry. " ". $$entry."<br>\n";
if (!isset($$entry) || $$entry == "" || $$entry < 0) {
$$entry = $Default[$entry];
$warning .= "\n<br>Using default value " . $$entry .
" for " . $Label[$entry] . " " . $entry;
}
}
if (($mo == 0 || $msys == 0) && ($na == 0 && $wl == 0)) {
$error .= "Wrong magnification value.<br>\n";
} else {
$M = $mo * $msys;
if ($extra1) $M *= $extra1;
if ($extra2) $M *= $extra2;
}
if ($c == 0)
$error .= "Wrong shape factor value.<br>\n";
if ($d == 0 || !isset($d))
$error .= "Wrong pinhole value. Please enter a value as reported " .
"by your microscope.<br>\n";
if ($table == 1) {
if ($micro == "Olympus_FV300") {
switch ($d) {
case 1:
$deff = 60;
break;
case 2:
$deff = 100;
break;
case 3:
$deff = 150;
break;
case 4:
$deff = 200;
break;
case 5:
$deff = 300;
break;
default:
$error .= "Unknown size parameter";
break;
}
} else $error .= "Undefined table for model $micro<br>\n";
} else {
$deff = $d;
}
#$out .= "d $deff";
if ($na != 0 && $wl != 0) { # Reported in Airy disks
$phr = $c * 1.22 * $wl * $deff / $na;
$M = 1; #Magnification doesn't apply in this case, don't divide at all.
} elseif ($a != 0) {
if (!is_numeric($ru)) {
$error .= "Wrong report units value $ru.<br>\n";
}
if (is_numeric($u)) {
$unitsf = pow(10, $u);
$phr = pow(10, -1 * $ru) * $unitsf * $c * ($a * $deff + $b);
#$out .= "rb = ".pow(10,9) * $unitsf." * $c * ($a * $deff plus $b)<br>";
} else
$error .= "Wrong units value $u.<br>\n";
} else {
$error .= "Wrong equation: not enough parameters.<br>\n";
}
if ($error) {
$out .= "<h3>Error!</h3>\n" . $error;
} else {
$out .= "<p>Parameters used for the calculation:</p>";
$out .= $warning;
$out .= "<p>";
$out .= "" . field("micro") . ": " . $micro . " ";
foreach ($reportparams as $entry) {
if ($$entry != 0 && isset($$entry)) {
$out .= "\n<br>" . field($entry) . ": " . $$entry . " ";
if ($entry == "msys") {
if ($extra1) $out .= "×$extra1 ";
if ($extra2) $out .= "×$extra2 ";
}
}
}
$out .= "</p>\n";
$out .= "<p> </p>";
$result = round($phr / $M, 2);
$out .= "<fieldset id='backproj_result'>";
$out .= "<legend>Result</legend>";
$out .= "Backprojected $rtag $runits: <em class='result_value'>$result</em>";
$out .= "</fieldset>";
}
$out .= "<div id=\"controls\">";
$toScript = $_SERVER['HTTP_REFERER'];
$out .= "<input type=\"button\" value=\"\" class=\"icon previous\"
onmouseover=\"Tip('Try again with other parameters.' )\"
onmouseout=\"UnTip()\"
onclick=\"document.location.href='" . $toScript . "'\" />";
$out .= "<input type=\"button\" value=\"\" class=\"icon next\"
onmouseover=\"Tip('Proceed to the optical parameters back.' )\"
onmouseout=\"UnTip()\"
onclick=\"document.location.href='" . $ref . "'\" /></div>";
$out .= "</div> <!-- content -->";
$out .= "<div id=\"rightpanel\">
<div id=\"info\">
<h3>Quick help</h3>";
if ($error) {
$out .= "<p>Please go back and correct the wrong or missing parameter(s) or
proceed to the optical parameter pages.</p>";
} else {
$out .= "<p>On the left you can see the result of the calculation and the
parameters used for it. <u>Please annotate the calculated value
and enter it in the image parameter pages. The value <strong>
will not</strong> be transferred automatically</u>.</p>
<p>You can repeat the calculation with different input values
(e.g. for other channels) or proceed to the image parameter
pages.</p>";
}
$out .= "</div>
</div> <!-- rightpanel -->";
return $out;
} # END calc
# --
############ Start page
$script = "settings.js";
include("header.inc.php");
?>
<div id="nav">
<div id="navleft">
<ul>
<?php
echo(Nav::linkWikiPage('BackprojectedPinholeCalculator'));
?>
</ul>
</div>
<div id="navright">
<ul>
<?php
echo(Nav::textUser($_SESSION['user']->name()));
?>
</ul>
</div>
<div class="clear"></div>
</div>
<?php
echo "<div id=\"content\"><h3><img alt=\"CalcPinhole\" src=\"./images/pinhole.png\"
width=\"40\"/> Backprojected pinhole calculator</h3>";
switch ($task) {
case 'calc':
$html = serve();
echo $html;
break;
case 'form':
form();
break;
default:
start();
# this case doesn't print html headers, it is intended to be called from
# a wiki article by inserting %%Nyquistcalculator%% there.
}
include("footer.inc.php");
?>