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ctfsimu.htm
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<body width=95% topmargin="0" onLoad="open('ctf/ctfapplet.html','ctfapplet','menubar=yes,location=no,toolbar=no,resizable=yes,scrollbars=yes',true)">
<script SRC="control.js" type="text/javascript"></script>
<script type="text/javascript">
<!--
CheckBrowser();
// -->
</script>
<center>
<h1><b><font color="#3333FF"><font size=+4>CTF Simulation</font></font></b></h1>
<p><p>
<form><input type="button" name="start" value="Start Applet" onClick='open("ctf/ctfapplet.html","ctfapplet","menubar=yes,location=no,toolbar=no,resizable=yes,scrollbars=yes")'>
</form>
</center>
<p><p>
<b>NOTE 1: New Web browsers are dropping Java support. If this CTF applet does not work, please use this page to <a href="https://www.java.com/verify">Verify Java Support</a></b> <br><br>
<b>NOTE 2: You need to disable pop-up blocking of this site to run the CTF simulation Java applet. You might also need to add a security exception in your Java settings for this site</b> <br><br>
<b>Please cite:</b> <a href="https://www.researchgate.net/publication/10890212_Web-based_Simulation_for_Contrast_Transfer_Function_and_Envelope_Functions
">Web-based Simulation for Contrast Transfer Function and Envelope Functions</a>. Microscopy and Microanalysis 7(4), 329-334, 2001
<p>
<font color="#000000"> Contrast
of an ectron image is influenced by the contrast transfer function (CTF)
and the envelope functions of the electron microscope. In order to plan
an experimental condition for data collection or to interpret the contrast
of an electron micrograph, one would often need to know the quantitative
values of these functions for a given set of microscope parameters. This
simulation program is written in <a href="http://java.sun.com">Java</a>
applet and <a href="http://developer.netscape.com/docs/manuals/communicator/jsguide4/index.htm">JavaScript</a>
programming language. The parameters of these functions can be adjusted
interactively with slider bars and the plot for the simulated function
would be updated instantaneously.
<p>
This applet is known to run on Windows (Netscape and Internet Explorer), Linux (i386) (Netscape), SGI IRIX (Netscape), OS/2 Warp and MacOS X. Please inform me if you found that
this applet runs or has problems to run on other platforms.
</font>
<br><font color="#000000"> </font>
<br><font color="#000000"> The
following is the detailed descriptions for some aspects of the applet page.</font>
<center>
<p><b><font size=+2>List of the special symbols/functions used in the applet</font></b></center>
<center><table BORDER WIDTH="95%" NOSAVE >
<tr>
<td><b> Term</b></td>
<td><b> Unit</b></td>
<td><b> Description</b></td>
</tr>
<tr>
<td> s</td>
<td> 1/Å</td>
<td> resolution</td>
</tr>
<tr>
<td> v</td>
<td> keV</td>
<td> accelerating voltage</td>
</tr>
<tr>
<td> Cs</td>
<td> mm</td>
<td> spherical aberration</td>
</tr>
<tr>
<td> Cc</td>
<td> mm</td>
<td> chromatic abbe ration</td>
</tr>
<tr>
<td> Q</td>
<td></td>
<td> amplitude contrast [0-1]</td>
</tr>
<tr>
<td> dE</td>
<td> eV</td>
<td> time variation of electron beam energy from the average</td>
</tr>
<tr>
<td> dI</td>
<td> ppm</td>
<td> time variation of object lens current from the average</td>
</tr>
<tr>
<td> dF</td>
<td> Å</td>
<td> vertical sinusoidal motion amplitude</td>
</tr>
<tr>
<td> dR</td>
<td> Å</td>
<td> horizontal drift amplitude</td>
</tr>
<tr>
<td> dZ</td>
<td> Å</td>
<td> defocus, positive for under-focus</td>
</tr>
<tr>
<td> B</td>
<td> Å<sup>2</sup></td>
<td> envelope decay parameter, exp(-B*s^2)</td>
</tr>
<tr>
<td> a</td>
<td> mrad</td>
<td> illumination angle</td>
</tr>
<tr>
<td> lambda(v)</td>
<td> Å</td>
<td> electron wavelength, automatically computed from voltage</td>
</tr>
<tr>
<td> gamma(s,v,Cs,dZ)</td>
<td></td>
<td> 2*pi*(2.5e6*Cs*lambda(v)^3*s^4-dZ*lambda(v)*s^2/2)</td>
</tr>
<tr>
<td> ctf(s,v,Cs,dZ,Q)</td>
<td></td>
<td> sqrt(1-Q*Q)*sin(gamma(s,v,Cs,dZ))-Q*cos(gamma(s,v,Cs,dZ))</td>
</tr>
<tr>
<td> Gsc(s,v,Cs,dZ,a)</td>
<td></td>
<td> spatial coherence decay: exp(-(pi*a*(1.0e7*Cs*lambda(v)^2*s^3-dZ*s))^2/1e6)</td>
</tr>
<tr>
<td> Gtc(s,v,Cc,dE)</td>
<td></td>
<td> temporal energy spread decay: exp(-1.0e8*(pi*Cc*lambda(v)*s^2*dE/v)^2/(16*ln(2)))</td>
</tr>
<tr>
<td> Gol(s,v,Cc,dE)</td>
<td></td>
<td> temporal lens current spread decay: exp(-1.0e2*(pi*Cc*lambda(v)*s^2*dI)^2/(4*ln(2)))</td>
</tr>
<tr>
<td> Glm(s,v,dF)</td>
<td></td>
<td> vertical motion decay: j0(pi*dF*lambda(v)*s*s)</td>
</tr>
<tr>
<td> Gtm(s,dR)</td>
<td></td>
<td> horizontal drift decay: sinc(pi*s*dR)</td>
</tr>
<tr>
<td> sinc(s)</td>
<td></td>
<td> sinc function: sin(s)/s</td>
</tr>
<tr>
<td> j0(s)</td>
<td></td>
<td> Bessel function of the first kind, order 0: <a href="http://lib-www.lanl.gov/numerical/bookcpdf/c6-5.pdf">(57568490574.0+s*s*(-13362590354.0+s*s*(651619640.7+s*s*(-11214424.18+s*s*(77392.33017+s*s*(-184.9052456))))))
/(57568490411.0+s*s*(1029532 985.0+s*s*(9494680.718+s*s*(59272.64853+s*s*(267.8532712+s*s*1.0)))))</a></td>
</tr>
</table></center>
<center>
<p><b>In addition to the symbols mentioned above, almost all the <a href="http://math.hws.edu/javamath/applets/index.html">common
function, operators, constants</a> could be used in the function definition
if you choose to plot you own function</b></center>
<center><table BORDER COLS=10 WIDTH="95%" >
<tr>
<td>
<center>sin</center>
</td>
<td>
<center>cos</center>
</td>
<td>
<center>tan</center>
</td>
<td>
<center>cot</center>
</td>
<td>
<center>sec</center>
</td>
<td>
<center>csc</center>
</td>
<td>
<center>arcsin</center>
</td>
<td>
<center>arccos</center>
</td>
<td>
<center>arctan</center>
</td>
<td>
<center>abs</center>
</td>
</tr>
<tr>
<td>
<center>sqrt</center>
</td>
<td>
<center>cubert</center>
</td>
<td>
<center>exp</center>
</td>
<td>
<center>ln</center>
</td>
<td>
<center>log2</center>
</td>
<td>
<center>log10</center>
</td>
<td>
<center>trunc</center>
</td>
<td>
<center>round</center>
</td>
<td>
<center>floor</center>
</td>
<td>
<center>ceiling</center>
</td>
</tr>
</table></center>
<center><table BORDER COLS=7 WIDTH="95%" >
<tr>
<td>
<center>+</center>
</td>
<td>
<center>-</center>
</td>
<td>
<center>*</center>
</td>
<td>
<center>/</center>
</td>
<td>
<center>^</center>
</td>
<td>
<center>**</center>
</td>
<td>
<center>!</center>
</td>
</tr>
<tr>
<td>
<center>?:</center>
</td>
<td>
<center><</center>
</td>
<td>
<center><=</center>
</td>
<td>
<center>=</center>
</td>
<td>
<center>></center>
</td>
<td>
<center>>=</center>
</td>
<td>
<center><></center>
</td>
</tr>
<tr>
<td>
<center><i>and</i></center>
</td>
<td>
<center><i>or</i></center>
</td>
<td>
<center><i> not</i></center>
</td>
<td COLSPAN="4">
<center>sum(sumationVariable, start, end, expression)</center>
</td>
</tr>
</table></center>
<center><table BORDER COLS=2 WIDTH="95%" NOSAVE >
<tr NOSAVE>
<td NOSAVE>
<center>pi</center>
</td>
<td>
<center>e</center>
</td>
</tr>
</table></center>
<center>
<p><b>This ctf simulation applet is written by <a href="http://jiang.bio.purdue.edu">Wen
Jiang</a> with help of the excellent <a href="http://math.hws.edu/javamath/index.html">Java
Components for Mathematics</a>.</b>
<p><form><input type="button" name="start" value="Start Applet" onClick='open("ctf/ctfapplet.html","ctfapplet","menubar=yes,location=no,toolbar=no,resizable=yes,scrollbars=yes")'><input type="button" name="close" value="Close" onClick="window.close()"></form></center>