ctfWeightMapCreation - Revision history

Kinoshita: Created page with "'''ctfWeightMapCreation''' is Eos's Command. == List of option == === Main option ===

Option Essential/Optional
2014-08-20T00:36:31Z

Created page with "'''ctfWeightMapCreation''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</..."

New page
'''ctfWeightMapCreation''' is [[Eos]]'s [[Command]].

== List of option ==
=== Main option ===
<table border="1">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-kV</td>
<td>Optional</td>
<td>[[Acceleration voltage]]: [kV]</td>
<td>200</td>
</tr>
<tr>
<td>-Cs</td>
<td>Optional</td>
<td>[[Spherical aberration coefficient]]: [mm]</td>
<td>1.7</td>
</tr>
<tr>
<td>-df</td>
<td>Essential</td>
<td>Defocus: [A] (+ is Underfocus)</td>
<td>2.7</td>
</tr>
<tr>
<td>-white</td>
<td>Optional</td>
<td>White Noise(Noise/Signal)</td>
<td>1.0</td>
</tr>
<tr>
<td>-noise</td>
<td>Optional</td>
<td>Noise Power Spectrum</td>
<td>NULL</td>
</tr>
<tr>
<td>-splusn</td>
<td>Optional</td>
<td>Signal+Noise Power Spectrum</td>
<td>NULL</td>
</tr>
<tr>
<td>-dRinv</td>
<td>Essential</td>
<td>dRinv[A]</td>
<td>10245/3</td>
</tr>
<tr>
<td>-dRmaxInv</td>
<td>Essential</td>
<td>dRmaxInv[A]</td>
<td>10.0</td>
</tr>
<tr>
<td>-SinWin</td>
<td>Optional</td>
<td>(RminInv[A], RmaxInv[A])</td>
<td>(20.0, 10.0)</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>
<br>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>No correction : F = G</td>
</tr>
<tr>
<td>1</td>
<td>Phase contrast : F = G(H/abs(H))(Only 1 or -1)</td>
</tr>
<tr>
<td>2</td>
<td>Phase contrast : F = GH (Winer filter (S/N << 1))</td>
</tr>
<tr>
<td>3</td>
<td>Phase contrast : F = G/H (Inverse filter)</td>
</tr>
<tr>
<td>4</td>
<td>Phase contrast : F = G(H/(HH + NN)) (Winer filter (white noise : Required Option -white))</td>
</tr>
<tr>
<td>5</td>
<td>Phase contrast : F = G(H/abs(H)abs(GG-NN)/(GG)) (Winer filter: Required Option -noise, -splusn))</td>
</tr>
</table>
<br>

== Execution example ==
=== Case: Options only essential ===
====Case: df=2.7, dRinv=10245/3, dRmaxInv=10.0====
<pre>
0.000000 1.000000 1.000000
0.000977 1.000000 -0.000000
0.001953 1.000000 -0.000001
0.002930 1.000000 -0.000002
0.003906 1.000000 -0.000003
0.004883 1.000000 -0.000005
0.005859 1.000000 -0.000007
0.006836 1.000000 -0.000009
0.007812 1.000000 -0.000011
0.008789 1.000000 -0.000014

...

0.090820 1.000000 0.026869
0.091797 1.000000 0.028082
0.092773 1.000000 0.029335
0.093750 1.000000 0.030629
0.094727 1.000000 0.031964
0.095703 1.000000 0.033343
0.096680 1.000000 0.034765
0.097656 1.000000 0.036232
0.098633 1.000000 0.037744
0.099609 1.000000 0.039302
</pre>
<br>

<div>In the following, Setting at df=2.7, dRinv=10245/3, dRmaxInv=10.0</div>

=== Option -kV===
====Case: kV=100====
<pre>
0.000000 1.000000 1.000000
0.000977 1.000000 -0.000000
0.001953 1.000000 -0.000001
0.002930 1.000000 -0.000003
0.003906 1.000000 -0.000004
0.004883 1.000000 -0.000007
0.005859 1.000000 -0.000009
0.006836 1.000000 -0.000012
0.007812 1.000000 -0.000014
0.008789 1.000000 -0.000016

...

0.090820 1.000000 0.089324
0.091797 1.000000 0.093274
0.092773 1.000000 0.097352
0.093750 1.000000 0.101561
0.094727 1.000000 0.105902
0.095703 1.000000 0.110378
0.096680 1.000000 0.114993
0.097656 1.000000 0.119748
0.098633 1.000000 0.124646
0.099609 1.000000 0.129690
</pre>
<br>

=== Option -Cs===
====Case: Cs=2====
<pre>
0.000000 1.000000 1.000000
0.000977 1.000000 -0.000000
0.001953 1.000000 -0.000001
0.002930 1.000000 -0.000002
0.003906 1.000000 -0.000003
0.004883 1.000000 -0.000005
0.005859 1.000000 -0.000007
0.006836 1.000000 -0.000009
0.007812 1.000000 -0.000011
0.008789 1.000000 -0.000013

...

0.090820 1.000000 0.031918
0.091797 1.000000 0.033352
0.092773 1.000000 0.034832
0.093750 1.000000 0.036361
0.094727 1.000000 0.037939
0.095703 1.000000 0.039567
0.096680 1.000000 0.041247
0.097656 1.000000 0.042979
0.098633 1.000000 0.044765
0.099609 1.000000 0.046605
</pre>
<br>

=== Option -m===
====Case: m=1====
<pre>
0.000000 1.000000 1.000000
0.000977 -1.000000 -0.000000
0.001953 -1.000000 -0.000001
0.002930 -1.000000 -0.000002
0.003906 -1.000000 -0.000003
0.004883 -1.000000 -0.000005
0.005859 -1.000000 -0.000007
0.006836 -1.000000 -0.000009
0.007812 -1.000000 -0.000011
0.008789 -1.000000 -0.000014

...

0.090820 1.000000 0.026869
0.091797 1.000000 0.028082
0.092773 1.000000 0.029335
0.093750 1.000000 0.030629
0.094727 1.000000 0.031964
0.095703 1.000000 0.033343
0.096680 1.000000 0.034765
0.097656 1.000000 0.036232
0.098633 1.000000 0.037744
0.099609 1.000000 0.039302
</pre>
<br>

====Case: m=2====
<pre>
0.000000 1.000000 1.000000
0.000977 -0.000000 -0.000000
0.001953 -0.000001 -0.000001
0.002930 -0.000002 -0.000002
0.003906 -0.000003 -0.000003
0.004883 -0.000005 -0.000005
0.005859 -0.000007 -0.000007
0.006836 -0.000009 -0.000009
0.007812 -0.000011 -0.000011
0.008789 -0.000014 -0.000014

...

0.090820 0.026869 0.026869
0.091797 0.028082 0.028082
0.092773 0.029335 0.029335
0.093750 0.030629 0.030629
0.094727 0.031964 0.031964
0.095703 0.033343 0.033343
0.096680 0.034765 0.034765
0.097656 0.036232 0.036232
0.098633 0.037744 0.037744
0.099609 0.039302 0.039302
</pre>
<br>

====Case: m=3====
=====Case: No other settings=====
<pre>
0.000000 1.000000 1.000000
0.000977 0.000000 -0.000000
0.001953 0.000000 -0.000001
0.002930 0.000000 -0.000002
0.003906 0.000000 -0.000003
0.004883 0.000000 -0.000005
0.005859 0.000000 -0.000007
0.006836 0.000000 -0.000009
0.007812 0.000000 -0.000011
0.008789 0.000000 -0.000014

...

0.090820 0.000000 0.026869
0.091797 0.000000 0.028082
0.092773 0.000000 0.029335
0.093750 0.000000 0.030629
0.094727 0.000000 0.031964
0.095703 0.000000 0.033343
0.096680 0.000000 0.034765
0.097656 0.000000 0.036232
0.098633 0.000000 0.037744
0.099609 0.000000 0.039302
</pre>
<br>

=====Case: df=2.7, dRinv=645/3, dRmaxInv=1.0=====
<pre>
0.000000 1.000000 1.000000
0.015625 0.000000 -0.000027
0.031250 0.000000 0.000194
0.046875 0.000000 0.001564
0.062500 0.000000 0.005590
0.078125 0.000000 0.014376
0.093750 0.000000 0.030629
0.109375 0.000000 0.057639
0.125000 0.000000 0.099237
0.140625 6.263639 0.159652
0.156250 4.112921 0.243136
0.171875 2.831935 0.353115

...

0.843750 -1.971417 -0.507249
0.859375 0.000000 0.005251
0.875000 1.009738 0.990356
0.890625 1.608352 0.621754
0.906250 1.289093 0.775739
0.921875 1.170360 0.854438
0.937500 -1.052999 -0.949668
0.953125 1.005029 0.994997
0.968750 -3.063165 -0.326460
0.984375 -1.204873 -0.829963
1.000000 -2.392987 -0.417888
</pre>
<br>

====Case: m=4====
=====Case: No other settings=====
<pre>
0.000000 1.000000 1.000000
0.000977 -4940297.000000 -0.000000
0.001953 -1242119.125000 -0.000001
0.002930 -557351.375000 -0.000002
0.003906 -317780.156250 -0.000003
0.004883 -207004.218750 -0.000005
0.005859 -146954.187500 -0.000007
0.006836 -110884.648438 -0.000009
0.007812 -87629.039062 -0.000011
0.008789 -71859.500000 -0.000014

...

0.090820 37.217903 0.026869
0.091797 35.610458 0.028082
0.092773 34.089443 0.029335
0.093750 32.649300 0.030629
0.094727 31.284903 0.031964
0.095703 29.991486 0.033343
0.096680 28.764643 0.034765
0.097656 27.600285 0.036232
0.098633 26.494612 0.037744
0.099609 25.444090 0.039302
</pre>
<br>

=====Case: SinWin=(15, 5)=====
<pre>
0.000000 1.000000 1.000000
0.000977 -4940297.000000 -0.000000
0.001953 -1242119.125000 -0.000001
0.002930 -557351.375000 -0.000002
0.003906 -317780.156250 -0.000003
0.004883 -207004.218750 -0.000005
0.005859 -146954.187500 -0.000007
0.006836 -110884.648438 -0.000009
0.007812 -87629.039062 -0.000011
0.008789 -71859.500000 -0.000014

...

0.090820 34.284809 0.026869
0.091797 32.579319 0.028082
0.092773 30.965157 0.029335
0.093750 29.436731 0.030629
0.094727 27.988871 0.031964
0.095703 26.616741 0.033343
0.096680 25.315859 0.034765
0.097656 24.082047 0.036232
0.098633 22.911407 0.037744
0.099609 21.800304 0.039302
</pre>
<br>

====Case: m=5, -noise, -splusn====
=====Case: df=2.7, dRinv=1024*5/3, dRmaxInv=32=====
<div>[[Media:Input-Noise.mrc|-noiseのfile]]'s image</div>
<table>
<tr>
<td>[[File:Input-Noise.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-3.42794 (71, 0, 0)<br>
3.56337 (70, 30, 0)<br>
0.00203425<br>
0.989485<br>
0.0123686<br></p>
</td>
</tr>
</table>
<br>

<div>[[Media:Input-1VOM-N-2D.mrc|-splusnのfile]]'s image</div>
<table>
<tr>
<td>[[File:Input-1VOM-N-2D.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-18651.7 (10, 1, 0)<br>
52942.7 (24, 39, 0)<br>
7214.87<br>
10067.6<br>
125.845<br></p>
</td>
</tr>
</table>
<br>

<div>Output</div>
<pre>
This mode will ignore -dRmax and -dR options
0.000000 1.000000 1.000000
0.012500 -1.000000 -0.000023
0.025000 1.000000 0.000031
0.037500 1.000000 0.000533
0.050000 1.000000 0.002098
0.062500 1.000000 0.005590
0.075000 1.000000 0.012116
0.087500 1.000000 0.023034
0.100000 1.000000 0.039938
0.112500 1.000000 0.064660
0.125000 1.000000 0.099237
0.137500 1.000000 0.145855
0.150000 1.000000 0.206721
0.162500 1.000000 0.283817
0.175000 1.000000 0.378439
0.187500 1.000000 0.490411
0.200000 1.000000 0.616825
0.212500 1.000000 0.750193
0.225000 1.000000 0.876038
0.237500 1.000000 0.970358
0.250000 1.000000 0.998231
0.262500 1.000000 0.916192
0.275000 1.000000 0.682602
0.287500 1.000000 0.280724
0.300000 -1.000000 -0.244868
0.312500 -1.000000 -0.751460
0.325000 -1.000000 -0.999174
0.337500 -1.000000 -0.750135
0.350000 1.000000 0.004719
0.362500 1.000000 0.815910
0.375000 1.000000 0.906149
0.387500 -1.000000 -0.030004
0.400000 -1.000000 -0.966833
</pre>
<br>