View source for ctfZeroPoint

'''ctfZeroPoint''' 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>-RMax</td> 
				<td>Optional</td> 
				<td>max Spatial frequency[/A]</td> 
				<td>0.1</td> 
			</tr> 
			<tr> 
				<td>-dR</td> 
				<td>Optional</td> 
				<td>delta Spatial frequency[/A]</td> 
				<td>0.0001</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>2.1</td> 
			</tr> 
			<tr> 
				<td>-df</td> 
				<td>Optional</td> 
				<td>defocus: [A]:under(+)</td> 
				<td>27000</td> 
			</tr> 
			<tr> 
				<td>-dfMin</td> 
				<td>Optional</td> 
				<td>min defocus: [A]</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-dfMax</td> 
				<td>Optional</td> 
				<td>max defocus: [A]</td> 
				<td>200000</td> 
			</tr> 
			<tr> 
				<td>-deltadf</td> 
				<td>Optional</td> 
				<td>delta defocus[A]</td> 
				<td>2000</td> 
			</tr> 
			<tr> 
				<td>-A</td> 
				<td>Optional</td> 
				<td>AmplitudeContrast/PhaseContrast</td> 
				<td>0.05</td> 
			</tr> 
			<tr> 
				<td>-N</td> 
				<td>Optional</td> 
				<td>Ordinal number of zero point</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-Ain</td> 
				<td>Optional</td> 
				<td>[[Illumination Aperture]][mrad]</td> 
				<td>0.02</td> 
			</tr> 
			<tr> 
				<td>-ctfMode</td> 
				<td>Optional</td> 
				<td>CTFMode</td> 
				<td>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> 

=== -m details ===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>0</td> 
				<td>One zero point</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>All zero points </td> 
			</tr> 
			<tr> 
				<td>2</td> 
				<td>All zero points along defocus </td> 
			</tr> 
		</table> 

===CTFMode details===
	<table border="1"> 
		<div align="left"> 
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>0</td> 
				<td>Phase CTF</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>PhaseCTF + ratio*AmpCTF </td> 
			</tr> 
		</div> 
	</table>


== Execution example ==
=== Case: Options only essential ===
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
   27000.000000 1        0.038443 
</pre>


=== Option -kV===
====Case: kV=100==== 
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
   27000.000000 1        0.031647 
</pre>


=== Option -Cs===
====Case: Cs=5.0==== 
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
   27000.000000 1        0.038453 
</pre>


=== Option -df===
====Case: df=20000==== 
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
   20000.000000 1        0.044674 
</pre>


=== Option -A===
====Case: A=0.1==== 
<pre>
[ZeroPointResult] AmpContrast        0.100000 
Amount of Defocus [A]  Number          R [A] ......... 
   27000.000000 1        0.038443 
</pre>


=== Option -N===
====Case: N=2==== 
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
   27000.000000 2        0.054377 
</pre>


=== Option -ctfMode===
====Case: ctfMode=1==== 
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
   27000.000000 1        0.038136 
</pre>


=== Option -m===
====Case: m=1, N=2==== 
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
   27000.000000 2       0.038443       0.054377
</pre>


====Case: m=2==== 
=====Case: No other settings=====
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
       0.000000               1       -1.000000
    2000.000000               1       -1.000000
    4000.000000               1       -1.000000
    6000.000000               1        0.081838
    8000.000000               1        0.070758
   10000.000000               1        0.063241
   12000.000000               1        0.057707
   14000.000000               1        0.053414
   16000.000000               1        0.049956

...

   80000.000000               1        0.022330
   82000.000000               1        0.022056
   84000.000000               1        0.021792
   86000.000000               1        0.021537
   88000.000000               1        0.021291
   90000.000000               1        0.021053
   92000.000000               1        0.020823
   94000.000000               1        0.020600
   96000.000000               1        0.020384
   98000.000000               1        0.020175
  100000.000000               1        0.019972

...

  190000.000000               1        0.014489
  192000.000000               1        0.014414
  194000.000000               1        0.014339
  196000.000000               1        0.014266
  198000.000000               1        0.014194
  200000.000000               1        0.014122
</pre>


=====Case: dfMin=8000, dfMax=100000, deltadf=4000=====
<pre>
[ZeroPointResult] AmpContrast        0.050000 
Amount of Defocus [A]  Number          R [A] ......... 
    8000.000000               1        0.070758
   12000.000000               1        0.057707
   16000.000000               1        0.049956
   20000.000000               1        0.044674
   24000.000000               1        0.040777
   28000.000000               1        0.037750
   32000.000000               1        0.035311
   36000.000000               1        0.033290
   40000.000000               1        0.031581
   44000.000000               1        0.030111
   48000.000000               1        0.028829
   52000.000000               1        0.027698
   56000.000000               1        0.026690
   60000.000000               1        0.025785
   64000.000000               1        0.024966
   68000.000000               1        0.024220
   72000.000000               1        0.023538
   76000.000000               1        0.022910
   80000.000000               1        0.022330
   84000.000000               1        0.021792
   88000.000000               1        0.021291
   92000.000000               1        0.020823
   96000.000000               1        0.020384
  100000.000000               1        0.019972
</pre>