View source for llExtractWithLayerSeparation

'''llExtractWithLayerSeparation''' 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>-i</td> 
				<td>Essential</td> 
				<td>Input: [[mrcImage]]([[FFT]])</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-I</td> 
				<td>Optional</td> 
				<td>Input: llData(Already separated): (InLLNea, InLLFar)</td> 
				<td>(NULL, NULL)</td> 
			</tr> 
			<tr> 
				<td>-r</td> 
				<td>Optional</td> 
				<td>Reference: llData(Gnl(R) Space)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o</td> 
				<td>Essential</td> 
				<td>Output: llData(Average File)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o2</td> 
				<td>Optional</td> 
				<td>OutputList: llData(Each Filament which has the same orientation as average)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o3</td> 
				<td>Optional</td> 
				<td>OutputList: llData(Difference of each filament)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o4</td> 
				<td>Optional</td> 
				<td>OutputList: llData(Each Filament which has the same orientaion as original filament)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o5</td> 
				<td>Optional</td> 
				<td>OutputList: llData(P-Value)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o6</td> 
				<td>Optional</td> 
				<td>OutputList: llData(Q-Value)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o7</td> 
				<td>Optional</td> 
				<td>Output: [[ASCII]](Two subsets for resolution estimation)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o8</td> 
				<td>Optional</td> 
				<td>Output: [[ASCII]](For Back Projection)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o9</td> 
				<td>Optional</td> 
				<td>OutputList: [[ASCII]](x shift, z shift and dY information)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-comment</td> 
				<td>Optional</td> 
				<td>Comment</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-symmetry</td> 
				<td>Optional</td> 
				<td>Symmetry for back projection text file</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-l</td> 
				<td>Essential</td> 
				<td>LayerLineInformation</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-lfinal</td> 
				<td>Optional</td> 
				<td>LayerLineInformation(Final)</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-li</td> 
				<td>Optional</td> 
				<td>LayerLineInformationImportant</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-liw</td> 
				<td>Optional</td> 
				<td>Weight of Important Layer</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-liwStart</td> 
				<td>Optional</td> 
				<td>Weight of Important Layer</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-liwStep/td> 
				<td>Optional</td> 
				<td>Weight of Important Layer</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-la</td> 
				<td>Optional</td> 
				<td>LayerLineInformationForAxisSearch</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-law</td> 
				<td>Optional</td> 
				<td>Weight of Important Layer for AS</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-lawStart</td> 
				<td>Optional</td> 
				<td>Weight of Important Layer for AS</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-lawStep</td> 
				<td>Optional</td> 
				<td>Weight of Important Layer for AS</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-truePitch</td> 
				<td>Essential</td> 
				<td>true pitch [A]</td> 
				<td>430.0</td> 
			</tr> 
			<tr> 
				<td>-rMax</td> 
				<td>Essential</td> 
				<td>rMax [A]</td> 
				<td>100.0</td> 
			</tr> 
			<tr> 
				<td>-rMaxMin</td> 
				<td>Optional</td> 
				<td>rMaxMin [A]</td> 
				<td>100.0</td> 
			</tr> 
			<tr> 
				<td>-RMax</td> 
				<td>Optional</td> 
				<td>RMax [/A]</td> 
				<td>0.1</td> 
			</tr> 
			<tr> 
				<td>-RMaxFirst</td> 
				<td>Optional</td> 
				<td>RMaxFirst [/A] (Def: RMax)</td> 
				<td>0.04</td> 
			</tr> 
			<tr> 
				<td>-RMaxStep</td> 
				<td>Optional</td> 
				<td>RMaxStep [/A]</td> 
				<td>0.02</td> 
			</tr> 
			<tr> 
				<td>-RRMax</td> 
				<td>Optional</td> 
				<td>Radial RMax [/A]</td> 
				<td>0.1</td> 
			</tr> 
			<tr> 
				<td>-RRMaxFirst</td> 
				<td>Optional</td> 
				<td>Radial RMaxFirst [/A] (Def: RMax)</td> 
				<td>0.04</td> 
			</tr> 
			<tr> 
				<td>-RRMaxStep</td> 
				<td>Optional</td> 
				<td>Radial RMaxStep [/A]</td> 
				<td>0.02</td> 
			</tr> 
			<tr> 
				<td>-delBR</td> 
				<td>Optional</td> 
				<td>delBR [/A]</td> 
				<td>0.0002</td> 
			</tr> 
			<tr> 
				<td>-rms</td> 
				<td>Optional</td> 
				<td>rms</td> 
				<td>1e-6</td> 
			</tr> 
			<tr> 
				<td>-narrowSearch</td> 
				<td>Optional</td> 
				<td>narrowSearch [Degree]: P-value and Q-value</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-nextTimes</td> 
				<td>Optional</td> 
				<td>nextTimes: rms</td> 
				<td>1e-4</td> 
			</tr> 
			<tr> 
				<td>-maxIter</td> 
				<td>Optional</td> 
				<td>max Iteration</td> 
				<td>10</td> 
			</tr> 
			<tr> 
				<td>-maxIter2</td> 
				<td>Optional</td> 
				<td>max Iteration on the same RMax and RRMax</td> 
				<td>1</td> 
			</tr> 
			<tr> 
				<td>-maxIter3</td> 
				<td>Optional</td> 
				<td>max Iteration on the same RMax, RRMax, and Weight</td> 
				<td>1</td> 
			</tr> 
			<tr> 
				<td>-lambda</td> 
				<td>Optional</td> 
				<td>lambda</td> 
				<td>1.0</td> 
			</tr> 
			<tr> 
				<td>-ctf</td> 
				<td>Optional</td> 
				<td>CTF Compensation</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-WhiteNoise</td> 
				<td>Optional</td> 
				<td>White Noise</td> 
				<td>0.0</td> 
			</tr> 
			<tr> 
				<td>-below</td> 
				<td>Optional</td> 
				<td>below</td> 
				<td>90.0</td> 
			</tr> 
			<tr> 
				<td>-noantipole</td> 
				<td>Optional</td> 
				<td>No Antipole</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-magLimit</td> 
				<td>Optional</td> 
				<td>magLimit</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-eachTime</td> 
				<td>Optional</td> 
				<td>each time</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-continue</td> 
				<td>Optional</td> 
				<td>continue</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-forContinue</td> 
				<td>Optional</td> 
				<td>For continue</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-phi</td> 
				<td>Optional</td> 
				<td>phi [degree]: (phimin, phimax, delphi))</td> 
				<td>(0.0, 360.0, 10.0)</td> 
			</tr> 
			<tr> 
				<td>-z</td> 
				<td>Optional</td> 
				<td>z [A]: (zmin, zmax, delz)</td> 
				<td>(0.0, 30.0, 5.0)</td> 
			</tr> 
			<tr> 
				<td>-shift</td> 
				<td>Optional</td> 
				<td>shift [A]: (shiftmin, shiftmax, delshift)</td> 
				<td>(-10.0, 10.0, 1.0)</td> 
			</tr> 
			<tr> 
				<td>-log</td> 
				<td>Optional</td> 
				<td>Logfile</td> 
				<td>stdout</td> 
			</tr> 
			<tr> 
				<td>-Normalization</td> 
				<td>Optional</td> 
				<td>Normalization</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-pvm</td> 
				<td>Optional</td> 
				<td>pvmNumber</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-pvmList</td> 
				<td>Optional</td> 
				<td>pvmList</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-pvmServer</td> 
				<td>Optional</td> 
				<td>Work as a server</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-pvmClient</td> 
				<td>Optional</td> 
				<td>Work as a client</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-wd</td> 
				<td>Optional</td> 
				<td>Working Directory</td> 
				<td>./</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> 

<pre>
If -ctf, the file list indicated by -i must include the below information
filename weight  defocus[A] Cs[mm] AccV[kV] ratioOfAmpToPhase mode
</pre>

<pre>
>> llDataSepartionControlFile <<
llMax(different)
nl Z numberOfN n0 n1 n2...
</pre>

===-m  details===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>0</td> 
				<td>The 1st version algorism(Sharing)</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>The 2nd version algorism(Least Square)</td> 
			</tr> 
		</table> 

===-ctf  details===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>0</td> 
				<td>|CTFi|/Sigma(SQR(CTFi))</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>CTFi /Sigma(SQR(CTFi))</td> 
			</tr> 
		</table> 


== Execution example ==