llExtractWithLayerSeparation - Revision history

Kinoshita: /* Main option */

2014-08-25T01:47:21Z

‎Main option

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

Option Essential/Op..."
2014-08-25T01:46:59Z

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

New page
'''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>Outputリスト: [[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 ==