Kinoshita: /* 設定の決め方 */

2014-08-25T00:55:18Z

‎設定の決め方

Kinoshita: Created page with "'''llExtractCtrlFileCreate''' is Eos's Command that creates configuration file for extracting llData from mrcImage(FFT). Output file is used by llExtrac..."

2014-08-25T00:40:03Z

Created page with "'''llExtractCtrlFileCreate''' is Eos's Command that creates configuration file for extracting llData from mrcImage(FFT). Output file is used by llExtrac..."

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'''llExtractCtrlFileCreate''' is [[Eos]]'s [[Command]] that creates configuration file for extracting [[llData]] from [[mrcImage]]([[FFT]]). Output file is used by [[llExtract]](-c).

== 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>-o</td>
<td>Essential</td>
<td>Output: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-t</td>
<td>Optional</td>
<td>Turn</td>
<td>-6</td>
</tr>
<tr>
<td>-u</td>
<td>Optional</td>
<td>Unit</td>
<td>13</td>
</tr>
<tr>
<td>-N</td>
<td>Optional</td>
<td>N-strand</td>
<td>1</td>
</tr>
<tr>
<td>-Y1</td>
<td>Optional</td>
<td>Y1 [pixel]<br>
The Position of LayerLine which l = |t| i.e., |n|=1&&m=0 for the first time<br>
<td>36</td>
</tr>
<tr>
<td>-Y0</td>
<td>Optional</td>
<td>Y0 [pixel]<br>
The Position of LayerLine which n = 0 , l != 0 for the first time</td>
<td>78</td>
</tr>
<tr>
<td>-rmax</td>
<td>Optional</td>
<td>rmax[A]</td>
<td>250</td>
</tr>
<tr>
<td>-Rmax</td>
<td>Optional</td>
<td>Rmax[/A]</td>
<td>0.1</td>
</tr>
<tr>
<td>-lx</td>
<td>Optional</td>
<td>PixelSize x: (For m=0)</td>
<td>5.0</td>
</tr>
<tr>
<td>-ly</td>
<td>Optional</td>
<td>PixelSize y: (For m=0)</td>
<td>5.0</td>
</tr>
<tr>
<td>-nx</td>
<td>Optional</td>
<td>Image Size x [Pixel]: (For m=0)</td>
<td>1000.0</td>
</tr>
<tr>
<td>-ny</td>
<td>Optional</td>
<td>Image Size y [Pixel]: (For m=0)</td>
<td>1000.0</td>
</tr>
<tr>
<td>-center</td>
<td>Optional</td>
<td>Center of nx(center of filament)[Pixel]: (For m=0)</td>
<td>500.0</td>
</tr>
<tr>
<td>-layerline</td>
<td>Optional</td>
<td>Number of Layer Line: (For m=0)</td>
<td>21.0</td>
</tr>
<tr>
<td>-Ax</td>
<td>Optional</td>
<td>Length of nx(lx * nx): [A]: (For m=0)</td>
<td>5000.0</td>
</tr>
<tr>
<td>-dY</td>
<td>Optional</td>
<td>Range of Layer Line[pixel]: (Form=0)</td>
<td>12.0</td>
</tr>
<tr>
<td>-truePitch</td>
<td>Optional</td>
<td>True Pitch</td>
<td>430</td>
</tr>
<tr>
<td>-PixelSize</td>
<td>Optional</td>
<td>PixelSize: [A]: (For m=0)</td>
<td>5</td>
</tr>
<tr>
<td>-deltadY</td>
<td>Optional</td>
<td>A range of deltadY to determine dY.[pixel]: (For m=0)</td>
<td>0.5</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>1</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>Myosin: t=1, u=9</td>
</tr>
<tr>
<td>1</td>
<td>Otherwise</td>
</tr>
</table>
<br>

== Execution example ==
===[[:Media:1ATOMFil.fft|Input file]] image===
<div>by [[mrcFFTExpression]](m=1)</div>
<table>
<tr>
<td><p align="Center">[[File:1ATOMFil-FFT.png]]<br>
Whole area<br></p>
</td>
<td><p align="Center">[[File:1ATOMFil-FFT1.png]]<br>
Around center<br></p>
</td>
<td><p align="left">Size<br>
Mode<br>
Length<br>
Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">( 512, 1146, 1)<br>
mrcComplexFloatFT <br>
( 2.000, 2.000, 0.000)<br>
4.08519e-10 (257, 572, 0)<br>
0.109661 (0, 0, 0)<br>
0.00909953<br>
0.00776913<br>
1.01425e-05<br></p>
</td>
</tr>
</table>
<br>

===設定の決め方===
<div>各設定はInput fileのフーリエパターンを確認して決定します。</div>
<br>

====-Y1, -Y0====
<div>[[Display2]]等を用いてInput fileを確認します。<br>
まず、基準(画像では中心)となる層線を選びます。そして、<br>
Y1: 基準の層線と同じパターンで最も近い距離<br>
Y0: 基準の層線から最も近い層線の距離<br>
として、Y0, Y1を決定することが出来ます。</div>
[[File:1ATOMFil-FFT2.png]]<br>
<br>

=== Case: Options only essential ===
<div>Output</div>
<pre>
nlMax: 43 nnMax: 159
</pre>
<br>

<div>Output file</div>
<pre>
llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
1055
1024
0
0 0 0 0 255 0 255 0.5
13 0 0 0 255 0 255 0.5
-13 0 0 0 255 0 255 0.5
26 0 0 0 255 0 255 0.5
-26 0 0 0 255 0 255 0.5

...

156 0 0 0 255 0 255 0.5
-156 0 0 0 255 0 255 0.5
2 1 6 0 255 0 255 1.0
-11 1 6 0 255 0 255 1.0
15 1 6 0 255 0 255 1.0
-24 1 6 0 255 0 255 1.0
28 1 6 0 255 0 255 1.0
-37 1 6 0 255 0 255 1.0
41 1 6 0 255 0 255 1.0
-50 1 6 0 255 0 255 1.0

...

97 42 252 0 255 0 255 1.0
-98 42 252 0 255 0 255 1.0
110 42 252 0 255 0 255 1.0
-111 42 252 0 255 0 255 1.0
123 42 252 0 255 0 255 1.0
-124 42 252 0 255 0 255 1.0
136 42 252 0 255 0 255 1.0
-137 42 252 0 255 0 255 1.0
149 42 252 0 255 0 255 1.0
-150 42 252 0 255 0 255 1.0

</pre>
<br>

=== Option -t, -u===
====Case: t=-13, u=28====
<div>Output file</div>
<pre>
llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
490
1024
0
0 0 0 0 255 0 255 0.5
28 0 6 0 255 0 255 1.0
-28 0 -6 0 255 0 255 1.0
56 0 12 0 255 0 255 1.0
-56 0 -12 0 255 0 255 1.0
84 0 18 0 255 0 255 1.0
-84 0 -18 0 255 0 255 1.0
112 0 24 0 255 0 255 1.0
-112 0 -24 0 255 0 255 1.0
140 0 30 0 255 0 255 1.0
-140 0 -30 0 255 0 255 1.0
-13 1 0 0 255 0 255 0.5
15 1 6 0 255 0 255 1.0
-41 1 -6 0 255 0 255 1.0
43 1 12 0 255 0 255 1.0
-69 1 -12 0 255 0 255 1.0
71 1 18 0 255 0 255 1.0
-97 1 -18 0 255 0 255 1.0
99 1 24 0 255 0 255 1.0
-125 1 -24 0 255 0 255 1.0
127 1 30 0 255 0 255 1.0
-153 1 -30 0 255 0 255 1.0
155 1 36 0 255 0 255 1.0
2 2 6 0 255 0 255 1.0
-26 2 0 0 255 0 255 0.5
30 2 12 0 255 0 255 1.0
-54 2 -6 0 255 0 255 1.0
58 2 18 0 255 0 255 1.0

...

42 42 126 0 255 0 255 1.0
-42 42 108 0 255 0 255 1.0
70 42 132 0 255 0 255 1.0
-70 42 102 0 255 0 255 1.0
98 42 138 0 255 0 255 1.0
-98 42 96 0 255 0 255 1.0
126 42 144 0 255 0 255 1.0
-126 42 90 0 255 0 255 1.0
154 42 150 0 255 0 255 1.0
-154 42 84 0 255 0 255 1.0
</pre>
<br>

<div>In the following, Setting at t=-13, u=28</div>
=== Option -N===
====Case: N=2====
<div>Output file</div>
<pre>
llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
488
1024
0
0 0 0 0 255 0 255 0.5
28 0 6 0 255 0 255 1.0
-28 0 -6 0 255 0 255 1.0
56 0 12 0 255 0 255 1.0
-56 0 -12 0 255 0 255 1.0
84 0 18 0 255 0 255 1.0
-84 0 -18 0 255 0 255 1.0
112 0 24 0 255 0 255 1.0
-112 0 -24 0 255 0 255 1.0
140 0 30 0 255 0 255 1.0
-140 0 -30 0 255 0 255 1.0
2 1 6 0 255 0 255 1.0
-26 1 0 0 255 0 255 0.5
30 1 12 0 255 0 255 1.0
-54 1 -6 0 255 0 255 1.0
58 1 18 0 255 0 255 1.0

...

28 42 240 0 255 0 255 1.0
-28 42 228 0 255 0 255 1.0
56 42 246 0 255 0 255 1.0
-56 42 222 0 255 0 255 1.0
84 42 252 0 255 0 255 1.0
-84 42 216 0 255 0 255 1.0
112 42 258 0 255 0 255 1.0
-112 42 210 0 255 0 255 1.0
140 42 264 0 255 0 255 1.0
-140 42 204 0 255 0 255 1.0
</pre>
<br>

=== Option -Y1, -Y0===
====Case: Y1=6, Y0=84====
<div>Output file</div>
<pre>
llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
490
1024
0
0 0 0 0 255 0 255 0.5
28 0 924 0 255 0 255 1.0
-28 0 -924 0 255 0 255 1.0
56 0 1848 0 255 0 255 1.0
-56 0 -1848 0 255 0 255 1.0
84 0 2772 0 255 0 255 1.0
-84 0 -2772 0 255 0 255 1.0
112 0 3696 0 255 0 255 1.0
-112 0 -3696 0 255 0 255 1.0
140 0 4620 0 255 0 255 1.0
-140 0 -4620 0 255 0 255 1.0
-13 1 -426 0 255 0 255 1.0
15 1 498 0 255 0 255 1.0
-41 1 -1350 0 255 0 255 1.0
43 1 1422 0 255 0 255 1.0
-69 1 -2274 0 255 0 255 1.0
71 1 2346 0 255 0 255 1.0
-97 1 -3198 0 255 0 255 1.0
99 1 3270 0 255 0 255 1.0
-125 1 -4122 0 255 0 255 1.0
127 1 4194 0 255 0 255 1.0
-153 1 -5046 0 255 0 255 1.0
155 1 5118 0 255 0 255 1.0
2 2 72 0 255 0 255 1.0
-26 2 -852 0 255 0 255 1.0
30 2 996 0 255 0 255 1.0
-54 2 -1776 0 255 0 255 1.0
58 2 1920 0 255 0 255 1.0

...

42 42 1512 0 255 0 255 1.0
-42 42 -1260 0 255 0 255 1.0
70 42 2436 0 255 0 255 1.0
-70 42 -2184 0 255 0 255 1.0
98 42 3360 0 255 0 255 1.0
-98 42 -3108 0 255 0 255 1.0
126 42 4284 0 255 0 255 1.0
-126 42 -4032 0 255 0 255 1.0
154 42 5208 0 255 0 255 1.0
-154 42 -4956 0 255 0 255 1.0
</pre>
<br>

<div>In the following, Setting at Y1=6, Y0=84</div>
=== Option -truePitch===
====Case: truePitch=364====
<div>Output</div>
<pre>
nlMax: 36 nnMax: 159
</pre>
<br>

<div>Output file</div>
<pre>
llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
410
1024
0
0 0 0 0 255 0 255 0.5
28 0 924 0 255 0 255 1.0
-28 0 -924 0 255 0 255 1.0
56 0 1848 0 255 0 255 1.0
-56 0 -1848 0 255 0 255 1.0
84 0 2772 0 255 0 255 1.0
-84 0 -2772 0 255 0 255 1.0
112 0 3696 0 255 0 255 1.0
-112 0 -3696 0 255 0 255 1.0
140 0 4620 0 255 0 255 1.0
-140 0 -4620 0 255 0 255 1.0
-13 1 -426 0 255 0 255 1.0
15 1 498 0 255 0 255 1.0
-41 1 -1350 0 255 0 255 1.0
43 1 1422 0 255 0 255 1.0
-69 1 -2274 0 255 0 255 1.0
71 1 2346 0 255 0 255 1.0
-97 1 -3198 0 255 0 255 1.0
99 1 3270 0 255 0 255 1.0
-125 1 -4122 0 255 0 255 1.0
127 1 4194 0 255 0 255 1.0
-153 1 -5046 0 255 0 255 1.0
155 1 5118 0 255 0 255 1.0
2 2 72 0 255 0 255 1.0
-26 2 -852 0 255 0 255 1.0
30 2 996 0 255 0 255 1.0
-54 2 -1776 0 255 0 255 1.0
58 2 1920 0 255 0 255 1.0

...

-91 35 -2898 0 255 0 255 1.0
105 35 3570 0 255 0 255 1.0
-119 35 -3822 0 255 0 255 1.0
133 35 4494 0 255 0 255 1.0
-147 35 -4746 0 255 0 255 1.0
</pre>
<br>

<div>In the following, Setting at truePitch=364</div>
=== Option -rmax===
====Case: rmax=4====
<div>Output</div>
<pre>
nlMax: 36 nnMax: 4
</pre>
<br>

<div>Output file</div>
<pre>
llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
12
1024
0
0 0 0 0 255 0 255 0.5
2 2 72 0 255 0 255 1.0
4 4 144 0 255 0 255 1.0
-3 11 -66 0 255 0 255 1.0
-1 13 6 0 255 0 255 1.0
1 15 78 0 255 0 255 1.0
3 17 150 0 255 0 255 1.0
-4 24 -60 0 255 0 255 1.0
-2 26 12 0 255 0 255 1.0
0 28 84 0 255 0 255 1.0
2 30 156 0 255 0 255 1.0
4 32 228 0 255 0 255 1.0

</pre>
<br>

<div>In the following, Setting at rmax=4</div>
=== Option -Rmax===
====Case: Rmax=0.02====
<div>Output</div>
<pre>
nlMax: 72 nnMax: 7
</pre>
<br>

<div>Output file</div>
<pre>
llData
2 2
255 572
In
Nea
Far
0.0
0.0
0.0
0
0.0
0.0
256
39
1024
0
0 0 0 0 255 0 255 0.5
2 2 72 0 255 0 255 1.0
4 4 144 0 255 0 255 1.0
6 6 216 0 255 0 255 1.0
-7 7 -210 0 255 0 255 1.0
-5 9 -138 0 255 0 255 1.0
-3 11 -66 0 255 0 255 1.0
-1 13 6 0 255 0 255 1.0
1 15 78 0 255 0 255 1.0
3 17 150 0 255 0 255 1.0
5 19 222 0 255 0 255 1.0
7 21 294 0 255 0 255 1.0
-6 22 -132 0 255 0 255 1.0
-4 24 -60 0 255 0 255 1.0
-2 26 12 0 255 0 255 1.0
0 28 84 0 255 0 255 1.0
2 30 156 0 255 0 255 1.0
4 32 228 0 255 0 255 1.0
6 34 300 0 255 0 255 1.0
-7 35 -126 0 255 0 255 1.0
-5 37 -54 0 255 0 255 1.0
-3 39 18 0 255 0 255 1.0
-1 41 90 0 255 0 255 1.0
1 43 162 0 255 0 255 1.0
3 45 234 0 255 0 255 1.0
5 47 306 0 255 0 255 1.0
7 49 378 0 255 0 255 1.0
-6 50 -48 0 255 0 255 1.0
-4 52 24 0 255 0 255 1.0
-2 54 96 0 255 0 255 1.0
0 56 168 0 255 0 255 1.0
2 58 240 0 255 0 255 1.0
4 60 312 0 255 0 255 1.0
6 62 384 0 255 0 255 1.0
-7 63 -42 0 255 0 255 1.0
-5 65 30 0 255 0 255 1.0
-3 67 102 0 255 0 255 1.0
-1 69 174 0 255 0 255 1.0
1 71 246 0 255 0 255 1.0

</pre>
<br>

@@ Line 204: / Line 204: @@
 <br>
-===設定の決め方===
+===How to set options===
-<div>各設定はInput fileのフーリエパターンを確認して決定します。</div>
+<div>Set each option with checking Fourier pattern of input file.</div>
 <br>
 ====-Y1, -Y0====
-<div>[[Display2]]等を用いてInput fileを確認します。<br>
+<div>Check the input file by [[Display2]].<br>
-まず、基準(画像では中心)となる層線を選びます。そして、<br>
+First, select a base layer line(around center in image). Then, <br>
-Y1: 基準の層線と同じパターンで最も近い距離<br>
+Y1: Distance between Base layer line and Same pattern nearest layer line.<br>
-Y0: 基準の層線から最も近い層線の距離<br>
+Y0: Distance between Base layer line and nearest layer line.<br>
-として、Y0, Y1を決定することが出来ます。</div>
+As the above, determine Y0 and Y1.</div>
 [[File:1ATOMFil-FFT2.png]]<br>
 <br>

llExtractCtrlFileCreate - Revision history

Kinoshita: /* 設定の決め方 */

Kinoshita: Created page with "'''llExtractCtrlFileCreate''' is Eos's Command that creates configuration file for extracting llData from mrcImage(FFT). Output file is used by llExtrac..."