Difference between revisions of "llExtractCtrlFileCreate"

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(Created page with "'''llExtractCtrlFileCreate''' is Eos's Command that creates configuration file for extracting llData from mrcImage(FFT). Output file is used by llExtrac...")
 
(→‎設定の決め方)
 
Line 204: Line 204:
 
<br>
 
<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>
 
<br>
  
 
====-Y1, -Y0====
 
====-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>
 
[[File:1ATOMFil-FFT2.png]]<br>
 
<br>
 
<br>

Latest revision as of 00:55, 25 August 2014

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

Option Essential/Optional Description Default
-i Essential Input: mrcImage(FFT) NULL
-o Essential Output: ASCII stdout
-t Optional Turn -6
-u Optional Unit 13
-N Optional N-strand 1
-Y1 Optional Y1 [pixel]

The Position of LayerLine which l = |t| i.e., |n|=1&&m=0 for the first time

36
-Y0 Optional Y0 [pixel]
The Position of LayerLine which n = 0 , l != 0 for the first time		 78
-rmax Optional rmax[A] 250
-Rmax Optional Rmax[/A] 0.1
-lx Optional PixelSize x: (For m=0) 5.0
-ly Optional PixelSize y: (For m=0) 5.0
-nx Optional Image Size x [Pixel]: (For m=0) 1000.0
-ny Optional Image Size y [Pixel]: (For m=0) 1000.0
-center Optional Center of nx(center of filament)[Pixel]: (For m=0) 500.0
-layerline Optional Number of Layer Line: (For m=0) 21.0
-Ax Optional Length of nx(lx * nx): [A]: (For m=0) 5000.0
-dY Optional Range of Layer Line[pixel]: (Form=0) 12.0
-truePitch Optional True Pitch 430
-PixelSize Optional PixelSize: [A]: (For m=0) 5
-deltadY Optional A range of deltadY to determine dY.[pixel]: (For m=0) 0.5
-c Optional ConfigurationFile NULL
-m Optional Mode 1
-h Optional Help 　


-m details

Value Description
0 Myosin: t=1, u=9
1 Otherwise


Execution example

Input file image

by mrcFFTExpression(m=1)

1ATOMFil-FFT.png
Whole area

1ATOMFil-FFT1.png
Around center

Size

Mode
Length
Min
Max
Mean
SD

SE

( 512, 1146, 1)

mrcComplexFloatFT
( 2.000, 2.000, 0.000)
4.08519e-10 (257, 572, 0)
0.109661 (0, 0, 0)
0.00909953
0.00776913

1.01425e-05


How to set options

Set each option with checking Fourier pattern of input file.


-Y1, -Y0

Check the input file by Display2.

First, select a base layer line(around center in image). Then,
Y1: Distance between Base layer line and Same pattern nearest layer line.
Y0: Distance between Base layer line and nearest layer line.

As the above, determine Y0 and Y1.

1ATOMFil-FFT2.png

Case: Options only essential

Output
nlMax: 43 nnMax: 159


Output file
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


Option -t, -u

Case: t=-13, u=28

Output file
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


In the following, Setting at t=-13, u=28

Option -N

Case: N=2

Output file
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


Option -Y1, -Y0

Case: Y1=6, Y0=84

Output file
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


In the following, Setting at Y1=6, Y0=84

Option -truePitch

Case: truePitch=364

Output
nlMax: 36 nnMax: 159


Output file
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


In the following, Setting at truePitch=364

Option -rmax

Case: rmax=4

Output
nlMax: 36 nnMax: 4


Output file
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


In the following, Setting at rmax=4

Option -Rmax

Case: Rmax=0.02

Output
nlMax: 72 nnMax: 7


Output file
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


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