Difference between revisions of "mrc2Dto3D"

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(Created page with "'''mrc2Dto3D''' is a command Eos to 3D images from 2D images which is an electron micrographs. From the angle information of the particle cut out, to r...")
 
(→‎Main option)
Line 41: Line 41:
 
<td>-O</td>  
 
<td>-O</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>Output: </td>  
+
<td>OutputDataFile[2DMulti]</td>  
 
<td>NULL</td>  
 
<td>NULL</td>  
 
</tr>  
 
</tr>  
Line 47: Line 47:
 
<td>-single</td>  
 
<td>-single</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>傾斜軸を一つに設定</td>  
+
<td>SingleTiltMode</td>  
 
<td>1</td>  
 
<td>1</td>  
 
</tr>  
 
</tr>  
Line 53: Line 53:
 
<td>-InterpolationMode</td>  
 
<td>-InterpolationMode</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>展開モード</td>  
+
<td>[[Interpolation Mode]]</td>  
 
<td>1</td>  
 
<td>1</td>  
 
</tr>  
 
</tr>  
Line 59: Line 59:
 
<td>-Double</td>  
 
<td>-Double</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>傾斜軸を２つに設定</td>  
+
<td>DoubleTiltMode</td>  
 
<td>　</td>  
 
<td>　</td>  
 
</tr>  
 
</tr>  
Line 65: Line 65:
 
<td>-DoubleCounter</td>  
 
<td>-DoubleCounter</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-Doubleを宣言した上で使用<br>  
+
<td>Only when setting -Double<br>  
−
２つの傾斜軸を選択し、設定する</td>  
+
DoubleCounter</td>  
 
<td>NULL</td>  
 
<td>NULL</td>  
 
</tr>  
 
</tr>  
Line 72: Line 72:
 
<td>-CounterThreshold</td>  
 
<td>-CounterThreshold</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-Doubleを宣言した上で使用<br>  
+
<td>Only when setting -Double<br>  
−
波形の谷の閾値</td>  
+
Threshold of the Valley of the waveform</td>  
 
<td>1e-6</td>  
 
<td>1e-6</td>  
 
</tr>  
 
</tr>  
Line 79: Line 79:
 
<td>-CounterThresholdMode</td>  
 
<td>-CounterThresholdMode</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-Doubleを宣言した上で使用<br>  
+
<td>Only when setting -Double<br>  
−
波形の谷の閾値のモード</td>  
+
Mode of threshold of the Valley of the waveform</td>  
 
<td>0</td>  
 
<td>0</td>  
 
</tr>  
 
</tr>  
Line 86: Line 86:
 
<td>-WeightMode</td>  
 
<td>-WeightMode</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-Doubleを宣言した上で使用<br>  
+
<td>Only when setting -Double<br>  
−
重心のモード</td>  
+
Mode of the center of gravity</td>  
 
<td>0</td>  
 
<td>0</td>  
 
</tr>  
 
</tr>  
Line 93: Line 93:
 
<td>-thicknessWeight</td>  
 
<td>-thicknessWeight</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-Doubleを宣言した上で使用<br>  
+
<td>Only when setting -Double<br>  
−
重心の深さ</td>  
+
The depth of the center of gravity</td>  
 
<td>　</td>  
 
<td>　</td>  
 
</tr>  
 
</tr>  
Line 100: Line 100:
 
<td>-Sub</td>  
 
<td>-Sub</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-Doubleを宣言した上で使用<br>  
+
<td>Only when setting -Double<br>  
−
下位サンプリング</td>  
+
SubSampling: [pixel]</td>  
 
<td>1</td>  
 
<td>1</td>  
 
</tr>  
 
</tr>  
Line 107: Line 107:
 
<td>-PlusXrot</td>  
 
<td>-PlusXrot</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>rasmolのためにｘ軸を180°回転</td>  
+
<td>The 180 ° rotation of the x-axis for rasmol</td>  
 
<td>　</td>  
 
<td>　</td>  
 
</tr>  
 
</tr>  
Line 113: Line 113:
 
<td>-SIRT</td>  
 
<td>-SIRT</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>同時反復再構成法</td>  
+
<td>[[SIRT]] (Simultaneous Iterative Reconstruction Technique)</td>  
 
<td>　</td>  
 
<td>　</td>  
 
</tr>  
 
</tr>  
Line 119: Line 119:
 
<td>-max</td>  
 
<td>-max</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-SIRTを宣言した上で使用<br>  
+
<td>Only when setting -SIRT<br>  
−
同時反復再構成法の最大値設定</td>  
+
Max Value setting of [[SIRT]]</td>  
 
<td>30</td>  
 
<td>30</td>  
 
</tr>  
 
</tr>  
Line 126: Line 126:
 
<td>-rms</td>  
 
<td>-rms</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-SIRTを宣言した上で使用<br>  
+
<td>Only when setting -SIRT<br>  
−
同時反復再構成法の平方２乗平均を設定</td>  
+
RMS (root mean square) setting of [[SIRT]]</td>  
 
<td>1.0</td>  
 
<td>1.0</td>  
 
</tr>  
 
</tr>  
Line 133: Line 133:
 
<td>-CTF</td>  
 
<td>-CTF</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>-SIRTを宣言した上で使用<br>  
+
<td>Only when setting -SIRT<br>  
−
CTFInfoファイルを設定</td>  
+
CTF information file setting</td>  
 
<td>NULL</td>  
 
<td>NULL</td>  
 
</tr>  
 
</tr>  
Line 150: Line 150:
 
</tr>  
 
</tr>  
 
</table>
 
</table>
 +
<br>
 +
 +
=== -m details ===
 +
Setting of the projected image mode.
 +
<table border="1">
 +
<tr>
 +
<th>Value</th>
 +
<th>Description</th>
 +
</tr>
 +
<tr>
 +
<td>0</td>
 +
<td>Simple back projection</td>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>Filtered back projection</td>
 +
</tr>
 +
<tr>
 +
<td>2</td>
 +
<td>Weighted back projection</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
=== -single details ===
 +
Setting of the tilt axis.
 +
<table border="1">
 +
<tr>
 +
<th>Value</th>
 +
<th>Description</th>
 +
</tr>
 +
<tr>
 +
<td>0</td>
 +
<td>The parallel to the x-axis tilt axis</td>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>The parallel to the y-axis tilt axis</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
=== -WeightMode details ===
 +
Setting of weights when calculating.
 +
<table border="1">
 +
<tr>
 +
<th>Value</th>
 +
<th>Description</th>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>Real space: Circle(same density)</td>
 +
</tr>
 +
<tr>
 +
<td>2</td>
 +
<td>Real space: Circle(weighted density)</td>
 +
</tr>
 +
<tr>
 +
<td>3</td>
 +
<td>Real space: Square(weighted density) </td>
 +
</tr>
 +
<tr>
 +
<td>4</td>
 +
<td>Fourier space: Plane(same density) -CounterThreshold 0.5</td>
 +
</tr>
 +
<tr>
 +
<td>5</td>
 +
<td>Fourier space: Plane(Linear Gradient)-CounterThreshold 0.5</td>
 +
</tr>
 +
<tr>
 +
<td>6</td>
 +
<td>Fourier space: Plane(Cosine Gradient) Current Recommende using -CounterThreshold 0.5</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
=== -InterpolationMode details ===
 +
Setting of [[Interpolation Mode]].
 +
<table border="1">
 +
<tr>
 +
<th>Value</th>
 +
<th>Description</th>
 +
</tr>
 +
<tr>
 +
<td>0</td>
 +
<td>Nearest neighbor method</td>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>Bi-linear interpolation method</td>
 +
</tr>
 +
<tr>
 +
<td>2</td>
 +
<td>Cubic convolution method</td>
 +
</tr>
 +
<tr>
 +
<td>3</td>
 +
<td>Polynomial interpolation method</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
=== -I format ===
 +
<pre>
 +
filename0 RotationOrder0 rot1 rot2 rot3
 +
filename1 RotationOrder1 rot1 rot2 rot3
 +
　　　　　　　・
 +
　　　　　　　・
 +
　　　　　　　・
 +
</pre>
 +
<br>
 +
 +
=== [[Rotation Order]] details ===
 +
<pre>
 +
1st digit: Setting the rotation axis of the first
 +
2nd digit: Setting the order-1 of the rotation axis
 +
O: Order Z -> Y-> X
 +
E: Order Z -> X-> Y
 +
3rd digit: Setting the order-2 of the rotation axis
 +
Y: Keep the order
 +
N: Reverse the order
 +
4th digit: Setting rotation method
 +
S: Rotate the object
 +
N: Move the coordinates
 +
</pre>
 +
<br>
 +
 +
== Execution example ==
 +
 +
===-i example===
 +
Is shown in Fig.1 the file that was used in the option -i as a specific example.
 +
Details of these images are as follows.
 +
 +
Min 0
 +
Max 0.175
 +
Mean 0.00302838
 +
SD 0.0129759
 +
SE 8.75794e-06
 +
 +
Output result is Fig.2 followed. Details are as follows.
 +
 +
Min 0
 +
Max 0.0872652
 +
Mean 0.00352428
 +
SD 0.00653417
 +
SE 9.13179e-06
 +
 +
[[File:121p.no2.out-In1-input1.png]]
 +
[[File:121p.no2.out-In1-input2.png]]
 +
[[File:opution-i.png]]
 +
<gallery>
 +
File:121p.no2.out-In1-input1.png|Fig.1-1:XY-plane of the input image
 +
File:121p.no2.out-In1-input2.png|Fig.1-2:ZX-plane of the input image
 +
File:opution-i.png|Fig.2:Output
 +
</gallery>
 +
<br>
 +
 +
===-I example===
 +
For more information about the file that was used in the option -I. The input file is as follows.
 +
 +
a000-2a.orgmrc YOYS 0 60 0
 +
a004-2a.orgmrc YOYS 0 56 0
 +
a008-2a.orgmrc YOYS 0 52 0
 +
a012-2a.orgmrc YOYS 0 48 0
 +
a016-2a.orgmrc YOYS 0 44 0
 +
a020-2a.orgmrc YOYS 0 40 0
 +
a024-2a.orgmrc YOYS 0 36 0
 +
            ・
 +
            ・
 +
            ・
 +
 +
Fig.3 shows a portion of the input image.
 +
In the same object a004-2.orgmrc and a000-2.orgmrc, it is an image tilt angle is different.
 +
Details of each are as follows.
 +
 +
a000-2.orgmrc:
 +
Min 0
 +
Max 37.8872
 +
Mean 0.833407
 +
SD 4.20486
 +
SE 0.0420486
 +
 +
a004-2.orgmrc:
 +
Min 0
 +
Max 38.0379
 +
Mean 0.833354
 +
SD 4.19112
 +
SE 0.0419112
 +
 +
<gallery>
 +
File:a000-2.png|Fig.3-1:a000-2.orgmrc Image
 +
File:a004-2.png|Fig.3-2:a004-2.orgmrc Image
 +
</gallery>
 +
<br>
 +
 +
===-single example===
 +
Tilt axis this is the y-axis from the details of the input file.
 +
 +
Min 0
 +
Max 33.7425
 +
Mean 0.92622
 +
SD 2.73412
 +
SE 0.00273412
 +
 +
<gallery>
 +
File:single.png|Fig.4-1:XY-plane of the input image
 +
File:single-yx.png|Fig.4-2:YZ-plane
 +
File:single-zx.png|Fig.4-3:ZX-plane
 +
</gallery>
 +
<br>
 +
 +
===-Double example===
 +
The combination option -WeightMode, -CounterThreshhold.
 +
 +
====-CounterThreshhold is 2====
 +
WeightMode: 1
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W1m1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-24.3363<br>
 +
115.7<br>
 +
-1.58352e-10<br>
 +
6.11368<br>
 +
0.00611368<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>WeightMode: 2</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W2m1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SE<br>
 +
SD<br></p>
 +
</td>
 +
<td><p align="left">-23.6896<br>
 +
117.242<br>
 +
-8.14329e-09<br>
 +
6.12488<br>
 +
0.00612488<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>WeightMode: 3</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W3m1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-23.6896<br>
 +
117.242<br>
 +
-8.14329e-09<br>
 +
6.12488<br>
 +
0.00612488<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>WeightMode: 4</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W4m1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-40.5762<br>
 +
174.198<br>
 +
0.821701<br>
 +
8.99569<br>
 +
0.00899569<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>WeightMode: 5</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W5m1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-41.7929<br>
 +
185.856<br>
 +
0.821701<br>
 +
8.94568<br>
 +
0.00894568<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>WeightMode: 6</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W6m1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-43.5065<br>
 +
190.759<br>
 +
0.821701<br>
 +
9.38459<br>
 +
0.00938459<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<br>
 +
<div>※-CounterThreshhold is left default, there is the case that is not handled well calculated for this image, the following image is processed.<br>
 +
[[File:121p-input-DW5m1.png]]</div>
 +
<br>
 +
 +
==== With option -CounterThresholdMode====
 +
Executing at the option -WeightMode=1, -CounterThreshhold=2.
 +
<div>-m: 0</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W1m1CTM0.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-24.3363<br>
 +
115.7<br>
 +
-1.58352e-10<br>
 +
6.11368<br>
 +
0.00611368<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>-m: 1</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W1m1CTM1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-20.1632<br>
 +
113.527<br>
 +
-8.04145e-10<br>
 +
5.91589<br>
 +
0.00591589<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
===-InterpolationMode example===
 +
Executing at the option -WeightMode=1, -CounterThreshhold=2.
 +
<div>InterpolationMode: 0</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-CT2W1m1IM0.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-24.6593<br>
 +
117.022<br>
 +
-4.08489e-09<br>
 +
6.13305<br>
 +
0.00613305<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>InterpolationMode: 1</div>
 +
<table>
 +
<tr>
 +
<td>[[File:Double-CT2W1m1IM1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-24.3363<br>
 +
115.7<br>
 +
-1.58352e-10<br>
 +
6.11368<br>
 +
0.00611368<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>InterpolationMode: 2</div>
 +
<table>
 +
<tr>
 +
<td>[[File:Double-CT2W1m1IM2.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-26.0299<br>
 +
118.253<br>
 +
2.86921e-09<br>
 +
6.1544<br>
 +
0.0061544<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>InterpolationMode: 3</div>
 +
<table>
 +
<tr>
 +
<td>[[File:Double-CT2W1m1IM3.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-40640.8<br>
 +
209412<br>
 +
3.35228e-06<br>
 +
10763.2<br>
 +
10.7632<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
===-SIRT example===
 +
Executing of [[SIRT]].
 +
 +
Option -max,-rms are default value, -WeightMode=1, -CounterThreshhold=2.
 +
<table>
 +
<tr>
 +
<td>[[File:double-m1SIRT.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-725.47<br>
 +
2563.64<br>
 +
6.83624e-07<br>
 +
130.514<br>
 +
0.130514<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>Executing at the option -max=5,-rms=1</div>
 +
<table>
 +
<tr>
 +
<td>[[File:Double-m1SIRTm5r1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-234.062<br>
 +
575.77<br>
 +
-7.42642e-08<br>
 +
35.0409<br>
 +
0.0350409<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
===-m example===
 +
<div>-m: 0 (Simple Back Projection)</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">0<br>
 +
30.514<br>
 +
0.916102<br>
 +
2.14263<br>
 +
0.00214263<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
<div>-m: 1 (Filtered Back Projection)</div>
 +
<table>
 +
<tr>
 +
<td>[[File:double-m1.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-54.8893<br>
 +
125.857<br>
 +
7.73532e-09<br>
 +
6.50251<br>
 +
0.00650251<br></p>
 +
</td>
 +
</tr>
 +
</table>

Revision as of 02:21, 15 July 2014

mrc2Dto3D is a command Eos to 3D images from 2D images which is an electron micrographs. From the angle information of the particle cut out, to reconstruct a three-dimensional structure using a back projection technique. The output is a 3d file dsn6, it is possible to display (such as chimera or VMD) molecule viewer density map.

List of option

Main option

The setting of the mode and each parameter.

Option Essential/Optional Description Default
-i Optional Input: mrcImage[2DSet] NULL
-I Optional InputDataFile NULL
-each Optional 一つ一つのファイルを必要なときに読み込む
-o Essential Output: mrcImage[3D] NULL
-O Optional OutputDataFile[2DMulti] NULL
-single Optional SingleTiltMode 1
-InterpolationMode Optional Interpolation Mode 1
-Double Optional DoubleTiltMode 　
-DoubleCounter Optional Only when setting -Double
DoubleCounter		 NULL
-CounterThreshold Optional Only when setting -Double
Threshold of the Valley of the waveform		 1e-6
-CounterThresholdMode Optional Only when setting -Double
Mode of threshold of the Valley of the waveform		 0
-WeightMode Optional Only when setting -Double
Mode of the center of gravity		 0
-thicknessWeight Optional Only when setting -Double
The depth of the center of gravity		 　
-Sub Optional Only when setting -Double
SubSampling: [pixel]		 1
-PlusXrot Optional The 180 ° rotation of the x-axis for rasmol 　
-SIRT Optional SIRT (Simultaneous Iterative Reconstruction Technique) 　
-max Optional Only when setting -SIRT
Max Value setting of SIRT		 30
-rms Optional Only when setting -SIRT
RMS (root mean square) setting of SIRT		 1.0
-CTF Optional Only when setting -SIRT
CTF information file setting		 NULL
-m Optional Mode 0
-h Optional Help 　


-m details

Setting of the projected image mode.

Value Description
0 Simple back projection
1 Filtered back projection
2 Weighted back projection


-single details

Setting of the tilt axis.

Value Description
0 The parallel to the x-axis tilt axis
1 The parallel to the y-axis tilt axis


-WeightMode details

Setting of weights when calculating.

Value Description
1 Real space: Circle(same density)
2 Real space: Circle(weighted density)
3 Real space: Square(weighted density)
4 Fourier space: Plane(same density) -CounterThreshold 0.5
5 Fourier space: Plane(Linear Gradient)-CounterThreshold 0.5
6 Fourier space: Plane(Cosine Gradient) Current Recommende using -CounterThreshold 0.5


-InterpolationMode details

Setting of Interpolation Mode.

Value Description
0 Nearest neighbor method
1 Bi-linear interpolation method
2 Cubic convolution method
3 Polynomial interpolation method


-I format

filename0 RotationOrder0 rot1 rot2 rot3
filename1 RotationOrder1 rot1 rot2 rot3
　　　　　　　・
　　　　　　　・
　　　　　　　・


Rotation Order details

1st digit: Setting the rotation axis of the first
2nd digit: Setting the order-1 of the rotation axis
	O: Order Z -> Y-> X 
	E: Order Z -> X-> Y 
3rd digit: Setting the order-2 of the rotation axis
	Y: Keep the order
	N: Reverse the order
4th digit: Setting rotation method
	S: Rotate the object
	N: Move the coordinates


Execution example

-i example

Is shown in Fig.1 the file that was used in the option -i as a specific example. Details of these images are as follows. 

Min		0
Max		0.175
Mean	0.00302838
SD		0.0129759
SE		8.75794e-06

Output result is Fig.2 followed. Details are as follows. 

Min		0
Max		0.0872652
Mean	0.00352428
SD		0.00653417
SE		9.13179e-06

121p.no2.out-In1-input1.png 121p.no2.out-In1-input2.png opution-i.png

  • Fig.1-1:XY-plane of the input image

  • Fig.1-2:ZX-plane of the input image

  • Fig.2:Output


-I example

For more information about the file that was used in the option -I. The input file is as follows. 

a000-2a.orgmrc YOYS 0 60 0
a004-2a.orgmrc YOYS 0 56 0
a008-2a.orgmrc YOYS 0 52 0
a012-2a.orgmrc YOYS 0 48 0
a016-2a.orgmrc YOYS 0 44 0
a020-2a.orgmrc YOYS 0 40 0
a024-2a.orgmrc YOYS 0 36 0
           ・
           ・
           ・

Fig.3 shows a portion of the input image. In the same object a004-2.orgmrc and a000-2.orgmrc, it is an image tilt angle is different. Details of each are as follows. 

a000-2.orgmrc:
Min		0
Max		37.8872
Mean	0.833407
SD		4.20486
SE		0.0420486

a004-2.orgmrc:
Min		0
Max		38.0379
Mean	0.833354
SD		4.19112
SE		0.0419112

  • Fig.3-1:a000-2.orgmrc Image

  • Fig.3-2:a004-2.orgmrc Image


-single example

Tilt axis this is the y-axis from the details of the input file. 

Min		0
Max		33.7425
Mean	0.92622
SD		2.73412
SE		0.00273412

  • Fig.4-1:XY-plane of the input image

  • Fig.4-2:YZ-plane

  • Fig.4-3:ZX-plane


-Double example

The combination option -WeightMode, -CounterThreshhold.

-CounterThreshhold is 2

WeightMode: 1

double-CT2W1m1.png

Min

Max
Mean
SD

SE

-24.3363

115.7
-1.58352e-10
6.11368

0.00611368
WeightMode: 2
double-CT2W2m1.png

Min

Max
Mean
SE

SD

-23.6896

117.242
-8.14329e-09
6.12488

0.00612488
WeightMode: 3
double-CT2W3m1.png

Min

Max
Mean
SD

SE

-23.6896

117.242
-8.14329e-09
6.12488

0.00612488
WeightMode: 4
double-CT2W4m1.png

Min

Max
Mean
SD

SE

-40.5762

174.198
0.821701
8.99569

0.00899569
WeightMode: 5
double-CT2W5m1.png

Min

Max
Mean
SD

SE

-41.7929

185.856
0.821701
8.94568

0.00894568
WeightMode: 6
double-CT2W6m1.png

Min

Max
Mean
SD

SE

-43.5065

190.759
0.821701
9.38459

0.00938459


※-CounterThreshhold is left default, there is the case that is not handled well calculated for this image, the following image is processed.
121p-input-DW5m1.png


With option -CounterThresholdMode

Executing at the option -WeightMode=1, -CounterThreshhold=2.

-m: 0
double-CT2W1m1CTM0.png

Min

Max
Mean
SD

SE

-24.3363

115.7
-1.58352e-10
6.11368

0.00611368
-m: 1
double-CT2W1m1CTM1.png

Min

Max
Mean
SD

SE

-20.1632

113.527
-8.04145e-10
5.91589

0.00591589


-InterpolationMode example

Executing at the option -WeightMode=1, -CounterThreshhold=2.

InterpolationMode: 0
double-CT2W1m1IM0.png

Min

Max
Mean
SD

SE

-24.6593

117.022
-4.08489e-09
6.13305

0.00613305
InterpolationMode: 1
Double-CT2W1m1IM1.png

Min

Max
Mean
SD

SE

-24.3363

115.7
-1.58352e-10
6.11368

0.00611368
InterpolationMode: 2
Double-CT2W1m1IM2.png

Min

Max
Mean
SD

SE

-26.0299

118.253
2.86921e-09
6.1544

0.0061544
InterpolationMode: 3
Double-CT2W1m1IM3.png

Min

Max
Mean
SD

SE

-40640.8

209412
3.35228e-06
10763.2

10.7632


-SIRT example

Executing of SIRT.

Option -max,-rms are default value, -WeightMode=1, -CounterThreshhold=2.

double-m1SIRT.png

Min

Max
Mean
SD

SE

-725.47

2563.64
6.83624e-07
130.514

0.130514
Executing at the option -max=5,-rms=1
Double-m1SIRTm5r1.png

Min

Max
Mean
SD

SE

-234.062

575.77
-7.42642e-08
35.0409

0.0350409


-m example

-m: 0 (Simple Back Projection)
double.png

Min

Max
Mean
SD

SE

0

30.514
0.916102
2.14263

0.00214263
-m: 1 (Filtered Back Projection)
double-m1.png

Min

Max
Mean
SD

SE

-54.8893

125.857
7.73532e-09
6.50251

0.00650251
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