EosPedia - User contributions [en]

mrcImageSmoothing

2015-03-04T06:08:13Z

Kinoshita:

'''mrcImageSmoothing''' is [[Eos]]'s [[Command]] that performs Nonlinear smoothing [[mrcImage]].

== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Essential</td>
<td>Input名: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output名: [[mrcImage]]</td>
<td>stdout(Standard output by default）</td>
</tr>
<tr>
<td>-sx</td>
<td>Optional</td>
<td>x of Kernel Size</td>
<td>3</td>
</tr>
<tr>
<td>-sy</td>
<td>Optional</td>
<td>y of Kernel Size</td>
<td>3</td>
</tr>
<tr>
<td>-sz</td>
<td>Optional</td>
<td>z of Kernel Size</td>
<td>3</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Radius of Kernel Size</td>
<td>1</td>
</tr>
<tr>
<td>-sigma</td>
<td>Optional</td>
<td>Sigma (For m=4)</td>
<td>2.0</td>
</tr>
<tr>
<td>-times</td>
<td>Optional</td>
<td>Repeat time</td>
<td>1</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>-M</td>
<td>Optional</td>
<td>Mode2</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</div>
</table>

===-m details===
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>1</td>
<td>Median filter</td>
</tr>
<tr>
<td>2</td>
<td>Mean filter </td>
</tr>
<tr>
<td>3</td>
<td>Surface Fit filter </td>
</tr>
<tr>
<td>4</td>
<td>Lee-Sigma filter</td>
</tr>
</div>
</table>
<div>m=0, at the default setting. Therefore, It is error if -m isn't set.</div>
 

===-M details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Kernel is cube. : required argumnent: -sx, -sy, [-sz]</td>
</tr>
<tr>
<td>1</td>
<td>Kernel is sphere.(Only mode 1 supported) : required argumnent: -r </td>
</tr>
</table>

== Execution example ==

Example of Option -h

$ mrcImageSmoothing -h
Usage: /home/people/tacyas/Eos/bin/X86LINUX64/mrcImageSmoothing
Options:
[-i[nput] In (NULL )] :Essential :InputDataFile
[-o[utput] Out (NULL )] :Essential :OutputDataFile
[-sx sx (3 )] :Optional :x of Kernel Size
[-sy sy (3 )] :Optional :y of Kernel Size
[-sz sz (3 )] :Optional :z of Kernel Size
[-r r (1 )] :Optional :Radius of Kernel Size
[-sigma sigma (2.0 )] :Optional :Sigma for Lee-Sigma
[-m[ode] mode (0 )] :Optional :Mode
[-M[ode2] mode2 (0 )] :Optional :Mode
[-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
>>> Mode <<<<
1: Median filter
2: Mean filter
3: Surface Fit filter
4: Lee-Sigma filter
>>> Mode2 <<<<
0: Kernel is cube. : required argumnent: -sx, -sy, [-sz]
1: Kernel is sphere.(Only mode 1 supported) : required argumnent: -r

===Input file's image===
<table>
<tr>
<td>[[File:B120.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-65.0178 
94.4699 
4.85274 
20.4635 
0.255794 
</td>
</tr>
</table>
 

===Option -m, -M===
====Case: m=1====
<table>
<tr>
<td>[[File:Smo.m1.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-41.8721 
65.9659 
4.7617 
14.3083 
0.178854 
</td>
<td>Case: M=0 
with -sx=9,-sy=9 
　　－－－－－－＞</td>
<td>[[File:Smo.m1M0x9y9.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-54.6403 
54.0815 
4.773 
13.5848 
0.16981 
</td>
</tr>
<tr>
<td></td>
<td></td>
<td></td>
<td>Case: M=1 
with -r=5 
　　－－－－－－＞</td>
<td>[[File:Smo.m1M1r5.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-54.6403 
55.7056 
4.73966 
13.9823 
0.174779 
</td>
</tr>
</table>
 

====Case: m=2====
<table>
<tr>
<td>[[File:Smo.m2.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-41.8721 
67.5276 
4.82079 
13.8056 
0.17257 
</td>
<td>Case: M=0 
with -sx=9,-sy=9 
　　－－－－－－＞</td>
<td>[[File:Smo.m2M0x9y9.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-54.6403 
54.0644 
4.89358 
13.5214 
0.169018 
</td>
</tr>
</table>
 

====Case: m=3====
<table>
<tr>
<td>[[File:Smo.m3.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-41.8721 
83.4967 
4.85411 
17.5032 
0.21879 
</td>
<td>Case: M=0 
with -sx=9,-sy=9 
　　－－－－－－＞</td>
<td>[[File:Smo.m3M0x9y9.center-mrcImageSmoothing.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-54.6403 
56.99 
4.87303 
14.4517 
0.180646 
</td>
</tr>
</table>

File:Outdata-m5hvp0.03-mrcImageLowPassFilter-FFT.png

2015-03-04T01:10:09Z

Kinoshita:

File:Outdata-m4hvp0.03-mrcImageLowPassFilter-FFT.png

2015-03-04T01:09:49Z

Kinoshita:

File:Outdata-m3hvp0.03-mrcImageLowPassFilter-FFT.png

2015-03-04T01:09:30Z

Kinoshita:

File:Outdata-m2hvp0.03-mrcImageLowPassFilter-FFT.png

2015-03-04T01:09:07Z

Kinoshita:

File:Outdata-m1hvp0.03-mrcImageLowPassFilter-FFT.png

2015-03-04T01:08:37Z

Kinoshita:

mrcImageLowPassFilter

2015-03-04T01:07:31Z

Kinoshita: /* Option -m */

'''mrcImageLowPassFilter''' is [[Eos]]'s [[Command]] that performs [[Low-Pass Filter]] to [[mrcImage]], and smoothing it.

== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<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]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-hvp</td>
<td>Optional</td>
<td>HalfValuePoint[A-1] (the spatial frequency that the intensity attenuate to half)</td>
<td>1.0</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Width of cos function of spatial frequency</td>
<td>1.0</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 (need to set ,because 0 is undefined)</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</div>
</table>

=== -m details ===
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>1</td>
<td>Step filter : required argumnent: -hvp</td>
</tr>
<tr>
<td>2</td>
<td>Cos filter : required argumnent: -hvp -w</td>
</tr>
<tr>
<td>3</td>
<td>Exp filter : required argumnent: -hvp</td>
</tr>

<tr>
<td>4</td>
<td>Gauss filter : required argumnent: -hvp</td>
</tr>
<tr>
<td>5</td>
<td>Lorenz filter : required argumnent: -hvp</td>
</tr>
</div>
</table>

== Execution example ==
=== [[:Media:Input-B120.mrc|Input file]]'s image ===
<table>
<tr>
<td>[[File:Input-B120.png]] 
Real Space 
</td>
<td>[[File:Input-B120-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 
255 
21.0538 
47.6709 
0.595886 
</td>
</tr>
</table>
 

=== Option -m===
====Case: m=1====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m1hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m1hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-13.3126 
219.107 
21.0538 
46.5599 
0.581999 
</td>
</tr>
</table>
The image on Real Space is seen blurry, because its high frequency signal is filtered. 
 

====Case: m=2====
=====Case: hvp=0.03, w=0.03=====
<table>
<tr>
<td>[[File:Outdata-m2hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m2hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-7.37665 
213.947 
21.0538 
46.0616 
0.57577 
</td>
</tr>
</table>
 

====Case: m=3====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m3hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m3hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1.13914 
183.815 
21.0538 
39.0991 
0.488739 
</td>
</tr>
</table>
 

=====Case: hvp=0.01=====
<table>
<tr>
<td>[[File:Outdata-m3hvp0.01-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m3hvp0.01-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>3.38997 
125.944 
21.0538 
28.4391 
0.355488 
</td>
</tr>
</table>
 

====Case: m=4====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m4hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m4hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-1.83105e-05 
199.777 
21.0538 
43.8691 
0.548364 
</td>
</tr>
</table>
 

====Case: m=5====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m5hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m5hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1.15871e-05 
199.081 
21.0538 
43.1827 
0.539784 
</td>
</tr>
</table>
 

Example of help by -h

$ mrcImageLowPassFilter -h
Usage: /home/people/tacyas/Eos/bin/X86LINUX64/mrcImageLowPassFilter
Options:
[-i[nput] In (NULL )] :Essential :InputDataFile
[-o[utput] Out (NULL )] :Essential :OutputDataFile
[-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
[-m[ode] mode (0 )] :Optional :Mode
[-h[alf]v[alue]p[oint]hvp (1.0 )] :Optional :HalfValuePoint[/A]
[-w[idth] width (1.0 )] :Optional :WidthOfDumping
>>> Mode <<<<
1: Step filter : required argumnent: -hvp
2: Cos filter : required argumnent: -hvp -w
3: Exp filter : required argumnent: -hvp
4: Gauss filter : required argumnent: -hvp
5: Lorenz filter : required argumnent: -hvp

mrcImageLowPassFilter

2015-03-04T01:07:18Z

Kinoshita: /* Execution example */

'''mrcImageLowPassFilter''' is [[Eos]]'s [[Command]] that performs [[Low-Pass Filter]] to [[mrcImage]], and smoothing it.

== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<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]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-hvp</td>
<td>Optional</td>
<td>HalfValuePoint[A-1] (the spatial frequency that the intensity attenuate to half)</td>
<td>1.0</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Width of cos function of spatial frequency</td>
<td>1.0</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 (need to set ,because 0 is undefined)</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</div>
</table>

=== -m details ===
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>1</td>
<td>Step filter : required argumnent: -hvp</td>
</tr>
<tr>
<td>2</td>
<td>Cos filter : required argumnent: -hvp -w</td>
</tr>
<tr>
<td>3</td>
<td>Exp filter : required argumnent: -hvp</td>
</tr>

<tr>
<td>4</td>
<td>Gauss filter : required argumnent: -hvp</td>
</tr>
<tr>
<td>5</td>
<td>Lorenz filter : required argumnent: -hvp</td>
</tr>
</div>
</table>

== Execution example ==
=== [[:Media:Input-B120.mrc|Input file]]'s image ===
<table>
<tr>
<td>[[File:Input-B120.png]] 
Real Space 
</td>
<td>[[File:Input-B120-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 
255 
21.0538 
47.6709 
0.595886 
</td>
</tr>
</table>
 

=== Option -m===
====Case: m=1====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m1hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m1hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-13.3126 
219.107 
21.0538 
46.5599 
0.581999 
</td>
</tr>
</table>
The image on Real Space is seen blurry, because its high frequency signal is filtered.
 

====Case: m=2====
=====Case: hvp=0.03, w=0.03=====
<table>
<tr>
<td>[[File:Outdata-m2hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m2hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-7.37665 
213.947 
21.0538 
46.0616 
0.57577 
</td>
</tr>
</table>
 

====Case: m=3====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m3hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m3hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1.13914 
183.815 
21.0538 
39.0991 
0.488739 
</td>
</tr>
</table>
 

=====Case: hvp=0.01=====
<table>
<tr>
<td>[[File:Outdata-m3hvp0.01-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m3hvp0.01-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>3.38997 
125.944 
21.0538 
28.4391 
0.355488 
</td>
</tr>
</table>
 

====Case: m=4====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m4hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m4hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-1.83105e-05 
199.777 
21.0538 
43.8691 
0.548364 
</td>
</tr>
</table>
 

====Case: m=5====
=====Case: hvp=0.03=====
<table>
<tr>
<td>[[File:Outdata-m5hvp0.03-mrcImageLowPassFilter.png]] 
Real Space 
</td>
<td>[[File:Outdata-m5hvp0.03-mrcImageLowPassFilter-FFT.png]] 
Fourier Space 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1.15871e-05 
199.081 
21.0538 
43.1827 
0.539784 
</td>
</tr>
</table>
 

Example of help by -h

$ mrcImageLowPassFilter -h
Usage: /home/people/tacyas/Eos/bin/X86LINUX64/mrcImageLowPassFilter
Options:
[-i[nput] In (NULL )] :Essential :InputDataFile
[-o[utput] Out (NULL )] :Essential :OutputDataFile
[-c[onfig] configFile (NULL )] :Optional :ConfigurationFile
[-m[ode] mode (0 )] :Optional :Mode
[-h[alf]v[alue]p[oint]hvp (1.0 )] :Optional :HalfValuePoint[/A]
[-w[idth] width (1.0 )] :Optional :WidthOfDumping
>>> Mode <<<<
1: Step filter : required argumnent: -hvp
2: Cos filter : required argumnent: -hvp -w
3: Exp filter : required argumnent: -hvp
4: Gauss filter : required argumnent: -hvp
5: Lorenz filter : required argumnent: -hvp

File:Outdata-m3hvp0.01-mrcImageLowPassFilter-FFT.png

2015-03-04T00:48:25Z

Kinoshita:

File:Outdata-m3hvp0.01-mrcImageLowPassFilter.png

2015-03-04T00:48:14Z

Kinoshita:

mrcImageCTFCompensationForTiltImage

2015-02-12T03:58:43Z

Kinoshita: /* Main option */

'''mrcImageCTFCompensationForTiltImage''' is [[Eos]]'s [[Command]] that performs [[CTF Correction]] for [[Tilt image]].

== 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]](for file size only)</td>
<td>NULL</td>
</tr>
<tr>
<td>-I</td>
<td>Essential</td>
<td>ROI information: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[mrcImage]]([[CTF]])</td>
<td>NULL</td>
</tr>
<tr>
<td>-cut</td>
<td>Optional</td>
<td>Range with no compensation (The number of pixels from the center)</td>
<td>6</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>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>

===-I format===
<div>cf [[mrcImageROIs]] about ROI information's format.</div>

== Execution example ==
===Input file's data===
====-i image====
<table>
<tr>
<td>[[File:Input-mrcImageCTFCompensationForTiltImage.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
255 (49, 32, 0) 
21.0538 
47.6709 
0.595886 
</td>
</tr>
</table>

====-I data====
<pre>
/Eos/img/ROISet0/inputnoise-0000.roi Rect 6 6 26 6 26 26 6 26
/Eos/img/ROISet0/inputnoise-0001.roi Rect 20 6 40 6 40 26 20 26
/Eos/img/ROISet0/inputnoise-0002.roi Rect 40 6 60 6 60 26 40 26
/Eos/img/ROISet0/inputnoise-0003.roi Rect 54 6 74 6 74 26 54 26
/Eos/img/ROISet0/inputnoise-0004.roi Rect 6 20 26 20 26 40 6 40
/Eos/img/ROISet0/inputnoise-0005.roi Rect 20 20 40 20 40 40 20 40
/Eos/img/ROISet0/inputnoise-0006.roi Rect 40 20 60 20 60 40 40 40
/Eos/img/ROISet0/inputnoise-0007.roi Rect 54 20 74 20 74 40 54 40
/Eos/img/ROISet0/inputnoise-0008.roi Rect 6 40 26 40 26 60 6 60
/Eos/img/ROISet0/inputnoise-0009.roi Rect 20 40 40 40 40 60 20 60
/Eos/img/ROISet0/inputnoise-0010.roi Rect 40 40 60 40 60 60 40 60
/Eos/img/ROISet0/inputnoise-0011.roi Rect 54 40 74 40 74 60 54 60
/Eos/img/ROISet0/inputnoise-0012.roi Rect 6 54 26 54 26 74 6 74
/Eos/img/ROISet0/inputnoise-0013.roi Rect 20 54 40 54 40 74 20 74
/Eos/img/ROISet0/inputnoise-0014.roi Rect 40 54 60 54 60 74 40 74
/Eos/img/ROISet0/inputnoise-0015.roi Rect 54 54 74 54 74 74 54 74

</pre>

Using ROI files: [[Media:Input-ROISet0.zip | Input file]]

=== Example of options only essential ===
<table>
<tr>
<td>[[File:Outdata-mrcImageCTFCompensationForTiltImage.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1 (7, 7, 0) 
255 (22, 7, 0) 
155.874 
73.4908 
0.918635 
</td>
</tr>
</table>

=== Option -cut===
====Case: cut=20====
<table>
<tr>
<td>[[File:Outdata-cut-mrcImageCTFCompensationForTiltImage.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0.01 (7, 7, 0) 
255 (25, 20, 0) 
118.004 
59.0793 
0.738491 
</td>
</tr>
</table>

mrcFFTSpectrum

2015-02-09T00:19:42Z

Kinoshita:

'''mrcFFTSpectrum''' is [[Eos]]'s [[Command]] that outputs [[FFT]] spectrums from each specified angle.

== 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>Optional</td>
<td>Output: spectrum: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-n</td>
<td>Optional</td>
<td>n-division: 2PI/n</td>
<td>1</td>
</tr>
<tr>
<td>-axis</td>
<td>Optional</td>
<td>axis</td>
<td>0.0</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>
 

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
 

===-o 's format===
<pre>
R F1 F2 ... Fn
. . . ... .
. . . ... .
. . . ... .
</pre>
It outputs spectrum at each R and each angle. 
 

== Execution example ==
=== Input file's image ===
<table>
<tr>
<td>[[File:Input-mrcFFTSpectrum.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>5.8388e-05 (34, 19, 25) 
269.463 (0, 0, 0) 
0.184947 
0.853561 
0.00121937 
</td>
</tr>
</table>

=== Example of options only essential ===
<pre>
0 72610.2
0.00285714 9403.77
0.00571429 424.22
0.00857143 72.3162
0.0114286 53.0119
0.0142857 16.8282
0.0171429 5.76959
0.02 6.58468
0.0228571 3.23293
0.0257143 1.55617
0.0285714 1.6768
0.0314286 1.20942
0.0342857 0.906873
0.0371429 0.818493
0.04 0.641874
0.0428571 0.463089
0.0457143 0.443777
0.0485714 0.361395
0.0514286 0.330671
0.0542857 0.206129
0.0571429 0.236484
0.06 0.159589
0.0628571 0.126009
0.0657143 0.155259
0.0685714 0.133023
0.0714286 0.0925122
0.0742857 0.116136
0.0771429 0.0917471
0.08 0.071327
0.0828571 0.0729114
0.0857143 0.0688022
0.0885714 0.0585575
0.0914286 0.0579214
0.0942857 0.0547112
0.0971429 0.051852
0.1 0.0563705
</pre>

=== Option -n===
====Case: n=2====
<pre>
0 72610.2 0
0.00285714 9540.94 9321.47
0.00571429 377.685 457.459
0.00857143 71.7113 72.7867
0.0114286 54.4599 51.7342
0.0142857 17.2292 16.4807
0.0171429 5.97049 5.58782
0.02 6.90724 6.29284
0.0228571 3.37276 3.10428
0.0257143 1.59725 1.51744
0.0285714 1.71636 1.63995
0.0314286 1.22438 1.19526
0.0342857 0.889703 0.923062
0.0371429 0.817146 0.819779
0.04 0.632989 0.650364
0.0428571 0.465223 0.461054
0.0457143 0.442187 0.445312
0.0485714 0.367417 0.355584
0.0514286 0.336318 0.325222
0.0542857 0.209724 0.202656
0.0571429 0.239088 0.233972
0.06 0.161831 0.157409
0.0628571 0.127638 0.124426
0.0657143 0.153156 0.157304
0.0685714 0.132966 0.133078
0.0714286 0.0932153 0.0918257
0.0742857 0.117086 0.115208
0.0771429 0.091885 0.0916127
0.08 0.0720596 0.0706101
0.0828571 0.0735423 0.0722951
0.0857143 0.0691698 0.0684419
0.0885714 0.0585733 0.0585419
0.0914286 0.0584944 0.0573604
0.0942857 0.0551845 0.0542469
0.0971429 0.0509491 0.0527389
0.1 0.0558718 0.0569212
</pre>

=== Option -axis===
====Case: axis=1, n=2====
<pre>
0 72610.2 0
0.00285714 9403.77 9403.77
0.00571429 424.22 424.22
0.00857143 72.3162 72.3162
0.0114286 53.0119 53.0119
0.0142857 16.8282 16.8282
0.0171429 5.76959 5.76958
0.02 6.58468 6.58468
0.0228571 3.23293 3.23293
0.0257143 1.55617 1.55617
0.0285714 1.6768 1.67679
0.0314286 1.20942 1.20942
0.0342857 0.906873 0.906873
0.0371429 0.818492 0.818492
0.04 0.641874 0.641874
0.0428571 0.463089 0.463089
0.0457143 0.443778 0.443777
0.0485714 0.361395 0.361395
0.0514286 0.330671 0.330671
0.0542857 0.206129 0.206129
0.0571429 0.236484 0.236484
0.06 0.159589 0.159589
0.0628571 0.126009 0.126009
0.0657143 0.155259 0.155259
0.0685714 0.133023 0.133023
0.0714286 0.0925122 0.0925122
0.0742857 0.116136 0.116136
0.0771429 0.0917471 0.0917472
0.08 0.071327 0.071327
0.0828571 0.0729114 0.0729114
0.0857143 0.0688022 0.0688022
0.0885714 0.0585574 0.0585574
0.0914286 0.0579214 0.0579214
0.0942857 0.0547111 0.0547112
0.0971429 0.051852 0.051852
0.1 0.0589118 0.0535082

</pre>

mrcFFTSpectrum

2015-02-09T00:07:37Z

Kinoshita:

'''mrcFFTSpectrum''' is [[Eos]]'s [[Command]] that outputs [[FFT]] spectrums from each specified angle.

== 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>Optional</td>
<td>Output: spectrum: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-n</td>
<td>Optional</td>
<td>n-division: 2PI/n</td>
<td>1</td>
</tr>
<tr>
<td>-axis</td>
<td>Optional</td>
<td>axis</td>
<td>0.0</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>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>

== Execution example ==
=== Input file's image ===
<table>
<tr>
<td>[[File:Input-mrcFFTSpectrum.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>5.8388e-05 (34, 19, 25) 
269.463 (0, 0, 0) 
0.184947 
0.853561 
0.00121937 
</td>
</tr>
</table>

=== Example of options only essential ===
<pre>
0 72610.2
0.00285714 9403.77
0.00571429 424.22
0.00857143 72.3162
0.0114286 53.0119
0.0142857 16.8282
0.0171429 5.76959
0.02 6.58468
0.0228571 3.23293
0.0257143 1.55617
0.0285714 1.6768
0.0314286 1.20942
0.0342857 0.906873
0.0371429 0.818493
0.04 0.641874
0.0428571 0.463089
0.0457143 0.443777
0.0485714 0.361395
0.0514286 0.330671
0.0542857 0.206129
0.0571429 0.236484
0.06 0.159589
0.0628571 0.126009
0.0657143 0.155259
0.0685714 0.133023
0.0714286 0.0925122
0.0742857 0.116136
0.0771429 0.0917471
0.08 0.071327
0.0828571 0.0729114
0.0857143 0.0688022
0.0885714 0.0585575
0.0914286 0.0579214
0.0942857 0.0547112
0.0971429 0.051852
0.1 0.0563705
</pre>

=== Option -n===
====Case: n=2====
<pre>
0 72610.2 0
0.00285714 9540.94 9321.47
0.00571429 377.685 457.459
0.00857143 71.7113 72.7867
0.0114286 54.4599 51.7342
0.0142857 17.2292 16.4807
0.0171429 5.97049 5.58782
0.02 6.90724 6.29284
0.0228571 3.37276 3.10428
0.0257143 1.59725 1.51744
0.0285714 1.71636 1.63995
0.0314286 1.22438 1.19526
0.0342857 0.889703 0.923062
0.0371429 0.817146 0.819779
0.04 0.632989 0.650364
0.0428571 0.465223 0.461054
0.0457143 0.442187 0.445312
0.0485714 0.367417 0.355584
0.0514286 0.336318 0.325222
0.0542857 0.209724 0.202656
0.0571429 0.239088 0.233972
0.06 0.161831 0.157409
0.0628571 0.127638 0.124426
0.0657143 0.153156 0.157304
0.0685714 0.132966 0.133078
0.0714286 0.0932153 0.0918257
0.0742857 0.117086 0.115208
0.0771429 0.091885 0.0916127
0.08 0.0720596 0.0706101
0.0828571 0.0735423 0.0722951
0.0857143 0.0691698 0.0684419
0.0885714 0.0585733 0.0585419
0.0914286 0.0584944 0.0573604
0.0942857 0.0551845 0.0542469
0.0971429 0.0509491 0.0527389
0.1 0.0558718 0.0569212
</pre>

=== Option -axis===
====Case: axis=1, n=2====
<pre>
0 72610.2 0
0.00285714 9403.77 9403.77
0.00571429 424.22 424.22
0.00857143 72.3162 72.3162
0.0114286 53.0119 53.0119
0.0142857 16.8282 16.8282
0.0171429 5.76959 5.76958
0.02 6.58468 6.58468
0.0228571 3.23293 3.23293
0.0257143 1.55617 1.55617
0.0285714 1.6768 1.67679
0.0314286 1.20942 1.20942
0.0342857 0.906873 0.906873
0.0371429 0.818492 0.818492
0.04 0.641874 0.641874
0.0428571 0.463089 0.463089
0.0457143 0.443778 0.443777
0.0485714 0.361395 0.361395
0.0514286 0.330671 0.330671
0.0542857 0.206129 0.206129
0.0571429 0.236484 0.236484
0.06 0.159589 0.159589
0.0628571 0.126009 0.126009
0.0657143 0.155259 0.155259
0.0685714 0.133023 0.133023
0.0714286 0.0925122 0.0925122
0.0742857 0.116136 0.116136
0.0771429 0.0917471 0.0917472
0.08 0.071327 0.071327
0.0828571 0.0729114 0.0729114
0.0857143 0.0688022 0.0688022
0.0885714 0.0585574 0.0585574
0.0914286 0.0579214 0.0579214
0.0942857 0.0547111 0.0547112
0.0971429 0.051852 0.051852
0.1 0.0589118 0.0535082

</pre>

File:Outdata2-filterCol3-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:09:50Z

Kinoshita:

File:Outdata1-filterCol3-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:09:38Z

Kinoshita:

File:Outdata-filterCol3-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:09:24Z

Kinoshita:

File:Outdata2-filter3-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:09:01Z

Kinoshita:

File:Outdata1-filter3-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:08:49Z

Kinoshita:

File:Outdata-filter3-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:08:37Z

Kinoshita:

File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter-FFT.png

2014-10-29T01:08:00Z

Kinoshita:

File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:07:49Z

Kinoshita:

File:Outdata-filterCol-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:07:35Z

Kinoshita:

File:Outdata1-filter2-mrcImageSpatialFrequencyFilter-FFT.png

2014-10-29T01:07:11Z

Kinoshita:

File:Outdata1-filter2-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:06:59Z

Kinoshita:

File:Outdata-filter2-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:06:47Z

Kinoshita:

File:Outdata1-H-mrcImageSpatialFrequencyFilter-FFT.png

2014-10-29T01:06:20Z

Kinoshita:

File:Outdata1-H-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:06:08Z

Kinoshita:

File:Outdata-H-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:05:56Z

Kinoshita:

File:Outdata-filter-mrcImageSpatialFrequencyFilter-FFT.png

2014-10-29T01:05:22Z

Kinoshita:

File:Outdata1-filter-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:05:11Z

Kinoshita:

File:Outdata-filter-mrcImageSpatialFrequencyFilter.png

2014-10-29T01:04:58Z

Kinoshita:

File:Input-1VOM.FNC.zip

2014-10-29T01:04:14Z

Kinoshita:

Input [[File:Input-1VOM-N.mrc]] 
use [[mrcImageFourierNeighborCorrelation]] 
c.f. Makefile in [[Tutorial List]]

File:Input-1VOM.FNC.zip

2014-10-29T01:01:54Z

Kinoshita:

File:Input-1VOM-N-FFT.png

2014-10-29T01:01:22Z

Kinoshita:

Input [[File:Input-1VOM-N.mrc]] 
use [[mrcImageFFT]] -> [[mrcFFTExpression]](m=1)

File:Input-1VOM-N-FFT.png

2014-10-29T01:00:29Z

Kinoshita:

mrcImageSpatialFrequencyFilter

2014-10-29T00:59:05Z

Kinoshita:

'''mrcImageSpatialFrequencyFilter''' is [[Eos]]'s [[Command]] that that filters depending on the weight for each set spatial frequency.

== 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]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-filter</td>
<td>Essential</td>
<td>Input: Filter file: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-filterCol</td>
<td>Optional</td>
<td>Filter Column: (R, W)</td>
<td>(1, 2)</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-L</td>
<td>Optional</td>
<td>LowCut: [/A]</td>
<td>-0.1</td>
</tr>
<tr>
<td>-H</td>
<td>Optional</td>
<td>HighCut: [/A]</td>
<td>1.0</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>
 

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
 

== Execution example ==
=== [[Media:Input-1VOM-N.mrc |Input file]]'s image ===
<table>
<tr>
<td>[[File:Input-1VOM-N.png]] 
xy-plane 
</td>
<td>[[File:Input1-1VOM-N.png]] 
yz-plane 
</td>
<td>[[File:Input-1VOM-N-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2390.42 (77, 14, 69) 
4374.62 (17, 62, 46) 
72.1487 
577.82 
0.722275 
</td>
</tr>
</table>
 

=== Example about -filter, -filterCol ===
[[:Media:Input-1VOM.FNC.zip|-filter 's file]](Create by using [[mrcImageFourierNeighborCorrelation]]) 
<pre>
0.000000 0.991796 1 FSC 9.519133 SNR -2.234766e+00 FNCF 0.887094 FNCN 0.921272 FSCfull 1.809870 Cref 1.345314 NoiseWeighted 1.345314
0.003906 0.982392 18 FSC 5.915698 SNR -2.406860e+00 FNCF 0.882438 FNCN 0.813045 FSCfull 1.710803 Cref 1.307977 NoiseWeighted 1.308476
0.007812 0.963411 62 FSC 3.088757 SNR -2.957507e+00 FNCF 0.864149 FNCN 0.779968 FSCfull 1.510854 Cref 1.229168 NoiseWeighted 1.231045
0.011719 0.934883 98 FSC 1.532664 SNR -5.754709e+00 FNCF 0.841882 FNCN 0.823140 FSCfull 1.210318 Cref 1.100144 NoiseWeighted 1.103928
0.015625 0.902410 210 FSC 0.767160 SNR 6.589575e+00 FNCF 0.843278 FNCN 0.833989 FSCfull 0.868240 Cref 0.931794 NoiseWeighted 0.937499

...

0.078125 0.874788 5034 FSC 0.405730 SNR 1.365474e+00 FNCF 0.918267 FNCN 0.805186 FSCfull 0.577252 Cref 0.759771 NoiseWeighted 0.885015
0.082031 0.881223 5714 FSC 0.476054 SNR 1.817189e+00 FNCF 0.920790 FNCN 0.818042 FSCfull 0.645036 Cref 0.803142 NoiseWeighted 0.950282
0.085938 0.887642 5982 FSC 0.553597 SNR 2.480260e+00 FNCF 0.918410 FNCN 0.819727 FSCfull 0.712665 Cref 0.844195 NoiseWeighted 1.015377
0.089844 0.888627 6602 FSC 0.566220 SNR 2.610627e+00 FNCF 0.914992 FNCN 0.811965 FSCfull 0.723040 Cref 0.850317 NoiseWeighted 1.040449
0.093750 0.887771 7130 FSC 0.555237 SNR 2.496775e+00 FNCF 0.913122 FNCN 0.820130 FSCfull 0.714022 Cref 0.844998 NoiseWeighted 1.052645
0.097656 0.892122 8034 FSC 0.612713 SNR 3.164125e+00 FNCF 0.914968 FNCN 0.817642 FSCfull 0.759854 Cref 0.871696 NoiseWeighted 1.106391
0.101562 0.896910 8606 FSC 0.681085 SNR 4.271264e+00 FNCF 0.915875 FNCN 0.815180 FSCfull 0.810292 Cref 0.900162 NoiseWeighted 1.164968
0.105469 0.889562 9066 FSC 0.578393 SNR 2.743754e+00 FNCF 0.913390 FNCN 0.816582 FSCfull 0.732888 Cref 0.856089 NoiseWeighted 1.130557
0.109375 0.879936 9962 FSC 0.461431 SNR 1.713548e+00 FNCF 0.915444 FNCN 0.824100 FSCfull 0.631479 Cref 0.794656 NoiseWeighted 1.071679
0.113281 0.873392 10550 FSC 0.391352 SNR 1.285974e+00 FNCF 0.917362 FNCN 0.826946 FSCfull 0.562550 Cref 0.750033 NoiseWeighted 1.033735

...

0.652344 0.820764 101724 FSC 0.004082 SNR 8.197289e-03 FNCF 0.914716 FNCN 0.819407 FSCfull 0.008131 Cref 0.090170 NoiseWeighted 3762.170730
0.656250 0.821992 98396 FSC 0.010648 SNR 2.152460e-02 FNCF 0.915023 FNCN 0.819700 FSCfull 0.021071 Cref 0.145159 NoiseWeighted 6882.065383
0.660156 0.820556 94632 FSC 0.002979 SNR 5.976104e-03 FNCF 0.915374 FNCN 0.820679 FSCfull 0.005941 Cref 0.077075 NoiseWeighted 4155.485366
0.664062 0.819228 90908 FSC -0.004008 SNR -7.984459e-03 FNCF 0.916605 FNCN 0.819217 FSCfull -0.008049 Cref 0.000000 NoiseWeighted 0.000000
0.667969 0.819197 86684 FSC -0.004168 SNR -8.302339e-03 FNCF 0.917529 FNCN 0.816882 FSCfull -0.008372 Cref 0.000000 NoiseWeighted 0.000000

...

0.847656 0.821916 392 FSC 0.010239 SNR 2.068939e-02 FNCF 0.910826 FNCN 0.841365 FSCfull 0.020270 Cref 0.142373 NoiseWeighted 0.000000
0.851562 0.765112 200 FSC -0.224245 SNR -3.663394e-01 FNCF 0.922496 FNCN 0.812100 FSCfull -0.578132 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.812369 72 FSC -0.038602 SNR -7.433483e-02 FNCF 0.958576 FNCN 0.817161 FSCfull -0.080304 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.777638 8 FSC -0.182399 SNR -3.085238e-01 FNCF 0.982674 FNCN 0.748480 FSCfull -0.446181 Cref 0.000000 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.811999 SNR -8.962464e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.638216 Cref 0.000000 NoiseWeighted 0.000000
</pre>
Because R is written at 1st column and Weight is written at 17th column, execute setting filterCol=(1, 17). 
 

==== Case: No other settings ====
You can also perform this command by using Makefile of [[Tutorial List#mrcImage]]. 
 
Setting 
<pre>
### For mrcImageSpatialFrequencyFilter
# -filterCol
FIL_COL_R=1
FIL_COL_W=17
# -H
FIL_H=
# -L
FIL_L=
</pre>
Command 
<pre>
make all
</pre>
 
<table>
<tr>
<td>[[File:Outdata-filter-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata-filter-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2.59766e+06 (8, 70, 17) 
2.64186e+06 (43, 75, 36) 
97.0626 
582169 
727.711 
</td>
</tr>
</table>
On default setting, weight is very large at high frequency component whose SN ratio is small. Therefore, the noise is emphasized and its shape is quite different to input file. 
 

==== Case: H=0.105469 ====
Execute the command setting the -H as R=0.105469. (FSC is more than 0.5, and SN ratio is about 3.) 
 
In the case of using Makefile, the following setting is required. 
<pre>
# -H
FIL_H=0.105469
</pre>
<table>
<tr>
<td>[[File:Outdata-H-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-H-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-H-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-178.789 (1, 26, 29) 
798.082 (42, 35, 41) 
97.0627 
149.022 
0.186278 
</td>
</tr>
</table>
The noise is reduced, and the frequency component which has large weight is emphasized. 
 

=== Example2 about -filter, -filterCol ===
filterCol makes possible to select reading columns in filter file, so you can filter to required components as the following. 
 
-filter 's file
<pre>
0 1 1 1 1 1 1 1 1 1 1 1
.100000 0 1 1 1 1 1 1 1 1 1 1
.200000 0 0 1 1 1 1 1 1 1 1 1
.300000 0 0 0 1 1 1 1 1 1 1 1
.400000 0 0 0 0 1 1 1 1 1 1 1
.500000 0 0 0 0 0 1 1 1 1 1 1
.600000 0 0 0 0 0 0 1 1 1 1 1
.700000 0 0 0 0 0 0 0 1 1 1 1
.800000 0 0 0 0 0 0 0 0 1 1 1
.900000 0 0 0 0 0 0 0 0 0 1 1
1.000000 0 0 0 0 0 0 0 0 0 0 1

</pre>
 

==== Case: No other settings ====
In the case of using Makefile, the following setting and command are required. 
Setting 
<pre>
# -filterCol
FIL_COL_R=
FIL_COL_W=
</pre>
Command 
<pre>
make all2
</pre>
<table>
<tr>
<td>[[File:Outdata-filter2-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter2-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-filter2-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-40.3107 (57, 52, 16) 
425.495 (29, 46, 54) 
72.1487 
110.072 
0.13759 
</td>
</tr>
</table>
-filterCol is set as R=1, W=2 by default setting. 
 

==== Case: filterCol=(1, 3) ====
In the case of using Makefile, the following setting is required. 
<pre>
# -filterCol
FIL_COL_R=1
FIL_COL_W=3
</pre>
<table>
<tr>
<td>[[File:Outdata-filterCol-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-259.771 (3, 53, 13) 
1001.51 (43, 71, 44) 
72.1487 
168.798 
0.210998 
</td>
</tr>
</table>
 

=== Example3 about -filter, -filterCol ===
Use the filter file whose weight is calculated by using R. 
 
-filter のfile
<pre>
0 1 1 1 1 1 1 1 1 1 1 1
.100000 .900000 .810000 .729000 .656100 .590490 .531441 .478296 .430466 .387419 .348677 .313809
.200000 .800000 .640000 .512000 .409600 .327680 .262144 .209715 .167772 .134217 .107373 .085898
.300000 .700000 .490000 .343000 .240100 .168070 .117649 .082354 .057647 .040352 .028246 .019772
.400000 .600000 .360000 .216000 .129600 .077760 .046656 .027993 .016795 .010077 .006046 .003627
.500000 .500000 .250000 .125000 .062500 .031250 .015625 .007812 .003906 .001953 .000976 .000488
.600000 .400000 .160000 .064000 .025600 .010240 .004096 .001638 .000655 .000262 .000104 .000041
.700000 .300000 .090000 .027000 .008100 .002430 .000729 .000218 .000065 .000019 .000005 .000001
.800000 .200000 .040000 .008000 .001600 .000320 .000064 .000012 .000002 0 0 0
.900000 .100000 .010000 .001000 .000100 .000010 .000001 0 0 0 0 0
1.000000 0 0 0 0 0 0 0 0 0 0 0
</pre>
Weight in this file is calculated as W=(1-R)^n: (n=column).
 

==== Case: No other settings ====
In the case of using Makefile, the following setting and command are required. 
Setting 
<pre>
# -filterCol
FIL_COL_R=
FIL_COL_W=
</pre>
Command 
<pre>
make all3
</pre>
<table>
<tr>
<td>[[File:Outdata-filter3-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter3-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata2-filter3-mrcImageSpatialFrequencyFilter.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-1268.05 (77, 14, 69) 
2769.86 (17, 62, 45) 
72.1487 
352.17 
0.440212 
</td>
</tr>
</table>
-filterCol is set as R=1, W=2 by default setting. 
 

==== Case: filterCol=(1, 3) ====
In the case of using Makefile, the following setting is required. 
<pre>
# -filterCol
FIL_COL_R=1
FIL_COL_W=3
</pre>
<table>
<tr>
<td>[[File:Outdata-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata2-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-721.031 (77, 14, 69) 
2011.1 (17, 62, 45) 
72.1487 
252.314 
0.315393 
</td>
</tr>
</table>

mrcImageSpatialFrequencyFilter

2014-10-29T00:52:35Z

Kinoshita:

'''mrcImageSpatialFrequencyFilter''' is [[Eos]]'s [[Command]] that that filters depending on the weight for each set spatial frequency.

== 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]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-filter</td>
<td>Essential</td>
<td>Input: Filter file: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-filterCol</td>
<td>Optional</td>
<td>Filter Column: (R, W)</td>
<td>(1, 2)</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-L</td>
<td>Optional</td>
<td>LowCut: [/A]</td>
<td>-0.1</td>
</tr>
<tr>
<td>-H</td>
<td>Optional</td>
<td>HighCut: [/A]</td>
<td>1.0</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>
 

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
 

== Execution example ==
=== [[Media:Input-1VOM-N.mrc |Input file]]'s image ===
<table>
<tr>
<td>[[File:Input-1VOM-N.png]] 
xy-plane 
</td>
<td>[[File:Input1-1VOM-N.png]] 
yz-plane 
</td>
<td>[[File:Input-1VOM-N-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2390.42 (77, 14, 69) 
4374.62 (17, 62, 46) 
72.1487 
577.82 
0.722275 
</td>
</tr>
</table>
 

=== Example about -filter, -filterCol ===
[[:Media:Input-1VOM.FNC.zip|-filter 's file]](Create by using [[mrcImageFourierNeighborCorrelation]]) 
<pre>
0.000000 0.991796 1 FSC 9.519133 SNR -2.234766e+00 FNCF 0.887094 FNCN 0.921272 FSCfull 1.809870 Cref 1.345314 NoiseWeighted 1.345314
0.003906 0.982392 18 FSC 5.915698 SNR -2.406860e+00 FNCF 0.882438 FNCN 0.813045 FSCfull 1.710803 Cref 1.307977 NoiseWeighted 1.308476
0.007812 0.963411 62 FSC 3.088757 SNR -2.957507e+00 FNCF 0.864149 FNCN 0.779968 FSCfull 1.510854 Cref 1.229168 NoiseWeighted 1.231045
0.011719 0.934883 98 FSC 1.532664 SNR -5.754709e+00 FNCF 0.841882 FNCN 0.823140 FSCfull 1.210318 Cref 1.100144 NoiseWeighted 1.103928
0.015625 0.902410 210 FSC 0.767160 SNR 6.589575e+00 FNCF 0.843278 FNCN 0.833989 FSCfull 0.868240 Cref 0.931794 NoiseWeighted 0.937499

...

0.078125 0.874788 5034 FSC 0.405730 SNR 1.365474e+00 FNCF 0.918267 FNCN 0.805186 FSCfull 0.577252 Cref 0.759771 NoiseWeighted 0.885015
0.082031 0.881223 5714 FSC 0.476054 SNR 1.817189e+00 FNCF 0.920790 FNCN 0.818042 FSCfull 0.645036 Cref 0.803142 NoiseWeighted 0.950282
0.085938 0.887642 5982 FSC 0.553597 SNR 2.480260e+00 FNCF 0.918410 FNCN 0.819727 FSCfull 0.712665 Cref 0.844195 NoiseWeighted 1.015377
0.089844 0.888627 6602 FSC 0.566220 SNR 2.610627e+00 FNCF 0.914992 FNCN 0.811965 FSCfull 0.723040 Cref 0.850317 NoiseWeighted 1.040449
0.093750 0.887771 7130 FSC 0.555237 SNR 2.496775e+00 FNCF 0.913122 FNCN 0.820130 FSCfull 0.714022 Cref 0.844998 NoiseWeighted 1.052645
0.097656 0.892122 8034 FSC 0.612713 SNR 3.164125e+00 FNCF 0.914968 FNCN 0.817642 FSCfull 0.759854 Cref 0.871696 NoiseWeighted 1.106391
0.101562 0.896910 8606 FSC 0.681085 SNR 4.271264e+00 FNCF 0.915875 FNCN 0.815180 FSCfull 0.810292 Cref 0.900162 NoiseWeighted 1.164968
0.105469 0.889562 9066 FSC 0.578393 SNR 2.743754e+00 FNCF 0.913390 FNCN 0.816582 FSCfull 0.732888 Cref 0.856089 NoiseWeighted 1.130557
0.109375 0.879936 9962 FSC 0.461431 SNR 1.713548e+00 FNCF 0.915444 FNCN 0.824100 FSCfull 0.631479 Cref 0.794656 NoiseWeighted 1.071679
0.113281 0.873392 10550 FSC 0.391352 SNR 1.285974e+00 FNCF 0.917362 FNCN 0.826946 FSCfull 0.562550 Cref 0.750033 NoiseWeighted 1.033735

...

0.652344 0.820764 101724 FSC 0.004082 SNR 8.197289e-03 FNCF 0.914716 FNCN 0.819407 FSCfull 0.008131 Cref 0.090170 NoiseWeighted 3762.170730
0.656250 0.821992 98396 FSC 0.010648 SNR 2.152460e-02 FNCF 0.915023 FNCN 0.819700 FSCfull 0.021071 Cref 0.145159 NoiseWeighted 6882.065383
0.660156 0.820556 94632 FSC 0.002979 SNR 5.976104e-03 FNCF 0.915374 FNCN 0.820679 FSCfull 0.005941 Cref 0.077075 NoiseWeighted 4155.485366
0.664062 0.819228 90908 FSC -0.004008 SNR -7.984459e-03 FNCF 0.916605 FNCN 0.819217 FSCfull -0.008049 Cref 0.000000 NoiseWeighted 0.000000
0.667969 0.819197 86684 FSC -0.004168 SNR -8.302339e-03 FNCF 0.917529 FNCN 0.816882 FSCfull -0.008372 Cref 0.000000 NoiseWeighted 0.000000

...

0.847656 0.821916 392 FSC 0.010239 SNR 2.068939e-02 FNCF 0.910826 FNCN 0.841365 FSCfull 0.020270 Cref 0.142373 NoiseWeighted 0.000000
0.851562 0.765112 200 FSC -0.224245 SNR -3.663394e-01 FNCF 0.922496 FNCN 0.812100 FSCfull -0.578132 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.812369 72 FSC -0.038602 SNR -7.433483e-02 FNCF 0.958576 FNCN 0.817161 FSCfull -0.080304 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.777638 8 FSC -0.182399 SNR -3.085238e-01 FNCF 0.982674 FNCN 0.748480 FSCfull -0.446181 Cref 0.000000 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.811999 SNR -8.962464e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.638216 Cref 0.000000 NoiseWeighted 0.000000
</pre>
Because R is written at 1st column and Weight is written at 17th column, execute setting filterCol=(1, 17). 
 

==== Case: No other settings ====
You can also perform this command by using Makefile of [[Tutorial List#mrcImage]]. 
 
Setting 
<pre>
### For mrcImageSpatialFrequencyFilter
# -filterCol
FIL_COL_R=1
FIL_COL_W=17
# -H
FIL_H=
# -L
FIL_L=
</pre>
Command 
<pre>
make all
</pre>
 
<table>
<tr>
<td>[[File:Outdata-filter-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata-filter-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2.59766e+06 (8, 70, 17) 
2.64186e+06 (43, 75, 36) 
97.0626 
582169 
727.711 
</td>
</tr>
</table>
On default setting, weight is very large at high frequency component whose SN ratio is small. Therefore, the noise is emphasized and its shape is quite different to input file. 
 

==== Case: H=0.105469 ====
Execute the command setting the -H as R=0.105469. (FSC is more than 0.5, and SN ratio is about 3.) 
 
In the case of using Makefile, the following setting is required. 
<pre>
# -H
FIL_H=0.105469
</pre>
<table>
<tr>
<td>[[File:Outdata-H-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-H-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-H-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-178.789 (1, 26, 29) 
798.082 (42, 35, 41) 
97.0627 
149.022 
0.186278 
</td>
</tr>
</table>
The noise is reduced, and the frequency component which has large weight is emphasized. 
 

=== Example2 about -filter, -filterCol ===
filterCol makes possible to select reading columns in filter file, so you can filter to required components as the following. 
 
-filter 's file
<pre>
0 1 1 1 1 1 1 1 1 1 1 1
.100000 0 1 1 1 1 1 1 1 1 1 1
.200000 0 0 1 1 1 1 1 1 1 1 1
.300000 0 0 0 1 1 1 1 1 1 1 1
.400000 0 0 0 0 1 1 1 1 1 1 1
.500000 0 0 0 0 0 1 1 1 1 1 1
.600000 0 0 0 0 0 0 1 1 1 1 1
.700000 0 0 0 0 0 0 0 1 1 1 1
.800000 0 0 0 0 0 0 0 0 1 1 1
.900000 0 0 0 0 0 0 0 0 0 1 1
1.000000 0 0 0 0 0 0 0 0 0 0 1

</pre>
 

==== Case: No other settings ====
In the case of using Makefile, the following setting and command are required. 
Setting 
<pre>
# -filterCol
FIL_COL_R=
FIL_COL_W=
</pre>
Command 
<pre>
make all2
</pre>
<table>
<tr>
<td>[[File:Outdata-filter2-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter2-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-filter2-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-40.3107 (57, 52, 16) 
425.495 (29, 46, 54) 
72.1487 
110.072 
0.13759 
</td>
</tr>
</table>
-filterCol is set as R=1, W=2 by default setting. 
 

==== Case: filterCol=(1, 3) ====
In the case of using Makefile, the following setting is required. 
<pre>
# -filterCol
FIL_COL_R=1
FIL_COL_W=3
</pre>
<table>
<tr>
<td>[[File:Outdata-filterCol-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-259.771 (3, 53, 13) 
1001.51 (43, 71, 44) 
72.1487 
168.798 
0.210998 
</td>
</tr>
</table>
 

=== Example3 about -filter, -filterCol ===
Rに応じた重みを計算したFilterfileで実行する. 
 
-filter のfile
<pre>
0 1 1 1 1 1 1 1 1 1 1 1
.100000 .900000 .810000 .729000 .656100 .590490 .531441 .478296 .430466 .387419 .348677 .313809
.200000 .800000 .640000 .512000 .409600 .327680 .262144 .209715 .167772 .134217 .107373 .085898
.300000 .700000 .490000 .343000 .240100 .168070 .117649 .082354 .057647 .040352 .028246 .019772
.400000 .600000 .360000 .216000 .129600 .077760 .046656 .027993 .016795 .010077 .006046 .003627
.500000 .500000 .250000 .125000 .062500 .031250 .015625 .007812 .003906 .001953 .000976 .000488
.600000 .400000 .160000 .064000 .025600 .010240 .004096 .001638 .000655 .000262 .000104 .000041
.700000 .300000 .090000 .027000 .008100 .002430 .000729 .000218 .000065 .000019 .000005 .000001
.800000 .200000 .040000 .008000 .001600 .000320 .000064 .000012 .000002 0 0 0
.900000 .100000 .010000 .001000 .000100 .000010 .000001 0 0 0 0 0
1.000000 0 0 0 0 0 0 0 0 0 0 0
</pre>
このfileの重みはW=(1-R)^n: (n=列)で算出している.
 

==== その他Optionなしで実行 ====
下記のSettingとCommandにより,Makefileからでも実行できる. 
Setting 
<pre>
# -filterCol
FIL_COL_R=
FIL_COL_W=
</pre>
Command 
<pre>
make all3
</pre>
<table>
<tr>
<td>[[File:Outdata-filter3-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter3-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata2-filter3-mrcImageSpatialFrequencyFilter.png]] 
FFT画像 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-1268.05 (77, 14, 69) 
2769.86 (17, 62, 45) 
72.1487 
352.17 
0.440212 
</td>
</tr>
</table>
-filterColはデフォルトではR=1, W=2として実行される. 
 

==== filterCol=(1, 3)で実行 ====
Makefileを使用する場合は下記のSetting変更を行うと実行できる. 
<pre>
# -filterCol
FIL_COL_R=1
FIL_COL_W=3
</pre>
<table>
<tr>
<td>[[File:Outdata-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata2-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
FFT画像 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-721.031 (77, 14, 69) 
2011.1 (17, 62, 45) 
72.1487 
252.314 
0.315393 
</td>
</tr>
</table>

mrcImageSpatialFrequencyFilter

2014-10-29T00:25:15Z

Kinoshita: /* Execution example */

'''mrcImageSpatialFrequencyFilter''' is [[Eos]]'s [[Command]] that that filters depending on the weight for each set spatial frequency.

== 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]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-filter</td>
<td>Essential</td>
<td>Input: Filter file: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-filterCol</td>
<td>Optional</td>
<td>Filter Column: (R, W)</td>
<td>(1, 2)</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-L</td>
<td>Optional</td>
<td>LowCut: [/A]</td>
<td>-0.1</td>
</tr>
<tr>
<td>-H</td>
<td>Optional</td>
<td>HighCut: [/A]</td>
<td>1.0</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>
 

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
 

== Execution example ==
=== [[Media:Input-1VOM-N.mrc |Input file]]'s image ===
<table>
<tr>
<td>[[File:Input-1VOM-N.png]] 
xy-plane 
</td>
<td>[[File:Input1-1VOM-N.png]] 
yz-plane 
</td>
<td>[[File:Input-1VOM-N-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2390.42 (77, 14, 69) 
4374.62 (17, 62, 46) 
72.1487 
577.82 
0.722275 
</td>
</tr>
</table>
 

=== Example about -filter, -filterCol ===
[[:Media:Input-1VOM.FNC.zip|-filter 's file]](Create by using [[mrcImageFourierNeighborCorrelation]]) 
<pre>
0.000000 0.991796 1 FSC 9.519133 SNR -2.234766e+00 FNCF 0.887094 FNCN 0.921272 FSCfull 1.809870 Cref 1.345314 NoiseWeighted 1.345314
0.003906 0.982392 18 FSC 5.915698 SNR -2.406860e+00 FNCF 0.882438 FNCN 0.813045 FSCfull 1.710803 Cref 1.307977 NoiseWeighted 1.308476
0.007812 0.963411 62 FSC 3.088757 SNR -2.957507e+00 FNCF 0.864149 FNCN 0.779968 FSCfull 1.510854 Cref 1.229168 NoiseWeighted 1.231045
0.011719 0.934883 98 FSC 1.532664 SNR -5.754709e+00 FNCF 0.841882 FNCN 0.823140 FSCfull 1.210318 Cref 1.100144 NoiseWeighted 1.103928
0.015625 0.902410 210 FSC 0.767160 SNR 6.589575e+00 FNCF 0.843278 FNCN 0.833989 FSCfull 0.868240 Cref 0.931794 NoiseWeighted 0.937499

...

0.078125 0.874788 5034 FSC 0.405730 SNR 1.365474e+00 FNCF 0.918267 FNCN 0.805186 FSCfull 0.577252 Cref 0.759771 NoiseWeighted 0.885015
0.082031 0.881223 5714 FSC 0.476054 SNR 1.817189e+00 FNCF 0.920790 FNCN 0.818042 FSCfull 0.645036 Cref 0.803142 NoiseWeighted 0.950282
0.085938 0.887642 5982 FSC 0.553597 SNR 2.480260e+00 FNCF 0.918410 FNCN 0.819727 FSCfull 0.712665 Cref 0.844195 NoiseWeighted 1.015377
0.089844 0.888627 6602 FSC 0.566220 SNR 2.610627e+00 FNCF 0.914992 FNCN 0.811965 FSCfull 0.723040 Cref 0.850317 NoiseWeighted 1.040449
0.093750 0.887771 7130 FSC 0.555237 SNR 2.496775e+00 FNCF 0.913122 FNCN 0.820130 FSCfull 0.714022 Cref 0.844998 NoiseWeighted 1.052645
0.097656 0.892122 8034 FSC 0.612713 SNR 3.164125e+00 FNCF 0.914968 FNCN 0.817642 FSCfull 0.759854 Cref 0.871696 NoiseWeighted 1.106391
0.101562 0.896910 8606 FSC 0.681085 SNR 4.271264e+00 FNCF 0.915875 FNCN 0.815180 FSCfull 0.810292 Cref 0.900162 NoiseWeighted 1.164968
0.105469 0.889562 9066 FSC 0.578393 SNR 2.743754e+00 FNCF 0.913390 FNCN 0.816582 FSCfull 0.732888 Cref 0.856089 NoiseWeighted 1.130557
0.109375 0.879936 9962 FSC 0.461431 SNR 1.713548e+00 FNCF 0.915444 FNCN 0.824100 FSCfull 0.631479 Cref 0.794656 NoiseWeighted 1.071679
0.113281 0.873392 10550 FSC 0.391352 SNR 1.285974e+00 FNCF 0.917362 FNCN 0.826946 FSCfull 0.562550 Cref 0.750033 NoiseWeighted 1.033735

...

0.652344 0.820764 101724 FSC 0.004082 SNR 8.197289e-03 FNCF 0.914716 FNCN 0.819407 FSCfull 0.008131 Cref 0.090170 NoiseWeighted 3762.170730
0.656250 0.821992 98396 FSC 0.010648 SNR 2.152460e-02 FNCF 0.915023 FNCN 0.819700 FSCfull 0.021071 Cref 0.145159 NoiseWeighted 6882.065383
0.660156 0.820556 94632 FSC 0.002979 SNR 5.976104e-03 FNCF 0.915374 FNCN 0.820679 FSCfull 0.005941 Cref 0.077075 NoiseWeighted 4155.485366
0.664062 0.819228 90908 FSC -0.004008 SNR -7.984459e-03 FNCF 0.916605 FNCN 0.819217 FSCfull -0.008049 Cref 0.000000 NoiseWeighted 0.000000
0.667969 0.819197 86684 FSC -0.004168 SNR -8.302339e-03 FNCF 0.917529 FNCN 0.816882 FSCfull -0.008372 Cref 0.000000 NoiseWeighted 0.000000

...

0.847656 0.821916 392 FSC 0.010239 SNR 2.068939e-02 FNCF 0.910826 FNCN 0.841365 FSCfull 0.020270 Cref 0.142373 NoiseWeighted 0.000000
0.851562 0.765112 200 FSC -0.224245 SNR -3.663394e-01 FNCF 0.922496 FNCN 0.812100 FSCfull -0.578132 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.812369 72 FSC -0.038602 SNR -7.433483e-02 FNCF 0.958576 FNCN 0.817161 FSCfull -0.080304 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.777638 8 FSC -0.182399 SNR -3.085238e-01 FNCF 0.982674 FNCN 0.748480 FSCfull -0.446181 Cref 0.000000 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.811999 SNR -8.962464e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.638216 Cref 0.000000 NoiseWeighted 0.000000
</pre>
Because R is written at 1st column and Weight is written at 17th column, execute setting filterCol=(1, 17). 
 

==== Case: No other settings ====
You can also perform this command by using Makefile of [[Tutorial List#mrcImage]]. 
 
Setting 
<pre>
### For mrcImageSpatialFrequencyFilter
# -filterCol
FIL_COL_R=1
FIL_COL_W=17
# -H
FIL_H=
# -L
FIL_L=
</pre>
Command 
<pre>
make all
</pre>
 
<table>
<tr>
<td>[[File:Outdata-filter-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata-filter-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2.59766e+06 (8, 70, 17) 
2.64186e+06 (43, 75, 36) 
97.0626 
582169 
727.711 
</td>
</tr>
</table>
On default setting, weight is very large at high frequency component whose SN ratio is small. Therefore, the noise is emphasized and its shape is quite different to input file. 
 

==== Case: H=0.105469 ====
Filterfileにおいて,FSCが0.5を上回りSN比が3であるR=0.105469を基準にして実行する. 
 
Makefileを使用する場合は下記のSettingを変更すると実行できる. 
<pre>
# -H
FIL_H=0.105469
</pre>
<table>
<tr>
<td>[[File:Outdata-H-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-H-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-H-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT画像 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-178.789 (1, 26, 29) 
798.082 (42, 35, 41) 
97.0627 
149.022 
0.186278 
</td>
</tr>
</table>
Input fileに対して周辺のNoiseが軽減され,重みの大きいFrequency成分が強調される. 
 

=== -filter, -filterCol の実行Example2 ===
FilterfileはfilterColを元に読み出し列を決めることができるので,下記のように好きな成分にFilterを掛けることができる. 
 
-filter のfile
<pre>
0 1 1 1 1 1 1 1 1 1 1 1
.100000 0 1 1 1 1 1 1 1 1 1 1
.200000 0 0 1 1 1 1 1 1 1 1 1
.300000 0 0 0 1 1 1 1 1 1 1 1
.400000 0 0 0 0 1 1 1 1 1 1 1
.500000 0 0 0 0 0 1 1 1 1 1 1
.600000 0 0 0 0 0 0 1 1 1 1 1
.700000 0 0 0 0 0 0 0 1 1 1 1
.800000 0 0 0 0 0 0 0 0 1 1 1
.900000 0 0 0 0 0 0 0 0 0 1 1
1.000000 0 0 0 0 0 0 0 0 0 0 1

</pre>
 

==== その他Optionなしで実行 ====
下記のSettingとCommandにより,Makefileからでも実行できる. 
Setting 
<pre>
# -filterCol
FIL_COL_R=
FIL_COL_W=
</pre>
Command 
<pre>
make all2
</pre>
<table>
<tr>
<td>[[File:Outdata-filter2-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter2-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-filter2-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT画像 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-40.3107 (57, 52, 16) 
425.495 (29, 46, 54) 
72.1487 
110.072 
0.13759 
</td>
</tr>
</table>
-filterColはデフォルトではR=1, W=2として実行される. 
 

==== filterCol=(1, 3)で実行 ====
Makefileを使用する場合は下記のSetting変更を行うと実行できる. 
<pre>
# -filterCol
FIL_COL_R=1
FIL_COL_W=3
</pre>
<table>
<tr>
<td>[[File:Outdata-filterCol-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata1-filterCol-mrcImageSpatialFrequencyFilter-FFT.png]] 
FFT画像 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-259.771 (3, 53, 13) 
1001.51 (43, 71, 44) 
72.1487 
168.798 
0.210998 
</td>
</tr>
</table>
 

=== -filter, -filterCol の実行Example3 ===
Rに応じた重みを計算したFilterfileで実行する. 
 
-filter のfile
<pre>
0 1 1 1 1 1 1 1 1 1 1 1
.100000 .900000 .810000 .729000 .656100 .590490 .531441 .478296 .430466 .387419 .348677 .313809
.200000 .800000 .640000 .512000 .409600 .327680 .262144 .209715 .167772 .134217 .107373 .085898
.300000 .700000 .490000 .343000 .240100 .168070 .117649 .082354 .057647 .040352 .028246 .019772
.400000 .600000 .360000 .216000 .129600 .077760 .046656 .027993 .016795 .010077 .006046 .003627
.500000 .500000 .250000 .125000 .062500 .031250 .015625 .007812 .003906 .001953 .000976 .000488
.600000 .400000 .160000 .064000 .025600 .010240 .004096 .001638 .000655 .000262 .000104 .000041
.700000 .300000 .090000 .027000 .008100 .002430 .000729 .000218 .000065 .000019 .000005 .000001
.800000 .200000 .040000 .008000 .001600 .000320 .000064 .000012 .000002 0 0 0
.900000 .100000 .010000 .001000 .000100 .000010 .000001 0 0 0 0 0
1.000000 0 0 0 0 0 0 0 0 0 0 0
</pre>
このfileの重みはW=(1-R)^n: (n=列)で算出している.
 

==== その他Optionなしで実行 ====
下記のSettingとCommandにより,Makefileからでも実行できる. 
Setting 
<pre>
# -filterCol
FIL_COL_R=
FIL_COL_W=
</pre>
Command 
<pre>
make all3
</pre>
<table>
<tr>
<td>[[File:Outdata-filter3-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filter3-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata2-filter3-mrcImageSpatialFrequencyFilter.png]] 
FFT画像 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-1268.05 (77, 14, 69) 
2769.86 (17, 62, 45) 
72.1487 
352.17 
0.440212 
</td>
</tr>
</table>
-filterColはデフォルトではR=1, W=2として実行される. 
 

==== filterCol=(1, 3)で実行 ====
Makefileを使用する場合は下記のSetting変更を行うと実行できる. 
<pre>
# -filterCol
FIL_COL_R=1
FIL_COL_W=3
</pre>
<table>
<tr>
<td>[[File:Outdata-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
xy-plane 
</td>
<td>[[File:Outdata1-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
yz-plane 
</td>
<td>[[File:Outdata2-filterCol3-mrcImageSpatialFrequencyFilter.png]] 
FFT画像 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-721.031 (77, 14, 69) 
2011.1 (17, 62, 45) 
72.1487 
252.314 
0.315393 
</td>
</tr>
</table>

mrcImageFourierNeighborCorrelation

2014-10-28T09:04:19Z

Kinoshita:

'''mrcImageFourierNeighborCorrelation''' is [[Eos]]'s [[Command]] to check a resolution by utilizing the redundancy of [[Fourier Space]].

== 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]](3D)</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[ASCII]]([[FNC]])</td>
<td>stdout</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>delta on [[Fourier Space]]</td>
<td>0.0</td>
</tr>
<tr>
<td>-C</td>
<td>Optional</td>
<td>CentreMode</td>
<td>0</td>
</tr>
<tr>
<td>-M</td>
<td>Optional</td>
<td>[[Interpolation Mode]]</td>
<td>0</td>
</tr>
<tr>
<td>-FSC</td>
<td>Optional</td>
<td>Output flag of predicted [[FSC]]</td>
<td></td>
</tr>
<tr>
<td>-Cref</td>
<td>Optional</td>
<td>Output flag of Cref</td>
<td></td>
</tr>
<tr>
<td>-FSCfull</td>
<td>Optional</td>
<td>Output flag of [[FSC]] full</td>
<td></td>
</tr>
<tr>
<td>-NoiseWeighted</td>
<td>Optional</td>
<td>NoiseWeighted: Cref*exp(-Brestore/(4*d^2)</td>
<td>-100.0</td>
</tr>
<tr>
<td>-mask</td>
<td>Optional</td>
<td>Input: [[mrcImage]](3D)(Mask for [[FSC]])</td>
<td>NULL</td>
</tr>
<tr>
<td>-maskBack</td>
<td>Optional</td>
<td>Input: [[mrcImage]](3D)(Mask for [[FSC]] Back)</td>
<td>NULL</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>
 

=== -mask details ===
Use the binary file as same shape as -i file. 
 
(Example) 
First, Get Low-frequency component of -i file by using [[mrcImageLowPassFilter]]. 
Next, binarize it by using [[mrcImageBinalization]](m=32). 
 

=== -maskBack details ===
Use the file. (The size is same as -i file, and the all value is 1) 
In addition, In addition, multiply the same windowing as -i file. 
 
(Example) 
First, get size of -i file by using [[mrcInfo]]. 
Next, create the image whose value of all is 1, by using [[mrcImageNullImageCreate]](v=1). 
Finally, multiply the same windowing by using [[mrcImageWindowing]]. 
 

=== -C details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Centre is ImageCentre Shift: (Nx/2.0, Ny/2.0, Nz/2.0 )</td>
</tr>
<tr>
<td>1</td>
<td>Centre is BottomLeft Shift: (0, 0, 0 )</td>
</tr>
<tr>
<td>2</td>
<td>Use StartN Shift: (StartNx,StartNy,StartNz)</td>
</tr>
</table>
 

=== -M details ===
c.f. [[Interpolation Mode]]

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
 

== Execution example ==
===[[Media:Input-1VOM-N.mrc|Input file]] image===
<table>
<tr>
<td>[[File:Input-1VOM-N.png]] 
xy-plane 
</td>
<td>[[File:Input1-1VOM-N.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2390.42 (77, 14, 69) 
4374.62 (17, 62, 46) 
72.1487 
577.82 
0.722275 
</td>
</tr>
</table>
 

<pre>
0.000000 0.863711 1
0.012500 0.553876 18
0.025000 0.170684 64
0.037500 0.221808 146
0.050000 0.230874 266
0.062500 0.280359 382
0.075000 0.269777 588
0.087500 0.280955 746
0.100000 0.322332 1002
0.112500 0.249747 1294

...

0.750000 -0.005313 2256
0.762500 0.036957 1688
0.775000 0.021723 1264
0.787500 0.010364 864
0.800000 -0.026498 568
0.812500 -0.009259 312
0.825000 -0.009356 144
0.837500 0.030291 72
0.850000 -0.109028 8
0.862500 0.000000 0
</pre>
 

[[File:Outdata-mrcImageFourierNeighborCorrelation.png]] 
Because this image does not have redundancy at all, the FNC decreases suddenly. 
 

=== Input file(Padding) ===
Padding of the above file by 0 adds redundancy to the image. 
This file can be created by [[Tutorial List#mrcImage]]. 
<table>
<tr>
<td>[[File:Input-1VOM-N-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-1VOM-N-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2390.42 (165, 102, 147) 
4374.62 (105, 150, 124) 
2.75226 
113.698 
0.0277584 
</td>
</tr>
</table>
 

Output 
<pre>
0.000000 0.991796 1
0.003906 0.982392 18
0.007812 0.963411 62
0.011719 0.934883 98
0.015625 0.902410 210
0.019531 0.864067 350
0.023438 0.841587 450
0.027344 0.856990 602
0.031250 0.887424 762
0.035156 0.887318 1142

...

0.828125 0.811470 1320
0.832031 0.812934 1352
0.835938 0.823354 1152
0.839844 0.817772 800
0.843750 0.824257 288
0.847656 0.821916 392
0.851562 0.765112 200
0.855469 0.812369 72
0.859375 0.777638 8
0.863281 0.000000 0
</pre>
 
[[File:Outdata1-mrcImageFourierNeighborCorrelation.png]] 
In the case of an image which has redundancy, FNC on high frequency area is also the high value. 
 

==== Option -d ====
===== Case: d=0.025 =====
<pre>
0.000000 0.961060 147
0.025000 0.884961 3596
0.050000 0.876699 13334
0.075000 0.884583 30012
0.100000 0.888691 53048
0.125000 0.873868 82634
0.150000 0.860938 118688
0.175000 0.862499 161322
0.200000 0.875542 211496
0.225000 0.882194 266468
0.250000 0.874374 330126
0.275000 0.868385 398912
0.300000 0.861123 473858
0.325000 0.852294 557496
0.350000 0.846181 647132
0.375000 0.842054 739454
0.400000 0.836904 845340
0.425000 0.836800 950870
0.450000 0.834607 1068284
0.475000 0.831828 1190048
0.500000 0.829300 1284690
0.525000 0.827369 1227836
0.550000 0.824926 1141760
0.575000 0.824884 1043124
0.600000 0.823838 930008
0.625000 0.822523 803708
0.650000 0.821119 663864
0.675000 0.820229 512012
0.700000 0.819524 348596
0.725000 0.818723 217808
0.750000 0.820472 135048
0.775000 0.825089 77288
0.800000 0.815167 38120
0.825000 0.816419 13488
0.850000 0.814605 1760

</pre>
 

[[File:Outdata-d-mrcImageFourierNeighborCorrelation.png]] 
 

==== Case: using -FSC and specifying files as -mask, -maskBack ====
-mask 's file: This file can be created by [[Tutorial List#mrcImage]]. 
 
Setting of Makefile 
<pre>
MASK_VALUE=0.0125
</pre>
<table>
<tr>
<td>[[File:Input-Noise1-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-Noise1-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (111, 135, 84) 
0.0158784 
0.125005 
3.05189e-05 
</td>
</tr>
</table>
 

-maskBack 's file: This file can be created by [[Tutorial List#mrcImage]]. 
<table>
<tr>
<td>[[File:Input-Null1-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-Null1-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1 (0, 0, 0) 
1 (88, 88, 78) 
0.038147 
0.191551 
4.67654e-05 
</td>
</tr>
</table>
 

Output 
<pre>
FNCF 0.894073 FNCN 0.820233
0.000000 0.991796 1 FSC -7.183377 SNR -1.755602e+00 FNCF 0.951711 FNCN -0.366379
0.003906 0.982392 18 FSC -11.199417 SNR -1.836058e+00 FNCF 0.903913 FNCN 0.595703
0.007812 0.963411 62 FSC 31.808857 SNR -2.064916e+00 FNCF 0.844130 FNCN 0.798653
0.011719 0.934883 98 FSC 3.471075 SNR -2.809364e+00 FNCF 0.845211 FNCN 0.799688
0.015625 0.902410 210 FSC 1.254576 SNR -9.856209e+00 FNCF 0.886035 FNCN 0.734901
0.019531 0.864067 350 FSC 0.422099 SNR 1.460802e+00 FNCF 0.893608 FNCN 0.787841
0.023438 0.841587 450 FSC 0.169033 SNR 4.068355e-01 FNCF 0.889512 FNCN 0.827210
0.027344 0.856990 602 FSC 0.331378 SNR 9.912261e-01 FNCF 0.873868 FNCN 0.811905
0.031250 0.887424 762 FSC 0.834791 SNR 1.010589e+01 FNCF 0.889606 FNCN 0.818398
0.035156 0.887318 1142 FSC 0.832380 SNR 9.931723e+00 FNCF 0.897804 FNCN 0.824152
0.039062 0.879608 1250 FSC 0.672387 SNR 4.104771e+00 FNCF 0.894009 FNCN 0.803585
0.042969 0.874892 1458 FSC 0.587592 SNR 2.849572e+00 FNCF 0.887004 FNCN 0.803368
0.046875 0.874435 1814 FSC 0.579834 SNR 2.760026e+00 FNCF 0.884325 FNCN 0.816900
0.050781 0.877405 2178 FSC 0.631676 SNR 3.429994e+00 FNCF 0.896430 FNCN 0.821318
0.054688 0.875931 2498 FSC 0.605536 SNR 3.070172e+00 FNCF 0.908684 FNCN 0.828866
0.058594 0.876247 2622 FSC 0.611065 SNR 3.142250e+00 FNCF 0.910457 FNCN 0.831098
0.062500 0.884193 3338 FSC 0.763974 SNR 6.473637e+00 FNCF 0.898597 FNCN 0.823882
0.066406 0.890079 3722 FSC 0.897373 SNR 1.748804e+01 FNCF 0.888997 FNCN 0.820916
0.070312 0.888096 4170 FSC 0.850229 SNR 1.135368e+01 FNCF 0.896541 FNCN 0.822739
0.074219 0.881947 4358 FSC 0.717896 SNR 5.089588e+00 FNCF 0.897502 FNCN 0.819764

...

0.789062 0.821038 8592 FSC 0.005476 SNR 1.101324e-02 FNCF 0.888864 FNCN 0.821332
0.792969 0.813430 7208 FSC -0.044041 SNR -8.436653e-02 FNCF 0.889662 FNCN 0.818472
0.796875 0.813393 6296 FSC -0.044265 SNR -8.477789e-02 FNCF 0.890629 FNCN 0.815216
0.800781 0.812815 5544 FSC -0.047832 SNR -9.129702e-02 FNCF 0.894048 FNCN 0.808839
0.804688 0.814086 5360 FSC -0.039964 SNR -7.685736e-02 FNCF 0.892404 FNCN 0.813711
0.808594 0.814528 4344 FSC -0.037196 SNR -7.172486e-02 FNCF 0.886577 FNCN 0.828553
0.812500 0.813960 3272 FSC -0.040749 SNR -7.830638e-02 FNCF 0.887005 FNCN 0.826397
0.816406 0.816745 3096 FSC -0.023074 SNR -4.510691e-02 FNCF 0.895393 FNCN 0.818955
0.820312 0.823611 2840 FSC 0.023408 SNR 4.793880e-02 FNCF 0.898811 FNCN 0.825501
0.824219 0.810629 2240 FSC -0.061066 SNR -1.151032e-01 FNCF 0.895444 FNCN 0.827601
0.828125 0.811470 1320 FSC -0.056018 SNR -1.060935e-01 FNCF 0.903966 FNCN 0.820170
0.832031 0.812934 1352 FSC -0.047100 SNR -8.996210e-02 FNCF 0.908462 FNCN 0.826379
0.835938 0.823354 1152 FSC 0.021585 SNR 4.412220e-02 FNCF 0.887402 FNCN 0.824615
0.839844 0.817772 800 FSC -0.016396 SNR -3.226391e-02 FNCF 0.869994 FNCN 0.815638
0.843750 0.824257 288 FSC 0.028007 SNR 5.762863e-02 FNCF 0.880944 FNCN 0.824954
0.847656 0.821916 392 FSC 0.011526 SNR 2.331998e-02 FNCF 0.899626 FNCN 0.837368
0.851562 0.765112 200 FSC -0.271800 SNR -4.274263e-01 FNCF 0.925513 FNCN 0.800424
0.855469 0.812369 72 FSC -0.050561 SNR -9.625498e-02 FNCF 0.902540 FNCN 0.779785
0.859375 0.777638 8 FSC -0.223864 SNR -3.658316e-01 FNCF 0.774510 FNCN 0.868126
0.863281 0.000000 0 FSC -0.847425 SNR -9.174121e-01 FNCF 0.000000 FNCN 0.000000
</pre>
Display the output of FSC, SNR, FNCF, FNCN. 
 

<table>
<tr>
<td>[[File:Outdata-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
<td>[[File:Outdata-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
</tr>
<tr>
<td>[[File:Outdata-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
</table>
These graphs are removed the first and last 10 point. 
 

Or later, use same files as -mask, -maskBack. 
 

===== Case: using -FSCfull, -Cref, and NoiseWeighted=-100 =====
Output 
<pre>
FNCF 0.893745 FNCN 0.820252
0.000000 0.991796 1 FSC -6.985231 SNR -1.749538e+00 FNCF 0.704805 FNCN 0.391308 FSCfull 2.334156 Cref 0.000000 NoiseWeighted 0.000000
0.003906 0.982392 18 FSC -10.699472 SNR -1.829052e+00 FNCF 0.821228 FNCN 0.684129 FSCfull 2.206197 Cref 0.000000 NoiseWeighted 0.000000
0.007812 0.963411 62 FSC 37.413739 SNR -2.054924e+00 FNCF 0.884407 FNCN 0.773688 FSCfull 1.947935 Cref 1.395685 NoiseWeighted 0.000000
0.011719 0.934883 98 FSC 3.542894 SNR -2.786505e+00 FNCF 0.896445 FNCN 0.837667 FSCfull 1.559752 Cref 1.248900 NoiseWeighted 0.000000
0.015625 0.902410 210 FSC 1.267348 SNR -9.480880e+00 FNCF 0.879666 FNCN 0.865827 FSCfull 1.117912 Cref 1.057314 NoiseWeighted 0.000000
0.019531 0.864067 350 FSC 0.424680 SNR 1.476325e+00 FNCF 0.881884 FNCN 0.835433 FSCfull 0.596176 Cref 0.772124 NoiseWeighted 0.000000
0.023438 0.841587 450 FSC 0.169793 SNR 4.090381e-01 FNCF 0.901388 FNCN 0.806285 FSCfull 0.290296 Cref 0.538791 NoiseWeighted 0.000000
0.027344 0.856990 602 FSC 0.333237 SNR 9.995687e-01 FNCF 0.897467 FNCN 0.819184 FSCfull 0.499892 Cref 0.707031 NoiseWeighted 0.000000
0.031250 0.887424 762 FSC 0.841616 SNR 1.062755e+01 FNCF 0.888027 FNCN 0.826006 FSCfull 0.913997 Cref 0.956032 NoiseWeighted 0.000000
0.035156 0.887318 1142 FSC 0.839175 SNR 1.043589e+01 FNCF 0.885703 FNCN 0.827937 FSCfull 0.912556 Cref 0.955278 NoiseWeighted 0.000000
0.039062 0.879608 1250 FSC 0.677353 SNR 4.198725e+00 FNCF 0.886124 FNCN 0.821982 FSCfull 0.807645 Cref 0.898691 NoiseWeighted 0.000000
0.042969 0.874892 1458 FSC 0.591685 SNR 2.898177e+00 FNCF 0.893947 FNCN 0.826635 FSCfull 0.743470 Cref 0.862247 NoiseWeighted 0.000000
0.046875 0.874435 1814 FSC 0.583850 SNR 2.805960e+00 FNCF 0.893287 FNCN 0.825939 FSCfull 0.737254 Cref 0.858635 NoiseWeighted 0.000000
0.050781 0.877405 2178 FSC 0.636213 SNR 3.497730e+00 FNCF 0.891071 FNCN 0.829329 FSCfull 0.777666 Cref 0.881854 NoiseWeighted 0.000000
0.054688 0.875931 2498 FSC 0.609808 SNR 3.125677e+00 FNCF 0.882848 FNCN 0.823179 FSCfull 0.757616 Cref 0.870411 NoiseWeighted 0.000000
0.058594 0.876247 2622 FSC 0.615393 SNR 3.200107e+00 FNCF 0.884282 FNCN 0.810449 FSCfull 0.761911 Cref 0.872875 NoiseWeighted 0.000000
0.062500 0.884193 3338 FSC 0.769958 SNR 6.694059e+00 FNCF 0.889011 FNCN 0.809316 FSCfull 0.870030 Cref 0.932754 NoiseWeighted 0.000000
0.066406 0.890079 3722 FSC 0.904980 SNR 1.904823e+01 FNCF 0.895025 FNCN 0.809225 FSCfull 0.950120 Cref 0.974741 NoiseWeighted 0.000000
0.070312 0.888096 4170 FSC 0.857243 SNR 1.200983e+01 FNCF 0.899517 FNCN 0.816330 FSCfull 0.923135 Cref 0.960799 NoiseWeighted 0.000000
0.074219 0.881947 4358 FSC 0.723358 SNR 5.229561e+00 FNCF 0.896087 FNCN 0.821250 FSCfull 0.839475 Cref 0.916229 NoiseWeighted 0.000000

...

0.789062 0.821038 8592 FSC 0.005374 SNR 1.080707e-02 FNCF 0.889648 FNCN 0.823173 FSCfull 0.010692 Cref 0.103400 NoiseWeighted 0.000000
0.792969 0.813430 7208 FSC -0.044355 SNR -8.494283e-02 FNCF 0.891566 FNCN 0.824518 FSCfull -0.092828 Cref 0.000000 NoiseWeighted 0.000000
0.796875 0.813393 6296 FSC -0.044580 SNR -8.535559e-02 FNCF 0.891161 FNCN 0.818115 FSCfull -0.093321 Cref 0.000000 NoiseWeighted 0.000000
0.800781 0.812815 5544 FSC -0.048161 SNR -9.189702e-02 FNCF 0.892987 FNCN 0.824486 FSCfull -0.101197 Cref 0.000000 NoiseWeighted 0.000000
0.804688 0.814086 5360 FSC -0.040262 SNR -7.740746e-02 FNCF 0.893581 FNCN 0.822037 FSCfull -0.083902 Cref 0.000000 NoiseWeighted 0.000000
0.808594 0.814528 4344 FSC -0.037483 SNR -7.225678e-02 FNCF 0.896030 FNCN 0.823916 FSCfull -0.077884 Cref 0.000000 NoiseWeighted 0.000000
0.812500 0.813960 3272 FSC -0.041049 SNR -7.886156e-02 FNCF 0.895996 FNCN 0.815310 FSCfull -0.085613 Cref 0.000000 NoiseWeighted 0.000000
0.816406 0.816745 3096 FSC -0.023301 SNR -4.554071e-02 FNCF 0.903188 FNCN 0.808224 FSCfull -0.047714 Cref 0.000000 NoiseWeighted 0.000000
0.820312 0.823611 2840 FSC 0.023389 SNR 4.789782e-02 FNCF 0.892511 FNCN 0.822457 FSCfull 0.045708 Cref 0.213795 NoiseWeighted 0.000000
0.824219 0.810629 2240 FSC -0.061448 SNR -1.157814e-01 FNCF 0.894149 FNCN 0.805167 FSCfull -0.130942 Cref 0.000000 NoiseWeighted 0.000000
0.828125 0.811470 1320 FSC -0.056380 SNR -1.067427e-01 FNCF 0.895955 FNCN 0.802224 FSCfull -0.119498 Cref 0.000000 NoiseWeighted 0.000000
0.832031 0.812934 1352 FSC -0.047426 SNR -9.055756e-02 FNCF 0.913658 FNCN 0.815504 FSCfull -0.099575 Cref 0.000000 NoiseWeighted 0.000000
0.835938 0.823354 1152 FSC 0.021557 SNR 4.406357e-02 FNCF 0.917390 FNCN 0.826730 FSCfull 0.042204 Cref 0.205436 NoiseWeighted 0.000000
0.839844 0.817772 800 FSC -0.016595 SNR -3.264812e-02 FNCF 0.886657 FNCN 0.834540 FSCfull -0.033750 Cref 0.000000 NoiseWeighted 0.000000
0.843750 0.824257 288 FSC 0.028009 SNR 5.763305e-02 FNCF 0.847956 FNCN 0.782642 FSCfull 0.054492 Cref 0.233436 NoiseWeighted 0.000000
0.847656 0.821916 392 FSC 0.011451 SNR 2.316754e-02 FNCF 0.862911 FNCN 0.801126 FSCfull 0.022643 Cref 0.150476 NoiseWeighted 0.000000
0.851562 0.765112 200 FSC -0.272800 SNR -4.286612e-01 FNCF 0.888032 FNCN 0.840993 FSCfull -0.750275 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.812369 72 FSC -0.050901 SNR -9.687171e-02 FNCF 0.851466 FNCN 0.740952 FSCfull -0.107262 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.777638 8 FSC -0.224759 SNR -3.670256e-01 FNCF 0.680124 FNCN 0.689641 FSCfull -0.579843 Cref 0.000000 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.848036 SNR -9.177697e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -11.160973 Cref 0.000000 NoiseWeighted 0.000000
</pre>
Display the output of FNCfull, Cref, NoiseWeighted. 
Because Cref at R=0 is negative, it is corrected 0. Therefore, all NoiseWeighted is output as 0. 
 

<table>
<tr>
<td>[[File:Outdata-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
<td>[[File:Outdata-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
</tr>
<tr>
<td>[[File:Outdata-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
</table>
These graphs are removed the last point. 
 

===== Case: using -FSCfull, -Cref, and d=0.025, NoiseWeighted=-100 =====
Output 
<pre>
0.000000 0.961060 147 FSC 19.604071 SNR -2.107503e+00 FNCF 0.881653 FNCN 0.813775 FSCfull 1.902932 Cref 1.379468 NoiseWeighted 1.379468
0.025000 0.884961 3596 FSC 0.778687 SNR 7.036960e+00 FNCF 0.890538 FNCN 0.819820 FSCfull 0.875575 Cref 0.935722 NoiseWeighted 0.950457
0.050000 0.876699 13334 FSC 0.618184 SNR 3.238129e+00 FNCF 0.901366 FNCN 0.819141 FSCfull 0.764047 Cref 0.874098 NoiseWeighted 0.930472
0.075000 0.884583 30012 FSC 0.770666 SNR 6.720909e+00 FNCF 0.893296 FNCN 0.821043 FSCfull 0.870482 Cref 0.932996 NoiseWeighted 1.073872
0.100000 0.888691 53048 FSC 0.862079 SNR 1.250108e+01 FNCF 0.894515 FNCN 0.820477 FSCfull 0.925932 Cref 0.962254 NoiseWeighted 1.235558
0.125000 0.873868 82634 FSC 0.569634 SNR 2.647204e+00 FNCF 0.893251 FNCN 0.822256 FSCfull 0.725817 Cref 0.851949 NoiseWeighted 1.259099
0.150000 0.860938 118688 FSC 0.380513 SNR 1.228478e+00 FNCF 0.892919 FNCN 0.822140 FSCfull 0.551263 Cref 0.742471 NoiseWeighted 1.303077
0.175000 0.862499 161322 FSC 0.400894 SNR 1.338309e+00 FNCF 0.895633 FNCN 0.819697 FSCfull 0.572341 Cref 0.756532 NoiseWeighted 1.626799
0.200000 0.875542 211496 FSC 0.597988 SNR 2.974978e+00 FNCF 0.892626 FNCN 0.820726 FSCfull 0.748426 Cref 0.865116 NoiseWeighted 2.351630
0.225000 0.882194 266468 FSC 0.721495 SNR 5.181196e+00 FNCF 0.893766 FNCN 0.819388 FSCfull 0.838219 Cref 0.915543 NoiseWeighted 3.245882
0.250000 0.874374 330126 FSC 0.578097 SNR 2.740421e+00 FNCF 0.892148 FNCN 0.819562 FSCfull 0.732650 Cref 0.855950 NoiseWeighted 4.083509
0.275000 0.868385 398912 FSC 0.483453 SNR 1.871867e+00 FNCF 0.893360 FNCN 0.818555 FSCfull 0.651794 Cref 0.807338 NoiseWeighted 5.347409
0.300000 0.861123 473858 FSC 0.382903 SNR 1.240984e+00 FNCF 0.894373 FNCN 0.819237 FSCfull 0.553767 Cref 0.744156 NoiseWeighted 7.060352
0.325000 0.852294 557496 FSC 0.277607 SNR 7.685764e-01 FNCF 0.894332 FNCN 0.820382 FSCfull 0.434573 Cref 0.659222 NoiseWeighted 9.243587
0.350000 0.846181 647132 FSC 0.213624 SNR 5.433115e-01 FNCF 0.893565 FNCN 0.819353 FSCfull 0.352043 Cref 0.593332 NoiseWeighted 12.685995
0.375000 0.842054 739454 FSC 0.173934 SNR 4.211135e-01 FNCF 0.894578 FNCN 0.820175 FSCfull 0.296326 Cref 0.544359 NoiseWeighted 18.310566
0.400000 0.836904 845340 FSC 0.127900 SNR 2.933142e-01 FNCF 0.895293 FNCN 0.819759 FSCfull 0.226793 Cref 0.476228 NoiseWeighted 26.001148
0.425000 0.836800 950870 FSC 0.127013 SNR 2.909839e-01 FNCF 0.894829 FNCN 0.820387 FSCfull 0.225397 Cref 0.474760 NoiseWeighted 43.409539
0.450000 0.834607 1068284 FSC 0.108519 SNR 2.434566e-01 FNCF 0.894605 FNCN 0.819227 FSCfull 0.195790 Cref 0.442482 NoiseWeighted 69.905495
0.475000 0.831828 1190048 FSC 0.085938 SNR 1.880360e-01 FNCF 0.893867 FNCN 0.819873 FSCfull 0.158275 Cref 0.397838 NoiseWeighted 112.046453
0.500000 0.829300 1284690 FSC 0.066183 SNR 1.417471e-01 FNCF 0.893855 FNCN 0.821343 FSCfull 0.124149 Cref 0.352348 NoiseWeighted 182.520960
0.525000 0.827369 1227836 FSC 0.051568 SNR 1.087446e-01 FNCF 0.894786 FNCN 0.820592 FSCfull 0.098079 Cref 0.313176 NoiseWeighted 307.856690
0.550000 0.824926 1141760 FSC 0.033639 SNR 6.962054e-02 FNCF 0.893119 FNCN 0.820052 FSCfull 0.065089 Cref 0.255125 NoiseWeighted 491.027655
0.575000 0.824884 1043124 FSC 0.033335 SNR 6.896969e-02 FNCF 0.894419 FNCN 0.819959 FSCfull 0.064520 Cref 0.254007 NoiseWeighted 987.556329
0.600000 0.823838 930008 FSC 0.025857 SNR 5.308599e-02 FNCF 0.894395 FNCN 0.819809 FSCfull 0.050410 Cref 0.224522 NoiseWeighted 1819.317450
0.625000 0.822523 803708 FSC 0.016596 SNR 3.375260e-02 FNCF 0.894275 FNCN 0.820134 FSCfull 0.032651 Cref 0.180695 NoiseWeighted 3148.491102
0.650000 0.821119 663864 FSC 0.006894 SNR 1.388304e-02 FNCF 0.894622 FNCN 0.820588 FSCfull 0.013693 Cref 0.117017 NoiseWeighted 4523.596884
0.675000 0.820229 512012 FSC 0.000838 SNR 1.678337e-03 FNCF 0.893624 FNCN 0.820495 FSCfull 0.001676 Cref 0.040933 NoiseWeighted 3622.105778
0.700000 0.819524 348596 FSC -0.003899 SNR -7.768473e-03 FNCF 0.894646 FNCN 0.819049 FSCfull -0.007829 Cref 0.000000 NoiseWeighted 0.000000
0.725000 0.818723 217808 FSC -0.009236 SNR -1.830228e-02 FNCF 0.893341 FNCN 0.820796 FSCfull -0.018643 Cref 0.000000 NoiseWeighted 0.000000
0.750000 0.820472 135048 FSC 0.002487 SNR 4.985434e-03 FNCF 0.891864 FNCN 0.822416 FSCfull 0.004961 Cref 0.070432 NoiseWeighted 0.000000
0.775000 0.825089 77288 FSC 0.034817 SNR 7.214486e-02 FNCF 0.895766 FNCN 0.818517 FSCfull 0.067290 Cref 0.259404 NoiseWeighted 0.000000
0.800000 0.815167 38120 FSC -0.032256 SNR -6.249550e-02 FNCF 0.898301 FNCN 0.823939 FSCfull -0.066662 Cref 0.000000 NoiseWeighted 0.000000
0.825000 0.816419 13488 FSC -0.024276 SNR -4.740110e-02 FNCF 0.894416 FNCN 0.824161 FSCfull -0.049760 Cref 0.000000 NoiseWeighted 0.000000
0.850000 0.814605 1760 FSC -0.035796 SNR -6.911783e-02 FNCF 0.894095 FNCN 0.806454 FSCfull -0.074250 Cref 0.000000 NoiseWeighted 0.000000
</pre>
On R=0.675000 (or below), Noiseweighted is outputted. 
 

<table>
<tr>
<td>[[File:Outdata-d-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata-d-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
<tr>
<td>[[File:Outdata-d-FNC-mrcImageFourierNeighborCorrelation.png]] 
FNC 
</td>
<td>[[File:Outdata-d-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
</tr>
<tr>
<td>[[File:Outdata-d-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
<td>[[File:Outdata-d-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
</tr>
<tr>
<td>[[File:Outdata-d-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
<td>[[File:Outdata-d-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
<tr>
<td>[[File:Outdata1-d-mrcImageFourierNeighborCorrelation.png]] 
FNC, FNCF, FNCN 
</td>
<td>[[File:Outdata1-d-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted(~ R=0.375000) 
</td>
</tr>
</table>
These graphs are removed the first point. 
 
As above, if FNC is between FNCF and FNCN, the estimate value of SNR, FSC, FSCfull is positive. Then, Cref and NoiseWeighted can be calculated as real value. 
 

==== Case: using -FSC and specifying files as -mask, -maskBack (vol.2)====
In [[#Case: using -FSC and specifying files as -mask, -maskBack|above example]], The half value point of Low-Pass Filter to create mask file is 0.0125(80Å). Therefore, it is coarse almost as an ellipse. 
This time prepare a mask file whose half value point is 0.05(20Å). 
-mask 's file: This file can be created by [[Tutorial List#mrcImage]]. 
 
Setting of Makefile 
<pre>
MASK_VALUE=0.05
</pre>
<table>
<tr>
<td>[[File:Input-Mask1-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-Mask1-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (114, 141, 82) 
0.00774205 
0.0876476 
2.13983e-05 
</td>
</tr>
</table>
 

-maskBack: Use same file. 
 

===== NoiseWeighted=-100, -FSCfull, -Cref =====
<pre>
FNCF 0.914907 FNCN 0.819953
0.000000 0.991796 1 FSC 9.512511 SNR -2.234948e+00 FNCF 0.982818 FNCN 0.771068 FSCfull 1.809750 Cref 1.345270 NoiseWeighted 1.345270
0.003906 0.982392 18 FSC 5.913521 SNR -2.407040e+00 FNCF 0.979065 FNCN 0.796796 FSCfull 1.710712 Cref 1.307942 NoiseWeighted 1.308441
0.007812 0.963411 62 FSC 3.088481 SNR -2.957634e+00 FNCF 0.971746 FNCN 0.760178 FSCfull 1.510821 Cref 1.229154 NoiseWeighted 1.231031
0.011719 0.934883 98 FSC 1.532837 SNR -5.753490e+00 FNCF 0.963111 FNCN 0.803158 FSCfull 1.210372 Cref 1.100169 NoiseWeighted 1.103953
0.015625 0.902410 210 FSC 0.767399 SNR 6.598402e+00 FNCF 0.955381 FNCN 0.827784 FSCfull 0.868393 Cref 0.931876 NoiseWeighted 0.937581
0.019531 0.864067 350 FSC 0.302572 SNR 8.676784e-01 FNCF 0.940646 FNCN 0.801457 FSCfull 0.464576 Cref 0.681598 NoiseWeighted 0.688129
0.023438 0.841587 450 FSC 0.128559 SNR 2.950497e-01 FNCF 0.929146 FNCN 0.807370 FSCfull 0.227829 Cref 0.477314 NoiseWeighted 0.483914
0.027344 0.856990 602 FSC 0.242277 SNR 6.394883e-01 FNCF 0.922377 FNCN 0.819179 FSCfull 0.390054 Cref 0.624543 NoiseWeighted 0.636326
0.031250 0.887424 762 FSC 0.551068 SNR 2.455017e+00 FNCF 0.922938 FNCN 0.811850 FSCfull 0.710566 Cref 0.842951 NoiseWeighted 0.863784
0.035156 0.887318 1142 FSC 0.549727 SNR 2.441751e+00 FNCF 0.924502 FNCN 0.804822 FSCfull 0.709450 Cref 0.842289 NoiseWeighted 0.868721
0.039062 0.879608 1250 FSC 0.457992 SNR 1.689984e+00 FNCF 0.927185 FNCN 0.798498 FSCfull 0.628251 Cref 0.792623 NoiseWeighted 0.823443
0.042969 0.874892 1458 FSC 0.407043 SNR 1.372928e+00 FNCF 0.927562 FNCN 0.809349 FSCfull 0.578580 Cref 0.760644 NoiseWeighted 0.796577
0.046875 0.874435 1814 FSC 0.402297 SNR 1.346145e+00 FNCF 0.920495 FNCN 0.820928 FSCfull 0.573769 Cref 0.757475 NoiseWeighted 0.800249
0.050781 0.877405 2178 FSC 0.433740 SNR 1.531945e+00 FNCF 0.907902 FNCN 0.804488 FSCfull 0.605047 Cref 0.777848 NoiseWeighted 0.829646
0.054688 0.875931 2498 FSC 0.417965 SNR 1.436221e+00 FNCF 0.903627 FNCN 0.813420 FSCfull 0.589528 Cref 0.767807 NoiseWeighted 0.827416
0.058594 0.876247 2622 FSC 0.421315 SNR 1.456114e+00 FNCF 0.912572 FNCN 0.826763 FSCfull 0.592853 Cref 0.769969 NoiseWeighted 0.838975
0.062500 0.884193 3338 FSC 0.511185 SNR 2.091527e+00 FNCF 0.916913 FNCN 0.821846 FSCfull 0.676535 Cref 0.822518 NoiseWeighted 0.906895
0.066406 0.890079 3722 FSC 0.585445 SNR 2.824450e+00 FNCF 0.917732 FNCN 0.820012 FSCfull 0.738524 Cref 0.859374 NoiseWeighted 0.959536
0.070312 0.888096 4170 FSC 0.559622 SNR 2.541557e+00 FNCF 0.918467 FNCN 0.831005 FSCfull 0.717638 Cref 0.847135 NoiseWeighted 0.958583
0.074219 0.881947 4358 FSC 0.484656 SNR 1.880902e+00 FNCF 0.920695 FNCN 0.829698 FSCfull 0.652886 Cref 0.808014 NoiseWeighted 0.927312

...

0.644531 0.822764 109556 FSC 0.015021 SNR 3.049937e-02 FNCF 0.914710 FNCN 0.819465 FSCfull 0.029597 Cref 0.172037 NoiseWeighted 5571.763528
0.648438 0.820426 104768 FSC 0.002494 SNR 5.000113e-03 FNCF 0.916695 FNCN 0.818935 FSCfull 0.004975 Cref 0.070535 NoiseWeighted 2591.879420
0.652344 0.820764 101724 FSC 0.004285 SNR 8.606361e-03 FNCF 0.915339 FNCN 0.815352 FSCfull 0.008533 Cref 0.092374 NoiseWeighted 3854.118436
0.656250 0.821992 98396 FSC 0.010851 SNR 2.194065e-02 FNCF 0.914227 FNCN 0.817587 FSCfull 0.021470 Cref 0.146525 NoiseWeighted 6946.843637
0.660156 0.820556 94632 FSC 0.003182 SNR 6.384020e-03 FNCF 0.912940 FNCN 0.820474 FSCfull 0.006344 Cref 0.079646 NoiseWeighted 4294.096180
0.664062 0.819228 90908 FSC -0.003806 SNR -7.583799e-03 FNCF 0.912924 FNCN 0.819343 FSCfull -0.007642 Cref 0.000000 NoiseWeighted 0.000000
0.667969 0.819197 86684 FSC -0.003967 SNR -7.901843e-03 FNCF 0.914583 FNCN 0.817105 FSCfull -0.007965 Cref 0.000000 NoiseWeighted 0.000000
0.671875 0.820568 82776 FSC 0.003245 SNR 6.510316e-03 FNCF 0.915174 FNCN 0.819274 FSCfull 0.006468 Cref 0.080425 NoiseWeighted 0.000000
0.675781 0.820683 80372 FSC 0.003858 SNR 7.746611e-03 FNCF 0.913751 FNCN 0.818000 FSCfull 0.007687 Cref 0.087676 NoiseWeighted 0.000000
0.679688 0.821076 75108 FSC 0.005946 SNR 1.196247e-02 FNCF 0.913970 FNCN 0.815727 FSCfull 0.011821 Cref 0.108725 NoiseWeighted 0.000000

...

0.828125 0.811470 1320 FSC -0.042763 SNR -8.201861e-02 FNCF 0.917130 FNCN 0.825454 FSCfull -0.089347 Cref 0.000000 NoiseWeighted 0.000000
0.832031 0.812934 1352 FSC -0.035646 SNR -6.883734e-02 FNCF 0.920492 FNCN 0.823277 FSCfull -0.073926 Cref 0.000000 NoiseWeighted 0.000000
0.835938 0.823354 1152 FSC 0.018231 SNR 3.713860e-02 FNCF 0.925875 FNCN 0.800023 FSCfull 0.035809 Cref 0.189232 NoiseWeighted 0.000000
0.839844 0.817772 800 FSC -0.011359 SNR -2.246248e-02 FNCF 0.931022 FNCN 0.818680 FSCfull -0.022979 Cref 0.000000 NoiseWeighted 0.000000
0.843750 0.824257 288 FSC 0.023185 SNR 4.747129e-02 FNCF 0.926149 FNCN 0.862458 FSCfull 0.045320 Cref 0.212885 NoiseWeighted 0.000000
0.847656 0.821916 392 FSC 0.010442 SNR 2.110497e-02 FNCF 0.912921 FNCN 0.826884 FSCfull 0.020669 Cref 0.143766 NoiseWeighted 0.000000
0.851562 0.765112 200 FSC -0.224072 SNR -3.661096e-01 FNCF 0.904654 FNCN 0.721120 FSCfull -0.577560 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.812369 72 FSC -0.038404 SNR -7.396801e-02 FNCF 0.878913 FNCN 0.789634 FSCfull -0.079876 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.777638 8 FSC -0.182221 SNR -3.082684e-01 FNCF 0.792984 FNCN 0.764045 FSCfull -0.445647 Cref 0.000000 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.811947 SNR -8.962150e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.635308 Cref 0.000000 NoiseWeighted 0.000000
</pre>
Data in interval of default setting can be expressed on range of R=0.660156. 
 

<table>
<tr>
<td>[[File:Outdata2-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata2-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
<tr>
<td>[[File:Outdata2-FNC-mrcImageFourierNeighborCorrelation.png]] 
FNC 
</td>
<td>[[File:Outdata2-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
</tr>
<tr>
<td>[[File:Outdata2-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
<td>[[File:Outdata2-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
</tr>
<tr>
<td>[[File:Outdata2-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
<td>[[File:Outdata2-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
</table>
These graphs are removed the first 4 points and last 1 point. 
 

=== Compare data with each SN ratio ===
Compare output for input data with each different SN ratio as the following.br>
You can perform by [[Tutorial List#mrcImage]] command. 
 
Setting of Makefile 
<pre>
#### Definition ####
# Path of Input File
INPUT_PATH=${EOS_HOME}/tutorial/SampleData/1VOM.mrc
#INPUT_PATH=${EOS_HOME}/tutorial/SampleData/1VOM-N.mrc

### SN or NS for Input file
INI_SN=0.3 1 3 10 100
</pre>
 

Each input image(before padding) 
<table>
<tr>
<td>SN比 
</td>
<td>SN=0.3 
</td>
<td>SN=1 
</td>
<td>SN=3 
</td>
<td>SN=10 
</td>
<td>SN=100 
</td>
</tr>
<tr>
<td>xy-plane 
</td>
<td>[[File:Input-SN0.3-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN1-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN3-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN10-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN100-mrcImageFourierNeighborCorrelation.png]]
</td>
</tr>
<tr>
<td>yz-plane 
</td>
<td>[[File:Input1-SN0.3-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN1-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN3-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN10-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN100-mrcImageFourierNeighborCorrelation.png]] 
</td>
</tr>
<tr>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-7489.39 (57, 54, 75) 
8066.02 (17, 29, 46) 
68.7388 
1679.17 
2.09896 
</td>
<td>-2225.59 (26, 40, 83) 
4567.91 (28, 50, 50) 
72.5953 
578.119 
0.722649 
</td>
<td>-784.63 (44, 6, 70) 
3724.44 (41, 60, 31) 
72.3035 
337.846 
0.422308 
</td>
<td>-246.726 (17, 25, 16) 
3406.43 (20, 24, 29) 
72.1722 
299.081 
0.373851 
</td>
<td>-22.8638 (79, 41, 2) 
3399.86 (23, 55, 41) 
72.133 
294.848 
0.368559 
</td>
</tr>
</table>
 

==== Compare [[:Media:Outdata-mrcImageFourierNeighborCorrelation.zip|Output file]]s ====
 

<table>
<tr>
<td>[[File:Outdata3-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata3-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
<tr>
<td>[[File:Outdata3-FNC-mrcImageFourierNeighborCorrelation.png]] 
FNC 
</td>
<td>[[File:Outdata3-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
</tr>
<tr>
<td>[[File:Outdata3-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
<td>[[File:Outdata3-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
</tr>
<tr>
<td>[[File:Outdata3-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
<td>[[File:Outdata3-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
</table>

==== Output for around the first point as Cref=0. ====
SN=0.3 
<pre>
...

0.125000 0.830285 12606 FSC 0.056542 SNR 1.198620e-01 FNCF 0.905793 FNCN 0.820589 FSCfull 0.107033 Cref 0.327159 NoiseWeighted 0.483509
0.128906 0.835033 13802 FSC 0.085415 SNR 1.867837e-01 FNCF 0.907524 FNCN 0.814605 FSCfull 0.157386 Cref 0.396720 NoiseWeighted 0.601033
0.132812 0.831848 14754 FSC 0.065877 SNR 1.410450e-01 FNCF 0.913083 FNCN 0.824672 FSCfull 0.123610 Cref 0.351583 NoiseWeighted 0.546440
0.136719 0.831254 15194 FSC 0.062310 SNR 1.329021e-01 FNCF 0.916913 FNCN 0.827674 FSCfull 0.117311 Cref 0.342507 NoiseWeighted 0.546532
0.140625 0.826966 16454 FSC 0.037254 SNR 7.739025e-02 FNCF 0.915416 FNCN 0.821369 FSCfull 0.071831 Cref 0.268013 NoiseWeighted 0.439405
0.144531 0.820016 17154 FSC -0.000933 SNR -1.863673e-03 FNCF 0.913586 FNCN 0.824382 FSCfull -0.001867 Cref 0.000000 NoiseWeighted 0.000000
0.148438 0.821502 18266 FSC 0.006992 SNR 1.408213e-02 FNCF 0.913122 FNCN 0.829752 FSCfull 0.013887 Cref 0.117841 NoiseWeighted 0.000000
0.152344 0.822031 18750 FSC 0.009847 SNR 1.989009e-02 FNCF 0.911698 FNCN 0.824485 FSCfull 0.019502 Cref 0.139650 NoiseWeighted 0.000000
0.156250 0.826508 20234 FSC 0.034651 SNR 7.179050e-02 FNCF 0.913992 FNCN 0.817147 FSCfull 0.066982 Cref 0.258808 NoiseWeighted 0.000000
0.160156 0.829598 21450 FSC 0.052491 SNR 1.107982e-01 FNCF 0.915240 FNCN 0.817627 FSCfull 0.099746 Cref 0.315827 NoiseWeighted 0.000000

...
</pre>
 

SN=1 
<pre>
...

0.625000 0.821968 125484 FSC 0.008655 SNR 1.746116e-02 FNCF 0.915959 FNCN 0.820807 FSCfull 0.017161 Cref 0.131002 NoiseWeighted 2282.625528
0.628906 0.822126 123668 FSC 0.009510 SNR 1.920304e-02 FNCF 0.915730 FNCN 0.818373 FSCfull 0.018841 Cref 0.137263 NoiseWeighted 2703.284812
0.632812 0.822135 118752 FSC 0.009556 SNR 1.929710e-02 FNCF 0.916420 FNCN 0.817706 FSCfull 0.018932 Cref 0.137593 NoiseWeighted 3065.097206
0.636719 0.822268 115748 FSC 0.010276 SNR 2.076605e-02 FNCF 0.916453 FNCN 0.821218 FSCfull 0.020344 Cref 0.142631 NoiseWeighted 3596.708750
0.640625 0.821682 111732 FSC 0.007114 SNR 1.432974e-02 FNCF 0.916046 FNCN 0.819347 FSCfull 0.014127 Cref 0.118858 NoiseWeighted 3395.432939
0.644531 0.819634 109556 FSC -0.003778 SNR -7.527926e-03 FNCF 0.915582 FNCN 0.818883 FSCfull -0.007585 Cref 0.000000 NoiseWeighted 0.000000
0.648438 0.820647 104768 FSC 0.001581 SNR 3.167601e-03 FNCF 0.915830 FNCN 0.819727 FSCfull 0.003158 Cref 0.056193 NoiseWeighted 0.000000
0.652344 0.820390 101724 FSC 0.000214 SNR 4.288445e-04 FNCF 0.914391 FNCN 0.820488 FSCfull 0.000429 Cref 0.020704 NoiseWeighted 0.000000
0.656250 0.821091 98396 FSC 0.003947 SNR 7.925782e-03 FNCF 0.913665 FNCN 0.822480 FSCfull 0.007863 Cref 0.088676 NoiseWeighted 0.000000
0.660156 0.821039 94632 FSC 0.003669 SNR 7.364323e-03 FNCF 0.913751 FNCN 0.819652 FSCfull 0.007310 Cref 0.085501 NoiseWeighted 0.000000

...
</pre>
 

SN=3 
<pre>
...

0.765625 0.821757 15104 FSC 0.009515 SNR 1.921255e-02 FNCF 0.922342 FNCN 0.820350 FSCfull 0.018850 Cref 0.137297 NoiseWeighted 317721.373090
0.769531 0.822221 13472 FSC 0.011996 SNR 2.428272e-02 FNCF 0.922754 FNCN 0.817671 FSCfull 0.023707 Cref 0.153971 NoiseWeighted 413936.197088
0.773438 0.821217 12312 FSC 0.006642 SNR 1.337191e-02 FNCF 0.918091 FNCN 0.817507 FSCfull 0.013195 Cref 0.114871 NoiseWeighted 359043.192167
0.777344 0.827075 11528 FSC 0.038716 SNR 8.055134e-02 FNCF 0.915129 FNCN 0.819965 FSCfull 0.074547 Cref 0.273032 NoiseWeighted 992931.202359
0.781250 0.824370 10056 FSC 0.023654 SNR 4.845502e-02 FNCF 0.915417 FNCN 0.814779 FSCfull 0.046216 Cref 0.214978 NoiseWeighted 910337.354456
0.785156 0.818701 8936 FSC -0.006536 SNR -1.298769e-02 FNCF 0.913984 FNCN 0.830604 FSCfull -0.013159 Cref 0.000000 NoiseWeighted 0.000000
0.789062 0.819627 8592 FSC -0.001726 SNR -3.446727e-03 FNCF 0.906964 FNCN 0.823014 FSCfull -0.003459 Cref 0.000000 NoiseWeighted 0.000000
0.792969 0.820210 7208 FSC 0.001325 SNR 2.654493e-03 FNCF 0.903543 FNCN 0.818116 FSCfull 0.002647 Cref 0.051454 NoiseWeighted 0.000000
0.796875 0.815899 6296 FSC -0.020810 SNR -4.077152e-02 FNCF 0.908125 FNCN 0.817338 FSCfull -0.042504 Cref 0.000000 NoiseWeighted 0.000000
0.800781 0.823119 5544 FSC 0.016835 SNR 3.424612e-02 FNCF 0.914006 FNCN 0.817025 FSCfull 0.033112 Cref 0.181967 NoiseWeighted 0.000000

...
</pre>
 

SN=10 
<pre>
...

0.828125 0.844910 1320 FSC 0.149342 SNR 3.511221e-01 FNCF 0.912374 FNCN 0.803915 FSCfull 0.259874 Cref 0.509779 NoiseWeighted 14231907.761588
0.832031 0.837728 1352 FSC 0.101517 SNR 2.259737e-01 FNCF 0.902768 FNCN 0.811758 FSCfull 0.184322 Cref 0.429327 NoiseWeighted 14095470.163758
0.835938 0.836067 1152 FSC 0.091023 SNR 2.002756e-01 FNCF 0.913173 FNCN 0.800848 FSCfull 0.166858 Cref 0.408483 NoiseWeighted 15783593.638134
0.839844 0.831098 800 FSC 0.060772 SNR 1.294080e-01 FNCF 0.910829 FNCN 0.797062 FSCfull 0.114580 Cref 0.338497 NoiseWeighted 15404941.069368
0.843750 0.829879 288 FSC 0.053609 SNR 1.132924e-01 FNCF 0.886515 FNCN 0.824411 FSCfull 0.101763 Cref 0.319004 NoiseWeighted 17112149.322272
0.847656 0.852127 392 FSC 0.201767 SNR 5.055348e-01 FNCF 0.880805 FNCN 0.817034 FSCfull 0.335784 Cref 0.579469 NoiseWeighted 36666886.878487
0.851562 0.819553 200 FSC -0.003419 SNR -6.815128e-03 FNCF 0.916154 FNCN 0.829615 FSCfull -0.006862 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.816624 72 FSC -0.018488 SNR -3.630448e-02 FNCF 0.925319 FNCN 0.796666 FSCfull -0.037672 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.917138 8 FSC 1.040065 SNR -5.191875e+01 FNCF 0.853931 FNCN 0.697182 FSCfull 1.019639 Cref 1.009772 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.811813 SNR -8.961335e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.627743 Cref 0.000000 NoiseWeighted 0.000000

...
</pre>
 

SN=100 
<pre>
...

0.828125 0.901847 1320 FSC 0.756211 SNR 6.203817e+00 FNCF 0.919589 FNCN 0.822237 FSCfull 0.861185 Cref 0.928000 NoiseWeighted 25907738.220224
0.832031 0.903973 1352 FSC 0.791551 SNR 7.594690e+00 FNCF 0.914005 FNCN 0.814800 FSCfull 0.883649 Cref 0.940026 NoiseWeighted 30862499.462702
0.835938 0.908114 1152 FSC 0.864634 SNR 1.277477e+01 FNCF 0.893985 FNCN 0.804227 FSCfull 0.927403 Cref 0.963018 NoiseWeighted 37210603.792030
0.839844 0.915035 800 FSC 1.001069 SNR -1.872989e+03 FNCF 0.903230 FNCN 0.814543 FSCfull 1.000534 Cref 1.000267 NoiseWeighted 45521947.697260
0.843750 0.918614 288 FSC 1.079756 SNR -2.707648e+01 FNCF 0.924216 FNCN 0.803353 FSCfull 1.038349 Cref 1.018994 NoiseWeighted 54661348.443263
0.847656 0.914517 392 FSC 0.990177 SNR 2.016063e+02 FNCF 0.929501 FNCN 0.780177 FSCfull 0.995064 Cref 0.997529 NoiseWeighted 63120364.126596
0.851562 0.898429 200 FSC 0.702229 SNR 4.716581e+00 FNCF 0.931254 FNCN 0.802611 FSCfull 0.825070 Cref 0.908334 NoiseWeighted 67850948.494955
0.855469 0.877008 72 FSC 0.427280 SNR 1.492108e+00 FNCF 0.926600 FNCN 0.805094 FSCfull 0.598733 Cref 0.773779 NoiseWeighted 68284951.426467
0.859375 0.899341 8 FSC 0.716309 SNR 5.049935e+00 FNCF 0.841373 FNCN 0.745881 FSCfull 0.834709 Cref 0.913624 NoiseWeighted 95324620.998659
0.863281 0.000000 0 FSC -0.812524 SNR -8.965661e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.668008 Cref 0.000000 NoiseWeighted 0.000000

...
</pre>
 
It is found that the higher SN ratio is the higher the resolution is. 
 

== References ==
[http://grigoriefflab.janelia.org/node/55 Ab initio resolution measurement for single particle structures] (Calculate FNC, FNCF, FNCN, and estimate SNR,FSC) 
[http://nramm.scripps.edu/wp-content/seminars/2004/dlecture/ Single particle electron microscopy] (Calculate Cref, NoiseWeighted from FSC)

mrcImageSpatialFrequencyFilter

2014-10-27T04:13:50Z

Kinoshita: Created page with "'''mrcImageSpatialFrequencyFilter''' is Eos's Command that that filters depending on the weight for each set spatial frequency. == List of option == === Main option..."

mrcImageFourierNeighborCorrelation

2014-10-27T03:48:18Z

Kinoshita: /* SN比毎のdata比較 */

'''mrcImageFourierNeighborCorrelation''' is [[Eos]]'s [[Command]] to check a resolution by utilizing the redundancy of [[Fourier Space]].

== 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]](3D)</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[ASCII]]([[FNC]])</td>
<td>stdout</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>delta on [[Fourier Space]]</td>
<td>0.0</td>
</tr>
<tr>
<td>-C</td>
<td>Optional</td>
<td>CentreMode</td>
<td>0</td>
</tr>
<tr>
<td>-M</td>
<td>Optional</td>
<td>[[Interpolation Mode]]</td>
<td>0</td>
</tr>
<tr>
<td>-FSC</td>
<td>Optional</td>
<td>Output flag of predicted [[FSC]]</td>
<td></td>
</tr>
<tr>
<td>-Cref</td>
<td>Optional</td>
<td>Output flag of Cref</td>
<td></td>
</tr>
<tr>
<td>-FSCfull</td>
<td>Optional</td>
<td>Output flag of [[FSC]] full</td>
<td></td>
</tr>
<tr>
<td>-NoiseWeighted</td>
<td>Optional</td>
<td>NoiseWeighted: Cref*exp(-Brestore/(4*d^2)</td>
<td>-100.0</td>
</tr>
<tr>
<td>-mask</td>
<td>Optional</td>
<td>Input: [[mrcImage]](3D)(Mask for [[FSC]])</td>
<td>NULL</td>
</tr>
<tr>
<td>-maskBack</td>
<td>Optional</td>
<td>Input: [[mrcImage]](3D)(Mask for [[FSC]] Back)</td>
<td>NULL</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>
 

=== -mask details ===
Use the binary file as same shape as -i file. 
 
(Example) 
First, Get Low-frequency component of -i file by using [[mrcImageLowPassFilter]]. 
Next, binarize it by using [[mrcImageBinalization]](m=32). 
 

=== -maskBack details ===
Use the file. (The size is same as -i file, and the all value is 1) 
In addition, In addition, multiply the same windowing as -i file. 
 
(Example) 
First, get size of -i file by using [[mrcInfo]]. 
Next, create the image whose value of all is 1, by using [[mrcImageNullImageCreate]](v=1). 
Finally, multiply the same windowing by using [[mrcImageWindowing]]. 
 

=== -C details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Centre is ImageCentre Shift: (Nx/2.0, Ny/2.0, Nz/2.0 )</td>
</tr>
<tr>
<td>1</td>
<td>Centre is BottomLeft Shift: (0, 0, 0 )</td>
</tr>
<tr>
<td>2</td>
<td>Use StartN Shift: (StartNx,StartNy,StartNz)</td>
</tr>
</table>
 

=== -M details ===
c.f. [[Interpolation Mode]]

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
 

== Execution example ==
===[[Media:Input-1VOM-N.mrc|Input file]] image===
<table>
<tr>
<td>[[File:Input-1VOM-N.png]] 
xy-plane 
</td>
<td>[[File:Input1-1VOM-N.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2390.42 (77, 14, 69) 
4374.62 (17, 62, 46) 
72.1487 
577.82 
0.722275 
</td>
</tr>
</table>
 

<pre>
0.000000 0.863711 1
0.012500 0.553876 18
0.025000 0.170684 64
0.037500 0.221808 146
0.050000 0.230874 266
0.062500 0.280359 382
0.075000 0.269777 588
0.087500 0.280955 746
0.100000 0.322332 1002
0.112500 0.249747 1294

...

0.750000 -0.005313 2256
0.762500 0.036957 1688
0.775000 0.021723 1264
0.787500 0.010364 864
0.800000 -0.026498 568
0.812500 -0.009259 312
0.825000 -0.009356 144
0.837500 0.030291 72
0.850000 -0.109028 8
0.862500 0.000000 0
</pre>
 

[[File:Outdata-mrcImageFourierNeighborCorrelation.png]] 
Because this image does not have redundancy at all, the FNC decreases suddenly. 
 

=== Input file(Padding) ===
Padding of the above file by 0 adds redundancy to the image. 
This file can be created by [[Tutorial List]]. 
<table>
<tr>
<td>[[File:Input-1VOM-N-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-1VOM-N-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-2390.42 (165, 102, 147) 
4374.62 (105, 150, 124) 
2.75226 
113.698 
0.0277584 
</td>
</tr>
</table>
 

Output 
<pre>
0.000000 0.991796 1
0.003906 0.982392 18
0.007812 0.963411 62
0.011719 0.934883 98
0.015625 0.902410 210
0.019531 0.864067 350
0.023438 0.841587 450
0.027344 0.856990 602
0.031250 0.887424 762
0.035156 0.887318 1142

...

0.828125 0.811470 1320
0.832031 0.812934 1352
0.835938 0.823354 1152
0.839844 0.817772 800
0.843750 0.824257 288
0.847656 0.821916 392
0.851562 0.765112 200
0.855469 0.812369 72
0.859375 0.777638 8
0.863281 0.000000 0
</pre>
 
[[File:Outdata1-mrcImageFourierNeighborCorrelation.png]] 
In the case of an image which has redundancy, FNC on high frequency area is also the high value. 
 

==== Option -d ====
===== Case: d=0.025 =====
<pre>
0.000000 0.961060 147
0.025000 0.884961 3596
0.050000 0.876699 13334
0.075000 0.884583 30012
0.100000 0.888691 53048
0.125000 0.873868 82634
0.150000 0.860938 118688
0.175000 0.862499 161322
0.200000 0.875542 211496
0.225000 0.882194 266468
0.250000 0.874374 330126
0.275000 0.868385 398912
0.300000 0.861123 473858
0.325000 0.852294 557496
0.350000 0.846181 647132
0.375000 0.842054 739454
0.400000 0.836904 845340
0.425000 0.836800 950870
0.450000 0.834607 1068284
0.475000 0.831828 1190048
0.500000 0.829300 1284690
0.525000 0.827369 1227836
0.550000 0.824926 1141760
0.575000 0.824884 1043124
0.600000 0.823838 930008
0.625000 0.822523 803708
0.650000 0.821119 663864
0.675000 0.820229 512012
0.700000 0.819524 348596
0.725000 0.818723 217808
0.750000 0.820472 135048
0.775000 0.825089 77288
0.800000 0.815167 38120
0.825000 0.816419 13488
0.850000 0.814605 1760

</pre>
 

[[File:Outdata-d-mrcImageFourierNeighborCorrelation.png]] 
 

==== Case: using -FSC and specifying files as -mask, -maskBack ====
-mask 's file: This file can be created by [[Tutorial List]]. 
 
Setting of Makefile 
<pre>
MASK_VALUE=0.0125
</pre>
<table>
<tr>
<td>[[File:Input-Noise1-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-Noise1-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (111, 135, 84) 
0.0158784 
0.125005 
3.05189e-05 
</td>
</tr>
</table>
 

-maskBack 's file: This file can be created by [[Tutorial List]]. 
<table>
<tr>
<td>[[File:Input-Null1-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-Null1-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>1 (0, 0, 0) 
1 (88, 88, 78) 
0.038147 
0.191551 
4.67654e-05 
</td>
</tr>
</table>
 

Output 
<pre>
FNCF 0.894073 FNCN 0.820233
0.000000 0.991796 1 FSC -7.183377 SNR -1.755602e+00 FNCF 0.951711 FNCN -0.366379
0.003906 0.982392 18 FSC -11.199417 SNR -1.836058e+00 FNCF 0.903913 FNCN 0.595703
0.007812 0.963411 62 FSC 31.808857 SNR -2.064916e+00 FNCF 0.844130 FNCN 0.798653
0.011719 0.934883 98 FSC 3.471075 SNR -2.809364e+00 FNCF 0.845211 FNCN 0.799688
0.015625 0.902410 210 FSC 1.254576 SNR -9.856209e+00 FNCF 0.886035 FNCN 0.734901
0.019531 0.864067 350 FSC 0.422099 SNR 1.460802e+00 FNCF 0.893608 FNCN 0.787841
0.023438 0.841587 450 FSC 0.169033 SNR 4.068355e-01 FNCF 0.889512 FNCN 0.827210
0.027344 0.856990 602 FSC 0.331378 SNR 9.912261e-01 FNCF 0.873868 FNCN 0.811905
0.031250 0.887424 762 FSC 0.834791 SNR 1.010589e+01 FNCF 0.889606 FNCN 0.818398
0.035156 0.887318 1142 FSC 0.832380 SNR 9.931723e+00 FNCF 0.897804 FNCN 0.824152
0.039062 0.879608 1250 FSC 0.672387 SNR 4.104771e+00 FNCF 0.894009 FNCN 0.803585
0.042969 0.874892 1458 FSC 0.587592 SNR 2.849572e+00 FNCF 0.887004 FNCN 0.803368
0.046875 0.874435 1814 FSC 0.579834 SNR 2.760026e+00 FNCF 0.884325 FNCN 0.816900
0.050781 0.877405 2178 FSC 0.631676 SNR 3.429994e+00 FNCF 0.896430 FNCN 0.821318
0.054688 0.875931 2498 FSC 0.605536 SNR 3.070172e+00 FNCF 0.908684 FNCN 0.828866
0.058594 0.876247 2622 FSC 0.611065 SNR 3.142250e+00 FNCF 0.910457 FNCN 0.831098
0.062500 0.884193 3338 FSC 0.763974 SNR 6.473637e+00 FNCF 0.898597 FNCN 0.823882
0.066406 0.890079 3722 FSC 0.897373 SNR 1.748804e+01 FNCF 0.888997 FNCN 0.820916
0.070312 0.888096 4170 FSC 0.850229 SNR 1.135368e+01 FNCF 0.896541 FNCN 0.822739
0.074219 0.881947 4358 FSC 0.717896 SNR 5.089588e+00 FNCF 0.897502 FNCN 0.819764

...

0.789062 0.821038 8592 FSC 0.005476 SNR 1.101324e-02 FNCF 0.888864 FNCN 0.821332
0.792969 0.813430 7208 FSC -0.044041 SNR -8.436653e-02 FNCF 0.889662 FNCN 0.818472
0.796875 0.813393 6296 FSC -0.044265 SNR -8.477789e-02 FNCF 0.890629 FNCN 0.815216
0.800781 0.812815 5544 FSC -0.047832 SNR -9.129702e-02 FNCF 0.894048 FNCN 0.808839
0.804688 0.814086 5360 FSC -0.039964 SNR -7.685736e-02 FNCF 0.892404 FNCN 0.813711
0.808594 0.814528 4344 FSC -0.037196 SNR -7.172486e-02 FNCF 0.886577 FNCN 0.828553
0.812500 0.813960 3272 FSC -0.040749 SNR -7.830638e-02 FNCF 0.887005 FNCN 0.826397
0.816406 0.816745 3096 FSC -0.023074 SNR -4.510691e-02 FNCF 0.895393 FNCN 0.818955
0.820312 0.823611 2840 FSC 0.023408 SNR 4.793880e-02 FNCF 0.898811 FNCN 0.825501
0.824219 0.810629 2240 FSC -0.061066 SNR -1.151032e-01 FNCF 0.895444 FNCN 0.827601
0.828125 0.811470 1320 FSC -0.056018 SNR -1.060935e-01 FNCF 0.903966 FNCN 0.820170
0.832031 0.812934 1352 FSC -0.047100 SNR -8.996210e-02 FNCF 0.908462 FNCN 0.826379
0.835938 0.823354 1152 FSC 0.021585 SNR 4.412220e-02 FNCF 0.887402 FNCN 0.824615
0.839844 0.817772 800 FSC -0.016396 SNR -3.226391e-02 FNCF 0.869994 FNCN 0.815638
0.843750 0.824257 288 FSC 0.028007 SNR 5.762863e-02 FNCF 0.880944 FNCN 0.824954
0.847656 0.821916 392 FSC 0.011526 SNR 2.331998e-02 FNCF 0.899626 FNCN 0.837368
0.851562 0.765112 200 FSC -0.271800 SNR -4.274263e-01 FNCF 0.925513 FNCN 0.800424
0.855469 0.812369 72 FSC -0.050561 SNR -9.625498e-02 FNCF 0.902540 FNCN 0.779785
0.859375 0.777638 8 FSC -0.223864 SNR -3.658316e-01 FNCF 0.774510 FNCN 0.868126
0.863281 0.000000 0 FSC -0.847425 SNR -9.174121e-01 FNCF 0.000000 FNCN 0.000000
</pre>
Display the output of FSC, SNR, FNCF, FNCN. 
 

<table>
<tr>
<td>[[File:Outdata-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
<td>[[File:Outdata-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
</tr>
<tr>
<td>[[File:Outdata-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
</table>
These graphs are removed the first and last 10 point. 
 

Or later, use same files as -mask, -maskBack. 
 

===== Case: using -FSCfull, -Cref, and NoiseWeighted=-100 =====
Output 
<pre>
FNCF 0.893745 FNCN 0.820252
0.000000 0.991796 1 FSC -6.985231 SNR -1.749538e+00 FNCF 0.704805 FNCN 0.391308 FSCfull 2.334156 Cref 0.000000 NoiseWeighted 0.000000
0.003906 0.982392 18 FSC -10.699472 SNR -1.829052e+00 FNCF 0.821228 FNCN 0.684129 FSCfull 2.206197 Cref 0.000000 NoiseWeighted 0.000000
0.007812 0.963411 62 FSC 37.413739 SNR -2.054924e+00 FNCF 0.884407 FNCN 0.773688 FSCfull 1.947935 Cref 1.395685 NoiseWeighted 0.000000
0.011719 0.934883 98 FSC 3.542894 SNR -2.786505e+00 FNCF 0.896445 FNCN 0.837667 FSCfull 1.559752 Cref 1.248900 NoiseWeighted 0.000000
0.015625 0.902410 210 FSC 1.267348 SNR -9.480880e+00 FNCF 0.879666 FNCN 0.865827 FSCfull 1.117912 Cref 1.057314 NoiseWeighted 0.000000
0.019531 0.864067 350 FSC 0.424680 SNR 1.476325e+00 FNCF 0.881884 FNCN 0.835433 FSCfull 0.596176 Cref 0.772124 NoiseWeighted 0.000000
0.023438 0.841587 450 FSC 0.169793 SNR 4.090381e-01 FNCF 0.901388 FNCN 0.806285 FSCfull 0.290296 Cref 0.538791 NoiseWeighted 0.000000
0.027344 0.856990 602 FSC 0.333237 SNR 9.995687e-01 FNCF 0.897467 FNCN 0.819184 FSCfull 0.499892 Cref 0.707031 NoiseWeighted 0.000000
0.031250 0.887424 762 FSC 0.841616 SNR 1.062755e+01 FNCF 0.888027 FNCN 0.826006 FSCfull 0.913997 Cref 0.956032 NoiseWeighted 0.000000
0.035156 0.887318 1142 FSC 0.839175 SNR 1.043589e+01 FNCF 0.885703 FNCN 0.827937 FSCfull 0.912556 Cref 0.955278 NoiseWeighted 0.000000
0.039062 0.879608 1250 FSC 0.677353 SNR 4.198725e+00 FNCF 0.886124 FNCN 0.821982 FSCfull 0.807645 Cref 0.898691 NoiseWeighted 0.000000
0.042969 0.874892 1458 FSC 0.591685 SNR 2.898177e+00 FNCF 0.893947 FNCN 0.826635 FSCfull 0.743470 Cref 0.862247 NoiseWeighted 0.000000
0.046875 0.874435 1814 FSC 0.583850 SNR 2.805960e+00 FNCF 0.893287 FNCN 0.825939 FSCfull 0.737254 Cref 0.858635 NoiseWeighted 0.000000
0.050781 0.877405 2178 FSC 0.636213 SNR 3.497730e+00 FNCF 0.891071 FNCN 0.829329 FSCfull 0.777666 Cref 0.881854 NoiseWeighted 0.000000
0.054688 0.875931 2498 FSC 0.609808 SNR 3.125677e+00 FNCF 0.882848 FNCN 0.823179 FSCfull 0.757616 Cref 0.870411 NoiseWeighted 0.000000
0.058594 0.876247 2622 FSC 0.615393 SNR 3.200107e+00 FNCF 0.884282 FNCN 0.810449 FSCfull 0.761911 Cref 0.872875 NoiseWeighted 0.000000
0.062500 0.884193 3338 FSC 0.769958 SNR 6.694059e+00 FNCF 0.889011 FNCN 0.809316 FSCfull 0.870030 Cref 0.932754 NoiseWeighted 0.000000
0.066406 0.890079 3722 FSC 0.904980 SNR 1.904823e+01 FNCF 0.895025 FNCN 0.809225 FSCfull 0.950120 Cref 0.974741 NoiseWeighted 0.000000
0.070312 0.888096 4170 FSC 0.857243 SNR 1.200983e+01 FNCF 0.899517 FNCN 0.816330 FSCfull 0.923135 Cref 0.960799 NoiseWeighted 0.000000
0.074219 0.881947 4358 FSC 0.723358 SNR 5.229561e+00 FNCF 0.896087 FNCN 0.821250 FSCfull 0.839475 Cref 0.916229 NoiseWeighted 0.000000

...

0.789062 0.821038 8592 FSC 0.005374 SNR 1.080707e-02 FNCF 0.889648 FNCN 0.823173 FSCfull 0.010692 Cref 0.103400 NoiseWeighted 0.000000
0.792969 0.813430 7208 FSC -0.044355 SNR -8.494283e-02 FNCF 0.891566 FNCN 0.824518 FSCfull -0.092828 Cref 0.000000 NoiseWeighted 0.000000
0.796875 0.813393 6296 FSC -0.044580 SNR -8.535559e-02 FNCF 0.891161 FNCN 0.818115 FSCfull -0.093321 Cref 0.000000 NoiseWeighted 0.000000
0.800781 0.812815 5544 FSC -0.048161 SNR -9.189702e-02 FNCF 0.892987 FNCN 0.824486 FSCfull -0.101197 Cref 0.000000 NoiseWeighted 0.000000
0.804688 0.814086 5360 FSC -0.040262 SNR -7.740746e-02 FNCF 0.893581 FNCN 0.822037 FSCfull -0.083902 Cref 0.000000 NoiseWeighted 0.000000
0.808594 0.814528 4344 FSC -0.037483 SNR -7.225678e-02 FNCF 0.896030 FNCN 0.823916 FSCfull -0.077884 Cref 0.000000 NoiseWeighted 0.000000
0.812500 0.813960 3272 FSC -0.041049 SNR -7.886156e-02 FNCF 0.895996 FNCN 0.815310 FSCfull -0.085613 Cref 0.000000 NoiseWeighted 0.000000
0.816406 0.816745 3096 FSC -0.023301 SNR -4.554071e-02 FNCF 0.903188 FNCN 0.808224 FSCfull -0.047714 Cref 0.000000 NoiseWeighted 0.000000
0.820312 0.823611 2840 FSC 0.023389 SNR 4.789782e-02 FNCF 0.892511 FNCN 0.822457 FSCfull 0.045708 Cref 0.213795 NoiseWeighted 0.000000
0.824219 0.810629 2240 FSC -0.061448 SNR -1.157814e-01 FNCF 0.894149 FNCN 0.805167 FSCfull -0.130942 Cref 0.000000 NoiseWeighted 0.000000
0.828125 0.811470 1320 FSC -0.056380 SNR -1.067427e-01 FNCF 0.895955 FNCN 0.802224 FSCfull -0.119498 Cref 0.000000 NoiseWeighted 0.000000
0.832031 0.812934 1352 FSC -0.047426 SNR -9.055756e-02 FNCF 0.913658 FNCN 0.815504 FSCfull -0.099575 Cref 0.000000 NoiseWeighted 0.000000
0.835938 0.823354 1152 FSC 0.021557 SNR 4.406357e-02 FNCF 0.917390 FNCN 0.826730 FSCfull 0.042204 Cref 0.205436 NoiseWeighted 0.000000
0.839844 0.817772 800 FSC -0.016595 SNR -3.264812e-02 FNCF 0.886657 FNCN 0.834540 FSCfull -0.033750 Cref 0.000000 NoiseWeighted 0.000000
0.843750 0.824257 288 FSC 0.028009 SNR 5.763305e-02 FNCF 0.847956 FNCN 0.782642 FSCfull 0.054492 Cref 0.233436 NoiseWeighted 0.000000
0.847656 0.821916 392 FSC 0.011451 SNR 2.316754e-02 FNCF 0.862911 FNCN 0.801126 FSCfull 0.022643 Cref 0.150476 NoiseWeighted 0.000000
0.851562 0.765112 200 FSC -0.272800 SNR -4.286612e-01 FNCF 0.888032 FNCN 0.840993 FSCfull -0.750275 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.812369 72 FSC -0.050901 SNR -9.687171e-02 FNCF 0.851466 FNCN 0.740952 FSCfull -0.107262 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.777638 8 FSC -0.224759 SNR -3.670256e-01 FNCF 0.680124 FNCN 0.689641 FSCfull -0.579843 Cref 0.000000 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.848036 SNR -9.177697e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -11.160973 Cref 0.000000 NoiseWeighted 0.000000
</pre>
Display the output of FNCfull, Cref, NoiseWeighted. 
Because Cref at R=0 is negative, it is corrected 0. Therefore, all NoiseWeighted is output as 0. 
 

<table>
<tr>
<td>[[File:Outdata-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
<td>[[File:Outdata-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
</tr>
<tr>
<td>[[File:Outdata-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
</table>
These graphs are removed the last point. 
 

===== Case: using -FSCfull, -Cref, and d=0.025, NoiseWeighted=-100 =====
Output 
<pre>
0.000000 0.961060 147 FSC 19.604071 SNR -2.107503e+00 FNCF 0.881653 FNCN 0.813775 FSCfull 1.902932 Cref 1.379468 NoiseWeighted 1.379468
0.025000 0.884961 3596 FSC 0.778687 SNR 7.036960e+00 FNCF 0.890538 FNCN 0.819820 FSCfull 0.875575 Cref 0.935722 NoiseWeighted 0.950457
0.050000 0.876699 13334 FSC 0.618184 SNR 3.238129e+00 FNCF 0.901366 FNCN 0.819141 FSCfull 0.764047 Cref 0.874098 NoiseWeighted 0.930472
0.075000 0.884583 30012 FSC 0.770666 SNR 6.720909e+00 FNCF 0.893296 FNCN 0.821043 FSCfull 0.870482 Cref 0.932996 NoiseWeighted 1.073872
0.100000 0.888691 53048 FSC 0.862079 SNR 1.250108e+01 FNCF 0.894515 FNCN 0.820477 FSCfull 0.925932 Cref 0.962254 NoiseWeighted 1.235558
0.125000 0.873868 82634 FSC 0.569634 SNR 2.647204e+00 FNCF 0.893251 FNCN 0.822256 FSCfull 0.725817 Cref 0.851949 NoiseWeighted 1.259099
0.150000 0.860938 118688 FSC 0.380513 SNR 1.228478e+00 FNCF 0.892919 FNCN 0.822140 FSCfull 0.551263 Cref 0.742471 NoiseWeighted 1.303077
0.175000 0.862499 161322 FSC 0.400894 SNR 1.338309e+00 FNCF 0.895633 FNCN 0.819697 FSCfull 0.572341 Cref 0.756532 NoiseWeighted 1.626799
0.200000 0.875542 211496 FSC 0.597988 SNR 2.974978e+00 FNCF 0.892626 FNCN 0.820726 FSCfull 0.748426 Cref 0.865116 NoiseWeighted 2.351630
0.225000 0.882194 266468 FSC 0.721495 SNR 5.181196e+00 FNCF 0.893766 FNCN 0.819388 FSCfull 0.838219 Cref 0.915543 NoiseWeighted 3.245882
0.250000 0.874374 330126 FSC 0.578097 SNR 2.740421e+00 FNCF 0.892148 FNCN 0.819562 FSCfull 0.732650 Cref 0.855950 NoiseWeighted 4.083509
0.275000 0.868385 398912 FSC 0.483453 SNR 1.871867e+00 FNCF 0.893360 FNCN 0.818555 FSCfull 0.651794 Cref 0.807338 NoiseWeighted 5.347409
0.300000 0.861123 473858 FSC 0.382903 SNR 1.240984e+00 FNCF 0.894373 FNCN 0.819237 FSCfull 0.553767 Cref 0.744156 NoiseWeighted 7.060352
0.325000 0.852294 557496 FSC 0.277607 SNR 7.685764e-01 FNCF 0.894332 FNCN 0.820382 FSCfull 0.434573 Cref 0.659222 NoiseWeighted 9.243587
0.350000 0.846181 647132 FSC 0.213624 SNR 5.433115e-01 FNCF 0.893565 FNCN 0.819353 FSCfull 0.352043 Cref 0.593332 NoiseWeighted 12.685995
0.375000 0.842054 739454 FSC 0.173934 SNR 4.211135e-01 FNCF 0.894578 FNCN 0.820175 FSCfull 0.296326 Cref 0.544359 NoiseWeighted 18.310566
0.400000 0.836904 845340 FSC 0.127900 SNR 2.933142e-01 FNCF 0.895293 FNCN 0.819759 FSCfull 0.226793 Cref 0.476228 NoiseWeighted 26.001148
0.425000 0.836800 950870 FSC 0.127013 SNR 2.909839e-01 FNCF 0.894829 FNCN 0.820387 FSCfull 0.225397 Cref 0.474760 NoiseWeighted 43.409539
0.450000 0.834607 1068284 FSC 0.108519 SNR 2.434566e-01 FNCF 0.894605 FNCN 0.819227 FSCfull 0.195790 Cref 0.442482 NoiseWeighted 69.905495
0.475000 0.831828 1190048 FSC 0.085938 SNR 1.880360e-01 FNCF 0.893867 FNCN 0.819873 FSCfull 0.158275 Cref 0.397838 NoiseWeighted 112.046453
0.500000 0.829300 1284690 FSC 0.066183 SNR 1.417471e-01 FNCF 0.893855 FNCN 0.821343 FSCfull 0.124149 Cref 0.352348 NoiseWeighted 182.520960
0.525000 0.827369 1227836 FSC 0.051568 SNR 1.087446e-01 FNCF 0.894786 FNCN 0.820592 FSCfull 0.098079 Cref 0.313176 NoiseWeighted 307.856690
0.550000 0.824926 1141760 FSC 0.033639 SNR 6.962054e-02 FNCF 0.893119 FNCN 0.820052 FSCfull 0.065089 Cref 0.255125 NoiseWeighted 491.027655
0.575000 0.824884 1043124 FSC 0.033335 SNR 6.896969e-02 FNCF 0.894419 FNCN 0.819959 FSCfull 0.064520 Cref 0.254007 NoiseWeighted 987.556329
0.600000 0.823838 930008 FSC 0.025857 SNR 5.308599e-02 FNCF 0.894395 FNCN 0.819809 FSCfull 0.050410 Cref 0.224522 NoiseWeighted 1819.317450
0.625000 0.822523 803708 FSC 0.016596 SNR 3.375260e-02 FNCF 0.894275 FNCN 0.820134 FSCfull 0.032651 Cref 0.180695 NoiseWeighted 3148.491102
0.650000 0.821119 663864 FSC 0.006894 SNR 1.388304e-02 FNCF 0.894622 FNCN 0.820588 FSCfull 0.013693 Cref 0.117017 NoiseWeighted 4523.596884
0.675000 0.820229 512012 FSC 0.000838 SNR 1.678337e-03 FNCF 0.893624 FNCN 0.820495 FSCfull 0.001676 Cref 0.040933 NoiseWeighted 3622.105778
0.700000 0.819524 348596 FSC -0.003899 SNR -7.768473e-03 FNCF 0.894646 FNCN 0.819049 FSCfull -0.007829 Cref 0.000000 NoiseWeighted 0.000000
0.725000 0.818723 217808 FSC -0.009236 SNR -1.830228e-02 FNCF 0.893341 FNCN 0.820796 FSCfull -0.018643 Cref 0.000000 NoiseWeighted 0.000000
0.750000 0.820472 135048 FSC 0.002487 SNR 4.985434e-03 FNCF 0.891864 FNCN 0.822416 FSCfull 0.004961 Cref 0.070432 NoiseWeighted 0.000000
0.775000 0.825089 77288 FSC 0.034817 SNR 7.214486e-02 FNCF 0.895766 FNCN 0.818517 FSCfull 0.067290 Cref 0.259404 NoiseWeighted 0.000000
0.800000 0.815167 38120 FSC -0.032256 SNR -6.249550e-02 FNCF 0.898301 FNCN 0.823939 FSCfull -0.066662 Cref 0.000000 NoiseWeighted 0.000000
0.825000 0.816419 13488 FSC -0.024276 SNR -4.740110e-02 FNCF 0.894416 FNCN 0.824161 FSCfull -0.049760 Cref 0.000000 NoiseWeighted 0.000000
0.850000 0.814605 1760 FSC -0.035796 SNR -6.911783e-02 FNCF 0.894095 FNCN 0.806454 FSCfull -0.074250 Cref 0.000000 NoiseWeighted 0.000000
</pre>
On R=0.675000 (or below), Noiseweighted is outputted. 
 

<table>
<tr>
<td>[[File:Outdata-d-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata-d-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
<tr>
<td>[[File:Outdata-d-FNC-mrcImageFourierNeighborCorrelation.png]] 
FNC 
</td>
<td>[[File:Outdata-d-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
</tr>
<tr>
<td>[[File:Outdata-d-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
<td>[[File:Outdata-d-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
</tr>
<tr>
<td>[[File:Outdata-d-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
<td>[[File:Outdata-d-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
<tr>
<td>[[File:Outdata1-d-mrcImageFourierNeighborCorrelation.png]] 
FNC, FNCF, FNCN 
</td>
<td>[[File:Outdata1-d-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted(~ R=0.375000) 
</td>
</tr>
</table>
These graphs are removed the first point. 
 
As above, if FNC is between FNCF and FNCN, the estimate value of SNR, FSC, FSCfull is positive. Then, Cref and NoiseWeighted can be calculated as real value. 
 

==== Case: using -FSC and specifying files as -mask, -maskBack (vol.2)====
In [[#Case: using -FSC and specifying files as -mask, -maskBack|above example]], The half value point of Low-Pass Filter to create mask file is 0.0125(80Å). Therefore, it is coarse almost as an ellipse. 
This time prepare a mask file whose half value point is 0.05(20Å). 
-mask 's file: This file can be created by [[Tutorial List]]. 
 
Setting of Makefile 
<pre>
MASK_VALUE=0.05
</pre>
<table>
<tr>
<td>[[File:Input-Mask1-P.png]] 
xy-plane 
</td>
<td>[[File:Input1-Mask1-P.png]] 
yz-plane 
</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
1 (114, 141, 82) 
0.00774205 
0.0876476 
2.13983e-05 
</td>
</tr>
</table>
 

-maskBack: Use same file. 
 

===== NoiseWeighted=-100, -FSCfull, -Cref =====
<pre>
FNCF 0.914907 FNCN 0.819953
0.000000 0.991796 1 FSC 9.512511 SNR -2.234948e+00 FNCF 0.982818 FNCN 0.771068 FSCfull 1.809750 Cref 1.345270 NoiseWeighted 1.345270
0.003906 0.982392 18 FSC 5.913521 SNR -2.407040e+00 FNCF 0.979065 FNCN 0.796796 FSCfull 1.710712 Cref 1.307942 NoiseWeighted 1.308441
0.007812 0.963411 62 FSC 3.088481 SNR -2.957634e+00 FNCF 0.971746 FNCN 0.760178 FSCfull 1.510821 Cref 1.229154 NoiseWeighted 1.231031
0.011719 0.934883 98 FSC 1.532837 SNR -5.753490e+00 FNCF 0.963111 FNCN 0.803158 FSCfull 1.210372 Cref 1.100169 NoiseWeighted 1.103953
0.015625 0.902410 210 FSC 0.767399 SNR 6.598402e+00 FNCF 0.955381 FNCN 0.827784 FSCfull 0.868393 Cref 0.931876 NoiseWeighted 0.937581
0.019531 0.864067 350 FSC 0.302572 SNR 8.676784e-01 FNCF 0.940646 FNCN 0.801457 FSCfull 0.464576 Cref 0.681598 NoiseWeighted 0.688129
0.023438 0.841587 450 FSC 0.128559 SNR 2.950497e-01 FNCF 0.929146 FNCN 0.807370 FSCfull 0.227829 Cref 0.477314 NoiseWeighted 0.483914
0.027344 0.856990 602 FSC 0.242277 SNR 6.394883e-01 FNCF 0.922377 FNCN 0.819179 FSCfull 0.390054 Cref 0.624543 NoiseWeighted 0.636326
0.031250 0.887424 762 FSC 0.551068 SNR 2.455017e+00 FNCF 0.922938 FNCN 0.811850 FSCfull 0.710566 Cref 0.842951 NoiseWeighted 0.863784
0.035156 0.887318 1142 FSC 0.549727 SNR 2.441751e+00 FNCF 0.924502 FNCN 0.804822 FSCfull 0.709450 Cref 0.842289 NoiseWeighted 0.868721
0.039062 0.879608 1250 FSC 0.457992 SNR 1.689984e+00 FNCF 0.927185 FNCN 0.798498 FSCfull 0.628251 Cref 0.792623 NoiseWeighted 0.823443
0.042969 0.874892 1458 FSC 0.407043 SNR 1.372928e+00 FNCF 0.927562 FNCN 0.809349 FSCfull 0.578580 Cref 0.760644 NoiseWeighted 0.796577
0.046875 0.874435 1814 FSC 0.402297 SNR 1.346145e+00 FNCF 0.920495 FNCN 0.820928 FSCfull 0.573769 Cref 0.757475 NoiseWeighted 0.800249
0.050781 0.877405 2178 FSC 0.433740 SNR 1.531945e+00 FNCF 0.907902 FNCN 0.804488 FSCfull 0.605047 Cref 0.777848 NoiseWeighted 0.829646
0.054688 0.875931 2498 FSC 0.417965 SNR 1.436221e+00 FNCF 0.903627 FNCN 0.813420 FSCfull 0.589528 Cref 0.767807 NoiseWeighted 0.827416
0.058594 0.876247 2622 FSC 0.421315 SNR 1.456114e+00 FNCF 0.912572 FNCN 0.826763 FSCfull 0.592853 Cref 0.769969 NoiseWeighted 0.838975
0.062500 0.884193 3338 FSC 0.511185 SNR 2.091527e+00 FNCF 0.916913 FNCN 0.821846 FSCfull 0.676535 Cref 0.822518 NoiseWeighted 0.906895
0.066406 0.890079 3722 FSC 0.585445 SNR 2.824450e+00 FNCF 0.917732 FNCN 0.820012 FSCfull 0.738524 Cref 0.859374 NoiseWeighted 0.959536
0.070312 0.888096 4170 FSC 0.559622 SNR 2.541557e+00 FNCF 0.918467 FNCN 0.831005 FSCfull 0.717638 Cref 0.847135 NoiseWeighted 0.958583
0.074219 0.881947 4358 FSC 0.484656 SNR 1.880902e+00 FNCF 0.920695 FNCN 0.829698 FSCfull 0.652886 Cref 0.808014 NoiseWeighted 0.927312

...

0.644531 0.822764 109556 FSC 0.015021 SNR 3.049937e-02 FNCF 0.914710 FNCN 0.819465 FSCfull 0.029597 Cref 0.172037 NoiseWeighted 5571.763528
0.648438 0.820426 104768 FSC 0.002494 SNR 5.000113e-03 FNCF 0.916695 FNCN 0.818935 FSCfull 0.004975 Cref 0.070535 NoiseWeighted 2591.879420
0.652344 0.820764 101724 FSC 0.004285 SNR 8.606361e-03 FNCF 0.915339 FNCN 0.815352 FSCfull 0.008533 Cref 0.092374 NoiseWeighted 3854.118436
0.656250 0.821992 98396 FSC 0.010851 SNR 2.194065e-02 FNCF 0.914227 FNCN 0.817587 FSCfull 0.021470 Cref 0.146525 NoiseWeighted 6946.843637
0.660156 0.820556 94632 FSC 0.003182 SNR 6.384020e-03 FNCF 0.912940 FNCN 0.820474 FSCfull 0.006344 Cref 0.079646 NoiseWeighted 4294.096180
0.664062 0.819228 90908 FSC -0.003806 SNR -7.583799e-03 FNCF 0.912924 FNCN 0.819343 FSCfull -0.007642 Cref 0.000000 NoiseWeighted 0.000000
0.667969 0.819197 86684 FSC -0.003967 SNR -7.901843e-03 FNCF 0.914583 FNCN 0.817105 FSCfull -0.007965 Cref 0.000000 NoiseWeighted 0.000000
0.671875 0.820568 82776 FSC 0.003245 SNR 6.510316e-03 FNCF 0.915174 FNCN 0.819274 FSCfull 0.006468 Cref 0.080425 NoiseWeighted 0.000000
0.675781 0.820683 80372 FSC 0.003858 SNR 7.746611e-03 FNCF 0.913751 FNCN 0.818000 FSCfull 0.007687 Cref 0.087676 NoiseWeighted 0.000000
0.679688 0.821076 75108 FSC 0.005946 SNR 1.196247e-02 FNCF 0.913970 FNCN 0.815727 FSCfull 0.011821 Cref 0.108725 NoiseWeighted 0.000000

...

0.828125 0.811470 1320 FSC -0.042763 SNR -8.201861e-02 FNCF 0.917130 FNCN 0.825454 FSCfull -0.089347 Cref 0.000000 NoiseWeighted 0.000000
0.832031 0.812934 1352 FSC -0.035646 SNR -6.883734e-02 FNCF 0.920492 FNCN 0.823277 FSCfull -0.073926 Cref 0.000000 NoiseWeighted 0.000000
0.835938 0.823354 1152 FSC 0.018231 SNR 3.713860e-02 FNCF 0.925875 FNCN 0.800023 FSCfull 0.035809 Cref 0.189232 NoiseWeighted 0.000000
0.839844 0.817772 800 FSC -0.011359 SNR -2.246248e-02 FNCF 0.931022 FNCN 0.818680 FSCfull -0.022979 Cref 0.000000 NoiseWeighted 0.000000
0.843750 0.824257 288 FSC 0.023185 SNR 4.747129e-02 FNCF 0.926149 FNCN 0.862458 FSCfull 0.045320 Cref 0.212885 NoiseWeighted 0.000000
0.847656 0.821916 392 FSC 0.010442 SNR 2.110497e-02 FNCF 0.912921 FNCN 0.826884 FSCfull 0.020669 Cref 0.143766 NoiseWeighted 0.000000
0.851562 0.765112 200 FSC -0.224072 SNR -3.661096e-01 FNCF 0.904654 FNCN 0.721120 FSCfull -0.577560 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.812369 72 FSC -0.038404 SNR -7.396801e-02 FNCF 0.878913 FNCN 0.789634 FSCfull -0.079876 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.777638 8 FSC -0.182221 SNR -3.082684e-01 FNCF 0.792984 FNCN 0.764045 FSCfull -0.445647 Cref 0.000000 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.811947 SNR -8.962150e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.635308 Cref 0.000000 NoiseWeighted 0.000000
</pre>
Data in interval of default setting can be expressed on range of R=0.660156. 
 

<table>
<tr>
<td>[[File:Outdata2-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata2-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
<tr>
<td>[[File:Outdata2-FNC-mrcImageFourierNeighborCorrelation.png]] 
FNC 
</td>
<td>[[File:Outdata2-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
</tr>
<tr>
<td>[[File:Outdata2-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
<td>[[File:Outdata2-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
</tr>
<tr>
<td>[[File:Outdata2-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
<td>[[File:Outdata2-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
</table>
These graphs are removed the first 4 points and last 1 point. 
 

=== Compare data with each SN ratio ===
Compare output for input data with each different SN ratio as the following.br>
You can perform by [[Tutorial List]] command. 
 
Setting of Makefile 
<pre>
#### Definition ####
# Path of Input File
INPUT_PATH=${EOS_HOME}/tutorial/SampleData/1VOM.mrc
#INPUT_PATH=${EOS_HOME}/tutorial/SampleData/1VOM-N.mrc

### SN or NS for Input file
INI_SN=0.3 1 3 10 100
</pre>
 

Each input image(before padding) 
<table>
<tr>
<td>SN比 
</td>
<td>SN=0.3 
</td>
<td>SN=1 
</td>
<td>SN=3 
</td>
<td>SN=10 
</td>
<td>SN=100 
</td>
</tr>
<tr>
<td>xy-plane 
</td>
<td>[[File:Input-SN0.3-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN1-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN3-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN10-mrcImageFourierNeighborCorrelation.png]]
</td>
<td>[[File:Input-SN100-mrcImageFourierNeighborCorrelation.png]]
</td>
</tr>
<tr>
<td>yz-plane 
</td>
<td>[[File:Input1-SN0.3-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN1-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN3-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN10-mrcImageFourierNeighborCorrelation.png]] 
</td>
<td>[[File:Input1-SN100-mrcImageFourierNeighborCorrelation.png]] 
</td>
</tr>
<tr>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-7489.39 (57, 54, 75) 
8066.02 (17, 29, 46) 
68.7388 
1679.17 
2.09896 
</td>
<td>-2225.59 (26, 40, 83) 
4567.91 (28, 50, 50) 
72.5953 
578.119 
0.722649 
</td>
<td>-784.63 (44, 6, 70) 
3724.44 (41, 60, 31) 
72.3035 
337.846 
0.422308 
</td>
<td>-246.726 (17, 25, 16) 
3406.43 (20, 24, 29) 
72.1722 
299.081 
0.373851 
</td>
<td>-22.8638 (79, 41, 2) 
3399.86 (23, 55, 41) 
72.133 
294.848 
0.368559 
</td>
</tr>
</table>
 

==== Compare [[:Media:Outdata-mrcImageFourierNeighborCorrelation.zip|Output file]]s ====
 

<table>
<tr>
<td>[[File:Outdata3-FNCF-mrcImageFourierNeighborCorrelation.png]] 
FNCF 
</td>
<td>[[File:Outdata3-FNCN-mrcImageFourierNeighborCorrelation.png]] 
FNCN 
</td>
</tr>
<tr>
<td>[[File:Outdata3-FNC-mrcImageFourierNeighborCorrelation.png]] 
FNC 
</td>
<td>[[File:Outdata3-FSC-mrcImageFourierNeighborCorrelation.png]] 
FSC 
</td>
</tr>
<tr>
<td>[[File:Outdata3-SNR-mrcImageFourierNeighborCorrelation.png]] 
SNR 
</td>
<td>[[File:Outdata3-FSCfull-mrcImageFourierNeighborCorrelation.png]] 
FSCfull 
</td>
</tr>
<tr>
<td>[[File:Outdata3-Cref-mrcImageFourierNeighborCorrelation.png]] 
Cref 
</td>
<td>[[File:Outdata3-NoiseWeighted-mrcImageFourierNeighborCorrelation.png]] 
NoiseWeighted 
</td>
</tr>
</table>

==== Output for around the first point as Cref=0. ====
SN=0.3 
<pre>
...

0.125000 0.830285 12606 FSC 0.056542 SNR 1.198620e-01 FNCF 0.905793 FNCN 0.820589 FSCfull 0.107033 Cref 0.327159 NoiseWeighted 0.483509
0.128906 0.835033 13802 FSC 0.085415 SNR 1.867837e-01 FNCF 0.907524 FNCN 0.814605 FSCfull 0.157386 Cref 0.396720 NoiseWeighted 0.601033
0.132812 0.831848 14754 FSC 0.065877 SNR 1.410450e-01 FNCF 0.913083 FNCN 0.824672 FSCfull 0.123610 Cref 0.351583 NoiseWeighted 0.546440
0.136719 0.831254 15194 FSC 0.062310 SNR 1.329021e-01 FNCF 0.916913 FNCN 0.827674 FSCfull 0.117311 Cref 0.342507 NoiseWeighted 0.546532
0.140625 0.826966 16454 FSC 0.037254 SNR 7.739025e-02 FNCF 0.915416 FNCN 0.821369 FSCfull 0.071831 Cref 0.268013 NoiseWeighted 0.439405
0.144531 0.820016 17154 FSC -0.000933 SNR -1.863673e-03 FNCF 0.913586 FNCN 0.824382 FSCfull -0.001867 Cref 0.000000 NoiseWeighted 0.000000
0.148438 0.821502 18266 FSC 0.006992 SNR 1.408213e-02 FNCF 0.913122 FNCN 0.829752 FSCfull 0.013887 Cref 0.117841 NoiseWeighted 0.000000
0.152344 0.822031 18750 FSC 0.009847 SNR 1.989009e-02 FNCF 0.911698 FNCN 0.824485 FSCfull 0.019502 Cref 0.139650 NoiseWeighted 0.000000
0.156250 0.826508 20234 FSC 0.034651 SNR 7.179050e-02 FNCF 0.913992 FNCN 0.817147 FSCfull 0.066982 Cref 0.258808 NoiseWeighted 0.000000
0.160156 0.829598 21450 FSC 0.052491 SNR 1.107982e-01 FNCF 0.915240 FNCN 0.817627 FSCfull 0.099746 Cref 0.315827 NoiseWeighted 0.000000

...
</pre>
 

SN=1 
<pre>
...

0.625000 0.821968 125484 FSC 0.008655 SNR 1.746116e-02 FNCF 0.915959 FNCN 0.820807 FSCfull 0.017161 Cref 0.131002 NoiseWeighted 2282.625528
0.628906 0.822126 123668 FSC 0.009510 SNR 1.920304e-02 FNCF 0.915730 FNCN 0.818373 FSCfull 0.018841 Cref 0.137263 NoiseWeighted 2703.284812
0.632812 0.822135 118752 FSC 0.009556 SNR 1.929710e-02 FNCF 0.916420 FNCN 0.817706 FSCfull 0.018932 Cref 0.137593 NoiseWeighted 3065.097206
0.636719 0.822268 115748 FSC 0.010276 SNR 2.076605e-02 FNCF 0.916453 FNCN 0.821218 FSCfull 0.020344 Cref 0.142631 NoiseWeighted 3596.708750
0.640625 0.821682 111732 FSC 0.007114 SNR 1.432974e-02 FNCF 0.916046 FNCN 0.819347 FSCfull 0.014127 Cref 0.118858 NoiseWeighted 3395.432939
0.644531 0.819634 109556 FSC -0.003778 SNR -7.527926e-03 FNCF 0.915582 FNCN 0.818883 FSCfull -0.007585 Cref 0.000000 NoiseWeighted 0.000000
0.648438 0.820647 104768 FSC 0.001581 SNR 3.167601e-03 FNCF 0.915830 FNCN 0.819727 FSCfull 0.003158 Cref 0.056193 NoiseWeighted 0.000000
0.652344 0.820390 101724 FSC 0.000214 SNR 4.288445e-04 FNCF 0.914391 FNCN 0.820488 FSCfull 0.000429 Cref 0.020704 NoiseWeighted 0.000000
0.656250 0.821091 98396 FSC 0.003947 SNR 7.925782e-03 FNCF 0.913665 FNCN 0.822480 FSCfull 0.007863 Cref 0.088676 NoiseWeighted 0.000000
0.660156 0.821039 94632 FSC 0.003669 SNR 7.364323e-03 FNCF 0.913751 FNCN 0.819652 FSCfull 0.007310 Cref 0.085501 NoiseWeighted 0.000000

...
</pre>
 

SN=3 
<pre>
...

0.765625 0.821757 15104 FSC 0.009515 SNR 1.921255e-02 FNCF 0.922342 FNCN 0.820350 FSCfull 0.018850 Cref 0.137297 NoiseWeighted 317721.373090
0.769531 0.822221 13472 FSC 0.011996 SNR 2.428272e-02 FNCF 0.922754 FNCN 0.817671 FSCfull 0.023707 Cref 0.153971 NoiseWeighted 413936.197088
0.773438 0.821217 12312 FSC 0.006642 SNR 1.337191e-02 FNCF 0.918091 FNCN 0.817507 FSCfull 0.013195 Cref 0.114871 NoiseWeighted 359043.192167
0.777344 0.827075 11528 FSC 0.038716 SNR 8.055134e-02 FNCF 0.915129 FNCN 0.819965 FSCfull 0.074547 Cref 0.273032 NoiseWeighted 992931.202359
0.781250 0.824370 10056 FSC 0.023654 SNR 4.845502e-02 FNCF 0.915417 FNCN 0.814779 FSCfull 0.046216 Cref 0.214978 NoiseWeighted 910337.354456
0.785156 0.818701 8936 FSC -0.006536 SNR -1.298769e-02 FNCF 0.913984 FNCN 0.830604 FSCfull -0.013159 Cref 0.000000 NoiseWeighted 0.000000
0.789062 0.819627 8592 FSC -0.001726 SNR -3.446727e-03 FNCF 0.906964 FNCN 0.823014 FSCfull -0.003459 Cref 0.000000 NoiseWeighted 0.000000
0.792969 0.820210 7208 FSC 0.001325 SNR 2.654493e-03 FNCF 0.903543 FNCN 0.818116 FSCfull 0.002647 Cref 0.051454 NoiseWeighted 0.000000
0.796875 0.815899 6296 FSC -0.020810 SNR -4.077152e-02 FNCF 0.908125 FNCN 0.817338 FSCfull -0.042504 Cref 0.000000 NoiseWeighted 0.000000
0.800781 0.823119 5544 FSC 0.016835 SNR 3.424612e-02 FNCF 0.914006 FNCN 0.817025 FSCfull 0.033112 Cref 0.181967 NoiseWeighted 0.000000

...
</pre>
 

SN=10 
<pre>
...

0.828125 0.844910 1320 FSC 0.149342 SNR 3.511221e-01 FNCF 0.912374 FNCN 0.803915 FSCfull 0.259874 Cref 0.509779 NoiseWeighted 14231907.761588
0.832031 0.837728 1352 FSC 0.101517 SNR 2.259737e-01 FNCF 0.902768 FNCN 0.811758 FSCfull 0.184322 Cref 0.429327 NoiseWeighted 14095470.163758
0.835938 0.836067 1152 FSC 0.091023 SNR 2.002756e-01 FNCF 0.913173 FNCN 0.800848 FSCfull 0.166858 Cref 0.408483 NoiseWeighted 15783593.638134
0.839844 0.831098 800 FSC 0.060772 SNR 1.294080e-01 FNCF 0.910829 FNCN 0.797062 FSCfull 0.114580 Cref 0.338497 NoiseWeighted 15404941.069368
0.843750 0.829879 288 FSC 0.053609 SNR 1.132924e-01 FNCF 0.886515 FNCN 0.824411 FSCfull 0.101763 Cref 0.319004 NoiseWeighted 17112149.322272
0.847656 0.852127 392 FSC 0.201767 SNR 5.055348e-01 FNCF 0.880805 FNCN 0.817034 FSCfull 0.335784 Cref 0.579469 NoiseWeighted 36666886.878487
0.851562 0.819553 200 FSC -0.003419 SNR -6.815128e-03 FNCF 0.916154 FNCN 0.829615 FSCfull -0.006862 Cref 0.000000 NoiseWeighted 0.000000
0.855469 0.816624 72 FSC -0.018488 SNR -3.630448e-02 FNCF 0.925319 FNCN 0.796666 FSCfull -0.037672 Cref 0.000000 NoiseWeighted 0.000000
0.859375 0.917138 8 FSC 1.040065 SNR -5.191875e+01 FNCF 0.853931 FNCN 0.697182 FSCfull 1.019639 Cref 1.009772 NoiseWeighted 0.000000
0.863281 0.000000 0 FSC -0.811813 SNR -8.961335e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.627743 Cref 0.000000 NoiseWeighted 0.000000

...
</pre>
 

SN=100 
<pre>
...

0.828125 0.901847 1320 FSC 0.756211 SNR 6.203817e+00 FNCF 0.919589 FNCN 0.822237 FSCfull 0.861185 Cref 0.928000 NoiseWeighted 25907738.220224
0.832031 0.903973 1352 FSC 0.791551 SNR 7.594690e+00 FNCF 0.914005 FNCN 0.814800 FSCfull 0.883649 Cref 0.940026 NoiseWeighted 30862499.462702
0.835938 0.908114 1152 FSC 0.864634 SNR 1.277477e+01 FNCF 0.893985 FNCN 0.804227 FSCfull 0.927403 Cref 0.963018 NoiseWeighted 37210603.792030
0.839844 0.915035 800 FSC 1.001069 SNR -1.872989e+03 FNCF 0.903230 FNCN 0.814543 FSCfull 1.000534 Cref 1.000267 NoiseWeighted 45521947.697260
0.843750 0.918614 288 FSC 1.079756 SNR -2.707648e+01 FNCF 0.924216 FNCN 0.803353 FSCfull 1.038349 Cref 1.018994 NoiseWeighted 54661348.443263
0.847656 0.914517 392 FSC 0.990177 SNR 2.016063e+02 FNCF 0.929501 FNCN 0.780177 FSCfull 0.995064 Cref 0.997529 NoiseWeighted 63120364.126596
0.851562 0.898429 200 FSC 0.702229 SNR 4.716581e+00 FNCF 0.931254 FNCN 0.802611 FSCfull 0.825070 Cref 0.908334 NoiseWeighted 67850948.494955
0.855469 0.877008 72 FSC 0.427280 SNR 1.492108e+00 FNCF 0.926600 FNCN 0.805094 FSCfull 0.598733 Cref 0.773779 NoiseWeighted 68284951.426467
0.859375 0.899341 8 FSC 0.716309 SNR 5.049935e+00 FNCF 0.841373 FNCN 0.745881 FSCfull 0.834709 Cref 0.913624 NoiseWeighted 95324620.998659
0.863281 0.000000 0 FSC -0.812524 SNR -8.965661e-01 FNCF 0.000000 FNCN 0.000000 FSCfull -8.668008 Cref 0.000000 NoiseWeighted 0.000000

...
</pre>
 
It is found that the higher SN ratio is the higher the resolution is. 
 

== References ==
[http://grigoriefflab.janelia.org/node/55 Ab initio resolution measurement for single particle structures] (Calculate FNC, FNCF, FNCN, and estimate SNR,FSC) 
[http://nramm.scripps.edu/wp-content/seminars/2004/dlecture/ Single particle electron microscopy] (Calculate Cref, NoiseWeighted from FSC)

File:Outdata-mrcImageFourierNeighborCorrelation.zip

2014-10-27T03:34:26Z

Kinoshita:

File:Input1-SN100-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:33:51Z

Kinoshita:

File:Input1-SN10-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:33:35Z

Kinoshita:

File:Input1-SN3-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:33:21Z

Kinoshita:

File:Input1-SN1-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:33:07Z

Kinoshita:

File:Input1-SN0.3-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:32:54Z

Kinoshita:

File:Input-SN100-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:32:41Z

Kinoshita:

File:Input-SN10-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:32:27Z

Kinoshita:

File:Input-SN3-mrcImageFourierNeighborCorrelation.png

2014-10-27T03:32:13Z

Kinoshita: