mrcImageSpatialFrequencyFilter

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


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage NULL
-filter Essential Input: Filter file: ASCII NULL
-filterCol Optional Filter Column: (R, W) (1, 2)
-o Essential Output: ASCII NULL
-L Optional LowCut: [/A] -0.1
-H Optional HighCut: [/A] 1.0
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　


-m details

Value Description
0


Execution example

Input file's image

Input-1VOM-N.png
xy-plane

Input1-1VOM-N.png
yz-plane

Input-1VOM-N-FFT.png
FFT

Min

Max
Mean
SD

SE

-2390.42 (77, 14, 69)

4374.62 (17, 62, 46)
72.1487
577.82

0.722275


Example about -filter, -filterCol

-filter 's file(Create by using mrcImageFourierNeighborCorrelation)

  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

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

### For mrcImageSpatialFrequencyFilter
# -filterCol
FIL_COL_R=1
FIL_COL_W=17
# -H
FIL_H=
# -L
FIL_L=

Command

make all


Outdata-filter-mrcImageSpatialFrequencyFilter.png
xy-plane

Outdata1-filter-mrcImageSpatialFrequencyFilter.png
yz-plane

Outdata-filter-mrcImageSpatialFrequencyFilter-FFT.png
FFT

Min

Max
Mean
SD

SE

-2.59766e+06 (8, 70, 17)

2.64186e+06 (43, 75, 36)
97.0626
582169

727.711

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.

# -H
FIL_H=0.105469

Outdata-H-mrcImageSpatialFrequencyFilter.png
xy-plane

Outdata1-H-mrcImageSpatialFrequencyFilter.png
yz-plane

Outdata1-H-mrcImageSpatialFrequencyFilter-FFT.png
FFT画像

Min

Max
Mean
SD

SE

-178.789 (1, 26, 29)

798.082 (42, 35, 41)
97.0627
149.022

0.186278

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 

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


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

# -filterCol
FIL_COL_R=
FIL_COL_W=

Command

make all2

Outdata-filter2-mrcImageSpatialFrequencyFilter.png
xy-plane

Outdata1-filter2-mrcImageSpatialFrequencyFilter.png
yz-plane

Outdata1-filter2-mrcImageSpatialFrequencyFilter-FFT.png
FFT画像

Min

Max
Mean
SD

SE

-40.3107 (57, 52, 16)

425.495 (29, 46, 54)
72.1487
110.072

0.13759

-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.

# -filterCol
FIL_COL_R=1
FIL_COL_W=3

Outdata-filterCol-mrcImageSpatialFrequencyFilter.png
xy-plane

Outdata1-filterCol-mrcImageSpatialFrequencyFilter.png
yz-plane

Outdata1-filterCol-mrcImageSpatialFrequencyFilter-FFT.png
FFT画像

Min

Max
Mean
SD

SE

-259.771 (3, 53, 13)

1001.51 (43, 71, 44)
72.1487
168.798

0.210998


-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 

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

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

# -filterCol
FIL_COL_R=
FIL_COL_W=

Command

make all3

Outdata-filter3-mrcImageSpatialFrequencyFilter.png
xy-plane

Outdata1-filter3-mrcImageSpatialFrequencyFilter.png
yz-plane

Outdata2-filter3-mrcImageSpatialFrequencyFilter.png
FFT画像

Min

Max
Mean
SD

SE

-1268.05 (77, 14, 69)

2769.86 (17, 62, 45)
72.1487
352.17

0.440212

-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.

# -filterCol
FIL_COL_R=1
FIL_COL_W=3

Outdata-filterCol3-mrcImageSpatialFrequencyFilter.png
xy-plane

Outdata1-filterCol3-mrcImageSpatialFrequencyFilter.png
yz-plane

Outdata2-filterCol3-mrcImageSpatialFrequencyFilter.png
FFT画像

Min

Max
Mean
SD

SE

-721.031 (77, 14, 69)

2011.1 (17, 62, 45)
72.1487
252.314

0.315393


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