mrcImagesSinogramCorrelation

From EosPedia
Revision as of 04:22, 25 August 2014 by Kinoshita (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

mrcImagesSinogramCorrelation is Eos's Command that performs correlation among multiple Sinograms. Output file is used by WeightCalculationOfCommonLineSearchByAllSinogram.


List of option

Main option

Option Essential/Optional Description Default
-I Essential Input: ASCII(FileList) NULL
-oH Optional OutputDataFileHeader test
-Rd Optional output results directory name Result
-Nd Optional irectory name of output normalcorrelation in results directory(Create in -Rd) Normal
-D1d Optional directory name of output derivation1Dcorrelation in results directory(Create in -Rd) Derivation1D
-D2d Optional directory name of output derivation2Dcorrelation in results directory(Create in -Rd) Derivation2D
-Ld Optional directory name of output lengthcorrelation in results directory(Create in -Rd) Length
-CE Optional output correlation file extension cor
-LE Optional output file list extension list
-Nm Optional NormalCorrelationMode 0
-D1m Optional Derivation1DCorrelationMode 0
-D2m Optional Derivation2DCorrelationMode 0
-Lm Optional LengthCorrelationMode 0
-LTM Optional LengthThresholdMode 0
-LTR Optional LengthThresholdRatio 0.25
-CM Optional CreateFileMode 0
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　


-m details

Value Description
0


-Nm details

Value Description
0 create normal correlation(-Nd (Specify Output Directory)
1 not create normal correlation


-D1m details

Value Description
0 create derivation1D correlation(-D1d (Specify Output Directory)
1 not create derivation1D correlation


-D2m details

Value Description
0 create derivation2D correlation(-D2d (Specify Output Directory)
1 not create derivation2D correlation


-Lm details

Value Description
0 create length correlation (-Ld(Specify Output Directory), -LTM, -LTR)
1 not creat length correlation


-CM details

Value Description
0 Output image of correlation and list
1 Output list only


-I format

file1,  EA1  Rot1-1  Rot1-2  Rot1-3
file2,  EA2  Rot2-1  Rot2-2  Rot2-3
file3,  EA3  Rot3-1  Rot3-2  Rot3-3
      .       ,     .        .            .           .
      .       ,     .        .            .           .
      .       ,     .        .            .           .
file名とEAの間には,(カンマ)を入れなければならない。
file名の先頭を/にすると命名規則により相関fileを作成できないので注意。


Created Directory and File

Directory

Rd
Rd/Nd (D1d, D2d, Ld)
Example: Result/Normal/
ディレクトリが既に存在している場合はdataを作成できないので注意。


ListFile

Rd/Nd/oH-Nd.LE
Example: Result/Normal/test-Normal.list


CorrelationFile

Rd/Nd/infile1_infile2.Nd.CE
Example: Result/Normal/test1_test2.Normal.cor


Execution example

Input file's data

Input-1VOM-2D-sin.mrc,	YOYS	0	0	0
Input-1VOM-Rot-2D-sin.mrc,	YOYS	90	0	0
Input-1VOM-Rot3-2D-sin.mrc,	YOYS	0	90	0


Input-1VOM-2D-sin.mrc's image
Input-1VOM-2D-sin.png

Min

Max
Mean
SD

SE

-3045.85 (79, 268, 0)

1.53325e+06 (27, 1, 0)
589315
378411

2229.81


Input-1VOM-Rot-2D-sin.mrc's image
Input-1VOM-Rot-2D-sin.png

Min

Max
Mean
SD

SE

-16429.6 (78, 357, 0)

1.31372e+06 (44, 38, 0)
536988
293780

1731.11


Input-1VOM-Rot3-2D-sin.mrc's image
Input-1VOM-Rot3-2D-sin.png

Min

Max
Mean
SD

SE

-1732.14 (3, 3, 0)

1.39371e+06 (51, 202, 0)
533594
366888

2161.91


Case: Options only essential

Output
LengthCorrelation=0.840580 InLength[0]=58 RefLength[0]=80
LengthCorrelation=0.840580 InLength[0]=58 RefLength[1]=80
LengthCorrelation=0.840580 InLength[0]=58 RefLength[2]=80
LengthCorrelation=0.840580 InLength[0]=58 RefLength[3]=80
LengthCorrelation=0.840580 InLength[0]=58 RefLength[4]=80
LengthCorrelation=0.872180 InLength[0]=58 RefLength[5]=75
LengthCorrelation=0.872180 InLength[0]=58 RefLength[6]=75

...

LengthCorrelation=0.852941 InLength[359]=58 RefLength[355]=78
LengthCorrelation=0.852941 InLength[359]=58 RefLength[356]=78
LengthCorrelation=0.840580 InLength[359]=58 RefLength[357]=80
LengthCorrelation=0.840580 InLength[359]=58 RefLength[358]=80
LengthCorrelation=0.840580 InLength[359]=58 RefLength[359]=80
LengthCorrelation=1.000000 InLength[0]=58 RefLength[0]=58
LengthCorrelation=0.945455 InLength[0]=58 RefLength[1]=52
LengthCorrelation=0.905660 InLength[0]=58 RefLength[2]=48
LengthCorrelation=0.862745 InLength[0]=58 RefLength[3]=44
LengthCorrelation=0.925926 InLength[0]=58 RefLength[4]=50

...

LengthCorrelation=0.973451 InLength[359]=58 RefLength[355]=55
LengthCorrelation=0.973451 InLength[359]=58 RefLength[356]=55
LengthCorrelation=0.973451 InLength[359]=58 RefLength[357]=55
LengthCorrelation=0.973451 InLength[359]=58 RefLength[358]=55
LengthCorrelation=0.973451 InLength[359]=58 RefLength[359]=55
LengthCorrelation=0.840580 InLength[0]=80 RefLength[0]=58
LengthCorrelation=0.787879 InLength[0]=80 RefLength[1]=52
LengthCorrelation=0.750000 InLength[0]=80 RefLength[2]=48
LengthCorrelation=0.709677 InLength[0]=80 RefLength[3]=44
LengthCorrelation=0.769231 InLength[0]=80 RefLength[4]=50

...

LengthCorrelation=0.840580 InLength[359]=80 RefLength[350]=58
LengthCorrelation=0.881119 InLength[359]=80 RefLength[351]=63
LengthCorrelation=0.881119 InLength[359]=80 RefLength[352]=63
LengthCorrelation=0.873239 InLength[359]=80 RefLength[353]=62
LengthCorrelation=0.796992 InLength[359]=80 RefLength[354]=53
LengthCorrelation=0.814815 InLength[359]=80 RefLength[355]=55
LengthCorrelation=0.814815 InLength[359]=80 RefLength[356]=55
LengthCorrelation=0.814815 InLength[359]=80 RefLength[357]=55
LengthCorrelation=0.814815 InLength[359]=80 RefLength[358]=55
LengthCorrelation=0.814815 InLength[359]=80 RefLength[359]=55


List of Output file
In the case of default setting, file structure is as the following.
$EOS_HOME/Result/Derivation1D/Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Derivation1D.cor
$EOS_HOME/Result/Derivation1D/Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation1D.cor
$EOS_HOME/Result/Derivation1D/Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation1D.cor
$EOS_HOME/Result/Derivation1D/test-Derivation1D.list
$EOS_HOME/Result/Derivation2D/Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Derivation2D.cor
$EOS_HOME/Result/Derivation2D/Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation2D.cor
$EOS_HOME/Result/Derivation2D/Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation2D.cor
$EOS_HOME/Result/Derivation2D/test-Derivation2D.list
$EOS_HOME/Result/Length/Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Length.cor
$EOS_HOME/Result/Length/Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor
$EOS_HOME/Result/Length/Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor
$EOS_HOME/Result/Length/test-Length.list
$EOS_HOME/Result/Normal/Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Normal.cor
$EOS_HOME/Result/Normal/Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Normal.cor
$EOS_HOME/Result/Normal/Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Normal.cor
$EOS_HOME/Result/Normal/test-Normal.list


Option -Nm

Case: Nm=0(Default)

Data in Normal directory


Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Normal.cor
Outdata-Nm-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-0.925733 (174, 223, 0)

0.986152 (271, 281, 0)
0.203463
0.411921

0.00114423


Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Normal.cor
Outdata-Nm1-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-0.969656 (10, 168, 0)

0.96977 (10, 357, 0)
0.199734
0.487223

0.0013534


Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Normal.cor
Outdata-Nm2-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-0.79716 (206, 183, 0)

0.986575 (190, 120, 0)
0.251101
0.368028

0.0010223


test-Normal.list
Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Normal.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot-2D-sin.mrc 1.570796 1.570796 1
Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Normal.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 0.000000 1
Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Normal.cor Input-1VOM-Rot-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 4.712389 1


Option -D1d

Case: D1d=0(Default)

data in Derivation1D directory


Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Derivation1D.cor
Outdata-D1d-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-0.999642 (131, 329, 0)

0.921779 (132, 73, 0)
0.0604004
0.241042

0.00066956


Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation1D.cor
Outdata-D1d1-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-0.995358 (132, 121, 0)

0.991247 (133, 4, 0)
0.0859721
0.247723

0.000688118


Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation1D.cor
Outdata-D1d2-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-0.98175 (356, 217, 0)

0.97865 (0, 217, 0)
0.0731451
0.245175

0.000681042


test-Derivation1D.list
Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Derivation1D.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot-2D-sin.mrc 1.570796 1.570796 1
Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation1D.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 0.000000 1
Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation1D.cor Input-1VOM-Rot-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 4.712389 1


Option -D2d

Case: D2d=0(Default)

data in Derivation2D directory


Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Derivation2D.cor
Outdata-D2d-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-1 (285, 75, 0)

1 (285, 61, 0)
nan
nan

nan


Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation2D.cor
Outdata-D2d1-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-1 (158, 33, 0)

1 (158, 30, 0)
0.0945901
0.227151

0.000630976


Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation2D.cor
Outdata-D2d2-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

-0.970911 (132, 30, 0)

1 (135, 30, 0)
0.104829
0.220026

0.000611183


test-Derivation2D.list
Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Derivation2D.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot-2D-sin.mrc 1.570796 1.570796 1
Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation2D.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 0.000000 1
Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Derivation2D.cor Input-1VOM-Rot-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 4.712389 1


Option -Ld

Case: Ld=0(Default)

data in Length directory


Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Length.cor
Outdata-Ld-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

0.778626 (27, 38, 0)

1 (27, 0, 0)
0.946219
0.047809

0.000132803


Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor
Outdata-Ld2-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

0.699187 (27, 191, 0)

1 (0, 0, 0)
0.93032
0.0611702

0.000169917


Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor
Outdata-Ld1-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

0.699187 (0, 191, 0)

1 (67, 0, 0)
0.93353
0.0580325

0.000161201


test-Length.list
Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Length.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot-2D-sin.mrc 1.570796 1.570796 1
Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 0.000000 1
Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor Input-1VOM-Rot-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 4.712389 1


Option -LTR

Case: LTR=0.5

data in Length directory


Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Length.cor
Outdata-LTR-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

0.0487805 (28, 303, 0)

1 (28, 0, 0)
0.864734
0.122153

0.000339315


Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor
Outdata-LTR1-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

0.16092 (28, 68, 0)

1 (1, 0, 0)
0.849408
0.121498

0.000337494


Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor
Outdata-LTR2-mrcImagesSinogramCorrelation.png

Min

Max
Mean
SD

SE

0.0487805 (303, 31, 0)

1 (31, 0, 0)
0.849326
0.135625

0.000376735


test-Length.list
Input-1VOM-2D-sin_Input-1VOM-Rot-2D-sin.Length.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot-2D-sin.mrc 1.570796 1.570796 1
Input-1VOM-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor Input-1VOM-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 0.000000 0.000000 z-rotation
Input-1VOM-Rot-2D-sin_Input-1VOM-Rot3-2D-sin.Length.cor Input-1VOM-Rot-2D-sin.mrc Input-1VOM-Rot3-2D-sin.mrc 1.570796 1.570796 1


Retrieved from "http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImagesSinogramCorrelation&oldid=3684"