mrcImagePCA

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mrcImagePCA is Eos's Command that performs PCA(Principal components analysis) from multiple images and creates the PCA images.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: ASCII(File List) NULL
-o Essential Output: ASCII(File List) NULL
-EPS Optional EPS: lambda<EPS, stop calculation. 1e2
-NX Optional Pixel: Nx 30
-NY Optional Pixel: Ny 30
-O Optional Output: vectorfile NULL
-EPSO Optional Output: EPSOutput: caletimefile NULL
-E Optional Output: eigenImage eigen
-numE Optional Number of eigenImages 10
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　


-m details

Value Description
0


-i, -o format

File1
File2
.
.


Execution example

Input file's data

Input-121P-2D-P.mrc
Input-121P-2D1-P.mrc
Input-121P-2D2-P.mrc
Input-121P-2D-P.mrc's image
Input-121P-2D-P.png

Min

Max
Mean
SD

SE

-1105.85 (0, 0, 0)

29741.8 (13, 23, 0)
5686.81
5820.04

145.501


Input-121P-2D1-P.mrc's image
Input-121P-2D1-P.png

Min

Max
Mean
SD

SE

-1105.85 (0, 0, 0)

30528.7 (8, 21, 0)
5656.23
6199.33

154.983


Input-121P-2D2-P.mrc's image
Input-121P-2D2-P.png

Min

Max
Mean
SD

SE

-1105.85 (0, 0, 0)

29425.9 (17, 12, 0)
5666.16
6154.34

153.858


-o 's file
Outdata0-mrcImagePCA.mrc
Outdata1-mrcImagePCA.mrc
Outdata2-mrcImagePCA.mrc


Example of options only essential

-o 's image
View image was corrected by mrcImageWindowing, because its first data far larger than others.


Outdata0-mrcImagePCA.mrc
Outdata0-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.00138839 (2, 0, 0)

107098 (1, 0, 0)
200.692
4325.59

144.186
By mrcImageMakeDump
0 0 73525.2 
1 0 107098 
2 0 -0.00138839 
3 0 -0.00137284 
4 0 -0.00128583 
5 0 0.000646963 
6 0 -0.000642849 

...

8 10 -2.65457e-06 
9 10 -6.40329e-06 
10 10 -6.56773e-06 
11 10 -9.83265e-05 
12 10 8.96691e-07 

...

25 29 -1.81996e-06 
26 29 -8.89436e-07 
27 29 1.35051e-06 
28 29 7.98696e-07 
29 29 -7.37277e-07


Outdata1-mrcImagePCA.mrc
Outdata1-mrcImagePCA.png

Min

Max
Mean
SD

SE

-105568 (1, 0, 0)

76769.3 (0, 0, 0)
-31.9984
4350.89

145.03
By mrcImageMakeDump
0 0 76769.3 
1 0 -105568 
2 0 0.00136864 
3 0 0.00135261 
4 0 0.00127105 
5 0 0.000675541 
6 0 -0.000672826 

...

8 10 -3.828e-06 
9 10 -6.76705e-06 
10 10 -6.8542e-06 
11 10 -9.83877e-05 
12 10 7.78496e-07 

...

25 29 1.8971e-06 
26 29 -1.24502e-06 
27 29 1.55392e-06 
28 29 1.16343e-06 
29 29 -1.05502e-06


Outdata2-mrcImagePCA.mrc
Outdata2-mrcImagePCA.png

Min

Max
Mean
SD

SE

-150295 (0, 0, 0)

0.00131568 (6, 0, 0)
-168.694
5007.24

166.908
By mrcImageMakeDump
0 0 -150295 
1 0 -1530.13 
2 0 1.97447e-05 
3 0 2.02311e-05 
4 0 1.47764e-05 
5 0 -0.0013225 
6 0 0.00131568 
7 0 0.00128579 

...

8 10 6.48256e-06 
9 10 1.31703e-05 
10 10 1.34219e-05 
11 10 0.000196714 
12 10 -1.67518e-06 

...

25 29 -7.71467e-08 
26 29 2.13446e-06 
27 29 -2.90443e-06 
28 29 -1.96212e-06 
29 29 1.7923e-06


Option -NX, -NY

NX=20, NY=20

-o 's image
View image was corrected by mrcImageWindowing, because its first data far larger than others.


Outdata0-mrcImagePCA.mrc
Outdata0-N-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.00138839 (2, 0, 0)

107098 (1, 0, 0)
451.558
6479.66

323.983
By mrcImageMakeDump
0 0 73525.2 
1 0 107098 
2 0 -0.00138839 
3 0 -0.00137284 
4 0 -0.00128583 
5 0 0.000646963 
6 0 -0.000642849 

...

8 15 -2.65457e-06 
9 15 -6.40329e-06 
10 15 -6.56773e-06 
11 15 -9.83265e-05 
12 15 8.96691e-07 

...

15 19 -5.82619e-07 
16 19 4.00663e-07 
17 19 6.01493e-07 
18 19 7.07807e-06 
19 19 6.33428e-06


Outdata1-mrcImagePCA.mrc
Outdata1-N-mrcImagePCA.png

Min

Max
Mean
SD

SE

-105568 (1, 0, 0)

76769.3 (0, 0, 0)
-71.9964
6526.11

326.305
By mrcImageMakeDump
0 0 76769.3 
1 0 -105568 
2 0 0.00136864 
3 0 0.00135261 
4 0 0.00127105 

...

8 15 -3.828e-06 
9 15 -6.76705e-06 
10 15 -6.8542e-06 
11 15 -9.83877e-05 
12 15 7.78496e-07 

...

15 19 -3.87463e-07 
16 19 4.56702e-07 
17 19 8.39118e-07 
18 19 7.15604e-06 
19 19 6.71392e-06


Outdata2-mrcImagePCA.mrc
Outdata2-N-mrcImagePCA.png

Min

Max
Mean
SD

SE

-150295 (0, 0, 0)

0.00131568 (6, 0, 0)
-379.562
7505.53

375.276
By mrcImageMakeDump
0 0 -150295 
1 0 -1530.13 
2 0 1.97447e-05 
3 0 2.02311e-05 
4 0 1.47764e-05 
5 0 -0.0013225 
6 0 0.00131568 

...

8 15 6.48256e-06 
9 15 1.31703e-05 
10 15 1.34219e-05 
11 15 0.000196714 
12 15 -1.67518e-06 

...

15 19 9.70083e-07 
16 19 -8.57366e-07 
17 19 -1.4406e-06 
18 19 -1.42341e-05 
19 19 -1.30482e-05


Option -O

-O 's data
   0   848  11295979840.68  59.97
   1   933  7538968371.30  100.00
   2  1077   0.00  100.00
   3   231   0.00  100.00
   4   122   0.00  100.00
   5   184   0.00  100.00
   6  1398   0.00  100.00

...

1595   450  -0.00  100.00
1596   888  -0.00  100.00
1597  1068  -0.00  100.00
1598  1259  -0.00  100.00
1599  1132  -0.00  100.00


Option -EPSO

-EPSO 's data
1000/1279200 = 0.078174 % current 9.66421e+07 EPS 100 2 sec
2000/1279200 = 0.156348 % current 7.96464e+07 EPS 100 4 sec
3000/1279200 = 0.234522 % current 1.3266e+07 EPS 100 6 sec
4000/1279200 = 0.312695 % current 2.07992e+06 EPS 100 9 sec
5000/1279200 = 0.390869 % current 76309.2 EPS 100 11 sec
6000/1279200 = 0.469043 % current 663.412 EPS 100 14 sec
EPSbreak
6080/1279200 = 0.475297 % current 99.6128 EPS 100 14 sec


Option -EPS

Case: EPS=1e3

-EPSO 's data
1000/1279200 = 0.078174 % current 9.66421e+07 EPS 1000 2 sec
2000/1279200 = 0.156348 % current 7.96464e+07 EPS 1000 4 sec
3000/1279200 = 0.234522 % current 1.3266e+07 EPS 1000 7 sec
4000/1279200 = 0.312695 % current 2.07992e+06 EPS 1000 9 sec
5000/1279200 = 0.390869 % current 76309.2 EPS 1000 11 sec
EPSbreak
5952/1279200 = 0.465291 % current 968.28 EPS 1000 13 sec


Option -E

-E 's data
10 files are output, because numE=10 on default setting.
eigen.00000
Outdata10-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.0991027 (17, 12, 0)

0.0947194 (8, 21, 0)
2.23033e-05
0.025

0.000625
eigen.00001
Outdata11-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.0995859 (18, 23, 0)

0.092875 (12, 22, 0)
0.000144147
0.0249996

0.00062499
eigen.00002
Outdata12-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.000641438 (8, 21, 0)

0.999987 (37, 26, 0)
0.000625099
0.0249922

0.000624805

...

eigen.00009
Outdata19-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.00053598 (13, 23, 0)

0.999988 (14, 4, 0)
0.000624184
0.0249922

0.000624805


Option -numE

Case: numE=2

-E 's data
eigen.00000
Outdata20-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.0991027 (17, 12, 0)

0.0947194 (8, 21, 0)
2.23033e-05
0.025

0.000625
eigen.00001
Outdata21-mrcImagePCA.png

Min

Max
Mean
SD

SE

-0.0995859 (18, 23, 0)

0.092875 (12, 22, 0)
0.000144147
0.0249996

0.00062499
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