mrcImageFourierShellCorrelation - Revision history

Kinoshita: Created page with "'''mrcImageFourierShellCorrelation''' is Eos's Command for displaying 3D image of mrcImage. == Algorithm == == List of option == === Main option ===
2014-07-24T04:54:17Z
Created page with "'''mrcImageFourierShellCorrelation''' is Eos's Command for displaying 3D image of mrcImage. == Algorithm == == List of option == === Main option === <table bord..."
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'''mrcImageFourierShellCorrelation''' is [[Eos]]'s [[Command]] for displaying 3D image of [[mrcImage]].

== Algorithm ==
== 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>-i1</td>
<td>Optional</td>
<td>Input: [[mrcImage]]: 3D from one set</td>
<td>NULL</td>
</tr>
<tr>
<td>-i2</td>
<td>Optional</td>
<td>Input: [[mrcImage]]: 3D from another set</td>
<td>NULL</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>Input: Delta [A-1] (Default 1/(Nx*size of pixel)</td>
<td>0</td>
</tr>
<tr>
<td>-z</td>
<td>Optional</td>
<td>z position of reference file to correlate.(For M=2 only)</td>
<td>0</td>
</tr>
<tr>
<td>-L</td>
<td>Optional</td>
<td>Low threshold (For m=+2)</td>
<td>0</td>
</tr>
<tr>
<td>-H</td>
<td>Optional</td>
<td>High threshold (For m=+2)</td>
<td>0</td>
</tr>
<tr>
<td>-I1</td>
<td>Optional</td>
<td>InputDataFiles</td>
<td>stdin</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>
</div>
</table>
<br>

===-m details===
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Fourier Shell Correlation(FSC)</td>
</tr>
<tr>
<td>1</td>
<td>Fourier Shell Phase Residual(FSPR)</td>
</tr>
<tr>
<td>+2</td>
<td>Correlation between L and H</td>
</tr>
<tr>
<td>+4</td>
<td>Without equator</td>
</tr>
</div>
</table>
<br>

===-M details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Correlation between same size images</td>
</tr>
<tr>
<td>1</td>
<td>Correlation between 2D image and image extracted from 3D image</td>
</tr>
<tr>
<td>+2</td>
<td>Correlation between 2D different size images. In1 is compared with center of In2</td>
</tr>
</table>
<br>

===-I1 format===
<pre>
mrcFile1
mrcFile2
.
.

</pre>
<br>

== Execution example ==
<pre>
$ mrcImageFourierCorrealation -i1 aa1 -i2 aa2 -d 0.005 > aa.FSC
</pre>
<div>The result is standard out. Therefore it can be written to aa.FSC by input as above.</div>
<br>

===Input file===
<div>[[Media:Input-1VOM-N.mrc |-i1 file]]'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Input-1VOM-N.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-1VOM-N.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-2390.42 (77, 14, 69)<br>
4374.62 (17, 62, 46)<br>
72.1487<br>
577.82<br>
0.722275<br></p>
</td>
</tr>
</table>
<br>

<div>[[Media:1VOM.mrc |-i2 file]]'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Input-1VOM.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-1VOM.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (0, 0, 0)<br>
3398.12 (23, 55, 41)<br>
72.129<br>
294.805<br>
0.368507<br></p>
</td>
</tr>
</table>
<br>

<div>-I1 's data</div>
<pre>
Input-1VOM-N.mrc
Input-1VOM-N-Rot5.mrc

</pre>
<div>Input-1VOM-N.mrc is -i1 file</div>

<div>[[Media:Input-1VOM-N-Rot5.mrc|Input-1VOM-N-Rot5.mrc]]'s image</div>
<table>
<tr>
<td><p align="Center">[[File:Input-1VOM-N-Rot5.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-1VOM-N-Rot5.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-2183.15 (44, 1, 42)<br>
4374.62 (17, 43, 72)<br>
65.2201<br>
444.739<br>
0.555924<br></p>
</td>
</tr>
</table>
<br>

===Using -i1, -i2===
====Case: No other settings====
<pre>
0.000000 1.000000 1
0.012500 0.999634 13
0.025000 0.995969 39
0.037500 0.988261 87
0.050000 0.957829 149
0.062500 0.947918 207
0.075000 0.917809 323
0.087500 0.887196 397
0.100000 0.889336 533
0.112500 0.821884 683

...

0.750000 0.065970 1483
0.762500 0.038822 1141
0.775000 0.053317 878
0.787500 0.044822 636
0.800000 0.056993 454
0.812500 0.017477 293
0.825000 0.028400 169
0.837500 0.011719 96
0.850000 0.072043 38
0.862500 0.271245 6
</pre>
<br>

====Case: d=0.025====
<pre>
0.000000 0.999930 3
0.025000 0.998200 80
0.050000 0.965491 275
0.075000 0.924165 624
0.100000 0.875124 1072
0.125000 0.783273 1647
0.150000 0.699995 2361
0.175000 0.689238 3192
0.200000 0.759293 4121
0.225000 0.789672 5267
0.250000 0.756202 6490
0.275000 0.722542 7712
0.300000 0.658240 9152
0.325000 0.588251 10943
0.350000 0.518991 12514
0.375000 0.477529 14361
0.400000 0.436295 16386
0.425000 0.413060 18422
0.450000 0.382743 20652
0.475000 0.351337 22943
0.500000 0.316665 25104
0.525000 0.267024 24196
0.550000 0.243536 22682
0.575000 0.205291 20736
0.600000 0.181078 18634
0.625000 0.150142 16132
0.650000 0.131186 13422
0.675000 0.121229 10614
0.700000 0.091703 7502
0.725000 0.093191 4733
0.750000 0.061833 2934
0.775000 0.040827 1751
0.800000 0.049153 897
0.825000 0.023844 361
0.850000 0.048584 84
0.875000 -1.000000 1
</pre>
<br>

====Case: m=1====
<pre>
0.000000 0.000000 1
0.012500 0.016997 13
0.025000 0.042363 39
0.037500 0.068608 87
0.050000 0.146883 149
0.062500 0.171470 207
0.075000 0.219479 323
0.087500 0.263114 397
0.100000 0.261232 533
0.112500 0.348648 683

...

0.750000 1.468900 1483
0.762500 1.503913 1141
0.775000 1.485309 878
0.787500 1.488339 636
0.800000 1.488236 454
0.812500 1.531858 293
0.825000 1.515839 169
0.837500 1.541283 96
0.850000 1.470908 38
0.862500 0.999492 6
</pre>
<br>

====Case: m=2, L=0.05, H=1.0====
<pre>
1.000000 0.050000 0.470159
</pre>
<br>

====Case: m=6, L=0.05, H=1.0====
<pre>
1.000000 0.050000 0.467996
</pre>
<br>

====Case: M=1====
<pre>
0.000000 1.000000 1
0.012500 -0.178747 13
0.025000 0.020397 39
0.037500 0.063693 87
0.050000 0.059777 149
0.062500 -0.074179 207
0.075000 -0.030089 323
0.087500 0.027561 397
0.100000 -0.008085 533
0.112500 -0.005067 683

...

0.750000 0.016127 1483
0.762500 -0.008485 1141
0.775000 -0.010831 878
0.787500 -0.026397 636
0.800000 -0.042493 454
0.812500 0.036403 293
0.825000 0.000491 169
0.837500 0.027535 96
0.850000 -0.036928 38
0.862500 -0.346569 6
</pre>
<br>

====Case: M=1, z=40====
<pre>
0.000000 1.000000 1
0.012500 -0.308974 13
0.025000 -0.081648 39
0.037500 0.114969 87
0.050000 -0.070818 149
0.062500 -0.147309 207
0.075000 0.039240 323
0.087500 -0.005340 397
0.100000 0.027345 533
0.112500 -0.005642 683

...

0.750000 -0.027752 1483
0.762500 0.012519 1141
0.775000 0.008470 878
0.787500 -0.009874 636
0.800000 0.031715 454
0.812500 0.009969 293
0.825000 0.081095 169
0.837500 -0.043615 96
0.850000 -0.187544 38
0.862500 0.500939 6
</pre>
<br>

====Case: M=2====
<pre>
0.000000 1.000000 1
0.012500 0.561919 5
0.025000 0.641637 7
0.037500 0.201681 9
0.050000 -0.218393 17
0.062500 0.180950 15
0.075000 -0.230490 21
0.087500 -0.009274 21
0.100000 0.183872 25
0.112500 0.119556 35

...

0.675000 -0.122544 16
0.687500 0.499015 5
0.700000 0.297501 3
0.712500 1.000000 1
0.725000 0.000000 0
0.737500 0.000000 0
0.750000 0.000000 0
0.762500 0.000000 0
0.775000 0.000000 0
0.787500 0.000000 0
0.800000 0.000000 0
0.812500 0.000000 0
0.825000 0.000000 0
0.837500 0.000000 0
0.850000 0.000000 0
0.862500 0.000000 0
</pre>
<br>

===Using -I1, -i2===
<pre>
Input-1VOM-N.mrc 0.000000 1.000000 1
0.012500 0.999634 13
0.025000 0.995969 39
0.037500 0.988261 87
0.050000 0.957829 149
0.062500 0.947918 207
0.075000 0.917809 323
0.087500 0.887196 397
0.100000 0.889336 533
0.112500 0.821884 683
0.125000 0.781489 833

...

0.750000 0.065970 1483
0.762500 0.038822 1141
0.775000 0.053317 878
0.787500 0.044822 636
0.800000 0.056993 454
0.812500 0.017477 293
0.825000 0.028400 169
0.837500 0.011719 96
0.850000 0.072043 38
0.862500 0.271245 6
Input-1VOM-N-Rot5.mrc 0.000000 1.000000 1
0.012500 0.773940 13
0.025000 0.016870 39
0.037500 0.145600 87
0.050000 0.022819 149
0.062500 0.018082 207
0.075000 0.069249 323
0.087500 -0.046304 397
0.100000 0.052714 533
0.112500 -0.006479 683

...

0.750000 -0.045042 1483
0.762500 -0.008477 1141
0.775000 -0.009835 878
0.787500 -0.019530 636
0.800000 0.024443 454
0.812500 0.096803 293
0.825000 0.009359 169
0.837500 -0.065044 96
0.850000 -0.184656 38
0.862500 -0.406431 6
</pre>
<br>

== References ==
[[http://en.wikipedia.org/wiki/Fourier_shell_correlation Fourier_Sell_Correlation]]