mrcImageVarianceMap - Revision history

Kinoshita: Created page with "'''mrcImageVarianceMap''' is Eos's Command that creates Variance Map from multiple mrcImages(2D). == List of option == === Main option === ..."
2014-08-04T06:25:12Z
Created page with "'''mrcImageVarianceMap''' is Eos's Command that creates Variance Map from multiple mrcImages(2D). == List of option == === Main option === <table border="1">..."
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'''mrcImageVarianceMap''' is [[Eos]]'s [[Command]] that creates Variance Map from multiple [[mrcImage]]s(2D).

== 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>Optional</td>
<td>Input: [[ASCII]] (File List)</td>
<td>NULL</td>
</tr>
<tr>
<td>-I</td>
<td>Optional</td>
<td>Input: (In2 In2Var In2N))</td>
<td>NULL NULL 0</td>
</tr>
<tr>
<td>-Nor</td>
<td>Optional</td>
<td>Input: A + Bx: NormalizingParameter (NorA NorB)</td>
<td>0.0 1.0</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Reference: [[ASCII]] (File List)</td>
<td>NULL</td>
</tr>
<tr>
<td>-R</td>
<td>Optional</td>
<td>Reference: (Ref2 Ref2Var Ref2N )</td>
<td>NULL NULL 0</td>
</tr>
<tr>
<td>-NorR</td>
<td>Optional</td>
<td>Input: A + Bx: NormalizingParameter for Ref (RNorARef RNorBRef)</td>
<td>0.0 1.0</td>
</tr>
<tr>
<td>-IR</td>
<td>Optional</td>
<td>Input and Reference: (InAndRef2 InAndRef2Var InAndRef2N)</td>
<td>NULL NULL 0</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: Variance Probability</td>
<td>NULL</td>
</tr>
<tr>
<td>-v</td>
<td>Optional</td>
<td>Output: Variance Map</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>

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

===-i, -r format===
<pre>
mrcFile1
mrcFile2
.
.

</pre>

===Variance Map===
<pre>
VarianceMap := VarinceOfAll/((VarianceOfDataSet1n1+VarianceOfDataSet2n2)/n1+n2)
VarinceOfAll: variance of all data from Set1 and Set2
VarinceOfDataSet1: variance of all data from Set1
VarinceOfDataSet2: variance of all data from Set2

Kai-distribution: Kai^2 = SumOf (Xi - AvgOfXi)^2/sigma^2
= s^2*(n-1)/sigma^2 : degree of freedom n-1
when variables Xi are due to N(u, sigma^2)
Kai-distribution: Kai^2 = Kai1^2 + Kai2^2 : degree of freedom m1 + m2
F-distribution: F = (Kai1^2/k1)/(Kai2^2/k2) : degree of freedom : (k1, k2)
(s1^2/sigma1^2)/(s2^2/sigma2^2) : degree of freedom : (k1-1, k2-1)
If sigma1 == sigma2, then
s1^2/s2^2 (Variance Ratio) : degree of freedom : (k1-1, k2-1)
</pre>

== Execution example ==
===Input file's data===
<pre>
/Eos/img/Input-ThickFilaments0-N-30.mrc
/Eos/img/Input-ThickFilaments0-N-40.mrc
/Eos/img/Input-ThickFilaments0-N-50.mrc

</pre>

<div>[[:Media:Input-ThickFilaments0-N-30.mrc | Input-ThickFilaments0-N-30.mrc]]'s image </div>
<table>
<tr>
<td>[[File:Input-ThickFilaments0-N-30.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0.242386 (63, 38, 0)<br>
1.18538 (46, 26, 0)<br>
0.00402522<br>
0.0987806<br>
0.0014316<br></p>
</td>
</tr>
</table>

<div>[[:Media:Input-ThickFilaments0-N-40.mrc | Input-ThickFilaments0-N-40.mrc]]'s image </div>
<table>
<tr>
<td>[[File:Input-ThickFilaments0-N-40.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0.284772 (20, 5, 0)<br>
1.39313 (24, 45, 0)<br>
0.00654313<br>
0.117719<br>
0.00170608<br></p>
</td>
</tr>
</table>

<div>[[:Media:Input-ThickFilaments0-N-50.mrc | Input-ThickFilaments0-N-50.mrc]]'s image </div>
<table>
<tr>
<td>[[File:Input-ThickFilaments0-N-50.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0.244921 (31, 53, 0)<br>
1.10864 (41, 21, 0)<br>
0.00225865<br>
0.096511<br>
0.00139871<br></p>
</td>
</tr>
</table>

===Reference file data===
<pre>
/Eos/img/Input-ThickFilaments0-30.mrc
/Eos/img/Input-ThickFilaments0-40.mrc
/Eos/img/Input-ThickFilaments0-50.mrc

</pre>

<div>[[:Media:Input-ThickFilaments0-30.mrc | Input-ThickFilaments0-30.mrc]]'s image </div>
<table>
<tr>
<td>[[File:Input-ThickFilaments0-30.png]]</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>
1.04379 (42, 46, 0)<br>
0.00425073<br>
0.0654553<br>
0.000948628<br></p>
</td>
</tr>
</table>

<div>[[:Media:Input-ThickFilaments0-40.mrc | Input-ThickFilaments0-40.mrc]]'s image </div>
<table>
<tr>
<td>[[File:Input-ThickFilaments0-40.png]]</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>
1.34347 (44, 23, 0)<br>
0.00812336<br>
0.0935823<br>
0.00135626<br></p>
</td>
</tr>
</table>

<div>[[:Media:Input-ThickFilaments0-50.mrc | Input-ThickFilaments0-50.mrc]]'s image </div>
<table>
<tr>
<td>[[File:Input-ThickFilaments0-50.png]]</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>
1 (32, 19, 0)<br>
0.0042008<br>
0.0646773<br>
0.000937352<br></p>
</td>
</tr>
</table>

=== Example of options only essential ===
<table>
<tr>
<td>[[File:Outdata-mrcImageVarianceMap.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-68.5414 (35, 18, 0)<br>
99.9999 (8, 46, 0)<br>
-26.8277<br>
60.764<br>
0.880638<br></p>
</td>
</tr>
</table>

=== Option -Nor===
====Case: Nor=(1, 3)====
<table>
<tr>
<td>[[File:Outdata-Nor-mrcImageVarianceMap.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-57.2844 (21, 42, 0)<br>
100 (67, 30, 0)<br>
96.1833<br>
11.7327<br>
0.170039<br></p>
</td>
</tr>
</table>

=== Option -NorR===
====Case: NorR=(1, 1)====
<table>
<tr>
<td>[[File:Outdata-NorR-mrcImageVarianceMap.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">50.3586 (23, 24, 0)<br>
100 (1, 0, 0)<br>
99.3951<br>
4.68716<br>
0.0679299<br></p>
</td>
</tr>
</table>