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Kinoshita: Created page with "'''mrcImageSuperResolution''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optiona..."
2014-08-04T00:05:23Z
<p>Created page with "'''mrcImageSuperResolution''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a>. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optiona..."</p>
<p><b>New page</b></p><div>'''mrcImageSuperResolution''' is [[Eos]]'s [[Command]].<br />
<br />
<br />
== List of option ==<br />
=== Main option ===<br />
<table border="1"><br />
<tr> <br />
<th>Option</th> <br />
<th>Essential/Optional</th> <br />
<th>Description</th> <br />
<th>Default</th> <br />
</tr> <br />
<tr> <br />
<td>-I</td> <br />
<td>Essential</td> <br />
<td>Input: Original </td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-i</td> <br />
<td>Essential</td> <br />
<td>Input: Previous </td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-ic</td> <br />
<td>Optional</td> <br />
<td>Input: CounterforWeight FourierSpace </td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Essential</td> <br />
<td>Output: Next</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-t</td> <br />
<td>Optional</td> <br />
<td>Number of time: Iteration(Real Space)</td> <br />
<td>1</td> <br />
</tr> <br />
<tr> <br />
<td>-fromp1</td> <br />
<td>Optional</td> <br />
<td>First value near origin of coordinates (x00[pixel], y00[pixel], z00[pixel])</td> <br />
<td>(0, 0, 0)</td> <br />
</tr> <br />
<tr> <br />
<td>-top1</td> <br />
<td>Optional</td> <br />
<td>target value ( x01[pixel], y01[pixel], z01[pixel])</td> <br />
<td>(2, 2, 2)</td> <br />
</tr> <br />
<tr> <br />
<td>-fromp2</td> <br />
<td>Optional</td> <br />
<td>First value far from origin of coordinates (x10[pixel], y10[pixel], z10[pixel])</td> <br />
<td>(0, 0, 0)</td> <br />
</tr> <br />
<tr> <br />
<td>-top2</td> <br />
<td>Optional</td> <br />
<td>target value (x11[pixel], y11[pixel], z11[pixel])</td> <br />
<td>(0, 0, 0)</td> <br />
</tr> <br />
<tr> <br />
<td>-LabelingMode</td> <br />
<td>Optional</td> <br />
<td>LabelingMode</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-max</td> <br />
<td>Optional</td> <br />
<td>Density Max value: Support Constraint()</td> <br />
<td>800</td> <br />
</tr> <br />
<tr> <br />
<td>-min</td> <br />
<td>Optional</td> <br />
<td>Density Min value: Support Constraint()</td> <br />
<td>200</td> <br />
</tr> <br />
<tr> <br />
<td>-sh</td> <br />
<td>Optional</td> <br />
<td>Shape</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-hvp</td> <br />
<td>Optional</td> <br />
<td>Half value point(/[A])</td> <br />
<td>0.0</td> <br />
</tr> <br />
<tr> <br />
<td>-Inverse</td> <br />
<td>Optional</td> <br />
<td>Inverse</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-nM</td> <br />
<td>Optional</td> <br />
<td>Number of Molecule</td> <br />
<td>1</td> <br />
</tr> <br />
<tr> <br />
<td>-M</td> <br />
<td>Optional</td> <br />
<td>MolecularWeight</td> <br />
<td>80000</td> <br />
</tr> <br />
<tr> <br />
<td>-D</td> <br />
<td>Optional</td> <br />
<td>Density: (g/cm3)</td> <br />
<td>1.35</td> <br />
</tr> <br />
<tr> <br />
<td>-counter</td> <br />
<td>Optional</td> <br />
<td>Counter(Fourier Space)</td> <br />
<td>3.0</td> <br />
</tr> <br />
<tr> <br />
<td>-dDensity</td> <br />
<td>Optional</td> <br />
<td>Delta (Convergence)</td> <br />
<td>100.0</td> <br />
</tr> <br />
<tr> <br />
<td>-dArea</td> <br />
<td>Optional</td> <br />
<td>Area(Convergence)</td> <br />
<td>100.0</td> <br />
</tr> <br />
<tr> <br />
<td>-sub</td> <br />
<td>Optional</td> <br />
<td>Subtraction(Convergence)</td> <br />
<td>0.2</td> <br />
</tr> <br />
<tr> <br />
<td>-ratio</td> <br />
<td>Optional</td> <br />
<td>Ratio(Convergence)</td> <br />
<td>0.3</td> <br />
</tr> <br />
<tr> <br />
<td>-tmax</td> <br />
<td>Optional</td> <br />
<td>Time Max(Convergence)</td> <br />
<td>1000</td> <br />
</tr> <br />
<tr> <br />
<td>-wd</td> <br />
<td>Optional</td> <br />
<td>WeightDelta(Fourier Space)</td> <br />
<td>0.1</td> <br />
</tr> <br />
<tr> <br />
<td>-wm</td> <br />
<td>Optional</td> <br />
<td>WeightMax(Fourier Space)</td> <br />
<td>2</td> <br />
</tr> <br />
<tr> <br />
<td>-Subtraction</td> <br />
<td>Optional</td> <br />
<td>Subtraction(Real Space)</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-c</td> <br />
<td>Optional</td> <br />
<td>ConfigurationFile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-m</td> <br />
<td>Essential</td> <br />
<td>RealSpaceCalculating</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-h</td> <br />
<td>Optional</td> <br />
<td>Help</td> <br />
<td> </td> <br />
</tr> <br />
</table> <br />
<pre><br />
-Inverse<br />
If high density means the location of protein, -Inverse is required for volume calculation.<br />
-wm and -wd<br />
weight = counter / (weightmax + counter)<br />
weightmax -> 0 (weightdelt by weightdelta) <br />
-Subtraction<br />
Real Space Constraint for desolving edge problem<br />
</pre><br />
<br><br />
<br />
=== -m details ===<br />
<table border="1"><br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
<td>513</td> <br />
<td>514</td> <br />
<td>515</td> <br />
<td>673</td> <br />
<td>672</td> <br />
<td>675</td> <br />
<td>736</td> <br />
<td>737</td> <br />
<td>742</td> <br />
<td>517</td> <br />
<td>518</td> <br />
<td>519</td> <br />
<td>534</td> <br />
<td>257</td> <br />
<td>258</td> <br />
<td>259</td> <br />
</tr> <br />
<tr> <br />
<td>+1</td> <br />
<td>AreaAndLocation</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
</tr> <br />
<tr> <br />
<td>+2</td> <br />
<td>Density</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
</tr> <br />
<tr> <br />
<td>+4</td> <br />
<td>Convergence(Option)</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>+16</td> <br />
<td>NonnegativeMode(before RealSpaceConstraint)</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>+32</td> <br />
<td>Binarization(before RealSpaceConstraint)</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>+64</td> <br />
<td>Labeling</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>+128</td> <br />
<td>SixOrientation</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>+256</td> <br />
<td>LowpassfilterMode(-hvp is required)</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
</tr> <br />
<tr> <br />
<td>+512</td> <br />
<td>CounterMode(-ic is required)</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td>◯</td> <br />
<td></td> <br />
<td></td> <br />
<td></td> <br />
</tr> <br />
</table> <br />
<div>They are used in combination.</div><br />
<br><br />
<br />
===-LabelinMode details===<br />
<table border="1"><br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td>TheLargestLabelingSearch</td> <br />
</tr> <br />
<tr> <br />
<td>1</td> <br />
<td>SomeVolumeLabelingSearch</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
===-sh details===<br />
<table border="1"><br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td>Rectangle</td> <br />
</tr> <br />
<tr> <br />
<td>1</td> <br />
<td>Globe</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
== Execution example ==<br />
=== Input file's image ===<br />
<div>[[:Media:Input-1VOM-2D.mrc|-I file]]'s image</div><br />
<table><br />
<tr><br />
<td>[[File:Input-1VOM-2D.png]]</td><br />
<td><p align="left">Min<br><br />
Max<br><br />
Mean<br><br />
SD<br><br />
SE<br></p><br />
</td><br />
<td><p align="left">0 (0, 0, 0)<br><br />
49749.7 (27, 28, 0)<br><br />
7212.9<br><br />
8827.15<br><br />
110.339<br></p><br />
</td><br />
</tr><br />
</table><br />
<br><br />
<br />
<div>[[Media:Input-1VOM-N-2D.mrc|-i file]]'s image</div><br />
<table> <br />
<tr> <br />
<td>[[File:Input-1VOM-N-2D.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-18651.7 (10, 1, 0)<br> <br />
52942.7 (24, 39, 0)<br> <br />
7214.87<br> <br />
10067.6<br> <br />
125.845<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br><br />
<br />
<div>[[:Media:Input-1VOM-2D.fft|-ic file]]'s image (For m=+512)</div><br />
<table><br />
<tr><br />
<td><p align="Center">[[File:Input-1VOM-2D-FFT.png]]<br><br />
by [[mrcFFTExpression]](m=1)<br></p> <br />
</td> <br />
<td><p align="left">Min<br><br />
Max<br><br />
Mean<br><br />
SD<br><br />
SE<br></p><br />
</td><br />
<td><p align="left">18.4637 (75, 36, 0)<br><br />
577032 (0, 0, 0)<br><br />
3573.53<br><br />
13475.7<br><br />
168.446<br></p><br />
</td><br />
</tr><br />
</table><br />
<br><br />
<br />
=== Option -m ===<br />
====Case: m=257, hvp=0.6==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m257-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-8991.5 (62, 67, 0)<br> <br />
45836.1 (18, 41, 0)<br> <br />
7214.87<br> <br />
9093.88<br> <br />
113.673<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
====Case: m=258, hvp=0.6==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m258-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-8601.65 (53, 3, 0)<br> <br />
53186.7 (24, 39, 0)<br> <br />
7214.87<br> <br />
9760.69<br> <br />
122.009<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
====Case: m=259, hvp=0.6==== <br />
=====Case: No other settings=====<br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m259-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-8999.82 (62, 67, 0)<br> <br />
45839 (18, 41, 0)<br> <br />
7214.87<br> <br />
9093.6<br> <br />
113.67<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
=====Case: t=100=====<br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-t-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-7536.4 (62, 67, 0)<br> <br />
45966.4 (18, 41, 0)<br> <br />
7214.87<br> <br />
9105.49<br> <br />
113.819<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
=====Case: top1=(20, 20, 0), tpo2=(60, 60, 0)=====<br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-top1top2-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-15758.5 (56, 22, 0)<br> <br />
52052.5 (24, 39, 0)<br> <br />
7214.87<br> <br />
9421.67<br> <br />
117.771<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
====Case: m=513==== <br />
=====Case: No other settings=====<br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m513-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-19348.5 (10, 1, 0)<br> <br />
53392.6 (24, 39, 0)<br> <br />
7214.87<br> <br />
10054.2<br> <br />
125.678<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
=====Case: counter=3000=====<br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-counter-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-22031.6 (0, 0, 0)<br> <br />
48805.4 (24, 39, 0)<br> <br />
7214.87<br> <br />
9538.88<br> <br />
119.236<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
<div>In the following, Setting atcounter=3000</div><br />
====Case: m=514==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m514-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-15917 (10, 1, 0)<br> <br />
52659.8 (24, 39, 0)<br> <br />
7214.87<br> <br />
9915.95<br> <br />
123.949<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
====Case: m=515==== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m515-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-20273.1 (0, 0, 0)<br> <br />
48844.2 (24, 39, 0)<br> <br />
7214.87<br> <br />
9539.42<br> <br />
119.243<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
====Case: m=736==== <br />
=====Case: No other settings=====<br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-m736-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-15814.1 (10, 1, 0)<br> <br />
52224.5 (24, 39, 0)<br> <br />
7214.87<br> <br />
9877.61<br> <br />
123.47<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
=====Case: LabelingMode=1===== <br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-LabelingMode1-mrcImageSuperResolution.png]]</td> <br />
<td><p align="left">Min<br> <br />
Max<br> <br />
Mean<br> <br />
SD<br> <br />
SE<br></p> <br />
</td> <br />
<td><p align="left">-19306.2 (10, 1, 0)<br> <br />
52834.2 (24, 39, 0)<br> <br />
7214.87<br> <br />
9993.85<br> <br />
124.923<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br></div>
Kinoshita