View source for mrcImageSuperResolution

'''mrcImageSuperResolution''' is [[Eos]]'s [[Command]].


== 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>Essential</td> 
				<td>Input: Original </td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-i</td> 
				<td>Essential</td> 
				<td>Input: Previous </td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-ic</td> 
				<td>Optional</td> 
				<td>Input: CounterforWeight FourierSpace </td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-o</td> 
				<td>Essential</td> 
				<td>Output: Next</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-t</td> 
				<td>Optional</td> 
				<td>Number of time: Iteration(Real Space)</td> 
				<td>1</td> 
			</tr> 
			<tr> 
				<td>-fromp1</td> 
				<td>Optional</td> 
				<td>First value near origin of coordinates (x00[pixel], y00[pixel], z00[pixel])</td> 
				<td>(0, 0, 0)</td> 
			</tr> 
			<tr> 
				<td>-top1</td> 
				<td>Optional</td> 
				<td>target value ( x01[pixel], y01[pixel], z01[pixel])</td> 
				<td>(2, 2, 2)</td> 
			</tr> 
			<tr> 
				<td>-fromp2</td> 
				<td>Optional</td> 
				<td>First value far from origin of coordinates (x10[pixel], y10[pixel], z10[pixel])</td> 
				<td>(0, 0, 0)</td> 
			</tr> 
			<tr> 
				<td>-top2</td> 
				<td>Optional</td> 
				<td>target value (x11[pixel], y11[pixel], z11[pixel])</td> 
				<td>(0, 0, 0)</td> 
			</tr> 
			<tr> 
				<td>-LabelingMode</td> 
				<td>Optional</td> 
				<td>LabelingMode</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-max</td> 
				<td>Optional</td> 
				<td>Density Max value: Support Constraint()</td> 
				<td>800</td> 
			</tr> 
			<tr> 
				<td>-min</td> 
				<td>Optional</td> 
				<td>Density Min value: Support Constraint()</td> 
				<td>200</td> 
			</tr> 
			<tr> 
				<td>-sh</td> 
				<td>Optional</td> 
				<td>Shape</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-hvp</td> 
				<td>Optional</td> 
				<td>Half value point(/[A])</td> 
				<td>0.0</td> 
			</tr> 
			<tr> 
				<td>-Inverse</td> 
				<td>Optional</td> 
				<td>Inverse</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-nM</td> 
				<td>Optional</td> 
				<td>Number of Molecule</td> 
				<td>1</td> 
			</tr> 
			<tr> 
				<td>-M</td> 
				<td>Optional</td> 
				<td>MolecularWeight</td> 
				<td>80000</td> 
			</tr> 
			<tr> 
				<td>-D</td> 
				<td>Optional</td> 
				<td>Density: (g/cm3)</td> 
				<td>1.35</td> 
			</tr> 
			<tr> 
				<td>-counter</td> 
				<td>Optional</td> 
				<td>Counter(Fourier Space)</td> 
				<td>3.0</td> 
			</tr> 
			<tr> 
				<td>-dDensity</td> 
				<td>Optional</td> 
				<td>Delta (Convergence)</td> 
				<td>100.0</td> 
			</tr> 
			<tr> 
				<td>-dArea</td> 
				<td>Optional</td> 
				<td>Area(Convergence)</td> 
				<td>100.0</td> 
			</tr> 
			<tr> 
				<td>-sub</td> 
				<td>Optional</td> 
				<td>Subtraction(Convergence)</td> 
				<td>0.2</td> 
			</tr> 
			<tr> 
				<td>-ratio</td> 
				<td>Optional</td> 
				<td>Ratio(Convergence)</td> 
				<td>0.3</td> 
			</tr> 
			<tr> 
				<td>-tmax</td> 
				<td>Optional</td> 
				<td>Time Max(Convergence)</td> 
				<td>1000</td> 
			</tr> 
			<tr> 
				<td>-wd</td> 
				<td>Optional</td> 
				<td>WeightDelta(Fourier Space)</td> 
				<td>0.1</td> 
			</tr> 
			<tr> 
				<td>-wm</td> 
				<td>Optional</td> 
				<td>WeightMax(Fourier Space)</td> 
				<td>2</td> 
			</tr> 
			<tr> 
				<td>-Subtraction</td> 
				<td>Optional</td> 
				<td>Subtraction(Real Space)</td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>-c</td> 
				<td>Optional</td> 
				<td>ConfigurationFile</td> 
				<td>NULL</td> 
			</tr> 
			<tr> 
				<td>-m</td> 
				<td>Essential</td> 
				<td>RealSpaceCalculating</td> 
				<td>0</td> 
			</tr> 
			<tr> 
				<td>-h</td> 
				<td>Optional</td> 
				<td>Help</td> 
				<td>　</td> 
			</tr> 
		</table> 
<pre>
-Inverse
If high density means the location of protein, -Inverse is required for volume calculation.
-wm and -wd
weight = counter / (weightmax + counter)
weightmax -> 0 (weightdelt by weightdelta) 
-Subtraction
Real Space Constraint for desolving edge problem
</pre>
<br>

=== -m details ===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
				<td>513</td> 
				<td>514</td> 
				<td>515</td> 
				<td>673</td> 
				<td>672</td> 
				<td>675</td> 
				<td>736</td> 
				<td>737</td> 
				<td>742</td> 
				<td>517</td> 
				<td>518</td> 
				<td>519</td> 
				<td>534</td> 
				<td>257</td> 
				<td>258</td> 
				<td>259</td> 
			</tr> 
			<tr> 
				<td>+1</td> 
				<td>AreaAndLocation</td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
			</tr> 
			<tr> 
				<td>+2</td> 
				<td>Density</td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
			</tr> 
			<tr> 
				<td>+4</td> 
				<td>Convergence(Option)</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>+16</td> 
				<td>NonnegativeMode(before RealSpaceConstraint)</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>+32</td> 
				<td>Binarization(before RealSpaceConstraint)</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>+64</td> 
				<td>Labeling</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>+128</td> 
				<td>SixOrientation</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
			</tr> 
			<tr> 
				<td>+256</td> 
				<td>LowpassfilterMode(-hvp is required)</td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td></td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
			</tr> 
			<tr> 
				<td>+512</td> 
				<td>CounterMode(-ic is required)</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td>◯</td> 
				<td></td> 
				<td></td> 
				<td></td> 
			</tr> 
		</table> 
<div>They are used in combination.</div>
<br>

===-LabelinMode  details===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>0</td> 
				<td>TheLargestLabelingSearch</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>SomeVolumeLabelingSearch</td> 
			</tr> 
		</table> 
<br>

===-sh  details===
		<table border="1">
			<tr> 
				<th>Value</th> 
				<th>Description</th> 
			</tr> 
			<tr> 
				<td>0</td> 
				<td>Rectangle</td> 
			</tr> 
			<tr> 
				<td>1</td> 
				<td>Globe</td> 
			</tr> 
		</table> 
<br>

== Execution example ==
=== Input file's image ===
<div>[[:Media:Input-1VOM-2D.mrc|-I file]]'s image</div>
	<table>
		<tr>
			<td>[[File:Input-1VOM-2D.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>
				49749.7 (27, 28, 0)<br>
				7212.9<br>
				8827.15<br>
				110.339<br></p>
			</td>
		</tr>
	</table>
<br>

<div>[[Media:Input-1VOM-N-2D.mrc|-i file]]'s image</div>
	<table> 
		<tr> 
			<td>[[File:Input-1VOM-N-2D.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-18651.7 (10, 1, 0)<br> 
				52942.7 (24, 39, 0)<br> 
				7214.87<br> 
				10067.6<br> 
				125.845<br></p> 
			</td> 
		</tr> 
	</table>
<br>

<div>[[:Media:Input-1VOM-2D.fft|-ic file]]'s image (For m=+512)</div>
	<table>
		<tr>
			<td><p align="Center">[[File:Input-1VOM-2D-FFT.png]]<br>
				by [[mrcFFTExpression]](m=1)<br></p> 
			</td> 
			<td><p align="left">Min<br>
				Max<br>
				Mean<br>
				SD<br>
				SE<br></p>
			</td>
			<td><p align="left">18.4637 (75, 36, 0)<br>
				577032 (0, 0, 0)<br>
				3573.53<br>
				13475.7<br>
				168.446<br></p>
			</td>
		</tr>
	</table>
<br>

=== Option -m ===
====Case: m=257, hvp=0.6==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-m257-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-8991.5 (62, 67, 0)<br> 
				45836.1 (18, 41, 0)<br> 
				7214.87<br> 
				9093.88<br> 
				113.673<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

====Case: m=258, hvp=0.6==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-m258-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-8601.65 (53, 3, 0)<br> 
				53186.7 (24, 39, 0)<br> 
				7214.87<br> 
				9760.69<br> 
				122.009<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

====Case: m=259, hvp=0.6==== 
=====Case: No other settings=====
	<table> 
		<tr> 
			<td>[[File:Outdata-m259-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-8999.82 (62, 67, 0)<br> 
				45839 (18, 41, 0)<br> 
				7214.87<br> 
				9093.6<br> 
				113.67<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

=====Case: t=100=====
	<table> 
		<tr> 
			<td>[[File:Outdata-t-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-7536.4 (62, 67, 0)<br> 
				45966.4 (18, 41, 0)<br> 
				7214.87<br> 
				9105.49<br> 
				113.819<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

=====Case: top1=(20, 20, 0), tpo2=(60, 60, 0)=====
	<table> 
		<tr> 
			<td>[[File:Outdata-top1top2-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-15758.5 (56, 22, 0)<br> 
				52052.5 (24, 39, 0)<br> 
				7214.87<br> 
				9421.67<br> 
				117.771<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

====Case: m=513==== 
=====Case: No other settings=====
	<table> 
		<tr> 
			<td>[[File:Outdata-m513-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-19348.5 (10, 1, 0)<br> 
				53392.6 (24, 39, 0)<br> 
				7214.87<br> 
				10054.2<br> 
				125.678<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

=====Case: counter=3000=====
	<table> 
		<tr> 
			<td>[[File:Outdata-counter-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-22031.6 (0, 0, 0)<br> 
				48805.4 (24, 39, 0)<br> 
				7214.87<br> 
				9538.88<br> 
				119.236<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

<div>In the following, Setting atcounter=3000</div>
====Case: m=514==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-m514-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-15917 (10, 1, 0)<br> 
				52659.8 (24, 39, 0)<br> 
				7214.87<br> 
				9915.95<br> 
				123.949<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

====Case: m=515==== 
	<table> 
		<tr> 
			<td>[[File:Outdata-m515-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-20273.1 (0, 0, 0)<br> 
				48844.2 (24, 39, 0)<br> 
				7214.87<br> 
				9539.42<br> 
				119.243<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

====Case: m=736==== 
=====Case: No other settings=====
	<table> 
		<tr> 
			<td>[[File:Outdata-m736-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-15814.1 (10, 1, 0)<br> 
				52224.5 (24, 39, 0)<br> 
				7214.87<br> 
				9877.61<br> 
				123.47<br></p> 
			</td> 
		</tr> 
	</table> 
<br>

=====Case: LabelingMode=1===== 
	<table> 
		<tr> 
			<td>[[File:Outdata-LabelingMode1-mrcImageSuperResolution.png]]</td> 
			<td><p align="left">Min<br> 
				Max<br> 
				Mean<br> 
				SD<br> 
				SE<br></p> 
			</td> 
			<td><p align="left">-19306.2 (10, 1, 0)<br> 
				52834.2 (24, 39, 0)<br> 
				7214.87<br> 
				9993.85<br> 
				124.923<br></p> 
			</td> 
		</tr> 
	</table> 
<br>