mrcImagePrint - Revision history

Kinoshita: Created page with "'''mrcImagePrint''' is Eos's Command. == List of option == === Main option === ..."
2014-07-29T03:43:52Z
Created page with "'''mrcImagePrint''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</th>..."
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'''mrcImagePrint''' 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: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: ps file</td>
<td>stdout</td>
</tr>
<tr>
<td>-H</td>
<td>Optional</td>
<td>High Threshold</td>
<td>0.0</td>
</tr>
<tr>
<td>-L</td>
<td>Optional</td>
<td>Low Threshold</td>
<td>1.0</td>
</tr>
<tr>
<td>-Section</td>
<td>Optional</td>
<td>[z|x|y]Section</td>
<td>z</td>
</tr>
<tr>
<td>-x</td>
<td>Optional</td>
<td>x section:(xMin, xMax)</td>
<td>(0, 0)</td>
</tr>
<tr>
<td>-y</td>
<td>Optional</td>
<td>y section:(yMin, yMax)</td>
<td>(0, 0)</td>
</tr>
<tr>
<td>-z</td>
<td>Optional</td>
<td>z section:(zMin, zMax)</td>
<td>(0, 0)</td>
</tr>
<tr>
<td>-S</td>
<td>Optional</td>
<td>Scale(Centre is Bottom Left): -S 1 := 1 mm/pixel</td>
<td>1.0</td>
</tr>
<tr>
<td>-AS</td>
<td>Optional</td>
<td>Scale(Centre is Bottom Left): -AS 1 := 1 mm/A (Real) or 1 mm/A-1 (Fourier Space)</td>
<td>1.0</td>
</tr>
<tr>
<td>-E</td>
<td>Optional</td>
<td>Enlargement(image center is center)</td>
<td>1.0</td>
</tr>
<tr>
<td>-center</td>
<td>Optional</td>
<td>Center of a printed image(in case of FT or N.x/2.0 in case of Image):(cx, cy)</td>
<td>(0.0, 0.0)</td>
</tr>
<tr>
<td>-C</td>
<td>Optional</td>
<td>[[Variable]]: ContourLevel</td>
<td>1.0 ...</td>
</tr>
<tr>
<td>-I</td>
<td>Optional</td>
<td>Black is High Density.</td>
<td></td>
</tr>
<tr>
<td>-A</td>
<td>Optional</td>
<td>HighThres=Mean-SD, LowThres=Mean+SD</td>
<td></td>
</tr>
<tr>
<td>-AC</td>
<td>Optional</td>
<td>Auto Contour(thresHigh <-> mean)</td>
<td>10</td>
</tr>
<tr>
<td>-PC</td>
<td>Optional</td>
<td>Peak Contour(thresHigh <-> (mean+thresHigh)/2</td>
<td>10</td>
</tr>
<tr>
<td>-AC2</td>
<td>Optional</td>
<td>Auto Contour2(thresHigh <-> thresLow)</td>
<td>10</td>
</tr>
<tr>
<td>-Y</td>
<td>Optional</td>
<td>Y-axis expanding</td>
<td>1</td>
</tr>
<tr>
<td>-RGB</td>
<td>Optional</td>
<td>Contour Color Mode: RGB:(Red, Green, Blue)</td>
<td>(0, 0, 0)</td>
</tr>
<tr>
<td>-RGBGradient</td>
<td>Optional</td>
<td>Contour Color GradientMode: RGB:(RedFirst, GreenFirst, BlueFirst, RedLast, GreenLast, BlueLast)</td>
<td>(0, 0, 0, 0, 0, 0)</td>
</tr>
<tr>
<td>-HSB</td>
<td>Optional</td>
<td>Contour Color Mode: HSB:(Hue, Saturation, Brightness)</td>
<td>(0, 0, 0)</td>
</tr>
<tr>
<td>-HSBGradient</td>
<td>Optional</td>
<td>Contour Color GradientMode: HSB:(HueFirst, SaturationFirst, BrightnessFirst, HueLast, SaturationLast, BrightnessLast)</td>
<td>(0, 0, 0, 0, 0, 0)</td>
</tr>
<tr>
<td>-LineColourRGB</td>
<td>Optional</td>
<td>Contour Color Mode: RGB:(LineRed, LineGreen, LineBlue)</td>
<td>(0, 0, 0)</td>
</tr>
<tr>
<td>-LineColourRGBGradient</td>
<td>Optional</td>
<td>Contour Color GradientMode: RGB:(LineRedFirst, LineGreenFirst, LineBlueFirst, LineRedLast, LineGreenLast, LineBlueLast)</td>
<td>(0, 0, 0, 0, 0, 0)</td>
</tr>
<tr>
<td>-LineColourHSB</td>
<td>Optional</td>
<td>Contour Color Mode: HSB:(LineHue, LineSaturation, LineBrightness)</td>
<td>(0, 0, 0)</td>
</tr>
<tr>
<td>-LineColourHSBGradient</td>
<td>Optional</td>
<td>Contour Color GradientMode: HSB:(LineHueFirst, LineSaturationFirst, LineBrightnessFirst, LineHueLast, LineSaturationLast, LineBrightnessLast)</td>
<td>(0, 0, 0, 0, 0, 0)</td>
</tr>
<tr>
<td>-LineChange</td>
<td>Optional</td>
<td>Contour Color Change</td>
<td>0.1</td>
</tr>
<tr>
<td>-LineWidthStart</td>
<td>Optional</td>
<td>Contour Line Width Start</td>
<td>0.1</td>
</tr>
<tr>
<td>-LineWidthStep</td>
<td>Optional</td>
<td>Contour Line Width Step</td>
<td>0.05</td>
</tr>
<tr>
<td>-ReverseOrder</td>
<td>Optional</td>
<td>Reverse Print Order</td>
<td></td>
</tr>
<tr>
<td>-Untwist</td>
<td>Optional</td>
<td>Untwist Angle [degree/A], example: (-13,28) = 0.4709576</td>
<td>0.0</td>
</tr>
<tr>
<td>-UpsideDown</td>
<td>Optional</td>
<td>Upside Down</td>
<td></td>
</tr>
<tr>
<td>-Centre</td>
<td>Optional</td>
<td>Image Centre is at the centre of paper.</td>
<td></td>
</tr>
<tr>
<td>-CircleRadius</td>
<td>Optional</td>
<td>Radius of circles in the case of imageCircles</td>
<td>0.5</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>49</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

<pre>
-C option is stronger than -AC and -PC
-PC option is stronger than -AC
-AC: (i+1)(max-maen) /(AC+1) + mean
-PC: (i )(max+mean)/2)/AC + (max+mean)/2
-AS option is stronger than -S option
The default value of -AS option is ignored.
The default value of -S option is used.
Both options are applied to y-axis.
</pre>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>1</td>
<td>ImageDensity</td>
</tr>
<tr>
<td>2</td>
<td>Contour(DiffrentLineWidth)</td>
</tr>
<tr>
<td>4</td>
<td>Contour(SameLineWidth)</td>
</tr>
<tr>
<td>8</td>
<td>BlackCircles</td>
</tr>
<tr>
<td>16</td>
<td>Scale</td>
</tr>
<tr>
<td>32</td>
<td>Centre Mark</td>
</tr>
<tr>
<td>16777216</td>
<td>Amplitude by AsciiFile</td>
</tr>
<tr>
<td>33554432</td>
<td>Log of Amplitude by AsciiFile</td>
</tr>
<tr>
<td>67108864</td>
<td>Phase by AsciiFile</td>
</tr>
</table>

== Execution example ==
=== Input file's image ===
<table>
<tr>
<td>[[File:Input-mrcImagePrint.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>
5 (34, 41, 36)<br>
0.00471829<br>
0.0933498<br>
0.000162869<br></p>
</td>
</tr>
</table>

=== Example of options only essential ===
<table>
<tr>
<th>[[File:Outdata-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
<tr>
<th>[[File:Outdata(s)-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>Thumbnail</th>
</tr>
</table>

=== Option -S===
====Case: S=2====
<table>
<tr>
<th>[[File:Outdata-S-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
<tr>
<th>[[File:Outdata2-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>Thumbnail</th>
</tr>
</table>

=== Option -H===
====Case: H=1, S=2====
<table>
<tr>
<th>[[File:Outdata-H-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -L===
====Case: L=1.5, S=2====
<table>
<tr>
<th>[[File:Outdata-L-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -Section===
====Case: Section=x, S=2====
<table>
<tr>
<th>[[File:Outdata-Section-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -x, -y, -z===
====Case: x=(10, 50), y=(0, 40), z=(30, 50), S=2====
<table>
<tr>
<th>[[File:Outdata-xyz-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>11/21 Page</th>
</tr>
</table>

=== Option -AS===
====Case: AS=1====
<table>
<tr>
<th>[[File:Outdata-AS-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -center===
====Case: center=(30, 30), S=2====
<table>
<tr>
<th>[[File:Outdata-center-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -I===
====Case: I, S=2====
<table>
<tr>
<th>[[File:Outdata-I-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -A===
====Case: A, S=2====
<table>
<tr>
<th>[[File:Outdata-A-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -Y===
====Case: Y=2====
<table>
<tr>
<th>[[File:Outdata-Y-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -ReverseOrder===
====Case: ReverseOrder, S=2====
<table>
<tr>
<th>[[File:Outdata-ReverseOrder-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>31/69 Page</th>
</tr>
<tr>
<th>[[File:Outdata2-ReverseOrder-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>Thumbnail</th>
</tr>
</table>

=== Option -untwist===
====Case: untwist=0.1, S=2====
<table>
<tr>
<th>[[File:Outdata-untwist-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
<tr>
<th>[[File:Outdata2-untwist-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>Thumbnail</th>
</tr>
</table>

=== Option -UpsideDown===
====Case: UpsideDown, S=2====
<table>
<tr>
<th>[[File:Outdata-UpsideDown-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>31/69 Page</th>
</tr>
<tr>
<th>[[File:Outdata2-UpsideDown-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>Thumbnail</th>
</tr>
</table>

=== Option -Centre===
====Case: Centre, S=2====
<table>
<tr>
<th>[[File:Outdata-Centre-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
<tr>
<th>[[File:Outdata2-Centre-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>Thumbnail</th>
</tr>
</table>

=== Option -m===
====Case: m=1, S=2====
<table>
<tr>
<th>[[File:Outdata-m1-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

====Case: m=17, S=2====
<table>
<tr>
<th>[[File:Outdata-m17-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

====Case: m=2, C=(1, 2, 3), S=2====
<table>
<tr>
<th>[[File:Outdata-m2-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

====Case: m=6, C=(1, 2, 3), S=2====
<table>
<tr>
<th>[[File:Outdata-m6-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

====Case: m=10, C=(1, 2, 3), S=2====
<table>
<tr>
<th>[[File:Outdata-m10-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

====Case: m=34, C=(1, 2, 3), S=2====
<table>
<tr>
<th>[[File:Outdata-m34-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

====Case: m=62, C=(1, 2, 3), S=2====
<table>
<tr>
<th>[[File:Outdata-m62-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -AC===
====Case: AC=3, m=62, S=2====
<table>
<tr>
<th>[[File:Outdata-AC-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -PC===
====Case: PC=1, m=62, S=2====
<table>
<tr>
<th>[[File:Outdata-PC-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -AC2===
====Case: AC2=4, m=62, S=2====
<table>
<tr>
<th>[[File:Outdata-AC2-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

=== Option -CircleRadius===
====Case: CircleRadius=0.75, m=62, C=(1, 2, 3), S=2====
<table>
<tr>
<th>[[File:Outdata-CircleRadius-mrcImagePrint.png]]</th>
</tr>
<tr>
<th>39/69 Page</th>
</tr>
</table>

Option Essential/Optional