http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?action=history&feed=atom&title=mrcImageROI
mrcImageROI - Revision history
2026-05-05T11:04:56Z
Revision history for this page on the wiki
MediaWiki 1.23.6
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageROI&diff=2070&oldid=prev
Kinoshita: /* List of option */
2014-07-30T00:56:06Z
<p><span dir="auto"><span class="autocomment">List of option</span></span></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 00:56, 30 July 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-i</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-i</td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Essential</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Essential</td>  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> <td>Input: [[mrcImage]]</td>  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> <td>Input: [[mrcImage]]<ins class="diffchange diffchange-inline">(2D)</ins></td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>NULL</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>NULL</td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td></tr>
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<td colspan="2" class="diff-lineno">Line 20:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-o</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>-o</td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Essential</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>Essential</td>  </div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> <td>Output: [[mrcImage]]</td>  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> <td>Output: [[mrcImage]]<ins class="diffchange diffchange-inline">(2D ROI)</ins></td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>NULL</td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td>NULL</td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </tr>  </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </div>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </div>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </table></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </table></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Execution example ==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>== Execution example ==</div></td></tr>
</table>
Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageROI&diff=2050&oldid=prev
Kinoshita: Created page with "'''mrcImageROI''' is Eos's Command that extracts the ROI from mrcImage file. == List of option == === Main option === <table border="1"> <div align="lef..."
2014-07-30T00:21:57Z
<p>Created page with "'''mrcImageROI''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a> that extracts the <a href="/Eos/index.php/ROI" title="ROI">ROI</a> from <a href="/Eos/index.php/mrcImage" title="mrcImage">mrcImage</a> file. == List of option == === Main option === <table border="1"> <div align="lef..."</p>
<p><b>New page</b></p><div>'''mrcImageROI''' is [[Eos]]'s [[Command]] that extracts the [[ROI]] from [[mrcImage]] file.<br />
<br />
== List of option ==<br />
=== Main option ===<br />
<table border="1"> <br />
<div align="left"> <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: [[mrcImage]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Essential</td> <br />
<td>Output: [[mrcImage]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-r</td> <br />
<td>Optional</td> <br />
<td>Rectangle ROI (blx, bly, brx, bry, trx, try, tlx, tly)</td> <br />
<td>(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)</td> <br />
</tr> <br />
<tr> <br />
<td>-x</td> <br />
<td>Optional</td> <br />
<td>Width before expansion</td> <br />
<td>1.0(Default is set by -r)</td> <br />
</tr> <br />
<tr> <br />
<td>-y</td> <br />
<td>Optional</td> <br />
<td>Height before expansion</td> <br />
<td>1.0(Default is set by -r)</td> <br />
</tr> <br />
<tr> <br />
<td>-a</td> <br />
<td>Optional</td> <br />
<td>This value [degree] is added to angle of current source image.</td> <br />
<td>0.0</td> <br />
</tr> <br />
<tr> <br />
<td>-W</td> <br />
<td>Optional</td> <br />
<td>Width after expansion[Pixel]</td> <br />
<td>1.0</td> <br />
</tr> <br />
<tr> <br />
<td>-H</td> <br />
<td>Optional</td> <br />
<td>Height after expansion[Pixel]</td> <br />
<td>1.0</td> <br />
</tr> <br />
<tr> <br />
<td>-Shift</td> <br />
<td>Optional</td> <br />
<td>ROI ARea Shift [Pixel](ShiftX, ShiftY)</td> <br />
<td>(0.0, 0.0)</td> <br />
</tr> <br />
<tr> <br />
<td>-truePitch</td> <br />
<td>Optional</td> <br />
<td>truePitch [A]</td> <br />
<td>430.0</td> <br />
</tr> <br />
<tr> <br />
<td>-dY</td> <br />
<td>Optional</td> <br />
<td>Number of turePitch</td> <br />
<td>0.0</td> <br />
</tr> <br />
<tr> <br />
<td>-Ly</td> <br />
<td>Optional</td> <br />
<td>Header Length y [A/Pixel]</td> <br />
<td>5.0</td> <br />
</tr> <br />
<tr> <br />
<td>-S</td> <br />
<td>Optional</td> <br />
<td>When inputfile is shrinked</td> <br />
<td>1</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>Optional</td> <br />
<td>Mode</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 />
</div> <br />
</table> <br />
<br />
=== -m details ===<br />
Setting of [[Interpolation]] method.<br />
<table border="1"> <br />
<div align="left"> <br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td>Nearest neighbor method</td> <br />
</tr> <br />
<tr> <br />
<td>1</td> <br />
<td>Bi-linear interpolation method</td> <br />
</tr> <br />
<tr> <br />
<td>2</td> <br />
<td>Cubic convolution method</td> <br />
</tr> <br />
<tr> <br />
<td>3</td> <br />
<td>Polynomial interpolation method</td> <br />
</tr> <br />
</div> <br />
</table><br />
<br />
<br />
== Execution example ==<br />
===------Input file's image------===<br />
<table><br />
<tr><br />
<td>[[File:Input-mrcImageROI.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<br><br />
255<br><br />
82.357<br><br />
119.241<br><br />
1.49051<br></p><br />
</td><br />
<td>Using image Added the Noise<br><br />
－－－－－－＞</td><br />
<td>[[File:Input.noiseadd-mrcImageROI.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<br><br />
255<br><br />
96.8606<br><br />
123.396<br><br />
1.54245<br></p><br />
</td><br />
</tr><br />
</table> <br />
<br />
===------Example of options only essential------===<br />
<table><br />
<tr><br />
<td>[[File:Outdata-mrcImageROI.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<br><br />
255<br><br />
96.8606<br><br />
123.396<br><br />
1.54245<br></p><br />
</td><br />
<td>* There is no change in particular.</td><br />
</tr><br />
</table><br />
<br />
===------Option -r------===<br />
====Case: -r 10 10 70 20 70 70 10 60====<br />
<table><br />
<tr><br />
<td>[[File:Inputnoise1.m0r2-mrcImageROI.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<br><br />
255<br><br />
123.636<br><br />
126.999<br><br />
2.2585<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
===------Option -x, -y------===<br />
<table><br />
<tr><td>Case: x=100, y=100</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.x100y100-mrcImageROI.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<br><br />
255<br><br />
82.5123<br><br />
118.972<br><br />
1.18972<br></p><br />
</td><br />
</tr><br />
<tr><td>Case: x=50, y=50</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.x50y50-mrcImageROI.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<br><br />
255<br><br />
125.118<br><br />
127.03<br><br />
2.5406<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
===------Option -a------===<br />
<table><br />
<tr><td>Case: a=30</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.a30-mrcImageROI.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<br><br />
255<br><br />
102.184<br><br />
124.572<br><br />
1.55715<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
===------Option -W, -H------===<br />
<table><br />
<tr><td>Case: W=100, H=100</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.w100h100-mrcImageROI.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<br><br />
255<br><br />
95.808<br><br />
123.128<br><br />
1.23128<br></p><br />
</td><br />
</tr><br />
<tr><td>Case: W=50, H=50</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.w50h50-mrcImageROI.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<br><br />
255<br><br />
95.5624<br><br />
123.048<br><br />
2.46095<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
<br><br />
<br><br />
===------Option -Shift------===<br />
<table><br />
<tr><td>Case: Shift=10</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.shift1010-mrcImageROI.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<br><br />
255<br><br />
96.8606<br><br />
124.572<br><br />
1.55715<br></p><br />
</td><br />
</tr><br />
<tr><td>Case: Shift=30</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.Shift3030-mrcImageROI.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<br><br />
255<br><br />
96.8606<br><br />
123.396<br><br />
1.54245<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
<br><br />
<br><br />
===------Option -S------===<br />
<table><br />
<tr><td>Case: S=2</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.S2-mrcImageROI.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<br><br />
255<br><br />
97.5262<br><br />
123.5572<br><br />
0.777089<br></p><br />
</td><br />
</tr><br />
<tr><td>Case: S=3</td></tr><br />
<tr><br />
<td>[[File:Inputnoise.S3-mrcImageROI.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<br><br />
255<br><br />
97.7599<br><br />
123.612<br><br />
0.519379<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
===------Option -m------===<br />
<div>The image processed -r was used as input file. (Since the change is easy to find.)</div><br />
<table><br />
<tr><td>Case: m=0</td></tr><br />
<tr><br />
<td>[[File:Inputnoise1.m0r2-mrcImageROI.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<br><br />
255<br><br />
96.8606<br><br />
123.396<br><br />
1.54245<br></p><br />
</td><br />
</tr><br />
<tr><td>Case: m=1</td></tr><br />
<tr><br />
<td>[[File:Inputnoise1.m1r2-mrcImageROI.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<br><br />
255<br><br />
123.29<br><br />
103.921<br><br />
1.84808<br></p><br />
</td><br />
</tr><br />
<tr><td>Case: m=2</td></tr><br />
<tr><br />
<td>[[File:Inputnoise1.m2r2-mrcImageROI.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">-89.3528<br><br />
354.475<br><br />
123.427<br><br />
120.789<br><br />
2.14806<br></p><br />
</td><br />
</tr><br />
<tr><td>Case: m=3</td></tr><br />
<tr><br />
<td>[[File:Inputnoise1.m3r2-mrcImageROI.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">-44414.5<br><br />
632802<br><br />
133351<br><br />
142680<br><br />
2537.36<br></p><br />
</td><br />
</tr><br />
</table></div>
Kinoshita