mrcImageROIs - Revision history

Kinoshita: Created page with "'''mrcImageROIs''' is Eos's Command that cuts out multiple ROIs required. == Algorithm == == List of option == === Main option ===

2014-07-30T01:35:49Z

Created page with "'''mrcImageROIs''' is Eos's Command that cuts out multiple ROIs required. == Algorithm == == List of option == === Main option === <table border="1"> <div align..."

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'''mrcImageROIs''' is [[Eos]]'s [[Command]] that cuts out multiple ROIs required.

== Algorithm ==
== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<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>-I</td>
<td>Essential</td>
<td>Input:[[ASCII]](ROI Information)</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: Montage file</td>
<td>stdout(Standard output by default）</td>
</tr>
<tr>
<td>-S</td>
<td>Optional</td>
<td>Input: when the shrink ratio between Input file and image with ROI Information is different.</td>
<td>NULL (No Shrink)</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Input: Width of all</td>
<td>0.0 (Depending to ROI Information)</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Input: Height of all</td>
<td>0.0 (Depending to ROI Information)</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Interpolation mode</td>
<td>0</td>
</tr>
<tr>
<td>-M</td>
<td>Optional</td>
<td>Output file's format</td>
<td>2</td>
</tr>
</div>
</table>

=== -m details ===
Setting of [[Interpolation]] method.
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Nearest neighbor method</td>
</tr>
<tr>
<td>1</td>
<td>Bi-linear interpolation method</td>
</tr>
<tr>
<td>2</td>
<td>Cubic convolution method</td>
</tr>
<tr>
<td>3</td>
<td>Polynomial interpolation method</td>
</tr>
</div>
</table>
<br>

===-M details ===
Setting format of output file.
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Char</td>
</tr>
<tr>
<td>1</td>
<td>Short</td>
</tr>
<tr>
<td>2</td>
<td>Float</td>
</tr>
</div>
</table>
<br>

=== ROI Information file's format===
OutputFileName　Shape　Parameter

Rectangle (4 corners)
OutFileName Rect blx bly brx bry trx try tlx tly

Rectangle (Center and Size)
OutFileName Rect2 centerx centery width height

Center and Radius
OutFileName Circle centerx centery radius

== Execution example ==
===------Input file's image------===
<table>
<tr>
<td>[[File:Input-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
255<br>
82.357<br>
119.241<br>
1.49051<br></p>
</td>
<td>Using image Added the Noise<br>
　　－－－－－－＞</td>
<td>[[File:Inputnoise.r1-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
255<br>
95.3804<br>
123.024<br>
1.51882<br></p>
</td>
</tr>
</table>

===------Infomation file's data------===
====Format pattern1: OutFileName Rect blx bly brx bry trx try tlx tly====
<div>Setting as coordinates of rectangle</div>
<pre>
inputnoise-0000.roi Rect 6 6 26 6 26 26 6 26
inputnoise-0001.roi Rect 20 6 40 6 40 26 20 26
inputnoise-0002.roi Rect 40 6 60 6 60 26 40 26
inputnoise-0003.roi Rect 54 6 74 6 74 26 54 26
inputnoise-0004.roi Rect 6 20 26 20 26 40 6 40
inputnoise-0005.roi Rect 20 20 40 20 40 40 20 40
inputnoise-0006.roi Rect 40 20 60 20 60 40 40 40
inputnoise-0007.roi Rect 54 20 74 20 74 40 54 40
inputnoise-0008.roi Rect 6 40 26 40 26 60 6 60
inputnoise-0009.roi Rect 20 40 40 40 40 60 20 60
inputnoise-0010.roi Rect 40 40 60 40 60 60 40 60
inputnoise-0011.roi Rect 54 40 74 40 74 60 54 60
inputnoise-0012.roi Rect 6 54 26 54 26 74 6 74
inputnoise-0013.roi Rect 20 54 40 54 40 74 20 74
inputnoise-0014.roi Rect 40 54 60 54 60 74 40 74
inputnoise-0015.roi Rect 54 54 74 54 74 74 54 74

</pre>

====Format pattern2: OutFileName Rect2 centerx centery width height====
<div>Setting center position, width and height.</div><br>
[[File:Infomation2-mrcImageROIs.png]]

===------Example of options only essential------===
====Case: Infomation file: Rect====
<div>Images of Infomation file's number are output</div>
<table>
<tr>
<td>[[File:Inputnoise-0000.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0001.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0002.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0003.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0004.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0005.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0006.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0007.roi-mrcImageROIs.png]]</td>
</tr>
<tr>
<td>[[File:Inputnoise-0008.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0009.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0010.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0011.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0012.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0013.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0014.roi-mrcImageROIs.png]]</td>
<td>[[File:Inputnoise-0015.roi-mrcImageROIs.png]]</td>
</tr>
</table>

====Case: Infomation file: Rect2====
[[File:Inputnoise1-0000-m0.roi-mrcImageROIs.png]]<br>

===------Option -o------===
<table>
<tr>
<td>[[File:Inputnoise.r1.out-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-168.927<br>
160.828<br>
-9.74867e-07<br>
111.57<br>
1.18799<br></p>
</td>
</tr>
</table>

===------Option -S------===
====Example of 15th image from Infomation file====
=====Case: -S=3=====
<table>
<tr>
<td>[[File:Inputnoise-0015-S3.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
255<br>
99.9307<br>
124.111<br>
2.03461<br></p>
</td>
</tr>
</table>

=====Case: -S=5=====
<table>
<tr>
<td>[[File:Inputnoise-0015-S5.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
255<br>
82.7682<br>
119.056<br>
1.17877<br></p>
</td>
</tr>
</table>

===------Option -width,-height------===
====Case: -width=10,-height=10====
<table>
<tr>
<td>[[File:Inputnoise-0015-w10h10.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
255<br>
203.47<br>
101.588<br>
10.1588<br></p>
</td>
</tr>
</table>

====Case: -width=50,-height=50====
<table>
<tr>
<td>[[File:Inputnoise-0015-w50h50.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
255<br>
84.2792<br>
119.61<br>
2.3922<br></p>
</td>
</tr>
</table>

===------Option -M------===
====Using Infomation file: Rect====
=====Case: M=0=====
<table>
<tr>
<td>[[File:Inputnoise.r1.M0-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
165<br>
99.2579<br>
54.0903<br>
0.575951<br></p>
</td>
</tr>
</table>

=====Case: M=1=====
<table>
<tr>
<td>[[File:Inputnoise-r1.M1-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0<br>
65445<br>
25411.9<br>
31831.5<br>
338.94<br></p>
</td>
</tr>
</table>

=====Case: M=2=====
<table>
<tr>
<td>[[File:Inputnoise.r1.out-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-168.927<br>
160.828<br>
-9.74867e-07<br>
111.57<br>
1.18799<br></p>
</td>
</tr>
</table>

===------Option -m------===
====Using Infomation file: Rect2====
=====Case: m=0=====
<table>
<tr>
<td>[[File:Inputnoise1-0000-m0.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
Sum<br></p>
</td>
<td><p align="left">0<br>
255<br>
106.696<br>
125.405<br>
2.92352<br>
196321<br></p>
</td>
</tr>
</table>

=====Case: m=1=====
<table>
<tr>
<td>[[File:Inputnoise1-0000-m1.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
Sum<br></p>
</td>
<td><p align="left">0<br>
255<br>
106.881<br>
105.188<br>
2.4522<br>
196661<br></p>
</td>
</tr>
</table>

=====Case: m=2=====
<table>
<tr>
<td>[[File:Inputnoise1-0000-m2.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
Sum<br></p>
</td>
<td><p align="left">-65.1789<br>
323.14<br>
106.754<br>
121.757<br>
2.83848<br>
196428<br></p>
</td>
</tr>
</table>

=====Case: m=3=====
<table>
<tr>
<td>[[File:Inputnoise1-0000-m3.roi-mrcImageROIs.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br>
Sum<br></p>
</td>
<td><p align="left">-13045.1<br>
399922<br>
81934.6<br>
82047.6<br>
1912.75<br>
1.5076e+08<br></p>
</td>
</tr>
</table>

== References ==