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− | === Matrix file === | + | <div id="MipavMtl"></div> |
| + | ==Matrix file== |
| + | ===What is it and what is its purpose?=== |
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− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">What is it and what is its purpose?</font>'''</span><br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> The matrix file provides identity information for an image. It describes the image's orientation, translations, offset scales, rotations, and shears. When any of this information changes in the image, the identity matrix changes. <br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">When and how is it created?</font>'''</span><br /></font>'''</div>
| + | The MIPAV matrix file provides identity information for an image. It describes the image's orientation, translations, offset scales, rotations, and shears. When any of this information changes in the image, the identity matrix changes. <br /> |
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| + | ===When and how is it created?=== |
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| Every image has an identity matrix. The matrix changes when you apply those algorithms or utilities to the image that change any of its identity information. | | Every image has an identity matrix. The matrix changes when you apply those algorithms or utilities to the image that change any of its identity information. |
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− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> W<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">hat does it look like?</font>'''</span><br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If the image is currently open and active, you can view its matrix information by selecting Image > Attributes > View Header in the MIPAV window. The Information dialog box (Figure 7) opens.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | ===What does it look like?=== |
| + | |
| + | If the image is currently open and active, you can view its matrix information by selecting Image > Attributes > View Header in the MIPAV window. The Information dialog box opens [[#MatrixFileFigure7| see below]].<br /> |
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| + | <div id="MatrixFileFigure7"></div> |
| {| border="1" cellpadding="5" | | {| border="1" cellpadding="5" |
− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 7. The original image (A) and transformed image (B). The Info dialog box displays the transformation matrix for the image when the Transform dialog box shows settings which determined that transformation<br /></font>'''</div> | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> The original image (A) and transformed image (B). The Info dialog box displays the transformation matrix for the image when the Transform dialog box shows settings which determined that transformation<br /></font>'''</div> |
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| |} | | |} |
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− | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Where is it stored, TBD?</font>'''</span><br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> MIPAV stores matrix files in the same directory as its associated image.
| + | ===Where is it stored?=== |
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− | === Plot file ===
| + | MIPAV stores matrix files in the same directory as its associated image. |
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− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> What is it and what is its purpose?<br /></font>'''</div> | + | <div id="MipavPlotFiles"></div> |
| + | == Plot file == |
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− | The plot (PLT) file contains plot data for an intensity profile, or graph, generated for an image.
| + | ===What is it and what is its purpose?=== |
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− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> When and how is it created?<br /></font>'''</div>
| + | The MIPAV plot (PLT) file contains plot data for an intensity profile, or a graph generated for a given image. |
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− | MIPAV generates the plot file when you delineate a VOI on an image and then do the following:
| + | ===When and how is it created?=== |
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− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Select one of the following in the MIPAV window:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> VOI > Graph > Boundary Intensity<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> VOI > Graph > 2.5D Total Intensity<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> VOI > Graph > 2.5D Average Intensity<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Select File > Save Graph or press Ctrl S in either the Contour VOI Graph window or Intensity Graph window.<br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> What does it look like?<br /></font>'''</div>
| + | MIPAV generates the plot file when you delineated a VOI on an image and then called the one of following intensity functions: Boundary Intensity, 2.5D Total Intensity, or 2.5D Average Intensity. |
| + | |
| + | To call the Intensity function(s): |
| + | |
| + | <ol> |
| + | <li>Select one of the following in the MIPAV window:</li> |
| + | <ul> |
| + | <li>VOI > Graph > Boundary Intensity</li> |
| + | <li>VOI > Graph > 2.5D Total Intensity</li> |
| + | <li>VOI > Graph > 2.5D Average Intensity</li> |
| + | </ul> |
| + | <li> Select File > Save Graph or press Ctrl S in either the Contour VOI Graph window or Intensity Graph window.</li> |
| + | </ol> |
| + | |
| + | <div id="PlotFileExamples"></div> |
| + | ===What does it look like?=== |
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| An example of a plot file appears in Figure 8, and Figure 9 shows a graph for this plot file. | | An example of a plot file appears in Figure 8, and Figure 9 shows a graph for this plot file. |
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| |} | | |} |
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− | <br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Where is it stored?<br /></font>'''</div>
| + | === Where is it stored?=== |
| | | |
| By default, the PLT file is stored in the same directory that holds the image. However, you can store it in any directory of your choice. | | By default, the PLT file is stored in the same directory that holds the image. However, you can store it in any directory of your choice. |
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− | === VOI file === | + | <div id="MipavLutFile"></div> |
| + | == LUT file == |
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− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> What is it and what is its purpose? <br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> The VOI file provides plots for contours that you have delineated on an image. Saving VOI information to a file means that it can be used again. In addition, if you create a script that includes algorithms that require VOIs, you need to save the VOIs so that the script can apply them to the images (refer to [MIPAV_Scripting.html#1298974 "Using Scripts (Macros) in MIPAV" ]).<br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> What does it look like? <br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [MIPAV_AppCSupportedFormats.html#1250734 Figure 10] shows an example of a VOI file.
| + | LUT is a vector file format used to store MIPAV Lookup Table (LUT) data. |
| + | |
| + | MIPAV provides a logical color map, which allows you to remap the original intensities to other intensities. Although technically the term look-up table (LUT) can be used for the physical and logical color maps, in this guide look-up table refers to the logical color map only. You can apply predefined, pseudo color or inverse LUTs, or you can manually manipulate the transfer function used to map the image data to the LUT. The LUT then translates the remapped values so that they can be interpreted by the physical color map and displayed on your monitor. |
| + | |
| + | === What is its purpose? === |
| + | |
| + | The lookup table (LUT) file holds lookup table values, which you can modify, for the active image currently being displayed. |
| + | |
| + | |
| + | === When and how is it created? === |
| + | |
| + | MIPAV generates the LUT file when, after opening an image, you either create or save a corresponding lookup table. For example: |
| + | |
| + | |
| + | [[Image:LUTIco.jpg]] |
| + | |
| + | <ul> |
| + | <li>Select the Lookup table icon, to call the Lookup Table window and display a lookup table for the image.</li> |
| + | <li>Save the Lookup table by selecting LUT > Save or pressing Ctrl+S.</li> |
| + | </ul> |
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| {| border="1" cellpadding="5" | | {| border="1" cellpadding="5" |
− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 10. An example of a VOI file<br /></font>'''</div> | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 5. Lookup Table window<br /></font>'''</div> |
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− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">MIPAV VOI FILE</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">0 # curveType of the VOI</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">255 # color of VOI - red component</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">0 # color of VOI - green component</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">0 # color of VOI - blue component</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">255 # color of VOI - alpha component</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">1 # number of slices for the VOI</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">8 # slice number</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">1 # number of contours in slice</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">38 # number of pts in contour</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">167.0 124.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">161.0 147.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">156.0 156.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">150.0 162.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">144.0 166.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">139.0 170.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">133.0 172.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">128.0 174.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">122.0 175.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">116.0 176.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">111.0 176.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">105.0 175.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">139.0 78.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">144.0 82.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">150.0 86.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">156.0 92.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">161.0 101.0</font></span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">24862902 # unique ID of the VOI</font></span><br /></font></div>
| + | [[Image:LookupTableDialogBox.jpg]] |
| |} | | |} |
| | | |
− | <br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> When and how is it created?<br /></font>'''</div>
| + | === Where is it stored? === |
| | | |
− | MIPAV creates a VOI file when you create one or more VOIs on an image and then select one of the following commands in the MIPAV window:
| + | By default, the LUT file is stored in the same directory that holds the image. |
| | | |
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> VOI > Save VOI<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> VOI > Save VOI as<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> VOI > Save All VOIs<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> VOI > Save All VOIs to<br /></font></div>
| |
| | | |
− | Because MIPAV VOI file format is a simple ASCII format, it can be easily adapted to other formats. The contours are given as simple closed polygons. One cross-section may contain several polygons. A contour can reside inside another contour. They are oriented so the inside of a contour (material) is on the right side. The <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">xy </font>''</span>coordinates range from 0 to 512.
| + | === What does it look like? === |
| | | |
− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Where is it stored?<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Although by default it is stored in same directory as the image, you can save it to another directory by selecting VOI > Save VOI as or VOI > Save All VOIs to, which open the Save window.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 1pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div>
| + | A figure below shows an example of a LUT file. The middle section of the file was removed in this example because of space limitations, and the column headings-alpha, red, green, and blue-were added to make it is easier to interpret the values. The column headings do not appear in the actual LUT file. |
| | | |
− | ==== VOI XML file ====
| |
| | | |
− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> What is it and what is its purpose? <br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> The VOI XML (<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">.xml</font></span>) file provides plots for contours in an XML format.<br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Where is it stored? <br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Like VOI files, VOI XML files are stored, by default, in the same directory as the image. However, you can save them to another directory by selecting either VOI > Save VOI as or VOI > Save All VOIs to. <br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> When and how is it created?<br /></font>'''</div>
| + | {| border="1" cellpadding="5" |
| + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Sample LUT file (bold column headings added to make it easier to interpret the values)<br /></font>'''</div> |
| + | |- |
| + | | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> </font></span><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Alpha Red Green Blue</font>'''</span> |
| | | |
− | You can save VOIs as VOI files or VOI XML files. To do so, you delineate one or more VOIs on an image and then select VOI > Save VOI as or VOI > Save All VOIs to. In the Save dialog box, you simply type the file name with a <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">.xml</font></span> extension and click Save.
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><LUT></font></span> |
| | | |
− | <div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> What does it look like?<br /></font>'''</div> | + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">256 # Size of LUT Arrays</font></span> |
| | | |
− | An example of a VOI XML file appears in [MIPAV_AppCSupportedFormats.html#1257794 Figure 11]. The middle part of the file was removed to save space.
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">0 1.0 0.0 0.0 0.0</font></span> |
| | | |
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">1 1.0 0.99609375 0.99609375 0.99609375</font></span> |
| | | |
− | {| border="1" cellpadding="5"
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">2 1.0 1.9921875 1.9921875 1.9921875</font></span> |
− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 11. An example of a VOI XML file <br /></font>'''</div>
| + | |
− | |-
| + | |
− | |
| + | |
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <?xml version="1.0" encoding="UTF-8" ?> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> - <!-- <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> MIPAV VOI file <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> --> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-transform: none; vertical-align: baseline"><u><font color="#0000ff">-</font></u></span> <VOI xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Unique-ID>24862902</Unique-ID> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Curve-type>0</Curve-type> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Color>255,255,0,0</Color> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-transform: none; vertical-align: baseline"><u><font color="#0000ff">-</font></u></span> <Contour> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Slice-number>8</Slice-number> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>167.0,124.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>161.0,147.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>144.0,166.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>139.0,170.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>133.0,172.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>128.0,174.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Â <br /></font></div>
| + | |
| | | |
− | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[This part of the LUT file was removed to save space.]</font></span> | + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">3 1.0 2.9882812 2.9882812 2.9882812</font></span> |
| | | |
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Â <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>144.0,82.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>150.0,86.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>156.0,92.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>161.0,101.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> </Contour> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; font-weight: normal; text-transform: none; vertical-align: baseline"><u><font color="#0000ff">-</font></u></span> <Contour> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Slice-number>8</Slice-number> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>159.0,55.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>190.0,55.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>190.0,85.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <Pt>159.0,85.0</Pt> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> </Contour> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 54pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> </VOI><br /></font></div> | + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">4 1.0 3.984375 3.984375 3.984375</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">5 1.0 4.9804688 4.9804688 4.9804688</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">6 1.0 5.9765625 5.9765625 5.9765625</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">7 1.0 6.9726562 6.9726562 6.9726562</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">8 1.0 7.96875 7.96875 7.96875</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">9 1.0 8.964844 8.964844 8.964844</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">10 1.0 9.9609375 9.9609375 9.9609375</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">11 1.0 10.957031 10.957031 10.957031</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">12 1.0 11.953125 11.953125 11.953125</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">13 1.0 12.949219 12.949219 12.949219</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">14 1.0 13.9453125 13.9453125 13.9453125</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"> </font></span><span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">[This part of the LUT file was removed to save space.]</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">251 1.0 250.01953 250.01953 250.01953</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">252 1.0 251.01562 251.01562 251.01562</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">253 1.0 252.01172 252.01172 252.01172</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">254 1.0 253.00781 253.00781 253.00781</font></span> |
| + | |
| + | <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">255 1.0 254.0039 254.0039 254.0039</font></span> |
| + | |
| + | <div class="CellBody"> </div> |
| |} | | |} |
| | | |
− | <br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 12pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> <br /></font>'''</div>
| |
| | | |
| + | The LUT file is arranged in table row-column format. The LUT file contains 256 rows, numbered 0 to 255, which correspond to the number of intensities that can be displayed in the image. The first number assigned to the intensity described by the other numbers in that row. The second number is the alpha channel value. The alpha channel is the portion of each pixel's that indicates the opacity level of the intensity value. The number 1.0 indicates that the intensity is opaque; 0.0 indicates the intensity is transparent. Numbers in-between indicate varying translucency levels. The last three numbers indicate the values for the red, green, and blue channels, respectively.<br /> |
| + | |
| + | |
| + | |
| + | <div id="MipavVoiFile"></div> |
| + | |
| + | == VOI file == |
| + | |
| + | === What is it and what is its purpose? === |
| + | |
| + | The MIPAV VOI file provides plots for contours that you have delineated on an image. Saving VOI information to a file means that it can be used again. In addition, if you create a script that includes algorithms that require VOIs, you need to save the VOIs so that the script can apply them to the images (refer to [MIPAV_Scripting.html#1298974 "Using Scripts (Macros) in MIPAV" ]).<br /> |
| + | |
| + | '''An example of a VOI file:''' |
| + | |
| + | <div style="font-family:courier"> |
| + | 0 # curveType of the VOI |
| + | |
| + | 255 # color of VOI - red component |
| + | |
| + | 0 # color of VOI - green component |
| + | |
| + | 0 # color of VOI - blue component |
| + | |
| + | 255 # color of VOI - alpha component |
| + | |
| + | 1 # number of slices for the VOI |
| + | |
| + | 8 # slice number |
| + | |
| + | 1 # number of contours in slice |
| + | |
| + | 38 # number of pts in contour |
| + | |
| + | 167.0 124.0 |
| + | |
| + | 161.0 147.0 |
| + | |
| + | 156.0 156.0 |
| + | |
| + | 150.0 162.0 |
| + | |
| + | 144.0 166.0 |
| + | |
| + | 139.0 170.0 |
| + | |
| + | 133.0 172.0 |
| + | |
| + | 128.0 174.0 |
| + | |
| + | 122.0 175.0 |
| + | |
| + | 116.0 176.0 |
| + | |
| + | 111.0 176.0 |
| + | |
| + | 105.0 175.0 |
| + | |
| + | 139.0 78.0 |
| + | |
| + | 144.0 82.0 |
| + | |
| + | 150.0 86.0 |
| + | |
| + | 156.0 92.0 |
| + | |
| + | 161.0 101.0 |
| + | |
| + | 24862902 # unique ID of the V |
| + | </div> |
| + | |
| + | === When and how is it created? === |
| + | |
| + | MIPAV creates a VOI file when you create one or more VOIs on an image and then select one of the following commands in the MIPAV window: |
| + | |
| + | <ul> |
| + | <li>VOI > Save VOI</li> |
| + | <li>VOI > Save VOI as</li> |
| + | <li>VOI > Save All VOIs</li> |
| + | <li>VOI > Save All VOIs to</li> |
| + | </ul> |
| + | |
| + | Because MIPAV VOI file format is a simple ASCII format, it can be easily adapted to other formats. The contours are given as simple closed polygons. One cross-section may contain several polygons. A contour can reside inside another contour. They are oriented so the inside of a contour (material) is on the right side. The xy coordinates range from 0 to 512. |
| + | |
| + | === Where is it stored? === |
| + | Although by default it is stored in same directory as the image, you can save it to another directory by selecting VOI > Save VOI as or VOI > Save All VOIs to, which open the Save window. |
| + | |
| + | <div id="MipavLutVoiXmlFile"></div> |
| + | ===VOI XML file=== |
| + | |
| + | ====What is it and what is its purpose?==== |
| + | The VOI XML (.xml) file provides plots for contours in an XML format. |
| + | |
| + | ====Where is it stored?==== |
| + | |
| + | Like VOI files, VOI XML files are stored, by default, in the same directory as the image. However, you can save them to another directory by selecting either VOI > Save VOI as or VOI > Save All VOIs to. |
| + | |
| + | ====When and how is it created?==== |
| + | |
| + | You can save VOIs as VOI files or VOI XML files. To do so, you delineate one or more VOIs on an image and then select VOI > Save VOI as or VOI > Save All VOIs to. In the Save dialog box, you simply type the file name with a .xml extension and click Save. |
| + | |
| + | ====What does it look like?==== |
| + | |
| + | An example of a VOI XML file is shown below. The middle part of the file was removed to save space. |
| + | |
| + | '''An example of a VOI XML file''' |
| + | <br /> |
| + | |
| + | <div style="font-family:courier"> |
| + | <?xml version="1.0" encoding="UTF-8" ?> |
| + | |
| + | - <!-- |
| + | |
| + | MIPAV VOI file |
| + | |
| + | --> |
| + | |
| + | - <VOI xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> |
| + | |
| + | <Unique-ID>24862902</Unique-ID> |
| + | |
| + | <Curve-type>0</Curve-type> |
| + | |
| + | <Color>255,255,0,0</Color> |
| + | |
| + | - <Contour> |
| + | |
| + | <Slice-number>8</Slice-number> |
| + | |
| + | <Pt>167.0,124.0</Pt> |
| + | |
| + | <Pt>161.0,147.0</Pt> |
| + | |
| + | <Pt>144.0,166.0</Pt> |
| + | |
| + | <Pt>139.0,170.0</Pt> |
| + | |
| + | <Pt>133.0,172.0</Pt> |
| + | |
| + | <Pt>128.0,174.0</Pt> |
| + | |
| + | |
| + | [This part of the LUT file was removed to save space.] |
| + | |
| + | <Pt>144.0,82.0</Pt> |
| + | |
| + | <Pt>150.0,86.0</Pt> |
| + | |
| + | <Pt>156.0,92.0</Pt> |
| + | |
| + | <Pt>161.0,101.0</Pt> |
| + | |
| + | </Contour> |
| + | |
| + | - <Contour> |
| + | |
| + | <Slice-number>8</Slice-number> |
| + | |
| + | <Pt>159.0,55.0</Pt> |
| + | |
| + | <Pt>190.0,55.0</Pt> |
| + | |
| + | <Pt>190.0,85.0</Pt> |
| + | |
| + | <Pt>159.0,85.0</Pt> |
| + | |
| + | </Contour> |
| + | |
| + | </VOI> |
| + | |
| + | </div> |
| + | |
| + | |
| + | <div id="MipavSurfaceFiles"></div> |
| + | == Surface files == |
| + | |
| + | A '''surface area''' is the measure of how much exposed area a solid object has. It is usually expressed in square units. In medical imaging, curves and surfaces allow for the modeling of body parts and organs with complex curvature(s) in multiple coordinate directions. |
| + | |
| + | MIPAV supports its own surface format (*.sur). A MIPAV surface file contains the information about the surface area and geometry, plus the additional information that describes the surface color and more. This is defined by [http://mipav.cit.nih.gov/documentation/xml-format/image/ an XML scheme], which can be found on [http://mipav.cit.nih.gov/documentation/xml-format/image/ the MIPAV web site]. |
| + | |
| + | |
| + | '''MIPAV Surface format (Triangle mesh or ClodMesh - Continuous level of details mesh)''' |
| + | <br /> |
| + | <div style="font-family:courier"> |
| + | Inverse Dicom matrix flag |
| + | |
| + | 3D mesh direction x, y, z |
| + | |
| + | Start location x, y, z |
| + | |
| + | Bounding box x, y, z |
| + | |
| + | Inverse Dicom matrix |
| + | |
| + | Vertex quantity |
| + | |
| + | Vertex position x, y, z |
| + | |
| + | Vertex normal x, y, z |
| + | |
| + | Index quantity |
| + | |
| + | Index connectivity x, y, z |
| + | |
| + | Surface material property |
| + | |
| + | Clodmesh collapse record |
| + | |
| + | </div> |
| + | |
| + | '''See also:''' [http://mipav.cit.nih.gov/documentation/api/gov/nih/mipav/view/renderer/J3D/model/file/package-summary.html| MIPAV API]. |
| + | |
| + | <div id="MipavTextFormat"></div> |
| + | ===MIPAV surface file in text file format=== |
| + | |
| + | MIPAV also uses ASCII text format to define surfaces. The text surface file records the triangle mesh vertices, normals and connectivity. |
| + | |
| + | A sample surface defined in ASCII format: |
| + | |
| + | <div style="font-family:courier;font-size:-1"> |
| + | Vertices |
| + | |
| + | x, y, z // vertex position |
| + | |
| + | Normal |
| + | |
| + | x, y, z // normal coordinate |
| + | |
| + | Connectivity |
| | | |
− | [[MIPAV Surface file ]]
| + | x, y, z // index connection |
| + | |
| + | </div> |
The MIPAV matrix file provides identity information for an image. It describes the image's orientation, translations, offset scales, rotations, and shears. When any of this information changes in the image, the identity matrix changes.
Every image has an identity matrix. The matrix changes when you apply those algorithms or utilities to the image that change any of its identity information.
If the image is currently open and active, you can view its matrix information by selecting Image > Attributes > View Header in the MIPAV window. The Information dialog box opens see below.
MIPAV stores matrix files in the same directory as its associated image.
The MIPAV plot (PLT) file contains plot data for an intensity profile, or a graph generated for a given image.
MIPAV generates the plot file when you delineated a VOI on an image and then called the one of following intensity functions: Boundary Intensity, 2.5D Total Intensity, or 2.5D Average Intensity.
An example of a plot file appears in Figure 8, and Figure 9 shows a graph for this plot file.
The graph has five functions. Each function has 32 points. This file is read vertically. The first two columns show the x and y values for the first function. The next two columns show the x and y values for the second function, and so on. The first point of the first function is (1, 8), the second is (2, 9), and the third is (3, 18).
The first point for the fifth function is (1, 22400), the second is (2, 21700), the third is (3, 21000), and so on. The graph for this plot file appears in Figure 9.