Difference between revisions of "MIPAV configuration files"

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== MIPAV configuration files ==
  
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== Understanding MIPAV-related files ==
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This section includes definitions and examples of the MIPAV configuration files: [[#PreferenceFile |preference]] and [[#MIpavLaxFile| LAX]].<br />
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<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"> This section includes examples of the following files: preference, LUT, IMG, matrix, plot, VOI, VOI XML, LAX, and Analyze.<br /></font></div>
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<div id="PreferenceFile"></div>
 
=== Preference file ===
 
=== Preference file ===
  
 
==== What is its purpose? ====
 
==== What is its purpose? ====
  
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<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 preference file (mipav.preference) contains either the default or customized settings for running MIPAV. These settings determine whether some features appear or how certain features look. <br /></font></div>
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The preference file (mipav.preference) contains either the default or customized settings for running MIPAV. These settings determine whether some features appear or how certain features look. See also: [[Customizing MIPAV#MipavOptions | MIPAV options]].
  
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You can customize the settings in the file by selecting Help &gt; Program Options in the MIPAV window. For example, you can change whether the splash screen appears when you start the program, whether the scripting toolbar appears, the color of the crosshair cursor, whether the log mode is turn on, and so on.
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You can customize the settings in the file by selecting Help > Program Options in the MIPAV window. For example, you can change whether the splash screen appears when you start the program, whether the scripting toolbar appears, the color of the crosshair cursor, whether the log mode is turn on, and so on.
  
 
==== When and how is it created? ====
 
==== When and how is it created? ====
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By default, MIPAV stores the preference file in your home directory.
 
By default, MIPAV stores the preference file in your home directory.
  
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{| border="1" cellpadding="5"
 
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|+  <div class="TableTitle">Table 4.  Default home directories</div>
 
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<div class="CellHeading">For . . .</div>
 
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<div class="CellHeading">The home directory is . . .</div>
 
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<div class="CellBody">Window users</div>
 
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<div class="CellBody">C:\Documents and Settings\userID</div>
 
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<div class="CellBody">Unix users</div>
 
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<div class="CellBody">Â </div>
 
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<div class="CellBody">MacIntosh users</div>
 
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<div class="CellBody">Â </div>
 
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However, if MIPAV is installed on a network and several users access it remotely, preference files are stored in the network home directory.
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However, if MIPAV is installed on a network drive and several users can access it remotely, preference files are stored in the network home directory.
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The system administrator for the network may select another directory on the network in which to store preference files. <br />
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==== What does it look like? ====
  
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<div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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">Note:</font>'''</span> The system administrator for the network may select another directory on the network in which to store proference files. <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"> An example of the preference file appears in [MIPAV_AppCSupportedFormats.html#1023375 Figure 4]. For ease of discussion, line numbers appear on the left of each line in the figure, although they don't appear in the actual preference file. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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">Note:</font>'''</span> Your preference file may not have the same ordering of information as in [MIPAV_AppCSupportedFormats.html#1023375 Figure 4]<nowiki>; as you customize MIPAV, your preference file changes to reflect the additional information.</nowiki><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">
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An example of the preference file appears in the figure below. For ease of discussion, line numbers appear on the left of each line in the figure, although they don't appear in the actual preference file. Your preference file may not have the same ordering of information as it shown below; as you customize MIPAV, your preference file changes to reflect the additional information.
  
 
{| border="1" cellpadding="5"
 
{| border="1" cellpadding="5"
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|+ <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 4. Example of MIPAV.preference file <br /></font>'''</div>
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|+ <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"> An example of MIPAV.preference file <br /></font>'''</div>
 
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<br /></font></div>
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<br />
  
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=== LUT file ===
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<div id="MIpavLaxFile"></div>
  
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<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">What is its purpose? </font>'''</span><span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">The lookup table (LUT) file holds lookup table values, which you can modify, for the active image currently being displayed. </font></span><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><span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">MIPAV generates the file when, after opening an image, you do the following:</font></span>
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<div id="LaunchAnywhere"></div>
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== MIPAV LaunchAnywhere executable (LAX) file ==
  
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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 [[Image:LUTIco.jpg]] select the Lookup table icon, to call the Lookup Table window and display a lookup table for the image. See [MIPAV_AppCSupportedFormats.html#1249199 Figure 5]. <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 Save the Lookup table by selecting LUT &gt; Save or pressing Ctrl S.<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">
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=== What is it and what is its purpose? ===
  
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{| border="1" cellpadding="5"
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The LAX file is a LaunchAnywhere Executable (LAX) file that contains MIPAV's runtime environmental options. It may be helpful to access the file if you contacting the software developers during the debugging process. To contact MIPAV developers, use [http://mipav.cit.nih.gov/contact.php the MIPAV contact page].
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|+ <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: 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 clear="all" />{| align="center"
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[[Image:LookupTableDialogBox.jpg]]
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|}<br clear="all" /><br /></font></div>
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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>
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[http://www.macrovision.com/products/installation/installanywhere.htm?tabContent=/products/installation/installanywhere/feat_6396.htm LaunchAnywhere] is a commercial program created by Macrovizion, Inc. and used to install and start the MIPAV software on your system.  
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<br />
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By default, the LUT file is stored in the same directory that holds the 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 does it look like?<br /></font>'''</div>
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[MIPAV_AppCSupportedFormats.html#1248570 Figure 6] is 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.
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<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">
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{| border="1" cellpadding="5"
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|+ <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 6. Sample LUT file (bold column headings added to make it easier to interpret the values)<br /></font>'''</div>
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<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>
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<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">&lt;LUT&gt;</font></span>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<div class="CellBody">Â </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: 1pt; 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: 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"> he 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 /></font></div>
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The runtime environmental options in the LAX file are set during the development of the MIPAV software. If you install MIPAV on any Windows, UNIX, or MAC OS operating system, the LaunchAnywhere program copies a LaunchAnywhere Executable (LAX) file to the same directory as your other MIPAV software files. <br />
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== See also: ==
 +
*[[Getting Started Quickly with MIPAV]]
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*[[Supported Formats]]
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**[[Supported Formats | Graphical and file formats supported by MIPAV]]
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**[[Image formats descriptions | Image formats' descriptions]]
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**[[FAQ: Understanding Image Basics#FilesExtensions | Image files supported by MIPAV]]
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*[[Customizing MIPAV]]
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**[[Customizing MIPAV#MipavOptions | MIPAV Options dialog box]]
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**[[Customizing MIPAV#SplashScreen | Showing and hiding the splash screen on start-up]]
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**[[Customizing MIPAV#DebuggingMipav | Debugging MIPAV]]
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**[[Customizing MIPAV#ActionsHistory | Saving a history of actions on images]]
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**[[Customizing MIPAV#DefaultFileTypes | Choosing the default file types to display or save]]
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**[[Customizing MIPAV#AddingShortcuts | Adding Shortcuts]]
  
  
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[[Matrix file]]
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[[Category: Help]]
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[[Category: Getting started]]

Latest revision as of 15:20, 26 April 2012

MIPAV configuration files

This section includes definitions and examples of the MIPAV configuration files: preference and LAX.

Preference file

What is its purpose?

The preference file (mipav.preference) contains either the default or customized settings for running MIPAV. These settings determine whether some features appear or how certain features look. See also: MIPAV options.

You can customize the settings in the file by selecting Help > Program Options in the MIPAV window. For example, you can change whether the splash screen appears when you start the program, whether the scripting toolbar appears, the color of the crosshair cursor, whether the log mode is turn on, and so on.

When and how is it created?

MIPAV generates a preference file for all users when the program is run for the first time. Usually, the first settings recorded in the preference file are the memory setting, or maximum heap size, and the default image directory. When you first customize one or more of the settings in the Program Options dialog box, MIPAV adds those settings to the preference file as well as the default settings for those features you did not change. If you later make changes to those same preferences, the program adds those new settings to the preference file. In other words, the initial preference file is very small. It grows in size as you customize the program with the latest changes appearing last in the file.

Where is it stored?

By default, MIPAV stores the preference file in your home directory.


However, if MIPAV is installed on a network drive and several users can access it remotely, preference files are stored in the network home directory.

The system administrator for the network may select another directory on the network in which to store preference files.

What does it look like?

An example of the preference file appears in the figure below. For ease of discussion, line numbers appear on the left of each line in the figure, although they don't appear in the actual preference file. Your preference file may not have the same ordering of information as it shown below; as you customize MIPAV, your preference file changes to reflect the additional information.

An example of MIPAV.preference file

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# MIPAV preference file
#Mon Mar 19 15:12:48 EST 2001
LightBoxGridRow=2
LightBoxBorderSize=3
EnableDICOMReceiver=true
TRIM=0.4
DEBUG=true
PlugInFile3=SpreadSheet
PlugInFile2=GraphPanel
PlugInFile1=Chart
Swing=true
LightBoxRowDependant=true
PlugInView1=DrawTest
PlugInAlgorithm1=GraphApplet
Server1=MRIPS;MARS;137.187.26.152;104;
Storage1=MIPAV;MIPAV;C\:\\images;3100
SplashGraphics=no
LightBoxGridColor=000000
LightBoxBorderColor=960000
LightBoxGridSize=5
LightBoxMagnification=45.0
LightBoxGridCol=2
ImageDirectory=D\:\\Java\\jdk1.3\\demo\\applets\\SpreadSheet LightBoxLocation=813,23
1-2
Indicate the type of file and the date and time of the last update (comment lines).
3-4
Indicate default settings the light box image window.
5
Shows DICOM information and indicates whether the DICOM Receiver is on by default. If the DICOM Receiver is on, you can receive or retrieve DICOM image files.
6
Indicates the default trim parameter. The trim parameter is discussed in detail in Chapter 7.
7
Indicates whether MIPAV is placed in debug mode. If MIPAV is placed in debug mode and technical problems occur while you use the software, error messages are logged in the Output window.
11
Indicates whether the Swing-generated graphical user interface (GUI) is displayed. If the preference is set to false, the Advanced Windows Toolkit (AWT)-generated GUI appears instead.
12
Indicates default settings the light box image window.
13-14
Shows plug-in file information.
15-16
Shows DICOM information and shows hosts table entries. (The hosts table is located in the DICOM Communication Panel window.)
Line 15 shows the server (device) entry.
Line 16 shows a storage destination entry, which indicates where image files are stored when they are received or retrieved. If you indicate more than one storage destination entry, more lines appear in the preference file.
For more information on MIPAV`s DICOM capabilities, refer to [MIPAV_DicomImages.html#1259465 "Working with DICOM Images" on page 85].
16
Shows DICOM information.
17
Indicates whether an introductory splash screen appears when you start MIPAV.
18-22
Indicates default settings the lightbox image window.
23
Shows the image directory.


MIPAV LaunchAnywhere executable (LAX) file

What is it and what is its purpose?

The LAX file is a LaunchAnywhere Executable (LAX) file that contains MIPAV's runtime environmental options. It may be helpful to access the file if you contacting the software developers during the debugging process. To contact MIPAV developers, use the MIPAV contact page.

LaunchAnywhere is a commercial program created by Macrovizion, Inc. and used to install and start the MIPAV software on your system.

The runtime environmental options in the LAX file are set during the development of the MIPAV software. If you install MIPAV on any Windows, UNIX, or MAC OS operating system, the LaunchAnywhere program copies a LaunchAnywhere Executable (LAX) file to the same directory as your other MIPAV software files.

See also:

Retrieved from "http://mipav.cit.nih.gov/pubwiki/index.php?title=MIPAV_configuration_files&oldid=41463"