<![CDATA[
<table cellspacing="0" cellpadding="0">
<tr height="150">
<td align="left"><img src="../../../../img/logo.gif" alt="IAC logo"></img></td>
<td width="100%" rowspan="2" align="left" valign="center">
<table cellspacing="0" cellpadding="0">
<tr>
<td>
<table class="navigate_doc" width="100%" border="0" align="center">
<tr bgcolor="c6c6e0" align="center">
<th nowrap width="1%" height="32">P0054</th>
<th nowrap width="98%">ReadAnalyze</th>
<th nowrap width="1%">7th June 2002</th>
</tr>
<tr>
<td align="left" colspan="3">
<p><b>Author:</b> Joanna Leng
<b>Version:</b> 1.2
<b>Path:</b> iac_proj/rd_anlyz/</p>
<a href="../../data_io.shtml" target="_top"><img src="../../../../img/data_io.gif" width="60" height="30" border="0" alt="Data IO"></a>
<a href="doc_mod.shtml" target="_top">
<img src="../../../../img/doc_mod.gif" border="0"
width="30" height="30"
alt="Module Document - ReadAnalyzeFile"></a>
<a href="doc_umac.shtml" target="_top">
<img src="../../../../img/doc_umac.gif" border="0"
width="30" height="30"
alt="User Macro Document - readAnalyze"></a>
<a href="source/data_io/rd_anlyz/rd_anlyz.tar.gz">
<img src="../../../../img/targz.gif"
border="0" width="52" height="30"
alt="Archive - rd_anlyz.tar.gz"></a>
<a href="source/data_io/rd_anlyz/rd_anlyz.tar.Z">
<img src="../../../../img/tarz.gif"
border="0" width="52" height="30"
alt="Archive - rd_anlyz.tar.Z"></a>
<a href="source/data_io/rd_anlyz/rd_anlyz.zip">
<img src="../../../../img/zip.gif"
border="0" width="52" height="30"
alt="Archive - rd_anlyz.zip"></a>
<img src="../../../../img/note.gif" width="15" height="30"
alt="May not work on non 32-bit systems">
</td>
</tr>
</table>
<br>
</td>
</tr>
<tr>
<td>
<!-- BEGIN CONTENT PAGE -->
<h1>ReadAnalyzeFile</h1>
<h3>Synopsis</h3>
<p>
Reads a Mayo Analyze file and outputs a uniform field representing the
data.
</p>
<p>
<hr>
<pre>
module ReadAnalyzeFile {
string filename_in<NEportLevels={2,0}>;
Mesh_Unif+Node_Data out<NEportLevels={1,2}>;
omethod+notify_inst+req update<src_file="rd_anlyz.c">(
filename_in+read+notify+req, out+write
) = "read_analyze_update";
};
</pre>
<hr>
</p>
<h3>Description</h3>
<p>
The ReadAnalyseFile module reads Mayo Analyze files and outputs a
uniform field for the data contained in the file. The Analyze file
format consists of at least two file. For the image named <I>foo</I> the
files need by this module are <I>foo.hdr</I> and <I>foo.img</I>. This
module reads the <I>foo.hdr</I> file and prints all the information from
the header to the standard output. It then uses this information to read
in the file <I>foo.img</I> and converts it into the appropriate uniform
field.
</p>
<p>
The output field is stretched in the z axis to account for the
difference in the interslice resolution. The module performs byte
swapping as appropriate so that it works correctly on little and big
endian platforms. Volumes containing RGB or Complex data cannot be dealt
with.
</p>
<h3>Input</h3>
<p>
<i><b>&filename_in</b></i>
</p>
<p>
The name of the header file that should be initially read from. This
parameter is of type string. If the file is not valid then module should
correctly detect this and report the error that has occured.
</p>
<h3>Outputs</h3>
<p>
<i><b>out</b></i>
</p>
<p>
The uniform field that represents the data read from the Analyze file.
The field has node data of the type specified in the Analyze header
file. The resultant field data is automatically stretched in the z axis
to account for the difference in the interslice distance. This scaling
should normally be correct. However it can be changed by altering the
<tt>out_points</tt> array in the field object.
</p>
<h3>Utility Macros</h3>
<p>
The low-level ReadAnalyzeFile module is used in the User Macro readAnalyze.
This module can be used directly in applications. The readAnalyze macro also
uses the ReadAnalyzeUI UI macro.
</p>
<h3>Example</h3>
<p>
An example application ReadAnalyzeEg is provided that reads a set of
Analyze files and renders three orthoslices through the volume. A sample
set of Analyze files, head.hdr and head.img, are provided with the
distribution of this module.
</p>
<h3>Files</h3>
<p>
<I>iac_proj/rd_anlyze/rdanmods.v</I> contains the ReadAnalyzeFile module
V definition.
</p>
<h3>Other Notes</h3>
<p>
The low-level ReadAnalyzeMods library containing the module
ReadAnalyzeFile does not specify a process. By default the express
process will be used.
</p>
<p>
The ReadAnalyzeFile module was designed to work on a 32-bit system. In
particular it assumes that the short variable type is 16 bits long, the
int and float variable types are 32 bits long and the double variable
type is 64 bits long. If this is not the case then it is unlikely that
the data will be read correctly. Correcting this problem will require
alterations to the <tt>rd_anlyz.c</tt> source code file.
</p>
<p>
Information for this module was obtained from David Clunies Medical Image
File Format web site, it can currently be accessed from:</p>
<p>
<a href="http://idt.net/~dclunie/medical-image-faq/html/index.html">
http://idt.net/~dclunie/medical-image-faq/html/index.html</a>
</p>
<p>
Analyze is the file format of the software produced by the Biomedical
Imageing Resource Group at the Mayo Clinic/Foundation.
</p>
<p>
<a href="http://www.mayo.edu/bir/">http://www.mayo.edu/bir/</a>
</p>
<h3>Authors</h3>
<p>
<pre>
Joanna Leng
Manchester Visualization Centre
</pre>
</p>
<h3>Modifications</h3>
<p>
<pre>
Andrew Dodd
Manchester Visualization Centre
</pre>
</p>
<h3>Contact</h3>
<p>
<pre>
International AVS Centre
Manchester Visualization Centre
Manchester Computing
University of Manchester
Oxford Road
Manchester
United Kingdom
M13 9PL
</pre>
</p>
<h3>See Also</h3>
<p>
readAnalyze, ReadAnalyzeUI and ReadAnalyzeEg
</p>
<!-- END CONTENT PAGE -->
</td>
</tr>
</table>
</td>
</tr>
<tr height="100%">
<td class="sideLink" width="25%" align="left" valign="top" nowrap="nowrap">
<p><a href="../../../../general/index.shtml" target="_top">General Information</a></p>
<p><a href="../../../../repository/index.shtml" target="_top">Repositories</a></p>
<p class="sideLinkLevel2"><a href="../../../new/index.shtml" target="_top"> New Releases</a></p>
<p class="sideLinkLevel2"><a href="../../../download/index.shtml" target="_top"> Download</a></p>
<p class="sideLinkLevel2"><a href="../../../submit/index.shtml" target="_top"> Submit</a></p>
<p class="sideLinkLevel2"><a href="../../../pfiles/index.shtml" target="_top"> Project Files</a></p>
<p class="sideLinkLevel2"><a href="../../../avs5/index.shtml" target="_top"> AVS5</a></p>
<p class="sideLinkLevel2"><a href="../../../express/index.shtml" target="_top"> AVS/Express</a></p>
<p class="sideLinkLevel3"><a href="../../atoz.shtml" target="_top"> A to Z</a></p>
<p class="sideLinkLevel3"><a href="../../number.shtml" target="_top"> Project #</a></p>
<p></p>
<p class="sideLinkLevel3"><a href="../../data_io.shtml" target="_top"> Data IO</a></p>
<p class="sideLinkLevel3"><a href="../../filters.shtml" target="_top"> Filters</a></p>
<p class="sideLinkLevel3"><a href="../../mappers.shtml" target="_top"> Mappers</a></p>
<p class="sideLinkLevel3"><a href="../../misc.shtml" target="_top"> Miscellaneous</a></p>
<p class="sideLinkLevel3"><a href="../../special.shtml" target="_top"> Special Projects</a></p>
<p class="sideLinkLevel2"><a href="../../../pog/index.shtml" target="_top"> Project Guidelines</a></p>
<p><a href="../../../../usergroup/index.shtml" target="_top">User Group</a></p>
<p><a href="../../../../training/index.shtml" target="_top">Training Materials</a></p>
</td>
</tr>
</table>
<table width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="c6c6e0">
<tr>
<td><img src="../../../../img/foot1.gif" alt="IAC" width="155" height="25"></td>
<td width="100%"> Last Updated:
<!-- #BeginEditable "date-stamp" -->
26th November 2002
<!-- #EndEditable --></td>
</tr>
</table>
]]>