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<th nowrap width="1%" height="32">P0055</th>
<th nowrap width="98%">ReadBioRadPic</th>
<th nowrap width="1%">29th June 1999</th>
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<p><b>Authors:</b> Chris Pudney, Joanna Leng and Andrew Dodd
<b>Version:</b> 1.0
<b>Path:</b> iac_proj/rd_brpic/</p>
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<h1>ReadPicData</h1>
<h3>Synopsis</h3>
<p>
Reads a Bio-Rad PIC file and outputs the dimensions and data array.
</p>
<p>
<hr>
<pre>
group ReadPicData {
string filename<NEportLevels={2,0}>;
file FILE {
name => <-.filename;
};
ReadPicDims ReadPicDims {
filename=> <-.filename;
};
int dims<NEportLevels={0,2}>[3] => ReadPicDims.dims;
byte data<NEportLevels={0,2}>[prod(dims)] => cache(file_obj(.FILE,76,1,,1));
};
</pre>
<hr>
</p>
<h3>Description</h3>
<p>
The ReadPicData module reads a Bio-Rad PIC file and outputs the dimensions of
the data and an array containing the image data. These outputs can then
be combined using a <TT>uniform_scalar_field</TT> module to create field data that
can then be visualized using any of the standard modules. The dimensions
are output as an array of integers and the data is output as an array of
bytes. The module will only handle 8-bit images. 16-bit and 24-bit images are
not handled correctly. Any notes appended to PIC files are also ignored.
</p>
<p>
Bio-Rad PIC files contain 3D confocal microscope images, <I>i.e.</I> 3D
scalar uniform fields. However 3D confocal microscope images are usually
anisotropic i.e. the x-y scale is different from the z scale. In this case
the <TT>scale</TT> module can be used to alter the scaling of the resultant
field data. For more information please see the <a href="source/data_io/rd_brpic/NOTE">NOTE</a> file.
</p>
<h3>Input</h3>
<p>
<i><b>&filename</b></i>
</p>
<p>
The name of the file that should be read from. This parameter is of type string.
The ReadPicData module does not check to ensure that the supplied file is a
valid Bio-Rad PIC file. If the file is not valid then errors could occur.
</p>
<h3>Low-Level Module</h3>
<p>
<i><b>ReadPicDims</b></i>
</p>
<p>
An internal module, written in C, that reads the image dimensions from the input
file. The read dimensions are then used to determine the amount of image data
that should be read from the input file and to generate the uniform field. The
dimensions are 16 bit long values. These values are read into a variable
of type short. If the length of the short type on your system is not 16 bits long
then the module may need alteration. The <TT>ReadPicDims</TT> module also performs the
necessary byte swapping so that the module can be used on both big and little
endian systems.
</p>
<h3>Outputs</h3>
<p>
<i><b>dims[3]</b></i>
</p>
<p>
This array contains the dimensions of the Bio-Rad PIC image. The array
is of type int. The dimensions can be used directly by field mapping
modules to help generate AVS field data. The dimensions are read by the
<TT>ReadPicDims</TT> module and are cast from the original short values to the
int values that AVS/Express uses.
</p>
<p>
<i><b>data[]</b></i>
</p>
<p>
This array contains the data read from the Bio-Rad PIC file. The array is
of type byte. The length of the array is calculated from the dimensions read
by the <TT>ReadPicDims</TT> module. The data is actually read by the standard
file I/O modules present in AVS/Express.
</p>
<h3>Utility Macros</h3>
<p>
The low-level ReadPicData module is used in the User Macro readBRPic.
This module be used directly in applications. The readBRPic macro also
uses the ReadBRPicUI UI macro. The ReadPicData module uses the ReadPicDims
module.
</p>
<h3>Example</h3>
<p>
An example application ReadBRPicEg is provided that reads a Bio-Rad
PIC file and produces a maximum intensity projection. A sample Bio-Rad PIC
file flea3.pic is provided with the distribution of this module.
</p>
<h3>Files</h3>
<p>
<I>iac_proj/rd_brpic/rdbrmods.v</I> contains the ReadPicData and
ReadPicDims module V definitions.
</p>
<h3>Other Notes</h3>
<p>
The low-level ReadBRPicMods library containing the module
ReadPicDims does not specify a process. By default the express
process will be used.
</p>
<h3>Authors</h3>
<p>
<pre>
Chris Pudney
Biomedical Confocal Microscopy Research Centre
Department of Pharmacology
The University of Western Australia
Nedlands, W.A. 6907
AUSTRALIA
E-mail: <A HREF="mailto:cpudney@alphapharm.pharm.uwa.edu.au">cpudney@alphapharm.pharm.uwa.edu.au</A>
Phone, Fax: (+61 8) 9346 4571, (+618) 9346 3469
</pre>
</p>
<h3>Modifications</h3>
<p>
<pre>
Andrew Dodd, Joanna Leng
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>
readBRPic, ReadPicDims, ReadBRPicEg, read_BioRad_PIC (AVS5 IAC module)
</p>
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