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<th nowrap width="1%" height="32">P0009</th>
<th nowrap width="98%">PIC_IO</th>
<th nowrap width="1%">23rd February 2002</th>
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<p><b>Author:</b> Chris Pudney, Andrew Dodd
<b>Version:</b> 1.2
<b>Path:</b> iac_proj/picio/</p>
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<H1>read_PIC_core</H1>
<H3>Synopsis</H3>
<p>
Reads a Bio-Rad PIC file and outputs the dimensions and data array.
</p>
<p>
<HR>
<pre>
module Read_PIC_core<data_import_module=1> {
file+IPort2 &FILE;
int bytes[6] => cache(file_obj_bin(.FILE,0,0));
int+OPort2 dims[3] => {
(bytes[0] + bytes[1]*256),
(bytes[2] + bytes[3]*256),
(bytes[4] + bytes[5]*256)
};
byte+OPort2 data[prod(dims)] => cache(file_obj_bin(.FILE,76,0));
};
</pre>
<HR>
</p>
<H3>Description</H3>
<p>
This module reads a Bio-Rad PIC file and outputs its dimensions and field data.
Bio-Rad PIC files contain 3D confocal microscope images, <I>i.e.</I> 3D scalar
uniform fields. read_PIC outputs the dimensions of the field as an array of
integers and the values of the field as an array of bytes. The outputs can be
combined using uniform_scalar_field to produce a 3D uniform scalar field
that can be visualized. This is done in the Read_Biorad_PIC functional macro.
</p>
<p>
This module performs the byte reordering necessary for it to work correctly on
either big or little endian platforms.
</p>
<H3>Inputs</H3>
<p>
<B><I>FILE</I></B>
</p>
<p>
The file object corresponding to the Bio-Rad PIC file that should be read.
</p>
<H3>Outputs</H3>
<p>
<B><I>dims</I></B>
</p>
<p>
An array of three integers corresponding to the <I>x</I>-, <I>y</I>-
and <I>z</I>-dimensions of the field.
</p>
<p>
<B><I>data</I></B>
</p>
<p>
An array of bytes corresponding to the field values.
</p>
<H3>Utility Macros</H3>
<p>
read_PIC_core is used in the Functional Macro, Read_BioRad_PIC. This macro
is in turn used by the User Macro, read_Biorad_PIC.
</p>
<H3>Example</H3>
<p>
An example application Read_BioRad_PIC_Eg 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/picio/pio_mods.v</I> contains the read_PIC_core module V
definition.
</p>
<H3>Other Notes</H3>
<p>
This module does not check that the file specified by the user is a
valid Bio-Rad PIC file. If it is not then errors can occur.
</p>
<p>
Notes, which are sometimes appended to PIC files, are ignored.
</p>
<p>
This module will only handle 8-bit images. 16-bit and 24-bit images are
not handled correctly.
</p>
<p>
The AVS5 module read_BioRad_PIC (available from the IAC) can also be
used to read Bio-Rad PIC files.
</p>
<p>
This module does not contain any C or Fortran code and hence does not need to
be compiled.
</p>
<H3>Author</H3>
<p>
<pre>
<A HREF="http://www.cs.uwa.edu.au/~chrisp">Chris Pudney</A>
Biomedical Confocal Microscopy Research Centre
<A HREF="http://www.pharm.uwa.edu.au">Department of Pharmacology</A>
<A HREF="http://www.uwa.edu.au">The University of Western Australia</A>
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>
Rob Fletcher, Andrew Dodd
</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>read_BioRad_PIC, read_BioRad_PIC (AVS5 IAC module)</p>
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