read_PIC_core

Synopsis

Reads a Bio-Rad PIC file and outputs the dimensions and data array.

  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));
  };

Description

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.e. 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.

This module performs the byte reordering necessary for it to work correctly on either big or little endian platforms.

Inputs

FILE

The file object corresponding to the Bio-Rad PIC file that should be read.

Outputs

dims

An array of three integers corresponding to the x-, y- and z-dimensions of the field.

data

An array of bytes corresponding to the field values.

Utility Macros

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.

Example

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.

Files

iac_proj/picio/pio_mods.v contains the read_PIC_core module V definition.

Other Notes

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.

Notes, which are sometimes appended to PIC files, are ignored.

This module will only handle 8-bit images. 16-bit and 24-bit images are not handled correctly.

The AVS5 module read_BioRad_PIC (available from the IAC) can also be used to read Bio-Rad PIC files.

This module does not contain any C or Fortran code and hence does not need to be compiled.

Author

<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

Modifications

Rob Fletcher, Andrew Dodd

Contact

International AVS Centre
Manchester Visualization Centre
Manchester Computing
University of Manchester
Oxford Road
Manchester
United Kingdom
M13 9PL