readBRPic

Synopsis

The readBRPic user macro reads a Bio-Rad PIC data file and outputs a uniform scalar field. It performs byte-swapping so that it works correctly on both little and big endian platforms.

Parameters

The following lists all of the parameters used by the readBRPic user macro.

Name	Type	Description	UI Control
filename	string	name of Bio-Rad PIC file to read	Filename text box

Output Ports

Name	Type	Description
out_fld	uniform scalar field	read 3D volume
out_obj	DataObject	directly renderable output object

Description

The readBRPic macro reads a Bio-Rad PIC file and outputs a uniform scalar field representing the data. The field data can then be visualized using any of the standard modules. The uniform scalar field has the dimensions specified in the Bio-Rad PIC file and the data is represented as 8 bit node data. 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.

Bio-Rad PIC files contain 3D confocal microscope images, i.e. 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 scale module can be used to alter the scaling of the resultant field data. For more information please see the NOTE file.

Parameters

filename

The name of the file that should be read from. This parameter is of type string and can be specified through either a text-box or a file browser. 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.

Output Ports

out_fld

The most primitive output field of the readBRPic macro. This contains the generated 3D volume in the form of a uniform scalar field with the dimensions specified in the Bio-Rad PIC file. The data present in the file is stored as node data within the field.

out_obj

The directly renderable output field of the readBRPic macro. This contains a DataObject object that can be rendered by the standard data viewers. The DataObject is generated directly from the field data created from the Bio-Rad PIC file.

Utility Macros

The User Macro readBRPic uses the low-level module ReadPicData which in turn uses the low-level module ReadPicDims.

Example

An example application ReadBRPicEg is provided, which loads Bio-Rad PIC files and visualizes them using the volume renderer. An example data file flea3.pic is provided so that the macro can be tested.

Files

iac_proj/rd_brpic/rdbrmacs.v contains the readBRPic User Macro, the ReadBRPicUI UI Macro, and the example application ReadBRPicEg V definitions.

Other Notes

The ReadBRPicMacs library inherits its process. As this library contains no procedural code, the process is not important.

The ReadPicDims module assumes that the short variable type is 16 bits long. If this is not the case then the dimensions read may not be correct and the macro will not work. Correcting this problem will require alterations to the rd_brpic.c source code file.

Authors

Chris Pudney

Biomedical Confocal Microscopy Research Centre
Department of Pharmacology
The University of Western Australia
Nedlands, W.A. 6907
AUSTRALIA

E-mail: cpudney@alphapharm.pharm.uwa.edu.au
Phone, Fax: (+61 8) 9346 4571, (+618) 9346 3469

Modifications

Andrew Dodd
Joanna Leng

Contact

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

See Also

ReadPicData, ReadPicDims, ReadBRPicUI and ReadBRPicEg.