AVS

An Introduction course

Acknowledgement

On site modifications have been completed by L. Geoghegan

Overview

• Introduction to AVS

• AVS Modules

• AVS components
  • The network editors

  • Geometry viewer

• Importing Data into AVS

• MRI data type

• Command Line Interpreter

• UCD

Intro to AVS

• Application Visualisation System is produced by Advanced Visual Systems

• Visualization is a method of computing that has emerged from advances in visualization techniques, graphics s/w, networking and HPC

• AVS provides a large number of techniques for visualization

• AVS users can construct their own visualization applications by combining software components into executable flow networks
  • The components called modules implement specific functions in the visualization cycle

• The flow networks are built from a menu of modules using a direct-manipulation, visual programming interface call the AVS Network Editor

• Can visualise different forms of scientific data, e.g., 2D images, volumes of data

• The geometry Viewer displays 3D geometrical objects. The image viewer displays 2D images

• AVS is extensible by allowing users to write modules in C or FORTRAN and integrate them into the system

• AVS is easily tailored, and applicable to a wide range of applications.
  • can be used in various academic fields e.g medical to engineering

• An advanced course will cover module writing

Modules

• Modules are the "software building" blocks with well-defined interfaces

• The connections between the modules represent the flow of data among the modules

• A module is general in its functionality

• Modules take typed data as inputs and produce typed data as outputs

• The basic data types in the system are:
  • 1D, 2D and 3D grids of numbers

  • unstructured cell data

  • geometric data

  • images

• In addition to input and output data, modules also have parameters that control the modules's computation

• When AVS executes the network users are allowed to interact with the application

Application Building
in the network editor

• The Network Editor is a powerful, easy-to-use tool for quickly developing complex visualization processing networks

• The AVS network editor supports rapid prototyping of visualization applications

• The network editor allows the user to connect modules together to achieve a certain task

• These tasks include:
  • Data input

  • Filter + processing data

  • Visualisation techniques

  • Displaying graphical results

Network Editor

Network of Modules

Ex1 - Network editor

Geometry Viewer

• A geometry is a collection of points in 3D
  space, along with additional information

• The geometries can enter the Geometry Viewer from two sources:-
  • Can read.geom format files directly in to Geometry Viewer through the Read Object button on the Objects submenu

  • Geometries can flow into the geometry viewer module from an AVS network.

• The geometry viewer displays 3D geometric objects by creating a 3D stage called a scene within which you view geometries

• It reads/saves objects & scenes (.geom)

• Can create multiple views of an object

• The geometry viewer allows manipulation of objects

• One can change the properties of an object

• Allows one to alter the lights

• Handles composite objects

• One can switch between rendering techniques

Geometry viewer panel

Geom Objects

• Objects are read into world space with the
  Geometry Viewer's Read Object function

• Objects are organized into a hierarchy

• Each object has:
  • its own object coordinate system

  • Its own extents

  • its own centre

  • its own name

  • its own surface properties

Manipulation of Objects

• You can transform the objects themselves (move, rotate, scale)
  • left mouse button selects the object

  • middle mouse button rotates the object

  • right mouse button translates the object

  • middle mouse button + SHIFT key scales the object

• more precise transformations can be specified by type-in widgets

Alterations of the Lights

• The original window of every scene is created with a uniformed, non-directional ambient white light.

• In AVS you can control the way the graphical images are rendered (lighting and shading).

• The "lights'' panel must be selected

• "Show Lights" provides a vector representation of the light direction

• The light colour, type and direction can be changed

Composite objects

• many scenes from AVS modules are composite objects e.g., isosurface, slice and volume bounds

• clicking the left button in an empty space selects the whole scene

• clicking on an object part selects it

• clicking in the small window cycles through the objects and scene

A composite scene

Software renderer

• All machine ranges support the software renderer

• The s/w renderer can produce many rendering capabilities e.g., transparency and texture mapping

• Software rendering implements its own graphics model (lighting, shading, texture mapping, clipping planes etc.)
  

• The software renderer allows AVS to display on an 8-bit remote display

Hardware Renderers

• The hardware renderer only provides a capability if the underlying graphics system supports it

• The hardware renderer provides the highest performance

• The user can switch between h/w and s/w renderers

• AVS attempts to use all of the graphics functionality present on a platform

Geometry Viewer

Ex2 - Geometry Viewer

Importing data into AVS

• The overall view

• Description of the data
  • mapping methods

  • describing data elements

  • reading the data

  • operators

  • formats

• Some examples

AVS Data Types

• Primitive Data
  • Byte, integer, single-precision floating point, double-precision floating point, text strings

• Aggregate Date
  • Aggregate data is used by AVS to represent the data types for scientific and engineering data visualization

Field Data

• The AVS field datatype is used to represent arrays of data in AVS

• Each element of an array has a single data value or can a list of data values

• Field data is an n-dimensional array with an m-dimensional vector of values at each array location

• The data is described by an ASCII header file that defines the structure of the AVS field

• The header file can optionally contain data or reference the data file(s)

• Referencing the file(s) is a better way of working

Overall View

read_field module

• The read_field module is used to import data into an AVS network.

• The read_field module has a file browser to select the header file.

• The read field module has two input modes:-
  • native field input

  • data-parsing input

Description of data

dimensions

• you must specify the dimensions of the data

• e.g., 1D: list of scattered data, 3D: volume of data

• these specify the computational space

• you must specify the dimensions of the data as it is passed to AVS

• these specify the coordinate space

Mapping methods

UNIFORM

• The data is not transformed as it is imported (direct & implicit)

• The dimensions of the computational and coordinate space should be the same

• A uniform field has no computational-to-
  physical space mapping between data element.

• used to import regular arrays of data

• A field with no coordinates data for each of the data values is said to have the field type uniform

Uniform mapping

Mapping methods

RECTILINEAR

• Each dimension in the data has an explicit coordinate mapping

• The spacing along the coordinate axes can be non-uniform

• The dimensions of the computational and coordinate space should be the same.

Rectilinear mapping

Mapping methods

IRREGULAR

• For irregular there is no restriction on the correspondence between computational space and physical space

• Each data element is mapped to a point in the coordinate space.

• The dimensions of the computational and coordinate space can be different

• e.g., 1D scattered data into 3D space

Irregular mapping

Format of the header file

• the file should have an extension of.fld

• the first line should be:

	# AVS field file

• the rest of the file contains a number of keywords and values

Format

• all the format keywords must be on a single line

• in each of the examples a "-'' indicates that the line is continued below e.g.,

	This is a very very very very very -
	very long line.

• N.B., you cannot do this in the real header files though!

• the format keywords are also optional

Description of the data elements

• Specify the dimensions of the data
  • ndim= number of dimensions in computational space

  • dim1= specify the size of dimension 1, which can be thought of as the x dimension

  • Example:-

	ndim=3		#number of computational dimensions
	dim1=40 	#dim of axis 1
	dim2=32 	# dim of axis 2
	dim3=32 	# dim of axis 3

• Specify number of physical coordinates per point
  • nspace= number of dimensions in coordinate space E.g

	nspace=3 	number of coordinates per point

• Specify number of components at each point
  • veclen= number of data components per element

	veclen=3 	number of components at each point

• also the datatype e.g., byte,integer,float,double

• Other keywords
  • data= type of the data components

  • field= mapping method

  • label= label for each data component

  • unit= units for each data component

	veclen		= 2
	label		= pressure				temperature
	unit		= kg/m**2				K

Reading the data

• once the data structure has been defined you specify the location and format of the data file(s).

• the data file(s) can be binary or ASCII

• there are three operators available to read the data.
  

Operators to read data

• skip: specifies the number of lines to skip before starting to read the data

• offset: number of columns to jump over before the data is read

• stride: how many steps forward before the next item is reached. Assumes you are standing on the "data value" just read
  

Specifying the format
of the data

• each data component needs a line:

	variable N < number of format keywords >

• each item of coordinate information needs a line:

	coord N < number of format keywords >

• each line can reference different files

Format Keywords

• file= location of data file

• filetype= format of the data file, binary or ascii

• skip=, offset= and stride= to read the data

• some examples will follow

Example 1: Image data

• The data set is a 2D image (512x256) consisting of greyscale values 0 - 255

• The data

	0 10 0 15 200 255...
	...
	...

Solution for example 1

	# AVS field file
	#
	ndim = 2
	dim1 = 512
	dim2 = 256
	nspace = 2
	veclen = 1
	data = integer
	field = uniform
	variable 1 file=image.dat -
		filetype=ascii skip=0 stride=1

Example 2: Volume data

• The data consists of a 3D array of density comps in a regular volume, 1283

• The file has a line of header info

• The data

	Patient: Steve 10/11/93
	0 255 2 1 7.
	5 6.........
	...

Solution for example 2

	# AVS field file
	#
	ndim = 3
	dim1 = 128
	dim2 = 128
	dim3 = 128
	nspace = 3
	veclen = 1
	data = integer
	field = uniform
	variable 1 file=volume.dat filetype= 
		ascii skip=1 offset=0 stride=1

Example 3: Irregular data

The complete header file

# AVS field file
#
ndim = 2
dim1 = 5
dim2 = 10
nspace = 2
veclen = 2
data = float
field = irregular
label = temp press
variable 1 file=flow.dat filetype=ascii -
	skip=0 offset=0 stride=2 
variable 2 file=flow.dat filetype=ascii -
	skip=0 offset=1 stride=2
coord 1 file=coord.dat filetype=ascii -
	skip=0 offset=0 stride=2
coord 2 file=coord.dat filetype=ascii -
	skip=0 offset=1 stride=2

Debugging

• A useful module to include in your networks is print_field

• The module will display information on the header and data elements

The MRI Exercise

• This data file represents a MRI scan of the brain

• The dataset is 2D binary, containing 512x512 single scalar byes for each data value

• Has regular arrays of data
  • i.e the data file is binary and the data is arranged contiguously with no header information

• the exercise is to examine each dataset

Importing the MRI data

Importing the MRI data

• generate_colourmap: provides a colourmap definition for other modules

• downsize: samples the data to decrease its overall size

• color_range: maps the colourmap to the extent of the data it receives

• colorizer: produces an image using the data values as an index to the colormap

Example of colorizer

Temperature profile Exercise

• Temperature profile is a series of float point values (ascii) containing data on a regular 31 x 31 grid

• This data represents temperatures taken from a cross section of an injection moulding system

• The data components at each element is a single floating point value and the first two numbers in the file indicate the X and Y dimensions of the grid respectively

• The exercise is to examine each dataset

Temperature profile

Modules

• generate_colourmap

• downsize

• color_range

• field_to_mesh: produces a 3D surface from a 2D array where the heights are produced from the data elements

• geometry_viewer: renders the output from field_to_mesh

Example of field_to_mesh

2D field exercise

3D Arrays Exercise

• importing a file of data showing the flow of air over a fin

• The data file is an ASCII file which represents an 10x8x8 irregular grid.

• Each element has five floating points data components

• Each element has some associated coordinate data to position it in 3D space

• The data format is as follows:-

	density x-mom y-mom z-mom stag x y z

Field descriptor

	ndim=
	dim1=
	dim2=
	dim3=
	nspace=
	veclen=
	data=
	field=
	variable 1 file=
	variable 2 file=
	variable 3 file=
	variable 4 file=
	variable 5 file=
	coord 1 file=
	coord 2 file=
	coord 3 file=

Visualising scalar components

Visualising vector components

volume_bounds module

• constructs a boundary around a 3D array of data

• it is useful to indicate your location in the array of data

• it allows you to switch on/off planes orthogonal to the axes

hedgehog module

• displays velocity data by drawing vectors which indicate the direction and magnitude of the velocity

• you can add arrow heads to the vectors

• the scale and number of samples can be altered

• various probes can be selected e.g., point, circle, line, plane, space

Example of hedgehog

3D field exercise

AVS command line options

• -version which version are you running

• -network file start AVS to use the network specified

• -nohw use the software renderer (essential if running remotely via X)

• -usage what are the other options ?

• -mod_time unsupported feature for timing a network

AVS Command Line Interpreter (CLI)

• CLI Description
  • The Image viewer, Geometry Viewer, Graph Viewer and Network viewer can also be driven through a Command language Interpreter(CLI).

  • You can type CLI commands in response to a prompt and interactively view the results

  • you can create a command script file that executes automatically.

• to access use avs -cli

• to record a session use avs> script -open myscript

• to stop recording use avs> script -close

• to playback use avs> script -p myscript

A sample CLI script

net_clear
module "read image.user.0" -xy 230,73 -ex $Path/avs_library/mongo
module contrast.user.1 -xy 230,129 -ex $Path/avs_library/mongo
module "display image.user.2" -xy 230,185
port_connect "read image.user.0":0 contrast.user.1:0
port_connect contrast.user.1:0 "display image.user.2":0
parm_set "read image.user.0":"Read Image Browser"
usr/avs/data/image/avs.x
parm_set contrast.user.1:cont_in_max 178.171722412
parm_set contrast.user.1:cont_out_min 78.480216980

script -close

Obtaining hard copy from AVS

• connect the module image_to_postscript to the geometry_viewer module

• you can specify landscape or portrait

• you can alter the size in inches

Practical uses

Customising AVS

• when AVS starts up it looks for the file .avsrc in your home directory

• if this file does not exist it uses the file

	/usr/avs/runtime/avsrc

• this file sets certain default attributes in AVS

The .avsrc file

	Path /usr/local/avs
	NetworkDirectory /usr/avs/networks
	DataDirectory /usr/avs/data
	NoHW 1
	Bounding Box off

What is unstructured cell data?

How does AVS provide support?

• Unstructured Cell Data (UCD)

• NODES: contain data and position

• CELLS: have a geometric shape and reference nodes

• STRUCTURE: a collection of cells

A closer look at UCD

• data at each node can be a collection of scalar and vector quantities

• the data can have labels and units

• each cell has a shape, material and cell data associated with it

Importing UCD data

• you can write a reader using the UCD routines to parse your data file and create the appropriate UCD structure

• this is the preferred method but is not covered in this course

• AVS has a module read_ucd which imports ASCII files (.inp)

• you can change your data to match this format

An example of a .inp file

	8 1 1 0 0
	1 0.0 0.0 1.0
	2 0.0 1.0 0.0
	...
	8 0.0 1.0 0.0
	1 1 hex 1 2 3 4 5 6 7 8
	1 1
	stress, lb/in**2
	1 499.999
	2 567.888
	...
	8 5000.00

A sample UCD network

Other modules

• cropping and slicing (ucd_crop & ucd_rslice)

• vector data (ucd_hedgehog & ucd_streamlines)

• debugging (ucd_print)

• isosurfaces (ucd_iso)

Closing Comments

We have covered!

• Modules

• AVS subsystem
  • Network system

  • Geometry viewer

• Read and defining data files
  • 2D examples

  • 3D examples

• Command lIne operations

• Unstructured Cell Types

• Not - Writing modules in C and FORTRAN