Advanced visualization with VisNow platform Case study #2 3D scalar data visualization

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UNIVERSITY OF WARSAW

Interdisciplinary Centre for Mathematical and Computational Modelling

www.icm.edu.pl

Advanced visualization with VisNow platform

Case study #2 – 3D scalar data visualization

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.

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3D data on regular grids examples:

•

Physical model: electrostatic field of a

quadrupole calculated in a box

•

Medical imaging: Computed Tomography

scan of a human foot

•

Aerodynamics – supersonic flow over

wing edge

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Examples

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1. Create

VisNow field reader

module by dragging from modules library

2. Click

browse

in module GUI to read

ct.vnf

file located in

sample_data\VisNowFields\

folder

3. In the

field info

tab the information on the field can be found

4. Select all

show extern faces

boxes in

presentation

->

content

tab and select

color extern faces by avg;

We have the overall preview of file contents.

How can we look inside?

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Simple scalar data – reading

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5.

Remove

show extern faces

option

6. You may choose one of

oint grid

or

line grid

options with grid density

(coarse/fine/very fine)

7. The presentation is not precise but we may see the general geometry and inside contents

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Simple scalar data – presentation

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•

Incase of regular grid data we have

two modules that can slice the

field:

regular field slice

and

interpolated field slice

.

•

Regular field slice

module presents

a ”logical” slice based on a user

selected grid index in a field

structure.

•

Interpolated field slice

interpolates

the data on a custom selected

plane.

•

In both cases the slice can be

coloured with any of the original

components.

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Regular field slicing

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8. The easiest slice: click RMB on the blue output port (with our 3D field), choose

attach->3D

field mappers->regular field slice

9. You may now change the slice orientation, position and choose colour map in

presentation

tab

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Regular field slice

module selects one of the slice indices with a slider.

We only have the three directions of slicing – the ij plane, jk plane or ik plane. To create a custom slice use

interpolated field slice.

This interface consists of resolution sliders of the plane on whitch the dat will be niterpolated and a set of dials,

which can be used to rotate, translate and scale the slice plane.

You may now select a significantly interesting crosssection – e.g. slice just over the soul plane of the foot and

paralel ones.

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Isosurface

module creates

isosurface

v(x)=t

for a selected

component

v

and threshold

t.

Warning: if a vector component

is selected the isosurface of a

vector norm |v(x)| = t will be

calculated

The network to create this

image consists of the following

modules:

•

Test regular field 3D

•

Isosurface

•

Axes 3D

•

Viewer 3D

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Isosurface

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10. Connect the

isosurface

module (from

3D field mappers

) to our 3D field

11. We will see the skeleton outline on the screen – a result of default values

12. Get to know the interface of this module

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Isosurface

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Choice of a component to draw the isosurface –

in our example there’s only one

The threshold interface you already know

If the field is quite big (e.g. 512x512x5000) and

complex (e.g. noisy) we may use only every

n

-th

node

If the isosurface is noisy or sharp-edged it can be

smoothed a bit.

The uncertainty field can be generated

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Isosurface GUI

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Example – foot anatomy

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In volume rendering we obtain an image of

the volume in which the colour and the

transparency depend on data values.

Contrary to the precise presentation with a

slice or isosurface we get a synthetic

presentation under some uncertainty.

A complex interface of this module allows

to choose the colour map and a detailed

manipulation of transparency ”transfer

function” (dependancy of transparency on

data component values).

In certain case it is useful to use different

components for colour and transparency.

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Volume rendering

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13. Create a new

volume rendering

module and connect in to our 3D field. Just simple

parameter tuning shows a correct visualization (change colour map to

medical

)

14. The most precise modifications of the visual effect is provided by the transparency

map manipulation

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Volume rendering

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Choice of the data componant mapped to

transparency.

Range of mapped values.

Global transparency of data set by vertical slider.

Transparency map drawing window:

- draw the function with LMB dragging (red line)

- Draw straight lines with shift_LMB dragging

- Smooth with RMB

- The values histogram is visible in the

backgroud.

Threshold slider – all values below are fully

transparent.

Gray line shows the resulting transparency map.

Visualization of transparency.

Predefined maps

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Volume rendering

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•

Clearly visible areas of high potential (plus/minus) – a

result of applying a transparency map with centered

minimum.

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Potential and transparency

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15. Create a network of differential operations (data filters), modify

components/coordinates

and volume renderer

16. In differential operations

select the gradient of density

component (start

module with run

buton)

17. In

modify components/coordinates

select

split density gradient and click

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Volume rendering and gradients

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18. In

volume renderer

module select as

transparency component

the

density_grad

(yes, vector components

can be used as scalar by vector norm) and notice that uniform areas (e.g. muscles) are transparent while

area boundaries are clearly visible.

19. To increase the image plastics we’ll apply shading: in

datamap

tab select one of the gradient coordinates

component and grayscale colour map

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Volume rendering and gradients

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UNIVERSITY OF WARSAW

Interdisciplinary Centre for Mathematical

visnow.icm.edu.pl

Contact:

[email protected]

University of Warsaw

This work is licensed under a Creative Commons