PhysioVisualizer

PhysioVisualizer interface

This document shows a brief introduction of PhysioVisualizer interface


Main canvas

The following is the main canvas of PhysioVisualizer.
At the top of the canvas, there is a tool bar including several icons.
At the bottom, there is a time slider, and play, rewind, and forward button. These slider and buttons are used when users have multiple data files corresponding to different time instances.
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Tool bar

Pasted Graphic

Icon Action
Pasted Graphic Open a preference dialog.
See below for the details of the preference window.
Pasted Graphic 1 Toggle the view between 4 panels and 1 panel as follows
Pasted Graphic 2and Pasted Graphic 3
Pasted Graphic Set a camera angle. Click this icon sets a camera angle to that time frame, and a little start mark appears below the time slider. This camera angle is used for auto-rotation in generation of animation.
Pasted Graphic 1 Reset the position of the object to default position.
Pasted Graphic Reset the camera position to show the object on the Y-Z plane (view the object from the direction of X axis)
Pasted Graphic 1 Reset the camera position to show the object on the X-Z plane (view the object from the direction of Y axis)
Pasted Graphic 2 Reset the camera position to show the object on the X-Y plane (view the object from the direction of Z axis)
Pasted Graphic 4 Flip the direction in an anteroposterior direction.
Pasted Graphic 5 Restrict the rotation in 3D to a rotation around the X-axis of the panel
Pasted Graphic 6 Restrict the rotation in 3D to a rotation around the Y-axis of the panel
Pasted Graphic 7 Restrict the rotation in 3D to a rotation around the Z-axis of the panel
Pasted Graphic 8 Zoom-in
Pasted Graphic 9 Zoom-out


Layer Window

Objects to be visualised are managed as layers.
Layers are visualised in the order shown in the Layers window. The first layer comes to top of the visualisation. This means that if there are overlaps among layers, the voxels in the overlaps are colorised with the color of the top layer.
There are two types of the layers, i.e. Data layer and Condition layer.
Condition layer is composed based on an existing data layer. Users can select voxels which satisfies the user-defined condition, and can colorize to those voxels.

In Layers window, users can swap layer's order by moving the layer with mouse operation.
Unchecking the layer hides the layer in the visualisation temporarily.
To delete the layer, once select the layer by single click, and click Delete button.
To create a new layer, click Add button.

A gear icon opens a dialog to configure the data related setting of the layer.
A note icon opens a dialog to configure the preferences related to the visualisation of the layer.

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After clicking Add button, the following small dialog opens, in which users can select the type of layer.
One is Data Layer which contains data to visualise from a file.
The other is Condition Layer, which is defined based on an existing data layer.
Select one of two radio buttons, click OK button to go next.

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Configuration of a Data Layer

Here on this dialog, users define the data to load and visualise.
Layer name is used just as a label of the layer. Any text can be set.

There are three data types that PhysioVisualizer can deal with.
1. Voxels in the whole volume (*.fld, *vm)
2. Voxels only on an object (*.raw; *.raw.gz)
3. Flint format (*.isd)

The type 1 data format is the same format with the one used by AVS (Cybernet Systems Co., LTD.). A VM file includes value information of all voxels in a cubic volume in which an object is in. Hence the file contains the zero values for voxels outside of the object (empty space). FLD file is a header file of VM file describing the size of the cubic volume etc.

On the contrary, a data file with the type 2 data format contains the value information of voxels only on an object. Hence the size of the data file can be smaller than VM file. Because of this, it is impossible to visualize this data file alone. A morphology data representing the whole cubic volume in VOL or RAW format must be provided as well.

In the case of the type 3 data format, it contains similarly only the value information of voxels on an object. However it includes additional meta-information, users do not need to provide a entire morphology data. Instead it is enough to provide the division size of each edge (x, y, and z).

In the cases of type 2 and 3 data formats, PhysioVisualizer creates VM and FLD files in the back. So if users wants to keep those files for future, The path to save those files must be given.

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Configuration of a Condition Layer

A condition layer is defined based on an existing data layer.
Hence it is required to select one of data layers by the combo box.

Conditions can be defined by two ways.
One is to use mathematical equations.
And the other is to specify voxels directly by an eternal file.

In the former case, the value of voxels is referred to as "x".
Hence using "x", for example, users can define a condition "x > 60".
Then the voxels that satisfy the condition are selected.

The value of the voxel at one step previous timeframe is referred to as "xprev".
So it is possible to define a condition, such as, "x - xprev > 0".

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In the latter case, the external file including certain voxels must be given here.
Using ImageViewer, users can select certain voxels by mouse operation and save the selected voxels into a file.


Layer Preference

In Layer Preference dialog, there are two tabs. One is Voxel Value, and the other is Color Map.

In Voxel Value tab, users can select if users want to use the value in the data file as it is for coloration, or convert the value to other scale.

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In Color Map tab, the value - color correspondence can be defined.
In the two text boxes above the color bar, lower and upper boundary values are set.
If the values which is lower than the lower boundary or larger than the upper boundary exist on voxels, the color at the boundary is applied for the voxels.

Left click on the color bar opens a color wheel to select a color for that position.
Left click on a color tag below the color bar also opens a color wheel to specify the color of the tag.
Those tags can be slide along the color bar.

Alpha value (opacity) can be adjusted as well.
Double click on a line in the white box under the color bar creates a operation point (open circle) on the line, which can be moved by mouse operation.
Right click on the open circle opens a context menu. Selecting "delete" in the menu users can delete the operation point.

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It is possible to save the color map configuration into a file by clicking Save button.
Of course it is also possible to load the configuration by clicking Load button.

If users want to export the color map as an image, click Export button.
It pops up a small dialog in which users can select the orientation of the color map (horizontal or vertical) and format (png, jpeg etc).

To set the color code or alpha value with exact values, users can use the following dialog popping up by clicking Table button.
In Show tab, the color codes and alpha values as a function of the voxel value are shown.

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In Edit tab, it is possible to edit the color map with inputting color codes and alpha values.

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Preferences

In Preferences window, users can configure data reading setting, color and font, and display setting.

In Data tab, a time interval between adjacent two data files, and thin out rate of data files for generating a cutoff animation.

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Color, font and font size on the main canvas can be set in Color \& Font tab.

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In Display tab, users can set on/off status of the title, color map and clock.
The location of color map and clock can be selected in combo boxes.
It is also possible to select the orientation of the color map (vertical / horizontal).

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