PhysioVisualizer

Getting started

This document shows how to use PhysioVisualizer, using the example data bundled int the PhysioVisualizer package.


1. Launch PhysioDesigner


Double click on PhysioVisualizer icon opens the following two windows. A list of layers are listed in the left window, and morphology data will be visualised in the wright window.

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2. Add a Data Layer


Image data to be visualised is managed as layers on Physiovisualizer.
Now let's add the first layer to load image data.
Click Add button on Layers window, showing a small dialog to select the layer type.
Since this is the first layer, only "data Layer" is available. Select it and click OK button.
The other type is "Condition Layer" in which uses can define condition on the existing data layer.
Details of the condition layer is explained in other document.

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In the following dialog, users need to define the layer name, data type, and data file.
In this document we will use the data bundled in the PhysioVisualizer package.
Set "heart" (actually this can be any text) at Layer Name and All voxels (*.fld, *.vm) at Data Type.
Select one of *.fld file in samples > heart_spiral_wave.

There are many FLD and VM files in the directory.
A VM file is a binary image file, and a FLD file is a text header file of a VM file with the corresponding file name.
The number such as 26000 in the file names means time in this case.

Please replace the number with "#" which represents "any number".
For example, h_v29_26000.vm should be h_v29_#.vm
By this replacement of the number in the file name, all data file become the target of visualisation and this is necessary to create movie.
If users do not want to create a movie and it's enough to visualise a single data, the replacement with "#" is not necessary.

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Then click OK button.


3. Configure Visualization


The heart is displayed as follows.

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Left click and drag on the object rotates the object.
Shift + left button drag shifts the object.
Mouse wheel will zoom in and out.

Click Pasted Graphic icon on the Layer window opens Layer Preference dialog.

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In the Layer Preference dialog, users can adjust the value - value conversion and value - colour map configuration.
Value - value conversion is the conversion from a value written in a data file to a value which is used, for example, in physiological models.
Note that usually the value in a data file is not the same as the one used in a model to reduce the data file size. For example, even in a model a value is a real number ranging from -80 to 90, the value is converted in a CHAR type (1 byte) value ranging 0 - 255 to reduce the data file size.
In such case, to visualize we need to consider opposite way. The value must be converted from a value between 0 - 255 to -80 - 90.

After selecting "Convert at follows" radio button, set values properly.
And click Apply button. Then the following dialog pops up.

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If users click Yes button, the value is automatically used in the color map configuration.

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At Color Map tab, it's possible to define the correspondence between value and color.
It's also possible to set alpha value (opacity. 1:opaque, 0:transparent).
Users can move open circles on the line in the alpha panel.
Double click on the line creates a new open circle. Right click on a open circle shows a popup menu.


4. Export Movie


To check the dynamics, click Pasted Graphic (play) icon to play a dynamics as a movie.
PhysioVisualizer starts to load data file one by one, and creates a cutoff animation.
This process can be very slow according to the size of the data file.

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To export a movie, select a command from the menu bar "File > Export Movie > Volume".
A dialog pops up, so fill in the file name and select the format of the movie in the dialog.

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