5.3.1 Visualization Software
The entire system was written using AVS/Express Visualization Edition 6.2. AVS uses libraries programmed in a proprietary V-code format, although custom developed C++
modules can be utilized. For this work, all modules used were standard to the AVS package. The modules used and corresponding functions are presented in Appendix C in greater detail. Data import is handled by LabView and AVS. The system was designed on a Dell
Dimensions 2.4 GHz Pentium 4 running Windows XP. All images are rendered by software as a suitable graphics card was not available.
5.3.2 Volume Formation
Data is obtained as single slices and must be combined into the full volume before
importing into the visualization methods. This process is shown schematically by Figure 5-2. Each slice is a 2D array in the form:
i i
j X i
Y
S = , , ( 5.1 )
where Xi and Yj represent the X,Y coordinates in Cartesian space and i is the electrospray ion
density mapped to current. The volume is formed by stacking the slices to give
i i j k Y X i Z V = , , , ( 5.2 )
where Zk is the Z-Cartesian coordinate in space. The overall dimensions of the three-
dimensional volume are therefore defined by i, j, and k. A LabView application handles the acquisition of the individual slices and combines them into the three-dimensional volume that can be visualized with AVS. This process, summarized by Figure 5-3, is somewhat tedious for the user, but eliminates the need for array manipulation inside AVS/Express.
5.3.3 Data Space, Sampling and Sets
The data is embedded in a 3D volume. It is collected as 2D slices and is then regenerated back into 3D space inside AVS. The data was sampled in a regular grid (X-Y) for each slice. Spacing of the slice grid ranges from 1 mm-0.1 mm over a 10x10 mm area. Z-spacing is 1 mm over 10 mm of travel. This results in a 50x50x50 grid at the highest resolution.
A single point reading is taken at each (X-Y) position in the Slice Plane. This consists of an instantaneous voltage reading from the DAQ card in the computer. Position is read from a motion control board at the same time by a serial port. The signal is first passed through a
current amplifier with a gain of 108V/A and then low pass filtered at 25 HZ to remove high frequency jitter or slew noise.
Data quantization as a result of analog to digital conversion, is present in this data set. The data collection system utilizes a 12-bit A/D converter which results in 4096 (2^12) discrete values that can be represented in the data. Data points were obtained from the entire data sampling gird (discussed above) without any missing values.
The electrospray plume is a dynamic field of ions. During data collection of each plane (on the order of minutes) minor fluctuations in the intensity exist. These fluctuations are random in nature and signal averaging is a potential solution if necessary. It is assumed that the fluctuations are low enough in magnitude to have no effect the visualization as a whole. When regenerating the volume, the field will be considered to be at a steady-state condition.
5.4 VISUALIZATION PROTOTYPING
Three methods were initially prototyped. They consist of an isovolume rendering of the data in 3-space, a direct volume rendering in 3-space and an isoline plot of an orthoslice plane through one of the three Cartesian axis. Sample images and a brief discussion of what the image advantages and disadvantages and why they were ultimately inadequate are presented below. The sample data was collected over a 10x10x10 mm area with an irregular sample grid of 150x20x10 points.
5.4.1 Isovolume Rendering
A sample isovolume rendering of the ESI plume is shown in Figure 5-4. The density of the ions is mapped to color, while the isovolume displays the shape of the plume for values greater than or equal to the isovalue. Densities that are less than the isovalue are mapped to null space and are transparent. A rainbow color map is presented since only the outer shell is
of interest for the image. It is not intended to show the intensity falloff inside the volume, but instead the shape of various ion densities.
Interpolation is accomplished by conversion to a uniform mesh. The isovolume then maps to this mesh and essentially connects the dots to give a single surface. Interpolation settings have a drastic effect on the final image and are therefore cause for concern.
Figure 5-5 shows three renderings from the same viewpoint with different interpolation settings. It is evident that the image is significantly changed, making it difficult to draw conclusions about the fine detail of the plume. A higher resolution data set hopefully will smooth some of these errors, but this has not been examined to date.
The isovolume shows shape in a certain region, as desired by the primary goal but limits the user to that particular view. It is not possible to explore the shape at high and low density levels simultaneously. Information about the density falloff is also non-existent. The color scales, as presented in Figure 5-4, are also not ideal since a scale with better gradation would prevent artifacts from appearing.
5.4.2 Direct Volume Rendering
Rendering of the ESI plume using a direct composite ray tracer volume rendering is shown by Figure 5-6. Data channels are similar to the isovolume as ion density is mapped to a rainbow color map and shape is conveyed by the rendering. The image is further modified to make certain values transparent. This allows the core of the plume to be seen while retaining some information about the shape of the lower density areas. A rainbow color map is used across all values. An ideal map would vary only one color at a time to prevent banding and show a smooth transition between various values.
The primary drawback of the DVR is the rendering time. It does not present any more information then the isovolume about shape, but prevents the user from interacting in real
time. Additionally, the DVR makes it difficult to tell which surface is being viewed at the outer levels due to the transparency. Density falloff is also limited by occlusion and a poor use of the color map.
5.4.3 Isoline Orthoplanes
A final method for visualizing the ESI plume is shown in Figure 5-7. This shows isoline images for two different orthoslice planes. As in the previous methods, density is mapped to color while shape is shown by the isolines. A rainbow color map was used since the data is being presented as intervals. Interpolation is achieved using the scat_to_unif function (see Appendix C), and results in similar hazards as discussed previously. The isoline plots main advantage is an easy ability to see falloff from a qualitative view. Areas with close line spacing indicate a rapid decay of ion current, while larger spacing signifies an almost constant value.
The drawback of the isoline plot is the inability to see the three-dimensional volume. While some information can be obtained, it is limited to a 2D plot and forces one to assume symmetry. Another drawback is limiting the user to a qualitative view of the density area. The ability to probe certain isolines, or plot the quantitative falloff offers additional
advantages.