Volume Series

Volume Series displays an ordered sequence of volume data sets. A sequence could represent a time series or a comparison of states not necessarily ordered in time. See also: Morph Map

There are several ways to start Volume Series, a tool in the Volume Data category (including from the Volume Viewer Tools menu).

Clicking Open... raises a file browser for opening a volume series as either of the following:

• multiple volume data files sorted by name
• a single volume series file in Priism time series format

Multiple volume series may co-exist in Chimera. A volume series is named after the single file it was read from, or the first file if read from multiple files. Choosing the name of a volume series from the Data listing switches the display to that series, and it can be closed with Close Series.

The members of a series are indexed 0, 1, 2, ... and these indices are referred to as the Time. Any numbers in the individual filenames are not used, except to sort the names.

The Time slider can be moved manually to show a particular set of data and make it the current set of data in Volume Viewer. Settings in Volume Viewer (display style, step size, threshold level/color, surface smoothing, etc.) control its appearance and will be applied automatically to other series members as they are displayed. For efficient playback, however, the Volume Viewer dialog will not update to show current settings until the Time value has not changed for 1 second.

Normalize threshold levels adjusts the thresholds (contour levels) to keep the enclosed volume constant throughout the series. This is useful when the signal level in the data changes over time or between states.

Clicking Play cycles through the series in the specified manner:

• forward - in increasing order, then back to the first (01230123...)
• backward - in decreasing order, then back to the last (32103210...)
• oscillate - alternating increasing and decreasing order (01232101...)

• reduce the size of the data by increasing its step size and/or limiting the displayed region in Volume Viewer
• adjust caching parameters:
  • Data cache size (Mb) [size] (default as specified in the data display options of Volume Viewer) - how much memory to allot for volume data. Increasing the value to retain more or all of the volume data can speed playback because it decreases how much time is spent reading the data from disk. However, it is important not to increase the value to exceed or come close to the computer's physical memory, as that will result in swapping of data to disk and poor performance. Clicking Current use shows how much of the data cache is being used in total and by each data set.
    
    
  • Cache [N] renderings - store volume rendering (surface triangle or solid voxel) information for the N most recent displays. This can speed playback because less time is spent recalculating display information. This information is stored separately from the data cache, but the data cache is used to store the N associated sets of volume data (even if that exceeds the specified data cache size). There is no hard limit to the memory used to cache rendering information. Surface renderings use memory proportional to the number of triangles composing the surface. Solid renderings use memory proportional to the number of data voxels displayed: about 6 bytes per grid point with colormapping (on by default), 20 bytes without. For 2-byte data values, this is up to 10 times more memory than the actual data set. Thus, it is generally only feasible to cache solid display information for small data sets.

Show markers enables using Volume Tracer to place spherical markers on the data and to trace spatial and temporal paths. Each marker is labeled with the time of the data set on which it was placed. The labels are not shown. They are used by Volume Series to display only the markers for the currently displayed time. Markers for specified numbers of earlier and later time points can also be shown.

Volume Series controls the display of markers in the active set (current set) of markers in Volume Tracer. Using Volume Tracer,

• multiple marker sets can be created and any one chosen for display
• the current marker set can be saved to a file for later use

The Color zone around markers option colors volume contour surfaces to match markers within a specified range. All of the markers associated with the current time are used to color the current surface. The coloring does not apply to solid displays.

No session support. The state of Volume Series is not included in session files. A saved and restored session will include the volume data sets in Volume Viewer, but the data sets will not be associated with Volume Series, and there is no way to specify that they should be. However, markers and paths can be saved for later use.

Slow playback when caching renderings. The second time a surface is displayed, a graphics optimization (building an OpenGL display list) is done to speed up future drawing of that same surface by putting it in graphics card memory. That optimization is time-consuming. The third time the surface is displayed will take much less time if the graphics card has sufficient memory.

Threshold normalization brightness glitches in solid mode. Sometimes a data set will appear dimmer than the preceding or following sets when solid rendering and threshold normalization are used. This can happen when only two nodes are used to specify the transfer function on the Volume Viewer histogram, with one of the nodes at the highest data value. If a particular data set has a maximum data value much higher than the adjacent sets, that will substantially lower the brightness at typical data values. This can be remedied by adding a third node between the high and low nodes by Ctrl-clicking on the Volume Viewer histogram.