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Command: vseries

Usage:
vseries  action   arguments

The vseries command manipulates a volume series, an ordered sequence of volume data sets such as density maps or optical microscopy data. See also: volume, volume morph, mousemode, mseries, making movies

Examples:

vseries play #1 loop true
vseries stop #1
vseries save #1 ~/Desktop/test.cmap subregion 100,0,0,200,511,150 threshold 140 valueType uint8

The action can be:

Arguments for each action are described below. Option keywords and Boolean (truth) values can be truncated, with synonyms for true: True, 1, and synonyms for false: False, 0. A vertical bar “|” designates mutually exclusive values, and default settings are indicated with bold.

The volume-spec is the model number of any member of the series. The members of a series are indexed 0, 1, 2, ... and these indices are referred to as the time. Any numbers in the input filenames are not used.

vseries align  volume-specencloseVolume  volume | fastEncloseVolume  volume ]
Align the maps in the specified volume series. (Alternatively, alignment can be done with the align option of vseries save.) The encloseVolume option indicates setting the threshold (contour level) to enclose the specified volume in distance units cubed (e.g., Å3) before aligning the maps. The contour level affects alignment because only values above the contour level are used. The level is determined by an iterative procedure (details...). The fastEncloseVolume option is similar but uses a faster, noniterative approximation (details...).
vseries play  volume-specplay-options ]
Play back the specified volume series, with play-options as follows:
jumpTo  time
Go directly to the specified time and stop. See also startTime.
startTime  time
Go to the specified time and continue playback. See also jumpTo.
range  time-range
Limit playback to the specified time range.
direction  mode
Specify the playback mode:
loop  true | false
Whether to loop playback continuously until it is halted with vseries stop.
normalize  true | false
Whether to adjust 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.
showMarkers  marker-spec  [ precedingMarkerFrames  N ] [ followingMarkerFrames  M ]
Display the specified markers to trace spatial and temporal paths. (A marker is implemented as an atom and can be specified similarly by model number, etc.) The markers could have been created manually with the mouse (see mousemode) or automatically with vseries measure. For marker display to be synchronized with playback, each marker should be labeled with the time of the data set on which it was placed. The labels are not shown, but used by vseries to limit marker display to the corresponding time. Simultaneously, markers can also be displayed for N earlier time points (default 0) and M later time points (default 0) using precedingMarkerFrames and followingMarkerFrames, respectively.

colorRange  cutoff
(not yet supported)
Whether to color volume contour surfaces to match markers within a specified distance cutoff (regardless of whether the markers are shown). All of the markers associated with the current time are used to color the current surface. The coloring does not apply to solid displays.
maxFrameRate  rate
Specify a maximum playback rate in steps per second. By default, playback is as fast as possible, which can be fairly slow for large data. This option can be used to slow playback when it is too fast; however, the number of image frames per time step will still depend on the speed of graphics rendering. The pauseFrames option slows playback more reproducibly and may be preferred.
pauseFrames  P
Make playback slower by updating the time only every P graphics redraw frames. Ignore maxFrameRate if also given.
cacheFrames  K
Whether to store volume rendering (surface/mesh triangle or solid voxel) information for the K most recent displays (default 1). This can speed playback because less time is spent recalculating display information. 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, and it is generally only feasible to cache solid display information for small data sets.
vseries stop  volume-spec
Halt playback of the specified volume series.
vseries slider  volume-spec
Show a graphical slider interface for the specified volume series. Usually this is not needed, since simply opening the series will show the slider; however, it allows assigning the same slider to two or more series (different channels/wavelengths) even if the series are not the same sizes.

In the interface, the slider can be dragged or a time value entered directly. The interface also includes a play/pause button and another that toggles between the full data (step 1) and every-other-point subsampling (step 2).

Volume series playback can also be assigned to a mouse mode such as scrolling.

vseries measure  volume-specoutput  filename ] [ centroids  true | false ] [ radius  centroid-radius ] [ color  centroid-color ]
For each time in the specified volume series, calculate centroid (x,y,z) coordinates, distance from the previous centroid (“step”), cumulative distance along the piecewise linear path from the first centroid, surface-enclosed volume, and surface area. The results are saved as plain text in filename specified with the output option, otherwise given in the Log.

The calculation uses the step size and threshold (contour level) of the first map in the series for every time point; i.e., the contour level is not adjusted to maintain a constant volume. The centroid is the center of mass of the density map based on map regions above the threshold. The surface area is a sum over the triangles of the contour surface. The surface-enclosed volume does not include interior bubbles (if any), and any holes in the surface are treated as if covered by planar caps.

If centroids is true, a marker will be placed at at each centroid, with radius centroid-radius (default is the minimum grid-spacing in the maps) and color centroid-color (default gray). The centroid-color can be any color name that specifies a single color. Successive markers are linked. The markers can be shown during playback with the showMarkers option of vseries play.

vseries save  volume-spec  filenamesave-options ]
Save the specified series as a single file (filename) in Chimera map format, optionally with processing such as cropping, normalization, and alignment. The save-options are listed below in order of application when used together:
subregion  i1,j1,k1,i2,j2,k2
Instead of saving the full dimensions, save the subregion delimited by grid indices i1–i2 along the X axis, j1–j2 along the Y axis, and k1–k2 along the Z axis.
step  N | Nx,Ny,Nz
Specify sampling density, where a step of 1 means all data points, 2 means every other data point along each axis, etc. Step sizes must be integers. If a single number is supplied, it is used in all three directions; if three numbers are supplied (separated by commas but not spaces), they are used in the X, Y, and Z directions, respectively.
valueType  value-type
Change grid value type before any processing with other save options. The related option finalValueType sets the value type after any processing. The value-type can be:
threshold  minimum
Replace all values below the specified mininum with zero.
zeroMean  true | false
Subtract the mean from each value so that the new mean will be zero.
scaleFactor  f
matchScale  other-series
Scale values by a multiplicative factor f, or (mutually exclusive option) to minimize the sum of squares of the differences with other-series specified by model number. The other series must be on the same grid and have the same map dimensions as the series to be scaled.
encloseVolume volume | fastEncloseVolume volume ]
Set the contour level of each map to enclose a specified volume in distance units cubed. Either of two methods can be used, as described above. The contour level affects alignment because only values above the contour level are used.
normalizeLevel  value
Scale map values so that the current threshold (contour level) equals the specified value.
align  true | false
Align the maps before saving them. Only values above the contour level are used for alignment; contour levels can be set to enclose a specified volume.
onGrid  gridmap 
Create the new map on the grid of another, where gridmap is a model number preceded by #. This allows using a consistent grid for maps after alignment.
mask  maskmap 
Mask by maskmap (multiply by the 0,1 values within that map). The maskmap must be on the same grid and have the same dimensions as the series maps.
finalValueType  value-type
Set grid value type after any processing with other save options. Possible types are as listed for the related option valueType, which sets the value type before processing.
compress  true | false
Compress the output file (Chimera map format).

UCSF Resource for Biocomputing, Visualization, and Informatics / May 2017