Chimera Commands Index

vseries action arguments

The vseries command manipulates an ordered sequence of volume data sets. It is the command-line implementation of Volume Series. See also: vop morph, volume, movie-related commands

Possible values of action:


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

Arguments for each action are described below. Option keywords for vseries can be truncated to unique strings and their case does not matter. A vertical bar “|” designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.

vseries open  filename
Read the volume series from one or more files specified by filename (including path/location). The wildcard * can be used to specify multiple files. If filename includes spaces, it should be enclosed in quotes. 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.
vseries close  volume-spec
Close the volume series, where volume-spec is the model number of any member of the series.
vseries play  volume-specplay-options ]
Play back the specified volume series. The play-options are as follows:
jumpTo  time
Go directly to the specified time.
direction  mode
Specify the playback mode:
loop true | false
Whether to loop playback continuously until it is halted with vseries stop.
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 is used to slow playback when it is too fast.
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 true | false [ precedingMarkerFrames  N ] [ followingMarkerFrames  M ]
Whether to display markers previously created manually with Volume Tracer (or automatically with vseries measure) 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, 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
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.
cacheFrames  K
Whether to store volume rendering (surface 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 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 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 Reply 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, enclosed in quotes if it contains spaces. Successive markers are linked. The markers can be shown during playback with the showMarkers option of vseries play.

See also: measure

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.
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
Scale values by a multiplicative factor f.
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).