RunProj can be used to quickly combine information from multiple parallel slices through a data set. Typically, the slices are perpendicular to the z axis, but you can also choose to use slices that are perpendicular to the x or y axes. When the slices are perpendicular to the x or y axes, RunProj proceeds as if the data had been processed by Flip to swap the projection axis with the z axis and then projects the data along the new z axis. A common use for RunProj is to combine all of the slices along an axis as a quick volume rendering of the data set as if a camera were pointed along the projection axis. The controls for selecting and processing a region are the same as in many other applications. There are additional controls to set the number of sequential slices combined, the slice number increment from the beginning of one group of combined slices to the next, the method for combining intensity information from different slices, and the projection axis.
Region processing | Step size | Group size | Method | Axis | Command line
T-RunProj | Volume Viewer | Flip | Priism
Use this text field to indicate how many slices to move ahead from the first slice in one combined group to the first slice in the next combined group. For instance, if you selected a step size of 4 and project along the z axis, regardless of how many z sections are grouped into one projection, the projected groups would start at zstart, zstart+4, zstart+8, .... zstart is the starting z section from the Z field.
Use this text field to indicate how many slices to combine for each projected image. For example, if the number of slices to combine is three and x is the projection axis, then the columns with the indices, xstart, xstart+1, and xstart+2, would be combined to form the first projection image in the output. xstart is the starting x index from the XY field. If the step size was also three, then the columns, xstart+3, xstart+4, and xstart+5, would be combined to create the second image in the output. If the step size was two, than the second image in the output would be a combination of the columns, xstart+2, xstart+3, and xstart+4.
Use the menu next to the "Method" button to select how different slices are combined. You can choose one of these:
Use the menu next to the "Axis" button to select the axis along which to perform the projection. When you project along the z axis, the default, you have the same point of view as in the original data. If you project along the x or y axes, you will get an orthogonal view: with x as the projection axis the resulting images are projections to the yz plane of the original data and with y as the projection axis the resulting images are projections to the xz plane of the original data.
RunProj accepts the command-line arguments described in Region.html. In addition, RunProj has the following options:
-average
-average_z as a synonym for -average.
-axis=p
x, y, or z.
If this option does not appear on the command line, RunProj computes the
projection along the z axis.
-group=m
-group is not specified, RunProj combines 3 slices
to form one output image. For compatibility with previous versions,
RunProj accepts -z_group=m as a synonym for
-group=m.
-max
-max_z as a synonym for
-max.
-step=n
-step is not
specified, RunProj jumps 3 slices between groups. For compatibility with
previous versions, RunProj accepts -z_step=n
as a synonym for -step=n.
-sum
-sum_z
as a synonym for -sum.
If more than one of -sum, -average,
or -max appear on the command line, the last one takes
precedence. If none of them appear on the command line, RunProj combines
slices by summing them.
As an example, if stack.dat has 10 z sections per wavelength/time point pair, the command line shown below generates proj.dat which, for each wavelength/time point pair, has a single z section that is the average of the 10 z sections.
RunProj stack.dat proj.dat -group=10 -step=10 -average