Rotfast is a program that calculates projections of a 3D volume for one or more different views corresponding to different rotations of the volume about the Y axis.
There is a graphical interface (rotfast_i) for specifying the inputs to Rotfast and then passing them to the command-line application to calculate the result. You can also use the command-line application directly. To run Rotfast with the input file, infile, and output file, outfile, use
rotfast infile outfile <options>
For descriptions of the possible options see the topics Y angles, Background value, and Z pixel size. Other options to set the region processed and aspects of the graphical front end that Rotfast shares with other applications are described in BatchRegion.html.
The maximum size of the 3D volume that can be handled is 512 x 512 x 128 pixels.
Overview | Y angles | Background value | Z pixel size
BatchRegion.html | Priism | Categories | Applications
The projected views that Rotfast calculates are at y angles ranging from a start value to a final value with a fixed angle increment. In the graphical interface these values are set in the Y Tilt (min,max,del) field. On the command-line, use the option
-ang=min:max:step
to specify the set of views to calculate. If the option is not set, one view at y rotation of zero degrees is calculated.
Overview | Y angles | Background value | Z pixel size
Rotfast can subtract a fixed value from all the input values before doing the projection calculation. Those input values that are less than zero after the subtraction are coerced to zero. The background value to subtract is set in the Background to subtract field in the graphical interface (the graphical interface currently only allows you to set the background for the first wave; the other waves will use zero for the background value). On the command-line, use the option
-bkg=wave1_bkg:wave2_bkg:wave3_bkg:wave4_bkg:wave5_bkg
to specify the background values. If the option is not set, a background value of zero is assumed for all waves.
Overview | Y angles | Background value | Z pixel size
Use this option to override the z pixel size in the input file header. This works well for thin data stacks because it gives it a pseudo 3-D feel by stretching spacing of the stack in the z direction. This option can only be specified when running Rotfast directly on the command-line. Use
-deltaz=pixel_size
to set the pixel size. Currently, the z pixel size will not be altered if the new size is less than one.
Overview | Y angles | Background value | Z pixel size