Content-type: text/html Manpage of modifyMotiveList

modifyMotiveList

Section: User Commands (1)
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NAME

modifyMotiveList - rotate / translate each particle in a motive list  

SYNOPSIS

modifyMotiveList inFile outFile rotation
modifyMotiveList inFile outFile rotation translation
modifyMotiveList inFile outFile rotation translation flgInvert
modifyMotiveList inFile outFile rotation translation flgInvert flgEuler  

DESCRIPTION

Generate a new motive list in which each particle has been rotated and / or translated by a specifed amount from the input motive list. This can be useful during symmetrization or prior to regenerating averages in a new orientation. It can also be useful when combining multiple tomograms which have previously been aligned separately in a single PEET run. Modifying the motive list(s) will change the orientation of the resulting averages unless "Align averages to have their Y axis vertical" is selected. (While it is not strictly required, we generally recommend unchecking this option while verifying that modified motive list(s) are behaving as intended).
inFile
The file name of the input motive list in csv format.
outFile
The name to which the output file will be written. Previous contents will be overwritten and lost if the file already exists.
rotation
A string which can be evaluated as a Matlab vector specifying 3 floating point IMOD Slicer angles in degrees, e.g. "xAngle,yAngle,zAngle", where xAngle, yAngle, and zAngle specify rotations about corresponding tomogram axes, to be applied in the order Z-Y-X . The composite rotation can be thought of as applied to either a) the implied reference particle, or b) the resulting average prior to any "align particles to have their Y axes vertical" (flgAlignAverages) operation. Conversely, the volumes containing the individual particles can be thought of as rotating in the opposite direction. If flgEuler is true (see below), the angles specified will be interpreted as Z-X-Z Euler angles rather than Slicer angles.
translation (optional)
A string which can be evaluated as a Matlab vector specifying floating point X, Y, and Z translations in tomogram pixels, e.g. "xShift,yShift,zShift" (default = "0,0,0"). The resulting shift can be thought of as applying directly to either a) the implied reference, or b) the resulting average after any rotation specified, but prior to any optional vertical alignment. Alternatively, the volumes containing the individual particles can be thought of as shifting in the opposite direction.
flgInvert (optional, default = 0)
If non-zero, perform the inverse of the usual transformation. Given a motive list a.csv, for example, the commands


  modifyMotiveList a.csv b.csv '131, -37, 28' '2, -3, 5'
  modifyMotiveList b.csv c.csv '131, -37, 28' '2, -3, 5' 1

would result in c.csv being equivalent to a.csv, except for round-off errors.

flgEuler (optional, default = 0)
If non-zero, interpret the input angles as Z-X-Z Euler angles (entered in the order "Z1,X,Z2") rather than Z-Y-X Slicer angles.
 

AUTHOR

John Heumann  

SEE ALSO

PEET(1)


 

Index

NAME
SYNOPSIS
DESCRIPTION
AUTHOR
SEE ALSO

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Time: 21:10:05 GMT, March 20, 2017