tomopitch(1) General Commands Manual tomopitch(1)
NAME
tomopitch - Determines tomogram shift and angles from models of section
SYNOPSIS
tomopitch [options]
DESCRIPTION
Tomopitch analyes simple models of the boundaries of the section in
slices from a tomogram and recommends how much to change tilt angles to
make the section flat, how much to shift the tilt axis in Z to produce
centered slices, and how thick to make the slices. It can also recom-
mend how much X-axis tilt is needed to make the section flat in the
orthogonal direction as well. It can also be used with a model drawn
on a whole tomogram, possibly binned down.
The typical use is with samples of the tomogram in separate files. For
each sample of the tomogram, make a model file with two contours in it.
Each contour should have two points, with the line between them lying
along the top or bottom surface of the section. The points do not have
to be entered in any particular order, and the lines do not need to be
any particular length (the program will extend them in X, if necessary,
to within 5% of each edge of the tomogram).
As an alternative to making a separate model file for each sample, you
can load all of the samples into 3dmod together and make a single model
file, creating a pair of contours at each different time index. Make
this model file be the sole entry to Tomopitch, and it will analyze
each of the time indexes separately, the same as if they were in sepa-
rate files.
A third alternative is to make a model on an entire tomogram. Such a
model can take two forms. It can consist of any number of pairs of
horizontal lines, where each par is drawn predominantly in the X direc-
tion along the top and bottom of the section. This can be done while
viewing the YZ planes of the tomogram, just as in the samples of YZ
slices. The lines can also be drawn while viewing the XY planes of the
tomogram in the Zap window, or they can be drawn in the Slicer window
with the angles adjusted to make a surface appear all at once in the
window. These lines do not need to be parallel to the X axis, but try
to draw the two lines of a pair at approximately the same location in
Y. The program expects the separation in Y between the two lines of a
pair to be less than 0.3 times the separation between successive pairs.
The second form for a model on a whole tomogram consists of a pair of
horizontal lines near the middle of the tomogram, and a pair of lines
oriented vertically (predominantly in the Y direction) along the top
and bottom of the tomogram. Only one pair of lines of each type is
allowed. With this input, the program will construct two more pairs of
horizontal lines by sliding the pair that were entered to the low Y and
high Y ends of the vertical lines. Analysis then proceeds with the
three pairs of horizontal lines.
If you make a model on an entire tomogram, you need not enter a value
for the spacing in Y. If the tomogram is binned down relative to the
final tomogram, enter the binning factor as a scale factor to get val-
ues appropriate for the final tomogram.
The program analyzes each pair of horizontal lines separately. It
determines what rotation is required to make the section be flat. It
reports the upward shift needed to center the section in Y, and the
slice thickness needed to contain the section. These values are
derived and reported before and after the recommended rotation is
applied. Thickness values include an additional amount that you spec-
ify and are rounded up to integers suitable for taking 3D FFTs. After
all pairs of lines are analyzed, the program makes the same analysis
and report based on the data from all of the files. It then computes
an X-axis tilt and reports thickness and rotation if that tilt is taken
into account as well.
OPTIONS
Tomopitch uses the PIP package for input (see the manual page for
pip) and can take input interactively for options that existed when
it was converted, to maintain compatibility with old command files.
The following options can be specified either as command line arguments
(with the -) or one per line in a command file or parameter file (with-
out the -). Options can be abbreviated to unique letters; the cur-
rently valid abbreviations for short names are shown in parentheses.
-model (-m) OR -ModelFile File name
Model file with lines to analyze. If there are multiple model
file entries, they should be in order that they will be consid-
ered in the program. (Successive entries accumulate)
-extra (-e) OR -ExtraThickness Floating point
Additional pixels of thickness to add to both the top and the
bottom of the tomogram, beyond the region described by the model
lines. Enter values as unbinned pixels, i.e. pixels after the
scaling factor has been applied.
-spacing (-sp) OR -SpacingInY Floating point
Spacing between tomogram samples (distance in Y in tilted
views). If a non-zero number is entered, the program will com-
pute the tilt around the X-axis that will make the tomogram be
flat in its Z dimension.
-scale (-sc) OR -ScaleFactor Floating point
Amount by which to scale the Z shift and thickness recommended
by the program. Use this entry if the model was drawn on
binned-down samples or a whole binned-down tomogram but you
intend to make an unbinned tomogram. The scale factor is the
binning factor.
-angle (-a) OR -AngleOffsetOld Floating point
Angle offset in the alignment used to make the samples. If this
entry is present, the program will output the original, added,
and total offset.
-zshift (-z) OR -ZShiftOld Floating point
Z shift value in the alignment used to make the samples, in
unbinned pixels. If this entry is present, the program will
output the original, added, and total Z shift.
-xtilt (-x) OR -XAxisTiltOld Floating point
X axis tilt applied when the samples were made. If this entry
is present, the program will output the original, added, and
total X axis tilt.
-noxtilt (-n) OR -NoXAxisTilt
Do not solve for X axis tilt or changes in other values when X-
axis tilt is compensated for. An incoming value of -xtilt will
be ignored, but if positioning tomogram(s) were remade with a
non-zero X-axis tilt, the reported values will still be appro-
priate for such an X-tilted tomogram. Thus, it is best to have
this option present on the first round of positioning, or to
remake the tomogram(s) with X-axis tilt set to 0.
-param (-p) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
INTERACTIVE INPUT
If the program is started with no command line arguments, it reverts to
interactive input with the following entries:
Additional pixels of thickness to add to both the top and the bottom of
the tomogram, beyond the region described by the model lines.
Spacing between tomogram samples (the distance in Y in the tilt
images.) If a non-zero number is entered, the program will compute the
tilt around the X-axis that will make the tomogram be flat in its Z
dimension.
Number of model files to analyze
For each file, then enter the name of the file.
HISTORY
Written by David Mastronarde, January 2000
5/20/01: Added analysis of single file with multiple time indexes
11/13/03: Converted to PIP, added ability to draw lines in whole tomogram
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.2.0 tomopitch(1)