tomodataplots(1) General Commands Manual tomodataplots(1)
NAME
tomodataplots - Make an X/Y plot of output from tilt series processing
SYNOPSIS
tomodataplots [options] data_file
DESCRIPTION
Tomodataplots is a Python script to plot selected output from various
stages of tilt series processing in a window, using Genhstplt via
Onegenplot. It can plot X and Y shifts from alignment transforms,
min and max values from running "clip stat", the errors from shifting
montage frames into alignment in Blendmont, various components of a
Tiltalign solution, or the mean residual error for each view. It
can plot the defocus and other values contained in a Ctfplotter
defocus file. It can plot total shifts and residual values from align-
ing tilt series frames with Alignframes. It can also plot X, Y, and
Z position versus tilt angle during tilt series acquisition.
Each kind of plot has defaults for whether points will be connected by
lines, whether a symbol is drawn at each point, and the kind of symbol.
These defaults can be overridden with the options below. However, the
Tiltalign mean residuals plots (types 9 and 10) define views that
are multiples of 5 as being in a separate group, so in this case, con-
necting points will not work as desired.
Note that the graph window can be saved as a PNG file or printed from a
popup menu brought up by right-clicking in the window. Left-clicking
will pop up a report of the coordinates clicked.
OPTIONS
Tomodataplots uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-input (-i) OR -InputFile File name
Name of file with data to plot. If this option is not entered,
the first non-option argument is used for the name.
-type (-t) OR -TypeOfDataToPlot Multiple integers
Type of data to plot.
1-3: Shifts from a transform file; 1 for X shift, 2 for Y
shifts, 3 for both.
4: Mean and maximum errors in a Blendmont log versus view
number.
5-10: Solution parameters from a Tiltalign log versus view
number:
5 for rotation,
6 for delta tilt and skew if present,
7 for magnification,
8 for X-stretch (dmag),
9 for global mean residual, and
10 for the average of the mean residual over all local
areas
11-13: 11 for minimum, 12 for maximum, and 13 for both values
from "clip stats" output plotted versus view number or versus
piece number for a montage.
14: X, Y, and Z position versus tilt angle from tilt series
acquisition, using a file where each line has one set of tilt
angle, X, Y, and Z positions.
15-19: 15 for defocus, 16 for astigmatism, 17 for axis of
astigmatism, 18 for phase shift, and 19 for cuton frequency in a
defocus file from Ctfplotter.
20-22: 20 for raw and smoothed shifts, 21 for weighted mean
residual and leave-out error if present, and 22 for maximum of
maximum weighted residuals in an Alignframes log file.
-connect (-c) OR -ConnectWithLines Integer
To override the default on whether connecting lines are drawn,
enter 1 draw lines between successive points, or 0 not to. This
entry has no effect if the symbol is 0 (no symbol).
-symbols (-sy) OR -SymbolsForGroups Multiple integers
One or more symbols to use for the different types or columns
being displayed. See onegenplot for a list of symbol types.
-hue (-hu) OR -HueOfGroup Text string
This option can be used to specify a color for each group being
plotted. If one type of data is being plotted, the group number
is 1 and default color is black. When two types of data are
being plotted, the group numbers are 1 and 2 and the default
colors are navy and maroon. Enter either 4 integers separated
by commas (the group number and the red, green, and blue values,
ranging from 0 to 255) or the group number and a stock color
name separated by a comma. An entry here replaces the default
for that group. Stock colors can be listed with "onegenplot
-stock". (Successive entries accumulate)
-axis (-ax) OR -XaxisLabel Text string
A label for the X axis to override the default for the given
data type. If the label entered contains "View number", this
substring will be replaced with "Piece number" for "clip stats"
output from a montage.
-append (-ap) OR -AppendToKey Text string
String to append to the key on the right. Enter "@time" for a
timestamp (HH:MM:SS) or "@file" for the input filename.
-size (-si) OR -SizeOfPlot Two integers
Size of graphics window in X and Y, in pixels
-position (-p) OR -PositionOfPlot Two integers
Coordinates of the top left corner of the graphics window in X
and Y, in pixels, where Y is 0 at the top of the screen.
-background (-b) OR -BackgroundProcess
Run onegenplot in the background and exit quickly
-PID Print process ID
-help (-he) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
AUTHOR
David Mastronarde
SEE ALSO
genhstplt, onegenplot, tiltxcorr, blendmont, tiltalign,
clip, alignframes
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 tomodataplots(1)