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 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                                4.11.0                    tomodataplots(1)