tomodataplots(1)            General Commands Manual           tomodataplots(1)

       tomodataplots - Make an X/Y plot of output from tilt series processing

       tomodataplots  [options]  data_file

       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 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
       mean residuals plots (types 9 and 10) define views that are multiples
       of 5 as being in a separate group, so in this case, connecting 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.

       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
                5-10: Solution parameters from a Tiltalign log versus view
                      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
                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.
                15-18: 15 for defocus, 16 for astigmatism, 17 for axis of
              astigmatism, and 18 for phase shift in a defocus file from Ctf-

       -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 (-s) 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 (-a) 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.

       -background (-b) OR -BackgroundProcess
              Run onegenplot in the background and exit quickly

       -PID   Print process ID

       -help (-he) OR -usage
              Print help output

              Read parameter entries from standard input

       David Mastronarde

       genhstplt, onegenplot, tiltxcorr, blendmont, tiltalign,

       Email bug reports to mast at colorado dot edu.

IMOD                                4.10.15                   tomodataplots(1)