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 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. 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. -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 -StandardInput Read parameter entries from standard input AUTHOR David Mastronarde SEE ALSO genhstplt, onegenplot, tiltxcorr, blendmont, tiltalign, clip Email bug reports to mast at colorado dot edu. IMOD 4.9.10 tomodataplots(1)