Usage: 1dplot [options] tsfile ...

Graphs the columns of a *.1D time series file to the X11 screen,
or to an image file (.jpg or .png).

 ** This is the original C-language plotting program in AFNI, first created  **
 **  in 1999 (by RW Cox), built on routines he first wrote in the 1980s.     **
 ** Also see the much newer and similar Python-language program 1dplot.py    **
 **  (created by PA Taylor in 2018), which can produce nicer looking graphs. **

 -install   = Install a new X11 colormap.
 -sep       = Plot each column in a separate sub-graph.
 -one       = Plot all columns together in one big graph.
                [default = -sep]
 -sepscl    = Plot each column in a separate sub-graph
              and allow each sub-graph to have a different
              y-scale.  -sepscl is meaningless with -one!
 -noline    = Don't plot the connecting lines (also implies '-box').
 -NOLINE    = Same as '-noline', but will not try to plot values outside
              the rectangular box that contains the graph axes.
 -box       = Plot a small 'box' at each data point, in addition
              to the lines connecting the points.
             * The box size can be set via the environment variable
               AFNI_1DPLOT_BOXSIZE; the value is a fraction of the
               overall plot size.  The standard box size is 0.006.
               Example with a bigger box:
                 1dplot -DAFNI_1DPLOT_BOXSIZE=0.01 -box A.1D
             * The box shapes are different for different time
               series columns.  At present, there is no way to
               control which shape is used for what column
               (unless you modify the source code, that is).
             * If you want some data columns plotted with boxes
               and some with lines, don't use '-box'. Instead, use
               option '-dashed'.
             * You can set environment variable AFNI_1DPLOT_RANBOX
               to YES to get the '-noline' boxes plotted in a
               pseudo-random order, so that one particular color
               doesn't dominate just because it is last in the
               plotting order; for example:
        1dplot -DAFNI_1DPLOT_RANBOX=YES -one -x X.1D -noline Y1.1D Y2.1D Y3.1D

 -hist      = Plot graphs in histogram style (i.e., vertical boxes).
             * Histograms can be generated from 3D or 1D files using
               program 3dhistog; for example
                3dhistog -nbin 50 -notitle -min 0 -max .04 err.1D > eh.1D
                1dplot -hist -x eh.1D'[0]' -xlabel err -ylabel hist eh.1D'[1]'
               or, for something a little more fun looking:
                1dplot -one -hist -dashed 1:2 -x eh.1D'[0]' \
                       -xlabel err -ylabel hist eh.1D'[1]' eh.1D'[1]'

           ** The '-norm' options below can be useful for plotting data
               with different value ranges on top of each other via '-one':
 -norm2     = Independently scale each time series plotted to
              have L_2 norm = 1 (sum of squares).
 -normx     = Independently scale each time series plotted to
              have max absolute value = 1 (L_infinity norm).
 -norm1     = Independently scale each time series plotted to
              have max sum of absolute values = 1 (L_1 norm).
 -demean    = This option will remove the mean from each time series
              (before normalizing).  The combination '-demean -normx -one'
              can be useful when plotting disparate data together.
             * If you use '-demean' twice, you will get linear detrending.
             * Et cetera (e.g,, 4 times gives you cubic detrending.)

 -x  X.1D   = Use for X axis the data in X.1D.
              Note that X.1D should have one column
              of the same length as the columns in tsfile.
            ** Coupled with '-box -noline', you can use '-x' to make
               a scatter plot, as in graphing file A1.1D along the
               x-axis and file A2.1D along the y-axis:
                 1dplot -box -noline -x A1.1D -xlabel A1 -ylabel A2 A2.1D
            ** '-x' will override -dx and -xzero; -xaxis still works

 -xl10 X.1D = Use log10(X.1D) as the X axis.

 -xmulti X1.1D X2.1D ...
              This new [Oct 2013] option allows you to plot different
              columns from the data with different values along the
              x-axis.  You can supply one or more 1D files after the
              '-xmulti' option.  The columns from these files are
              catenated, and then the first xmulti column is used as
              as x-axis values for the first data column plotted, the
              second xmulti column gives the x-axis values for the
              second data column plotted, and so on.
           ** The command line arguments after '-xmulti' are taken
              as 1D filenames to read, until an argument starts with
              a '-' character -- this would either be another option,
              or just a single '-' to separate the xmulti 1D files
              from the data files to be plotted.
           ** If you don't provide enough xmulti columns for all the
              data files, the last xmulti column will be re-used.
           ** Useless but fun example:
               1deval -num 100 -expr '(i-i)+z+gran(0,6)' > X1.1D
               1deval -num 100 -expr '(i-i)+z+gran(0,6)' > X2.1D
               1dplot -one -box -xmulti X1.1D X2.1D - X2.1D X1.1D

 -dx xx     = Spacing between points on the x-axis is 'xx'
                [default = 1] SYNONYMS: '-dt' and '-del'
 -xzero zz  = Initial x coordinate is 'zz' [default = 0]
                SYNONYMS: '-tzero' and '-start'
 -nopush    = Don't 'push' axes ranges outwards.
 -ignore nn = Skip first 'nn' rows in the input file
                [default = 0]
 -use mm    = Plot 'mm' points [default = all of them]
 -xlabel aa = Put string 'aa' below the x-axis
                [default = no axis label]
 -ylabel aa = Put string 'aa' to the left of the y-axis
                [default = no axis label]
 -plabel pp = Put string 'pp' atop the plot.
              Some characters, such as '_' have
              special formatting effects. You
              can escape that with ''. For example:
        echo 2 4.5 -1 | 1dplot -plabel 'test_underscore' -stdin
        echo 2 4.5 -1 | 1dplot -plabel 'test\_underscore' -stdin
 -title pp = Same as -plabel, but only works with -ps/-png/-jpg/-pnm options.
 -wintitle pp = Set string 'pp' as the title of the frame
                containing the plot. Default is based on input.

 -naked     = Do NOT plot axes or labels, just the graph(s).
              You might want to use '-nopush' with '-naked'.
 -aspect A  = Set the width-to-height ratio of the plot region to 'A'.
              Default value is 1.3. Larger 'A' means a wider graph.

 -stdin     = Don't read from tsfile; instead, read from
              stdin and plot it. You cannot combine input
              from stdin and tsfile(s).  If you want to do so,
              use program 1dcat first.

 -ps        = Don't draw plot in a window; instead, write it
              to stdout in PostScript format.
             * If you view the result in 'gv', you should turn
               'anti-alias' off, and switch to landscape mode.
             * You can use the 'gs' program to convert PostScript
               to other formats; for example, a .bmp file:
                 1dplot -ps ~/data/verbal/cosall.1D |
                  gs -r100 -sOutputFile=fred.bmp -sDEVICE=bmp256 -q -dBATCH -
             * 1dplot is built on some line drawing software written
               a long time ago in a galaxy far away, which is why PostScript
               output was a natural thing to do -- I doubt that anyone uses
               this feature in these decadent modern times.

 -jpg fname  } = Render plot to an image and save to a file named
 -jpeg fname } = 'fname', in JPEG mode or in PNG mode or in PNM mode.
 -png fname  } = The default image width is 1024 pixels; to change
 -pnm fname  } = this value to 2048 pixels (say), do
                   setenv AFNI_1DPLOT_IMSIZE 2048
                 before running 1dplot, or add
                 to the 1dplot command line. Widths over 4096 might
                 start to look odd in some cases. The largest allowed
                 size is 8192 pixels.
               * PNG files created by 1dplot will be smaller than JPEG,
                 and are compressed without loss.
               * PNG output requires that the netpbm program
                 pnmtopng be installed somewhere in your PATH.
                 This program is NOT supplied with AFNI, but must
                 be installed separately:
               * PNM output files are not compressed, and are manipulable
                 by the netpbm package: http://netpbm.sourceforge.net/
                 Otherwise, this format isn't very useful anymore.
               * There will be small drawing differences between the
                 X11 (interactive) plotting window and the images saved
                 by these options -- or by the interactive button.
                 These differences arise from the use of different line
                 drawing functions for X11 windows and for off-screen
                 bitmap images.

 -pngs size fname } = convenience options equivalent to
 -jpgs size fname } = -DAFNI_1DPLOT_IMSIZE=size followed by
 -jpegs size fname} = -png fname (or -jpg or -jpeg or -pnm)
 -pnms size fname } = The largest allowed size is 8192 pixels.

 -ytran 'expr'   = Transform the data along the y-axis by
                   applying the expression to each input value.
                   For example:
                     -ytran 'log10(z)'
                   will take log10 of each input time series value
                   before plotting it.
                 * The expression should have one variable (any letter
                   from a-z will do), which stands for the time series
                   data to be transformed.
                 * An expression such as 'sqrt(x*x+i)' will use 'x'
                   for the time series value and use 'i' for the time
                   index (starting at 0) -- in this way, you can use
                   time-dependent transformations, if needed.
                 * This transformation applies to all input time series
                   (at present, there is no way to transform different
                   time series in distinct ways inside 1dplot).
                 * '-ytran' is applied BEFORE the various '-norm' options.

 -xtran 'expr'    = Similar, but for the x-axis.
                  ** Applies to '-xmulti' , '-x' , or the default x-axis.

 -xaxis b:t:n:m  = Set the x-axis to run from value 'b' to
                   value 't', with 'n' major divisions and
                   'm' minor tic marks per major division.
                   For example:
                     -xaxis 0:100:5:20
                   Setting 'n' to 0 means no tic marks or labels.
                 * You can set 'b' to be greater than 't', to
                   have the x-coordinate decrease from left-to-right.
                 * This is the only way to have this effect in 1dplot.
                 * In particular, '-dx' with a negative value will not work!

 -yaxis b:t:n:m  = Similar to above, for the y-axis.  These
                   options override the normal autoscaling
                   of their respective axes.

 -ynames a b ... = Use the strings 'a', 'b', etc., as
                   labels to the right of the graphs,
                   corresponding to each input column.
                   These strings CANNOT start with the
                   '-' character.
             N.B.: Each separate string after '-ynames'
                   is taken to be a new label, until the
                   end of the command line or until some
                   string starts with a '-'.  In particular,
                   This means you CANNOT do something like
                     1dplot -ynames a b c file.1D
                   since the input filename 'file.1D' will
                   be used as a label string, not a filename.
                   Instead, you must put another option between
                   the end of the '-ynames' label list, OR you
                   can put a single '-' at the end of the label
                   list to signal its end:
                     1dplot -ynames a b c - file.1D
        TSV files: When plotting a TSV file, where the first row
                   is the set of column labels, you can use this
                   Unix trick to put the column labels here:
                     -ynames `head -1 file.tsv`
                   The 'head' command copies just the first line
                   of the file to stdout, and the backquotes `...`
                   capture stdout and put it onto the command line.
                 * You might need to put a single '-' after this
                   option to prevent the problem alluded to above.
                   In any case, it can't hurt to use '-' as an option
                   after '-ynames'.
                 * If any of the TSV labels start with the '-' character,
                   peculiar and unpleasant things might transpire.

 -volreg         = Makes the 'ynames' be the same as the
                   6 labels used in plug_volreg for
                   Roll, Pitch, Yaw, I-S, R-L, and A-P
                   movements, in that order.

 -thick          = Each time you give this, it makes the line
                   thickness used for plotting a little larger.
                   [An alternative to using '-DAFNI_1DPLOT_THIK=...']
 -THICK          = Twice the power of '-thick' at no extra cost!!

 -dashed codes   = Plot dashed lines between data points.  The 'codes'
                   are a colon-separated list of dash values, which
                   can be 1 (solid), 2 (longer dashes), or 3 (shorter dashes).
                   0 can be used to indicate that a time series is to be
                   plotted without lines but with boxes instead.
                ** Example: '-dashed 1:2:3' means to plot the first time
                   series with solid lines, the second with long dashes,
                   and the third with short dashes.

 -Dname=val      = Set environment variable 'name' to 'val'
                   for this run of the program only:
 1dplot -DAFNI_1DPLOT_THIK=0.01 -DAFNI_1DPLOT_COLOR_01=blue '1D:3 4 5 3 1 0'

You may also select a subset of columns to display using
a tsfile specification like 'fred.1D[0,3,5]', indicating
that columns #0, #3, and #5 will be the only ones plotted.
For more details on this selection scheme, see the output
of '3dcalc -help'.

Example: graphing a 'dfile' output by 3dvolreg, when TR=5:
   1dplot -volreg -dx 5 -xlabel Time 'dfile[1..6]'

You can also input more than one tsfile, in which case the files
will all be plotted.  However, if the files have different column
lengths, the shortest one will rule.

The colors for the line graphs cycle between black, red, green, and
blue.  You can alter these colors by setting Unix environment
variables of the form AFNI_1DPLOT_COLOR_xx -- cf. README.environment.
You can alter the thickness of the lines by setting the variable
AFNI_1DPLOT_THIK to a value between 0.00 and 0.05 -- the units are
fractions of the page size; of course, you can also use the options
'-thick' or '-THICK' if you prefer.

On 30 Apr 2012, a new method of rendering the 1dplot graph into an X11
window was introduced -- this method uses 'anti-aliasing' to produce
smoother-looking lines and characters.  If you want the old coarser-looking
rendering method, set environment variable AFNI_1DPLOT_RENDEROLD to YES.

The program always uses the new rendering method when drawing to a JPEG
or PNG or PNM file (which is not and never has been just a screen capture).
There is no way to disable the new rendering method for image-file saves.

Besides normal alphabetic text, the various labels can include some
special characters, using TeX-like escapes starting with '\'.
Also, the '^' and '_' characters denote super- and sub-scripts,
respectively.  The following command shows many of the escapes:
 1deval -num 100 -expr 'J0(t/4)' | 1dplot -stdin -thick \
 -xlabel '\alpha\beta\gamma\delta\epsilon\zeta\eta^{\oplus\dagger}\times c' \
 -ylabel 'Bessel Function \green J_0(t/4)'     \
 -plabel '\Upsilon\Phi\Chi\Psi\Omega\red\leftrightarrow\blue\partial^{2}f/\partial x^2'

A timeseries file is in the form of a 1D or 2D table of ASCII numbers;
for example:   3 5 7
               2 4 6
               0 3 3
               7 2 9
This example has 4 rows and 3 columns.  Each column is considered as
a timeseries in AFNI.  The convention is to store this type of data
in a filename ending in '.1D'.

When specifying a timeseries file to an command-line AFNI program, you
can select a subset of columns using the '[...]' notation:
  'fred.1D[5]'            ==> use only column #5
  'fred.1D[5,9,17]'       ==> use columns #5, #9, and #17
  'fred.1D[5..8]'         ==> use columns #5, #6, #7, and #8
  'fred.1D[5..13(2)]'     ==> use columns #5, #7, #9, #11, and #13
Column indices start at 0.  You can use the character '$'
to indicate the last column in a 1D file; for example, you
can select every third column in a 1D file by using the selection list
  'fred.1D[0..$(3)]'      ==> use columns #0, #3, #6, #9, ....

Similarly, you select a subset of the rows using the '{...}' notation:
  'fred.1D{0..$(2)}'      ==> use rows #0, #2, #4, ....
You can also use both notations together, as in
  'fred.1D[1,3]{1..$(2)}' ==> columns #1 and #3; rows #1, #3, #5, ....

You can also input a 1D time series 'dataset' directly on the command
line, without an external file. The 'filename' for such input has the
general format
where each 'n_i' is an integer and each 'val_i' is a float.  For
   -a '1D:5@0,10@1,5@0,10@1,5@0'
specifies that variable 'a' be assigned to a 1D time series of 35,
alternating in blocks between values 0 and value 1.
 * Spaces or commas can be used to separate values.
 * A '|' character can be used to start a new input "line":
   Try 1dplot '1D: 3 4 3 5 | 3 5 4 3'

Finally, you can force most AFNI programs to transpose a 1D file on
input by appending a single ' character at the end of the filename.
N.B.: Since the ' character is also special to the shell, you'll
      probably have to put a \ character before it. Examples:
       1dplot '1D: 3 2 3 4 | 2 3 4 3'   and
       1dplot '1D: 3 2 3 4 | 2 3 4 3'\'
When you have reached this level of understanding, you are ready to
take the AFNI Jedi Master test.  I won't insult you by telling you
where to find this examination.

These files are used in BIDS http://bids.neuroimaging.io and AFNI
programs can read these in a few places.

The format of a .tsv file is a set of columns, where the values in
each row are separated by tab characters -- spaces are NOT separators.
Each element is string, some of which are numeric (e.g. 3.1416).
The first row of a .tsv file is a set of strings which are column
desciptors (separated by tabs, of course). For the most part, the
following data in each column are exclusively numeric or exclusively
strings. Strings can contain blanks/spaces since only tabs are used
to separate values.

A .tsv file can be read in most places where a .1D file is read.
However, columns (after the header row) that are not purely numeric
will be ignored, since the internal usage of .1D data in AFNI is numeric.
Thus, you can do something like
  1dplot -nopush -sepscl sub-10506_task-pamenc_events.tsv
and you will get a plot of all the numeric columns in this BIDS file.
Column selection '[]' can be done, using numbers to specify columns
or using the column labels in the .tsv file.

N.B.: The string 'N/A' or 'n/a' in a column that is otherwise numeric
      will be considered to be a number, and will be replaced on input
      with the mean of the "true" numbers in the column -- there is
      no concept of missing data in an AFNI .1D file.
    ++ If you don't like this, well ... too bad for you.

Program 1dcat has special knowledge of .tsv files, and will cat
(sideways - along rows) .tsv and .1D files together. It also has an
option to write the output in .tsv format.

For example, to get the 'onset', 'duration', and 'trial_type' columns
out of a BIDS task .tsv file, a command like this could be used:
  1dcat sub-10506_task-pamenc_events.tsv'[onset,duration,trial_type]'
Note that the column headers are lost in this output, but could be kept
if the 1dcat '-tsvout' option were used. In reverse, a numeric .1D file
can be converted to .tsv format by a command like:
  1dcat -tsvout Fred.1D
In this case, since a the data for .1D file doesn't have headers for its
columns, 1dcat will invent some column names.

At this time, other programs don't 'know' much about .tsv files, and will
ignore the header row and non-numeric columns when reading a .tsv file.
in place of a .1D file.

MARKING BLOCKS (e.g., censored time points)
The following options let you mark blocks along the x-axis, by drawing
colored vertical boxes over the standard white background.
 * The intended use is to mark blocks of time points that are censored
   out of an analysis, which is why the options are the same as those
   in 3dDeconvolve -- but you can mark blocks for any reason, of course.
 * These options don't do anything when the '-x' option is used to
   alter the x-axis spacings.
 * To see what the various color markings look like, try this silly example:

   1deval -num 100 -expr 'lran(2)' > zz.1D
   1dplot -thick -censor_RGB red    -CENSORTR 3-8   \
                 -censor_RGB green  -CENSORTR 11-16 \
                 -censor_RGB blue   -CENSORTR 22-27 \
                 -censor_RGB yellow -CENSORTR 34-39 \
                 -censor_RGB violet -CENSORTR 45-50 \
                 -censor_RGB pink   -CENSORTR 55-60 \
                 -censor_RGB gray   -CENSORTR 65-70 \
                 -censor_RGB #2cf   -CENSORTR 75-80 \
          -plabel 'red green blue yellow violet pink gray #2cf' zz.1D &

 -censor_RGB clr   = set the color used for the marking to 'clr', which
                     can be one of the strings below:
                       red green blue yellow violet pink gray (OR grey)
                   * OR 'clr' can be in the form '#xyz' or '#xxyyzz', where
                     'x', 'y', and 'z' are hexadecimal digits -- for example,
                     '#2cf' is sort of a cyan color.
                   * OR 'clr' can be in the form 'rgbi:rf/gf/bf' where
                     each color intensity (rf, gf, bf) is a number between
                     0.0 and 1.0 -- e.g., white is 'rgbi:1.0/1.0/1.0'.
                     Since the background is white, dark colors don't look
                     good here, and will obscure the graphs; for example,
                     pink is defined here as 'rgbi:1.0/0.5/0.5'.
                   * The default color is (a rather pale) yellow.
                   * You can use '-censor_RGB' more than once.  The color
                     most recently specified previous on the command line
                     is what will be used with the '-censor' and '-CENSORTR'
                     options.  This allows you to mark different blocks
                     with different colors (e.g., if they were censored
                     for different reasons).
                   * The feature of allowing multiple '-censor_RGB' options
                     means that you must put this option BEFORE the
                     relevant '-censor' and/or '-CENSORTR' options.
                     Otherwise, you'll get the default yellow color!

 -censor cname     = cname is the filename of censor .1D time series
                   * This is a file of 1s and 0s, indicating which
                     time points are to be un-marked (1) and which are
                     to be marked (0).
                   * Please note that only one '-censor' option can be
                     used, for compatibility with 3dDeconvolve.
                   * The option below may be simpler to use!
                     (And can be used multiple times.)

 -CENSORTR clist   = clist is a list of strings that specify time indexes
                     to be marked in the graph(s).  Each string is of
                     one of the following forms:
                           37 => mark global time index #37
                         2:37 => mark time index #37 in run #2
                       37..47 => mark global time indexes #37-47
                       37-47  => same as above
                     *:0-2    => mark time indexes #0-2 in all runs
                     2:37..47 => mark time indexes #37-47 in run #2
                   * Time indexes within each run start at 0.
                   * Run indexes start at 1 (just be to confusing).
                   * Multiple -CENSORTR options may be used, or
                     multiple -CENSORTR strings can be given at
                     once, separated by spaces or commas.
                   * Each argument on the command line after
                     '-CENSORTR' is treated as a censoring string,
                     until an argument starts with a '-' or an
                     alphabetic character, or it contains the substring
                     '1D'.  This means that if you want to plot a file
                     named '9zork.xyz', you may have to do this:
                       1dplot -CENSORTR 3-7 18-22 - 9zork.xyz
                     The stand-alone '-' will stop the processing
                     of censor strings; otherwise, the '9zork.xyz'
                     string, since it doesn't start with a letter,
                     would be treated as a censoring string, which
                     you would find confusing.
                  ** N.B.: 2:37,47 means index #37 in run #2 and
                     global time index 47; it does NOT mean
                     index #37 in run #2 AND index #47 in run #2.

 -concat rname      = rname is the filename for list of concatenated runs
                      * 'rname' can be in the format
                          '1D: 0 100 200 300'
                        which indicates 4 runs, the first of which
                        starts at time index=0, second at index=100,
                        and so on.
                      * The ONLY function of '-concat' is for use with
                        '-CENSORTR', to be compatible with 3dDeconvolve
                          [e.g., for plotting motion parameters from]
                          [3dvolreg -1Dfile, where you've cat-enated]
                          [the 1D files from separate runs into one ]
                          [long file for plotting with this program.]

 -rbox x1 y1 x2 y2 color1 color2
                    = Draw a rectangular box with corners (x1,y1) to
                      (x2,y2), in color1, with an outline in color2.
                      Colors are names, such as 'green'.
                        [This option lets you make bar]
                        [charts, *if* you care enough.]

 -Rbox x1 y1 x2 y2 y3 color1 color2
                    = As above, with an extra horizontal line at y3.

 -line x1 y1 x2 y2 color dashcode
                    = Draw one line segment.

Another fun fun example:

  1dplot -censor_RGB #ffa -CENSORTR '0-99'           \
         `1deval -1D: -num 61 -dx 0.3 -expr 'J0(x)'`

which illustrates the use of 'censoring' to mark the entire graph
background in pale yellow '#ffa', and also illustrates the use
of the '-1D:' option in 1deval to produce output that can be
used directly on the command line, via the backquote `...` operator.

++ Compile date = Sep  1 2021 {AFNI_21.2.06:linux_ubuntu_16_64}