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1dplot.json
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1dplot.json
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{
"command-line": "1dplot [INSTALL] [SEP] [ONE] [SEPSCL] [NOLINE] [BOX] [HIST] [X] [NORM2] [NORMX] [NORM1] [DEMEAN] [XL10] [DX] [XZERO] [NOPUSH] [IGNORE] [USE] [XLABEL] [YLABEL] [PLABEL] [TITLE] [WINTITLE] [NAKED] [ASPECT] [STDIN] [PS] [JPG] [JPEG] [PNG] [PNM] [PNGS] [JPGS] [JPEGS] [PNMS] [YTRAN] [XTRAN] [XAXIS] [YAXIS] [YNAMES] [VOLREG] [THICK] [DASHED] [DNAME] [A] [CENSOR_RGB] [CENSOR] [CENSORTR] [CONCAT] [RBOX] [LINE] [TSFILE] [...]",
"description": "tool description",
"inputs": [
{
"command-line-flag": "-install",
"description": "Install a new X11 colormap.",
"id": "INSTALL",
"name": "INSTALL",
"optional": true,
"type": "String",
"value-key": "[INSTALL]"
},
{
"command-line-flag": "-sep",
"description": "Plot each column in a separate sub-graph.",
"id": "SEP",
"name": "SEP",
"optional": true,
"type": "String",
"value-key": "[SEP]"
},
{
"command-line-flag": "-one",
"description": "Plot all columns together in one big graph. [default = -sep]",
"id": "ONE",
"name": "ONE",
"optional": true,
"type": "String",
"value-key": "[ONE]"
},
{
"command-line-flag": "-sepscl",
"description": "Plot each column in a separate sub-graph and allow each sub-graph to have a different y-scale. -sepscl is meaningless with -one!",
"id": "SEPSCL",
"name": "SEPSCL",
"optional": true,
"type": "String",
"value-key": "[SEPSCL]"
},
{
"command-line-flag": "-noline",
"description": "Don't plot the connecting lines (also implies '-box').",
"id": "NOLINE",
"name": "NOLINE",
"optional": true,
"type": "String",
"value-key": "[NOLINE]"
},
{
"command-line-flag": "-box",
"description": "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). * 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",
"id": "BOX",
"name": "BOX",
"optional": true,
"type": "String",
"value-key": "[BOX]"
},
{
"command-line-flag": "-hist",
"description": "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]' \\",
"id": "HIST",
"name": "HIST",
"optional": true,
"type": "String",
"value-key": "[HIST]"
},
{
"command-line-flag": "-x",
"description": "-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':",
"id": "X",
"name": "X",
"optional": true,
"type": "String",
"value-key": "[X]"
},
{
"command-line-flag": "-norm2",
"description": "Independently scale each time series plotted to have L_2 norm = 1 (sum of squares).",
"id": "NORM2",
"name": "NORM2",
"optional": true,
"type": "String",
"value-key": "[NORM2]"
},
{
"command-line-flag": "-normx",
"description": "Independently scale each time series plotted to have max absolute value = 1 (L_infinity norm).",
"id": "NORMX",
"name": "NORMX",
"optional": true,
"type": "String",
"value-key": "[NORMX]"
},
{
"command-line-flag": "-norm1",
"description": "Independently scale each time series plotted to have max sum of absolute values = 1 (L_1 norm).",
"id": "NORM1",
"name": "NORM1",
"optional": true,
"type": "String",
"value-key": "[NORM1]"
},
{
"command-line-flag": "-demean",
"description": "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.)",
"id": "DEMEAN",
"name": "DEMEAN",
"optional": true,
"type": "String",
"value-key": "[DEMEAN]"
},
{
"command-line-flag": "-xl10",
"description": "-xl10 X.1D = Use log10(X.1D) as the X axis.",
"id": "XL10",
"name": "XL10",
"optional": true,
"type": "String",
"value-key": "[XL10]"
},
{
"command-line-flag": "-dx",
"description": "Spacing between points on the x-axis is 'xx' [default = 1] SYNONYMS: '-dt' and '-del'",
"id": "DX",
"name": "DX",
"optional": true,
"type": "String",
"value-key": "[DX]"
},
{
"command-line-flag": "-xzero",
"description": "Initial x coordinate is 'zz' [default = 0] SYNONYMS: '-tzero' and '-start'",
"id": "XZERO",
"name": "XZERO",
"optional": true,
"type": "String",
"value-key": "[XZERO]"
},
{
"command-line-flag": "-nopush",
"description": "Don't 'push' axes ranges outwards.",
"id": "NOPUSH",
"name": "NOPUSH",
"optional": true,
"type": "String",
"value-key": "[NOPUSH]"
},
{
"command-line-flag": "-ignore",
"description": "Skip first 'nn' rows in the input file [default = 0]",
"id": "IGNORE",
"name": "IGNORE",
"optional": true,
"type": "String",
"value-key": "[IGNORE]"
},
{
"command-line-flag": "-use",
"description": "Plot 'mm' points [default = all of them]",
"id": "USE",
"name": "USE",
"optional": true,
"type": "String",
"value-key": "[USE]"
},
{
"command-line-flag": "-xlabel",
"description": "Put string 'aa' below the x-axis [default = no axis label]",
"id": "XLABEL",
"name": "XLABEL",
"optional": true,
"type": "String",
"value-key": "[XLABEL]"
},
{
"command-line-flag": "-ylabel",
"description": "Put string 'aa' to the left of the y-axis [default = no axis label]",
"id": "YLABEL",
"name": "YLABEL",
"optional": true,
"type": "String",
"value-key": "[YLABEL]"
},
{
"command-line-flag": "-plabel",
"description": "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 versus echo 2 4.5 -1 | 1dplot -plabel 'test\\_underscore' -stdin",
"id": "PLABEL",
"name": "PLABEL",
"optional": true,
"type": "String",
"value-key": "[PLABEL]"
},
{
"command-line-flag": "-title",
"description": "Same as -plabel, but only works with -ps/-png/-jpg/-pnm options.",
"id": "TITLE",
"name": "TITLE",
"optional": true,
"type": "String",
"value-key": "[TITLE]"
},
{
"command-line-flag": "-wintitle",
"description": "Set string 'pp' as the title of the frame containing the plot. Default is based on input.",
"id": "WINTITLE",
"name": "WINTITLE",
"optional": true,
"type": "String",
"value-key": "[WINTITLE]"
},
{
"command-line-flag": "-naked",
"description": "Do NOT plot axes or labels, just the graph(s). You might want to use '-nopush' with '-naked'.",
"id": "NAKED",
"name": "NAKED",
"optional": true,
"type": "String",
"value-key": "[NAKED]"
},
{
"command-line-flag": "-aspect",
"description": "Set the width-to-height ratio of the plot region to 'A'. Default value is 1.3. Larger 'A' means a wider graph.",
"id": "ASPECT",
"name": "ASPECT",
"optional": true,
"type": "String",
"value-key": "[ASPECT]"
},
{
"command-line-flag": "-stdin",
"description": "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.",
"id": "STDIN",
"name": "STDIN",
"optional": true,
"type": "String",
"value-key": "[STDIN]"
},
{
"command-line-flag": "-ps",
"description": "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 -",
"id": "PS",
"name": "PS",
"optional": true,
"type": "String",
"value-key": "[PS]"
},
{
"command-line-flag": "-jpg",
"description": "= Render plot to an image and save to a file named",
"id": "JPG",
"name": "JPG",
"optional": true,
"type": "String",
"value-key": "[JPG]"
},
{
"command-line-flag": "-jpeg",
"description": "= 'fname', in JPEG mode or in PNG mode or in PNM mode.",
"id": "JPEG",
"name": "JPEG",
"optional": true,
"type": "String",
"value-key": "[JPEG]"
},
{
"command-line-flag": "-png",
"description": "= The default image width is 1024 pixels; to change",
"id": "PNG",
"name": "PNG",
"optional": true,
"type": "String",
"value-key": "[PNG]"
},
{
"command-line-flag": "-pnm",
"description": "= this value to 2000 pixels (say), do setenv AFNI_1DPLOT_IMSIZE 2000 before running 1dplot. Widths over 2000 may start to look odd, and will run more slowly. * PNG files will be smaller than JPEG, and are compressed without loss. * PNG output requires that the netpbm program pnmtopng be installed somewhere in your PATH. * PNM output files are not compressed, and are manipulable by the netpbm package: http://netpbm.sourceforge.net/",
"id": "PNM",
"name": "PNM",
"optional": true,
"type": "String",
"value-key": "[PNM]"
},
{
"command-line-flag": "-pngs",
"description": "= a convenience function equivalent to",
"id": "PNGS",
"name": "PNGS",
"optional": true,
"type": "String",
"value-key": "[PNGS]"
},
{
"command-line-flag": "-jpgs",
"description": "= setenv AFNI_1DPLOT_IMSIZE SIZE and",
"id": "JPGS",
"name": "JPGS",
"optional": true,
"type": "String",
"value-key": "[JPGS]"
},
{
"command-line-flag": "-jpegs",
"description": "= -png (or -jpg or -pnm) fname",
"id": "JPEGS",
"name": "JPEGS",
"optional": true,
"type": "String",
"value-key": "[JPEGS]"
},
{
"command-line-flag": "-pnms",
"description": "-pnms SIZE fname }",
"id": "PNMS",
"name": "PNMS",
"optional": true,
"type": "String",
"value-key": "[PNMS]"
},
{
"command-line-flag": "-ytran",
"description": "-ytran 'expr' = Transform the data along the y-axis by applying the expression to each input value. For example:",
"id": "YTRAN",
"name": "YTRAN",
"optional": true,
"type": "String",
"value-key": "[YTRAN]"
},
{
"command-line-flag": "-xtran",
"description": "-xtran 'expr' = Similar, but for the x-axis. ** Applies to '-xmulti' , '-x' , or the default x-axis.",
"id": "XTRAN",
"name": "XTRAN",
"optional": true,
"type": "String",
"value-key": "[XTRAN]"
},
{
"command-line-flag": "-xaxis",
"description": ":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:",
"id": "XAXIS",
"name": "XAXIS",
"optional": true,
"type": "String",
"value-key": "[XAXIS]"
},
{
"command-line-flag": "-yaxis",
"description": ":n:m = Similar to above, for the y-axis. These options override the normal autoscaling of their respective axes.",
"id": "YAXIS",
"name": "YAXIS",
"optional": true,
"type": "String",
"value-key": "[YAXIS]"
},
{
"command-line-flag": "-ynames",
"description": "-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",
"id": "YNAMES",
"name": "YNAMES",
"optional": true,
"type": "String",
"value-key": "[YNAMES]"
},
{
"command-line-flag": "-volreg",
"description": "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.",
"id": "VOLREG",
"name": "VOLREG",
"optional": true,
"type": "String",
"value-key": "[VOLREG]"
},
{
"command-line-flag": "-thick",
"description": "Each time you give this, it makes the line thickness used for plotting a little larger. [An alternative to using '-DAFNI_1DPLOT_THIK=...']",
"id": "THICK",
"name": "THICK",
"optional": true,
"type": "String",
"value-key": "[THICK]"
},
{
"command-line-flag": "-dashed",
"description": "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). ** 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.",
"id": "DASHED",
"name": "DASHED",
"optional": true,
"type": "String",
"value-key": "[DASHED]"
},
{
"command-line-flag": "-Dname",
"description": "al = 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. ---------------- RENDERING METHOD ---------------- 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. ------ LABELS ------ 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 \\",
"id": "DNAME",
"name": "DNAME",
"optional": true,
"type": "String",
"value-key": "[DNAME]"
},
{
"command-line-flag": "-a",
"description": "-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' ** TRANSPOSITION WITH \\' ** 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. -------------- 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 &",
"id": "A",
"name": "A",
"optional": true,
"type": "String",
"value-key": "[A]"
},
{
"command-line-flag": "-censor_RGB",
"description": "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!",
"id": "CENSOR_RGB",
"name": "CENSOR_RGB",
"optional": true,
"type": "String",
"value-key": "[CENSOR_RGB]"
},
{
"command-line-flag": "-censor",
"description": "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.)",
"id": "CENSOR",
"name": "CENSOR",
"optional": true,
"type": "String",
"value-key": "[CENSOR]"
},
{
"command-line-flag": "-CENSORTR",
"description": "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.",
"id": "CENSORTR",
"name": "CENSORTR",
"optional": true,
"type": "String",
"value-key": "[CENSORTR]"
},
{
"command-line-flag": "-concat",
"description": "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.]",
"id": "CONCAT",
"name": "CONCAT",
"optional": true,
"type": "String",
"value-key": "[CONCAT]"
},
{
"command-line-flag": "-rbox",
"description": "-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.]",
"id": "RBOX",
"name": "RBOX",
"optional": true,
"type": "String",
"value-key": "[RBOX]"
},
{
"command-line-flag": "-line",
"description": "-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 7 2018 {:}",
"id": "LINE",
"name": "LINE",
"optional": true,
"type": "String",
"value-key": "[LINE]"
},
{
"description": "NA",
"id": "tsfile",
"name": "tsfile",
"optional": false,
"type": "String",
"value-key": "[TSFILE]"
},
{
"description": "NA",
"id": "...",
"name": "...",
"optional": false,
"type": "String",
"value-key": "[...]"
}
],
"name": "tool name",
"schema-version": "0.5",
"suggested-resources": {
"cpu-cores": 1,
"ram": 1,
"walltime-estimate": 60
},
"tags": {},
"tool-version": "v0.1.0"
}