SEEPLN
seepln is used to display or plot one-dimensional data, including 1-D traces through multi-dimensional data.
seepln can generate graphical displays using X-Windows, or output suitable for generating hard-copy using HPGL or PostScript. When invoked without any command line arguments, seepln uses X11 to display the data. The environment variable DISPLAY must be set in order for seepln to work. If the display you are using is the workstation console, it should be set to unix:0, which is the default. If you are running the Toolkit on a remote computer, DISPLAY should be set to the host name of the display, e.g. mumin:0 or mumin.med.harvard.edu:0.
As with other programs in the Toolkit, multiple instances of seepln can be invoked, all attached to the same (or different) shared memory sections. This is useful if you want to compare several rows or rows along different dimensions of multi-dimensional data.
Alphabetical list of commands
Command-line features in seepln
HP7550A HPGLfile;l
HPGL plotter output. The device size is 17" by 11", the plot size is 20cm by 20cm, and the origin offset is 5cm by 5cm.
HPDRAFT HPGLfile;l [D or E]
HPGL plotter output. For 'D' format the device size is 34" by 2", the plot size is 45cm by 45cm, and the origin offset is 5cm by 5cm. For 'E' format (which is the default) the device size is 44" by 34", the plot size is 75cm by 75cm, and the origin offset is 8cm by 8cm.
PS PostScriptfile;l [P or L]
PostScript output. The device size is 11" by 8.5". The P or L literal selects between Portrait and Landscape mode; the default is Landscape. In either mode, the plot size is 15cm by 15cm and the origin offset is 4cm by 4cm.
PSL PostScriptfile;l [P or L]
PostScript output (legal size). The device size is 14" by 8.5". Otherwise this mode is the same as the previous one.
X [-geometry =[WxH][+X+Y]]
Interactive X11 windowed output. This is the default output device selection. However, note that if the standard X geometry argument is given, the X specifier must also be present. If it is not given, the window size is taken to be one-half the width and height of the screen.
Commands in seepln
AUTOCLEAR
Turn on autoclear mode, so that the display is cleared before each new row is shown. To turn autoclear off, use NOCLEAR.
BORDER
Draw the border around the plot.
CHARSIZE x;f [y;f]
Specify the character horizontal and vertical sizes in cm. If the y-charsize is not given, it is taken to be the same as the x-charsize.
CLEAR
Clear the display. For plot file output, go to a new page.
COL [column;{i or f} [R or I]]
COL [NOSCALE]
Select a column for display. If column is given, it is taken as a column number (or ppm value). If column is not given, the program interactively prompts for columns to display. Enter a column number or ppm value, with an optional R or I (for the real or imaginary component in the column dimension). In interactive mode, each column is automatically scaled to fit the plot window unless the NOSCALE keyword is given.
COLOR color-value;i
Select a new color or line style. The possible choices are:
Value Color
0 Tan
1 White for X, Black for HPGL and PostScript
2 Red
3 Green
4 Blue
5 Yellow
6 Magenta
7 Cyan
8 Black for X, White for HPGL and PostScript
Note: if the resulting output is printed on a black-and-white PostScript device, the colors will only show up as shades of gray.
COM ...
Arbitrary comment text.
CUBE [cube;{i or f} [R or I]]
CUBE [NOSCALE]
Select a cube for display. See COL.
CURSOR color-value;i
Select a new cursor color (see COLOR). This command is only useful for interactive display.
DIM dom-1;l ... dom-n;l
Set the display order of the dimensions. Seepln is inherently row oriented, and this command specifies that dom-n is the row dimension, dom-(n-1) is the column dimension, and so on.
DRAW CM x;f y;f
DRAW x;f y;f [xoff;f yoff;f]
Draw a line from the current drawing location to the specified coordinates (see MOVE).
EXIT
Leave Seepln or stop reading the current stream file.
FLUSH
Flush the line output buffer for interactive DRAW commands.
FONT 'fontname' [pointsize;i]
Select a font for future TEXT commands. The font name must be in quotes and must be valid for the current output device. The pointsize argument duplicates (to some extent) the function of the CHARSIZE command, but the units are in points (1/72 in). Warning: errors in font names are not reported. For instance, using an incorrect font name for PostScript output will result in a PostScript error when the output file is printed.
GO [left-limit;i right-limit;i]
Plot the current row. If left-limit and right-limit are given, the plot is cropped to those limits.
GOTO dom-1;l coord;{i or f} [R or I] ...
Specify the coordinates for display by dimension name. The coordinates can be in points (integer) or ppm (float). An optional R or I can be used to select the real or imaginary component in each dimension.
IMAG
Select the imaginary component along the current dimension.
INT [left-limit;i right-limit;i] [TRAP or SIMP or PEAK percentage;f]
Integrate the data currently displayed. There is no correction to account for a non-zero baseline. If the right and left limits are specified, they will be used rather than the current window limits. If TRAP or SIMP is given, the trapezoid rule or Simpson's rule will be used for integration, rather than simple summation. If PEAK is given, the integration is over the interval in which the data is at least as high as the specified percentage of the largest peak within the limits.
LINETYPE type;i
Select a new line type. The possible choices are:
type Line style
1 Thick solid line
2 Thick dotted line
3 Thick dashed line
4 Thick dot-dash line
5 Thin solid line
6 Thin dotted line
7 Thin dashed line
8 Thin dot-dash line
This command is only valid for PostScript output.
LLIM x;{i or f}
Specify the left-hand limit for zooming, in points or ppm.
MOVE CM x;f y;f
MOVE x;f y;f [xoff;f yoff;f]
Set the drawing position to the specified coordinates in cm or ppm-intensity (with an optional offset in cm)
NOCLEAR
Turn off autoclear mode, so that the display is not cleared before each new row is shown.
NSKIP nskip;i
Specify the interval of points to be plotted. The original value is 1.
ORIGIN x;f y;f
Specify the plot origin in cm relative to the lower left corner of the page. For interactive windowed output the values are relative to the lower left corner of the window; but if the SIZE command has not been given (or specified a negative value) then the ORIGIN command is ignored and the plot always fills the entire window.
PEAK [x;{i or f}]
Enter interactive peak-picking mode. The initial cursor position can be specified, in points or ppm. The digits 4, 3, 2, 1 move the cursor to the left by 1, 5, 10, 30 points; the digits 6, 7, 8, 9 move the cursor to the right by 1, 5, 10, 30 points. Also, the mouse can be used to move the cursor directly.
Points can be flagged by striking an alphabetic key (optionally preceded by the 5 key) as follows:
B Add the current point to the baseline list
I Integrate between the left and right limits
L Specify the current point as the left limit for zooming or integration
P Specify the current point as the pivot for linear phase corrections
R Specify the current point as the right limit for zooming or integration
PEAK mode is terminated by pressing RETURN or any control-key combination.
PHASE [ABS or SET] p0;{i or f} [p1;{i or f}]
PHASE
Apply a phase correction to the current row. p0 and p1 can be entered as integers or floating point numbers, and are interpreted in degrees. The ABS keyword uses p0 and p1 as the final resulting phase; the SET keyword sets the phase variables to p0 and p1 without changing the data; otherwise p0 and p1 are used as phase increments.
When used without arguments, PHASE enters interactive phasing mode. The digits 4, 3, 2, 1 decrease the current phase value by 1, 5, 10, 30 degrees; the digits 6, 7, 8, 9 increase the phase value by 1, 5, 10, 30 degrees. Also, the mouse can be used to select the linear phase pivot point directly. The 5 key switches between constant and linear phase correction. Interactive phasing is terminated by pressing RETURN or any control-key combination.
PLANE [plane;{i or f} [R or I]]
PLANE [NOSCALE]
Select a plane for display. See COL.
PLOT [diameter;f] index1;i [index2;i ...]
PLOT [diameter;f] index1;i BY nskip;i [TO index2;i]
Plot filled circular dots at the index values listed. The dots' diameter is specified in cm; the default diameter is 0.2 cm. Currently the program is limited to plotting 100 dots at one time.
REAL
Select the real component along the current dimension.
RESET
Resets the display parameters to show the entire row, scaled to fit the window. It is no longer necessary to use this command to synchronize the NMR parameters with changes made in other programs.
RLIM x;{i or f}
Specify the right-hand limit for zooming, in points or ppm.
RMS [left-limit;i right-limit;i]
Compute the root mean square value of the data currently displayed. The signal-to-noise ratio is reported for the largest peak. If the right and left limits are specified, they will be used rather than the current window limits.
ROW [row;{i or f} [R or I]]
ROW [NOSCALE]
Select a row for display. See COL.
SCALE [ON or OFF]
SCALE loc;f
Enable or disable display of the ppm scale, and specify its vertical location as a percentage of the plot height.
SHELL 'Shell-command'
Spawns a sub-shell to execute the specified command (which must be surrounded by quotation marks).
SIZE x;f y;f
Specify the plot size in cm. For interactive windowed output, a negative size indicates the entire window should be used.
STREAM filename;l
Read input from a disk file. Stream files may be nested 3 deep.
TEXT CM x;f y;f 'string'
TEXT x;f y;f [xoff;f yoff;f] 'string'
Draw a text string at the specified coordinates (see MOVE).
TICK delta;f
Specify the tick spacing in ppm. If the spacing is not specified, the program will select a value that results in no more than ten tick marks along the horizontal axis.
TICKOFFSET voffset;f [hoffset;f]
Specify the vertical and optionally the horizontal offsets of the tick numbers, in cm.
UNZOOM
Display the entire row (not just the zoomed portion).
WHERE
Print the coordinate values of the row or column currently being displayed.
WRITE [BASELINE] filename;l
Write out (and clear) the list of baseline points for later use with LBC in Rnmrtk.
XMAX x;{i or f}
Specify the right-hand limit of the display, in points or ppm.
XMIN x;{i or f}
Specify the left-hand limit of the display, in points or ppm.
YMAX y;f
YMAX SYM
Specify the top limit of the display. The SYM keyword sets ymax equal to -ymin.
YMIN y;f
YMIN SYM
Specify the bottom limit of the display. The SYM keyword sets ymin equal to -ymax.
YSCALE factor;f
YSCALE [AUTO]
Scale the vertical axis by the specified factor. The optional AUTO form of the command scales the display to match the range of the data.
ZOOM
Display only the portion of the row between the zoom limits (see LLIM, RLIM, and PEAK).