axis · graph · graphmode · plot · plotx · ploty · plt · regraph · setcolor · settext

Obsolete Plotting

Warning

The functions on this page should be considered obsolete and avoided in new code; use Graph instead.

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graphmode()

obsolete. Use Graph instead.

Syntax:

h.graphmode(1)
Executes the list of setup statements. This is also done on the first call to h.graph(t) after a new setup statement is added to the list.

h.graphmode(-1)
Flushes the stored plots. Subsequent calls to h.graph(t) will start new lines. Should be executed just before a h.plt(-1) to ensure the entire lines are plotted.

h.graphmode(2)
Flushes the stored plots. Subsequent calls to h.graph(t) will continue the lines. Graphs are normally flushed every 50 points.

graph()

Name:

graph — multiple line plots (obsolete; use Graph instead)

Syntax:

h.graph()

h.graph(expression, setup)

h.graph(t)

h.graphmode(mode)

Description:

The graph() function solves the problem of obtaining multiple line plots during a single run. During calls to h.graph(t), specified variables are stored and plotted using scales determined by calls to axis().

Options:

h.graph()
erases the old list and starts a new (empty) list of plot expressions and setup statements.

h.graph(s1, s2)
Adds a new plot specification to the graph list. s1 must be a HOC string which contains an expression, usually a variable. e.g “y”. s2 is a HOC string which contains any number of statements used to initialize axes. etc. E.G “axis(0,5,1,-1,1,2) axis()”.

h.graph(t)
The current value of each expression in the graph list is saved along with the abscissa value, t. The line plots are flushed every 50 points.

Example:

from neuron import h, gui

# define a HOC variable x
h('x = 0')


def p(): # plot ramp
    h.axis(100, 300, 450, 200)
    h.axis(0, 15, 3, -1, 1, 2)
    h.axis()
    h.plot(1)
    for i in range(150):
        h.x = i * 0.1
        h.plot(h.x, h.x / 15.)    # ramp
        h.graph(h.x)  # plots graph list if any
    h.graph(-1) # flush remaining part of graphs, if any
    h.plt(-1)


p()    # plots the ramp alone

h.graph()
h.graph("sin(x)","axis(100, 300, 100, 300) axis()")
h.graph("cos(x)", "")  # same axes as previous call to graph

p()    # plots the sin and cos along with the ramp

Diagnostics:

The strings are parsed when h.graph(s1, s2) is executed. The strings are executed on calls to h.graph(t).

The best method for complicated plots is to make the setup string a simple call to a user defined procedure. This procedure can setup the axes, write the labels, etc. Newlines and strings within strings are possible by quoting with the \ character but generally are too confusing to be practical.

Local variables in graph strings make no sense.

Note

All expressions for initialization and for plotting must be specified as HOC expressions not as Python callables. These functions are maintained solely to maintain backward compatability, so this limitation is likely to never be lifted. New code should use Graph instead, which does not have this limitation.

Note

On some modern systems, the graph window may have to be interacted with (e.g. resized) before the first graph will appear.

See also

plot()

axis()

Syntax:

h.axis()

h.axis(clip)

h.axis(xorg, xsize, yorg, ysize)

h.axis(xstart, xstop, nticx, ystart, ystop, nticy)

Options:

h.axis()
draw axes with label values. Closes plot device.

h.axis(clip)
points are not plotted if they are a factor clip off the axis scale. Default is no clipping. Set clip to 1 to not plot out of axis region. A value of 1.1 allows plotting slightly outside the axis boundaries.

h.axis(xorg, xsize, yorg, ysize)
Size and location of the plot region. (Use the h.plt() absolute coordinates.)

h.axis(xstart, xstop, nticx, ystart, ystop, nticy)
Determines relative scale and origin.

Specification of the precision of axis tic labels is available by recompiling hoc/SRC/plot.c with #define Jaslove 1+. With this definition, the number of tics specified in the 3rd and 6th arguments of axis() should be of the form m.n. m is the number of tic marks, and n is the number of digits after the decimal point which are printed. This contribution was made by Stewart Jaslove.

See also

plot()

plotx()

ploty()

regraph(): See graph()

plot()

Name:: plot - plot relative to scale given by axis()

Syntax:

h.plot(mode)

inrange = h.plot(x,y)

Description:: h.plot() plots relative to the origin and scale defined by calls to axis(). The default x and y axes have relative units of 0 to 1 with the plot located in a 5x3.5 inch area.

Options:

h.plot()
print parameter usage help lines.

h.plot(0)
subsequent calls will plot points.

h.plot(1)
next call will be a move, subsequent call will draw lines.

h.plot(x, y)
plots a point (or vector) relative to the axis scale. Return value is 0 if the point is clipped (out of range).

h.plot(mode, x, y)
Like plt() but with scale and origin given by axis().

Example:

from neuron import h, gui
import math

# plot the sin function from 0 to 10 radians
h.axis(0, 10, 5, -1, 1, 2) #/* setup scale */
h.plot(1)
for i in range(101):
    x = i * 0.1
    h.plot(x, math.sin(x))  # plot the function

h.axis()

See also

plt(), setcolor(), axis()

setcolor()

obsolete.

Name:: setcolor - low level plot function

Syntax:

h.setcolor(colorval)

Description:

h.setcolor() sets the color (or pen number for HP plotter) used for plt().

Argument to setcolor() produces the following screen colors with an EGA adapter (left), X11 graphics (right):

    black  (pen 1 on HP plotter)         black
    blue                                 white
    green                                yellow
    cyan                                 red
    red                                  green
    magenta                              blue
    brown                                violet
    light gray  (pen 1 on HP plotter)    cyan
...
   white                                green

settext(): obsolete. See plt().

plt()

Name:

plt - low level plot function

Syntax:

h.plt(mode)

h.plt(mode, x, y)

Description:

h.plt() plots points, lines, and text using the Tektronix 4010 standard. Absolute coordinates of the lower left corner and upper right corner of the plot region are (0,0) and (1000, 780) respectively.

TURBO-C graphics drivers for VGA, EGA, CGA, and Hercules are automatically selected when the first plotting command is executed. An HP7475 compatible plotter may be connected to COM1:.

Options:

h.plt(-1)
Place cursor in home position.

h.plt(-2)
Subsequent text printed starting at current coordinate position.

h.plt(-3)
Erase screen, cursor in home position.

h.plt(-5)
Open HP plotter on PC; the plotter will stay open until another h.plt(-5) is executed.

h.plt(0, x, y)
Plot point.

h.plt(1, x, y)
Move to point without plotting.

h.plt(2, x, y)
Draw vector from former position to new position given by (x,y). (mode can be any number >= 2)

Several extra options are available for X11 graphics.

h.plt(-4, x, y)
Erases area defined by previous plot position and the point, (x, y).

h.plt(-5)
Fast mode. By default, the X11 server is flushed on every plot command so one can see the plot as it develops. Fast mode caches plot commands and only flushes on plt(-1) and setcolor(). Fast mode is three times faster than the default mode. It is most useful when plotting is the rate limiting step of the simulation.

h.plt(-6)
X11 server flushed on every plot call.

When the graphic window is resized, NEURON is notified after the next erase command.

Example:

from neuron import h, gui
import math

h.setcolor(3)      # color 3 is red for X11; to use with EGA, change to 4
h.plt(1, 100, 500)
h.plt(2, 100, 100) # y-axis
h.plt(1, 100, 300)
h.plt(2, 600, 300) # x-axis (NOTE: does not correspond to origin of sine wave)
h.plt(1, 200, 550)
h.plt(-2)
for i in range(1001):
    h.plt(i + 1, i * 5, 300 + 200 * math.sin(2 * math.pi * i / 100.))

h.plt(-1) # close plot

Warning

EGA adaptor used extensively but CGA and Hercules used hardly at all.

When the X11 graphic window is killed, NEURON exits without asking about unsaved edit buffers.