Warning
The functions on this page should be considered obsolete and avoided in new code; use :class:`Graph` instead.
.fa
.. function:: graphmode
obsolete. Use :class:`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.
.. function:: graph
Name:
graph --- multiple line plots (obsolete; use :class:`Graph` instead)
Syntax:
``h.graph()``
``h.graph(expression, setup)``
``h.graph(t)``
``h.graphmode(mode)``
Description:
The :func:`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 :func:`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:
.. code-block::
python
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
.. image:: ../images/oldgrph.png
:align: center
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 :class:`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.
.. seealso::
:func:`plot`
.. function:: 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 :file:`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.
.. seealso::
:func:`plot`
.. function:: plotx
.. function:: ploty
.. function:: regraph
See :func:`graph`
.. function:: plot
Name:
plot - plot relative to scale given by :func:`axis`
Syntax:
``h.plot(mode)``
``inrange = h.plot(x,y)``
Description:
``h.plot()`` plots relative to the origin and scale defined by
calls to :func:`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 :func:`plt` but with scale and origin given by :func:`axis`.
Example:
.. code-block::
python
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()
.. image:: ../images/plotsin.png
:align: center
.. seealso::
:func:`plt`, :func:`setcolor`, :func:`axis`
.. function:: 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 :func:`plt`.
Argument to \ ``setcolor()`` produces the following screen
colors with an EGA adapter (left), X11 graphics (right):
.. code-block::
none
0 black (pen 1 on HP plotter) black
1 blue white
2 green yellow
3 cyan red
4 red green
5 magenta blue
6 brown violet
7 light gray (pen 1 on HP plotter) cyan
...
15 white green
.. seealso:
:func:`plt`
.. function:: settext
obsolete. See :func:`plt`.
.. function:: 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:
.. code-block::
python
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
.. image:: ../images/plotsin2.png
:align: center
.. seealso::
:func:`plot`, :func:`axis`, :func:`lw`, :func:`setcolor`, :class:`Graph`
.. 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.