RangeVarPlot
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RangeVarPlot

class RangeVarPlot
Syntax:

h.RangeVarPlot("rangevar")

h.RangeVarPlot(py_callable)

Description:

Class for making a space plot. eg. voltage as function of path between two points on a cell. For plotting, an object of this type needs to be inserted in a Graph with g.addobject(rvp) By default, the location of the path nearest the root is location 0 (the origin) of the space plot.

If the rangevar does not exist at certain places in the path it is assumed to have a value of 0.

The first form where rangevar is “v” or “m_hh”, etc. is very efficient since the object can store pointers to the variables for fast plotting.

The second form is much slower since the expression must be executed by the interpreter for each point along the path for each plot. Execution of the expression is equivalent to for sec in h.allsec(): for seg in sec: f(seg.x) where the expression is the body of f. All section-dependent NEURON functions will default to the correct section for the call; i.e. there is no need to say sec= unless you want to refer to a section that is not the one whose data is being plotted. The current section may be read via h.cas().

Example (plotting by name):

from neuron import h, gui

dend1 = h.Section(name='dend1')
dend2 = h.Section(name='dend2')

for sec in h.allsec():
    sec.nseg = sec.L = 501
    sec.diam = 1

dend2.connect(dend1)

ic = h.IClamp(dend1(0.5))
ic.amp = 0.5
ic.delay = 0
ic.dur = 1

h.finitialize(-65)
h.continuerun(1)

rvp = h.RangeVarPlot('v')
rvp.begin(0, sec=dend1)
rvp.end(1, sec=dend2)
g = h.Graph()
g.addobject(rvp)
g.size(0, 1002, -70, 50)
../_images/rangevarplot1.png

Example (plotting a function):

from neuron import h, gui

dend1 = h.Section(name='dend1')
dend2 = h.Section(name='dend2')

for sec in h.allsec():
    sec.nseg = sec.L = 501
    sec.diam = 1

dend2.connect(dend1)

def my_func(x):
    sec = h.cas()  # find out which section
    if sec == dend1:
        y = x ** 2
    else:
        y = 1 + x ** 2
    return y

rvp = h.RangeVarPlot(my_func)
rvp.begin(0, sec=dend1)
rvp.end(1, sec=dend2)
g = h.Graph()
g.addobject(rvp)
g.size(0, 1002, 0, 2)
g.flush()
../_images/rangevarplot2.png
Example (transfer impedance):
imp = h.Impedance()

rvp = h.RangeVarPlot(imp.transfer)
rvp... #specify range begin and end
imp... #specify impedance computation
g = h.Graph()
g.addobject(rvp)

RangeVarPlot.begin()
Syntax:
rvp.begin(x, sec=section)
Description:
Starts the path for the space plot at the segment section(x).

RangeVarPlot.end()
Syntax:
rvp.end(x, sec=section)
Description:
Ends the path for the space plot at the segment section(x).

RangeVarPlot.origin()
Syntax:
rvp.origin(x, sec=section)
Description:
Defines the origin (location 0) of the space plot as section(x). The default is usually suitable unless you want to have several rangvarplots in one graph in which case this function is used to arrange all the plots relative to each other.

RangeVarPlot.left()
Syntax:
rvp.left()
Description:
returns the coordinate of the beginning of the path.

RangeVarPlot.right()
Syntax:
rvp.right()
Description:
returns the coordinate of the end of the path. The total length of the path is rvp.right() - rvp.left().

RangeVarPlot.list()
Syntax:
rvp.list(sectionlist)
Description:
append the path of sections to the SectionList object argument.

RangeVarPlot.color()
Syntax:
rvp.color(index)
Description:
Change the color property. To see the change on an already plotted RangeVarPlot in a Graph, the Graph should be flush()ed.

RangeVarPlot.to_vector()
Syntax:

rvp.to_vector(yvec)

rvp.to_vector(yvec, xvec)

Description:
Copy the range variable values to the Vector() yvec. yvec is resized to the number of range points. If the second arg is present then the locations are copied to xvec. A plot of yvec.line(g, xvec) would be identical to a plot using g.addobject(rvp).

RangeVarPlot.from_vector()
Syntax:
rvp.from_vector(yvec)
Description:
Copy the values in yvec to the range variables along the rvp path. The size of the vector must be consistent with rvp.