.. _pltshape_doc: PlotShape --------- .. class:: PlotShape Class for making a Shape window useful for coloring a shape according to a variable value and creating time and space graphs of a variable. The default variable is *v*. The first arg may be a SectionList. ---- .. method:: PlotShape.plot Syntax: ``ps.plot(matplotlib_object)`` Description: In NEURON 7.7+, PlotShape.plot works both with and without Interviews support. Variables, sectionlists, and scale are supported. Clicking on a segment displays the value and the segment id. Extra arguments and keyword arguments are passed to the underlying graphics library (currently only matplotlib ``Figure`` objects and ``pyplot`` are supported). .. note:: If Interviews is enabled, the flag ``False`` must be passed to the ``h.PlotShape`` constructor to avoid additionally displaying a PlotShape using Interviews graphics. See the example: Example: If no seclist argument is provided, PlotShape.plot will plot all sections .. code-block:: python from neuron import h from matplotlib import pyplot h.load_file('c91662.ses') # a morphology file for sec in h.allsec(): if 'apic' in str(sec): sec.v = 0 ps = h.PlotShape(False) # False tells h.PlotShape not to use NEURON's gui ps.plot(pyplot) pyplot.show() .. note:: In Jupyter, you can use %matplotlib notebook to get interactive PlotShape Example: You can also pass in a SectionList argument to only plot specific sections .. code-block:: python from neuron import h from matplotlib import pyplot, cm h.load_file('c91662.ses') sl = h.SectionList([sec for sec in h.allsec() if 'apic' in str(sec)]) for sec in sl: sec.v = 0 ps = h.PlotShape(sl, False) ps.scale(-80, 40) ps.variable('v') ax = ps.plot(pyplot, cmap=cm.jet) pyplot.show() ---- .. method:: PlotShape.scale Syntax: ``.scale(low, high)`` Description: Sets blue and red values for the color scale and default axes for time and space plots. ---- .. method:: PlotShape.view .. seealso:: :meth:`Shape.view` ---- .. method:: PlotShape.size .. seealso:: :meth:`Shape.size` ---- .. method:: PlotShape.view_count .. seealso:: :meth:`Shape.view_count` ---- .. method:: PlotShape.show .. seealso:: :meth:`Shape.show` ---- .. method:: PlotShape.flush .. seealso:: :meth:`Shape.flush` ---- .. method:: PlotShape.fastflush Syntax: ``shapeplot.fastflush()`` Description: Speeds up drawing of :meth:`PlotShape.hinton` elements. ---- .. method:: PlotShape.variable Syntax: ``.variable("rangevar")`` Description: Range variable (v, m_hh, etc.) to be used for time, space, and shape plots. ---- .. method:: PlotShape.save_name .. seealso:: :meth:`Shape.save_name` ---- .. method:: PlotShape.unmap .. seealso:: :meth:`Shape.unmap` ---- .. method:: PlotShape.printfile .. seealso:: :meth:`Shape.printfile` ---- .. method:: PlotShape.menu_action .. seealso:: :meth:`Graph.menu_action` ---- .. method:: PlotShape.menu_tool .. seealso:: :meth:`Shape.menu_tool` ---- .. method:: PlotShape.observe .. seealso:: :meth:`Shape.observe` ---- .. method:: PlotShape.nearest .. seealso:: :meth:`Shape.nearest` ---- .. method:: PlotShape.push_selected .. seealso:: :meth:`Shape.push_selected` ---- .. method:: PlotShape.exec_menu .. seealso:: :meth:`Graph.exec_menu` ---- .. method:: PlotShape.erase .. seealso:: :meth:`Graph.erase` ---- .. method:: PlotShape.erase_all Description: Erases everything in the PlotShape, including all Sections and hinton plots .. seealso:: :meth:`Graph.erase_all`, :meth:`PlotShape.observe`, :meth:`PlotShape.hinton` ---- .. method:: PlotShape.beginline .. seealso:: :meth:`Graph.beginline` ---- .. method:: PlotShape.line .. seealso:: :meth:`Graph.line` ---- .. method:: PlotShape.mark Syntax: ``ps = h.PlotShape(False)`` ``ps.plot(pyplot).mark(h.soma[0](0.5)).mark(h.apical_dendrite[68](1))`` ``plt.show`` Description: Above syntax is allowed in NEURON 7.7+, for older versions: .. seealso:: :meth:`Graph.mark` ---- .. method:: PlotShape.label .. seealso:: :meth:`Graph.label` ---- .. method:: PlotShape.color Syntax: ``shape.color(i, sec=sec)`` Description: colors the specified section according to color index (index same as specified in Graph class). If there are several sections to color it is more efficient to make a SectionList and use \ ``.color_list`` ---- .. method:: PlotShape.color_all Syntax: ``.color_all(i)`` Description: colors all the sections ---- .. method:: PlotShape.color_list Syntax: ``.color_list(SectionList, i)`` Description: colors the sections in the list ---- .. method:: PlotShape.colormap Syntax: ``s.colormap(size, [global = 0])`` ``s.colormap(index, red, green, blue)`` Description: If the optional global argument is 1 then these functions refer to the global (default) Colormap and a change will affect all PlotShape instances that use it. Otherwise these function create a colormap that is local to this PlotShape. With a single argument, destroys the old and creates a new colormap for shape plots with space for size colors. All colors are initialized to gray. The four argument syntax, specifies the color of the index element of the colormap. the red, green, and blue must be integers within the range 0-255 and specify the intensity of these colors. If an existing colormap is displayed in the view, it will be redrawn with the proper colors when :meth:`PlotShape.scale` is called. ---- .. method:: PlotShape.hinton Syntax: ``s.hinton(_ref_varname, x, y, size)`` ``s.hinton(_ref_varname, x, y, xsize, ysize)`` Description: A filled square or rectangle is drawn with center at (x, y) and edge length given by size. The color depends on the :meth:`PlotShape.colormap` and :meth:`PlotShape.scale` and is redrawn on :meth:`PlotShape.flush`. If there are many of these elements then :meth:`PlotShape.fastflush` can speed plotting by up to a factor of 4 if not too many elements change color between fastflush calls. Example: .. code-block:: python from neuron import h, gui soma = h.Section() sl = h.SectionList() s = h.PlotShape(sl) s.colormap(3) s.colormap(0, 255, 0, 0) s.colormap(1, 255, 255, 0) s.colormap(2, 200, 200, 200) s.scale(0, 2) nx = 30 ny = 30 vec = h.Vector(nx*ny) vec.fill(0) for i in range(nx): for j in range(ny): s.hinton(vec._ref_x[i*ny + j], float(i)/nx, float(j)/ny, 1./nx) s.size(-.5, 1, 0, 1) s.exec_menu("Shape Plot") r = h.Random() r.poisson(.01) h.doNotify() def p(): for i in range(1,1001): vec.setrand(r) s.fastflush() # faster by up to a factor of 4 h.doNotify() h.startsw() p() print(h.stopsw()) ---- .. method:: PlotShape.len_scale Syntax: ``shape.len_scale(scl, sec=sec)`` Description: See :meth:`Shape.len_scale` ---- .. method:: PlotShape.rotate Syntax: ``shape.rotate()`` ``shape.rotate(xorg, yorg, zorg, xrad, yrad, zrad)`` Description: See :meth:`Shape.rotate`