Class for making a Shape window for executing a user defined action when a section is clicked on. (When the section mode is selected from the mouse menu.) An argument of 0 will prevent default mapping of the window. If the first arg is a :class:`SectionList` (then a second arg of 0 will prevent default mapping) then only the sections in the list are drawn. Shape is redrawn automatically whenever length or diameter of a section changes.
Warning
The form of the constructor that takes a :class:`SectionList` does not currently work in Python.
.. method:: Shape.view
Syntax:
``.view(mleft, mbottom, mwidth, mheight, sleft, stop, swidth, sheight)``
Description:
maps a view of the Shape scene. m stands for model coordinates,
s stands for screen pixel coordinates where 0,0 is the top left
corner of the screen.
.. method:: Shape.size
Syntax:
``.size(mleft, mright, mbottom, mtop)``
``...``
Description:
Model coordinates for the scene.
This is the "whole scene" size.
Since, the aspect ratio for shape views is unity, the bounding box expressed
by the arguments may not fit exactly on the screen window. The scale factor
is decreased so that the first view window displays the entire bounding box
with the center of the bounding box in the center of the view.
See :meth:`Graph.size` for other, more rarely use argument sequences.
.. method:: Shape.show
Syntax:
``shape.show(mode)``
Description:
mode = 0
displays diameters
mode = 1
displays centroid. ie line through all the 3d points.
mode = 2
displays schematic. ie line through 1st and last 2d points of each
section.
.. method:: Shape.flush
Syntax:
``.flush()``
Description:
Redraws all views into this scene.
.. method:: Shape.observe
Syntax:
``shape.observe()``
``shape.observe(sectionlist)``
Description:
Replace the list of observed sections in the Shape with the specified
list. With no arguments, all sections are observed.
Example:
In the context of the pyramidal cell demo of neurondemo (launch via
``neurondemo --python``) the following
will change the Shape shown in the point process manager
to show only the soma and the main part of the primary dendrite.
.. code-block::
python
from neuron import h
sl = h.SectionList()
sl.append(h.soma)
sl.append(h.dendrite_1[8])
h.Shape[0].observe(sl)
.. method:: Shape.view_count
Syntax:
``.view_count()``
Description:
Returns number of views into this scene. (stdrun.hoc removes
scenes from the \ ``flush_list`` and \ ``graphList[]`` when this goes to
0. If no other \ ``objectvar`` points to the scene, it will be
freed.)
.. method:: Shape.select
Syntax:
``.select(sec=section)``
Description:
Colors red the specified section.
.. method:: Shape.action
Syntax:
``.action("command")``
Description:
command is executed whenever the user clicks on a section.
The clicked section is pushed before execution and popped after.
\ :data:`hoc_ac_` contains the arc position 0 - 1 of the nearest node.
.. method:: Shape.color
Syntax:
``shape.color(i, sec=section)``
Description:
colors the specified section according to color index
(index same as specified in :class:`Graph` class). If there are several
sections to color it is more efficient to make a :class:`SectionList` and
use \ ``.color_list``
.. method:: Shape.color_all
Syntax:
``.color_all(i)``
Description:
colors all the sections
.. method:: Shape.color_list
Syntax:
``.color_list(SectionList, i)``
Description:
colors the sections in the list
.. method:: Shape.point_mark
Syntax:
``.point_mark(objvar, colorindex)``
``.point_mark(objvar, colorindex, style)``
``.point_mark(objvar, colorindex, style, size)``
Description:
draw a little filled circle with indicated color where the point process
referenced by \ ``objvar`` is located. Note, if you subsequently relocate
the point process or destroy it the proper thing will happen to the
mark. (at least after a flush)
The optional arguments specify the style and size as in the
:meth:`Graph.mark` method of :class:`Graph`. This extension was contributed
by Yichun Wei ``yichunwe@usc.edu``.
.. method:: Shape.point_mark_remove
Syntax:
``.point_mark_remove([objvar])``
Description:
With no arg, removes all the point process marks.
.. method:: Shape.save_name
Syntax:
``.save_name("name")``
Description:
The \ ``objectvar`` used to save the scene when the print window
manager is used to save a session.
.. method:: Shape.unmap
Syntax:
``.unmap()``
Description:
dismisses all windows that are a direct view into this scene.
(does not unmap boxes containing scenes.) \ ``unmap`` is called
automatically when no hoc object variable references the Shape.
.. method:: Shape.printfile
Syntax:
``.printfile("filename")``
Description:
prints the first view of the graph as an encapsulated post script
file
.. method:: Shape.menu_action
.. seealso::
:meth:`Graph.menu_action`
.. method:: Shape.exec_menu
.. seealso::
:meth:`Graph.exec_menu`
.. method:: Shape.erase
.. seealso::
:meth:`Graph.erase`
.. method:: Shape.erase_all
Description:
Erases everything in the Shape, including all PointMarks and Sections.
.. seealso::
:meth:`Graph.erase_all`, :meth:`Shape.observe`, :meth:`Shape.point_mark`
.. method:: Shape.beginline
.. seealso::
:meth:`Graph.beginline`
.. method:: Shape.line
.. seealso::
:meth:`Graph.line`
.. method:: Shape.mark
.. seealso::
:meth:`Graph.mark`
.. method:: Shape.label
.. seealso::
:meth:`Graph.label`
.. method:: Shape.menu_tool
Syntax:
``s.menu_tool("label", "procname")``
Description:
Same as :meth:`Graph.menu_tool` for the :func:`Graph` class. When procname is
called it is given four arguments: type, x, y, keystate. Type = 1,2,3 means
move, press, release respectively and x and are in model coordinates.
Keystate reflects the
state of control (bit 1), shift (bit 2), and meta (bit 3) keys, ie
control and shift down has a value of 3.
.. seealso::
:meth:`Graph.menu_tool`, :meth:`Shape.nearest`, :meth:`Shape.push_selected`
Example:
The following example will work if executed in the context of the
pyramidal cell demo of the neurondemo. It colors red the section
you click nearest and prints the name and position of the selected section
as well as the mouse distance the selection.
.. code-block::
python
from neuron import h
ss = h.Shape[0]
def p(type, x, y, keystate):
if type == 2:
ss.color_all(1)
d = ss.nearest(x, y)
arc = ss.push_selected()
if arc >= 0:
ss.select()
print('%g from %s(%g)' % (d, h.secname(), a))
h.pop_section()
ss.menu_tool('test', p)
ss.exec_menu('test')
.. method:: Shape.nearest
Syntax:
``d = shape.nearest(x, y)``
Description:
returns the distance (in model coordinates) to the nearest section.
The section becomes the selected section of the Shape. It is NOT
pushed onto the section stack and it is NOT colored. The nearest
arc position of the selected section as well
as the section is available from :func:`push_section`.
.. method:: Shape.push_selected
Syntax:
.. code-block::
python
arc = shape.push_selected()
if arc >= 0:
# do something, then end with:
h.pop_section()
Description:
If there is a selection for the Shape class, then it is pushed onto
the section stack (becomes the currently accessed section) and the
arc position (0 to 1) returned. If no section is selected the function
returns -1 and no section is pushed.
.. note::
The pushed section can be read via ``h.cas()``.
.. note::
It is important that a :func:`pop_section` be executed if a section
is pushed onto the stack.
.. warning::
The arc position is relevant only if the section was selected using
:meth:`Shape.nearest`. Note, e.g., that :meth:`Shape.select` does not
set the arc position.
.. method:: Shape.len_scale
Syntax:
``shape.len_scale(scl, sec=section)``
Description:
The drawing of the section length (for the specified section) in the Shape
scene is scaled by the factor. Diameter is drawn normally.
Note that this does not change the physical length of the section but
only its appearance in this Shape instance.
.. method:: Shape.rotate
Syntax:
``shape.rotate()``
``shape.rotate(xorg, yorg, zorg, xrad, yrad, zrad)``
Description:
With no args the view is in the xy plane.
With args, incrementally rotate about the indicated origin by the
amount given in radians around the current view coordinates (order is
sequentially about x,y,z axes)