MoveText       Section        SpacePlot      
   PlotWhat       ShapePlot      TimePlot       
   Rotate3D       ShapeStyle     VariableScale  
A picture of all the sections in a scene. This is designed for use with 3-d reconstructions in which the 3-d shape is not usually tampered with. However it can also be used with stylized neurons with the following caveat: If you do invoke a shape scene with a stylized neuron, the system will impose its own 3-d information on those sections consistent with the current connections, diam, and L values of the sections.

Note: when define_shape is called, 3d info for sections that were not cleared is translated in order to appear connected to its parent.


It is a vestigial menu item for PlotShape's and does nothing. In Shape it selects the tool for calling various actions when clicking on a part of the shape.


Dragging rotates about an axis in the view plane that is perpendicular to the direction of mouse movement. During rotation the schematic style is used to give decent performance. During a rotation a 3-d axis appears indicating the direction of view. At this time rotations are about the origin at (0,0,0). Because rotations are non commutative, returning to the original position will not return you to the original orientation. However, WHILE THE MOUSE IS PRESSED, you can use various keys to impose fixed rotations.

z or space: returns to the original xy-plane view with model z-axis out of the screen.

x : model x-axis into screen.

y or a: model y-axis into screen (the a is near the shift and control keys and its a difficult reach to use y sometimes).

X,Y,Z,A : rotate about the indicated (view) axis by 10 degrees.

^X,^Y,^Z,^A : rotate in the opposite direction by 10 degrees. The repeat key property during a key press causes the appearance of a rotational velocity.


Show Diam: Shape is drawn using trapezoids between 3-d points. If the view is large and the diameters small not all of them may appear. (slowest)

Centroid: Shape is drawn as lines between 3-d points.

Schematic: Shape is drawn as line between first and last 3-d point of each section. (fastest)


The default plot variable is v. A browser pops up with all the range variables that can be plotted as a function of position on the shape. At this time only range variables can be plotted, not arbitrary functions. The PlotShape scene has a label indicating the chosen variable. A small bug prevents label from being updated since it is occluded by the dialog box. Refreshing (or any other drawing action) will update the label.


A field editor dialog pops up. Enter the scale as two space separated numbers (first less than the second). This range scale is used for the color scale. Purple is the first number, yellow is the second number, and 20 colors in between are intermediate values. This scale is also used to construct the default y axis for time and space plots of the variable.


Press a location on the shape and a graph will be created in which the range variable at that location will be plotted. You can select several locations to add more plots to the graph. The sections selected are highlighted in different colors. A new graph will be created if you select another tool and then come back to this one.


Press the left mouse button at one location and drag the mouse to another location on the cell. A graph will be created which contains a range variable plot between the two selected locations. (Actually the nearest ends (arc position 0 or 1) of the sections of the selected locations. The path is highlighted). A range variable plot is like a movie. The variable plotted does not have to exist at each section in the path. It is plotted as 0 where it does not exist. (Range variables, except v, do not exist at arc positions 0 and 1. At these points the value plotted is that just interior to the section.)


A color scale is used to show the value of the variable on the shape. Purple is low, yellow is high. The colorbar appears in the top left part of the view when you are in this mode. To change its location, back to the top left, manipulate the view then toggle to another plot style and back to shape or else change the scale. Performance could be better.


Drag the variable label to another location.

neuron/agui/pltshape.hel : May 13 2012