Developer Information: SpineCreator Annotations and Project file

SpineCreator Annotations

SpineCreator stores information about the 2D layout of networks, the 3D layout of neurons, the 2D routing of inputs and projections, and python scripts used to generate some ConnectionList data, as Annotations using the new SpineML Annotations tags. Annotations about an object (population/projection etc…) are stored inside that tag, and SpineCreator will respect existing Annotations in the tags it modifies. In order for other software to be built that can utilise the SpineCreator information we present a guide to the tags and information that can be stored in Annotations through SpineCreator.

Population

An annotations tag within a Population stores the following information.

  <LL:Annotation>
    <SpineCreator>
      <xPos value="-11.2353"/>
      <yPos value="12.5792"/>
      <animSpeed value="0.2"/>
      <aspectRatio value="1.66667"/>
      <colour red="0" green="0" blue="0"/>
      <size value="1"/>
      <tag value="2"/>
      <x3D value="0"/>
      <y3D value="0"/>
      <z3D value="0"/>
      <is_visualised value="0"/>
    </SpineCreator>
  </LL:Annotation>

xPos

Contains	Description
@value::float	The 2D X position of the Population

yPos

Contains	Description
@value::float	The 2D Y position of the Population

animSpeed

Contains	Description
@value::float	The speed that a moved Population follows the mouse cursor

aspectRatio

Contains	Description
@value::float	The ratio of the width to the height of the Population icon

colour

Contains	Description
@red::unit	The red component of the Population icon colour (0:255)
@green::unit	The green component of the Population icon colour (0:255)
@blue::unit	The blue component of the Population icon colour (0:255)

size

Contains	Description
@value::float	The size of the Population icon

tag

Contains	Description
@value::int	Not currently used by SpineCreator

x3D

Contains	Description
@value::int	The initial 3D X offset for drawing the neurons in the Population in 3D space

y3D

Contains	Description
@value::int	The initial 3D Y offset for drawing the neurons in the Population in 3D space

z3D

Contains	Description
@value::int	The initial 3D Z offset for drawing the neurons in the Population in 3D space

Projection

An annotations tag within a Projection stores the following information.

  <LL:Annotation>
    <SpineCreator>
      <DrawOptions style="0" showlabel="0"/>
      <start x="9.27878" y="7.23497"/>
      <curves>
        <curve>
          <C1 xpos="9.4914" ypos="7.23497"/>
          <C2 xpos="9.4914" ypos="7.22533"/>
          <end xpos="9.56297" ypos="7.22533"/>
        </curve>
      </curves>
    </SpineCreator>
  </LL:Annotation>

DrawOptions

Contains	Description
@style::int	Identifies the style used to draw the Projection in SpineCreator
@showlabel::bool	Used to indicate if a label describing the Projection type should be displayed

start

Contains	Description
@x::float	The X start point of the bezier curves used to describe the 2D form of the Projection
@y::float	The Y start point of the bezier curves used to describe the 2D form of the Projection

curves

Contains	Description
curve [1:…]	Container for the bezier curve points used to describe the 2D form of the Projection

curve

Contains	Description
C1 [1]	Bezier cubic curve C1 control point (See Qt documentation for QPainterPath::cubicTo for more details)
C2 [1]	Bezier cubic curve C2 control point (See Qt documentation for QPainterPath::cubicTo for more details)
end [1]	Bezier cubic curve end point (See Qt documentation for QPainterPath::cubicTo for more details)

C1

Contains	Description
@xpos::float	X location of C1 bezier point
@ypos::float	Y location of C1 bezier point

C2

Contains	Description
@xpos::float	X location of C2 bezier point
@ypos::float	Y location of C2 bezier point

end

Contains	Description
@xpos::float	X location of end bezier point
@ypos::float	Y location of end bezier point

Input

An annotations tag within a Input stores the following information.

  <LL:Annotation>
    <SpineCreator>
      <start x="9.21702" y="5.48872"/>
      <curves>
        <curve>
          <C1 xpos="8.94197" ypos="6.10971"/>
          <C2 xpos="8.94197" ypos="6.10971"/>
          <end xpos="8.66691" ypos="6.7307"/>
        </curve>
      </curves>
    </SpineCreator>
  </LL:Annotation>

For descriptions of these tags please refer to the Projection section

ConnectionList

An annotations tag within a ConnectionList stores the following information.

  <SpineCreator>
    <Script text="#!/usr/bin/python&#10;&#10;#PARNAME=size #LOC=1,1&#10;#PARNAME=scale #LOC=2,1&#10;#PARNAME=inhib #LOC=3,1&#10;#HASWEIGHT&#10;&#10;def connectionFunc( srclocs, dstlocs, size, scale, inhib ): &#10;..."/>
    <Config weightProperty="w"/>
  </SpineCreator>

Script

Contains	Description
@text:string	The text describing a script for generating a ConnectionList of connectivity

Config

Contains	Description
@weightProperty:string	A reference to the WeightUpdate Property name where an ExplictList is created by the Python script

SpineCreator Project file

SpineCreator stores the details of the xml files that compose the current Project in a file with the .proj extension. The format of this files is as follows:

<SpineCreatorProject>
 <Network>
  <File name="model.xml"/>
 </Network>
 <Components>
  <File name="LIN_adap.xml"/>
  <File name="LIF_det.xml"/>
  <File name="LIF_det1.xml"/>
  <File name="LIFposneg.xml"/>
  <File name="LIF1.xml"/>
 </Components>
 <Layouts>
  <File name="none.xml"/>
  <File name="hexagonal.xml"/>
 </Layouts>
 <Experiments>
  <File name="experiment0.xml"/>
  <File name="experiment1.xml"/>
 </Experiments>
 <AdditionalFiles>
  <File name="luminances.json"/>
  <File name="external.xsl"/>
 </AdditionalFiles>
</SpineCreatorProject>

SpineCreatorProject

Contains	Description
Network [1]	Contains the SpineML Network for the project
Conponents [1]	Contains the SpineML Components for the project
Layouts [1]	Contains the SpineML Layouts for the project
Experiments [1]	Contains the SpineML Experiments for the project
AdditionalFiles [1]	List of non-SpineML files for the project

Network

Contains	Description
File [1]	The network file name

Components

Contains	Description
File [1:…]	The component file names

Layouts

Contains	Description
File [1:…]	The layout file names

Experiments

Contains	Description
File [1:…]	The experiment file names

AdditionalFiles

Contains	Description
File [1:…]	Additional file name

File

Contains	Description
@name:string	The name of a file

SpineML The Spiking Neural Mark-up Language