|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectde.unihalle.informatik.Alida.operator.ALDData
de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
public class MTBNeurite2D
Class for neurite objects. An neurite consists of its neurite skeleton graph (NSG), at least two feature lines, which are to borderlines to separate the soma from the neurite shaft and the neurite shaft from the growth cone(s). And there is a maximum spine (filopodia-like protrusions) length value that indicates, which paths of the neurite are spines. TODO updated comments about measurements
MTBNeuriteSkelGraph
Constructor Summary | |
---|---|
MTBNeurite2D(MTBNeuriteSkelGraph _neuriteGraph,
Vector<Vector<Point2D.Double>> _featurePoints,
Vector<Vector<Line2D.Double>> _featureLines,
MTBRegion2D _neuriteRegion,
int _maxSpineLength,
int[] _neuriteShaftLengths,
Vector<Vector<Double>> _neuriteWidths)
Constructor to generate a new neurite object. |
Method Summary | |
---|---|
boolean |
addData(Vector<Vector<Point2D.Double>> p,
Vector<Vector<Line2D.Double>> f,
int[] n,
Vector<Vector<Double>> w)
Add data to the current neurite object. |
MTBImageByte |
drawLine2D(Line2D.Double line,
Point2D.Double point,
MTBImageByte tmpNeuronImg)
Draws a 2D line into the neuron image. |
double[] |
getAvgConeWidths()
Get average widths of each neurite growth cone. |
double[] |
getAvgNeuriteWidths()
Get average widths of each complete neurite branch. |
double[] |
getAvgShaftWidths()
Get average widths of each neurite shaft. |
int |
getBrancheCount()
Get number of neurite branches. |
int[] |
getBranchLengths()
Get lengths of neurite branches along the complete neurite skeleton graph. |
int[] |
getConeAreas()
Get areas of growth cone regions. |
int[] |
getConeLengths()
Get length of the growth cone region along the neurite skeleton graph without neurite shaft areas. |
double[] |
getConeRoundness()
Get roundness of growth cone regions, 1 means a perfect circle. |
int[] |
getConeSpineCount()
Get number of spines (filopodia-like protrusions) per growth cones. |
int |
getDefinedSpineLength()
Get length to define a neurite branch as spine (filopodia-like protrusions). |
int |
getEndCount()
Get number of end points. |
Vector<Vector<Line2D.Double>> |
getFeatureLines()
Get neurite corresponding feature lines of borders between soma and neurite shafts and neurite shafts and growth cones. |
Vector<Vector<Point2D.Double>> |
getFeaturePoints()
Get neurite corresponding feature points of borders between soma and neurite shafts and neurite shafts and growth cones. |
Point2D.Double |
getfirstFeatureAt(int index)
Get first feature of neurite corresponding feature points from borders between soma and neurite shafts. |
MTBRegion2DSet |
getGrowthConeRegions()
Get regions of the separated growth cones. |
MTBNeuriteSkelGraph |
getNeuriteGraph()
Get neurite corresponding skeleton graph. |
MTBRegion2D |
getNeuriteRegion()
Get neurite corresponding region. |
int |
getNeuriteShaftArea()
Get area of neurite shaft region (without growth cone). |
MTBRegion2D |
getNeuriteShaftRegion()
Get neurite shaft region (without growth cone). |
Vector<Vector<Double>> |
getNeuriteWidths()
Get average widths of each neurite branch, including the average widths of the whole branches, the shafts and the growth cones. |
Point2D.Double |
getsecondFeatureAt(int index)
Get second feature of neurite corresponding feature points from borders between neurite shafts and growth cones. |
int[] |
getShaftLengths()
Get neurite shaft lengths of all branches without growth cone areas. |
int |
getSpineCount()
Get number of spines (filopodia-like protrusions). |
MTBImageRGB |
toImage(Color regionColor)
Visualize the neurites skeleton graph as RGB image. |
MTBImageRGB |
toImage(MTBImageRGB rgbImage,
Color regionColor)
Visualize the neurites skeleton graph in the given RGB image. |
void |
updateRegions()
Update neurite shaft and growth cone regions, due to changes of this regions by adding features or something else. |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDData |
---|
cloneProperties, getLocation, getProperty, getPropertyKeys, print, setLocation, setProperty |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public MTBNeurite2D(MTBNeuriteSkelGraph _neuriteGraph, Vector<Vector<Point2D.Double>> _featurePoints, Vector<Vector<Line2D.Double>> _featureLines, MTBRegion2D _neuriteRegion, int _maxSpineLength, int[] _neuriteShaftLengths, Vector<Vector<Double>> _neuriteWidths)
_neuriteGraph
- NSG of the current neurite_featurePoints
- vector of feature points_featureLines
- vector of feature lines_neuriteRegion
- 2D region of the neurite_maxSpineLength
- maximum spine (filopodia-like protrusions) length_neuriteShaftLengths
- array of neurite branch lengths_neuriteWidths
- average widths of neurite branches, shafts and growth cones for
the current neurite objectMethod Detail |
---|
public MTBNeuriteSkelGraph getNeuriteGraph()
public Vector<Vector<Point2D.Double>> getFeaturePoints()
public Point2D.Double getfirstFeatureAt(int index)
public Point2D.Double getsecondFeatureAt(int index)
public Vector<Vector<Line2D.Double>> getFeatureLines()
public MTBRegion2D getNeuriteRegion()
public boolean addData(Vector<Vector<Point2D.Double>> p, Vector<Vector<Line2D.Double>> f, int[] n, Vector<Vector<Double>> w)
p
- vector of feature points to addf
- vector of feature lines to addn
- array of neurite branch lengths to addw
- vector of average widths to add
public void updateRegions()
public MTBRegion2DSet getGrowthConeRegions()
public MTBRegion2D getNeuriteShaftRegion()
public int getNeuriteShaftArea()
public int[] getConeAreas()
public double[] getConeRoundness()
public int[] getConeSpineCount()
public int getDefinedSpineLength()
public int[] getBranchLengths()
public int[] getShaftLengths()
public int[] getConeLengths()
public Vector<Vector<Double>> getNeuriteWidths()
public double[] getAvgNeuriteWidths()
public double[] getAvgShaftWidths()
public double[] getAvgConeWidths()
public int getBrancheCount()
public int getSpineCount()
public int getEndCount()
public MTBImageRGB toImage(Color regionColor)
regionColor
- neurite region color in 3-element RGB array red[0], green[1],
blue[2], if null no regions are drawn
public MTBImageRGB toImage(MTBImageRGB rgbImage, Color regionColor)
rgbImage
- image to draw neurite intoregionColor
- neurite region color in 3-element RGB array red[0], green[1],
blue[2], if null no regions are drawn
public MTBImageByte drawLine2D(Line2D.Double line, Point2D.Double point, MTBImageByte tmpNeuronImg)
This function implements the Bresenham algorithm. Code was 'stolen' from
Wikipedia, http://de.wikipedia.org/wiki/Bresenham-Algorithmus
, and
then translated into Java (German comments where kept).
xstart
- x-coordinate of start point.ystart
- y-coordinate of start point.xend
- x-coordinate of end point.yend
- y-coordinate of end point.value
- Color/gray-scale value of the polygon.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |