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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
Field Summary | |
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private java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> |
featureLines
Borderlines that separate the neurite from the soma and additionally separate the neurite from its growth cone. |
private java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> |
featurePoints
Features of the single neurite branches. |
private MTBRegion2DSet |
growthCones
Neurite corresponding growth cone regions as MTBRegion2D objects. |
private int |
maxSpineLength
Given maximum lengths for definition of spines. |
private MTBNeuriteSkelGraph |
neuriteGraph
Neurite skeleton Graph (NSG) of the current neurite. |
private MTBRegion2D |
neuriteRegion
Neurite corresponding region as MTBRegion2D object. |
private MTBRegion2D |
neuriteShaft
Neurite corresponding neurite shaft region as MTBRegion2D object. |
private int[] |
neuriteShaftLengths
Lengths of the single branches of a neurite shaft. |
private java.util.Vector<java.util.Vector<java.lang.Double>> |
neuriteWidths
Average widths of the whole neurite, the neurite shaft and the growth cone. |
Constructor Summary | |
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MTBNeurite2D(MTBNeuriteSkelGraph _neuriteGraph,
java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> _featurePoints,
java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> _featureLines,
MTBRegion2D _neuriteRegion,
int _maxSpineLength,
int[] _neuriteShaftLengths,
java.util.Vector<java.util.Vector<java.lang.Double>> _neuriteWidths)
Constructor to generate a new neurite object. |
Method Summary | |
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boolean |
addData(java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> p,
java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> f,
int[] n,
java.util.Vector<java.util.Vector<java.lang.Double>> w)
Add data to the current neurite object. |
MTBImageByte |
drawLine2D(java.awt.geom.Line2D.Double line,
java.awt.geom.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. |
java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> |
getFeatureLines()
Get neurite corresponding feature lines of borders between soma and neurite shafts and neurite shafts and growth cones. |
java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> |
getFeaturePoints()
Get neurite corresponding feature points of borders between soma and neurite shafts and neurite shafts and growth cones. |
java.awt.geom.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). |
java.util.Vector<java.util.Vector<java.lang.Double>> |
getNeuriteWidths()
Get average widths of each neurite branch, including the average widths of the whole branches, the shafts and the growth cones. |
java.awt.geom.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(java.awt.Color regionColor)
Visualize the neurites skeleton graph as RGB image. |
MTBImageRGB |
toImage(MTBImageRGB rgbImage,
java.awt.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 |
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cloneProperties, getLocation, getProperty, getPropertyKeys, print, setLocation, setProperty |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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private java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> featureLines
private java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> featurePoints
private MTBRegion2DSet growthCones
private int maxSpineLength
private MTBNeuriteSkelGraph neuriteGraph
private MTBRegion2D neuriteRegion
private MTBRegion2D neuriteShaft
private int[] neuriteShaftLengths
private java.util.Vector<java.util.Vector<java.lang.Double>> neuriteWidths
Constructor Detail |
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public MTBNeurite2D(MTBNeuriteSkelGraph _neuriteGraph, java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> _featurePoints, java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> _featureLines, MTBRegion2D _neuriteRegion, int _maxSpineLength, int[] _neuriteShaftLengths, java.util.Vector<java.util.Vector<java.lang.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 |
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public boolean addData(java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> p, java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> f, int[] n, java.util.Vector<java.util.Vector<java.lang.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 MTBImageByte drawLine2D(java.awt.geom.Line2D.Double line, java.awt.geom.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.public double[] getAvgConeWidths()
public double[] getAvgNeuriteWidths()
public double[] getAvgShaftWidths()
public int getBrancheCount()
public int[] getBranchLengths()
public int[] getConeAreas()
public int[] getConeLengths()
public double[] getConeRoundness()
public int[] getConeSpineCount()
public int getDefinedSpineLength()
public int getEndCount()
public java.util.Vector<java.util.Vector<java.awt.geom.Line2D.Double>> getFeatureLines()
public java.util.Vector<java.util.Vector<java.awt.geom.Point2D.Double>> getFeaturePoints()
public java.awt.geom.Point2D.Double getfirstFeatureAt(int index)
public MTBRegion2DSet getGrowthConeRegions()
public MTBNeuriteSkelGraph getNeuriteGraph()
public MTBRegion2D getNeuriteRegion()
public int getNeuriteShaftArea()
public MTBRegion2D getNeuriteShaftRegion()
public java.util.Vector<java.util.Vector<java.lang.Double>> getNeuriteWidths()
public java.awt.geom.Point2D.Double getsecondFeatureAt(int index)
public int[] getShaftLengths()
public int getSpineCount()
public MTBImageRGB toImage(java.awt.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, java.awt.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 void updateRegions()
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