Exemple #1
0
  private Segment addRelativeDendrite(Segment parent, Point3f relPosition) {
    Point3f newPosition = (new Point3f(parent.getEndPointPosition()));
    newPosition.add(relPosition);

    float newRadius = parent.getRadius() * .6f;

    String newName = "Dend_" + getOnlyDendriticSegments().size();

    Segment tempDend =
        addDendriticSegment(newRadius, newName, newPosition, parent, 1, newName + "_Sec", true);
    return tempDend;
  }
  public boolean isCellWithinRegion(Point3f point, Cell cell, boolean completelyInside) {
    logger.logComment("Checking point: " + point + " in: " + toString());

    float minXLoc, minYLoc, minZLoc;
    float maxXLoc, maxYLoc, maxZLoc;

    Segment firstSeg = cell.getFirstSomaSegment();

    if (completelyInside) logger.logComment("Cell needs to be completely inside");
    else
      logger.logComment(
          "Only cell centre (" + firstSeg.getStartPointPosition() + ") needs to be inside");

    int factor = 0;
    if (completelyInside) factor = 1;

    minXLoc = parameterList[0].value + factor * firstSeg.getSection().getStartRadius();
    minYLoc = parameterList[1].value + factor * firstSeg.getSection().getStartRadius();
    minZLoc = parameterList[2].value + factor * firstSeg.getSection().getStartRadius();
    maxXLoc =
        parameterList[0].value
            + parameterList[3].value
            - factor * firstSeg.getSection().getStartRadius();
    maxYLoc =
        parameterList[1].value
            + parameterList[4].value
            - factor * firstSeg.getSection().getStartRadius();
    maxZLoc =
        parameterList[2].value
            + parameterList[5].value
            - factor * firstSeg.getSection().getStartRadius();

    Point3f actualStartOfSoma =
        new Point3f(
            point.x + firstSeg.getSection().getStartPointPositionX(),
            point.y + firstSeg.getSection().getStartPointPositionY(),
            point.z + firstSeg.getSection().getStartPointPositionZ());

    logger.logComment(
        "actualStartOfSoma: "
            + actualStartOfSoma
            + ", radius: "
            + firstSeg.getSection().getStartRadius());

    if (actualStartOfSoma.x < minXLoc
        || actualStartOfSoma.x > maxXLoc
        || actualStartOfSoma.y < minYLoc
        || actualStartOfSoma.y > maxYLoc
        || actualStartOfSoma.z < minZLoc
        || actualStartOfSoma.z > maxZLoc) return false;

    if (completelyInside) {
      Vector somaSegments = cell.getOnlySomaSegments();

      for (int i = 0; i < somaSegments.size(); i++) {
        Segment nextSeg = (Segment) somaSegments.elementAt(i);

        Point3f actualEndPoint =
            new Point3f(
                point.x + nextSeg.getEndPointPositionX(),
                point.y + nextSeg.getEndPointPositionY(),
                point.z + nextSeg.getEndPointPositionZ());

        logger.logComment("actualEndPoint: " + actualEndPoint + ", radius: " + nextSeg.getRadius());

        if (actualEndPoint.x < parameterList[0].value + nextSeg.getRadius()
            || actualEndPoint.x
                > parameterList[0].value + parameterList[3].value - nextSeg.getRadius()
            || actualEndPoint.y < parameterList[1].value + nextSeg.getRadius()
            || actualEndPoint.y
                > parameterList[1].value + parameterList[4].value - nextSeg.getRadius()
            || actualEndPoint.z < parameterList[2].value + nextSeg.getRadius()
            || actualEndPoint.z
                > parameterList[2].value + parameterList[5].value - nextSeg.getRadius())
          return false;
      }
    }
    return true;
  }