/** Test of evaluateAt method, of class ParameterisedGroup. */
@Test
public void testEvaluateAt() throws ParameterException {
System.out.println("--- testEvaluateAt...");
// SegmentLocation loc1 = new PostSynapticTerminalLocation(d2.getSegmentId(), 0.5f);
assertEquals(0.5, pg1.evaluateAt(cell, d2, 0.5f), 0);
assertEquals(15, pg2.evaluateAt(cell, d2, 0.5f), 0);
//////// assertEquals(15, pg5.evaluateAt(cell, loc1), 0);
// SegmentLocation loc2 = new PostSynapticTerminalLocation(d3.getSegmentId(), 0.5f);
assertEquals(5d / 6d, pg1.evaluateAt(cell, d3, 0.5f), 1e-7);
assertEquals(25, pg2.evaluateAt(cell, d3, 0.5f), 0);
assertEquals(0.5, pg3.evaluateAt(cell, d3, 0.5f), 0);
assertEquals(0, pg4.evaluateAt(cell, d3, 0), 0);
assertEquals(5, pg4.evaluateAt(cell, d3, 0.5f), 0);
SegmentLocation sl1 = new SegmentLocation(d3.getSegmentId(), 0.5f);
assertEquals(
25,
pg5.evaluateAt(cell, cell.getSegmentWithId(sl1.getSegmentId()), sl1.getFractAlong()),
0);
assertEquals(30, pg5.evaluateAt(cell, d3, 1), 0);
GenesisCompartmentalisation g = new GenesisCompartmentalisation();
Cell gCell = g.getCompartmentalisation(cell);
System.out.println(CellTopologyHelper.printDetails(cell, null));
System.out.println(
"Changed from morph: " + cell.getMorphSummary() + ", to morph: " + gCell.getMorphSummary());
System.out.println("getSegmentMapper: " + g.getSegmentMapper());
System.out.println(CellTopologyHelper.printDetails(gCell, null));
SegmentLocation sl1_g = g.getSegmentMapper().mapSegmentLocation(sl1);
System.out.println("Mapped: " + sl1 + " to " + sl1_g);
assertEquals(
25,
pg5.evaluateAt(gCell, gCell.getSegmentWithId(sl1_g.getSegmentId()), sl1_g.getFractAlong()),
0);
}
public static void main(String[] args) {
RectangularBox rb = new RectangularBox();
System.out.println("Created: " + rb);
Point3f p = new Point3f(95, 18f, 98);
System.out.println("Moved: " + rb.getTranslatedRegion(new Vector3f(p)));
System.out.println("Sphere around: " + RectangularBox.getEnclosingSphere(rb));
SimpleCell cell = new SimpleCell("fff");
Vector3f origLoc = new Vector3f(cell.getFirstSomaSegment().getStartPointPosition());
origLoc.scale(-1);
CellTopologyHelper.translateAllPositions(cell, origLoc);
System.out.println("Cell: " + CellTopologyHelper.printShortDetails(cell));
System.out.println("Is point: " + p + " in region: " + rb.isCellWithinRegion(p, cell, true));
}
protected Point3f generateNextPosition() throws CellPackingException {
Point3f proposedPoint = null;
logger.logComment(
"---- Generating next position. positionsAlreadyTaken.size() = "
+ getNumPosAlreadyTaken());
float minXLoc, minYLoc, minZLoc, maxXLoc, maxYLoc, maxZLoc;
if (mustBeCompletelyInsideRegion()) {
// limit the extent for possible location of soma centre to box which
// will preclude soma wall impacting region boundary.
minXLoc = myRegion.getLowestXValue() - CellTopologyHelper.getMinXExtent(myCell, true, false);
minYLoc = myRegion.getLowestYValue() - CellTopologyHelper.getMinYExtent(myCell, true, false);
minZLoc = myRegion.getLowestZValue() - CellTopologyHelper.getMinZExtent(myCell, true, false);
maxXLoc = myRegion.getHighestXValue() - CellTopologyHelper.getMaxXExtent(myCell, true, false);
maxYLoc = myRegion.getHighestYValue() - CellTopologyHelper.getMaxYExtent(myCell, true, false);
maxZLoc = myRegion.getHighestZValue() - CellTopologyHelper.getMaxZExtent(myCell, true, false);
} else {
// in this case the soma centre can be anywhere inside the region..
minXLoc = myRegion.getLowestXValue();
minYLoc = myRegion.getLowestYValue();
minZLoc = myRegion.getLowestZValue();
maxXLoc = myRegion.getHighestXValue();
maxYLoc = myRegion.getHighestYValue();
maxZLoc = myRegion.getHighestZValue();
}
Point3f startPoint = new Point3f(minXLoc, minYLoc, minZLoc);
logger.logComment("minXLoc: " + minXLoc + ", maxXLoc: " + maxXLoc);
if (maxXLoc - minXLoc < 0 || maxYLoc - minYLoc < 0 || maxZLoc - minZLoc < 0) {
throw new CellPackingException("Diameter of cell is smaller than region");
}
if (getNumPosAlreadyTaken() >= getNumberCells()) {
throw new CellPackingException("All cells successfully placed");
}
if (getNumberCells() == 0) {
throw new CellPackingException("Cell number set to zero!!");
} else if (getNumberCells() == 1) {
if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_X) {
proposedPoint = new Point3f((minXLoc + maxXLoc) / 2, minYLoc, minZLoc);
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Y) {
proposedPoint = new Point3f(minXLoc, (minYLoc + maxYLoc) / 2, minZLoc);
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Z) {
proposedPoint = new Point3f(minXLoc, minYLoc, (minZLoc + maxZLoc) / 2);
}
} else {
// Point3f lastPositionedPoint = getLastPosTaken();
if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_X) {
float distanceApart = (maxXLoc - minXLoc) / (getNumberCells() - 1);
proposedPoint = new Point3f(startPoint);
proposedPoint.add(new Point3f(distanceApart * numProposedPoints, 0, 0));
logger.logComment(
"Placing one of "
+ getNumberCells()
+ " cells in x dim..."
+ distanceApart
+ " apart, new: "
+ proposedPoint
+ ", already proposed: "
+ numProposedPoints);
if (proposedPoint.x > maxXLoc) throw new CellPackingException("Reached end of x dimension");
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Y) {
logger.logComment("Placing cell in y dim...");
float distanceApart = (maxYLoc - minYLoc) / (getNumberCells() - 1);
proposedPoint = new Point3f(startPoint);
proposedPoint.add(new Point3f(0, distanceApart * numProposedPoints, 0));
if (proposedPoint.y > maxYLoc) throw new CellPackingException("Reached end of y dimension");
} else if (parameterList[DIMENSION_PARAM].value == DIMENSION_PARAM_Z) {
logger.logComment("Placing cell in z dim...");
float distanceApart = (maxZLoc - minZLoc) / (getNumberCells() - 1);
proposedPoint = new Point3f(startPoint);
proposedPoint.add(new Point3f(0, 0, distanceApart * numProposedPoints));
if (proposedPoint.z > maxZLoc) throw new CellPackingException("Reached end of z dimension");
}
if (proposedPoint == null) throw new CellPackingException("Cannot successfully place cell.");
}
// lastProposedPoint = new Point3d(proposedPoint);
numProposedPoints++;
return new Point3f(proposedPoint);
}
public static void main(String[] args) {
GolgiCell g = new GolgiCell("Test golgi");
System.out.println(CellTopologyHelper.printDetails(g, null));
}