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/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* CARET is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include "BorderFile.h"
#include "BorderProjectionFile.h"
#include "BorderProjectionUnprojector.h"
#include "BrainModelSurface.h"
#include "BrainSet.h"
#include "CellFileProjector.h"
#include "CommandSurfaceBorderIntersection.h"
#include "FileFilters.h"
#include "FociFile.h"
#include "FociProjectionFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandSurfaceBorderIntersection::CommandSurfaceBorderIntersection()
: CommandBase("-surface-border-intersection",
"SURFACE BORDER INTERSECTION")
{
}
/**
* destructor.
*/
CommandSurfaceBorderIntersection::~CommandSurfaceBorderIntersection()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceBorderIntersection::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Border Projection File", FileFilters::getBorderProjectionFileFilter());
paramsOut.addFile("Input Foci Projection File", FileFilters::getFociProjectionFileFilter());
paramsOut.addFile("Output Foci Projection File", FileFilters::getFociProjectionFileFilter());
paramsOut.addString("Border 1 Name");
paramsOut.addString("Border 2 Name");
paramsOut.addString("Focus Name");
paramsOut.addFloat("Intersection Tolerance", 3.0, 0.0, 100000.0);
}
/**
* get full help information.
*/
QString
CommandSurfaceBorderIntersection::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<coordinate-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<border-projection-file-name>\n"
+ indent9 + "<input-foci-projection-file-name>\n"
+ indent9 + "<output-foci-projection-file-name>\n"
+ indent9 + "<border-1-name>\n"
+ indent9 + "<border-2-name>\n"
+ indent9 + "<focus-name>\n"
+ indent9 + "<intersection-tolerance>\n"
+ indent9 + "\n"
+ indent9 + "Starting at the first border point in border 1, find the closest\n"
+ indent9 + "point in border 2. If the distance between these two border\n"
+ indent9 + "points is less than \"intersection-tolerance\", place a focus\n"
+ indent9 + "at this location. Otherwise, continue use successive points\n"
+ indent9 + "in border 1.\n"
+ indent9 + "\n"
+ indent9 + "The input foci projection file does not need to exist.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceBorderIntersection::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get parameters
//
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topologyFileName =
parameters->getNextParameterAsString("Topology File Name");
const QString borderProjectionFileName =
parameters->getNextParameterAsString("Border Projection File Name");
const QString inputFociProjectionFileName =
parameters->getNextParameterAsString("Input Foci Projection File Name");
const QString outputFociProjectionFileName =
parameters->getNextParameterAsString("Output Foci Projection File Name");
const QString border1Name =
parameters->getNextParameterAsString("Border 1 Name");
const QString border2Name =
parameters->getNextParameterAsString("Border 2 Name");
const QString focusName =
parameters->getNextParameterAsString("Focus Name");
const float intersectionTolerance =
parameters->getNextParameterAsFloat("Intersection Tolerance");
checkForExcessiveParameters();
//
// Create a brain set
//
BrainSet brainSet(topologyFileName,
coordinateFileName,
"",
true);
BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("unable to find surface.");
}
bms->setSurfaceType(BrainModelSurface::SURFACE_TYPE_FIDUCIAL); // need for projection to work
const TopologyFile* tf = bms->getTopologyFile();
if (tf == NULL) {
throw CommandException("unable to find topology.");
}
const int numNodes = bms->getNumberOfNodes();
if (numNodes == 0) {
throw CommandException("surface contains no nodes.");
}
//
// Read the border projection file
//
BorderProjectionFile borderProjectionFile;
borderProjectionFile.readFile(borderProjectionFileName);
//
// Find the borders
//
BorderProjection* bp1 = borderProjectionFile.getLastBorderProjectionByName(border1Name);
if (bp1 == NULL) {
throw CommandException("unable to find border named "
+ border1Name);
}
BorderProjection* bp2 = borderProjectionFile.getLastBorderProjectionByName(border2Name);
if (bp2 == NULL) {
throw CommandException("unable to find border named "
+ border2Name);
}
//
// Create another border projection file containing just the two borders
//
BorderProjectionFile tempBorderProjFile;
tempBorderProjFile.addBorderProjection(*bp1);
tempBorderProjFile.addBorderProjection(*bp2);
//
// Unproject the two borders
//
BorderFile borderFile;
BorderProjectionUnprojector unprojector;
unprojector.unprojectBorderProjections(*(bms->getCoordinateFile()),
tempBorderProjFile,
borderFile);
if (borderFile.getNumberOfBorders() != 2) {
throw CommandException("unprojection of borders failed.");
}
//
// Find intersection of two borders
//
const Border* border1 = borderFile.getBorder(0);
const Border* border2 = borderFile.getBorder(1);
int border1IntersectionLink, border2IntersectionLink;
if (border1->intersection3D(border2,
intersectionTolerance,
border1IntersectionLink,
border2IntersectionLink) == false) {
throw CommandException("no intersection within tolerance.");
}
//
// Read input foci projection file
//
FociProjectionFile fociProjectionFile;
if (QFile::exists(inputFociProjectionFileName)) {
fociProjectionFile.readFile(inputFociProjectionFileName);
}
//
// Add a focus at border intersection
//
const float* focusXYZ = border1->getLinkXYZ(border1IntersectionLink);
CellData focus(focusName, focusXYZ[0], focusXYZ[1], focusXYZ[2]);
FociFile fociFile;
fociFile.addCell(focus);
//
// Project the focus
//
CellProjectionFile tempFociProjFile;
tempFociProjFile.appendFiducialCellFile(fociFile);
CellFileProjector fociProjector(bms);
fociProjector.projectFile(&tempFociProjFile,
0,
CellFileProjector::PROJECTION_TYPE_ALL,
0.0,
false,
NULL);
//
// Get projected focus
//
fociProjectionFile.append(tempFociProjFile);
//
// Write the foci projection file
//
fociProjectionFile.writeFile(outputFociProjectionFileName);
}
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