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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 <limits>
#include "BorderFile.h"
#include "BorderProjectionFile.h"
#include "BorderProjectionUnprojector.h"
#include "BrainModelSurface.h"
#include "BrainSet.h"
#include "CommandSurfaceRegionOfInterestSelection.h"
#include "CoordinateFile.h"
#include "FileFilters.h"
#include "FociProjectionFile.h"
#include "LatLonFile.h"
#include "MetricFile.h"
#include "NodeRegionOfInterestFile.h"
#include "PaintFile.h"
#include "ProgramParameters.h"
#include "SurfaceShapeFile.h"
#include "TopologyFile.h"
/**
* constructor.
*/
CommandSurfaceRegionOfInterestSelection::CommandSurfaceRegionOfInterestSelection()
: CommandBase("-surface-region-of-interest-selection",
"SURFACE REGION OF INTEREST SELECTION")
{
}
/**
* destructor.
*/
CommandSurfaceRegionOfInterestSelection::~CommandSurfaceRegionOfInterestSelection()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceRegionOfInterestSelection::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Coordinate File Name", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Input Region of Interest File Name", FileFilters::getRegionOfInterestFileFilter());
paramsOut.addFile("Output Region of Interest File Name", FileFilters::getRegionOfInterestFileFilter());
paramsOut.addVariableListOfParameters("ROI Options");
}
/**
* get full help information.
*/
QString
CommandSurfaceRegionOfInterestSelection::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-coord-file-name> \n"
+ indent9 + "<input-topology-file-name> \n"
+ indent9 + "<input-region-of-interest-file-name.roi> \n"
+ indent9 + "<output-region-of-interest-file-name.roi> \n"
+ indent9 + "[-all-nodes] \n"
+ indent9 + "[-border-projection \n"
+ indent9 + " border-projection-file-name \n"
+ indent9 + " border-projection-name \n"
+ indent9 + " surface-view \n"
+ indent9 + " dimension \n"
+ indent9 + " z-minimum \n"
+ indent9 + " SEL-TYPE] \n"
+ indent9 + "[-boundary-only] \n"
+ indent9 + "[-dilate iterations] \n"
+ indent9 + "[-dilate-paint paint-file-name column paint-name iterations]\n"
+ indent9 + "[-edges SEL-TYPE] \n"
+ indent9 + "[-erode iterations] \n"
+ indent9 + "[-limit-x-lateral x-value] \n"
+ indent9 + "[-limit-x-medial x-value] \n"
+ indent9 + "[-limit-x-min x-value] \n"
+ indent9 + "[-limit-x-max x-value] \n"
+ indent9 + "[-limit-y-min y-value] \n"
+ indent9 + "[-limit-y-max y-value] \n"
+ indent9 + "[-limit-z-min z-value] \n"
+ indent9 + "[-limit-z-max z-value] \n"
+ indent9 + "[-limit-x-min-focus fociProjectionFile focusName] \n"
+ indent9 + "[-limit-x-max-focus fociProjectionFile focusName] \n"
+ indent9 + "[-limit-y-min-focus fociProjectionFile focusName] \n"
+ indent9 + "[-limit-y-max-focus fociProjectionFile focusName] \n"
+ indent9 + "[-limit-z-min-focus fociProjectionFile focusName] \n"
+ indent9 + "[-limit-z-max-focus fociProjectionFile focusName] \n"
+ indent9 + "[-metric metric-file-name column min max SEL-TYPE]\n"
+ indent9 + "[-invert-selection] \n"
+ indent9 + "[-latlon file-name column min-lat max-lat min-lon max-lon SEL_TYPE]\n"
+ indent9 + "[-paint paint-file-name column paint-name SEL-TYPE]\n"
+ indent9 + "[-remove-islands] \n"
+ indent9 + "[-shape shape-file-name column min max SEL-TYPE]\n"
+ indent9 + "\n"
+ indent9 + "The input region of interest file does not need to exist.\n"
+ indent9 + "\n"
+ indent9 + "Perform a surface node region of interest selection\n"
+ indent9 + "\n"
+ indent9 + "SEL-TYPE is one of \n"
+ indent9 + " NORMAL Applies selection to all nodes.\n"
+ indent9 + " AND And (intersection) new selection with the\n"
+ indent9 + " existing selection.\n"
+ indent9 + " OR Or (union) new selection with the\n"
+ indent9 + " existing selection.\n"
+ indent9 + " ANDNOT And the inverse of the new selection with\n"
+ indent9 + " existing selection.\n"
+ indent9 + "\n"
+ indent9 + "OPERATIONS\n"
+ indent9 + "\"-all-nodes\" will place all connected nodes into the ROI.\n"
+ indent9 + "\n"
+ indent9 + "\"-border-projection\" will place nodes that are inside of\n"
+ indent9 + " the border into the ROI. When \"dimension\" is 3D, nodes\n"
+ indent9 + " within the border and whose screen Z-coordinate is greater\n"
+ indent9 + " than \"z-minimum\" are assigned to the ROI. In most cases,\n"
+ indent9 + " a \"z-minimum\" of zero is sufficient. If areas within the\n"
+ indent9 + " border are not assigned, load the surface, click the mouse\n"
+ indent9 + " on the unassigned nodes to find the value needed for \n"
+ indent9 + " \"z-minimum\" and create the ROI again.\n"
+ indent9 + "\n"
+ indent9 + " \"surface-view\" is one of these single characters:\n"
+ indent9 + " A - Anterior\n"
+ indent9 + " D - Dorsal\n"
+ indent9 + " L - Lateral\n"
+ indent9 + " M - Medial\n"
+ indent9 + " P - Posterior\n"
+ indent9 + " R - Reset (default view)\n"
+ indent9 + " V - Ventral\n"
+ indent9 + " \"dimension\" is one of:\n"
+ indent9 + " 2D \n"
+ indent9 + " 3D \n"
+ indent9 + "\n"
+ indent9 + "\"-boundary-only\" will retain only those nodes that have\n"
+ indent9 + " at least one neighbor that is NOT in the ROI (interior\n"
+ indent9 + " nodes are removed).\n"
+ indent9 + "\n"
+ indent9 + "\"-dilate\" will dilate the ROI for the specified iterations.\n"
+ indent9 + "\n"
+ indent9 + "\"-dilate-paint\" will dilate the ROI but only nodes that have\n"
+ indent9 + " the specified paint are added to the ROI.\n"
+ indent9 + "\n"
+ indent9 + "\"-erode\" will erode the ROI for the specified iterations.\n"
+ indent9 + "\n"
+ indent9 + "\"-invert-selection\" will invert the node selection.\n"
+ indent9 + "\n"
+ indent9 + "\"-latlon\" will add nodes to the ROI if the nodes lat/long values\n"
+ indent9 + " are within the specified range of the column.\n"
+ indent9 + "\n"
+ indent9 + "\"-metric\" will add nodes to the ROI if the nodes metric value\n"
+ indent9 + " is within the specified range of the column.\n"
+ indent9 + "\n"
+ indent9 + "\"-paint\" will add nodes to the ROI if the nodes paint name\n"
+ indent9 + " is the specified paint name for the column.\n"
+ indent9 + "\n"
+ indent9 + "\"-remove-islands\" will retain only largest set of \n"
+ indent9 + " connected nodes in the ROI.\n"
+ indent9 + "\n"
+ indent9 + "\"-shape\" will add nodes to the ROI if the nodes shape value\n"
+ indent9 + " is within the specified range of the column.\n"
+ indent9 + "\n"
+ indent9 + "NOTES:\n"
+ indent9 + " The optional parameters (those enclosed in square\n"
+ indent9 + " brackets) are performed in the order they are\n"
+ indent9 + " listed on the command line.\n"
+ indent9 + "\n"
+ indent9 + " \"column\" is either the number of the column, which\n"
+ indent9 + " starts at one, or the name of the column. If a\n"
+ indent9 + " a name contains spaces, it must be enclosed in double \n"
+ indent9 + " quotes. Name has priority over number.\n"
+ indent9 + "\n"
+ indent9 + " When finding nodes enclosed inside a border projection\n"
+ indent9 + " use a dimension of 2D for flat surfaces. When the \n"
+ indent9 + " dimension is 2D, the surface view is ignored.\n"
+ indent9 + " \n"
+ indent9 + " For three dimensional surfaces (fiducial, inflated,\n"
+ indent9 + " spherical, etc.), set the dimension to 3D. When determining \n"
+ indent9 + " nodes within a border projection on a 3D surface, the \n"
+ indent9 + " surface-view is applied and those nodes with a Z-coordinate\n"
+ indent9 + " that is greater than Z-coordinate of the center of gravity\n"
+ indent9 + " and within the border projection are added to the region\n"
+ indent9 + " of interest.\n"
+ indent9 + "\n"
+ indent9 + " When limits are specified with foci, the last focus \n"
+ indent9 + " with \"focus-name\" found in the file is used.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceRegionOfInterestSelection::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get coord, topo, and roi file names
//
const QString coordFileName =
parameters->getNextParameterAsString("Input Coordinate File Name");
const QString topoFileName =
parameters->getNextParameterAsString("Input Topology File Name");
const QString inputRoiFileName =
parameters->getNextParameterAsString("Input Region of Interest File Name");
const QString outputRoiFileName =
parameters->getNextParameterAsString("Output Region of Interest File Name");
//
// Create a brain set
//
BrainSet brainSet(topoFileName,
coordFileName,
"",
true);
const BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("unable to find surface.");
}
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 not nodes.");
}
//
// Get the region of interest node selection
//
BrainModelSurfaceROINodeSelection* roi =
brainSet.getBrainModelSurfaceRegionOfInterestNodeSelection();
roi->deselectAllNodes();
//
// Read input ROI file
//
if (inputRoiFileName.isEmpty() == false) {
if (QFile::exists(inputRoiFileName)) {
NodeRegionOfInterestFile inputROIFile;
inputROIFile.readFile(inputRoiFileName);
roi->getRegionOfInterestFromFile(inputROIFile);
}
}
//
// Process the parameters for node selection
//
while (parameters->getParametersAvailable()) {
//
// Get the parameter
//
const QString parameterName =
parameters->getNextParameterAsString("ROI Operation");
if (parameterName == "-all-nodes") {
const QString msg = roi->selectAllNodes(bms);
if (msg.isEmpty() == false) {
throw CommandException(msg);
}
}
else if (parameterName == "-border-projection") {
const QString borderProjectionFileName =
parameters->getNextParameterAsString("Border Projection File Name");
const QString borderName =
parameters->getNextParameterAsString("Border Projection Name");
const QString surfaceViewString =
parameters->getNextParameterAsString("Surface View");
const QString dimensionString =
parameters->getNextParameterAsString("Dimension");
const float zMinimum =
parameters->getNextParameterAsFloat("Z-Minimum");
const BrainModelSurfaceROINodeSelection::SELECTION_LOGIC
selectionType = getSelectionType(
parameters->getNextParameterAsString("Lat Lon Selection Type"));
BrainModel::STANDARD_VIEWS surfaceView = BrainModel::VIEW_NONE;
if (surfaceViewString == "A") {
surfaceView = BrainModel::VIEW_ANTERIOR;
}
else if (surfaceViewString == "D") {
surfaceView = BrainModel::VIEW_DORSAL;
}
else if (surfaceViewString == "L") {
surfaceView = BrainModel::VIEW_LATERAL;
}
else if (surfaceViewString == "M") {
surfaceView = BrainModel::VIEW_MEDIAL;
}
else if (surfaceViewString == "P") {
surfaceView = BrainModel::VIEW_POSTERIOR;
}
else if (surfaceViewString == "R") {
surfaceView = BrainModel::VIEW_RESET;
}
else if (surfaceViewString == "V") {
surfaceView = BrainModel::VIEW_VENTRAL;
}
else {
throw CommandException("invalid surface view: "
+ surfaceViewString);
}
bool dim3D = false;
if (dimensionString == "2D") {
dim3D = false;
}
else if (dimensionString == "3D") {
dim3D = true;
}
else {
throw CommandException("invalid dimension: "
+ dimensionString);
}
//
// Read the border projection file
//
BorderProjectionFile borderProjectionFile;
borderProjectionFile.readFile(borderProjectionFileName);
//
// Find the border
//
BorderProjection* borderProjection =
borderProjectionFile.getLastBorderProjectionByName(borderName);
if (borderProjection == NULL) {
throw CommandException("no border projection with name: "
+ borderName);
}
//
// Copy the surface
//
BrainModelSurface borderSurface(*bms);
//
// 3D
//
if (dim3D) {
//
// Set view
//
if ((bms->getStructure().getType() != Structure::STRUCTURE_TYPE_CORTEX_LEFT) &&
(bms->getStructure().getType() != Structure::STRUCTURE_TYPE_CORTEX_RIGHT)) {
throw CommandException("Structure is neither right nor left for for 3D"
"within border test.");
}
borderSurface.applyViewToCoordinates(surfaceView);
//
// Translate to center of mass
//
borderSurface.translateToCenterOfMass();
}
const CoordinateFile* borderCoordinateFile = borderSurface.getCoordinateFile();
//
// Create a border projection file with the single projection
//
BorderProjectionFile tempBorderProjectionFile;
tempBorderProjectionFile.addBorderProjection(*borderProjection);
//
// Unproject the border
//
BorderFile borderFile;
BorderProjectionUnprojector unprojector;
unprojector.unprojectBorderProjections(*borderCoordinateFile,
tempBorderProjectionFile,
borderFile);
if (borderFile.getNumberOfBorders() <= 0) {
throw CommandException("unprojecting border projection: "
+ borderName);
}
//
// Get the border from unprojecting
//
const Border* border = borderFile.getBorder(0);
//
// select the nodes
//
const QString msg = roi->selectNodesWithinBorder(selectionType,
&borderSurface,
border,
dim3D,
zMinimum);
if (msg.isEmpty() == false) {
throw CommandException(msg);
}
}
else if (parameterName == "-boundary-only") {
roi->boundaryOnly(bms);
}
else if (parameterName == "-dilate") {
const int numberOfIterations =
parameters->getNextParameterAsInt("Dilation Iterations");
roi->dilate(bms, numberOfIterations);
}
else if (parameterName == "-dilate-paint") {
const QString paintFileName =
parameters->getNextParameterAsString("Dilate Paint File Name");
const QString paintColumn =
parameters->getNextParameterAsString("Dilate Paint Column Name or Number");
const QString paintName =
parameters->getNextParameterAsString("Dilate Paint Name");
const int iterations =
parameters->getNextParameterAsInt("Dilate Paint Iterations");
//
// Read the paint file
//
PaintFile paintFile;
paintFile.readFile(paintFileName);
//
// Get the column number
//
const int paintColumnNumber = paintFile.getColumnFromNameOrNumber(paintColumn, false);
//
// Select the nodes
//
roi->dilatePaintConstrained(bms,
&paintFile,
paintColumnNumber,
paintName,
iterations);
}
else if (parameterName == "-edges") {
const BrainModelSurfaceROINodeSelection::SELECTION_LOGIC
selectionType = getSelectionType(
parameters->getNextParameterAsString("Lat Lon Selection Type"));
roi->selectNodesThatAreEdges(selectionType, bms);
}
else if (parameterName == "-erode") {
const int numberOfIterations =
parameters->getNextParameterAsInt("Erosion Iterations");
roi->erode(bms, numberOfIterations);
}
else if (parameterName == "-invert-selection") {
roi->invertSelectedNodes(bms);
}
else if (parameterName == "-latlon") {
//
// Get the parameters
//
const QString latLonFileName =
parameters->getNextParameterAsString("Lat Lon File Name");
const QString latLonColumn =
parameters->getNextParameterAsString("Lat Lon Column Name or Number");
const float minLatValue =
parameters->getNextParameterAsFloat("Lat Min Value");
const float maxLatValue =
parameters->getNextParameterAsFloat("Lat Max Value");
const float minLonValue =
parameters->getNextParameterAsFloat("Lon Min Value");
const float maxLonValue =
parameters->getNextParameterAsFloat("Lon Max Value");
const BrainModelSurfaceROINodeSelection::SELECTION_LOGIC
selectionType = getSelectionType(
parameters->getNextParameterAsString("Lat Lon Selection Type"));
//
// Read the metric file
//
LatLonFile latLonFile;
latLonFile.readFile(latLonFileName);
//
// Get the column number
//
const int latLonColumnNumber = latLonFile.getColumnFromNameOrNumber(latLonColumn, false);
//
// Select the nodes
//
const QString msg = roi->selectNodesWithLatLong(selectionType,
bms,
&latLonFile,
latLonColumnNumber,
minLatValue,
maxLatValue,
minLonValue,
maxLonValue);
if (msg.isEmpty() == false) {
throw CommandException(msg);
}
}
else if ((parameterName == "-limit-x-lateral") ||
(parameterName == "-limit-x-medial") ||
(parameterName == "-limit-x-min") ||
(parameterName == "-limit-x-max") ||
(parameterName == "-limit-y-min") ||
(parameterName == "-limit-y-max") ||
(parameterName == "-limit-z-min") ||
(parameterName == "-limit-z-max")) {
const float value = parameters->getNextParameterAsFloat("ROI "
+ parameterName
+ " value");
extentLimit(bms,
roi,
parameterName,
value);
}
else if ((parameterName == "-limit-x-min-focus") ||
(parameterName == "-limit-x-max-focus") ||
(parameterName == "-limit-y-min-focus") ||
(parameterName == "-limit-y-max-focus") ||
(parameterName == "-limit-z-min-focus") ||
(parameterName == "-limit-z-max-focus")) {
//
// limit the ROI
//
focusLimit(bms,
roi,
parameterName);
}
else if (parameterName == "-metric") {
//
// Get the parameters
//
const QString metricFileName =
parameters->getNextParameterAsString("Metric File Name");
const QString metricColumn =
parameters->getNextParameterAsString("Metric Column Name or Number");
const float minValue =
parameters->getNextParameterAsFloat("Metric Min Value");
const float maxValue =
parameters->getNextParameterAsFloat("Metric Max Value");
const BrainModelSurfaceROINodeSelection::SELECTION_LOGIC
selectionType = getSelectionType(
parameters->getNextParameterAsString("Metric Selection Type"));
//
// Read the metric file
//
MetricFile metricFile;
metricFile.readFile(metricFileName);
//
// Get the column number
//
const int metricColumnNumber = metricFile.getColumnFromNameOrNumber(metricColumn, false);
//
// Select the nodes
//
const QString msg = roi->selectNodesWithMetric(selectionType,
bms,
&metricFile,
metricColumnNumber,
minValue,
maxValue);
if (msg.isEmpty() == false) {
throw CommandException(msg);
}
}
else if (parameterName == "-paint") {
//
// Get the parameters
//
const QString paintFileName =
parameters->getNextParameterAsString("Paint File Name");
const QString paintColumn =
parameters->getNextParameterAsString("Paint Column Name or Number");
const QString paintName =
parameters->getNextParameterAsString("Paint Name");
const BrainModelSurfaceROINodeSelection::SELECTION_LOGIC
selectionType = getSelectionType(
parameters->getNextParameterAsString("Paint Selection Type"));
//
// Read the paint file
//
PaintFile paintFile;
paintFile.readFile(paintFileName);
//
// Get the column number
//
const int paintColumnNumber = paintFile.getColumnFromNameOrNumber(paintColumn, false);
//
// Select the nodes
//
const QString msg = roi->selectNodesWithPaint(selectionType,
bms,
&paintFile,
paintColumnNumber,
paintName);
if (msg.isEmpty() == false) {
throw CommandException(msg);
}
}
else if (parameterName == "-remove-islands") {
roi->discardIslands(bms);
}
else if (parameterName == "-shape") {
//
// Get the parameters
//
const QString shapeFileName =
parameters->getNextParameterAsString("Shape File Name");
const QString shapeColumn =
parameters->getNextParameterAsString("Shape Column Name or Number");
const float minValue =
parameters->getNextParameterAsFloat("Shape Min Value");
const float maxValue =
parameters->getNextParameterAsFloat("Shape Max Value");
const BrainModelSurfaceROINodeSelection::SELECTION_LOGIC
selectionType = getSelectionType(
parameters->getNextParameterAsString("Shape Selection Type"));
//
// Read the surface shape file
//
SurfaceShapeFile shapeFile;
shapeFile.readFile(shapeFileName);
//
// Get the column number
//
const int shapeColumnNumber = shapeFile.getColumnFromNameOrNumber(shapeColumn, false);
//
// Select the nodes
//
const QString msg = roi->selectNodesWithSurfaceShape(selectionType,
bms,
&shapeFile,
shapeColumnNumber,
minValue,
maxValue);
if (msg.isEmpty() == false) {
throw CommandException(msg);
}
}
else {
throw CommandException("Unrecognized operation = \""
+ parameterName
+ "\".");
}
}
//
// Place the selections in a file and write it
//
NodeRegionOfInterestFile roiFile;
roi->setRegionOfInterestIntoFile(roiFile);
roiFile.writeFile(outputRoiFileName);
}
/**
* get the selection type.
*/
BrainModelSurfaceROINodeSelection::SELECTION_LOGIC
CommandSurfaceRegionOfInterestSelection::getSelectionType(const QString& selectionTypeName) const
throw (CommandException)
{
BrainModelSurfaceROINodeSelection::SELECTION_LOGIC selType;
if (selectionTypeName == "NORMAL") {
selType = BrainModelSurfaceROINodeSelection::SELECTION_LOGIC_NORMAL;
}
else if (selectionTypeName == "AND") {
selType = BrainModelSurfaceROINodeSelection::SELECTION_LOGIC_AND;
}
else if (selectionTypeName == "OR") {
selType = BrainModelSurfaceROINodeSelection::SELECTION_LOGIC_OR;
}
else if (selectionTypeName == "ANDNOT") {
selType = BrainModelSurfaceROINodeSelection::SELECTION_LOGIC_AND_NOT;
}
else {
throw CommandException("Invalid selection type: "
+ selectionTypeName);
}
return selType;
}
/**
* focus xyz limit.
*/
void
CommandSurfaceRegionOfInterestSelection::focusLimit(const BrainModelSurface* bms,
BrainModelSurfaceROINodeSelection* roi,
const QString& operationName)
{
//
// Get parameters
//
const QString fociProjectionFileName =
parameters->getNextParameterAsString("Limit Foci Projection File Name");
const QString focusName =
parameters->getNextParameterAsString("Limit Focus Name");
//
// Get the position of the focus
//
FociProjectionFile fpf;
fpf.readFile(fociProjectionFileName);
const CellProjection* focus = fpf.getLastCellProjectionWithName(focusName);
if (focus == NULL) {
throw CommandException("ROI LIMIT: focus name "
+ focusName
+ " not found.");
}
const bool fiducialSurfaceFlag =
(bms->getSurfaceType() == BrainModelSurface::SURFACE_TYPE_FIDUCIAL);
const bool flatSurfaceFlag =
((bms->getSurfaceType() == BrainModelSurface::SURFACE_TYPE_FLAT) ||
(bms->getSurfaceType() == BrainModelSurface::SURFACE_TYPE_FLAT_LOBAR));
float focusXYZ[3];
if (focus->getProjectedPosition(bms->getCoordinateFile(),
bms->getTopologyFile(),
fiducialSurfaceFlag,
flatSurfaceFlag,
false,
focusXYZ) == false) {
throw CommandException("ROI LIMIT: unable to get projected position for "
+ focusName);
}
//
// Set the extent for limiting
//
float extent[6] = {
-std::numeric_limits<float>::max(),
std::numeric_limits<float>::max(),
-std::numeric_limits<float>::max(),
std::numeric_limits<float>::max(),
-std::numeric_limits<float>::max(),
std::numeric_limits<float>::max()
};
if (operationName == "-limit-x-min-focus") {
extent[0] = focusXYZ[0];
}
else if (operationName == "-limit-x-max-focus") {
extent[1] = focusXYZ[0];
}
else if (operationName == "-limit-y-min-focus") {
extent[2] = focusXYZ[1];
}
else if (operationName == "-limit-y-max-focus") {
extent[3] = focusXYZ[1];
}
else if (operationName == "-limit-z-min-focus") {
extent[4] = focusXYZ[2];
}
else if (operationName == "-limit-z-max-focus") {
extent[5] = focusXYZ[2];
}
else {
throw CommandException("Invalid limit command "
+ operationName);
}
//
// Limit the ROI
//
roi->limitExtent(bms, extent);
}
/**
* extent xyz limit.
*/
void
CommandSurfaceRegionOfInterestSelection::extentLimit(const BrainModelSurface* bms,
BrainModelSurfaceROINodeSelection* roi,
const QString& operationName,
const float extentValue)
{
//
// Set the extent for limiting
//
float extent[6] = {
-std::numeric_limits<float>::max(),
std::numeric_limits<float>::max(),
-std::numeric_limits<float>::max(),
std::numeric_limits<float>::max(),
-std::numeric_limits<float>::max(),
std::numeric_limits<float>::max()
};
if (operationName == "-limit-x-lateral") {
if (bms->getStructure().getType() == Structure::STRUCTURE_TYPE_CORTEX_LEFT) {
extent[0] = -extentValue;
}
else if (bms->getStructure().getType() == Structure::STRUCTURE_TYPE_CORTEX_RIGHT) {
extent[1] = extentValue;
}
else {
throw CommandException("Structure is neither right nor left for lateral x limit");
}
}
else if (operationName == "-limit-x-medial") {
if (bms->getStructure().getType() == Structure::STRUCTURE_TYPE_CORTEX_LEFT) {
extent[1] = extentValue;
}
else if (bms->getStructure().getType() == Structure::STRUCTURE_TYPE_CORTEX_RIGHT) {
extent[0] = -extentValue;
}
else {
throw CommandException("Structure is neither right nor left for lateral x limit");
}
}
else if (operationName == "-limit-x-min") {
extent[0] = extentValue;
}
else if (operationName == "-limit-x-max") {
extent[1] = extentValue;
}
else if (operationName == "-limit-y-min") {
extent[2] = extentValue;
}
else if (operationName == "-limit-y-max") {
extent[3] = extentValue;
}
else if (operationName == "-limit-z-min") {
extent[4] = extentValue;
}
else if (operationName == "-limit-z-max") {
extent[5] = extentValue;
}
//
// Limit the ROI
//
roi->limitExtent(bms, extent);
}
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