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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 <iostream>
#include "BrainModelSurfaceBorderLandmarkIdentification.h"
#include "BrainModelVolumeSureFitSegmentation.h"
#include "BrainSet.h"
#include "CommandVolumeSegmentation.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "StringUtilities.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeSegmentation::CommandVolumeSegmentation()
: CommandBase("-volume-segment",
"VOLUME SEGMENTATION")
{
}
/**
* destructor.
*/
CommandVolumeSegmentation::~CommandVolumeSegmentation()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeSegmentation::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<QString> values, descriptions;
values.push_back("NIFTI"); descriptions.push_back("NIFTI");
values.push_back("AFNI"); descriptions.push_back("AFNI");
values.push_back("SPM"); descriptions.push_back("SPM");
values.push_back("WUNIL"); descriptions.push_back("WUNIL");
std::vector<QString> structValues, structDescriptions;
structValues.push_back("LEFT"); structDescriptions.push_back("LEFT");
structValues.push_back("RIGHT"); structDescriptions.push_back("RIGHT");
std::vector<BrainModelVolumeSureFitSegmentation::ERROR_CORRECTION_METHOD> errorCorrectionValues;
std::vector<QString> errorCorrectionNames;
BrainModelVolumeSureFitSegmentation::getErrorCorrectionMethodsAndNames(
errorCorrectionNames, errorCorrectionValues);
paramsOut.clear();
paramsOut.addFile("Input Anatomy Volume File Name", FileFilters::getVolumeAnatomyFileFilter());
paramsOut.addFile("Input Segmentation Volume File Name", FileFilters::getVolumeSegmentationFileFilter());
paramsOut.addFile("Spec File Name", FileFilters::getSpecFileFilter());
paramsOut.addString("Operation Code", "YYYYYYYYYNYYYYYY");
paramsOut.addFloat("Gray Peak", 100.0);
paramsOut.addFloat("White Peak", 170.0);
paramsOut.addString("Padding Code", "NNNNNN");
paramsOut.addListOfItems("Structure", structValues, structDescriptions);
paramsOut.addListOfItems("Error Correction", errorCorrectionNames, errorCorrectionNames);
paramsOut.addListOfItems("Volume Write Type", values, descriptions);
}
/**
* get full help information.
*/
QString
CommandVolumeSegmentation::getHelpInformation() const
{
std::vector<BrainModelVolumeSureFitSegmentation::ERROR_CORRECTION_METHOD> errorCorrectionValues;
std::vector<QString> errorCorrectionNames;
BrainModelVolumeSureFitSegmentation::getErrorCorrectionMethodsAndNames(
errorCorrectionNames, errorCorrectionValues);
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-anatomy-volume-file-name>\n"
+ indent9 + "<input-segmentation-volume-file-name>\n"
+ indent9 + "<spec-file-name>\n"
+ indent9 + "<operation-code>\n"
+ indent9 + "<gray-peak>\n"
+ indent9 + "<white-peak>\n"
+ indent9 + "<padding-code>\n"
+ indent9 + "<structure>\n"
+ indent9 + "<error-correction-method>\n"
+ indent9 + "<write-volume-type>\n"
+ indent9 + " \n"
+ indent9 + "Perform segmentation operations.\n"
+ indent9 + " \n"
+ indent9 + " Operation_Code characters \n"
+ indent9 + " Specify each with either a \"Y\" or \"N\". \n"
+ indent9 + " All characters must be specified. \n"
+ indent9 + " Character Operation Description \n"
+ indent9 + " --------- --------------------- \n"
+ indent9 + " 1 Disconnect Eye and Skull \n"
+ indent9 + " 2 Disconnect Hindbrain \n"
+ indent9 + " 3 Use High Threshold for Hindbrain disconnection \n"
+ indent9 + " 4 Cut Corpus Callossum \n"
+ indent9 + " 5 Generate Segmentation \n"
+ indent9 + " 6 Fill Ventricles \n"
+ indent9 + " 7 Generate Raw and Fiducial Surfaces \n"
+ indent9 + " 8 Reduce polygons in surfaces \n"
+ indent9 + " 9 Correct topological errors in surfaces \n"
+ indent9 + " 10 Generate Inflated Surface \n"
+ indent9 + " 11 Generate Very Inflated Surface \n"
+ indent9 + " 12 Generate Ellipsoid Surface (For Flattening) \n"
+ indent9 + " 13 Generate Spherical Surface \n"
+ indent9 + " 14 Generate Comp Med Wall Surface \n"
+ indent9 + " 15 Generate Hull Surface \n"
+ indent9 + " 16 Generate Curvature, Depth, and Paint Attributes \n"
+ indent9 + " 17 Generate Registration and Flattening Landmark Borders\n"
+ indent9 + " \n"
+ indent9 + " gray-peak specifies the intensity of the gray matter peak in the \n"
+ indent9 + " anatomy volume. \n"
+ indent9 + " \n"
+ indent9 + " white-peak specifies the intensity of the white matter peak in the \n"
+ indent9 + " anatomy volume. \n"
+ indent9 + " \n"
+ indent9 + " padding-code \n"
+ indent9 + " Specify padding for any cut faces when segmenting a partial hemisphere. \n"
+ indent9 + " Specify each with either a \"Y\" for padding or \"N\" for no padding. \n"
+ indent9 + " All characters must be specified. \n"
+ indent9 + " Character Padding Description \n"
+ indent9 + " --------- ------------------- \n"
+ indent9 + " 1 Pad Negative X \n"
+ indent9 + " 2 Pad Positive X \n"
+ indent9 + " 3 Pad Posterior Y \n"
+ indent9 + " 4 Pad Anterior Y \n"
+ indent9 + " 5 Pad Inferior Z \n"
+ indent9 + " 6 Pad Superior Z \n"
+ indent9 + " \n"
+ indent9 + " structure Specifies the brain structure. \n"
+ indent9 + " Acceptable values are RIGHT or LEFT \n"
+ indent9 + " \n"
+ indent9 + " spec-file-name Name of specification file. \n"
+ indent9 + " \n"
+ indent9 + " input-anatomy-volume-file-name \n"
+ indent9 + " If there is not an anatomy volume file, leave this\n"
+ indent9 + " item blank (two consecutive double quotes).\n"
+ indent9 + " \n"
+ indent9 + " input-segmentation-volume-file-name \n"
+ indent9 + " If there is not a segmentation volume file, leave this\n"
+ indent9 + " item blank (two consecutive double quotes).\n"
+ indent9 + " \n"
+ indent9 + " error-correction-method\n");
for (unsigned int i = 0; i < errorCorrectionNames.size(); i++) {
helpInfo += (
indent9 + indent9 + errorCorrectionNames[i] + "\n");
}
helpInfo += ("\n"
+ indent9 + " write-volume-type Type of volume files to write. \n"
+ indent9 + " Specifies the type of the volume files that will be written \n"
+ indent9 + " during the segmentation process. Valid values are \n"
+ indent9 + " AFNI \n"
+ indent9 + " NIFTI \n"
+ indent9 + " NIFTI_GZIP (RECOMMENDED!!!!) \n"
+ indent9 + " SPM \n"
+ indent9 + " WUNIL \n"
+ indent9 + " \n"
+ indent9 + " All input volumes must be in a Left-Posterior-Inferior orientation \n"
+ indent9 + " and their stereotaxic coordinates must be set so that the origin is \n"
+ indent9 + " at the anterior commissure. \n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeSegmentation::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputAnatomyVolumeFileName =
parameters->getNextParameterAsString("Input Anatomy Volume File Name");
const QString inputSegmentationVolumeFileName =
parameters->getNextParameterAsString("Input Segmentation Volume File Name");
const QString specFileName =
parameters->getNextParameterAsString("Spec File Name");
const QString operationCode =
parameters->getNextParameterAsString("Operation Code");
const float grayPeak =
parameters->getNextParameterAsFloat("Gray Peak");
const float whitePeak =
parameters->getNextParameterAsFloat("White Peak");
const QString paddingCode =
parameters->getNextParameterAsString("Padding Code");
const QString structureName =
parameters->getNextParameterAsString("Structure Name").toUpper();
const QString errorCorrectionName =
parameters->getNextParameterAsString("Error Correction Name");
const QString writeVolumeTypeString =
parameters->getNextParameterAsString("Write Volume Type");
checkForExcessiveParameters();
VolumeFile::FILE_READ_WRITE_TYPE writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_NIFTI_GZIP;
if (writeVolumeTypeString == "AFNI") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_AFNI;
}
else if (writeVolumeTypeString == "NIFTI") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_NIFTI;
}
else if (writeVolumeTypeString == "NIFTI_GZIP") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_NIFTI_GZIP;
}
else if (writeVolumeTypeString == "SPM") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_SPM_OR_MEDX;
}
else if (writeVolumeTypeString == "WUNIL") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_WUNIL;
}
else {
throw CommandException("Invalid volume file write type: "
+ writeVolumeTypeString);
}
//
// Check the operation code
//
const int operationCodeLength = 17;
if (operationCode.length() != operationCodeLength) {
throw CommandException("Operation code must contain exactly "
+ QString::number(operationCodeLength)
+ " characters.");
}
for (int i = 0; i < operationCodeLength; i++) {
if ((operationCode[i] != 'Y') && (operationCode[i] != 'N')) {
throw CommandException("Operation code character "
+ QString::number(i + 1)
+ " must be \"Y\" or \"N\".");
}
}
const bool disconnectEyeFlag = (operationCode[0] == 'Y');
const bool disconnectHindbrainFlag = (operationCode[1] == 'Y');
const bool disconnectHindHiThreshFlag = (operationCode[2] == 'Y');
const bool cutCorpusCallossumFlag = (operationCode[3] == 'Y');
const bool generateSegmentationFlag = (operationCode[4] == 'Y');
const bool fillVentriclesFlag = (operationCode[5] == 'Y');
const bool rawFiducialSurfaceFlag = (operationCode[6] == 'Y');
const bool reduceSurfacePolygonsFlag = (operationCode[7] == 'Y');
const bool topologicalCorrectFlag = (operationCode[8] == 'Y');
const bool inflatedSurfaceFlag = (operationCode[9] == 'Y');
const bool veryInflatedSurfaceFlag = (operationCode[10] == 'Y');
const bool ellipsoidSurfaceFlag = (operationCode[11] == 'Y');
const bool sphericalSurfaceFlag = (operationCode[12] == 'Y');
const bool compMedWallSurfaceFlag = (operationCode[13] == 'Y');
const bool hullSurfaceFlag = (operationCode[14] == 'Y');
const bool depthCurveGeographyFlag = (operationCode[15] == 'Y');
const bool landmarksFlag = (operationCode[16] == 'Y');
//
// Get the structure
//
Structure::STRUCTURE_TYPE structure;
if (structureName == "RIGHT") {
structure = Structure::STRUCTURE_TYPE_CORTEX_RIGHT;
}
else if (structureName == "LEFT") {
structure = Structure::STRUCTURE_TYPE_CORTEX_LEFT;
}
else {
throw CommandException("Structure must be either RIGHT or LEFT.\n"
" Value entered \"" + structureName + "\"");
}
//
// Determine padding
//
const int paddingCodeLength = 6;
if (paddingCode.length() != paddingCodeLength) {
throw CommandException("Padding code must have exactly "
+ QString::number(paddingCodeLength)
+ " characters.");
}
int paddingAmount[6] = { 0, 0, 0, 0, 0, 0 };
for (int i = 0; i < paddingCodeLength; i++) {
if (paddingCode[i] == 'Y') {
paddingAmount[i] = 30;
}
else if (paddingCode[i] == 'N') {
paddingAmount[i] = 0;
}
else {
throw CommandException("Padding code character "
+ QString::number(i + 1)
+ " must be \"Y\" or \"N\".");
}
}
//
// Get error correction
//
std::vector<BrainModelVolumeSureFitSegmentation::ERROR_CORRECTION_METHOD> errorCorrectionValues;
std::vector<QString> errorCorrectionNames;
BrainModelVolumeSureFitSegmentation::getErrorCorrectionMethodsAndNames(
errorCorrectionNames, errorCorrectionValues);
BrainModelVolumeSureFitSegmentation::ERROR_CORRECTION_METHOD errorCorrectionMethod =
BrainModelVolumeSureFitSegmentation::ERROR_CORRECTION_METHOD_NONE;
bool foundErrorCorrectionFlag = false;
for (unsigned int i = 0; i < errorCorrectionNames.size(); i++) {
if (errorCorrectionName == errorCorrectionNames[i]) {
errorCorrectionMethod = errorCorrectionValues[i];
foundErrorCorrectionFlag = true;
break;
}
}
if (foundErrorCorrectionFlag == false) {
throw CommandException("Invalid error correction: " + errorCorrectionName);
}
//
// Check if generating landmarks is valid
//
if (landmarksFlag) {
SpecFile sf;
sf.readFile(specFileName);
const StereotaxicSpace space = sf.getSpace();
const bool validLandmarkSpaceFlag =
BrainModelSurfaceBorderLandmarkIdentification::isStereotaxicSpaceSupported(space);
if (validLandmarkSpaceFlag == false) {
throw CommandException("Generation of flattening/landmark landmark borders "
"not supported for stereotaxic space: "
+ space.getName());
}
}
//
// Create a brain set
//
BrainSet brainSet(specFileName, false, true);
//
// For anterior commissure voxel index
//
const float zeros[3] = { 0.0, 0.0, 0.0 };
int acIJK[3];
//
// Read the anatomy volume file
//
VolumeFile inputAnatomyVolume;
if (inputAnatomyVolumeFileName.isEmpty() == false) {
inputAnatomyVolume.readFile(inputAnatomyVolumeFileName);
inputAnatomyVolume.convertCoordinatesToVoxelIJK(zeros, acIJK);
}
//
// Read the segmentation volume file
//
VolumeFile inputSegmentationVolume;
if (inputSegmentationVolumeFileName.isEmpty() == false) {
inputSegmentationVolume.readFile(inputSegmentationVolumeFileName);
inputSegmentationVolume.convertCoordinatesToVoxelIJK(zeros, acIJK);
}
//
// Create the segmentation object
//
BrainModelVolumeSureFitSegmentation
segmentationObject(&brainSet,
&inputAnatomyVolume,
&inputSegmentationVolume,
writeVolumeType,
acIJK,
paddingAmount,
whitePeak,
grayPeak,
0.0,
structure,
disconnectEyeFlag,
disconnectHindbrainFlag,
disconnectHindHiThreshFlag,
cutCorpusCallossumFlag,
generateSegmentationFlag,
fillVentriclesFlag,
errorCorrectionMethod,
rawFiducialSurfaceFlag,
(reduceSurfacePolygonsFlag == false),
topologicalCorrectFlag,
inflatedSurfaceFlag,
veryInflatedSurfaceFlag,
ellipsoidSurfaceFlag,
sphericalSurfaceFlag,
compMedWallSurfaceFlag,
hullSurfaceFlag,
depthCurveGeographyFlag,
landmarksFlag,
true);
//
// Execute the segmentation
//
segmentationObject.execute();
const QString warningMessages = segmentationObject.getWarningMessages();
if (warningMessages.isEmpty() == false) {
std::cout << "Segmentation Warnings: " << warningMessages.toAscii().constData() << std::endl;
}
}
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