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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 <QGlobalStatic>
#include <fstream>
#include <iostream>
#include <sstream>
#include <QFile>
#include <QGlobalStatic>
#include <QTime>
#include "BrainVoyagerFile.h"
#include "ByteSwapping.h"
#include "DebugControl.h"
#include "FileUtilities.h"
#include "SpecFile.h"
/**
* Constructor.
*/
BrainVoyagerFile::BrainVoyagerFile()
: AbstractFile("Brain Voyager File",
SpecFile::getBrainVoyagerFileExtension(),
false,
AbstractFile::FILE_FORMAT_BINARY,
FILE_IO_NONE,
FILE_IO_READ_ONLY,
FILE_IO_NONE,
FILE_IO_NONE)
{
verticesX = NULL;
verticesY = NULL;
verticesZ = NULL;
vertexRedComponent = NULL;
vertexGreenComponent = NULL;
vertexBlueComponent = NULL;
vertexAlphaComponent = NULL;
vertexColorTableIndices = NULL;
triangles = NULL;
clear();
}
/**
* Destructor.
*/
BrainVoyagerFile::~BrainVoyagerFile()
{
clear();
}
/**
* clear the files contents.
*/
void
BrainVoyagerFile::clear()
{
clearAbstractFile();
version = -1.0;
numberOfVertices = 0;
numberOfTriangles = 0;
if (verticesX != NULL) {
delete[] verticesX;
verticesX = NULL;
}
if (verticesY != NULL) {
delete[] verticesY;
verticesY = NULL;
}
if (verticesZ != NULL) {
delete[] verticesZ;
verticesZ = NULL;
}
if (vertexRedComponent != NULL) {
delete[] vertexRedComponent;
vertexRedComponent = NULL;
}
if (vertexGreenComponent != NULL) {
delete[] vertexGreenComponent;
vertexGreenComponent = NULL;
}
if (vertexBlueComponent != NULL) {
delete[] vertexBlueComponent;
vertexBlueComponent = NULL;
}
if (vertexAlphaComponent != NULL) {
delete[] vertexAlphaComponent;
vertexAlphaComponent = NULL;
}
if (vertexColorTableIndices != NULL) {
delete[] vertexColorTableIndices;
vertexColorTableIndices = NULL;
}
if (triangles != NULL) {
delete[] triangles;
triangles = NULL;
}
colorTable.clear();
}
/**
* get coordinates of a vertex.
*/
void
BrainVoyagerFile::getVertexCoordinates(const int vertexNumber, float xyz[3]) const
{
if (vertexNumber < numberOfVertices) {
xyz[0] = verticesX[vertexNumber];
xyz[1] = verticesY[vertexNumber];
xyz[2] = verticesZ[vertexNumber];
}
}
/**
* get vertices of a tile.
*/
void
BrainVoyagerFile::getTriangle(const int triangleNumber, int verts[3]) const
{
if (triangleNumber < numberOfTriangles) {
verts[0] = triangles[triangleNumber * 3];
verts[1] = triangles[triangleNumber * 3 + 1];
verts[2] = triangles[triangleNumber * 3 + 2];
}
}
/**
* get the vertex color.
*/
void
BrainVoyagerFile::getVertexColor(const int vertexNumber, unsigned char rgb[3]) const
{
if (vertexNumber < numberOfVertices) {
rgb[0] = static_cast<unsigned char>(vertexRedComponent[vertexNumber]);
rgb[1] = static_cast<unsigned char>(vertexGreenComponent[vertexNumber]);
rgb[2] = static_cast<unsigned char>(vertexBlueComponent[vertexNumber]);
}
}
/**
* Write the file's data (not used).
*/
void
BrainVoyagerFile::readFileData(QFile& /*file*/, QTextStream& /*stream*/, QDataStream&,
QDomElement& /* rootElement */) throw (FileException)
{
throw FileException(filename,
"Program Error: BrainVoyagerFile::readFileData should never be called");
}
/**
* Read the file's data (not used).
*/
void
BrainVoyagerFile::writeFileData(QTextStream& /*stream*/, QDataStream&,
QDomDocument& /* xmlDoc */,
QDomElement& /* rootElement */) throw (FileException)
{
throw FileException(filename,
"Program Error: BrainVoyagerFile::writeFileData should never be called");
}
/**
* Read the file (overrides AbstractFile method).
*/
void
BrainVoyagerFile::readFile(const QString& filenameIn) throw (FileException)
{
const QString filename2(filenameIn);
clear();
filename = filename2;
//
// MSB systems will need to byte swap
//
//int wordSize;
//bool bigEndian;
//qSysInfo(&wordSize, &bigEndian);
const bool needToByteSwap = (QSysInfo::ByteOrder == QSysInfo::BigEndian);
QTime timer;
timer.start();
std::ifstream file(filename.toAscii().constData(), std::ios::in | std::ios::binary);
if (file.bad() || file.fail()) {
throw FileException(filename, "Failure trying to open: ");
}
else {
try {
int intDummy;
float floatDummy;
file.read((char*)&version, sizeof(version));;
file.read((char*)&intDummy, sizeof(intDummy));
file.read((char*)&numberOfVertices, sizeof(numberOfVertices));
file.read((char*)&numberOfTriangles, sizeof(numberOfTriangles));
if (DebugControl::getDebugOn()) {
float fv = version;
ByteSwapping::swapBytes(&fv, 1);
std::cout << "version: " << version
<< " version byte swapped: " << fv << std::endl;
}
file.read((char*)&floatDummy, sizeof(floatDummy)); // mesh center x
file.read((char*)&floatDummy, sizeof(floatDummy)); // mesh center y
file.read((char*)&floatDummy, sizeof(floatDummy)); // mesh center z
if (needToByteSwap) {
ByteSwapping::swapBytes(&version, 1);
ByteSwapping::swapBytes(&numberOfVertices, 1);
ByteSwapping::swapBytes(&numberOfTriangles, 1);
}
if (numberOfVertices > 0) {
//
// Read vertices
//
verticesX = new float[numberOfVertices];
verticesY = new float[numberOfVertices];
verticesZ = new float[numberOfVertices];
file.read((char*)verticesX, (numberOfVertices * 4));
file.read((char*)verticesY, (numberOfVertices * 4));
file.read((char*)verticesZ, (numberOfVertices * 4));
if (needToByteSwap) {
ByteSwapping::swapBytes(verticesX, numberOfVertices);
ByteSwapping::swapBytes(verticesY, numberOfVertices);
ByteSwapping::swapBytes(verticesZ, numberOfVertices);
}
//
// Skip normals
//
file.seekg(numberOfVertices * 4 * 3, std::ios::cur);
}
float redConvexCurvature, greenConvexCurvature, blueConvexCurvature;
file.read((char*)&redConvexCurvature, sizeof(redConvexCurvature));
file.read((char*)&greenConvexCurvature, sizeof(greenConvexCurvature));
file.read((char*)&blueConvexCurvature, sizeof(blueConvexCurvature));
file.read((char*)&floatDummy, sizeof(floatDummy)); // alpha convex curvature
if (needToByteSwap) {
ByteSwapping::swapBytes(&redConvexCurvature, 1);
ByteSwapping::swapBytes(&greenConvexCurvature, 1);
ByteSwapping::swapBytes(&blueConvexCurvature, 1);
}
const unsigned char redConvex =
static_cast<unsigned char>(redConvexCurvature * 255.0);
const unsigned char greenConvex =
static_cast<unsigned char>(greenConvexCurvature * 255.0);
const unsigned char blueConvex =
static_cast<unsigned char>(blueConvexCurvature * 255.0);
float redConcaveCurvature, greenConcaveCurvature, blueConcaveCurvature;
file.read((char*)&redConcaveCurvature, sizeof(redConcaveCurvature));
file.read((char*)&greenConcaveCurvature, sizeof(greenConcaveCurvature));
file.read((char*)&blueConcaveCurvature, sizeof(blueConcaveCurvature));
file.read((char*)&floatDummy, sizeof(floatDummy)); // alpha concave curvature
if (needToByteSwap) {
ByteSwapping::swapBytes(&redConcaveCurvature, 1);
ByteSwapping::swapBytes(&greenConcaveCurvature, 1);
ByteSwapping::swapBytes(&blueConcaveCurvature, 1);
}
const unsigned char redConcave =
static_cast<unsigned char>(redConcaveCurvature * 255.0);
const unsigned char greenConcave =
static_cast<unsigned char>(greenConcaveCurvature * 255.0);
const unsigned char blueConcave =
static_cast<unsigned char>(blueConcaveCurvature * 255.0);
//
// Color indicies - Create color table
//
if (numberOfVertices > 0) {
vertexColorTableIndices = new int[numberOfVertices];
unsigned char dummyUnsignedChar;
for (int i = 0; i < numberOfVertices; i++) {
unsigned char index;
file.read((char*)&index, sizeof(index));
file.read((char*)&dummyUnsignedChar, sizeof(dummyUnsignedChar));
file.read((char*)&dummyUnsignedChar, sizeof(dummyUnsignedChar));
file.read((char*)&dummyUnsignedChar, sizeof(dummyUnsignedChar));
//
// See if color index already in color table
//
int colorTableIndex = -1;
for (unsigned int j = 0; j < colorTable.size(); j++) {
if (colorTable[j].brainVoyagerIndex == index) {
colorTableIndex = static_cast<int>(j);
}
}
//
// Create new color table element ?
//
if (colorTableIndex < 0) {
colorTable.push_back(BrainVoyagerColorTableElement(index));
colorTableIndex = static_cast<int>(colorTable.size()) - 1;
}
//
// set vertice's color table index
//
vertexColorTableIndices[i] = colorTableIndex;
}
//
// Set the convex and concave colors that are colors 0 & 1
//
if (colorTable.size() > 1) {
colorTable[0].name.append("_convex");
colorTable[0].rgb[0] = redConvex;
colorTable[0].rgb[1] = greenConvex;
colorTable[0].rgb[2] = blueConvex;
colorTable[1].name.append("_concave");
colorTable[1].rgb[0] = redConcave;
colorTable[1].rgb[1] = greenConcave;
colorTable[1].rgb[2] = blueConcave;
}
}
/*
//
// Color components
//
if (numberOfVertices > 0) {
vertexRedComponent = new unsigned char[numberOfVertices];
vertexGreenComponent = new unsigned char[numberOfVertices];
vertexBlueComponent = new unsigned char[numberOfVertices];
vertexAlphaComponent = new unsigned char[numberOfVertices];
for (int i = 0; i < numberOfVertices; i++) {
stream >> vertexRedComponent[i];
stream >> vertexGreenComponent[i];
stream >> vertexBlueComponent[i];
stream >> vertexAlphaComponent[i];
if (vertexRedComponent[i] == 0) {
vertexRedComponent[i] = redConvex;
vertexGreenComponent[i] = greenConvex;
vertexBlueComponent[i] = blueConvex;
}
else if (vertexRedComponent[i] == 1) {
vertexRedComponent[i] = redConcave;
vertexGreenComponent[i] = greenConcave;
vertexBlueComponent[i] = blueConcave;
}
//if (vertexRedComponent[i] != 0) {
std::cout << "node " << i
<< " (" << static_cast<int>(vertexRedComponent[i])
<< " ," << static_cast<int>(vertexGreenComponent[i])
<< " ," << static_cast<int>(vertexBlueComponent[i])
<< " ," << static_cast<int>(vertexAlphaComponent[i])
<< ")" << std::endl;
//}
}
}
*/
//
// Vertex Neighbors
//
for (int i = 0; i < numberOfVertices; i++) {
int numNeighbors;
file.read((char*)&numNeighbors, sizeof(numNeighbors));
if (needToByteSwap) {
ByteSwapping::swapBytes(&numNeighbors, 1);
}
if (i == 147644) {
std::cout << "Node " << i << " has "
<< numNeighbors << " neighbors." << std::endl;
}
for (int j = 0; j < numNeighbors; j++) {
file.read((char*)&intDummy, sizeof(intDummy));
}
}
//
// Triangles
//
triangles = new int[numberOfTriangles * 3];
file.read((char*)triangles, numberOfTriangles * 3 * 4);
if (needToByteSwap) {
ByteSwapping::swapBytes(triangles, numberOfTriangles * 3);
}
//
// Number of string elements
//
int numberOfStripElements;
file.read((char*)&numberOfStripElements, sizeof(numberOfStripElements));
if (needToByteSwap) {
ByteSwapping::swapBytes(&numberOfStripElements, 1);
}
//if (DebugControl::getDebugOn()) {
std::cout << "Version: " << version << std::endl;
std::cout << "Number of vertices: " << numberOfVertices << std::endl;
std::cout << "Number of triangles: " << numberOfTriangles << std::endl;
std::cout << "Number of strip elements: " << numberOfStripElements
<< std::endl;
std::cout << "Color table size: " << colorTable.size() << std::endl;
//}
clearModified();
}
catch (FileException& e) {
file.close();
clearModified();
throw e;
}
file.close();
}
if (DebugControl::getDebugOn()) {
std::cout << "Time to read " << FileUtilities::basename(filename).toAscii().constData()
<< " was "
<< (static_cast<float>(timer.elapsed()) / 1000.0)
<< " seconds." << std::endl;
}
}
/**
* Read the file.
*/
/*
void
BrainVoyagerFile::readFile(const QString& filenameIn) throw (FileException)
{
const QString filename2(filenameIn);
clear();
filename = filename2);
//
// We always need to byte swap on both MSB & LSB systems. It is
// something to do with the way QDataStream works.
//
const bool needToByteSwap = true;
QTime timer;
timer.start();
QFile file(filename);
if (file.open(IO_ReadOnly)) {
try {
QDataStream stream(&file);
if (DebugControl::getDebugOn()) {
switch(stream.byteOrder()) {
case QDataStream::BigEndian:
std::cout << "Brain Voyager File stream is big endian" << std::endl;
break;
case QDataStream::LittleEndian:
std::cout << "Brain Voyager File stream is little endian" << std::endl;
break;
}
}
int intDummy;
float floatDummy;
stream >> version;
stream >> intDummy;
stream >> numberOfVertices;
stream >> numberOfTriangles;
if (DebugControl::getDebugOn()) {
float fv = version;
ByteSwapping::swapBytes(&fv, 1);
std::cout << "version: " << version
<< " version byte swapped: " << fv << std::endl;
}
stream >> floatDummy; // mesh center x
stream >> floatDummy; // mesh center y
stream >> floatDummy; // mesh center z
if (needToByteSwap) {
ByteSwapping::swapBytes(&version, 1);
ByteSwapping::swapBytes(&numberOfVertices, 1);
ByteSwapping::swapBytes(&numberOfTriangles, 1);
}
if (numberOfVertices > 0) {
//
// Read vertices
//
verticesX = new float[numberOfVertices];
verticesY = new float[numberOfVertices];
verticesZ = new float[numberOfVertices];
stream.readRawBytes((char*)verticesX, (numberOfVertices * 4));
stream.readRawBytes((char*)verticesY, (numberOfVertices * 4));
stream.readRawBytes((char*)verticesZ, (numberOfVertices * 4));
if (needToByteSwap) {
ByteSwapping::swapBytes(verticesX, numberOfVertices);
ByteSwapping::swapBytes(verticesY, numberOfVertices);
ByteSwapping::swapBytes(verticesZ, numberOfVertices);
}
//
// Skip normals
//
QIODevice::Offset pos = file.at();
pos += numberOfVertices * 4 * 3;
file.at(pos);
}
float redConvexCurvature, greenConvexCurvature, blueConvexCurvature;
stream >> redConvexCurvature;
stream >> greenConvexCurvature;
stream >> blueConvexCurvature;
stream >> floatDummy; // alpha convex curvature
if (needToByteSwap) {
ByteSwapping::swapBytes(&redConvexCurvature, 1);
ByteSwapping::swapBytes(&greenConvexCurvature, 1);
ByteSwapping::swapBytes(&blueConvexCurvature, 1);
}
const unsigned char redConvex =
static_cast<unsigned char>(redConvexCurvature * 255.0);
const unsigned char greenConvex =
static_cast<unsigned char>(greenConvexCurvature * 255.0);
const unsigned char blueConvex =
static_cast<unsigned char>(blueConvexCurvature * 255.0);
float redConcaveCurvature, greenConcaveCurvature, blueConcaveCurvature;
stream >> redConcaveCurvature;
stream >> greenConcaveCurvature;
stream >> blueConcaveCurvature;
stream >> floatDummy; // alpha concave curvature
if (needToByteSwap) {
ByteSwapping::swapBytes(&redConcaveCurvature, 1);
ByteSwapping::swapBytes(&greenConcaveCurvature, 1);
ByteSwapping::swapBytes(&blueConcaveCurvature, 1);
}
const unsigned char redConcave =
static_cast<unsigned char>(redConcaveCurvature * 255.0);
const unsigned char greenConcave =
static_cast<unsigned char>(greenConcaveCurvature * 255.0);
const unsigned char blueConcave =
static_cast<unsigned char>(blueConcaveCurvature * 255.0);
//
// Color indicies - Create color table
//
if (numberOfVertices > 0) {
vertexColorTableIndices = new int[numberOfVertices];
unsigned char dummyUnsignedChar;
for (int i = 0; i < numberOfVertices; i++) {
unsigned char index;
stream >> index;
stream >> dummyUnsignedChar;
stream >> dummyUnsignedChar;
stream >> dummyUnsignedChar;
//
// See if color index already in color table
//
int colorTableIndex = -1;
for (unsigned int j = 0; j < colorTable.size(); j++) {
if (colorTable[j].brainVoyagerIndex == index) {
colorTableIndex = static_cast<int>(j);
}
}
//
// Create new color table element ?
//
if (colorTableIndex < 0) {
colorTable.push_back(BrainVoyagerColorTableElement(index));
colorTableIndex = static_cast<int>(colorTable.size());
}
//
// set vertice's color table index
//
vertexColorTableIndices[i] = colorTableIndex;
}
//
// Set the convex and concave colors that are colors 0 & 1
//
if (colorTable.size() > 1) {
colorTable[0].name.append("_convex");
colorTable[0].rgb[0] = redConvex;
colorTable[0].rgb[1] = greenConvex;
colorTable[0].rgb[2] = blueConvex;
colorTable[1].name.append("_concave");
colorTable[1].rgb[0] = redConcave;
colorTable[1].rgb[1] = greenConcave;
colorTable[1].rgb[2] = blueConcave;
}
}
//
// Vertex Neighbors
//
for (int i = 0; i < numberOfVertices; i++) {
int numNeighbors;
stream >> numNeighbors;
if (needToByteSwap) {
ByteSwapping::swapBytes(&numNeighbors, 1);
}
if (i == 147644) {
std::cout << "Node " << i << " has "
<< numNeighbors << " neighbors." << std::endl;
}
for (int j = 0; j < numNeighbors; j++) {
stream >> intDummy;
}
}
//
// Triangles
//
triangles = new int[numberOfTriangles * 3];
stream.readRawBytes((char*)triangles, numberOfTriangles * 3 * 4);
if (needToByteSwap) {
ByteSwapping::swapBytes(triangles, numberOfTriangles * 3);
}
//
// Number of string elements
//
int numberOfStripElements;
stream >> numberOfStripElements;
if (needToByteSwap) {
ByteSwapping::swapBytes(&numberOfStripElements, 1);
}
//if (DebugControl::getDebugOn()) {
std::cout << "Version: " << version << std::endl;
std::cout << "Number of vertices: " << numberOfVertices << std::endl;
std::cout << "Number of triangles: " << numberOfTriangles << std::endl;
std::cout << "Number of strip elements: " << numberOfStripElements
<< std::endl;
//}
clearModified();
}
catch (FileException& e) {
file.close();
clearModified();
throw e;
}
file.close();
}
else {
throw FileException(filename, "Failure trying to open: ");
}
if (DebugControl::getDebugOn()) {
std::cout << "Time to read " << FileUtilities::basename(filename)
<< " was "
<< (static_cast<float>(timer.elapsed()) / 1000.0)
<< " seconds." << std::endl;
}
}
*/
/**
* Write the file.
*/
void
BrainVoyagerFile::writeFile(const QString& filenameIn) throw (FileException)
{
throw FileException(filenameIn, "Writing brain voyager file not supported.");
}
//---------------------------------------------------------------------------------
/**
* Constructor.
*/
BrainVoyagerColorTableElement::BrainVoyagerColorTableElement(const int brainVoyagerIndexIn)
{
initialize();
brainVoyagerIndex = brainVoyagerIndexIn;
std::ostringstream str;
str << "Color_"
<< brainVoyagerIndex;
name = str.str().c_str();
switch(brainVoyagerIndex) {
case 24:
name.append("_white_med_wall_and_cuts");
rgb[0] = 255;
rgb[1] = 255;
rgb[2] = 255;
break;
case 32:
name.append("_bright_blue");
rgb[0] = 24;
rgb[1] = 93;
rgb[2] = 255;
break;
case 33:
name.append("_dark_blue");
rgb[0] = 16;
rgb[1] = 80;
rgb[2] = 222;
break;
case 34:
name.append("_bright_green");
rgb[0] = 16;
rgb[1] = 255;
rgb[2] = 98;
break;
case 35:
name.append("_dark_green");
rgb[0] = 24;
rgb[1] = 218;
rgb[2] = 82;
break;
case 240:
name.append("_light_gray_cuts");
rgb[0] = 200;
rgb[1] = 200;
rgb[2] = 200;
break;
}
}
/**
* Constructor.
*/
BrainVoyagerColorTableElement::BrainVoyagerColorTableElement()
{
initialize();
}
/**
* Destructor.
*/
BrainVoyagerColorTableElement::~BrainVoyagerColorTableElement()
{
}
/**
*
*/
void
BrainVoyagerColorTableElement::getRgb(unsigned char rgbOut[3]) const
{
rgbOut[0] = rgb[0];
rgbOut[1] = rgb[1];
rgbOut[2] = rgb[2];
}
/**
* Initialize the elements.
*/
void
BrainVoyagerColorTableElement::initialize()
{
brainVoyagerIndex = -1;
rgb[0] = 255;
rgb[1] = 0;
rgb[2] = 0;
}
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