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FiberODFAnalysis.cpp
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/*This file is part of the FEBio Studio source code and is licensed under the MIT license
listed below.
See Copyright-FEBio-Studio.txt for details.
Copyright (c) 2021 University of Utah, The Trustees of Columbia University in
the City of New York, and others.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.*/
#include "FiberODFAnalysis.h"
#include <qopengl.h>
#include "ImageModel.h"
#include <FEAMR/sphericalHarmonics.h>
#include <FEAMR/SpherePointsGenerator.h>
#include <MeshTools/FENNQuery.h>
#include <PostLib/ColorMap.h>
#include <MeshLib/GMesh.h>
#include <GLLib/GLCamera.h>
#include <complex>
#include <sstream>
#include "SITKTools.h"
#include <FECore/besselIK.h>
#include <GLWLib/GLWidgetManager.h>
#include <GLLib/glx.h>
#include <FEBioOpt/FEBioOpt.h>
#ifdef min
#undef min
#endif
#ifdef max
#undef max
#endif
#include <algorithm>
#ifdef __APPLE__
#include <OpenGL/GLU.h>
#else
#include <GL/glu.h>
#endif
#ifndef M_PI
#define M_PI 3.141592653589793
#endif
using std::vector;
using std::complex;
using sphere = SpherePointsGenerator;
//==================================================================
CODF::CODF() : m_odf(sphere::GetNumNodes(FULL), 0.0), m_meanIntensity(0)
{
m_el[0] = m_el[1] = m_el[2] = 1.0;
m_ev[0] = vec3d(1, 0, 0);
m_ev[1] = vec3d(0, 1, 0);
m_ev[2] = vec3d(0, 0, 1);
m_radius = 1.0;
m_meanIntensity = 0.0;
m_EFD_FRD = 0.0;
m_VM3_FRD = 0.0;
m_FA = 0.0;
m_GFA = 0.0;
};
//==================================================================
#ifdef HAS_ITK
#include <SimpleITK.h>
namespace sitk = itk::simple;
#endif
class CFiberODFAnalysis::Imp
{
public:
Imp(CFiberODFAnalysis* parent) : parent(parent) {}
#ifdef HAS_ITK
// calculate root-mean-square of vector x
double rms(const vector<double>& x)
{
if (x.empty()) return 0.0;
double rms = 0.0;
for (double xi : x) rms += xi * xi;
rms = sqrt(rms / (double)x.size());
return rms;
}
// calculate standard deviation of vector x
double stddev(const vector<double>& x)
{
if (x.empty()) return 0.0;
double mu = 0.0;
size_t n = x.size();
for (size_t i = 0; i < n; ++i) mu += x[i];
mu /= (double)x.size();
double sum = 0.0;
for (size_t i = 0; i < n; ++i) sum += (x[i] - mu) * (x[i] - mu);
sum = sqrt(sum / ((double)n - 1.0));
return sum;
}
// This function generates the ODF from the subvolume image
bool generateODF(CODF& odf, sitk::Image& img, int nsh)
{
// process the image (apply butterworth and calculate power spectrum)
// Note that the image is overwritten with the filtered power spectrum
processImage(img);
// allocate odf
odf.m_sphHarmonics.resize(nsh);
// project image onto unit sphere
std::vector<double> reduced = std::vector<double>(sphere::GetNumNodes(FULL), 0);
reduceAmp(img, reduced);
// see if user cancelled
if (parent->IsCanceled()) { parent->clear(); return false; }
// odf = A*B*reduced
vector<double> Bxr(parent->m_B.rows(), 0.0);
parent->m_B.mult(reduced, Bxr);
parent->m_A.mult(Bxr, odf.m_odf);
parent->updateProgressIncrement(0.75);
// normalize odf
parent->normalizeODF(odf.m_odf);
// Calculate spherical harmonics
parent->m_B.mult(odf.m_odf, odf.m_sphHarmonics);
// Recalc ODF based on spherical harmonics
parent->m_T.mult(odf.m_sphHarmonics, odf.m_odf);
parent->normalizeODF(odf.m_odf);
// Calcualte ODF_GFA
odf.m_GFA = stddev(odf.m_odf) / rms(odf.m_odf);
// build the meshes
parent->buildMesh(&odf);
parent->buildRemesh(&odf);
parent->normalizeODF(odf.m_remeshODF);
// do the fitting stats
if (parent->GetBoolValue(FITTING)) parent->calculateFits(&odf);
return true;
}
// Note that the returned image is now a filtered power spectrum
void processImage(sitk::Image& current)
{
// Apply Butterworth filter
butterworthFilter(current);
current = sitk::Cast(current, sitk::sitkFloat32);
// Apply FFT and FFT shift
current = sitk::FFTPad(current);
current = sitk::ForwardFFT(current);
current = sitk::FFTShift(current);
// Obtain Power Spectrum
current = powerSpectrum(current);
// Remove DC component (does not have a direction and does not
// constitute fibrillar structures)
// NOTE: For some reason, this doesn't perfectly match zeroing out the same point in MATLAB
// and results in a slightly different max value in the ODF
auto currentSize = current.GetSize();
std::vector<uint32_t> index{ currentSize[0] / 2 + 1, currentSize[1] / 2 + 1, currentSize[2] / 2 + 1 };
current.SetPixelAsFloat(index, 0);
// Apply Radial FFT Filter
fftRadialFilter(current);
}
void butterworthFilter(sitk::Image& img)
{
double fraction = parent->GetFloatValue(BW_FRACTION);
double steepness = parent->GetFloatValue(BW_STEEPNESS);
uint32_t* data = img.GetBufferAsUInt32();
int nx = img.GetSize()[0];
int ny = img.GetSize()[1];
int nz = img.GetSize()[2];
double xStep = img.GetSpacing()[0];
double yStep = img.GetSpacing()[1];
double zStep = img.GetSpacing()[2];
double height = nx*xStep;
double width = ny*yStep;
double depth = nz*zStep;
double radMax = std::min({height, width, depth})/2;
radMax = 1;
double decent = radMax - radMax * fraction;
#pragma omp parallel for
for(int z = 0; z < nz; z++)
{
for(int y = 0; y < ny; y++)
{
for(int x = 0; x < nx; x++)
{
int xPos = x - nx/2;
int yPos = y - ny/2;
int zPos = z - nz/2;
int xPercent = xPos/nx;
int yPercent = yPos/ny;
int zPercent = zPos/nz;
double rad = sqrt(xPercent*xPercent + yPercent*yPercent + zPercent*zPercent);
int index = x + y*nx + z*nx*ny;
data[index] = data[index]/(1 + pow(rad/decent, 2*steepness));
}
}
}
}
sitk::Image powerSpectrum(sitk::Image& img)
{
int nx = img.GetSize()[0];
int ny = img.GetSize()[1];
int nz = img.GetSize()[2];
// create a new image that will store the power spectrum
sitk::Image PS(nx, ny, nz, sitk::sitkFloat32);
PS.SetSpacing(img.GetSpacing());
PS.SetOrigin(img.GetOrigin());
float* data = PS.GetBufferAsFloat();
float* cd = (float*) (img.GetBufferAsVoid());
#pragma omp parallel for
for (int z = 0; z < nz; z++)
{
float* ci = cd + 2 * z * nx * ny;
for (int y = 0; y < ny; y++)
{
for(int x = 0; x <nx; x++)
{
// NOTE: ITK's indexing is really slow.
// std::vector<uint32_t> index = {(unsigned int)x,(unsigned int)y,(unsigned int)z};
// complex<float> val = img.GetPixelAsComplexFloat32(index);
complex<float> val = { (*ci++), (*ci++) };
float ps = abs(val);
int newIndex = x + y*nx + z*nx*ny;
data[newIndex] = ps*ps;
}
}
}
return PS;
}
// This function filters the power spectrum.
void fftRadialFilter(sitk::Image& img)
{
float fLow = 1/parent->GetFloatValue(T_LOW);
float fHigh = 1/parent->GetFloatValue(T_HIGH);
int nx = img.GetSize()[0];
int ny = img.GetSize()[1];
int nz = img.GetSize()[2];
int minSize = std::min({nx, ny, nz})/2;
float* data = img.GetBufferAsFloat();
#pragma omp parallel for
for(int z = 0; z < nz; z++)
{
for(int y = 0; y < ny; y++)
{
for(int x = 0; x < nx; x++)
{
int xPos = x - nx/2;
int yPos = y - ny/2;
int zPos = z - nz/2;
double rad = sqrt(xPos*xPos + yPos*yPos + zPos*zPos);
double val = rad/minSize;
if ((val < fLow) || (val > fHigh))
{
size_t index = x + y*nx + z*nx*ny;
data[index] = 0;
}
}
}
}
}
void reduceAmp(sitk::Image& img, std::vector<double>& reduced)
{
float* data = img.GetBufferAsFloat();
int nx = img.GetSize()[0];
int ny = img.GetSize()[1];
int nz = img.GetSize()[2];
double xSize = img.GetSpacing()[0];
double ySize = img.GetSpacing()[1];
double zSize = img.GetSpacing()[2];
double zcount = 0;
auto& points = sphere::GetNodes(FULL);
#pragma omp parallel shared(img)
{
FSNNQuery query(&points);
query.Init();
std::vector<double> tmp(points.size(), 0.0);
#pragma omp for schedule(dynamic)
for (int z = 0; z < nz; z++)
{
if (parent->IsCanceled()) continue;
double wz = (z - nz / 2) / (nz*0.5);
for (int y = 0; y < ny; y++)
{
double wy = (y - ny / 2) / (ny * 0.5);
for (int x = 0; x < nx; x++)
{
double wx = (x - nx / 2) / (nx * 0.5);
double realX = wx/xSize;
double realY = wy/ySize;
double realZ = wz/zSize;
double rad = sqrt(realX*realX + realY*realY + realZ*realZ);
if(rad == 0) continue;
int closestIndex = query.Find(vec3d(realX/rad, realY/rad, realZ/rad));
int index = x + y*nx + z*nx*ny;
tmp[closestIndex] += data[index];
}
}
#pragma omp critical
{
zcount++;
parent->updateProgressIncrement(0.5*zcount / nz);
}
}
#pragma omp critical
for (int i = 0; i < points.size(); ++i)
{
reduced[i] += tmp[i];
}
}
}
#endif
private:
CFiberODFAnalysis* parent;
};
//==================================================================
CFiberODFAnalysis::CFiberODFAnalysis(CImageModel* img)
: CImageAnalysis(CImageAnalysis::FIBERODF, img), m_imp(new Imp(this)), m_lengthScale(10), m_hausd(0.05),
m_grad(1.3)
{
static int n = 1;
std::stringstream ss;
ss << "Fiber ODF Analysis" << n++;
SetName(ss.str());
m_processSelectedOnly = false;
m_overlapFraction = 0.2;
m_renderScale = 1;
m_nshowMesh = 0;
m_bshowRadial = false;
m_nshowSelectionBox = true;
m_ncolormode = 0;
m_rangeOption = 0;
m_userMin = 0;
m_userMax = 1;
m_ndivs = 10;
m_FAmin = m_FAmax = 0.0;
// Define the parameters
// (note that we are hiding the parameters that control the ODF. These are presented elsewhere.)
AddIntParam(16, "Harmonic Order")->SetState(Param_HIDDEN);
AddDoubleParam(30, "Low Freq Cutoff (pixels)")->SetState(Param_HIDDEN);
AddDoubleParam(2.0, "High Freq Cutoff (pixels)")->SetState(Param_HIDDEN);
AddIntParam(1, "X Divisions")->SetState(Param_HIDDEN);
AddIntParam(1, "Y Divisions")->SetState(Param_HIDDEN);
AddIntParam(1, "Z Divisions")->SetState(Param_HIDDEN);
AddDoubleParam(m_overlapFraction, "Overlap Fraction")->SetState(Param_HIDDEN);
AddBoolParam(true, "Do fitting analysis")->SetState(Param_HIDDEN);
AddDoubleParam(m_renderScale, "renderScale", "Render Scale")->SetFloatRange(0,1);
AddBoolParam(false, "Render Mesh Lines");
AddBoolParam(m_bshowRadial, "Show Radial Mesh");
AddIntParam(m_nshowMesh, "Show ODF", "Render ODF As...")->SetEnumNames("ODF\0ODF remeshed\0EFD\0VM3\0");
AddBoolParam(true, "Show Bounding boxes");
AddBoolParam(m_nshowSelectionBox, "Show Selection box");
AddIntParam(m_ncolormode, "Coloring mode")->SetEnumNames("ODF\0Fractional anisotropy\0");
AddIntParam(m_ndivs, "Divisions", "Legend Divisions")->SetIntRange(1,100);
AddIntParam(m_rangeOption, "Range", "Legend Range")->SetEnumNames("automatic\0user\0");
AddDoubleParam(m_userMin, "User min", "Legend Min");
AddDoubleParam(m_userMax, "User max", "Legend Max");
AddDoubleParam(0.2, "Butterworth fraction")->SetState(Param_HIDDEN);
AddDoubleParam(10., "Butterworth steepness")->SetState(Param_HIDDEN);
m_tex.SetDivisions(10);
m_tex.SetSmooth(true);
m_map.jet();
m_remeshMap.jet();
m_pbar = new GLLegendBar(&m_tex, 0, 0, 120, 600, GLLegendBar::ORIENT_VERTICAL);
m_pbar->align(GLW_ALIGN_LEFT | GLW_ALIGN_VCENTER);
m_pbar->SetType(GLLegendBar::GRADIENT);
m_pbar->copy_label("ODF");
m_pbar->ShowTitle(true);
m_pbar->hide();
CGLWidgetManager::GetInstance()->AddWidget(m_pbar);
}
CFiberODFAnalysis::~CFiberODFAnalysis()
{
clear();
CGLWidgetManager::GetInstance()->RemoveWidget(m_pbar);
delete m_imp;
}
void CFiberODFAnalysis::clear()
{
for(auto odf : m_ODFs)
{
delete odf;
}
m_ODFs.clear();
if (m_pbar) m_pbar->hide();
}
#ifdef HAS_ITK
void CFiberODFAnalysis::GenerateSubVolumes()
{
clear();
sitk::Image img = SITKImageFrom3DImage(m_img->Get3DImage());
img = sitk::Cast(img, sitk::sitkUInt32);
auto size = img.GetSize();
// get the requested subdivisions
int xDiv = GetIntValue(XDIV);
int yDiv = GetIntValue(YDIV);
int zDiv = GetIntValue(ZDIV);
double xOverlap = 0;
double yOverlap = 0;
double zOverlap = 0;
m_overlapFraction = GetFloatValue(OVERLAP);
int xppd = 0, yppd = 0, zppd = 0;
if (xDiv > 1 || yDiv > 1 || zDiv > 1)
{
xppd = size[0] / (xDiv - (xDiv - 1) * m_overlapFraction);
yppd = size[1] / (yDiv - (yDiv - 1) * m_overlapFraction);
zppd = size[2] / (zDiv - (zDiv - 1) * m_overlapFraction);
if (xDiv != 1) xOverlap = ((int)size[0] - xDiv * xppd) / (double)(-(xDiv - 1) * xppd);
if (yDiv != 1) yOverlap = ((int)size[1] - yDiv * yppd) / (double)(-(yDiv - 1) * yppd);
if (zDiv != 1) zOverlap = ((int)size[2] - zDiv * zppd) / (double)(-(zDiv - 1) * zppd);
}
else
{
xppd = size[0];
yppd = size[1];
zppd = size[2];
}
unsigned int xDivSize = xppd;
unsigned int yDivSize = yppd;
unsigned int zDivSize = zppd;
auto spacing = img.GetSpacing();
auto origin = img.GetOrigin();
double xDivSizePhys = xppd * spacing[0];
double yDivSizePhys = yppd * spacing[1];
double zDivSizePhys = zppd * spacing[2];
double radius = std::min({ xDivSizePhys, yDivSizePhys, zDivSizePhys }) * 0.375;
for (int currentZ = 0; currentZ < zDiv; ++currentZ)
for (int currentY = 0; currentY < yDiv; ++currentY)
for (int currentX = 0; currentX < xDiv; ++currentX)
{
CODF* odf = new CODF;
odf->m_position = vec3d(xDivSizePhys / 2 * (currentX * 2 + 1) - xDivSizePhys * xOverlap * currentX + origin[0], yDivSizePhys / 2 * (currentY * 2 + 1) - yDivSizePhys * yOverlap * currentY + origin[1], zDivSizePhys / 2 * (currentZ * 2 + 1) - zDivSizePhys * zOverlap * currentZ + origin[2]);
odf->m_radius = radius;
odf->m_box = BOX(-xDivSizePhys / 2.0, -yDivSizePhys / 2.0, -zDivSizePhys / 2.0, xDivSizePhys / 2.0, yDivSizePhys / 2.0, zDivSizePhys / 2.0);
m_ODFs.push_back(odf);
}
}
// calculate mean image intensity
double meanImageIntensity(sitk::Image& img)
{
double meanIntensity = 0;
auto data = img.GetBufferAsUInt32();
auto size = img.GetNumberOfPixels();
for (int index = 0; index < size; index++)
{
meanIntensity += data[index];
}
meanIntensity /= size;
return meanIntensity;
}
// run the ODF analysis
void CFiberODFAnalysis::run()
{
resetProgress();
setCurrentTask("Starting ODF Analysis ...");
// generate the subvolumes
if (m_ODFs.empty()) GenerateSubVolumes();
sitk::Image img = SITKImageFrom3DImage(m_img->Get3DImage());
img = sitk::Cast(img, sitk::sitkUInt32);
int xDiv = GetIntValue(XDIV);
int yDiv = GetIntValue(YDIV);
int zDiv = GetIntValue(ZDIV);
auto size = img.GetSize();
double xOverlap = 0;
double yOverlap = 0;
double zOverlap = 0;
int xppd = 0, yppd = 0, zppd = 0;
if(xDiv > 1 || yDiv > 1 || zDiv > 1)
{
xppd = size[0]/(xDiv-(xDiv-1)*m_overlapFraction);
yppd = size[1]/(yDiv-(yDiv-1)*m_overlapFraction);
zppd = size[2]/(zDiv-(zDiv-1)*m_overlapFraction);
if(xDiv != 1) xOverlap = ((int)size[0] - xDiv*xppd)/(double)(-(xDiv-1)*xppd);
if(yDiv != 1) yOverlap = ((int)size[1] - yDiv*yppd)/(double)(-(yDiv-1)*yppd);
if(zDiv != 1) zOverlap = ((int)size[2] - zDiv*zppd)/(double)(-(zDiv-1)*zppd);
}
else
{
xppd = size[0];
yppd = size[1];
zppd = size[2];
}
unsigned int xDivSize = xppd;
unsigned int yDivSize = yppd;
unsigned int zDivSize = zppd;
auto spacing = img.GetSpacing();
auto origin = img.GetOrigin();
double xDivSizePhys = xppd*spacing[0];
double yDivSizePhys = yppd*spacing[1];
double zDivSizePhys = zppd*spacing[2];
double radius = std::min({xDivSizePhys, yDivSizePhys, zDivSizePhys})*0.375;
sitk::ExtractImageFilter extractFilter;
extractFilter.SetSize(std::vector<unsigned int> {xDivSize, yDivSize, zDivSize});
vector<vec3d>& points = sphere::GetNodes(FULL);
// calculate the spherical coordinates of the points
vector<double> theta;
vector<double> phi;
getSphereCoords(points, theta, phi);
// Calculate spherical harmonics coefficients
m_T = *compSH(GetIntValue(ORDER), theta, phi);
auto C = complLapBel_Coef();
m_A = m_T*(*C);
// Calculate "inverse" of T. (i.e. if a=T*b, then b = B*a)
// TODO: maybe make this a member of matrix
matrix transposeT = m_T.transpose();
m_B = (transposeT*(m_T)).inverse()*transposeT;
// start the loop over the subvolumes
m_totalSteps = xDiv * yDiv * zDiv;
assert(m_totalSteps == m_ODFs.size());
m_progress = 0;
double maxIntensity = -1;
setCurrentTask("Building ODFs ...");
for (int currentZ = 0; currentZ < zDiv; ++currentZ)
for (int currentY = 0; currentY < yDiv; ++currentY)
for (int currentX = 0; currentX < xDiv; ++currentX)
{
// see if user cancelled
if (IsCanceled()) { clear(); return; }
// calculate sub-volume index
m_stepsCompleted = currentX + currentY * xDiv + currentZ * xDiv * yDiv;
// process the next subvolume
CODF& odf = *(m_ODFs[m_stepsCompleted]);
if ((m_processSelectedOnly == false) || (odf.m_selected))
{
// check and report progress
std::stringstream ss;
Log("\n\n");
ss << "Building ODFs (" << m_stepsCompleted + 1 << "/" << m_totalSteps << ")...";
m_task = ss.str();
setCurrentTask(m_task.c_str(), m_progress);
// extract the sub-image
extractFilter.SetIndex(std::vector<int> {
(int)(xDivSize* currentX* (1 - xOverlap)),
(int)(yDivSize* currentY* (1 - yOverlap)),
(int)(zDivSize* currentZ* (1 - zOverlap))});
sitk::Image current = extractFilter.Execute(img);
// Let's check the mean intensity of subvolume
// If the mean intensity is zero, all voxel values are zero and the analysis will just produce nans.
double meanIntensity = meanImageIntensity(current);
if (meanIntensity != 0)
{
if (meanIntensity > maxIntensity) maxIntensity = meanIntensity;
// generate the odf from the image
bool b = m_imp->generateODF(odf, current, C->columns());
odf.m_meanIntensity = meanIntensity;
// delete image
current = sitk::Image();
}
else Log("subvolume %d skipped due to zero mean intensity\n", m_stepsCompleted);
}
updateProgressIncrement(1.0);
}
// normalize mean intensities
for(auto odf : m_ODFs)
{
odf->m_meanIntensity /= maxIntensity;
}
setProgress(100);
SelectODF(0);
UpdateStats();
UpdateColorBar();
UpdateAllMeshes();
m_pbar->show();
}
#else
void CFiberODFAnalysis::run() {}
void CFiberODFAnalysis::GenerateSubVolumes() {}
#endif
bool CFiberODFAnalysis::UpdateData(bool bsave)
{
if (bsave)
{
bool updateMeshes = false;
if ((m_bshowRadial != GetBoolValue(RADIAL)) ||
(m_nshowMesh != GetIntValue(SHOW_MESH)))
{
m_bshowRadial = GetBoolValue(RADIAL);
m_nshowMesh = GetIntValue(SHOW_MESH);
updateMeshes = true;
}
if(m_renderScale != GetFloatValue(RENDERSCALE))
{
m_renderScale = GetFloatValue(RENDERSCALE);
}
if (m_ncolormode != GetIntValue(COLOR_MODE))
{
m_ncolormode = GetIntValue(COLOR_MODE);
updateMeshes = true;
}
if (m_rangeOption != GetIntValue(RANGE))
{
m_rangeOption = GetIntValue(RANGE);
updateMeshes = true;
}
if ((m_userMin != GetFloatValue(USERMIN)) ||
(m_userMax != GetFloatValue(USERMAX)))
{
m_userMin = GetFloatValue(USERMIN);
m_userMax = GetFloatValue(USERMAX);
updateMeshes = true;
}
if (m_ndivs != GetIntValue(DIVS))
{
m_ndivs = GetIntValue(DIVS);
m_pbar->SetDivisions(m_ndivs);
}
if (m_overlapFraction != GetFloatValue(OVERLAP))
{
m_overlapFraction = GetFloatValue(OVERLAP);
updateMeshes = true;
}
if (updateMeshes)
{
UpdateColorBar();
UpdateAllMeshes();
}
}
return false;
}
void CFiberODFAnalysis::UpdateAllMeshes()
{
bool bradial = GetBoolValue(RADIAL);
int nshow = GetIntValue(SHOW_MESH);
int odfs = m_ODFs.size();
#pragma omp parallel for
for (int index = 0; index < odfs; index++)
{
auto odf = m_ODFs[index];
if (odf->IsValid())
{
switch (nshow)
{
// Don't break here so remesh is always updated
case 0: UpdateMesh(odf, odf->m_odf, m_ODFmin, m_ODFmax, bradial);
case 1: UpdateRemesh(odf, bradial); break;
case 2: UpdateSmallMesh(odf, odf->m_EFD_ODF, bradial); break;
case 3: UpdateSmallMesh(odf, odf->m_VM3_ODF, bradial); break;
}
}
}
}
void CFiberODFAnalysis::UpdateStats()
{
// collect some global stats
if (m_ODFs.empty()) return;
// global ODF ranges
m_ODFmin = 1e12;
m_ODFmax = 0;
for (auto odf : m_ODFs)
{
vector<double>& val = odf->m_odf;
if (val.empty() == false)
{
double min = *std::min_element(val.begin(), val.end());
double max = *std::max_element(val.begin(), val.end());
if (min < m_ODFmin) m_ODFmin = min;
if (max > m_ODFmax) m_ODFmax = max;
}
}
// global remeshed ODF ranges
m_remeshMin = 1e12;
m_remeshMax = 0;
for (auto odf : m_ODFs)
{
vector<double>& val = odf->m_remeshODF;
if (val.empty() == false)
{
double min = *std::min_element(val.begin(), val.end());
double max = *std::max_element(val.begin(), val.end());
if (min < m_remeshMin) m_remeshMin = min;
if (max > m_remeshMax) m_remeshMax = max;
}
}
// global EFD ranges
m_EFDmin = 1e12;
m_EFDmax = 0;
for (auto odf : m_ODFs)
{
vector<double>& val = odf->m_EFD_ODF;
if (val.empty() == false)
{
double min = *std::min_element(val.begin(), val.end());
double max = *std::max_element(val.begin(), val.end());
if (min < m_EFDmin) m_EFDmin = min;
if (max > m_EFDmax) m_EFDmax = max;
}
}
// global VM3 ranges
m_VM3min = 1e12;
m_VM3max = 0;
for (auto odf : m_ODFs)
{
vector<double>& val = odf->m_VM3_ODF;
if (val.empty() == false)
{
double min = *std::min_element(val.begin(), val.end());
double max = *std::max_element(val.begin(), val.end());
if (min < m_VM3min) m_VM3min = min;
if (max > m_VM3max) m_VM3max = max;
}
}
// global FA
m_FAmin = m_FAmax = m_ODFs[0]->m_FA;
for (auto odf : m_ODFs)
{
double fa = odf->m_FA;
if (fa < m_FAmin) m_FAmin = fa;
if (fa > m_FAmax) m_FAmax = fa;
}
}
void CFiberODFAnalysis::UpdateColorBar()
{
int colorMode = GetIntValue(COLOR_MODE);
if (colorMode == 0)
{
int nshow = GetIntValue(SHOW_MESH);
double vmin = 0, vmax = 1.0;
const char* szlabel = "";
switch (nshow)
{
case 0: vmin = m_ODFmin; vmax = m_ODFmax; szlabel = "ODF"; break;
case 1: vmin = m_remeshMin; vmax = m_remeshMax; szlabel = "ODF"; break;
case 2: vmin = m_EFDmin; vmax = m_EFDmax; szlabel = "EFD"; break;
case 3: vmin = m_VM3min; vmax = m_VM3max; szlabel = "VM3"; break;
}
if (m_rangeOption != 0)
{
vmin = m_userMin;
vmax = m_userMax;
// The remshed ODFs are shown when the camera is moving even when the option to display the
// full resultoion ODFs is selected. To keep the color mapping consistent, we need to adjust
// the range of the remeshed ODFs to match the full resolution ODFs.
if(nshow == 0)
{
double low = m_userMin - (m_userMax - m_userMin) * (m_remeshMin - m_ODFmin) / (m_ODFmax - m_ODFmin);
double high = m_userMin + (m_userMax - m_userMin) * (m_remeshMax - m_ODFmin) / (m_ODFmax - m_ODFmin);
m_remeshMap.SetRange(low, high);
}
// Otherwise, we just use the user defined range
else m_remeshMap.SetRange(m_userMin, m_userMax);
}
else
{
// Here we set the range of the remeshed ODFs in the event that we are displaying the
// full resolution ODFs. This keeps the color mapping consistent while the camera is moving.
m_remeshMap.SetRange(m_remeshMin, m_remeshMax);
}
m_pbar->SetRange(vmin, vmax);
m_pbar->copy_label(szlabel);
m_map.SetRange(vmin, vmax);
}
else
{
double vmin = m_FAmin;
double vmax = m_FAmax;
if (m_rangeOption != 0)
{
vmin = m_userMin;
vmax = m_userMax;
}
m_pbar->SetRange(vmin, vmax);
m_pbar->copy_label("FA");
m_map.SetRange(vmin, vmax);
}
}
void CFiberODFAnalysis::normalizeODF(std::vector<double>& odf)
{
double sum = 0;
for (int index = 0; index < odf.size(); index++)
{
double val = odf[index];
if (val < 0)
{
odf[index] = 0;
}
else
{
odf[index] = val;
}
sum += odf[index];
}
for (int index = 0; index < odf.size(); index++)
{
odf[index] /= sum;
}
}
void RenderEllipsoid(GLUquadricObj* po, float* l, vec3f* e)
{
float smax = 0.f;
float sx = fabs(l[0]); if (sx > smax) smax = sx;
float sy = fabs(l[1]); if (sy > smax) smax = sy;
float sz = fabs(l[2]); if (sz > smax) smax = sz;
if (smax < 1e-7f) return;
if (sx < 0.01 * smax) sx = 0.01f * smax;
if (sy < 0.01 * smax) sy = 0.01f * smax;
if (sz < 0.01 * smax) sz = 0.01f * smax;
glPushMatrix();
vec3f n = e[0] ^ e[1];
if (n * e[2] < 0) e[2] = -e[2];
GLfloat m[4][4] = { 0 };
m[3][3] = 1.f;
m[0][0] = e[0].x; m[0][1] = e[0].y; m[0][2] = e[0].z;
m[1][0] = e[1].x; m[1][1] = e[1].y; m[1][2] = e[1].z;
m[2][0] = e[2].x; m[2][1] = e[2].y; m[2][2] = e[2].z;
glMultMatrixf(&m[0][0]);
glScalef(sx, sy, sz);
gluSphere(po, 1.f, 32, 32);
glPopMatrix();
}
void CFiberODFAnalysis::render(CGLCamera* cam)
{
if (IsActive() == false)
{
m_pbar->hide();
return;
}
else if (m_ODFs.empty() == false)
{
m_pbar->show();
}
glPushAttrib(GL_ENABLE_BIT);
glEnable(GL_COLOR_MATERIAL);
GLfloat spc[4] = { 0, 0, 0, 1.f };
glMaterialfv(GL_FRONT_AND_BACK, GL_SPECULAR, spc);
// render the meshes (and selection box)
bool showBoundingBoxes = GetBoolValue(SHOW_BOUND_BOX);
bool showSelBox = GetBoolValue(SHOW_SELBOX);
CODF* sel = nullptr;
int showMesh = GetIntValue(SHOW_MESH);