void subtractBackgroundRamp(Image<DOUBLE> &I, int bg_radius)
{
int bg_radius2 = bg_radius * bg_radius;
fit_point3D point;
std::vector<fit_point3D> allpoints;
DOUBLE pA, pB, pC, avgbg, stddevbg, minbg, maxbg;
if (I().getDim() == 3)
REPORT_ERROR("ERROR %% calculateBackgroundRamp is not implemented for 3D data!");
FOR_ALL_ELEMENTS_IN_ARRAY2D(I())
{
if (i*i + j*j > bg_radius2)
{
point.x = j;
point.y = i;
point.z = A2D_ELEM(I(), i, j);
point.w = 1.;
allpoints.push_back(point);
}
}
fitLeastSquaresPlane(allpoints, pA, pB, pC);
// Substract the plane from the image
FOR_ALL_ELEMENTS_IN_ARRAY2D(I())
{
A2D_ELEM(I(), i, j) -= pA * j + pB * i + pC;
}
}
TEST( MultidimTest, getRealFromComplex)
{
MultidimArray<std::complex <double> > mSource(2,2);
MultidimArray<double> mdTarget;
A2D_ELEM(mSource,0,0) = (std::complex<double>(0,0));
A2D_ELEM(mSource,1,0) = (std::complex<double>(1,0));
A2D_ELEM(mSource,0,1) = (std::complex<double>(2,0));
A2D_ELEM(mSource,1,1) = (std::complex<double>(3,0));
mSource.getReal(mdTarget);
EXPECT_EQ(DIRECT_MULTIDIM_ELEM(mSource, 0).real(),DIRECT_MULTIDIM_ELEM(mdTarget,0));
EXPECT_EQ(DIRECT_MULTIDIM_ELEM(mSource, 1).real(),DIRECT_MULTIDIM_ELEM(mdTarget,1));
EXPECT_EQ(DIRECT_MULTIDIM_ELEM(mSource, 2).real(),DIRECT_MULTIDIM_ELEM(mdTarget,2));
EXPECT_EQ(DIRECT_MULTIDIM_ELEM(mSource, 3).real(),DIRECT_MULTIDIM_ELEM(mdTarget,3));
}
//#define DEBUG
blobtype best_blob(double alpha_0, double alpha_F, double inc_alpha,
double a_0, double a_F, double inc_a, double w, double *target_att,
int target_length)
{
blobtype retval;
retval.order = 2;
int alpha_size = FLOOR((alpha_F - alpha_0) / inc_alpha + 1);
int a_size = FLOOR((a_F - a_0) / inc_a + 1);
Image<double> att, ops;
att().resize(alpha_size, a_size);
ops().resize(alpha_size, a_size);
int i, j;
double a, alpha, best_a = -1, best_alpha = -1;
double best_ops = 1e10, best_att = 0;
for (i = 0, alpha = alpha_0; i < alpha_size; alpha += inc_alpha, i++)
for (j = 0, a = a_0; j < a_size; a += inc_a, j++)
{
retval.radius = a;
retval.alpha = alpha;
A2D_ELEM(att(), i, j) = blob_att(w, retval);
A2D_ELEM(ops(), i, j) = blob_ops(w, retval);
if (j > 0)
for (int n = target_length - 1; n >= 0; n--)
if (A2D_ELEM(att(), i, j - 1) > target_att[n] &&
A2D_ELEM(att(), i, j) < target_att[n])
{
A2D_ELEM(att(), i, j) = 0;
if (A2D_ELEM(ops(), i, j - 1) < best_ops &&
A2D_ELEM(att(), i, j - 1) >= best_att)
{
best_alpha = alpha;
best_a = a - inc_a;
best_ops = A2D_ELEM(ops(), i, j - 1);
best_att = target_att[n];
}
}
}
#ifdef DEBUG
att.write((std::string)"att" + floatToString(w) + ".xmp");
ops.write((std::string)"ops" + floatToString(w) + ".xmp");
#endif
retval.radius = best_a;
retval.alpha = best_alpha;
return retval;
}
void CTF::getCenteredImage(MultidimArray<DOUBLE> &result, DOUBLE Tm,
bool do_abs, bool do_only_flip_phases, bool do_intact_until_first_peak, bool do_damping)
{
result.setXmippOrigin();
DOUBLE xs = (DOUBLE)XSIZE(result) * Tm;
DOUBLE ys = (DOUBLE)YSIZE(result) * Tm;
FOR_ALL_ELEMENTS_IN_ARRAY2D(result)
{
DOUBLE x = (DOUBLE)j / xs;
DOUBLE y = (DOUBLE)i / ys;
A2D_ELEM(result, i, j) = getCTF(x, y, do_abs, do_only_flip_phases, do_intact_until_first_peak, do_damping);
}
}
//#define DEBUG
void normalize_tomography(MultidimArray<double> &I, double tilt, double &mui,
double &sigmai, bool tiltMask, bool tomography0,
double mu0, double sigma0)
{
// Tilt series are always 2D
I.checkDimension(2);
const int L=2;
// Build a mask using the tilt angle
I.setXmippOrigin();
MultidimArray<int> mask;
mask.initZeros(I);
int Xdimtilt=(int)XMIPP_MIN(FLOOR(0.5*(XSIZE(I)*cos(DEG2RAD(tilt)))),
0.5*(XSIZE(I)-(2*L+1)));
int N=0;
for (int i=STARTINGY(I); i<=FINISHINGY(I); i++)
for (int j=-Xdimtilt; j<=Xdimtilt;j++)
{
A2D_ELEM(mask,i,j)=1;
N++;
}
// Estimate the local variance
MultidimArray<double> localVariance;
localVariance.initZeros(I);
double meanVariance=0;
FOR_ALL_ELEMENTS_IN_ARRAY2D(I)
{
// Center a mask of size 5x5 and estimate the variance within the mask
double meanPiece=0, variancePiece=0;
double Npiece=0;
for (int ii=i-L; ii<=i+L; ii++)
{
if (INSIDEY(I,ii))
for (int jj=j-L; jj<=j+L; jj++)
{
if (INSIDEX(I,jj))
{
double pixval=A2D_ELEM(I,ii,jj);
meanPiece+=pixval;
variancePiece+=pixval*pixval;
++Npiece;
}
}
}
meanPiece/=Npiece;
variancePiece=variancePiece/(Npiece-1)-
Npiece/(Npiece-1)*meanPiece*meanPiece;
A2D_ELEM(localVariance,i,j)=variancePiece;
meanVariance+=variancePiece;
}
meanVariance*=1.0/N;
// Test the hypothesis that the variance in this piece is
// the same as the variance in the whole image
double iFu=1/icdf_FSnedecor(4*L*L+4*L,N-1,0.975);
double iFl=1/icdf_FSnedecor(4*L*L+4*L,N-1,0.025);
double iMeanVariance=1.0/meanVariance;
FOR_ALL_ELEMENTS_IN_ARRAY2D(localVariance)
{
if (A2D_ELEM(localVariance,i,j)==0)
A2D_ELEM(mask,i,j)=-2;
if (A2D_ELEM(mask,i,j)==1)
{
double ratio=A2D_ELEM(localVariance,i,j)*iMeanVariance;
double thl=ratio*iFu;
double thu=ratio*iFl;
if (thl>1 || thu<1)
A2D_ELEM(mask,i,j)=-1;
}
}
#ifdef DEBUG
Image<double> save;
save()=I;
save.write("PPP.xmp");
save()=localVariance;
save.write("PPPLocalVariance.xmp");
Image<int> savemask;
savemask()=mask;
savemask.write("PPPmask.xmp");
#endif
// Compute the statistics again in the reduced mask
double avg, stddev, min, max;
computeStats_within_binary_mask(mask, I, min, max, avg, stddev);
double cosTilt=cos(DEG2RAD(tilt));
double iCosTilt=1.0/cosTilt;
if (tomography0)
{
double iadjustedStddev=1.0/(sigma0*cosTilt);
FOR_ALL_ELEMENTS_IN_ARRAY2D(I)
switch (A2D_ELEM(mask,i,j))
{
case -2:
A2D_ELEM(I,i,j)=0;
break;
case 0:
if (tiltMask)
A2D_ELEM(I,i,j)=0;
else
A2D_ELEM(I,i,j)=(A2D_ELEM(I,i,j)*iCosTilt-mu0)*iadjustedStddev;
break;
case -1:
case 1:
A2D_ELEM(I,i,j)=(A2D_ELEM(I,i,j)*iCosTilt-mu0)*iadjustedStddev;
break;
}
}
else
{
TEST( MultidimTest, modulo)
{
MultidimArray<double> mSource(3,3);
MultidimArray<double> mTarget(3,3);
A2D_ELEM(mSource,0,0) = 0;
A2D_ELEM(mSource,0,1) = 10;
A2D_ELEM(mSource,0,2) = 3.14159265;
A2D_ELEM(mSource,1,0) = (20*3.14159265);
A2D_ELEM(mSource,1,1) = (3.14159265/2);
A2D_ELEM(mSource,1,2) = (3*3.14159265/2);
A2D_ELEM(mSource,2,0) = (10*3.14159265/2);
A2D_ELEM(mSource,2,1) = (50*3.14159265);
A2D_ELEM(mSource,2,2) = (2*3.14159265);
double value = 2*3.14159265;
mod(mSource,mTarget,value);
//We test the obtained values with the results obtained from method "mod" of Matlab
ASSERT_NEAR( A2D_ELEM(mTarget,0,0), 0, 1e-3);
ASSERT_NEAR( A2D_ELEM(mTarget,0,1), 3.7168, 1e-3 );
ASSERT_NEAR( A2D_ELEM(mTarget,0,2), 3.1416, 1e-3);
ASSERT_NEAR( A2D_ELEM(mTarget,1,0), 0, 1e-3);
ASSERT_NEAR( A2D_ELEM(mTarget,1,1), 1.5708, 1e-3);
ASSERT_NEAR( A2D_ELEM(mTarget,1,2), 4.7124, 1e-2);
ASSERT_NEAR( A2D_ELEM(mTarget,2,0), 3.1416, 1e-3);
if (A2D_ELEM(mTarget,2,1) > (value - 1e-3))
ASSERT_NEAR( A2D_ELEM(mTarget,2,1), value, 1e-3);
else
ASSERT_NEAR( A2D_ELEM(mTarget,2,1), 0, 1e-3);
ASSERT_NEAR( A2D_ELEM(mTarget,2,2), 0, 1e-3);
}
TEST( MultidimTest, sincos)
{
MultidimArray<double> mSource(2,2);
MultidimArray<double> mdSIN;
MultidimArray<double> mdCOS;
A2D_ELEM(mSource,0,0) = 0;
A2D_ELEM(mSource,1,0) = 3.14159265/2;
A2D_ELEM(mSource,0,1) = 3.14159265;
A2D_ELEM(mSource,1,1) = (3*3.14159265)/2;
sincos(mSource,mdSIN,mdCOS);
ASSERT_TRUE( (A2D_ELEM(mdSIN,0,0) - 0)<0.0001);
ASSERT_TRUE( (A2D_ELEM(mdSIN,1,0) - 1)<0.0001);
ASSERT_TRUE( (A2D_ELEM(mdSIN,0,1) - 0)<0.0001);
ASSERT_TRUE( (A2D_ELEM(mdSIN,1,1) + 1)<0.0001);
ASSERT_TRUE( (A2D_ELEM(mdCOS,0,0) - 1)<0.0001);
ASSERT_TRUE( (A2D_ELEM(mdCOS,1,0) - 0)<0.0001);
ASSERT_TRUE( (A2D_ELEM(mdCOS,0,1) + 1)<0.0001);
ASSERT_TRUE( (A2D_ELEM(mdCOS,1,1) - 0)<0.0001);
}
TEST( MultidimTest, selfCoreArrayByArrayMask)
{
MultidimArray<double> m1(2,2);
MultidimArray<double> m2(2,2);
MultidimArray<double> mOut(2,2);
MultidimArray<double> mref(2,2);
MultidimArray<double> mask(2,2);
A2D_ELEM(m1,0,0) = 1.;
A2D_ELEM(m1,1,0) = 2.;
A2D_ELEM(m1,0,1) = 3.;
A2D_ELEM(m1,1,1) = 4.;
A2D_ELEM(m2,0,0) = 11.;
A2D_ELEM(m2,1,0) = 22.;
A2D_ELEM(m2,0,1) = 33.;
A2D_ELEM(m2,1,1) = 44.;
A2D_ELEM(mask,0,0) = 0.;
A2D_ELEM(mask,1,0) = 1.;
A2D_ELEM(mask,0,1) = 1.;
A2D_ELEM(mask,1,1) = 1.;
A2D_ELEM(mOut,0,0) = 0.;
A2D_ELEM(mOut,1,0) = 0.;
A2D_ELEM(mOut,0,1) = 0.;
A2D_ELEM(mOut,1,1) = 1.;
selfCoreArrayByArrayMask(m1, m2, mOut, '+', &mask);
A2D_ELEM(mref,0,0) = 1.;
A2D_ELEM(mref,1,0) = 22.;
A2D_ELEM(mref,0,1) = 33.;
A2D_ELEM(mref,1,1) = 45.;
EXPECT_EQ(mOut,mref);
}
TEST( MultidimTest, coreArrayByArray)
{
MultidimArray<double> m1(2,2);
MultidimArray<double> m2(2,2);
MultidimArray<double> mOut(2,2);
MultidimArray<double> mref(2,2);
A2D_ELEM(m1,0,0) = 1.;
A2D_ELEM(m1,1,0) = 2.;
A2D_ELEM(m1,0,1) = 3.;
A2D_ELEM(m1,1,1) = 4.;
A2D_ELEM(m2,0,0) = 11.;
A2D_ELEM(m2,1,0) = 22.;
A2D_ELEM(m2,0,1) = 33.;
A2D_ELEM(m2,1,1) = 44.;
coreArrayByArray(m1, m2, mOut, '+');
A2D_ELEM(mref,0,0) = 12.;
A2D_ELEM(mref,1,0) = 24.;
A2D_ELEM(mref,0,1) = 36.;
A2D_ELEM(mref,1,1) = 48.;
EXPECT_EQ(mOut,mref);
}
void Projector::rotate2D(MultidimArray<Complex > &f2d, Matrix2D<DOUBLE> &A, bool inv)
{
DOUBLE fx, fy, xp, yp;
int x0, x1, y0, y1, y, y2, r2;
bool is_neg_x;
Complex d00, d01, d10, d11, dx0, dx1;
Matrix2D<DOUBLE> Ainv;
// f2d should already be in the right size (ori_size,orihalfdim)
// AND the points outside max_r should already be zero...
// f2d.initZeros();
// Use the inverse matrix
if (inv)
Ainv = A;
else
Ainv = A.transpose();
// The f2d image may be smaller than r_max, in that case also make sure not to fill the corners!
int my_r_max = XMIPP_MIN(r_max, XSIZE(f2d) - 1);
// Go from the 2D slice coordinates to the map coordinates
Ainv *= (DOUBLE)padding_factor; // take scaling into account directly
int max_r2 = my_r_max * my_r_max;
int min_r2_nn = r_min_nn * r_min_nn;
#ifdef DEBUG
std::cerr << " XSIZE(f2d)= "<< XSIZE(f2d) << std::endl;
std::cerr << " YSIZE(f2d)= "<< YSIZE(f2d) << std::endl;
std::cerr << " XSIZE(data)= "<< XSIZE(data) << std::endl;
std::cerr << " YSIZE(data)= "<< YSIZE(data) << std::endl;
std::cerr << " STARTINGX(data)= "<< STARTINGX(data) << std::endl;
std::cerr << " STARTINGY(data)= "<< STARTINGY(data) << std::endl;
std::cerr << " STARTINGZ(data)= "<< STARTINGZ(data) << std::endl;
std::cerr << " max_r= "<< r_max << std::endl;
std::cerr << " Ainv= " << Ainv << std::endl;
#endif
for (int i=0; i < YSIZE(f2d); i++)
{
// Don't search beyond square with side max_r
if (i <= my_r_max)
{
y = i;
}
else if (i >= YSIZE(f2d) - my_r_max)
{
y = i - YSIZE(f2d);
}
else
continue;
y2 = y * y;
for (int x=0; x <= my_r_max; x++)
{
// Only include points with radius < max_r (exclude points outside circle in square)
r2 = x * x + y2;
if (r2 > max_r2)
continue;
// Get logical coordinates in the 3D map
xp = Ainv(0,0) * x + Ainv(0,1) * y;
yp = Ainv(1,0) * x + Ainv(1,1) * y;
if (interpolator == TRILINEAR || r2 < min_r2_nn)
{
// Only asymmetric half is stored
if (xp < 0)
{
// Get complex conjugated hermitian symmetry pair
xp = -xp;
yp = -yp;
is_neg_x = true;
}
else
{
is_neg_x = false;
}
// Trilinear interpolation (with physical coords)
// Subtract STARTINGY to accelerate access to data (STARTINGX=0)
// In that way use DIRECT_A3D_ELEM, rather than A3D_ELEM
x0 = FLOOR(xp);
fx = xp - x0;
x1 = x0 + 1;
y0 = FLOOR(yp);
fy = yp - y0;
y0 -= STARTINGY(data);
y1 = y0 + 1;
// Matrix access can be accelerated through pre-calculation of z0*xydim etc.
d00 = DIRECT_A2D_ELEM(data, y0, x0);
d01 = DIRECT_A2D_ELEM(data, y0, x1);
d10 = DIRECT_A2D_ELEM(data, y1, x0);
d11 = DIRECT_A2D_ELEM(data, y1, x1);
// Set the interpolated value in the 2D output array
#ifndef FLOAT_PRECISION
__m256d __interpx = LIN_INTERP_AVX(_mm256_setr_pd(d00.real, d00.imag, d10.real, d10.imag),
_mm256_setr_pd(d01.real, d01.imag, d11.real, d11.imag),
_mm256_set1_pd(fx));
#else
__m128 __interpx = LIN_INTERP_AVX(_mm_setr_ps(d00.real, d00.imag, d10.real, d10.imag),
_mm_setr_ps(d01.real, d01.imag, d11.real, d11.imag),
_mm_set1_ps(fx));
#endif
Complex* interpx = (Complex*)&__interpx;
DIRECT_A2D_ELEM(f2d, i, x) = LIN_INTERP(fy, interpx[0], interpx[1]);
// Take complex conjugated for half with negative x
if (is_neg_x)
DIRECT_A2D_ELEM(f2d, i, x) = conj(DIRECT_A2D_ELEM(f2d, i, x));
} // endif TRILINEAR
else if (interpolator == NEAREST_NEIGHBOUR )
{
x0 = ROUND(xp);
y0 = ROUND(yp);
if (x0 < 0)
DIRECT_A2D_ELEM(f2d, i, x) = conj(A2D_ELEM(data, -y0, -x0));
else
DIRECT_A2D_ELEM(f2d, i, x) = A2D_ELEM(data, y0, x0);
} // endif NEAREST_NEIGHBOUR
else
REPORT_ERROR("Unrecognized interpolator in Projector::project");
} // endif x-loop
} // endif y-loop
}
//majorAxis and minorAxis is the estimated particle size in px
void ProgSortByStatistics::processInprocessInputPrepareSPTH(MetaData &SF, bool trained)
{
//#define DEBUG
PCAMahalanobisAnalyzer tempPcaAnalyzer0;
PCAMahalanobisAnalyzer tempPcaAnalyzer1;
PCAMahalanobisAnalyzer tempPcaAnalyzer2;
PCAMahalanobisAnalyzer tempPcaAnalyzer3;
PCAMahalanobisAnalyzer tempPcaAnalyzer4;
//Morphology
tempPcaAnalyzer0.clear();
//Signal to noise ratio
tempPcaAnalyzer1.clear();
tempPcaAnalyzer2.clear();
tempPcaAnalyzer3.clear();
//Histogram analysis, to detect black points and saturated parts
tempPcaAnalyzer4.clear();
double sign = 1;//;-1;
int numNorm = 3;
int numDescriptors0=numNorm;
int numDescriptors2=4;
int numDescriptors3=11;
int numDescriptors4 = 10;
MultidimArray<float> v0(numDescriptors0);
MultidimArray<float> v2(numDescriptors2);
MultidimArray<float> v3(numDescriptors3);
MultidimArray<float> v4(numDescriptors4);
if (verbose>0)
{
std::cout << " Sorting particle set by new xmipp method..." << std::endl;
}
int nr_imgs = SF.size();
if (verbose>0)
init_progress_bar(nr_imgs);
int c = XMIPP_MAX(1, nr_imgs / 60);
int imgno = 0, imgnoPCA=0;
bool thereIsEnable=SF.containsLabel(MDL_ENABLED);
bool first=true;
// We assume that at least there is one particle
size_t Xdim, Ydim, Zdim, Ndim;
getImageSize(SF,Xdim,Ydim,Zdim,Ndim);
//Initialization:
MultidimArray<double> nI, modI, tempI, tempM, ROI;
MultidimArray<bool> mask;
nI.resizeNoCopy(Ydim,Xdim);
modI.resizeNoCopy(Ydim,Xdim);
tempI.resizeNoCopy(Ydim,Xdim);
tempM.resizeNoCopy(Ydim,Xdim);
mask.resizeNoCopy(Ydim,Xdim);
mask.initConstant(true);
MultidimArray<double> autoCorr(2*Ydim,2*Xdim);
MultidimArray<double> smallAutoCorr;
Histogram1D hist;
Matrix2D<double> U,V,temp;
Matrix1D<double> D;
MultidimArray<int> radial_count;
MultidimArray<double> radial_avg;
Matrix1D<int> center(2);
MultidimArray<int> distance;
int dim;
center.initZeros();
v0.initZeros(numDescriptors0);
v2.initZeros(numDescriptors2);
v3.initZeros(numDescriptors3);
v4.initZeros(numDescriptors4);
ROI.resizeNoCopy(Ydim,Xdim);
ROI.setXmippOrigin();
FOR_ALL_ELEMENTS_IN_ARRAY2D(ROI)
{
double temp = std::sqrt(i*i+j*j);
if ( temp < (Xdim/2))
A2D_ELEM(ROI,i,j)= 1;
else
A2D_ELEM(ROI,i,j)= 0;
}
Image<double> img;
FourierTransformer transformer(FFTW_BACKWARD);
FOR_ALL_OBJECTS_IN_METADATA(SF)
{
if (thereIsEnable)
{
int enabled;
SF.getValue(MDL_ENABLED,enabled,__iter.objId);
if ( (enabled==-1) )
{
imgno++;
continue;
}
}
img.readApplyGeo(SF,__iter.objId);
if (targetXdim!=-1 && targetXdim!=XSIZE(img()))
selfScaleToSize(LINEAR,img(),targetXdim,targetXdim,1);
MultidimArray<double> &mI=img();
mI.setXmippOrigin();
mI.statisticsAdjust(0,1);
mask.setXmippOrigin();
//The size of v1 depends on the image size and must be declared here
int numDescriptors1 = XSIZE(mI)/2; //=100;
MultidimArray<float> v1(numDescriptors1);
v1.initZeros(numDescriptors1);
double var = 1;
normalize(transformer,mI,tempI,modI,0,var,mask);
modI.setXmippOrigin();
tempI.setXmippOrigin();
nI = sign*tempI*(modI*modI);
tempM = (modI*modI);
A1D_ELEM(v0,0) = (tempM*ROI).sum();
int index = 1;
var+=2;
while (index < numNorm)
{
normalize(transformer,mI,tempI,modI,0,var,mask);
modI.setXmippOrigin();
tempI.setXmippOrigin();
nI += sign*tempI*(modI*modI);
tempM += (modI*modI);
A1D_ELEM(v0,index) = (tempM*ROI).sum();
index++;
var+=2;
}
nI /= tempM;
tempPcaAnalyzer0.addVector(v0);
nI=(nI*ROI);
auto_correlation_matrix(mI,autoCorr);
if (first)
{
radialAveragePrecomputeDistance(autoCorr, center, distance, dim);
first=false;
}
fastRadialAverage(autoCorr, distance, dim, radial_avg, radial_count);
for (int n = 0; n < numDescriptors1; ++n)
A1D_ELEM(v1,n)=(float)DIRECT_A1D_ELEM(radial_avg,n);
tempPcaAnalyzer1.addVector(v1);
#ifdef DEBUG
//String name = "000005@Images/Extracted/run_002/extra/BPV_1386.stk";
String name = "000010@Images/Extracted/run_001/extra/KLH_Dataset_I_Training_0028.stk";
//String name = "001160@Images/Extracted/run_001/DefaultFamily5";
std::cout << img.name() << std::endl;
if (img.name()==name2)
{
FileName fpName = "test_1.txt";
mI.write(fpName);
fpName = "test_2.txt";
nI.write(fpName);
fpName = "test_3.txt";
tempM.write(fpName);
fpName = "test_4.txt";
ROI.write(fpName);
//exit(1);
}
#endif
nI.binarize(0);
int im = labelImage2D(nI,nI,8);
compute_hist(nI, hist, 0, im, im+1);
size_t l;
int k,i,j;
hist.maxIndex(l,k,i,j);
A1D_ELEM(hist,j)=0;
hist.maxIndex(l,k,i,j);
nI.binarizeRange(j-1,j+1);
double x0=0,y0=0,majorAxis=0,minorAxis=0,ellipAng=0;
size_t area=0;
fitEllipse(nI,x0,y0,majorAxis,minorAxis,ellipAng,area);
A1D_ELEM(v2,0)=majorAxis/((img().xdim) );
A1D_ELEM(v2,1)=minorAxis/((img().xdim) );
A1D_ELEM(v2,2)= (fabs((img().xdim)/2-x0)+fabs((img().ydim)/2-y0))/((img().xdim)/2);
A1D_ELEM(v2,3)=area/( (double)((img().xdim)/2)*((img().ydim)/2) );
for (int n=0 ; n < numDescriptors2 ; n++)
{
if ( std::isnan(std::abs(A1D_ELEM(v2,n))))
A1D_ELEM(v2,n)=0;
}
tempPcaAnalyzer2.addVector(v2);
//mI.setXmippOrigin();
//auto_correlation_matrix(mI*ROI,autoCorr);
//auto_correlation_matrix(nI,autoCorr);
autoCorr.window(smallAutoCorr,-5,-5, 5, 5);
smallAutoCorr.copy(temp);
svdcmp(temp,U,D,V);
for (int n = 0; n < numDescriptors3; ++n)
A1D_ELEM(v3,n)=(float)VEC_ELEM(D,n); //A1D_ELEM(v3,n)=(float)VEC_ELEM(D,n)/VEC_ELEM(D,0);
tempPcaAnalyzer3.addVector(v3);
double minVal=0.;
double maxVal=0.;
mI.computeDoubleMinMax(minVal,maxVal);
compute_hist(mI, hist, minVal, maxVal, 100);
for (int n=0 ; n <= numDescriptors4-1 ; n++)
{
A1D_ELEM(v4,n)= (hist.percentil((n+1)*10));
}
tempPcaAnalyzer4.addVector(v4);
#ifdef DEBUG
if (img.name()==name1)
{
FileName fpName = "test.txt";
mI.write(fpName);
fpName = "test3.txt";
nI.write(fpName);
}
#endif
imgno++;
imgnoPCA++;
if (imgno % c == 0 && verbose>0)
progress_bar(imgno);
}
tempPcaAnalyzer0.evaluateZScore(2,20,trained);
tempPcaAnalyzer1.evaluateZScore(2,20,trained);
tempPcaAnalyzer2.evaluateZScore(2,20,trained);
tempPcaAnalyzer3.evaluateZScore(2,20,trained);
tempPcaAnalyzer4.evaluateZScore(2,20,trained);
pcaAnalyzer.push_back(tempPcaAnalyzer0);
pcaAnalyzer.push_back(tempPcaAnalyzer1);
pcaAnalyzer.push_back(tempPcaAnalyzer1);
pcaAnalyzer.push_back(tempPcaAnalyzer3);
pcaAnalyzer.push_back(tempPcaAnalyzer4);
}
void PolyZernikes::fit(const Matrix1D<int> & coef, MultidimArray<double> & im, MultidimArray<double> &weight,
MultidimArray<bool> & ROI, int verbose)
{
this->create(coef);
size_t xdim = XSIZE(im);
size_t ydim = YSIZE(im);
//int numZer = (size_t)coef.sum();
int numZer = (size_t)coef.sum();
//Actually polOrder corresponds to the polynomial order +1
int polOrder=(int)ZERNIKE_ORDER(coef.size());
im.setXmippOrigin();
Matrix2D<double> polValue(polOrder,polOrder);
//First argument means number of images
//Second argument means number of pixels
WeightedLeastSquaresHelper weightedLeastSquaresHelper;
Matrix2D<double>& zerMat=weightedLeastSquaresHelper.A;
zerMat.resizeNoCopy((size_t)ROI.sum(), numZer);
double iMaxDim2 = 2./std::max(xdim,ydim);
size_t pixel_idx=0;
weightedLeastSquaresHelper.b.resizeNoCopy((size_t)ROI.sum());
weightedLeastSquaresHelper.w.resizeNoCopy(weightedLeastSquaresHelper.b);
FOR_ALL_ELEMENTS_IN_ARRAY2D(im)
{
if ( (A2D_ELEM(ROI,i,j)))
{
//For one i we swap the different j
double y=i*iMaxDim2;
double x=j*iMaxDim2;
//polValue = [ 0 y y2 y3 ...
// x xy xy2 xy3 ...
// x2 x2y x2y2 x2y3 ]
//dMij(polValue,py,px) py es fila, px es columna
for (int py = 0; py < polOrder; ++py)
{
double ypy=std::pow(y,py);
for (int px = 0; px < polOrder; ++px)
dMij(polValue,px,py) = ypy*std::pow(x,px);
}
Matrix2D<int> *fMat;
//We generate the representation of the Zernike polynomials
for (int k=0; k < numZer; ++k)
{
fMat = &fMatV[k];
if (fMat == NULL)
continue;
double temp = 0;
for (size_t px = 0; px < (*fMat).Xdim(); ++px)
for (size_t py = 0; py < (*fMat).Ydim(); ++py)
temp += dMij(*fMat,py,px)*dMij(polValue,py,px);
dMij(zerMat,pixel_idx,k) = temp;
}
VEC_ELEM(weightedLeastSquaresHelper.b,pixel_idx)=A2D_ELEM(im,i,j);
VEC_ELEM(weightedLeastSquaresHelper.w,pixel_idx)=std::abs(A2D_ELEM(weight,i,j));
++pixel_idx;
}
}
Matrix1D<double> zernikeCoefficients;
weightedLeastSquares(weightedLeastSquaresHelper, zernikeCoefficients);
fittedCoeffs = zernikeCoefficients;
// Pointer to the image to be fitted
MultidimArray<double> reconstructed;
reconstructed.resizeNoCopy(im);
pixel_idx=0;
FOR_ALL_ELEMENTS_IN_ARRAY2D(im)
if (A2D_ELEM(ROI,i,j))
{
double temp=0;
for (int k=0; k < numZer; ++k)
temp+=dMij(zerMat,pixel_idx,k)*VEC_ELEM(fittedCoeffs,k);
A2D_ELEM(reconstructed,i,j)=temp;
if ( fabs(A2D_ELEM(reconstructed,i,j)-A2D_ELEM(im,i,j)) > PI)
A2D_ELEM(ROI,i,j) = false;
++pixel_idx;
}
pixel_idx=0;
if (verbose > 0)
{
Image<double> save;
save()=reconstructed;
save.write("reconstructedZernikes.xmp");
ROI.write("ROI.txt");
}
}
void PolyZernikes::zernikePols(const Matrix1D<int> coef, MultidimArray<double> & im, MultidimArray<bool> & ROI, int verbose)
{
this->create(coef);
int polOrder=(int)ZERNIKE_ORDER(coef.size());
int numZer = coef.size();
int xdim = XSIZE(im);
int ydim = YSIZE(im);
im.setXmippOrigin();
Matrix2D<double> polValue(polOrder,polOrder);
double iMaxDim2 = 2./std::max(xdim,ydim);
double temp = 0;
FOR_ALL_ELEMENTS_IN_ARRAY2D(im)
{
if (A2D_ELEM(ROI,i,j))
{
//For one i we swap the different j
double y=i*iMaxDim2;
double x=j*iMaxDim2;
//polValue = [ 0 y y2 y3 ...
// x xy xy2 xy3 ...
// x2 x2y x2y2 x2y3 ]
//dMij(polValue,py,px) py es fila, px es columna
for (int py = 0; py < polOrder; ++py)
{
double ypy=std::pow(y,py);
for (int px = 0; px < polOrder; ++px)
dMij(polValue,px,py) = ypy*std::pow(x,px);
}
Matrix2D<int> *fMat;
//We generate the representation of the Zernike polynomials
for (int k=0; k < numZer; ++k)
{
fMat = &fMatV[k];
if ( (dMij(*fMat,0,0) == 0) && MAT_SIZE(*fMat) == 1 )
continue;
for (size_t px = 0; px < (*fMat).Xdim(); ++px)
for (size_t py = 0; py < (*fMat).Ydim(); ++py)
temp += dMij(*fMat,py,px)*dMij(polValue,py,px)*VEC_ELEM(coef,k);
}
A2D_ELEM(im,i,j) = temp;
temp = 0;
}
}
STARTINGX(im)=STARTINGY(im)=0;
if (verbose == 1)
{
Image<double> save;
save()=im;
save.write("PPP1.xmp");
}
}