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SLIMMER
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Functions for File Name Manipulation. More...
Classes | |
| class | BasicHeader |
| Medical Image Volume Info. More... | |
| class | GaussianKernels< T > |
| class | LinTransList< T > |
| Class for holding a List of Linear Transformations. More... | |
| class | ReadDataType |
| Read Low Level Data Types From File. More... | |
| class | SimpleBaseTMat< TM, TS2 > |
| Templated Base Class for Matrices. More... | |
| class | SimpleBaseTVec< T, TS > |
| Templated Base Class for Vectors. More... | |
| class | ExpLinearApprox< T > |
| Linear approximation of exp for faster evaluation. More... | |
| class | SimpleGlobalLog |
| Keep a text file log for command line programs. More... | |
| class | SimpleInterp< TOUT > |
| Class for Interpolation of Values on a regular 2D or 3D grid. More... | |
| class | LinTransParam< T > |
| Linear Transformation Parameters. More... | |
| class | SimpleNumericArrayIO |
| Class for Simple formated IO of Numeric Arrays. More... | |
| class | SimpleTField< T, TS > |
| Templated Spatio-Temporal Field of Values. More... | |
| class | SimpleTFieldList< T, TD, TS > |
| Class for holding a List of TFields with Associated Data. More... | |
| class | SimpleTMat< TM, MATX, MATY, TS > |
| Fixed Size Templated Matrix Class. More... | |
| class | SimpleTVec< T, STVEC_LEN, TS > |
| Fixed Size Templated Vector Class. More... | |
| class | SimpleVoxIO |
| Voxel Input/Output Class. More... | |
| class | SimpleVTMat< TM, TS > |
| Variable Size Templated Matrix Class. More... | |
| class | SimpleVTVec< T, TS > |
| Variable Size Templated Vector Class. More... | |
| class | Class |
| This class can generate 1D Gaussian kernels and 1D derived Gaussian kernels. In addition it contains an implementation of the error function. More... | |
| class | Transforms |
| A class for Transforms. More... | |
Functions | |
| float | keyvp (int argc, char **argv, char *tag, float def) |
| Return Floating Point Number value following a given string tag in the argument list, with default value def. | |
| float | keyvp (int argc, char **argv, char *tag, char *tag2, float def, int off=0) |
| Return Floating Point Number value following a given string tag in the argument list, with default value def. | |
| int | keyvp (int argc, char **argv, char *tag, int def) |
| Return Integer number value follwing a given string tag in the argument list, with default value def. | |
| int | keyv (int argc, char **argv, char *tag) |
| Return True if a given tag is in the comman line list. | |
| char | keyvp (int argc, char **argv, char *tag, char def) |
| Return char value following a given string tag in the argument list, with default value def. | |
| char * | keyvp (int argc, char **argv, char *tag) |
| Return string following a given string tag in comman line argumant list. | |
| template<typename T > | |
| int | MaskSpotClean (int maskThresh, T *refimMask, int neighb, int BackGround=-32768) |
| Spot Clean Mask: ==========================. | |
| template<typename T > | |
| SimpleTVec< float, 3 > | CentOfMass (SimpleTField< T > &LabelsIn, T Threshold=0) |
| Calcuate Center of mass of the Labels. | |
| template<typename T > | |
| void | Label2MultiFrame (SimpleTField< T > &LabelsIn, SimpleTField< T > &multiFrameOut, const int LabelVal=100) |
| Convert a Label Image Into a Multi Frame Image with Each Frame Holding One Label. | |
| template<typename T > | |
| void | MaskExtent (SimpleTField< T > *Mask, T maskThresh, SimpleTVec< int, 3 > &min, SimpleTVec< int, 3 > &max, bool Update=(1==0)) |
| Mask Extent=============================. | |
| template<typename T > | |
| void | MaskDilate (int maskThresh, T *refimMask, int ndil) |
| Dilate mask =============================. | |
| template<typename T > | |
| void | MaskDilate (int maskThresh, T *refim, T *transim, T *refimMask, int ndil) |
| Dilate mask =============================. | |
| template<typename T > | |
| void | maskTruncate (T *refimMask, unsigned int width) |
| Truncate mask Around Image Boundaries. | |
| template<typename T > | |
| int | Mask2TargetLinTrans (T *refimMask, T *transim, LinTransParam< float > &tp, int bound) |
| Adapt Mask to be within the Overlap with a Second Image Volume. | |
| template<typename T1 , typename T2 > | |
| void | EigenDecomp (SimpleTField< T1 > &stf, SimpleTField< T1 > &eVec, SimpleTField< T2 > &eVal) |
| template<typename T1 > | |
| void | Gradient (SimpleTField< T1 > &stf, SimpleTField< T1 > &out) |
| template<typename T1 , typename T2 > | |
| SimpleTField< T2 > | Convolve (SimpleTField< T1 > &stf, SimpleTField< T2 > &kernel) |
| Convolve two TFields: Btter use the Built in Function! | |
| template<typename T > | |
| void | GaussianKernel (const SimpleTVec< int, 3 > &nVox, const SimpleTVec< float, 3 > &VoxSz, const SimpleTMat< float, 3, 3 > &cov, SimpleTField< T > &w, int normalized=1) |
| Make a Gaussian Kernel: Better use the Built in Functions for blurring ! | |
| template<typename T > | |
| void | GaussianKernel (const SimpleTVec< int, 3 > &nVox, const SimpleTVec< float, 3 > &VoxSz, const SimpleTVec< float, 3 > &sigma, SimpleTField< T > &w, int normalized=1) |
| Make a Gaussian Kernel: Better use the Built in Functions for blurring ! | |
| SimpleTField< float > | GaussianKernel (const SimpleTVec< int, 3 > &nVox, const SimpleTVec< float, 3 > &VoxSz, const SimpleTVec< float, 3 > &sigma) |
| Make a Gaussian Kernel: Better use the Built in Functions for blurring ! | |
| template<typename T1 , typename T2 > | |
| void | Blur (const SimpleTField< T1 > &in, SimpleTField< T2 > &out, float sx=1.0f, float sy=-1.0f, float sz=-1.0f) |
| Blur an Image: Better use SimpleGaussFilt() in SimpleTField class. | |
| int | Pattern2FileName (char *name, char *pattern, int index=0) |
| Return the file corresponding to a given File Path/Name Pattern. | |
| void | LogToFile (char *entry) |
| Store a string in the Log File. | |
| FILE * | LogFileFP () |
| Return File Pointer to Log. | |
| void | LogTime () |
| Log the current time to the log file. | |
| template<typename T > | |
| void | BubbleSort (int *index, T *val, int num) |
| template<typename T , unsigned int LEN> | |
| void | BubbleSortVec (SimpleTVec< unsigned int, LEN > *index, SimpleTVec< T, LEN > *val, int num) |
| template<typename T , unsigned int LEN, unsigned int LEN2> | |
| void | BubbleSortMat (SimpleTMat< unsigned int, LEN, LEN2 > *index, SimpleTMat< T, LEN, LEN2 > *val, unsigned int num) |
| void | RandomIndex (int *index, int num) |
| void | RandomSampleIndex (int *index, int num) |
| SimpleTMat< float, 4, 4 > | LinTrans_mm2vox (const SimpleTMat< float, 4, 4 > &mm2mm, const BasicHeader &hdR, const BasicHeader &hdT) |
| template<typename T > | |
| LinTransParam< T > | ComposeRigid (const LinTransParam< T > &f, const LinTransParam< T > &g) |
| int | RANDOM_rint (float f) |
| float | gammln (float xx) |
| gammln From Numerical Recipies pp. 218 | |
| int | gser (float &gamser, float a, float x, float &gln) |
| void | gcf (float &gammcf, float a, float x, float gln) |
| gcf From Numerical Recipies pp. 218 | |
| float | gammq (float a, float x) |
| gammq From Numerical Recipies pp. 218 | |
| float | gammp (float a, float x) |
| gammap function from numeric. recip. | |
| float | betacf (float a, float b, float x) |
| betacf function from numerical recip. | |
| float | betai (float a, float b, float x) |
| Betaai function from numerical recip. | |
| template<typename T > | |
| T | cubicBST (T k1, T k2, T k3, T k4, const float &t, float tn) |
| Cubic BSpline (A Templated Version) | |
| template<typename T > | |
| T | cubicBST (T k1, T k2, T k3, T k4, const float &t) |
| Cubic BSpline (A Templated Version) | |
| template<typename T > | |
| T | cubicBST1 (T k1, T k2, T k3, T k4, const float &t) |
| Cubic BSpline First Derivative (A Templated Version) | |
| double | cubicBS1 (double k1, double k2, double k3, double k4, const float &t, const float &tn) |
| Derivative of Cubic B-Spline. | |
| double | AVGW (double k1, double k2, double k3, double k4, const float &t, const float &tn) |
| Simple Weighted Averaging Function. | |
| double | AVG (double k1, double k2, double k3, double k4, const float &t, const float &tn) |
| Very Simple Weighted Averaging Function. | |
| float | ran1 (long *idum) |
| famous ran1 from numeric recip in c p280 | |
| void | seedran1 (long *rs) |
| Set random number. | |
| float | ranrange (float min, float max, long *r) |
| return random number in range | |
| int | ranirange (int min, int max, long *r) |
| return random integer number in range | |
| float | gaussdev (long *idum) |
| return random floating point number with gaussian distribution sigma=1 | |
| int | igaussdev (long *idum, float mean, float std) |
| return random integer with gaussian distribution with required mean and stdev | |
| float | ricedev (long *idum, float v, float std) |
| Return a random number with Rician Distribution. | |
| float | poidev (float xm, long *idum) |
| Return a Random number with Poisson Distribution. | |
| float | GaussVar1D (const float &d, const float &variance) |
| Returns Value of Gaussian Distribution, mean 0, given variance, at a given point. | |
| float | Gauss1D (const float &d, const float &sigma) |
| Returns Value of Gaussian Distribution, mean 0, given sigma, at a given point. | |
| float | GaussFWHM1D (const float &d, const float &fwhm) |
| Returns Value of Gaussian Distribution, mean 0, given FWHM (1D), at a given point. | |
| float | GaussFWHM3Dsq (const float &dsq, const float &fwhm) |
| Returns Value of Gaussian Distribution, mean 0, given FWHM (1D), at a given point(squared) | |
| float | GaussFWHM3D (const float &d, const float &fwhm) |
| Returns Value of Gaussian Distribution, mean 0, given FWHM (1D), at a given point. | |
| template<typename T > | |
| T | PsiA (const T &vR, const T &v, const float &K) |
| Anisotropic Affinity Function. | |
| template<typename T > | |
| T | Psi (const T &vR, const T &v, const float &K) |
| Anisotropic Diffusion kernel. | |
| template<typename T > | |
| SimpleTMat< T, 3, 3 > | logSO3 (SimpleTMat< T, 3, 3 > R) |
| template<typename T > | |
| SimpleTMat< T, 3, 3 > | expso3 (SimpleTMat< T, 3, 3 > A) |
| template<typename T > | |
| void | eig3x3SymmetricMatrix (const SimpleTVec< T, 6 > &m, SimpleTMat< T, 3, 3 > &V, SimpleTVec< T, 3 > &ev) |
| template<typename T > | |
| void | expm3x3 (SimpleTMat< T, 3, 3 > M, SimpleTMat< T, 3, 3 > dM, SimpleTMat< T, 3, 3 > &F, SimpleTMat< T, 3, 3 > &dF) |
| template<typename T1 > | |
| void | WriteMat (T1 &svtm, const char *filename) |
| template<typename T1 > | |
| SimpleVTMat< T1 > | Diag (SimpleVTVec< T1 > &svtv) |
| template<typename T1 , int L> | |
| SimpleTVec< T1, L > | p2p (SimpleTVec< T1, L > v1, SimpleTVec< T1, L > v2) |
| template<typename T1 > | |
| T1 | Sum (SimpleVTMat< T1 > &svtm) |
| template<typename T > | |
| void | HouseholdReflection (SimpleVTVec< T > &v1, SimpleVTVec< T > &v2, SimpleVTVec< T > &u) |
| template<typename T > | |
| void | QR (const SimpleVTMat< T > &A, SimpleVTMat< T > &Q, SimpleVTMat< T > &R) |
| template<typename T1 , typename T2 > | |
| T1 | SIGN (T1 a, T2 b) |
| template<typename T1 , typename T2 > | |
| T1 | FMAX (T1 a, T2 b) |
| template<typename T1 , typename T2 > | |
| T1 | IMIN (T1 a, T2 b) |
| template<typename T1 , typename T2 > | |
| T1 | pythag (T1 a, T2 b) |
| template<typename T > | |
| void | svdcmp (SimpleBaseTMat< T > &a, SimpleBaseTVec< T > &w, SimpleBaseTMat< T > &v) |
| SVD. | |
| template<typename T > | |
| void | SVD (const SimpleVTMat< T > &a, SimpleVTMat< T > &u, SimpleVTMat< T > &w, SimpleVTMat< T > &v) |
| template<typename T > | |
| void | NullSpace (const SimpleVTMat< T > &in, SimpleVTMat< T > &out) |
| Returns a matrix, where the columns are the bases of the null space. n_rows>n_cols is assumed. | |
| template<typename Tdata > | |
| bool | SymLinSlvM (SimpleVTMat< Tdata > &A, SimpleVTMat< Tdata > &B, SimpleVTMat< Tdata > &X) |
| template<typename T1 , typename T2 , typename T3 > | |
| bool | PseudoInvSlv (SimpleVTMat< T1 > &A, SimpleVTVec< T2 > &B, SimpleVTVec< T3 > &X) |
| Pseudo-inverse solver of a linear problem. | |
| template<typename T1 , typename T2 , typename T3 , typename TS > | |
| SimpleVTVec< int > | PseudoInvSlv (SimpleVTMat< T1, TS > &A, SimpleVTVec< T2, TS > &B, SimpleVTVec< T3, TS > &X, T2 d_good, unsigned int n_rep=10000) |
| RANSAC version of Pseudo-inverse solver of a linear problem AX=B. | |
| bool | FileExists (const char *filename) |
| template<typename TM , unsigned int MATXY> | |
| SimpleTVec< TM, MATXY > | DecompEigenSym (SimpleTMat< TM, MATXY, MATXY, unsigned int > mat, SimpleTMat< TM, MATXY, MATXY, unsigned int > &eVec, int nit=50, int flag=(1==1)) |
| Decompose Eigen Values/Vectors from Sym. Matrix. | |
| template<typename TM , unsigned int MATXY, typename TS > | |
| SimpleTMat< TM, MATXY, MATXY > | ComposeEigenSym (const SimpleTMat< TM, MATXY, MATXY, TS > &eVec, const SimpleTVec< TM, MATXY, TS > &eVals) |
| Compose Matrix from Eigen Values/Vectors. | |
| template<typename TM , int MATXY, typename TS > | |
| SimpleTMat< TM, MATXY, MATXY > | Sqrt (SimpleTMat< TM, MATXY, MATXY > &mat) |
| Matrix Square Root (Sym Matrix) | |
| template<typename TM , unsigned int MATXY> | |
| SimpleTMat< TM, MATXY, MATXY, unsigned int > | ExpSym (const SimpleTMat< TM, MATXY, MATXY, unsigned int > &mat) |
| Matrix Exponent. | |
| template<typename TM , unsigned int MATXY> | |
| SimpleTMat< TM, MATXY, MATXY, unsigned int > | LogSym (const SimpleTMat< TM, MATXY, MATXY, unsigned int > &mat) |
| Matrix Log. | |
| template<typename TM , unsigned int MATXY> | |
| SimpleTMat< TM, MATXY, MATXY, unsigned int > | SqrtND (const SimpleTMat< TM, MATXY, MATXY, unsigned int > &mat) |
| template<typename TM > | |
| SimpleTMat< TM, 3, 3, unsigned int > | RotationDecomp (const SimpleTMat< TM, 3, 3, unsigned int > &mat) |
| Decompose Rigid Rotations Transformation from Affine 3x3. | |
| template<typename TM , int MATX, typename TS > | |
| SimpleTMat< TM, MATX, MATX, TS > | QRdecomp (SimpleTMat< TM, MATX, MATX, TS > &input, SimpleTMat< TM, MATX, MATX, TS > &Q) |
| QR Decomposition. | |
| template<typename TOUT , typename TIN1 , typename TIN2 > | |
| void | cross (SimpleBaseTVec< TOUT > &out, const SimpleBaseTVec< TIN1 > &v1, const SimpleBaseTVec< TIN2 > &v2) |
| template<typename TOUT , typename TIN1 , typename TIN2 > | |
| void | outer (SimpleVTMat< TOUT > &out, const SimpleVTVec< TIN1 > &v1, const SimpleVTVec< TIN2 > &v2) |
| template<typename T1 > | |
| T1 | VecMedian (SimpleVTVec< T1 > &vvec) |
| template<typename TOUT > | |
| void | gaussianKernel1D (SimpleBaseTVec< TOUT, unsigned int > &out, double sigma=0.0) |
| template<typename TOUT > | |
| void | legendreTVec (SimpleBaseTVec< TOUT > &out, int n) |
| Fills a SimpleBaseTVec with the n-th degree Legendre polynomial. | |
| template<typename TOUT > | |
| void | discreteCosineTVec (SimpleBaseTVec< TOUT > &out, int n) |
| Fills a SimpleBaseTVec with the n-th discrete Cosine Kernel. | |
| template<typename TOUT > | |
| void | tchebichefMomentsTVec (SimpleBaseTVec< TOUT > &out, int n) |
| Fills a SimpleBaseTVec with the n-th degree Tchebichef Moments (another discrete basis function) | |
| BasicHeader * | CreateHeaderFromFile (char *name) |
| Create a Basic Header From a File (without Loading Voxel data) | |
| template<typename T > | |
| void | MakeSphereVox (SimpleTField< T > &f, T outVal, T inVal, SimpleTVec< int, 3 > cen, float radiusMM, bool addShape=(1==0), int frame=0) |
| Make A Sphere at given voxel coordinates. | |
| template<typename T > | |
| void | MakePacManVox (SimpleTField< T > &f, T outVal, T inVal, SimpleTVec< int, 3 > cen, float radiusMM, float radiusMM2, float ReqAng=20, int frame=0) |
| template<typename T > | |
| void | MakeCubeVox (SimpleTField< T > &f, T outVal, T inVal, SimpleTVec< int, 3 > cen, float sideMM, int addShape=(1==0), int frame=0) |
| Make aa Cube at a given location and with a given size. | |
| void | SimpleBaseTVec< float, unsigned int >::Null () |
| Set All Elements to Zero. | |
| void | SimpleBaseTVec< float, unsigned long int >::Null () |
| Set All Elements to Zero. | |
Variables | |
| const char | SimpleFileNames_versionID [] = "$Id: SimpleFileNames.h,v 1.1 2011/06/19 02:05:38 bicg Exp $" |
| const char | SimpleMathsFunc_versionID [] = "$Id: SimpleMathsFunc.h,v 1.11 2011/10/17 16:08:20 cs Exp $" |
| const char | SimpleVectorFunc_versionID [] = "$Id: SimpleVectorFunc.h,v 1.10 2011/06/19 02:30:09 bicg Exp $" |
| static const char | BasicHeader::_versionID [] = "$Id: BasicHeader.h,v 1.40 2011/12/07 21:56:09 bicg Exp $" |
| static const char | SimpleBaseTVec< float, unsigned long int >::_versionID [] = "$Id: SimpleBaseTVec.h,v 1.55 2011/11/21 20:48:11 bicg Exp $" |
| static const char | SimpleBaseTVec< float, unsigned int >::_versionID [] = "$Id: SimpleBaseTVec.h,v 1.55 2011/11/21 20:48:11 bicg Exp $" |
| static const char | SimpleBaseTVec< int, unsigned int >::_versionID [] = "$Id: SimpleBaseTVec.h,v 1.55 2011/11/21 20:48:11 bicg Exp $" |
| static FILE * | SimpleGlobalLog::_fplog |
| static int | SimpleGlobalLog::_noLog |
| static int | SimpleGlobalLog::_numLog |
| static const char | LinTransParam< float >::_versionID [] = "$Id: SimpleLinTrans.h,v 1.36 2011/11/02 21:03:35 mads Exp $" |
| static const char | SimpleNumericArrayIO::_versionID [] = "$Id: SimpleNumericArrayIO.h,v 1.8 2010/05/07 18:31:46 cs Exp $" |
| static const char | SimpleVTVec< float, unsigned long int >::_versionID [] = "$Id: SimpleVTVec.h,v 1.36 2011/10/20 18:19:07 bicg Exp $" |
Functions for File Name Manipulation.
Functions to Create shapes in SimpleTFields.
Functions for Simple Indexed Data Manpilations.
##################################################################### A Collection of Functions working on Matrices
KeyValue Pair Functions for extracting values from command line arguments
MaskTools.h Colin Studholme, 1995-2007
Functions To Operate on a Volume Mask
Mask is templated needs BasicHeader Properties + DataPtr
Mask is specified by integer threshold in image volume
Older Functions to operate on SimpleTFields Better to use Built in Functions in SimpleTField!
##################################################################### A Collection of Maths Functions
Many From Numerical Recipies
##################################################################### A Collection of Functions working on Matrices
Many From Numerical Recipies or calling lapack
##################################################################### A Collection of Maths Functions for Matrices
| void MakePacManVox | ( | SimpleTField< T > & | f, |
| T | outVal, | ||
| T | inVal, | ||
| SimpleTVec< int, 3 > | cen, | ||
| float | radiusMM, | ||
| float | radiusMM2, | ||
| float | ReqAng = 20, |
||
| int | frame = 0 |
||
| ) |
---------- Create a 3D PacMan Mouth Open by a Given Angle
| void SimpleBaseTVec< float, unsigned long int >::Null | ( | ) | [inline] |
Set All Elements to Zero.
| void SimpleBaseTVec< float, unsigned int >::Null | ( | ) | [inline] |
Set All Elements to Zero.
1.7.4
