Inheritance diagram for sirf::NiftiImageData< dataType >:
Classes | |
| class | Iterator |
| class | Iterator_const |
Public Types | |
| typedef ImageData::Iterator | BaseIter |
| typedef ImageData::Iterator_const | BaseIter_const |
Public Member Functions | |
| NiftiImageData () | |
| Constructor. | |
| virtual | ~NiftiImageData () |
| Destructor. | |
| NiftiImageData (const NiftiImageData &to_copy) | |
| Copy constructor. | |
| NiftiImageData & | operator= (const NiftiImageData &to_copy) |
| Assignment. | |
| NiftiImageData (const ImageData &to_copy) | |
| Copy constructor. | |
| NiftiImageData & | operator= (const ImageData &to_copy) |
| Assignment. | |
| NiftiImageData (const std::string &filename) | |
| Filename constructor. | |
| NiftiImageData (const nifti_image &image_nifti) | |
| Nifti constructor. | |
| template<class inputType > | |
| NiftiImageData (const inputType *const data, const VoxelisedGeometricalInfo3D &geom, const bool is_tensor=false) | |
| Construct from array. | |
| bool | operator== (const NiftiImageData &other) const |
| Equality operator. | |
| bool | operator!= (const NiftiImageData &other) const |
| Equality operator. | |
| NiftiImageData & | operator+= (const NiftiImageData &rhs) |
| Addition operator. | |
| NiftiImageData & | operator-= (const NiftiImageData &rhs) |
| Subtraction operator. | |
| NiftiImageData & | operator+= (const float) |
| Addition operator. | |
| NiftiImageData & | operator-= (const float) |
| Subtraction operator. | |
| NiftiImageData & | operator*= (const float) |
| Multiplication operator. | |
| NiftiImageData & | operator*= (const NiftiImageData &rhs) |
| Multiplication operator. | |
| NiftiImageData & | operator/= (const float) |
| Division operator. | |
| NiftiImageData & | operator/= (const NiftiImageData &rhs) |
| float | operator() (const int index) const |
| Access data element via 1D index (const) | |
| float & | operator() (const int index) |
| Access data element via 1D index. | |
| float | operator() (const int index[7]) const |
| Access data element via 7D index (const) | |
| float & | operator() (const int index[7]) |
| Access data element via 7D index. | |
| float | operator() (const int x, const int y, const int z, const int t=0, const int u=0, const int v=0, const int w=0) const |
| Access data element via 7D index (const) | |
| float & | operator() (const int x, const int y, const int z, const int t=0, const int u=0, const int v=0, const int w=0) |
| Access data element via 7D index. | |
| bool | is_initialised () const |
| Is the image initialised? (Should be unless default constructor was used.) | |
| std::shared_ptr< const nifti_image > | get_raw_nifti_sptr () const |
| Get image as nifti as const. | |
| std::shared_ptr< nifti_image > | get_raw_nifti_sptr () |
| Get image as nifti. | |
| virtual void | write (const std::string &filename, const int datatype) const |
| virtual void | write (const std::string &filename) const |
| Write. | |
| float | get_max () const |
| Get max. | |
| float | get_min () const |
| Get min. | |
| float | get_mean () const |
| Get mean. | |
| float | get_variance () const |
| Get variance. | |
| float | get_standard_deviation () const |
| Get standard deviation. | |
| float | get_sum () const |
| Get sum. | |
| unsigned | get_nan_count () const |
| Get nan count. | |
| void | fill (const float v) |
| Fill. | |
| void | fill (const dataType *v) |
| Fill from array. | |
| void | fill (const NiftiImageData &im) |
| Fill from array. | |
| float | get_norm (const NiftiImageData &) const |
| Get norm. | |
| const int * | get_dimensions () const |
| Get data size in each dimension. | |
| size_t | get_num_voxels () const |
| Get total number of voxels. | |
| void | print_header () const |
| Print header info. More... | |
| void | crop (const int min_index[7], const int max_index[7]) |
| Crop. Set to -1 to leave unchanged. | |
| void | pad (const int min_index[7], const int max_index[7], const dataType val=0) |
| Pad image with value. Give number of voxels to increase in min and max directions. Set values to -1 to leave unchanged. | |
| int | get_1D_index (const int idx[7]) const |
| get 1D index from ND index | |
| int | get_original_datatype () const |
| Get original datatype. | |
| bool | is_in_bounds (const int index[7]) const |
| Point is in bounds? | |
| bool | is_in_bounds (const int index) const |
| Point is in bounds? | |
| bool | is_same_size (const NiftiImageData &im) const |
| Images are same size. | |
| void | set_voxel_spacing (const float factors[3], const int interpolation_order) |
| void | kernel_convolution (const float sigma, NREG_CONV_KERNEL_TYPE conv_type=GAUSSIAN_KERNEL) |
| Kernel convolution. | |
| bool | get_contains_nans () const |
| Does the image contain any NaNs? | |
| void | flip_along_axis (const unsigned axis) |
| Flip the image along a given axis (Rotation of 180 degrees about axis) | |
| void | mirror_along_axis (const unsigned axis) |
| Mirror the image along a given axis (This will change handedness of image) | |
| dataType | get_inner_product (const NiftiImageData &other) const |
| Inner product of two images. | |
| void | normalise_zero_and_one () |
| Normalise image between 0 and 1. | |
| void | standardise () |
| Standardise (subtract mean and divide by standard deviation). | |
| std::unique_ptr< NiftiImageData > | clone () const |
| Clone and return as unique pointer. | |
| virtual Iterator & | begin () |
| virtual Iterator_const & | begin () const |
| virtual Iterator & | end () |
| virtual Iterator_const & | end () const |
| unsigned int | items () const |
| virtual void | sum (void *ptr) const |
| below all void* are actually float* | |
| virtual void | max (void *ptr) const |
| calculates the value of this container's element with the largest real part | |
| virtual void | dot (const DataContainer &a_x, void *ptr) const |
| calculates the dot product of this container with another one More... | |
| virtual void | axpby (const void *ptr_a, const DataContainer &a_x, const void *ptr_b, const DataContainer &a_y) |
*this = the linear combination of x and y | |
| virtual void | xapyb (const DataContainer &a_x, const void *ptr_a, const DataContainer &a_y, const void *ptr_b) |
| alternative interface to the above | |
| virtual void | xapyb (const DataContainer &a_x, const DataContainer &a_a, const DataContainer &a_y, const DataContainer &a_b) |
*this = elementwise sum of two elementwise products x*a and y*b | |
| virtual void | xapyb (const DataContainer &a_x, const void *ptr_a, const DataContainer &a_y, const DataContainer &a_b) |
*this = elementwise sum of x*a and elementwise y*b | |
| virtual float | norm () const |
| returns the norm of this container viewed as a vector | |
| virtual void | multiply (const DataContainer &a_x, const DataContainer &a_y) |
*this = the elementwise product x*y | |
| virtual void | divide (const DataContainer &a_x, const DataContainer &a_y) |
*this = the elementwise ratio x / y | |
| virtual void | maximum (const DataContainer &x, const DataContainer &y) |
*this = the elementwise max(x, y) | |
| virtual void | minimum (const DataContainer &x, const DataContainer &y) |
*this = the elementwise min(x, y) | |
| virtual void | power (const DataContainer &x, const DataContainer &y) |
*this = the elementwise pow(x, y) | |
| virtual void | multiply (const DataContainer &a_x, const void *a_y) |
*this = the product x * y with scalar y | |
| virtual void | add (const DataContainer &a_x, const void *a_y) |
*this = the sum x + y with scalar y | |
| virtual void | maximum (const DataContainer &x, const void *a_y) |
| virtual void | minimum (const DataContainer &x, const void *a_y) |
| virtual void | power (const DataContainer &x, const void *a_y) |
| virtual void | exp (const DataContainer &x) |
*this = the elementwise exp(x) | |
| virtual void | log (const DataContainer &x) |
*this = the elementwise log(x) | |
| virtual void | sqrt (const DataContainer &x) |
*this = the elementwise sqrt(x) | |
| virtual void | sign (const DataContainer &x) |
*this = the elementwise sign(x) | |
| virtual void | abs (const DataContainer &x) |
*this = the elementwise abs(x) | |
| virtual Dimensions | dimensions () const |
| void | unary_op (const DataContainer &a_x, dataType(*f)(dataType)) |
| void | semibinary_op (const DataContainer &a_x, const void *a_y, dataType(*f)(dataType, dataType)) |
| void | binary_op (const DataContainer &a_x, const DataContainer &a_y, dataType(*f)(dataType, dataType)) |
| virtual void | set_up_geom_info () |
| Set up the geometrical info. Use qform preferentially over sform. | |
 Public Member Functions inherited from sirf::ImageData | |
| virtual void | scale (float s)=0 |
| virtual bool | ordered () const |
| void | copy (Iterator_const &src, Iterator &dst, Iterator &end) const |
| void | fill (const ImageData &im) |
| void | fill (float v) |
| virtual bool | operator== (const ImageData &id) const |
| Write image to file. | |
| virtual bool | operator!= (const ImageData &id) const |
| std::shared_ptr< const VoxelisedGeometricalInfo3D > | get_geom_info_sptr () const |
| Get geometrical info. | |
| std::unique_ptr< ImageData > | clone () const |
| Clone and return as unique pointer. | |
| virtual bool | is_complex () const |
| Is complex? Unless overwridden (Gadgetron), assume not complex. | |
| virtual void | reorient (const VoxelisedGeometricalInfo3D &) |
| Reorient image. Requires that dimesions and spacing match. | |
| Public Member Functions inherited from sirf::DataContainer | |
| virtual int | bits () const |
| returns the size of data elements | |
| void | xapyb (const DataContainer &a_x, const DataContainer &a_a, const DataContainer &a_y, const void *ptr_b) |
*this = elementwise sum of elementwise x*a and y*b | |
| bool | is_empty () const |
| std::unique_ptr< DataContainer > | clone () const |
| void | conjugate () |
| overwrites this container's complex data with complex conjugate values | |
| std::unique_ptr< DataContainer > | conjugate () const |
| returns unique pointer to the complex-conjugated copy of this container | |
Static Public Member Functions | |
| static std::shared_ptr< nifti_image > | create_from_geom_info (const VoxelisedGeometricalInfo3D &geom, const bool is_tensor=false, const NREG_TRANS_TYPE tensor_type=NREG_TRANS_TYPE::DEF_FIELD) |
| Create NiftiImageData from geometrical info. | |
| static void | construct_NiftiImageData_from_complex_im_real_component (std::shared_ptr< NiftiImageData > &out_sptr, const std::shared_ptr< const ImageData > in_sptr) |
| Construct NiftiImageData from the real component of a complex SIRF ImageData. | |
| static void | construct_NiftiImageData_from_complex_im_imag_component (std::shared_ptr< NiftiImageData > &out_sptr, const std::shared_ptr< const ImageData > in_sptr) |
| Construct NiftiImageData from the imaginary component of a complex SIRF ImageData. | |
| static void | construct_NiftiImageData_from_complex_im (std::shared_ptr< NiftiImageData > &out_real_sptr, std::shared_ptr< NiftiImageData > &out_imag_sptr, const std::shared_ptr< const ImageData > in_sptr) |
| Construct two NiftiImageData from a complex SIRF ImageData. | |
| static void | print_headers (const std::vector< const NiftiImageData * > &ims) |
| Print multiple header info. More... | |
| static bool | are_equal_to_given_accuracy (const NiftiImageData &im1, const NiftiImageData &im2, const float required_accuracy_compared_to_max) |
| Check if the norms of two images are equal to a given accuracy. | |
| static bool | do_nifti_image_metadata_match (const NiftiImageData &im1, const NiftiImageData &im2, bool verbose) |
| Do nifti image metadatas match? | |
| static void | dump_headers (const std::vector< const NiftiImageData * > &ims) |
| Dump info of multiple nifti images. | |
| template<typename T > | |
| static void | dump_nifti_element (const std::vector< const NiftiImageData * > &ims, const std::string &name, const T &call_back) |
| Dump nifti element. | |
| template<typename T > | |
| static void | dump_nifti_element (const std::vector< const NiftiImageData * > &ims, const std::string &name, const T &call_back, const unsigned num_elems) |
| Dump nifti element. | |
| static std::string | get_headers (const std::vector< const NiftiImageData< dataType > * > &ims) |
| template<typename T > | |
| static std::string | get_nifti_element (const std::vector< const NiftiImageData * > &ims, const std::string &name, const T &call_back) |
| template<typename T > | |
| static std::string | get_nifti_element (const std::vector< const NiftiImageData * > &ims, const std::string &name, const T &call_back, const unsigned num_elems) |
| Static Public Member Functions inherited from sirf::ImageData | |
| static bool | can_reorient (const VoxelisedGeometricalInfo3D &geom_1, const VoxelisedGeometricalInfo3D &geom_2, const bool throw_error) |
| Can reorient? (check dimensions and spacing) | |
| Static Public Member Functions inherited from sirf::DataContainer | |
| template<typename T > | |
| static T | product (T x, T y) |
| template<typename T > | |
| static T | ratio (T x, T y) |
| template<typename T > | |
| static T | inverse_ratio (T x, T y) |
| template<typename T > | |
| static T | sum (T x, T y) |
| template<typename T > | |
| static T | maximum (T x, T y) |
| template<typename T > | |
| static T | maxabs (T x, T y) |
| template<typename T > | |
| static T | maxreal (T x, T y) |
| template<typename T > | |
| static T | minimum (T x, T y) |
| template<typename T > | |
| static T | minabs (T x, T y) |
| template<typename T > | |
| static T | minreal (T x, T y) |
| static std::complex< float > | power (std::complex< float > x, std::complex< float > y) |
| static std::complex< float > | exp (std::complex< float > x) |
| static std::complex< float > | log (std::complex< float > x) |
| static std::complex< float > | sqrt (std::complex< float > x) |
| template<typename T > | |
| static T | sign (T x) |
| template<typename T > | |
| static T | abs (T x) |
Protected Types | |
| enum | NiftiImageDataType { _general , _3D , _3DTensor , _3DDisp , _3DDef } |
| enum | MathsType { ADD , sub , mul , div } |
Protected Member Functions | |
| void | check_dimensions (const enum NiftiImageDataType image_type=_general) |
| Check dimensions. Don't require anything for this class. | |
| void | set_up_data (const int original_datatype) |
| Set up datatype. Set to float if not already, store the original type. | |
| void | maths (const NiftiImageData &c, const MathsType type) |
| Add, subract image from another. | |
| void | maths (const float val, const MathsType type) |
| Add, subract, multiply value to image. | |
| virtual NiftiImageData * | clone_impl () const |
| Clone helper function. Don't use. | |
| virtual ObjectHandle< DataContainer > * | new_data_container_handle () const |
| Protected Member Functions inherited from sirf::ImageData | |
| void | set_geom_info (const std::shared_ptr< VoxelisedGeometricalInfo3D > geom_info_sptr) |
| Set geom info. | |
| Protected Member Functions inherited from sirf::DataContainer | |
| virtual void | conjugate_impl () |
| we assume data to be real, complex data containers must override this | |
Static Protected Member Functions | |
| static void | open_nifti_image (std::shared_ptr< nifti_image > &image, const std::string &filename) |
| Open nifti image. | |
| static void | copy_nifti_image (std::shared_ptr< nifti_image > &output_image_sptr, const std::shared_ptr< nifti_image > &image_to_copy_sptr) |
| Copy nifti image. | |
Protected Attributes | |
| std::shared_ptr< nifti_image > | _nifti_image |
| Image data as a nifti object. | |
| float * | _data = NULL |
| Data. | |
| int | _original_datatype = -1 |
| Original datatype. | |
| std::shared_ptr< Iterator > | _begin |
| std::shared_ptr< Iterator > | _end |
| std::shared_ptr< Iterator_const > | _begin_const |
| std::shared_ptr< Iterator_const > | _end_const |
Friends | |
| NiftiImageData | operator+ (NiftiImageData lhs, const NiftiImageData &rhs) |
| Addition operator. | |
| NiftiImageData | operator- (NiftiImageData lhs, const NiftiImageData &rhs) |
| Subtraction operator. | |
| NiftiImageData | operator+ (NiftiImageData lhs, const float val) |
| Addition operator. | |
| NiftiImageData | operator- (NiftiImageData lhs, const float val) |
| Subtraction operator. | |
| NiftiImageData | operator* (NiftiImageData lhs, const float val) |
| Multiplication operator. | |
| NiftiImageData | operator* (NiftiImageData lhs, const NiftiImageData &rhs) |
| Multiplication operator. | |
| NiftiImageData | operator/ (NiftiImageData lhs, const float val) |
| NiftiImageData | operator/ (NiftiImageData lhs, const NiftiImageData &rhs) |
| Division operator. | |
Member Function Documentation
◆ dot()
template<class dataType >
|
virtual |
calculates the dot product of this container with another one
below all void* are actually either float* (STIR containers and NiftiImageData) or complex_float_t* (Gadgetron containers)
Implements sirf::DataContainer.
◆ print_header()
template<class dataType >
| void NiftiImageData::print_header |
Print header info.
Dump header info.
◆ print_headers()
template<class dataType >
|
static |
Print multiple header info.
Dump multiple header info.
◆ set_voxel_spacing()
template<class dataType >
| void NiftiImageData::set_voxel_spacing | ( | const float | factors[3], |
| const int | interpolation_order | ||
| ) |
Set the voxel spacing. Requires resampling image, and so interpolation order is required. As per NiftyReg, interpolation_order can be either 0, 1 or 3 meaning nearest neighbor, linear or cubic spline interpolation.
◆ write()
template<class dataType >
|
virtual |
Save to file. Templated so the user can choose the datatype they save to. This defaults to -1, which is the original datatype of that image (stored as _original_datatype).
The documentation for this class was generated from the following files:
- /home/sirfuser/devel/buildVM/sources/SIRF/src/Registration/cReg/include/sirf/Reg/ImageWeightedMean.h
- /home/sirfuser/devel/buildVM/sources/SIRF/src/Registration/cReg/include/sirf/Reg/NiftiImageData.h
- /home/sirfuser/devel/buildVM/sources/SIRF/src/Registration/cReg/NiftiImageData.cpp
