iRoCS Toolbox
1.1.0
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The Array class is an extension to the blitz++ Array class providing additional parameters element size in microns and a transformation. More...
#include "libArrayToolbox/Array.hh"
Public Member Functions | |
Array (std::string const &fileName, std::string const &dataset, iRoCS::ProgressReporter *progress=NULL) | |
Constructor from BlitzH5File. More... | |
template<typename T_expr > | |
Array (blitz::_bz_ArrayExpr< T_expr > expr, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one)) | |
Constructor from Array expression. More... | |
Array (blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Default Constructor. More... | |
Array (BlitzIndexT extent0, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking one extent parameter. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking two extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking three extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking four extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, BlitzIndexT extent4, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking five extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, BlitzIndexT extent4, BlitzIndexT extent5, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking six extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, BlitzIndexT extent4, BlitzIndexT extent5, BlitzIndexT extent6, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking seven extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, BlitzIndexT extent4, BlitzIndexT extent5, BlitzIndexT extent6, BlitzIndexT extent7, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking eight extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, BlitzIndexT extent4, BlitzIndexT extent5, BlitzIndexT extent6, BlitzIndexT extent7, BlitzIndexT extent8, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking nine extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, BlitzIndexT extent4, BlitzIndexT extent5, BlitzIndexT extent6, BlitzIndexT extent7, BlitzIndexT extent8, BlitzIndexT extent9, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking ten extent parameters. More... | |
Array (BlitzIndexT extent0, BlitzIndexT extent1, BlitzIndexT extent2, BlitzIndexT extent3, BlitzIndexT extent4, BlitzIndexT extent5, BlitzIndexT extent6, BlitzIndexT extent7, BlitzIndexT extent8, BlitzIndexT extent9, BlitzIndexT extent10, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Constructor taking eleven extent parameters. More... | |
Array (DataT *restrict data, blitz::TinyVector< BlitzIndexT, Dim > const &shape, blitz::TinyVector< BlitzIndexT, Dim > const &stride, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Pre-existing data constructor with strides without ownership passing. More... | |
Array (DataT *restrict data, blitz::TinyVector< BlitzIndexT, Dim > const &shape, blitz::preexistingMemoryPolicy deletionPolicy, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Pre-existing data constructor with ownership passing (if requested). More... | |
Array (DataT *restrict data, blitz::TinyVector< BlitzIndexT, Dim > const &shape, blitz::TinyVector< BlitzIndexT, Dim > const &stride, blitz::preexistingMemoryPolicy deletionPolicy, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Pre-existing data constructor with strides and ownership passing (if requested). More... | |
Array (blitz::TinyVector< BlitzIndexT, Dim > const &extents, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array Constructor of specified size and storage format. More... | |
Array (blitz::TinyVector< BlitzIndexT, Dim > const &lbounds, blitz::TinyVector< BlitzIndexT, Dim > const &extents, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array Constructor of specified size and storage format with index offset. More... | |
Array (blitz::Range const &r0, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for one dimension. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for two dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for three dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for four dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::Range const &r4, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for five dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::Range const &r4, blitz::Range const &r5, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for six dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::Range const &r4, blitz::Range const &r5, blitz::Range const &r6, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for seven dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::Range const &r4, blitz::Range const &r5, blitz::Range const &r6, blitz::Range const &r7, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for eight dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::Range const &r4, blitz::Range const &r5, blitz::Range const &r6, blitz::Range const &r7, blitz::Range const &r8, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for nine dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::Range const &r4, blitz::Range const &r5, blitz::Range const &r6, blitz::Range const &r7, blitz::Range const &r8, blitz::Range const &r9, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for ten dimensions. More... | |
Array (blitz::Range const &r0, blitz::Range const &r1, blitz::Range const &r2, blitz::Range const &r3, blitz::Range const &r4, blitz::Range const &r5, blitz::Range const &r6, blitz::Range const &r7, blitz::Range const &r8, blitz::Range const &r9, blitz::Range const &r10, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one), blitz::GeneralArrayStorage< Dim > storage=blitz::GeneralArrayStorage< Dim >()) | |
Empty Array constructor with specified addressing space for eleven dimensions. More... | |
Array (Array< DataT, Dim > const &array) | |
Reference Constructor. More... | |
template<int Dim2, typename R0 , typename R1 , typename R2 , typename R3 , typename R4 , typename R5 , typename R6 , typename R7 , typename R8 , typename R9 , typename R10 > | |
Array (Array< DataT, Dim2 > &array, R0 r0, R1 r1, R2 r2, R3 r3, R4 r4, R5 r5, R6 r6, R7 r7, R8 r8, R9 r9, R10 r10) | |
Mixed type Constructor. More... | |
Array (blitz::Array< DataT, Dim > const &array, blitz::TinyVector< double, Dim > const &elementSizeUm=1.0, blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation=(traits< blitz::TinyMatrix< double, Dim+1, Dim+1 > >::one)) | |
blitz++ Array Copy Constructor. More... | |
~Array () | |
Destructor. More... | |
blitz::TinyVector< double, Dim > const & | elementSizeUm () const |
Get the element size of this Array. More... | |
Array< DataT, Dim > & | filterDeriche (double sigmaUm, int dim) |
Filter this Array with a recursive filter approximating a Gaussian (Deriche filter) along the selected dimension. More... | |
Interpolator< DataT, Dim > const & | interpolator () const |
Get a read-only reference to the ArrayInterpolator applied to this Array. More... | |
void | load (std::string const &fileName, std::string const &dataset, iRoCS::ProgressReporter *progress=NULL) |
Set the Array data and meta-data according to a specification stored in an HDF5 file. More... | |
void | load (BlitzH5File const &inFile, std::string const &dataset, iRoCS::ProgressReporter *progress=NULL) |
Set the Array data and meta-data according to a specification stored in an HDF5 file. More... | |
blitz::TinyVector< double, Dim > | lowerBoundUm () const |
Get the lower bound of the Array bounding box after application of the transformation in micrometers. More... | |
Array< DataT, Dim > & | operator= (Array< DataT, Dim > const &array) |
(Copy) Assignment operator. More... | |
Array< DataT, Dim > & | operator= (blitz::Array< DataT, Dim > const &array) |
Assignment operator from blitz++ Array. More... | |
template<typename T_expr > | |
Array< DataT, Dim > & | operator= (blitz::ETBase< T_expr > const &expr) |
Assignment operator from blitz++ Array expression. More... | |
blitz::ListInitializationSwitch< typename blitz::Array< DataT, Dim >, DataT * > | operator= (DataT x) |
List assignment operator. More... | |
Array< DataT, Dim > & | rescale (blitz::TinyVector< double, Dim > const &targetElementSizeUm, iRoCS::ProgressReporter *pr=NULL) |
Rescale the Array so that the new Array element size is the given target element size. More... | |
void | save (std::string const &fileName, std::string const &dataset, int compression=0, iRoCS::ProgressReporter *progress=NULL) const |
Save the Array data and meta-data to an HDF5 file. More... | |
void | save (BlitzH5File &outFile, std::string const &dataset, int compression=0, iRoCS::ProgressReporter *progress=NULL) const |
Save the Array data and meta-data to an HDF5 file. More... | |
void | setElementSizeUm (blitz::TinyVector< double, Dim > const &elementSizeUm) |
Set the element size of this Array. More... | |
void | setInterpolator (Interpolator< DataT, Dim > const &interpolator) |
Set the Interpolator applied to this Array. More... | |
void | setTransformation (blitz::TinyMatrix< double, Dim+1, Dim+1 > const &transformation) |
Set the homogeneous transformation matrix of this Array. More... | |
blitz::TinyMatrix< double, Dim+1, Dim+1 > const & | transformation () const |
Get the homogeneous transformation matrix of this Array. More... | |
blitz::TinyVector< double, Dim > | upperBoundUm () const |
Get the upper bound of the Array bounding box after application of the transformation in micrometers. More... | |
DataT | valueAt (blitz::TinyVector< double, Dim > const &positionUm) const |
Get the Array value at the model (sub-pixel) position given. More... | |
Protected Attributes | |
blitz::TinyVector< double, Dim > | _elementSizeUm |
The voxel extents in micrometers per voxel. More... | |
blitz::TinyMatrix< double, Dim+1, Dim+1 > | _transformation |
The transformation matrix to apply when accessing the Array using valueAt() and setValueAt() More... | |
Interpolator< DataT, Dim > * | p_interpolator |
The ArrayInterpolator to use when accessing sub-pixel Array positions using valueAt() and setValueAt() More... | |
The Array class is an extension to the blitz++ Array class providing additional parameters element size in microns and a transformation.
This class adds relevant metadata to the general purpose blitz++ Arrays to handle microscopic datasets in a unified way. Along with the raw data with the known manipulation options of blitz++ Arrays, it additionally specifies the voxel extents in micormeters and you can specify a transformation to apply before querying the Array. Application of the transformation may yield sub-pixel positions. You can specify the interpolation behaviour by specifying an Interpolator and passing it via the setInterpolator() function. By default a linear interpolator with zero boundary treatment is used.
DataT | The datatype of the Array elements to store. These can be basic or complex numeric types but also TinyVectors or TinyMatrices. Bool or user-defined types are not allowed and compilation will fail when trying to build Arrays using a type with undefined arithmetic operations. |
Dim | The rank of the Array |
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explicit |
Constructor from BlitzH5File.
fileName | The hdf5 file name |
dataset | The hdf5 dataset name |
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inlineexplicit |
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inline |
Default Constructor.
This constructor calls the blitz::Array default constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
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inlineexplicit |
Constructor taking one extent parameter.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zero's dimension (If the Array has more than one dimension this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking two extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension (If the Array has more than two dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking three extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension (If the Array has more than three dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking four extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension (If the Array has more than four dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking five extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension |
extent4 | The Array extent for the fourth dimension (If the Array has more than five dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking six extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension |
extent4 | The Array extent for the fourth dimension |
extent5 | The Array extent for the fifth dimension (If the Array has more than six dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking seven extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension |
extent4 | The Array extent for the fourth dimension |
extent5 | The Array extent for the fifth dimension |
extent6 | The Array extent for the sixth dimension (If the Array has more than seven dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking eight extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension |
extent4 | The Array extent for the fourth dimension |
extent5 | The Array extent for the fifth dimension |
extent6 | The Array extent for the sixth dimension |
extent7 | The Array extent for the seventh dimension (If the Array has more than eight dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking nine extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension |
extent4 | The Array extent for the fourth dimension |
extent5 | The Array extent for the fifth dimension |
extent6 | The Array extent for the sixth dimension |
extent7 | The Array extent for the seventh dimension |
extent8 | The Array extent for the eighth dimension (If the Array has more than nine dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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inline |
Constructor taking ten extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension |
extent4 | The Array extent for the fourth dimension |
extent5 | The Array extent for the fifth dimension |
extent6 | The Array extent for the sixth dimension |
extent7 | The Array extent for the seventh dimension |
extent8 | The Array extent for the eighth dimension |
extent9 | The Array extent for the nineth dimension (If the Array has more than ten dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Constructor taking eleven extent parameters.
This constructor calls the corresponding blitz::Array constructor, sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
extent0 | The Array extent for the zeroth dimension |
extent1 | The Array extent for the first dimension |
extent2 | The Array extent for the second dimension |
extent3 | The Array extent for the third dimension |
extent4 | The Array extent for the fourth dimension |
extent5 | The Array extent for the fifth dimension |
extent6 | The Array extent for the sixth dimension |
extent7 | The Array extent for the seventh dimension |
extent8 | The Array extent for the eighth dimension |
extent9 | The Array extent for the nineth dimension |
extent10 | The Array extent for the tenth dimension (If the Array has more than eleven dimensions this will be used for all remaining dimensions as well) |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Pre-existing data constructor with strides without ownership passing.
This constructor creates an Array from an existing data block with the given set of strides. Data ownership is not passed to the Array.
The constructor sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
data | The pointer to the first data element of the pre-allocated memory block |
shape | The shape of the resulting Array |
stride | The strides for the different dimensions |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Pre-existing data constructor with ownership passing (if requested).
This constructor creates an Array from an existing data block.
The constructor sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
data | The pointer to the first data element of the pre-allocated memory block |
shape | The shape of the resulting Array |
deletionPolicy | The deletion policy to apply. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Pre-existing data constructor with strides and ownership passing (if requested).
This constructor creates an Array from an existing data block.
The constructor sets the given element size and transformation matrix. The interpolator will be set to linear with ZeroBoundaryTreatment.
data | The pointer to the first data element of the pre-allocated memory block |
shape | The shape of the resulting Array |
stride | The strides for the different dimensions |
deletionPolicy | The deletion policy to apply. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply when accessing Array entries with valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array Constructor of specified size and storage format.
This constructor creates an Array of specified dimensions and sets the element size and transformation to the given values. The interpolator will be set to linear with ZeroBoundaryTreatment.
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Empty Array Constructor of specified size and storage format with index offset.
This constructor creates an Array of specified dimensions and sets the element size and transformation to the given values. The interpolator will be set to linear with ZeroBoundaryTreatment.
lbounds | The Array lower index bounds |
extents | The Array extents |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for one dimension.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. If the Array has more than one dimension this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for two dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. If the Array has more than two dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for three dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. If the Array has more than three dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for four dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. If the Array has more than four dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for five dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. |
r4 | The range of the fourth dimension. If the Array has more than five dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for six dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. |
r4 | The range of the fourth dimension. |
r5 | The range of the fifth dimension. If the Array has more than six dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for seven dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. |
r4 | The range of the fourth dimension. |
r5 | The range of the fifth dimension. |
r6 | The range of the sixth dimension. If the Array has more than seven dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for eight dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. |
r4 | The range of the fourth dimension. |
r5 | The range of the fifth dimension. |
r6 | The range of the sixth dimension. |
r7 | The range of the seventh dimension. If the Array has more than eight dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for nine dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. |
r4 | The range of the fourth dimension. |
r5 | The range of the fifth dimension. |
r6 | The range of the sixth dimension. |
r7 | The range of the seventh dimension. |
r8 | The range of the eighth dimension. If the Array has more than nine dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for ten dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. |
r4 | The range of the fourth dimension. |
r5 | The range of the fifth dimension. |
r6 | The range of the sixth dimension. |
r7 | The range of the seventh dimension. |
r8 | The range of the eighth dimension. |
r9 | The range of the nineth dimension. If the Array has more than ten dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Empty Array constructor with specified addressing space for eleven dimensions.
The Range argument indicates that the Array indices should start at the lower bound of the Range and end at the upper bound. e.g. Array<float,1>(blitz::Range(5, 15))
will create a new 1-D Array of length 11, starting at index 5.
r0 | The range of the zeroth dimension. |
r1 | The range of the first dimension. |
r2 | The range of the second dimension. |
r3 | The range of the third dimension. |
r4 | The range of the fourth dimension. |
r5 | The range of the fifth dimension. |
r6 | The range of the sixth dimension. |
r7 | The range of the seventh dimension. |
r8 | The range of the eighth dimension. |
r9 | The range of the nineth dimension. |
r10 | The range of the tenth dimension. If the Array has more than eleven dimensions this range is used for the remaining dimensions as well. |
elementSizeUm | The voxel extents in micrometers |
transformation | The transformation to apply to the query position before accessing the Array using valueAt() and setValueAt() |
storage | The GeneralArrayStorage to use for the underlying blitz++ Array |
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Reference Constructor.
This constructor creates a reference to another Array. This resembles the copy-Constructor of the blitz++ Arrays. It will not copy the array data. This is necessary to allow automatic type promotion and several Array assignment tricks known from blitz++. The meta-data will be copied to the new Array.
array | The Array to create a reference to |
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Mixed type Constructor.
This constructor is internally used by the () operators, don't use it directly to actually create an Array.
array | The Array to pick a sub-Array from |
r0 | The zeroth Range or index |
r1 | The first Range or index |
r2 | The second Range or index |
r3 | The third Range or index |
r4 | The fourth Range or index |
r5 | The fifth Range or index |
r6 | The sixth Range or index |
r7 | The seventh Range or index |
r8 | The eighth Range or index |
r9 | The nineth Range or index |
r10 | The tenth Range or index |
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blitz++ Array Copy Constructor.
This constructor creates an Array from the given blitz::Array. The data will be copied to the new Array and metadata set as given.
atb::Array< DataT, Dim >::~Array | ( | ) |
Destructor.
Referenced by atb::Array< unsigned char, 3 >::Array().
Array<DataT,Dim>& atb::Array< DataT, Dim >::operator= | ( | Array< DataT, Dim > const & | array | ) |
(Copy) Assignment operator.
This operator copies the values from the given Array into this Array, but leaves the meta-data of both Array untouched.
array | The Array to copy |
Referenced by atb::Array< unsigned char, 3 >::Array().
Array<DataT,Dim>& atb::Array< DataT, Dim >::operator= | ( | blitz::Array< DataT, Dim > const & | array | ) |
Array<DataT,Dim>& atb::Array< DataT, Dim >::operator= | ( | blitz::ETBase< T_expr > const & | expr | ) |
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Get the element size of this Array.
Definition at line 1308 of file Array.hh.
Referenced by atb::Array< unsigned char, 3 >::setElementSizeUm().
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Get the homogeneous transformation matrix of this Array.
Definition at line 1332 of file Array.hh.
Referenced by atb::Array< unsigned char, 3 >::setTransformation().
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Get a read-only reference to the ArrayInterpolator applied to this Array.
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Set the Interpolator applied to this Array.
interpolator | The new Interpolator for this Array |
Array<DataT,Dim>& atb::Array< DataT, Dim >::filterDeriche | ( | double | sigmaUm, |
int | dim | ||
) |
Filter this Array with a recursive filter approximating a Gaussian (Deriche filter) along the selected dimension.
Let and
be a line of this Array to be filtered, then the recursive filter is defined by
where
and
sigmaUm | The standard deviation of the Gaussian that is approximated by the recursive filter in micrometers |
dim | The dimension along the filtering is performed |
Referenced by atb::Array< unsigned char, 3 >::setInterpolator().
Array<DataT,Dim>& atb::Array< DataT, Dim >::rescale | ( | blitz::TinyVector< double, Dim > const & | targetElementSizeUm, |
iRoCS::ProgressReporter * | pr = NULL |
||
) |
Rescale the Array so that the new Array element size is the given target element size.
If down-scaling in any dimension is requested (increase in element size), the according dimension will first be convolved with a Gaussian to avoid aliasing. The Interpolator associated with this Array will be applied.
targetElementSizeUm | The target voxel extents in micrometers |
Referenced by atb::Array< unsigned char, 3 >::setInterpolator().
void atb::Array< DataT, Dim >::load | ( | std::string const & | fileName, |
std::string const & | dataset, | ||
iRoCS::ProgressReporter * | progress = NULL |
||
) |
Set the Array data and meta-data according to a specification stored in an HDF5 file.
This function loads the specified HDF5 dataset and associated meta-data. If meta-data are missing, they will be set to default values, i. e. unit element size and identity transformation. The meta-data are expected to be found in dataset attributes 'element_size_um' (double vector of length Dim) and 'transformation' (double vector of length (Dim + 1) * (Dim + 1)).
fileName | The hdf5 file to read the Array data from |
dataset | The hdf5 dataset to read the Array data from |
BlitzH5Error | If the dataset cannot be read this exception is thrown. |
Referenced by atb::Array< unsigned char, 3 >::setInterpolator().
void atb::Array< DataT, Dim >::load | ( | BlitzH5File const & | inFile, |
std::string const & | dataset, | ||
iRoCS::ProgressReporter * | progress = NULL |
||
) |
Set the Array data and meta-data according to a specification stored in an HDF5 file.
This function loads the specified HDF5 dataset and associated meta-data. If meta-data are missing, they will be set to default values, i. e. unit element size and identity transformation. The meta-data are expected to be found in dataset attributes 'element_size_um' (double vector of length Dim) and 'transformation' (double vector of length (Dim + 1) * (Dim + 1)).
inFile | The hdf5 file to read the Array data from |
dataset | The hdf5 dataset to read the Array data from |
BlitzH5Error | If the dataset cannot be read this exception is thrown. |
void atb::Array< DataT, Dim >::save | ( | std::string const & | fileName, |
std::string const & | dataset, | ||
int | compression = 0 , |
||
iRoCS::ProgressReporter * | progress = NULL |
||
) | const |
Save the Array data and meta-data to an HDF5 file.
This function saves this Array to the specified HDF5 dataset. The meta-data are stored in dataset attributes 'element_size_um' (double vector of length Dim) and 'transformation' (double vector of length (Dim + 1) * (Dim + 1)).
fileName | The hdf5 file to write the Array data to |
dataset | The hdf5 dataset to write the Array data to |
compression | The compression level to apply (0-9). 0 is no compression. Usually a good trade-off is a compression level of 3 |
BlitzH5Error | If the dataset cannot be written this exception is thrown. |
Referenced by atb::Array< unsigned char, 3 >::setInterpolator().
void atb::Array< DataT, Dim >::save | ( | BlitzH5File & | outFile, |
std::string const & | dataset, | ||
int | compression = 0 , |
||
iRoCS::ProgressReporter * | progress = NULL |
||
) | const |
Save the Array data and meta-data to an HDF5 file.
This function saves this Array to the specified HDF5 dataset. The meta-data are stored in dataset attributes 'element_size_um' (double vector of length Dim) and 'transformation' (double vector of length (Dim + 1) * (Dim + 1)).
outFile | The hdf5 file to write the Array data to |
dataset | The hdf5 dataset to write the Array data to |
compression | The compression level to apply (0-9). 0 is no compression. Usually a good trade-off is a compression level of 3 |
BlitzH5Error | If the dataset cannot be written this exception is thrown. |
blitz::TinyVector<double,Dim> atb::Array< DataT, Dim >::lowerBoundUm | ( | ) | const |
Get the lower bound of the Array bounding box after application of the transformation in micrometers.
Referenced by atb::Array< unsigned char, 3 >::setInterpolator().
blitz::TinyVector<double,Dim> atb::Array< DataT, Dim >::upperBoundUm | ( | ) | const |
Get the upper bound of the Array bounding box after application of the transformation in micrometers.
Referenced by atb::Array< unsigned char, 3 >::setInterpolator().
DataT atb::Array< DataT, Dim >::valueAt | ( | blitz::TinyVector< double, Dim > const & | positionUm | ) | const |
Get the Array value at the model (sub-pixel) position given.
To obtain the Array value first the transform is applied to the given micrometer position, the resulting position is divided by the element size to obtain the (sub-pixel) Array index to access. Then the ArrayInterpolator (with associated BoundaryTreatment) is applied to obtain the interpolated Array value.
positionUm | The micrometer position to query |
Referenced by atb::Array< unsigned char, 3 >::setInterpolator().
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The voxel extents in micrometers per voxel.
Definition at line 1561 of file Array.hh.
Referenced by atb::Array< unsigned char, 3 >::elementSizeUm(), and atb::Array< unsigned char, 3 >::setElementSizeUm().
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The transformation matrix to apply when accessing the Array using valueAt() and setValueAt()
Definition at line 1569 of file Array.hh.
Referenced by atb::Array< unsigned char, 3 >::setTransformation(), and atb::Array< unsigned char, 3 >::transformation().
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The ArrayInterpolator to use when accessing sub-pixel Array positions using valueAt() and setValueAt()
Definition at line 1577 of file Array.hh.
Referenced by atb::Array< unsigned char, 3 >::interpolator(), and atb::Array< unsigned char, 3 >::setInterpolator().