38 #ifndef OME_FILES_PIXELBUFFER_H 39 #define OME_FILES_PIXELBUFFER_H 51 #define BOOST_DISABLE_ASSERTS 1 52 #include <boost/multi_array.hpp> 54 #include <ome/files/PixelProperties.h> 58 #include <ome/xml/model/enums/DimensionOrder.h> 113 typedef boost::multi_array_types::index
index;
116 typedef std::array<boost::multi_array_types::index,
123 typedef boost::detail::multi_array::extent_gen<dimensions>
range_type;
135 pixeltype(pixeltype),
136 endiantype(endiantype)
178 static storage_order_type
190 static storage_order_type
252 typedef boost::multi_array<value_type, dimensions>
array_type;
262 multiarray(
std::shared_ptr<array_type>(new array_type(
boost::extents[1][1][1][1][1][1][1][1][1],
277 template<
class ExtentList>
284 multiarray(
std::shared_ptr<array_type>(new array_type(extents, storage)))
301 template<
class ExtentList>
304 const ExtentList& extents,
309 multiarray(
std::shared_ptr<array_ref_type>(new array_ref_type(pixeldata, extents, storage)))
329 multiarray(
std::shared_ptr<array_type>(new array_type(range, storage)))
353 multiarray(
std::shared_ptr<array_ref_type>(new array_ref_type(pixeldata, range, storage)))
367 multiarray(buffer.multiarray)
389 const array_ref_type&
403 return array().data();
417 return array().data();
433 bool is_valid =
true;
439 catch (
const std::runtime_error&)
457 return (boost::get<std::shared_ptr<array_type>>(&multiarray) !=
nullptr);
466 return array().num_elements();
475 return array().num_dimensions();
488 return array().shape();
498 const boost::multi_array_types::index *
501 return array().strides();
512 const boost::multi_array_types::index *
515 return array().index_bases();
531 return array().origin();
542 return array().storage_order();
558 array() = rhs.
array();
573 operator = (
const array_ref_type& rhs)
588 return array() == rhs.
array();
598 operator == (
const array_ref_type& rhs)
const 600 return array() == rhs;
612 return array() != rhs.
array();
622 operator != (
const array_ref_type& rhs)
const 624 return array() != rhs;
636 return array() < rhs.
array();
646 operator < (
const array_ref_type& rhs)
const 648 return array() < rhs;
660 return array() <= rhs.
array();
670 operator <= (
const array_ref_type& rhs)
const 672 return array() <= rhs;
684 return array() > rhs.
array();
694 operator > (
const array_ref_type& rhs)
const 696 return array() > rhs;
708 return array() >= rhs.
array();
718 operator >= (
const array_ref_type& rhs)
const 720 return array() >= rhs;
731 template <
typename InputIterator>
736 array().assign(begin, end);
752 return array()(indices);
768 return array()(indices);
781 template<
class charT,
class traits>
783 read(std::basic_istream<charT,traits>& stream)
785 stream.read(reinterpret_cast<char *>(data()),
786 static_cast<std::streamsize>(num_elements() *
sizeof(value_type)));
799 template<
class charT,
class traits>
801 write(std::basic_ostream<charT,traits>& stream)
const 803 stream.write(reinterpret_cast<const char *>(data()),
804 static_cast<std::streamsize>(num_elements() *
sizeof(value_type)));
823 boost::variant<std::shared_ptr<array_type>,
840 template <
typename U>
842 operator() (U& v)
const 845 throw std::runtime_error(
"Null array type");
860 template <
typename U>
862 operator() (U& v)
const 865 throw std::runtime_error(
"Null array type");
877 return boost::apply_visitor(v, multiarray);
885 return boost::apply_visitor(v, multiarray);
901 template<
typename T,
class charT,
class traits>
902 inline std::basic_istream<charT,traits>&
903 operator>> (std::basic_istream<charT,traits>& is,
917 template<
typename T,
class charT,
class traits>
918 inline std::basic_ostream<charT,traits>&
919 operator<< (std::basic_ostream<charT,traits>& os,
920 const ::ome::files::PixelBuffer<T>& buf)
928 #endif // OME_FILES_PIXELBUFFER_H const value_type * origin() const
Get the origin of the array.
Definition: PixelBuffer.h:529
boost::multi_array_ref< value_type, dimensions > array_ref_type
Type for multi-dimensional pixel array view referencing external data.
Definition: PixelBuffer.h:246
size_type num_dimensions() const
Get the number of dimensions in the multi-dimensional array.
Definition: PixelBuffer.h:473
Buffer for a specific pixel type.
Definition: PixelBuffer.h:235
PixelBuffer(value_type *pixeldata, const range_type &range, ::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, EndianType endiantype=ENDIAN_NATIVE, const storage_order_type &storage=PixelBufferBase::default_storage_order())
Construct from ranges (external storage).
Definition: PixelBuffer.h:347
void assign(InputIterator begin, InputIterator end)
Assign pixel values.
Definition: PixelBuffer.h:733
virtual ~PixelBuffer()
Destructor.
Definition: PixelBuffer.h:371
Spatial y dimension (Y).
Definition: PixelBuffer.h:81
value_type * data()
Get the raw data.
Definition: PixelBuffer.h:401
boost::variant< std::shared_ptr< array_type >, std::shared_ptr< array_ref_type > > multiarray
Multi-dimensional pixel array.
Definition: PixelBuffer.h:824
boost::multi_array_types::index index
Index type.
Definition: PixelBuffer.h:113
Base class for all PixelBuffer types.
Definition: PixelBuffer.h:103
Logical subdivision of the temporal t dimension (t).
Definition: PixelBuffer.h:87
value_type & at(const indices_type &indices)
Get the pixel value at an index.
Definition: PixelBuffer.h:750
PixelBufferBase(::ome::xml::model::enums::PixelType pixeltype, EndianType endiantype)
Constructor.
Definition: PixelBuffer.h:133
const boost::multi_array_types::index * index_bases() const
Get the index bases of the multi-dimensional array.
Definition: PixelBuffer.h:513
Logical subdivision of the logical channel dimension (c).
Definition: PixelBuffer.h:88
Spatial x dimension (X).
Definition: PixelBuffer.h:80
::ome::xml::model::enums::PixelType pixelType() const
Get the pixel type in use.
Definition: PixelBuffer.h:150
Open Microscopy Environment C++.
boost::general_storage_order< dimensions > storage_order_type
Storage ordering type for controlling pixel memory layout.
Definition: PixelBuffer.h:120
Native endian.
Definition: Types.h:71
Find a PixelBuffer data array of a specific pixel type.
Definition: PixelBuffer.h:832
static storage_order_type make_storage_order(ome::xml::model::enums::DimensionOrder order, bool interleaved)
Generate storage ordering for a given dimension order.
Definition: PixelBuffer.cpp:54
const value_type & at(const indices_type &indices) const
Get the pixel value at an index.
Definition: PixelBuffer.h:766
PixelBuffer(const range_type &range, ::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, EndianType endiantype=ENDIAN_NATIVE, const storage_order_type &storage=PixelBufferBase::default_storage_order())
Construct from ranges (internal storage).
Definition: PixelBuffer.h:324
virtual ~PixelBufferBase()
Destructor.
Definition: PixelBuffer.h:141
EndianType
Endianness.
Definition: Types.h:67
const boost::multi_array_types::index * strides() const
Get the strides of the multi-dimensional array.
Definition: PixelBuffer.h:499
const size_type * shape() const
Get the shape of the multi-dimensional array.
Definition: PixelBuffer.h:486
void write(std::basic_ostream< charT, traits > &stream) const
Write raw pixel data to a stream in physical storage order.
Definition: PixelBuffer.h:801
bool managed() const
Check if the buffer is internally managed.
Definition: PixelBuffer.h:455
EndianType endianType() const
Get the endian type in use.
Definition: PixelBuffer.h:161
size_type num_elements() const
Get the number of pixel elements in the multi-dimensional array.
Definition: PixelBuffer.h:464
void read(std::basic_istream< charT, traits > &stream)
Read raw pixel data from a stream in physical storage order.
Definition: PixelBuffer.h:783
Temporal t dimension (T).
Definition: PixelBuffer.h:83
Dimensions
Dimensions.
Definition: PixelBuffer.h:78
Find a PixelBuffer data array of a specific pixel type.
Definition: PixelBuffer.h:852
PixelBuffer(const ExtentList &extents, ::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, EndianType endiantype=ENDIAN_NATIVE, const storage_order_type &storage=PixelBufferBase::default_storage_order())
Construct from extents (internal storage).
Definition: PixelBuffer.h:279
boost::detail::multi_array::extent_gen< dimensions > range_type
Extent range type.
Definition: PixelBuffer.h:123
boost::multi_array_types::size_type size_type
Size type.
Definition: PixelBuffer.h:110
PixelBuffer(const PixelBuffer &buffer)
Copy constructor.
Definition: PixelBuffer.h:365
array_ref_type & array()
Get the pixel data.
Definition: PixelBuffer.h:874
const ::ome::xml::model::enums::PixelType pixeltype
Pixel type stored in this buffer.
Definition: PixelBuffer.h:195
static const uint16_t dimensions
Total number of supported dimensions.
Definition: PixelBuffer.h:107
PixelBuffer()
Default constructor.
Definition: PixelBuffer.h:260
Spatial z dimension (Z).
Definition: PixelBuffer.h:82
boost::multi_array< value_type, dimensions > array_type
Type for multi-dimensional pixel array view.
Definition: PixelBuffer.h:252
static storage_order_type default_storage_order()
Generate default storage ordering.
Definition: PixelBuffer.cpp:133
const EndianType endiantype
Endian type stored in this buffer.
Definition: PixelBuffer.h:198
std::array< boost::multi_array_types::index, PixelBufferBase::dimensions > indices_type
Type used to index all dimensions in public interfaces.
Definition: PixelBuffer.h:117
Logical subdivision of the spatial z dimension (z).
Definition: PixelBuffer.h:86
PixelBuffer(value_type *pixeldata, const ExtentList &extents, ::ome::xml::model::enums::PixelType pixeltype=::ome::xml::model::enums::PixelType::UINT8, EndianType endiantype=ENDIAN_NATIVE, const storage_order_type &storage=PixelBufferBase::default_storage_order())
Construct from extents (external storage).
Definition: PixelBuffer.h:303
Logical channel (typically detectors of specific wavelengths) (C).
Definition: PixelBuffer.h:84
const value_type * data() const
Get the raw data.
Definition: PixelBuffer.h:415
const storage_order_type & storage_order() const
Get the array storage order.
Definition: PixelBuffer.h:540
T value_type
Pixel value type.
Definition: PixelBuffer.h:239
bool valid() const
Check the buffer validity.
Definition: PixelBuffer.h:431
Logical sub-channel (typically used for RGB channel sub-components) (S).
Definition: PixelBuffer.h:85