thomas.forbriger committed Dec 20, 2002 1 /*! \file libaff/README  thomas.forbriger committed Dec 06, 2002 2  * \brief C++ containers for numbers (libaff)  thomas.forbriger committed Dec 06, 2002 3 4 5  * * ---------------------------------------------------------------------------- *  thomas.forbriger committed Aug 10, 2010 6  * $Id$  thomas.forbriger committed Dec 06, 2002 7 8 9  * * Copyright (c) 2002 by Thomas Forbriger (IMG Frankfurt) *  thomas.forbriger committed Dec 06, 2002 10  * C++ containers for numbers (libaff)  thomas.forbriger committed Dec 06, 2002 11 12  * * This file contains:  thomas.forbriger committed Dec 06, 2002 13  * - documentation of namespace aff  thomas.forbriger committed Dec 06, 2002 14 15  * - mainpage text * - documentation for pages:  thomas.forbriger committed Dec 08, 2002 16  * - \ref page_design  thomas.forbriger committed Dec 06, 2002 17 18  * - \ref page_using * - \ref page_notes  thomas.forbriger committed Dec 08, 2002 19  * - \ref page_naming  thomas.forbriger committed Dec 06, 2002 20 21  * * REVISIONS and CHANGES  thomas.forbriger committed Dec 06, 2002 22  * - 06/12/2002 V1.0 Thomas Forbriger (copied from libcontxx)  thomas.forbriger committed Dec 20, 2002 23 24 25 26 27  * - 20/12/2002 V1.1 (thof) * - complete revision of this file * - there are major gaps in * -# \ref sec_design_multidimensional * -# \ref page_using  thomas.forbriger committed Dec 29, 2002 28 29 30 31 32  * - 28/12/2002 V1.2 (thof) * - new term for containers of const elements * - added documentation regarding the concept of * const correctness * - added documentation regarding member typedefs  thomas.forbriger committed Dec 29, 2002 33 34 35 36 37 38 39  * - 29/12/2002 V1.3 (thof) * - added section about replicated shared heap base * class (\ref sec_design_replicated) * - added section about sparse interface * (\ref sec_design_interface_sparse) * - added section about accessing internals * (\ref sec_design_interface_internals)  thomas.forbriger committed Dec 29, 2002 40 41 42  * - reflect changes to Subarray and Slice * - tell about class hierarchies and member data vs. * inheritance  thomas.forbriger committed Jan 04, 2003 43 44 45  * - 04/01/2003 V1.4 (thof) * - added section about Tcontainer typedef * (\ref sec_design_interface_tcontainer)  thomas.forbriger committed Feb 10, 2004 46 47 48 49  * - 10/02/2004 V1.5 (thof) * - added section about decision against interface * base classes * (\ref sec_design_interface_nobaseclass)  thomas.forbriger committed Nov 10, 2010 50 51 52  * - 10/11/2010 V1.6 (thof) * - code fragments for precompiled templates are * removed from the library (\ref sec_design_binary)  thomas.forbriger committed May 14, 2011 53 54  * - 14/05/2011 V1.7 (thof) * - add info on raw-major and column-major order  thomas.forbriger committed Dec 06, 2002 55 56 57 58 59 60 61  * * ============================================================================ */ /*! \brief Root namespace of library This namespace contains all modules of the library  thomas.forbriger committed Dec 20, 2002 62 63 64  (see \ref sec_main_modules). Here you should find all components, the user needs to work with this library.  thomas.forbriger committed Dec 06, 2002 65  */  thomas.forbriger committed Dec 08, 2002 66 67 namespace aff { } // namespace aff  thomas.forbriger committed Dec 06, 2002 68 69 70 71 72 73  /*======================================================================*/ /*! \mainpage \author Thomas Forbriger  thomas.forbriger committed Dec 06, 2002 74 75 76 \author Wolfgang Friederich \since December 2002 \date December 2002  thomas.forbriger committed Dec 06, 2002 77 \version V1.0  thomas.forbriger committed Aug 10, 2010 78 $Id$  thomas.forbriger committed Dec 06, 2002 79 80  Contents of this page:  thomas.forbriger committed Dec 08, 2002 81  - \ref sec_main_aims  thomas.forbriger committed Dec 06, 2002 82  - \ref sec_main_modules  thomas.forbriger committed Dec 20, 2002 83 84  - \ref sec_main_modules_basic - \ref sec_main_modules_extended  thomas.forbriger committed Dec 20, 2002 85  - \ref sec_main_peculiar  thomas.forbriger committed Dec 06, 2002 86 87  Additional information:  thomas.forbriger committed May 14, 2011 88  - \ref page_array_layout  thomas.forbriger committed Dec 08, 2002 89 90 91 92  - \ref page_design - \ref page_using - \ref page_notes - \ref page_naming  thomas.forbriger committed Dec 06, 2002 93  - \ref page_representation  thomas.forbriger committed Dec 23, 2002 94  - \ref page_fortran  thomas.forbriger committed Dec 17, 2002 95  - \ref page_changelog  thomas.forbriger committed Dec 19, 2002 96  - \ref page_project_status  thomas.forbriger committed Dec 08, 2002 97 98 99 100 101 102 103  \section sec_main_aims Aims of the library The AFF (Array of Friederich and Forbriger) is a lightweight class library. It offers a simple and easy to use container for numbers as is necessary in numerical code. The offered array always has a rectangular strided layout, reference semantics (through counted references) and a Fortran layout in  thomas.forbriger committed Dec 20, 2002 104  memory. The interface is intentionally kept sparse to keep compilation times  thomas.forbriger committed Dec 08, 2002 105 106 107 108 109 110  small. The array itself is meant to be used to pass numbers from one program module to the other. If you want to exploit the power of expression templates, pass the array contents to something like Blitz++. \sa \ref sec_notes_need  thomas.forbriger committed Dec 06, 2002 111 112 \section sec_main_modules Modules of the library  thomas.forbriger committed Dec 08, 2002 113 114  The main module is the array class aff::Array. It provides basic functionality through its interface. See the explanation there.  thomas.forbriger committed Nov 10, 2010 115  It is presented in aff/array.h  thomas.forbriger committed Dec 29, 2002 116  The object code is placed in libaff.a.  thomas.forbriger committed Dec 20, 2002 117 118 119 120 121  \subsection sec_main_modules_basic Basic array modules By including aff/array.h you will get access to the following modules:  thomas.forbriger committed Dec 29, 2002 122  -# aff::Array is the main array interface (see example tests/arraytest.cc).  thomas.forbriger committed Dec 20, 2002 123  -# aff::Strided is the shape of a strided Fortran array and defines the  thomas.forbriger committed Dec 29, 2002 124 125  memory layout of aff::Array objects (see example tests/shapetest.cc).  thomas.forbriger committed Dec 20, 2002 126 127 128  -# aff::SharedHeap is the representation used by aff::Array. It holds the data in memory and provides an interface to it. This interface may be passed separately from the array object (see also  thomas.forbriger committed Jun 27, 2003 129  \ref page_representation and example tests/reprtest.cc).  thomas.forbriger committed Dec 20, 2002 130 131  -# aff::SimpleRigidArray is a linear array with size fixed at compile-time. There are several inline functions defined for operations with  thomas.forbriger committed Dec 29, 2002 132 133  this array class (see example tests/simplearraytest.cc). -# aff::Exception is the exception base class used in the library.  thomas.forbriger committed Dec 20, 2002 134  -# aff::AllocException is the exception that indicated a failed memory  thomas.forbriger committed Jun 27, 2003 135  allocation(see also \ref group_error).  thomas.forbriger committed Dec 20, 2002 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150  It additionally offers the following type definitions: -# aff::Tsubscript is the type of subscripts to arrays (positive and negative). -# aff::Tsize is the type of size values (non-negative). -# aff::Tdim is the type of the dimension index (small, non-negative). \subsection sec_main_modules_extended Extensions The library provides some additional modules. You need only include the header file of those modules that you really want to use in addition to the basic aff::Array functionality. These additional modules are:  thomas.forbriger committed Dec 23, 2002 151  -# aff::Shaper presented in aff/shaper.h and used to pass Fortran layouts  thomas.forbriger committed Dec 29, 2002 152  to array constructors (see example tests/shapetest.cc).  thomas.forbriger committed Dec 20, 2002 153  -# aff::Series presented in aff/series.h which is used to interface linear  thomas.forbriger committed Oct 02, 2007 154  sequences of data (like time series or Fourier coefficients).  thomas.forbriger committed Dec 20, 2002 155  -# aff::Iterator presented in aff/iterator.h which is an iterator interface  thomas.forbriger committed Dec 29, 2002 156 157  to containers like aff::Array or aff::Series (see example tests/helpertest.cc).  thomas.forbriger committed Dec 29, 2002 158  -# aff::subarray presented in aff/subarray.h to conveniently create  thomas.forbriger committed Dec 29, 2002 159 160  subarrays from aff::Array objects (see example tests/helpertest.cc).  thomas.forbriger committed Dec 29, 2002 161  -# aff::slice presented in aff/slice.h to conveniently create  thomas.forbriger committed Dec 29, 2002 162 163  slices from aff::Array objects (see example tests/helpertest.cc).  thomas.forbriger committed Dec 23, 2002 164 165  -# aff::FortranArray and its associate aff::util::FortranShape are presented in aff/fortranshape.h. They calculate a Fortran 77 array  thomas.forbriger committed Dec 29, 2002 166 167  layout (leading dimensions) from a given AFF array (see example tests/f77test.cc).  thomas.forbriger committed Dec 20, 2002 168 169  -# aff::dump and its associates, presented in aff/dump.h. They are used to dump shape or contents of containers and are thus useful when  thomas.forbriger committed Jun 27, 2003 170  debugging your code. See also \ref group_helpers.  thomas.forbriger committed Dec 20, 2002 171   thomas.forbriger committed Dec 08, 2002 172 173  \sa \ref sec_design_namespaces  thomas.forbriger committed Dec 29, 2002 174  \sa \ref sec_naming_files  thomas.forbriger committed Dec 06, 2002 175   thomas.forbriger committed Dec 20, 2002 176 \section sec_main_peculiar Peculiarities  thomas.forbriger committed Dec 06, 2002 177   thomas.forbriger committed Dec 29, 2002 178 179 180 181 \par Containers use counted references All containers (e.g. aff::Array, aff::Series) use counted references to access global memory. Assigning one container object to another just assigns the reference. Both will use the same data in memory afterwards.  thomas.forbriger committed Jun 27, 2003 182 See also \ref page_representation.  thomas.forbriger committed Dec 29, 2002 183   thomas.forbriger committed Dec 20, 2002 184 185 186 \par Const-correctness for array elements In this library we follow provide functionality to write const-correct code with regard to the array container and with regard to its element values.  thomas.forbriger committed Jun 27, 2003 187 See also \ref sec_design_const.  thomas.forbriger committed Dec 06, 2002 188   thomas.forbriger committed Dec 20, 2002 189 190 191 192 193 \par Multidimensional arrays Every aff::Array of this class has aff::Strided::Mmax_dimen dimensions. Construction and access for lower dimensionality is provided. In the case of using less dimensions, the size of the unused dimensions is 1 by default and its index is inherently set to the first index.  thomas.forbriger committed Jun 27, 2003 194 See also \ref sec_design_multidimensional.  thomas.forbriger committed Dec 06, 2002 195   thomas.forbriger committed Dec 08, 2002 196 */  thomas.forbriger committed Dec 06, 2002 197   thomas.forbriger committed Dec 08, 2002 198 /*======================================================================*/  thomas.forbriger committed Dec 06, 2002 199   thomas.forbriger committed Dec 08, 2002 200 /*! \page page_design Design decisions  thomas.forbriger committed Dec 06, 2002 201   thomas.forbriger committed Dec 08, 2002 202  Contents of this page:  thomas.forbriger committed Dec 29, 2002 203  - \ref sec_design_interface  thomas.forbriger committed Dec 29, 2002 204 205  - \ref sec_design_interface_sparse - \ref sec_design_interface_typedef  thomas.forbriger committed Jan 04, 2003 206  - \ref sec_design_interface_tcontainer  thomas.forbriger committed Dec 29, 2002 207  - \ref sec_design_interface_internals  thomas.forbriger committed Feb 10, 2004 208  - \ref sec_design_interface_nobaseclass  thomas.forbriger committed Dec 29, 2002 209  - \ref sec_design_hierarchy  thomas.forbriger committed Dec 29, 2002 210  - \ref sec_design_replicated  thomas.forbriger committed Dec 29, 2002 211 212 213  - \ref sec_design_replicated_fact - \ref sec_design_replicated_problem - \ref sec_design_replicated_solution  thomas.forbriger committed Dec 08, 2002 214 215 216 217 218  - \ref sec_design_copy - \ref sec_design_namespaces - \ref sec_design_binary - \ref sec_design_multidimensional - \ref sec_design_const  thomas.forbriger committed Dec 29, 2002 219 220 221 222  - \ref sec_design_const_problem - \ref sec_design_const_approach - \ref sec_design_const_alternatives - \ref sec_design_const_general  thomas.forbriger committed Dec 06, 2002 223   thomas.forbriger committed Dec 29, 2002 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 \section sec_design_interface Common interface concepts \subsection sec_design_interface_sparse Sparse interfaces The class library is intended to be a light-weight library. This means it should offer basic functionality in terms of multidimensional containers with counted references (and not more in first place). We do not like to include a tremendous amount of code for specialized concepts (like subranges or expression templates in Blitz++) each time we just need a small array. Thus the header files providing array declarations (aff/array.h and the files included therein) should be as sparse as possible. All extra functionality like iterators (aff::Iterator presented in aff/iterator.h) or slices (aff::Slice presented in aff/slice.h) should be external to the aff::Array class. This allows us to load their definitions only where needed. However, this approach requires that the internals of aff::Array are  thomas.forbriger committed Jun 27, 2003 239 240  exposed to the outside through appropriate functions (see \ref sec_design_interface_internals).  thomas.forbriger committed Dec 29, 2002 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282  \subsection sec_design_interface_typedef Member typedefs Class templates like aff::Iterator may be used with any container class, that provides an appropriate interface. This interface convention concerns the access to the type of related objects. I will explain by example: We use an iterator \c i which was declared \code aff::Iterator i \endcode for a container of type \c Cont, it expects to find a corresponding container class that promises constness of the elements through \code Cont::Tcontainer_of_const \endcode or short \code Cont::Tcoc \endcode For aff::ConstArray the type aff::ConstArray::Tcoc is just the class itself. However aff::Array::Tcoc gives an aff::ConstArray. \sa aff::SharedHeap::Tcontainer_of_const \sa aff::ConstSharedHeap::Tcontainer_of_const \sa aff::Array::Tcontainer_of_const \sa aff::ConstArray::Tcontainer_of_const \sa aff::Series::Tcontainer_of_const \sa aff::ConstSeries::Tcontainer_of_const In the same way we may access the appropriate element type through \code Cont::Tvalue \endcode which is \c T for aff::Array and \c const \T for aff::ConstArray. However a \code Cont::Tconst_value \endcode will always provide a type with const qualifier. \sa aff::Array::Tvalue \sa aff::Array::Tconst_value \sa aff::ConstArray::Tvalue \sa aff::ConstArray::Tconst_value \sa aff::Series::Tvalue \sa aff::Series::Tconst_value \sa aff::ConstSeries::Tvalue \sa aff::ConstSeries::Tconst_value In the same way we may access the type of the appropriate representation  thomas.forbriger committed Jan 02, 2003 283  by \code Cont::Trepresentation \endcode  thomas.forbriger committed Dec 29, 2002 284 285 286 287 288 289 290 291 292 293 294 295  \sa aff::Array::Trepresentation \sa aff::ConstArray::Trepresentation \sa aff::Series::Trepresentation \sa aff::ConstSeries::Trepresentation \b Notice: Using these typedefs (and also the typedefs for the shape class, etc.) improves the maintainability of your code. Think of using the $HOME variable in shell scripts. Once the name of your home directory changes, you need not modify all your shell scripts. Now consider one day your shape class might be renamed...  thomas.forbriger committed Jan 04, 2003 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 \subsection sec_design_interface_tcontainer Member typedef Tcontainer \par Design decision: Every class that can be converted to a container type, should provide a member typedef \c Tcontainer and an appropriate conversion operator. \sa aff::util::Slice \sa aff::util::Subarray \sa aff::deepcopy \par Background aff::deepcopy is a good example for function designed to deal with any container. There may be others in the future, like global arithmetic operators or sum-reduction. Due to its generality the function template puts no restrictions on its template arguments. You may instantiate that template for any class. In some sense this is bad practice and we have to resolve ambiguities and support type conversions. In particular, think of feeding a subarray (class aff::util::Subarray) to one of these whole-array functions (this might be one of the most interesting uses). aff::util::Subarray easily matches the template parameter, but does not offer the member functions necessary for element access. \par Hence we must ensure conversion of the aff::util::Subarray to its container class. In our concept this is done with in aff::deepcopy. It looks for a Tcontainer typedef in the argument class definitions and converts the class objects to its corresponding container class before the copy operation. \par Barton and Nackman propose another concept. Using their scheme we would introduce a general Container class, \code template class Container { public: typedef C& Tcontainer_reference; Container(Tcontainer_reference c): M(c) { } operator Tcontainer_reference() { return(M); } private: Tcontainer_reference M; }; \endcode that takes a special container class as a template argument and initializes a member data reference to an object of this class in its constructors. We would then derive aff::Array from this class by \code template class Array: public Container > { }; \endcode This way any reference to a container (aff::Array, aff:Series, aff::ConstArray, etc.) can be converted to a Container class object, which agein offers a conversion operator to a reference to its leaf class. Container-specific functions then are declared \code template void deecopy(const Container& source, Container& target); \endcode deepcopy than can only be called for objects that are derived from Container. \par Trade-offs The Barton and Nackman trick involves another member data field in each container class to hold the reference in the Container base class. aff::Array would have to extra member data fields, because aff::Array and aff::ConstArray both must inherit from Container. I regard this as a partial violation to our concept of sparse interfaces. and small data types and discard this option. \par However, our concept requires to create a full copy of at least the target container in each whole-array operation. This would not be necessary generally. Generally we would operate directly on the aff::Array reference passed as target of the operation. \par With the Barton and Nackman trick this copy operation would only be necessary with class objects, that are not directly derived from Container, as are aff::util::Subarray and companions. However, for those we would have to introduce specializations (overloaded functions) of whole-array operations, that first perform the conversion (creating an aff::Array or else) and then call the function that takes Container arguments. \par Alternative The cheapest alternative (with respect to runtime overhead in the whole-array function and in the container classes aff::Array, etc.) is to delegate the problem to aff::util::Subarray and companions. We could introduce a member data field in them of type Tarray. This would allow for a member function returning a reference to this member. There should be no runtime overhead, since every subarray must once be converted to an array to be useful (now this conversion takes place outside aff::util::Subarray). But this would involve the inconvenience to call an extra member function in Subarray, when passing to a whole-array function. The template argument type of the corresponding whole-array function remains unrestricted (totally unchecked).  thomas.forbriger committed Dec 29, 2002 392 393 394 \subsection sec_design_interface_internals Accessing internals Providing extended functionality outside of aff::Array (see  thomas.forbriger committed Jun 27, 2003 395  \ref sec_design_interface_sparse) requires, that aff::Array,  thomas.forbriger committed Dec 29, 2002 396 397 398 399 400 401 402 403 404 405 406 407 408 409  aff::ConstArray, aff::Series, and aff::ConstSeries expose some of their internals. This concerns the underlying shape as well as the represented data. aff::ConstArray and aff::ConstSeries provide a read-only reference to the data (i.e. an aff::ConstSharedHeap object) through their member-functions aff::ConstArray::representation and aff::ConstSeries::representation, respectively. In the same way aff::Array and aff::Series return an aff::SharedHeap through their representation member function. All of them return a copy of their shape through the member functions aff::Array::shape, aff::ConstArray::shape, aff::Series::shape, and aff::ConstSeries::shape, respectively. The type of the appropriate shape is  thomas.forbriger committed Jun 27, 2003 410  available through a member typedef (see \ref sec_design_interface_typedef).  thomas.forbriger committed Dec 29, 2002 411 412 413 414  In return all containers provide a constructor that takes a representation and a shape object and checks for their consistency.  thomas.forbriger committed Feb 10, 2004 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 \subsection sec_design_interface_nobaseclass Decision against a base class to express common interface This library contains different classes that provide common interfaces. For example all aff::ConstArray, aff::Array, aff::Series and aff::ConstSeries provide the necessary interface to be used together with aff::Iterator or aff::Browser. A rather elegant way to express this commonality in a template context is the Barton and Nackman trick. All containers that can work together with aff::Iterater sould have to inherit from a class aff::Iteratable. The base class is templated, takes the iteratable class as template parameter and stores a reference to the instance of the iteratable class. This way each iteratable class can be converted to aff::Iteratable, which again returns a reference to the classes iteratable features in the appropriate context. This way of expressing common interfaces makes the whole classes more complicated than necessary to provide their elementary functionality. We have to store an extra reference to the leaf class object for each feature, we will express this way. And we have to include a whole bunsch of extra code for each feature. Since we prefer \ref sec_design_interface_sparse this method was rejected.  thomas.forbriger committed Dec 29, 2002 436   thomas.forbriger committed Dec 29, 2002 437 438 439 \section sec_design_hierarchy Class hierarchy: member data vs. inheritance Containers like aff::Array rely on functionality provided by other classes.  thomas.forbriger committed Jan 02, 2003 440  They are based on shapes like aff::Strided and memory representations like  thomas.forbriger committed Jun 27, 2003 441  aff::SharedHeap (see \ref page_representation).  thomas.forbriger committed Dec 29, 2002 442 443 444 445 446  \par An array isn't a shape. Thus it would look like better design to use shapes as member data. We prefer, \b however, to derive privately from the shape classes. This hides them from the outside (apart from explicit access -  thomas.forbriger committed Jun 27, 2003 447  see \ref sec_design_interface_internals).  thomas.forbriger committed Dec 29, 2002 448 449 450 451 452 453 454 455 456 457 458 459  At the same time we make use of using declarations to provide access to member functions like aff::Strided::size() that make also sense as a member of aff::Array. \par An array is some kind of memory representation. Thus it would look like proper design to derive an array from a representation class. We prefer, \b however, to use the memory representation as a private member. We think of the representation as an individual and independent object that can be passed (e.g.) from an aff::Array to and aff::Series. Also due to the replication of the representation in aff::Array  thomas.forbriger committed Jun 27, 2003 460  (see \ref sec_design_replicated) and the distinction between containers  thomas.forbriger committed Dec 29, 2002 461 462 463 464 465 466 467 468 469 470 471  that allow data modification and containers that allow only read access this leads to a clearer design. This is reflected by the conciseness of the array constructors. Use the representation class as member data should introduce no runtime overhead. The full class specification including member data is available at compile-time. This should enable compilers to do excessive inlining. \section sec_design_replicated Replicated ConstSharedHeap  thomas.forbriger committed Dec 29, 2002 472 473  \subsection sec_design_replicated_fact Design decision  thomas.forbriger committed Dec 29, 2002 474 475 476 477 478 479 480 481 482  aff::Array has a member of type aff::SharedHeap (which is exposed to the outside through aff::Array::representation), which itself inherits from aff::ConstSharedHeap. At the same time aff::ConstArray has a member of type aff::Array and inherits itself from aff::ConstSharedHeap (which is exposed to the outside through aff::ConstArray::representation). Thus the class aff::ConstSharedHeap is replicated in aff::Array and it is not replicated by deriving from virtual base classes a virtual base class.  thomas.forbriger committed Dec 29, 2002 483 484 485 486 487 488 489  The same applies to aff::Series and aff::ConstSeries. \subsection sec_design_replicated_problem Where is the problem? Having an array object \c a declared \code aff::Array a; \endcode where \c T is any type, we want to pass this object to a function that promises constness of the elements (see  thomas.forbriger committed Jun 27, 2003 490  \ref sec_design_const). The function is thus declared  thomas.forbriger committed Dec 29, 2002 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538  \code void func(const aff::ConstArray&); \endcode and we want to use it like \code func(a) \endcode Consequently we must offer a way to convert an \code aff::Array& \endcode to an \code aff::ConstArray& \endcode implicitely. This is done by deriving aff::Array publicly from aff::ConstArray. The memory representation is needed by both, aff::Array and its base class. Hence aff::ConstArray has to inherit from the representation. It would be natural for aff::ConstArray to inherit from aff::ConstSharedHeap only. However, since the derived aff::Array needs full access to an aff::SharedHeap (to expose the representation to the outside), we might tend to derive aff::ConstArray from aff::SharedHeap privately, allowing only read access and conversion to aff::ConstSharedHeap. Why is this a problem? Consider the inside of the above function. We might know, that the columns of the passed array contain seismogram waveforms. And we might like to access them in an appropriate way (i.e. through an interface that provides waveform operations), though just reading - not modifying - the data. Then we would like to code something like \code template void func(const aff::ConstArray& a) { // cycle all seismograms for (Tsubscript iseis=a.f(1); iseis<=a.l(1); iseis++) { // extract shape aff::Strided shape(a.shape()); // collapse to waveform iseis shape.collapse(1,iseis); // create a time series aff::ConstSeries waveform(a.representation(), shape.size(), shape.first_offset()); // operate on time series (e.g. recursive filter) some_waveform_operation(waveform); } } \endcode The above example requires that we can construct an aff::ConstSeries from an aff::ConstSharedHeap (which is returned by aff::ConstArray::representation). The same problem appears together with aff::ConstArray, when creating a subarray or slice from an aff::ConstArray  thomas.forbriger committed Jan 02, 2003 539  with aff::subarray or aff::slice and aff::ConstArray itself knowing nothing  thomas.forbriger committed Dec 29, 2002 540 541 542 543 544  about slices, etc. Constructing aff::ConstArray from an aff::ConstSharedHeap sounds a natural operation. However, aff::ConstArray will ask for an aff::SharedHeap, if we derive from aff::SharedHeap (as sketched above). Conclusion: aff::ConstArray  thomas.forbriger committed Dec 29, 2002 545 546  must use an aff::ConstSharedHeap only. At the same time we must hold the full aff::SharedHeap together with the aff::Array object, since this must  thomas.forbriger committed Dec 29, 2002 547 548  return an aff::SharedHeap through aff::Array::representation to allow the above operation (accessing data through aff::Series or constructing a  thomas.forbriger committed Jun 27, 2003 549  slice - see \ref sec_design_interface_sparse).  thomas.forbriger committed Dec 29, 2002 550 551  \subsection sec_design_replicated_solution Solution  thomas.forbriger committed Dec 29, 2002 552 553  The most convincing solution (IMHO) to this problem is to use an (additional) member of type aff::SharedHeap in aff::Array which  thomas.forbriger committed Jun 27, 2003 554  inherits from aff::ConstArray.  thomas.forbriger committed Dec 29, 2002 555  In consequence aff::ConstSharedHeap is then a replicated within  thomas.forbriger committed Dec 29, 2002 556 557 558 559 560 561 562 563 564 565 566 567 568  aff::Array. For a proper design we might consider to make aff::ConstSharedHeap a virtual base, thus avoiding member data duplication. This would, however, introduce an extra level of indirection (additional to the indirection when accessing the heap data through the pointer to the aff::util::SHeap struct in aff::ConstSharedHeap). On the other hand, fully replicating the base aff::ConstSharedHeap just adds one member data pointer (the pointer to the aff::util::SHeap struct) to the data block in aff::Array (which already contains many bytes from the aff::Strided base). This overhead is not considered significant. \b But \b notice: We now must take care to synchronize the aff::SharedHeap base of aff::Array and the aff::ConstSharedHeap base of aff::ConstArray during construction. This is no major concern, but it is error-prone to some  thomas.forbriger committed Dec 29, 2002 569  degree. It is, however, much easier to keep them synchronous when using  thomas.forbriger committed Jun 27, 2003 570  member data instead of inheritance.  thomas.forbriger committed Dec 29, 2002 571 572   thomas.forbriger committed Dec 08, 2002 573 574 575 576 577 578 579 580 581 \section sec_design_copy Copy constructor and copy operator Usually we would expect the copy operator and the copy constructor to have the same semantics. Here the copy constructor of aff::Array must have reference semantics (it does a shallow copy). This is necessary to allow arrays as return values from functions. In this case the copy constructor is automatically invoked. Reference semantics ensure a minimal overhead. in terms of memory usage and execution time.  thomas.forbriger committed Dec 20, 2002 582 583  In the case of the copy (assignment) operator things are less clear: If we define the  thomas.forbriger committed Dec 08, 2002 584  copy operator to have reference semantics, it has the same behaviour as the  thomas.forbriger committed Dec 20, 2002 585  copy constructor. That is what we usually would expect. An expression like  thomas.forbriger committed Dec 06, 2002 586  \code  thomas.forbriger committed Dec 08, 2002 587  A=B;  thomas.forbriger committed Dec 06, 2002 588  \endcode  thomas.forbriger committed Dec 08, 2002 589 590 591 592  means that array \c A drops its reference to the memory location it was pointing to and forgets its previous shape. Following this statement array \c A will refer to the same memory location as array \c B and will have the same shape. Both are indistinguishable.  thomas.forbriger committed Dec 06, 2002 593   thomas.forbriger committed Dec 20, 2002 594 595 596  However, in many cases (most cases?) we will use the copy (assignment) operator in the sense of a mathematical equation. This may read like  thomas.forbriger committed Dec 06, 2002 597  \code  thomas.forbriger committed Dec 08, 2002 598  A=B+C;  thomas.forbriger committed Dec 06, 2002 599  \endcode  thomas.forbriger committed Dec 08, 2002 600  although expressions like this are not yet supported by the library  thomas.forbriger committed Dec 20, 2002 601  features. In this case we do not mean that \c A should drop it reference.  thomas.forbriger committed Dec 08, 2002 602 603 604  \c A may refer to an array in memory which is also referred by other array instances. And we want these values to be set to the result of the operation \c B + \c C. In that case the copy operator should have deep copy semantics.  thomas.forbriger committed Dec 06, 2002 605   thomas.forbriger committed Dec 20, 2002 606 607 608  \par Design decision The classes aff::Array and aff::Series provide copy (assignment) operators with shallow copy semantics.  thomas.forbriger committed Dec 29, 2002 609 610  The automatically created copy constructor and copy operator do just right for this.  thomas.forbriger committed Dec 20, 2002 611 612 613 614  This is sensible, because we are not offering mathematical array operations. This operations may be delegated to a wrapper class in the future, which then also may provide expression templates and an appropriate assignment operator.  thomas.forbriger committed Dec 06, 2002 615   thomas.forbriger committed Dec 29, 2002 616   thomas.forbriger committed Dec 08, 2002 617 \section sec_design_namespaces Namespaces  thomas.forbriger committed Dec 06, 2002 618   thomas.forbriger committed Dec 08, 2002 619  We group all code in two namespaces. Major modules which will be accessed by  thomas.forbriger committed Dec 20, 2002 620 621 622 623 624 625 626 627 628 629 630  the user are placed in namepsace aff. Modules meant to be used internally are placed in aff::util. Use directives like \code using namespace aff; \endcode or \code using aff::Array; \endcode for convenient access.  thomas.forbriger committed Dec 06, 2002 631   thomas.forbriger committed Dec 29, 2002 632   thomas.forbriger committed Dec 08, 2002 633 \section sec_design_binary Binary library  thomas.forbriger committed Dec 06, 2002 634   thomas.forbriger committed Dec 20, 2002 635 \note  thomas.forbriger committed Nov 10, 2010 636 637 638  The option to provide precompiled templates is finally removed from the library. \date 10/11/2010  thomas.forbriger committed Dec 06, 2002 639   thomas.forbriger committed Dec 29, 2002 640   thomas.forbriger committed Dec 08, 2002 641 \section sec_design_multidimensional Multidimensional arrays  thomas.forbriger committed Dec 06, 2002 642   thomas.forbriger committed Dec 08, 2002 643 644  \todo Explain Wolfgangs idea of multidimensional arrays.  thomas.forbriger committed Dec 06, 2002 645   thomas.forbriger committed Dec 29, 2002 646   thomas.forbriger committed Dec 08, 2002 647 648 \section sec_design_const Notes on the const-correctness of arrays  thomas.forbriger committed Dec 29, 2002 649 650 651 652 653 \subsection sec_design_const_problem Where is the problem? When passing a container (i.e. an array) to a function, we would like to promise that the values in the container are not modified, in case the function uses only read-access. Consider a declaration \code void func(const int& v) \endcode  thomas.forbriger committed Jan 02, 2003 654  of a function that takes and argument of type \c int an promises that this  thomas.forbriger committed Dec 29, 2002 655 656  will not be modified. Passing by reference is used, because this is more efficient than passing by value (in particular for large objects - which is  thomas.forbriger committed Jan 02, 2003 657 658  not the case for \c int, but for an array). And qualifying the type \c const promises that the  thomas.forbriger committed Dec 29, 2002 659 660 661 662  value passed by reference will not be changed. A declaration \code void func(const Array& v) \endcode  thomas.forbriger committed Jun 27, 2003 663  does not what we want (see \ref sec_design_const_general). It just  thomas.forbriger committed Dec 29, 2002 664 665  promises the constness of the container, not of the data. Within the function the passed reference may be assigned to a non-const \c Array,  thomas.forbriger committed Jun 27, 2003 666  which allows modification of the data (see \ref page_representation).  thomas.forbriger committed Dec 29, 2002 667 668 669 670 671 672 673 674 675  Thus we must use something like \code void func(const ConstArray& v) \endcode where \c ConstArray does not allow modification of the data (be no means - copying and conversions included) and may be derived from an \c Array by a trivial conversion (like a conversion to a public base class). \subsection sec_design_const_approach The approach used in this library  thomas.forbriger committed Dec 20, 2002 676 677 678 679 680 681 682 683 684 685 686 687 688 689  We distinguish between the constness of the array and the constness of the elements. A definition \code aff::Array A(12,12); const aff::Array B(A); \endcode means that array \c B is a constant array initialized to array \c A. This means, that the container is constant. Its shape and reference may not be changed. If you want to define constness of the contained values (e.g. when passing an array to a function), you have to use \code  thomas.forbriger committed Dec 29, 2002 690  aff::ConstArray C(A);  thomas.forbriger committed Dec 20, 2002 691 692 693 694 695 696 697 698 699 700  \endcode which defines that the contents of \c C may not be changed (i.e. they are of type \c const \c int. They are still refering to the same data in memory. If you modify data elements through \c A, this will be visible through \c C. An array for elements of type \c T is derived from an array for elements of type \c const \c T. Functions that only need read access to arrays should be declared like \code  thomas.forbriger committed Dec 29, 2002 701  void func(const aff::ConstArray& array);  thomas.forbriger committed Dec 20, 2002 702 703 704 705 706 707  \endcode and may be called like \code aff::Array A(12,12); func(A); \endcode  thomas.forbriger committed Dec 29, 2002 708 709  The type conversion from \code aff::Array \endcode to \code const aff::ConstArray& \endcode is trivial and has no runtime  thomas.forbriger committed Dec 20, 2002 710 711  overhead.  thomas.forbriger committed Dec 29, 2002 712 713 714 715 716 717 718  Each container class must deal with this issue on its own. Sorry... \sa aff::ConstSharedHeap \sa aff::ConstArray \sa aff::ConstSeries \par Restrictions for containers with const qualifier  thomas.forbriger committed Jul 04, 2005 719 720  In 7/2005 we changed the design decision of not allowing data modification through containers that are declared const.  thomas.forbriger committed Dec 29, 2002 721  Strictly distinguishing between constness of the container and constness of  thomas.forbriger committed Jul 04, 2005 722  the contained data allows to modify data through an object \c c that  thomas.forbriger committed Dec 29, 2002 723 724  was declared \code const Array c; \endcode  thomas.forbriger committed Jul 04, 2005 725 726 727 728 729 730  The containers in this library (aff::Array, etc.) allow data modification through instances declared const. This may appear surprising to users of the library. However, since it is possible to create a copy of a const container at any place and modifying the data through this copy, we would regard a different behaviour as a false promise.  thomas.forbriger committed Dec 29, 2002 731 732 733 734 735 736  To ensure true constness of the data, you have to assign to the base class of the container. Any container class (e.g. \c Cont) provides the type of container for const elements through a typedef Tcontainer_of_const (i.e. \c Cont::Tcontainer_of_const) or short Tcoc. Remember that a \c const \c aff::Array always  thomas.forbriger committed Dec 20, 2002 737 738 739  may be assigned to a mutable aff::Array, which in turn allows modification of the data!  thomas.forbriger committed Dec 29, 2002 740 741 742 743 744 745 746 747 \subsection sec_design_const_alternatives Alternatives Three alternatives to this concept have been discussed (and discarded). Both have the appealing property of needing only one class definition for each container (in contrast to a class and a base class in our case). Additionally both would offer name commonality for containers of non-const elements and containers of const elements.  thomas.forbriger committed Dec 29, 2002 748 \par Using arrays with element type const T  thomas.forbriger committed Dec 29, 2002 749 750 751 752  A rather straight approach is to use the element type \c const \c T where an array of elements of type \c T should be used, that we do not allow to be changed. This design concept can be accomplished with a special traits class that is specialized for \c const \c T and allows to derive a mutable  thomas.forbriger committed Jun 27, 2003 753  or const version of any type. By further providing appropriate conversion  thomas.forbriger committed Dec 29, 2002 754 755 756 757 758 759 760 761 762 763 764 765  operators, an \code Array \endcode could be converted to an \code Array, \endcode both sharing the same elements in memory. In this approach, however, both container classes are completely independent (although having the same name) due to their different template arguments. The conversion to the container for const elements is not a trivial conversion (like for a reference to a reference of a public base class) and must be done explicitely. That's inconvenient for the most common use (i.e. passing a container to a function). \par Deriving from a template specialization The name commonality could still be achieved by deriving the Array from template specialization Array. In this case the specialization must  thomas.forbriger committed Jun 27, 2003 766  be used as a base class before it is actually defined. That's improper  thomas.forbriger committed Dec 29, 2002 767 768 769 770 771 772  design. \par Ensuring constness of elements through const qualifier of functions We could strictly follow the concept (as we do anyway to some extent) to couple the constness of the container to the constness of the contained data. This is done by const qualifiers to member functions that allow  thomas.forbriger committed Jun 27, 2003 773 774  modification of the data. To avoid pitfalls, we have to consider copy operators  thomas.forbriger committed Dec 29, 2002 775 776 777 778 779  and copy constructors then too. Both must not promise const-ness to their arguments. While this works in principle, we would end up with a container class which doesn't allow copies of const instances. Hence we could not return a container from a function, that ensures that the accessed data cannot be modified.  thomas.forbriger committed Dec 20, 2002 780 781 782  \subsection sec_design_const_general General considerations  thomas.forbriger committed Dec 08, 2002 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805  Arrays using the shared heap representation have reference semantics. Different instances will access the same data in memory. Copying an array instance just copies a reference to the data. This mechanism is not obvious to the compiler. The array instances are values in the sense of C++ types and not references. Passing an \c const \c aff::Array to a function does not prohibit the function from assigning this instance to a non-const \c aff::Array, which then references the same memory area and allows the modification of the values contained in the array. Generally it has to be defined, what is meant by declaring an array instance to be \c const. In the first place this means constness of the container to the compiler. The compiler will ensure, that the container (array class) is not changed, thus no data member of the array is changed. This means that the array will keep the reference to the same data and that the index-mapping defined by the array shape may not be changed. However, the compiler will not prevent to change any data, the array refers to. We may define access operators that have a non-const version that returns a reference to the data, allowing to change the data values together with a const version that returns a value of const reference, thus preventing the data from being changed through an instance that is declared const. However, the compiler will always allow to create a non-const copy of a const array instance. In the sense of const-ness of C++ data, this does not violate the  thomas.forbriger committed Dec 20, 2002 806  const-ness of the source of the copy. The shape of the original array may  thomas.forbriger committed Dec 08, 2002 807 808 809 810 811 812 813 814 815  not be changed. Only the shape of the copy may be changed. But the data of the original array may now be changed through the copied instance, since our array classes implicitly have reference semantic. Thus we have to distinguish between const-ness of the container (array class instance) and the contained data (values in memory the arrays refers to). In this library we will not provide a const and a non-const version of the array classes. With templated code it is more convenient to use an array with element type \c const \c T as the const version of an array with  thomas.forbriger committed Dec 20, 2002 816 817 818  element type \c T. To allow conversion of an instance with element type \c T to an instance of type \c const \c T, we use the version for elements of type \c const \c T as a base classe.  thomas.forbriger committed Dec 08, 2002 819 820 821 822 823 824 825 826 827 828 829 830  - The need of const-correctness is discussed in "Chapter 1 Introduction, C++ Conventions, Implementation of Vector and Matrix Classes" of "Numerical Recipes in C++". A link to a PDF file of this chapter is provided at "http://www.nr.com/cpp-blurb.html". - The "C++ FAQ Lite" discusses many aspects of const-correctness in Chapter 18, which you find at "http://www.inf.uni-konstanz.de/~kuehl/cpp/cppfaq.htm/const-correctness.html". - You may find my thoughts about const-correctness with containers that have reference semantics at "http://www.geophysik.uni-frankfurt.de/~forbrig/txt/cxx/tutorial/consthandle.doc/doc/html/index.html".  thomas.forbriger committed Dec 06, 2002 831 832 833 834 */ /*======================================================================*/  thomas.forbriger committed Dec 08, 2002 835 /*! \page page_using HOWTO use this library  thomas.forbriger committed Dec 06, 2002 836   thomas.forbriger committed Dec 08, 2002 837 838  Contents of this page: - \ref sec_using_constructor  thomas.forbriger committed Dec 20, 2002 839  - \ref sec_using_examples  thomas.forbriger committed Dec 06, 2002 840 841  \section sec_using_constructor Constructing arrays  thomas.forbriger committed Dec 20, 2002 842 843 844 845  Arrays are most easy constructed by means of the aff::Shaper. If you want e.g. define an array \c A of element type int with Fortran layout, three dimensions and the index ranges [-2:2], [1:4], and [6:10] you have to code  thomas.forbriger committed Dec 06, 2002 846  \code  thomas.forbriger committed Dec 20, 2002 847 848  using namespace aff; Array A(Shaper(-2,2)(4)(6,10));  thomas.forbriger committed Dec 06, 2002 849  \endcode  thomas.forbriger committed Dec 20, 2002 850  The shaper is presented in aff/shaper.h.  thomas.forbriger committed Dec 06, 2002 851   thomas.forbriger committed Dec 20, 2002 852 853 854 855 856 857 \section sec_using_examples Example code The test programs may serve as examples for using this library: - tests/arraytest.cc - tests/shapetest.cc - tests/reprtest.cc - tests/simplearraytest.cc  thomas.forbriger committed Dec 08, 2002 858 859  \todo  thomas.forbriger committed Dec 20, 2002 860 861 We need more text and examples.  thomas.forbriger committed Dec 08, 2002 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 */ /*======================================================================*/ /*! \page page_notes General notes Contents of this page: - \ref sec_notes_need \section sec_notes_need The need of an array library One major reason for replacing Fortran77 by C++ in numerical code is the convenience in expressing logistics. Data of different type and size may be packed into classes and encapsulated from the outside world. Most numerical results are to be stored in arrays, multi-dimensional arrays in particular. This library provides the basic functionality for storing many data of the same type in memory, passing them around between subroutines in an efficient way and accessing them through convenient interfaces. The main purpose of this library is not calculation but managing (passing between program modules, selection of subsets of the data) large amounts of numbers. In the future it might provide interfaces to libraries like blitz++ for finite difference calculations, MTL for linear algebra calculations, and POOMA for parallel computations.  thomas.forbriger committed Dec 06, 2002 887 888 889 890 */ /*======================================================================*/  thomas.forbriger committed Dec 08, 2002 891 892 893 /*! \page page_naming Naming conventions Contents of this page:  thomas.forbriger committed Dec 29, 2002 894 895 896  - \ref sec_naming_identifiers - \ref sec_naming_macros - \ref sec_naming_files  thomas.forbriger committed Dec 08, 2002 897   thomas.forbriger committed Dec 29, 2002 898 \section sec_naming_identifiers Classes, Typedefs, etc.  thomas.forbriger committed Dec 08, 2002 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916  During coding it is sometimes helpfull to recognize the meaning of an identifier due to some signals in irs name. Therefor the following guidelines are used. The nameing of template parameters is left free for convenience. \par Classes Class names always start with a capital letter. \par Typedefs Typedefs always start with a capital \c T. \par Member data Member data identifiers always start with a capital \c M.  thomas.forbriger committed Dec 29, 2002 917 \section sec_naming_macros Preprocessor macros  thomas.forbriger committed Dec 08, 2002 918 919  Preprocessor macros like include-guards should have the prefix "AFF_".  thomas.forbriger committed Dec 19, 2002 920  The macros in the \ref group_helpers are an exception to this rule.  thomas.forbriger committed Dec 08, 2002 921   thomas.forbriger committed Dec 29, 2002 922 \section sec_naming_files Filenames  thomas.forbriger committed Dec 08, 2002 923 924 925 926 927 928 929  Files with the extension \c .cc contain only non-template definitions. Files with the extension \c .h may contain prototypes, class declarations or template code. Files ending on \c def.h contain template code definitions that is factored out to be compilable into a binary library for explicit instantiation.  thomas.forbriger committed Dec 20, 2002 930 931  The main directory %aff contains headers that are usually included by the user. A subdirectory %aff/lib contains additional headers that are mostly  thomas.forbriger committed Dec 08, 2002 932 933  used internally.  thomas.forbriger committed Dec 06, 2002 934 935 */  thomas.forbriger committed May 14, 2011 936 937 938 939 940 941 942 943 944 945 946 947 948 /*======================================================================*/ /*! \page page_array_layout Array layout The array class template aff::Array uses the shape class aff::Strided. Usually and in particular when constructed by using aff::Shaper, aff::Strided uses a Fortran like column-major layout in memory. aff::FortranArray and aff::util::FortranShape are provided to interface Fortran code with such kind of arrays. Nevertheless aff::Array together with aff::Strided is able to address a row-major C like memory layout too. Classes to interface raw memory arrays are presented in Carray.h.  thomas.forbriger committed May 14, 2011 949 950 951 952 953 954  By definition the first index \f$ i \f$on a two-dimenional matrix \f$ A_{ij} \f$as represented by the array \c A(i,j) is the row index while the second index \f$ j \f\$ is the column index. If elements of the two-dimensional matrix or array are arranged in linear computer memory, there are two options:  thomas.forbriger committed May 14, 2011 955 956  \section sec_array_layout_column_major Column major layout  thomas.forbriger committed May 14, 2011 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986  When traversing the linear representation in memory byte by byte in increasing address order the elements of the first column in order of increasing row index are passed first. Next the elements of the second column are passed in increasing row order and so forth. When labelling the array elements in linear memory, the first index varies quicker than the second index of the array if the elements are traversed in increasing address order. This is called the "column major order" and is the usualy layout of Fortran arrays. Column major layout is described in detail at http://en.wikipedia.org/wiki/Row-major_order#Column-major_order \section sec_array_layout_row_major Row major layout When traversing the linear representation in memory byte by byte in increasing address order the elements of the first row in order of increasing column index are passed first. Next the elements of the second row are passed in increasing column order and so forth. When labelling the array elements in linear memory, the second index varies quicker than the first index of the array if the elements are traversed in increasing address order. This is called the "row major order" and is the usualy layout of C arrays. Row major layout is described in detail at http://en.wikipedia.org/wiki/Row-major_order#Row-major_order  thomas.forbriger committed May 14, 2011 987   thomas.forbriger committed May 14, 2011 988 989  \todo Provide details on indexing raw memory in both layouts here.  thomas.forbriger committed May 14, 2011 990 991  */  thomas.forbriger committed Dec 06, 2002 992 // ----- END OF README -----