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annotate doc/interpreter/dynamic.txi @ 11039:4cbb08163a1f
Use Octave to create pdf versions of plots for documentation.
| author | Rik <octave@nomad.inbox5.com> |
|---|---|
| date | Tue, 28 Sep 2010 19:22:01 -0700 |
| parents | a4f482e66b65 |
| children | 746609dd54fd |
| rev | line source |
|---|---|
| 8920 | 1 @c Copyright (C) 2007, 2008, 2009 John W. Eaton and David Bateman |
| 7018 | 2 @c Copyright (C) 2007 Paul Thomas and Christoph Spiel |
| 3 @c | |
| 4 @c This file is part of Octave. | |
| 5 @c | |
| 6 @c Octave is free software; you can redistribute it and/or modify it | |
| 7 @c under the terms of the GNU General Public License as published by the | |
| 8 @c Free Software Foundation; either version 3 of the License, or (at | |
| 9 @c your option) any later version. | |
| 10 @c | |
| 11 @c Octave is distributed in the hope that it will be useful, but WITHOUT | |
| 12 @c ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or | |
| 13 @c FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License | |
| 14 @c for more details. | |
| 15 @c | |
| 16 @c You should have received a copy of the GNU General Public License | |
| 17 @c along with Octave; see the file COPYING. If not, see | |
| 18 @c <http://www.gnu.org/licenses/>. | |
| 6578 | 19 |
| 6569 | 20 @node Dynamically Linked Functions |
| 21 @appendix Dynamically Linked Functions | |
| 22 @cindex dynamic-linking | |
| 23 | |
| 24 Octave has the possibility of including compiled code as dynamically | |
| 25 linked extensions and then using these extensions as if they were part | |
| 8828 | 26 of Octave itself. Octave can call C++ code |
| 6569 | 27 through its native oct-file interface or C code through its mex |
| 6571 | 28 interface. It can also indirectly call functions written in any other |
| 29 language through a simple wrapper. The reasons to write code in a | |
| 6569 | 30 compiled language might be either to link to an existing piece of code |
| 31 and allow it to be used within Octave, or to allow improved performance | |
| 32 for key pieces of code. | |
| 33 | |
| 34 Before going further, you should first determine if you really need to | |
| 6571 | 35 use dynamically linked functions at all. Before proceeding with writing |
| 6569 | 36 any dynamically linked function to improve performance you should |
| 37 address ask yourself | |
| 38 | |
| 39 @itemize @bullet | |
| 40 @item | |
| 6939 | 41 Can I get the same functionality using the Octave scripting language only? |
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42 |
| 6569 | 43 @item |
| 6572 | 44 Is it thoroughly optimized Octave code? Vectorization of Octave code, |
| 6569 | 45 doesn't just make it concise, it generally significantly improves its |
| 6571 | 46 performance. Above all, if loops must be used, make sure that the |
| 6569 | 47 allocation of space for variables takes place outside the loops using an |
| 8828 | 48 assignment to a matrix of the right size, or zeros. |
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49 |
| 6569 | 50 @item |
| 51 Does it make as much use as possible of existing built-in library | |
| 6572 | 52 routines? These are highly optimized and many do not carry the overhead |
| 6569 | 53 of being interpreted. |
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54 |
| 6569 | 55 @item |
| 56 Does writing a dynamically linked function represent useful investment | |
| 57 of your time, relative to staying in Octave? | |
| 58 @end itemize | |
| 59 | |
| 8475 | 60 Also, as oct- and mex-files are dynamically linked to Octave, they |
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61 introduce the possibility of Octave crashing due to errors in |
| 7001 | 62 the user code. For example a segmentation violation in the user's code |
| 6569 | 63 will cause Octave to abort. |
| 64 | |
| 65 @menu | |
| 6572 | 66 * Oct-Files:: |
| 67 * Mex-Files:: | |
| 68 * Standalone Programs:: | |
| 6569 | 69 @end menu |
| 70 | |
| 71 @node Oct-Files | |
| 72 @section Oct-Files | |
| 73 @cindex oct-files | |
| 74 @cindex mkoctfile | |
| 75 @cindex oct | |
| 76 | |
| 77 @menu | |
| 6572 | 78 * Getting Started with Oct-Files:: |
| 79 * Matrices and Arrays in Oct-Files:: | |
| 80 * Character Strings in Oct-Files:: | |
| 81 * Cell Arrays in Oct-Files:: | |
| 82 * Structures in Oct-Files:: | |
| 83 * Sparse Matrices in Oct-Files:: | |
| 84 * Accessing Global Variables in Oct-Files:: | |
| 85 * Calling Octave Functions from Oct-Files:: | |
| 86 * Calling External Code from Oct-Files:: | |
| 87 * Allocating Local Memory in Oct-Files:: | |
| 88 * Input Parameter Checking in Oct-Files:: | |
| 89 * Exception and Error Handling in Oct-Files:: | |
| 90 * Documentation and Test of Oct-Files:: | |
| 6593 | 91 @c * Application Programming Interface for Oct-Files:: |
| 6569 | 92 @end menu |
| 93 | |
| 94 @node Getting Started with Oct-Files | |
| 95 @subsection Getting Started with Oct-Files | |
| 96 | |
| 97 The basic command to build oct-files is @code{mkoctfile} and it can be | |
| 98 call from within octave or from the command line. | |
| 99 | |
| 100 @DOCSTRING(mkoctfile) | |
| 101 | |
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102 Consider the short example: |
| 6569 | 103 |
| 9906 | 104 @example |
| 105 @group | |
| 106 @EXAMPLEFILE(helloworld.cc) | |
| 107 @end group | |
| 108 @end example | |
| 6569 | 109 |
| 110 This example although short introduces the basics of writing a C++ | |
| 6571 | 111 function that can be dynamically linked to Octave. The easiest way to |
| 6569 | 112 make available most of the definitions that might be necessary for an |
| 113 oct-file in Octave is to use the @code{#include <octave/oct.h>} | |
| 6571 | 114 header. |
| 6569 | 115 |
| 116 The macro that defines the entry point into the dynamically loaded | |
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117 function is @w{@code{DEFUN_DLD}}. This macro takes four arguments, these being |
| 6569 | 118 |
| 119 @enumerate 1 | |
| 6571 | 120 @item The function name as it will be seen in Octave, |
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121 |
| 6572 | 122 @item The list of arguments to the function of type @code{octave_value_list}, |
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123 |
| 6569 | 124 @item The number of output arguments, which can and often is omitted if |
| 125 not used, and | |
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126 |
| 6569 | 127 @item The string that will be seen as the help text of the function. |
| 128 @end enumerate | |
| 129 | |
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130 The return type of functions defined with @w{@code{DEFUN_DLD}} is always |
| 6572 | 131 @code{octave_value_list}. |
| 6569 | 132 |
| 133 There are a couple of important considerations in the choice of function | |
| 6571 | 134 name. Firstly, it must be a valid Octave function name and so must be a |
| 6569 | 135 sequence of letters, digits and underscores, not starting with a |
| 6571 | 136 digit. Secondly, as Octave uses the function name to define the filename |
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137 it attempts to find the function in, the function name in the |
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138 @w{@code{DEFUN_DLD}} macro must match the filename of the oct-file. Therefore, |
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139 the above function should be in a file @file{helloworld.cc}, and it should be |
| 6572 | 140 compiled to an oct-file using the command |
| 6569 | 141 |
| 142 @example | |
| 143 mkoctfile helloworld.cc | |
| 144 @end example | |
| 145 | |
| 8828 | 146 This will create a file called @file{helloworld.oct}, that is the compiled |
| 6571 | 147 version of the function. It should be noted that it is perfectly |
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148 acceptable to have more than one @w{@code{DEFUN_DLD}} function in a source |
| 6571 | 149 file. However, there must either be a symbolic link to the oct-file for |
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150 each of the functions defined in the source code with the @w{@code{DEFUN_DLD}} |
| 6569 | 151 macro or the autoload (@ref{Function Files}) function should be used. |
| 152 | |
| 153 The rest of this function then shows how to find the number of input | |
| 154 arguments, how to print through the octave pager, and return from the | |
| 6571 | 155 function. After compiling this function as above, an example of its use |
| 6569 | 156 is |
| 157 | |
| 158 @example | |
| 159 @group | |
| 6572 | 160 helloworld (1, 2, 3) |
| 161 @print{} Hello World has 3 input arguments and 0 output arguments. | |
| 6569 | 162 @end group |
| 163 @end example | |
| 164 | |
| 165 @node Matrices and Arrays in Oct-Files | |
| 166 @subsection Matrices and Arrays in Oct-Files | |
| 167 | |
| 168 Octave supports a number of different array and matrix classes, the | |
| 6571 | 169 majority of which are based on the Array class. The exception is the |
| 170 sparse matrix types discussed separately below. There are three basic | |
| 171 matrix types | |
| 6569 | 172 |
| 6572 | 173 @table @code |
| 6569 | 174 @item Matrix |
| 175 A double precision matrix class defined in dMatrix.h, | |
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176 |
| 6569 | 177 @item ComplexMatrix |
| 178 A complex matrix class defined in CMatrix.h, and | |
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179 |
| 6569 | 180 @item BoolMatrix |
| 181 A boolean matrix class defined in boolMatrix.h. | |
| 182 @end table | |
| 183 | |
| 6571 | 184 These are the basic two-dimensional matrix types of octave. In |
| 6569 | 185 additional there are a number of multi-dimensional array types, these |
| 186 being | |
| 187 | |
| 6572 | 188 @table @code |
| 6569 | 189 @item NDArray |
| 6572 | 190 A double precision array class defined in @file{dNDArray.h} |
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191 |
| 6569 | 192 @item ComplexNDarray |
| 6572 | 193 A complex array class defined in @file{CNDArray.h} |
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194 |
| 6569 | 195 @item boolNDArray |
| 6572 | 196 A boolean array class defined in @file{boolNDArray.h} |
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197 |
| 6572 | 198 @item int8NDArray |
| 199 @itemx int16NDArray | |
| 200 @itemx int32NDArray | |
| 201 @itemx int64NDArray | |
| 202 8, 16, 32 and 64-bit signed array classes defined in | |
| 203 @file{int8NDArray.h}, @file{int16NDArray.h}, etc. | |
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204 |
| 6572 | 205 @item uint8NDArray |
| 206 @itemx uint16NDArray | |
| 207 @itemx uint32NDArray | |
| 208 @itemx uint64NDArray | |
| 209 8, 16, 32 and 64-bit unsigned array classes defined in | |
| 210 @file{uint8NDArray.h}, @file{uint16NDArray.h}, etc. | |
| 6569 | 211 @end table |
| 212 | |
| 213 There are several basic means of constructing matrices of | |
| 6572 | 214 multi-dimensional arrays. Considering the @code{Matrix} type as an |
| 215 example | |
| 6569 | 216 |
| 217 @itemize @bullet | |
| 6571 | 218 @item |
| 219 We can create an empty matrix or array with the empty constructor. For | |
| 6569 | 220 example |
| 221 | |
| 222 @example | |
| 223 Matrix a; | |
| 224 @end example | |
| 225 | |
| 226 This can be used on all matrix and array types | |
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227 |
| 6571 | 228 @item |
| 229 Define the dimensions of the matrix or array with a dim_vector. For | |
| 6569 | 230 example |
| 231 | |
| 232 @example | |
| 233 @group | |
| 6572 | 234 dim_vector dv (2); |
| 6569 | 235 dv(0) = 2; dv(1) = 2; |
| 6572 | 236 Matrix a (dv); |
| 6569 | 237 @end group |
| 238 @end example | |
| 239 | |
| 240 This can be used on all matrix and array types | |
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241 |
| 6569 | 242 @item |
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243 Define the number of rows and columns in the matrix. For example: |
| 6569 | 244 |
| 245 @example | |
| 6572 | 246 Matrix a (2, 2) |
| 6569 | 247 @end example |
| 248 | |
| 249 However, this constructor can only be used with the matrix types. | |
| 250 @end itemize | |
| 251 | |
| 252 These types all share a number of basic methods and operators, a | |
| 253 selection of which include | |
| 254 | |
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255 @deftypefn Method T& {operator ()} (octave_idx_type) |
| 6572 | 256 @deftypefnx Method T& elem (octave_idx_type) |
| 257 The @code{()} operator or @code{elem} method allow the values of the | |
| 258 matrix or array to be read or set. These can take a single argument, | |
| 259 which is of type @code{octave_idx_type}, that is the index into the matrix or | |
| 6571 | 260 array. Additionally, the matrix type allows two argument versions of the |
| 6572 | 261 @code{()} operator and elem method, giving the row and column index of the |
| 6569 | 262 value to obtain or set. |
| 6572 | 263 @end deftypefn |
| 6569 | 264 |
| 7001 | 265 Note that these functions do significant error checking and so in some |
| 266 circumstances the user might prefer to access the data of the array or | |
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267 matrix directly through the @nospell{fortran_vec} method discussed below. |
| 6572 | 268 |
| 269 @deftypefn Method octave_idx_type nelem (void) const | |
| 6569 | 270 The total number of elements in the matrix or array. |
| 6572 | 271 @end deftypefn |
| 272 | |
| 273 @deftypefn Method size_t byte_size (void) const | |
| 6569 | 274 The number of bytes used to store the matrix or array. |
| 6572 | 275 @end deftypefn |
| 276 | |
| 277 @deftypefn Method dim_vector dims (void) const | |
| 6569 | 278 The dimensions of the matrix or array in value of type dim_vector. |
| 6572 | 279 @end deftypefn |
| 280 | |
| 281 @deftypefn Method void resize (const dim_vector&) | |
| 282 A method taking either an argument of type @code{dim_vector}, or in the | |
| 283 case of a matrix two arguments of type @code{octave_idx_type} defining | |
| 284 the number of rows and columns in the matrix. | |
| 285 @end deftypefn | |
| 286 | |
| 287 @deftypefn Method T* fortran_vec (void) | |
| 6569 | 288 This method returns a pointer to the underlying data of the matrix or a |
| 289 array so that it can be manipulated directly, either within Octave or by | |
| 290 an external library. | |
| 6572 | 291 @end deftypefn |
| 6569 | 292 |
| 6572 | 293 Operators such an @code{+}, @code{-}, or @code{*} can be used on the |
| 294 majority of the above types. In addition there are a number of methods | |
| 295 that are of interest only for matrices such as @code{transpose}, | |
| 296 @code{hermitian}, @code{solve}, etc. | |
| 6569 | 297 |
| 298 The typical way to extract a matrix or array from the input arguments of | |
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299 @w{@code{DEFUN_DLD}} function is as follows |
| 6569 | 300 |
| 9906 | 301 @example |
| 302 @group | |
| 303 @EXAMPLEFILE(addtwomatrices.cc) | |
| 304 @end group | |
| 305 @end example | |
| 6569 | 306 |
| 307 To avoid segmentation faults causing Octave to abort, this function | |
| 308 explicitly checks that there are sufficient arguments available before | |
| 6571 | 309 accessing these arguments. It then obtains two multi-dimensional arrays |
| 6572 | 310 of type @code{NDArray} and adds these together. Note that the array_value |
| 311 method is called without using the @code{is_matrix_type} type, and instead the | |
| 6571 | 312 error_state is checked before returning @code{A + B}. The reason to |
| 6569 | 313 prefer this is that the arguments might be a type that is not an |
| 6572 | 314 @code{NDArray}, but it would make sense to convert it to one. The |
| 315 @code{array_value} method allows this conversion to be performed | |
| 316 transparently if possible, and sets @code{error_state} if it is not. | |
| 6569 | 317 |
| 6572 | 318 @code{A + B}, operating on two @code{NDArray}'s returns an |
| 319 @code{NDArray}, which is cast to an @code{octave_value} on the return | |
| 320 from the function. An example of the use of this demonstration function | |
| 321 is | |
| 6569 | 322 |
| 323 @example | |
| 324 @group | |
| 6572 | 325 addtwomatrices (ones (2, 2), ones (2, 2)) |
| 6569 | 326 @result{} 2 2 |
| 327 2 2 | |
| 328 @end group | |
| 329 @end example | |
| 330 | |
| 6572 | 331 A list of the basic @code{Matrix} and @code{Array} types, the methods to |
| 332 extract these from an @code{octave_value} and the associated header is | |
| 333 listed below. | |
| 6569 | 334 |
| 335 @multitable @columnfractions .3 .4 .3 | |
| 6572 | 336 @item @code{RowVector} @tab @code{row_vector_value} @tab @file{dRowVector.h} |
| 337 @item @code{ComplexRowVector} @tab @code{complex_row_vector_value} @tab @file{CRowVector.h} | |
| 338 @item @code{ColumnVector} @tab @code{column_vector_value} @tab @file{dColVector.h} | |
| 339 @item @code{ComplexColumnVector} @tab @code{complex_column_vector_value} @tab @file{CColVector.h} | |
| 340 @item @code{Matrix} @tab @code{matrix_value} @tab @file{dMatrix.h} | |
| 341 @item @code{ComplexMatrix} @tab @code{complex_matrix_value} @tab @file{CMatrix.h} | |
| 342 @item @code{boolMatrix} @tab @code{bool_matrix_value} @tab @file{boolMatrix.h} | |
| 343 @item @code{charMatrix} @tab @code{char_matrix_value} @tab @file{chMatrix.h} | |
| 344 @item @code{NDArray} @tab @code{array_value} @tab @file{dNDArray.h} | |
| 345 @item @code{ComplexNDArray} @tab @code{complex_array_value} @tab @file{CNDArray.h} | |
| 346 @item @code{boolNDArray} @tab @code{bool_array_value} @tab @file{boolNDArray.h} | |
| 347 @item @code{charNDArray} @tab @code{char_array_value} @tab @file{charNDArray.h} | |
| 348 @item @code{int8NDArray} @tab @code{int8_array_value} @tab @file{int8NDArray.h} | |
| 349 @item @code{int16NDArray} @tab @code{int16_array_value} @tab @file{int16NDArray.h} | |
| 350 @item @code{int32NDArray} @tab @code{int32_array_value} @tab @file{int32NDArray.h} | |
| 351 @item @code{int64NDArray} @tab @code{int64_array_value} @tab @file{int64NDArray.h} | |
| 352 @item @code{uint8NDArray} @tab @code{uint8_array_value} @tab @file{uint8NDArray.h} | |
| 353 @item @code{uint16NDArray} @tab @code{uint16_array_value} @tab @file{uint16NDArray.h} | |
| 354 @item @code{uint32NDArray} @tab @code{uint32_array_value} @tab @file{uint32NDArray.h} | |
| 355 @item @code{uint64NDArray} @tab @code{uint64_array_value} @tab @file{uint64NDArray.h} | |
| 6569 | 356 @end multitable |
| 357 | |
| 6572 | 358 @node Character Strings in Oct-Files |
| 359 @subsection Character Strings in Oct-Files | |
| 360 | |
| 361 In Octave a character string is just a special @code{Array} class. | |
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362 Consider the example: |
| 6572 | 363 |
| 9906 | 364 @example |
| 365 @EXAMPLEFILE(stringdemo.cc) | |
| 366 @end example | |
| 6572 | 367 |
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368 An example of the use of this function is |
| 6572 | 369 |
| 370 @example | |
| 371 @group | |
| 372 s0 = ["First String"; "Second String"]; | |
| 373 [s1,s2] = stringdemo (s0) | |
| 374 @result{} s1 = Second String | |
| 375 First String | |
| 376 | |
| 377 @result{} s2 = First String | |
| 378 Second String | |
| 379 | |
| 380 typeinfo (s2) | |
| 381 @result{} sq_string | |
| 382 typeinfo (s1) | |
| 383 @result{} string | |
| 384 @end group | |
| 385 @end example | |
| 386 | |
| 387 One additional complication of strings in Octave is the difference | |
| 388 between single quoted and double quoted strings. To find out if an | |
| 389 @code{octave_value} contains a single or double quoted string an example is | |
| 390 | |
| 391 @example | |
| 392 @group | |
| 393 if (args(0).is_sq_string ()) | |
| 7081 | 394 octave_stdout << |
| 395 "First argument is a singularly quoted string\n"; | |
| 6572 | 396 else if (args(0).is_dq_string ()) |
| 7081 | 397 octave_stdout << |
| 398 "First argument is a doubly quoted string\n"; | |
| 6572 | 399 @end group |
| 400 @end example | |
| 401 | |
| 402 Note however, that both types of strings are represented by the | |
| 403 @code{charNDArray} type, and so when assigning to an | |
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404 @code{octave_value}, the type of string should be specified. For example: |
| 6572 | 405 |
| 406 @example | |
| 407 @group | |
| 408 octave_value_list retval; | |
| 409 charNDArray c; | |
| 410 @dots{} | |
| 6577 | 411 // Create single quoted string |
| 412 retval(1) = octave_value (ch, true, '\''); | |
| 413 | |
| 414 // Create a double quoted string | |
| 415 retval(0) = octave_value (ch, true); | |
| 6572 | 416 @end group |
| 417 @end example | |
| 418 | |
| 419 @node Cell Arrays in Oct-Files | |
| 420 @subsection Cell Arrays in Oct-Files | |
| 421 | |
| 7001 | 422 Octave's cell type is equally accessible within oct-files. A cell |
| 6572 | 423 array is just an array of @code{octave_value}s, and so each element of the cell |
| 424 array can then be treated just like any other @code{octave_value}. A simple | |
| 425 example is | |
| 426 | |
| 9906 | 427 @example |
| 428 @group | |
| 429 @EXAMPLEFILE(celldemo.cc) | |
| 430 @end group | |
| 431 @end example | |
| 6572 | 432 |
| 433 Note that cell arrays are used less often in standard oct-files and so | |
| 434 the @file{Cell.h} header file must be explicitly included. The rest of this | |
| 435 example extracts the @code{octave_value}s one by one from the cell array and | |
| 436 returns be as individual return arguments. For example consider | |
| 437 | |
| 438 @example | |
| 439 @group | |
| 440 [b1, b2, b3] = celldemo (@{1, [1, 2], "test"@}) | |
| 441 @result{} | |
| 442 b1 = 1 | |
| 443 b2 = | |
| 444 | |
| 445 1 2 | |
| 446 | |
| 447 b3 = test | |
| 448 @end group | |
| 449 @end example | |
| 450 | |
| 451 @node Structures in Oct-Files | |
| 452 @subsection Structures in Oct-Files | |
| 453 | |
| 454 A structure in Octave is map between a number of fields represented and | |
| 455 their values. The Standard Template Library @code{map} class is used, | |
| 456 with the pair consisting of a @code{std::string} and an octave | |
| 457 @code{Cell} variable. | |
| 458 | |
| 459 A simple example demonstrating the use of structures within oct-files is | |
| 460 | |
| 9906 | 461 @example |
| 462 @EXAMPLEFILE(structdemo.cc) | |
| 463 @end example | |
| 6572 | 464 |
| 465 An example of its use is | |
| 466 | |
| 467 @example | |
| 468 @group | |
| 469 x.a = 1; x.b = "test"; x.c = [1, 2]; | |
| 470 structdemo (x, "b") | |
| 471 @result{} selected = test | |
| 472 @end group | |
| 473 @end example | |
| 474 | |
| 7001 | 475 The commented code above demonstrates how to iterate over all of the |
| 6572 | 476 fields of the structure, where as the following code demonstrates finding |
| 477 a particular field in a more concise manner. | |
| 478 | |
| 479 As can be seen the @code{contents} method of the @code{Octave_map} class | |
| 480 returns a @code{Cell} which allows structure arrays to be represented. | |
| 481 Therefore, to obtain the underlying @code{octave_value} we write | |
| 482 | |
| 483 @example | |
| 484 octave_value tmp = arg0.contents (p1) (0); | |
| 485 @end example | |
| 486 | |
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487 @noindent |
| 6593 | 488 where the trailing (0) is the () operator on the @code{Cell} object. We |
| 489 can equally iterate of the elements of the Cell array to address the | |
| 490 elements of the structure array. | |
| 6572 | 491 |
| 492 @node Sparse Matrices in Oct-Files | |
| 493 @subsection Sparse Matrices in Oct-Files | |
| 6569 | 494 |
| 495 There are three classes of sparse objects that are of interest to the | |
| 496 user. | |
| 497 | |
| 6572 | 498 @table @code |
| 6569 | 499 @item SparseMatrix |
| 500 A double precision sparse matrix class | |
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501 |
| 6569 | 502 @item SparseComplexMatrix |
| 503 A complex sparse matrix class | |
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504 |
| 6569 | 505 @item SparseBoolMatrix |
| 506 A boolean sparse matrix class | |
| 507 @end table | |
| 508 | |
| 509 All of these classes inherit from the @code{Sparse<T>} template class, | |
| 6571 | 510 and so all have similar capabilities and usage. The @code{Sparse<T>} |
| 6569 | 511 class was based on Octave @code{Array<T>} class, and so users familiar |
| 6572 | 512 with Octave's @code{Array} classes will be comfortable with the use of |
| 6569 | 513 the sparse classes. |
| 514 | |
| 515 The sparse classes will not be entirely described in this section, due | |
| 6572 | 516 to their similarity with the existing @code{Array} classes. However, |
| 517 there are a few differences due the different nature of sparse objects, | |
| 518 and these will be described. Firstly, although it is fundamentally | |
| 519 possible to have N-dimensional sparse objects, the Octave sparse classes do | |
| 6571 | 520 not allow them at this time. So all operations of the sparse classes |
| 6569 | 521 must be 2-dimensional. This means that in fact @code{SparseMatrix} is |
| 522 similar to Octave's @code{Matrix} class rather than its | |
| 523 @code{NDArray} class. | |
| 524 | |
| 525 @menu | |
| 6572 | 526 * Array and Sparse Differences:: |
| 527 * Creating Sparse Matrices in Oct-Files:: | |
| 528 * Using Sparse Matrices in Oct-Files:: | |
| 6569 | 529 @end menu |
| 530 | |
| 6572 | 531 @node Array and Sparse Differences |
| 6569 | 532 @subsubsection The Differences between the Array and Sparse Classes |
| 533 | |
| 534 The number of elements in a sparse matrix is considered to be the number | |
| 6571 | 535 of non-zero elements rather than the product of the dimensions. Therefore |
| 6569 | 536 |
| 537 @example | |
| 6577 | 538 @group |
| 539 SparseMatrix sm; | |
| 540 @dots{} | |
| 541 int nel = sm.nelem (); | |
| 542 @end group | |
| 6569 | 543 @end example |
| 544 | |
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545 @noindent |
| 6571 | 546 returns the number of non-zero elements. If the user really requires the |
| 6569 | 547 number of elements in the matrix, including the non-zero elements, they |
| 6571 | 548 should use @code{numel} rather than @code{nelem}. Note that for very |
| 7001 | 549 large matrices, where the product of the two dimensions is larger than |
| 550 the representation of an unsigned int, then @code{numel} can overflow. | |
| 6569 | 551 An example is @code{speye(1e6)} which will create a matrix with a million |
| 6571 | 552 rows and columns, but only a million non-zero elements. Therefore the |
| 6569 | 553 number of rows by the number of columns in this case is more than two |
| 554 hundred times the maximum value that can be represented by an unsigned int. | |
| 555 The use of @code{numel} should therefore be avoided useless it is known | |
| 556 it won't overflow. | |
| 557 | |
| 558 Extreme care must be take with the elem method and the "()" operator, | |
| 6571 | 559 which perform basically the same function. The reason is that if a |
| 6569 | 560 sparse object is non-const, then Octave will assume that a |
| 6571 | 561 request for a zero element in a sparse matrix is in fact a request |
| 562 to create this element so it can be filled. Therefore a piece of | |
| 6569 | 563 code like |
| 564 | |
| 565 @example | |
| 6577 | 566 @group |
| 567 SparseMatrix sm; | |
| 568 @dots{} | |
| 569 for (int j = 0; j < nc; j++) | |
| 570 for (int i = 0; i < nr; i++) | |
| 571 std::cerr << " (" << i << "," << j << "): " << sm(i,j) | |
| 572 << std::endl; | |
| 573 @end group | |
| 6569 | 574 @end example |
| 575 | |
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576 @noindent |
| 6569 | 577 is a great way of turning the sparse matrix into a dense one, and a |
| 578 very slow way at that since it reallocates the sparse object at each | |
| 579 zero element in the matrix. | |
| 580 | |
| 581 An easy way of preventing the above from happening is to create a temporary | |
| 6571 | 582 constant version of the sparse matrix. Note that only the container for |
| 6569 | 583 the sparse matrix will be copied, while the actual representation of the |
| 6571 | 584 data will be shared between the two versions of the sparse matrix. So this |
| 585 is not a costly operation. For example, the above would become | |
| 6569 | 586 |
| 587 @example | |
| 6577 | 588 @group |
| 589 SparseMatrix sm; | |
| 590 @dots{} | |
| 591 const SparseMatrix tmp (sm); | |
| 592 for (int j = 0; j < nc; j++) | |
| 593 for (int i = 0; i < nr; i++) | |
| 594 std::cerr << " (" << i << "," << j << "): " << tmp(i,j) | |
| 595 << std::endl; | |
| 596 @end group | |
| 6569 | 597 @end example |
| 598 | |
| 599 Finally, as the sparse types aren't just represented as a contiguous | |
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600 block of memory, the @nospell{@code{fortran_vec}} method of the @code{Array<T>} |
| 6571 | 601 is not available. It is however replaced by three separate methods |
| 6569 | 602 @code{ridx}, @code{cidx} and @code{data}, that access the raw compressed |
| 603 column format that the Octave sparse matrices are stored in. | |
| 604 Additionally, these methods can be used in a manner similar to @code{elem}, | |
| 6571 | 605 to allow the matrix to be accessed or filled. However, in that case it is |
| 6569 | 606 up to the user to respect the sparse matrix compressed column format |
| 607 discussed previous. | |
| 608 | |
| 6572 | 609 @node Creating Sparse Matrices in Oct-Files |
| 610 @subsubsection Creating Sparse Matrices in Oct-Files | |
| 6569 | 611 |
| 6572 | 612 You have several alternatives for creating a sparse matrix. |
| 613 You can first create the data as three vectors representing the | |
| 6569 | 614 row and column indexes and the data, and from those create the matrix. |
| 6572 | 615 Or alternatively, you can create a sparse matrix with the appropriate |
| 6571 | 616 amount of space and then fill in the values. Both techniques have their |
| 6569 | 617 advantages and disadvantages. |
| 618 | |
| 6572 | 619 Here is an example of how to create a small sparse matrix with the first |
| 620 technique | |
| 6569 | 621 |
| 622 @example | |
| 6577 | 623 @group |
| 624 int nz = 4, nr = 3, nc = 4; | |
| 625 | |
| 626 ColumnVector ridx (nz); | |
| 627 ColumnVector cidx (nz); | |
| 628 ColumnVector data (nz); | |
| 6569 | 629 |
| 6577 | 630 ridx(0) = 0; ridx(1) = 0; ridx(2) = 1; ridx(3) = 2; |
| 631 cidx(0) = 0; cidx(1) = 1; cidx(2) = 3; cidx(3) = 3; | |
| 632 data(0) = 1; data(1) = 2; data(2) = 3; data(3) = 4; | |
| 6569 | 633 |
| 6577 | 634 SparseMatrix sm (data, ridx, cidx, nr, nc); |
| 635 @end group | |
| 6569 | 636 @end example |
| 637 | |
| 6572 | 638 @noindent |
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639 which creates the matrix given in section |
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640 @ref{Storage of Sparse Matrices}. Note that the compressed matrix |
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641 format is not used at the time of the creation of the matrix itself, |
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642 however it is used internally. |
| 6569 | 643 |
| 644 As previously mentioned, the values of the sparse matrix are stored | |
| 6571 | 645 in increasing column-major ordering. Although the data passed by the |
| 6569 | 646 user does not need to respect this requirement, the pre-sorting the |
| 647 data significantly speeds up the creation of the sparse matrix. | |
| 648 | |
| 649 The disadvantage of this technique of creating a sparse matrix is | |
| 6571 | 650 that there is a brief time where two copies of the data exists. Therefore |
| 6569 | 651 for extremely memory constrained problems this might not be the right |
| 652 technique to create the sparse matrix. | |
| 653 | |
| 654 The alternative is to first create the sparse matrix with the desired | |
| 6571 | 655 number of non-zero elements and then later fill those elements in. The |
| 656 easiest way to do this is | |
| 6569 | 657 |
| 6571 | 658 @example |
| 6577 | 659 @group |
| 660 int nz = 4, nr = 3, nc = 4; | |
| 661 SparseMatrix sm (nr, nc, nz); | |
| 662 sm(0,0) = 1; sm(0,1) = 2; sm(1,3) = 3; sm(2,3) = 4; | |
| 663 @end group | |
| 6569 | 664 @end example |
| 665 | |
| 6571 | 666 That creates the same matrix as previously. Again, although it is not |
| 6569 | 667 strictly necessary, it is significantly faster if the sparse matrix is |
| 668 created in this manner that the elements are added in column-major | |
| 6571 | 669 ordering. The reason for this is that if the elements are inserted |
| 6569 | 670 at the end of the current list of known elements then no element |
| 671 in the matrix needs to be moved to allow the new element to be | |
| 6571 | 672 inserted. Only the column indexes need to be updated. |
| 6569 | 673 |
| 674 There are a few further points to note about this technique of creating | |
| 6572 | 675 a sparse matrix. Firstly, it is possible to create a sparse matrix |
| 6571 | 676 with fewer elements than are actually inserted in the matrix. Therefore |
| 6569 | 677 |
| 6571 | 678 @example |
| 6577 | 679 @group |
| 680 int nz = 4, nr = 3, nc = 4; | |
| 681 SparseMatrix sm (nr, nc, 0); | |
| 682 sm(0,0) = 1; sm(0,1) = 2; sm(1,3) = 3; sm(2,3) = 4; | |
| 683 @end group | |
| 6569 | 684 @end example |
| 685 | |
| 6572 | 686 @noindent |
| 687 is perfectly valid. However it is a very bad idea. The reason is that | |
| 6569 | 688 as each new element is added to the sparse matrix the space allocated |
| 6571 | 689 to it is increased by reallocating the memory. This is an expensive |
| 6569 | 690 operation, that will significantly slow this means of creating a sparse |
| 6572 | 691 matrix. Furthermore, it is possible to create a sparse matrix with |
| 692 too much storage, so having @var{nz} above equaling 6 is also valid. | |
| 6569 | 693 The disadvantage is that the matrix occupies more memory than strictly |
| 694 needed. | |
| 695 | |
| 6572 | 696 It is not always easy to know the number of non-zero elements prior |
| 6571 | 697 to filling a matrix. For this reason the additional storage for the |
| 6569 | 698 sparse matrix can be removed after its creation with the |
| 6571 | 699 @dfn{maybe_compress} function. Furthermore, the maybe_compress can |
| 6569 | 700 deallocate the unused storage, but it can equally remove zero elements |
| 701 from the matrix. The removal of zero elements from the matrix is | |
| 702 controlled by setting the argument of the @dfn{maybe_compress} function | |
| 6572 | 703 to be @samp{true}. However, the cost of removing the zeros is high because it |
| 6571 | 704 implies resorting the elements. Therefore, if possible it is better |
| 705 is the user doesn't add the zeros in the first place. An example of | |
| 6569 | 706 the use of @dfn{maybe_compress} is |
| 707 | |
| 708 @example | |
| 6577 | 709 @group |
| 6569 | 710 int nz = 6, nr = 3, nc = 4; |
| 6577 | 711 |
| 6569 | 712 SparseMatrix sm1 (nr, nc, nz); |
| 713 sm1(0,0) = 1; sm1(0,1) = 2; sm1(1,3) = 3; sm1(2,3) = 4; | |
| 714 sm1.maybe_compress (); // No zero elements were added | |
| 715 | |
| 716 SparseMatrix sm2 (nr, nc, nz); | |
| 6571 | 717 sm2(0,0) = 1; sm2(0,1) = 2; sm(0,2) = 0; sm(1,2) = 0; |
| 6569 | 718 sm1(1,3) = 3; sm1(2,3) = 4; |
| 719 sm2.maybe_compress (true); // Zero elements were added | |
| 6577 | 720 @end group |
| 6569 | 721 @end example |
| 722 | |
| 723 The use of the @dfn{maybe_compress} function should be avoided if | |
| 724 possible, as it will slow the creation of the matrices. | |
| 725 | |
| 726 A third means of creating a sparse matrix is to work directly with | |
| 6571 | 727 the data in compressed row format. An example of this technique might |
| 6569 | 728 be |
| 729 | |
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730 @c Note the @verbatim environment is a relatively new addition to Texinfo. |
| 6571 | 731 @c Therefore use the @example environment and replace @, with @@, |
| 6569 | 732 @c { with @{, etc |
| 733 | |
| 734 @example | |
| 6577 | 735 octave_value arg; |
| 736 @dots{} | |
| 737 int nz = 6, nr = 3, nc = 4; // Assume we know the max no nz | |
| 738 SparseMatrix sm (nr, nc, nz); | |
| 739 Matrix m = arg.matrix_value (); | |
| 6569 | 740 |
| 6577 | 741 int ii = 0; |
| 742 sm.cidx (0) = 0; | |
| 743 for (int j = 1; j < nc; j++) | |
| 744 @{ | |
| 745 for (int i = 0; i < nr; i++) | |
| 746 @{ | |
| 747 double tmp = foo (m(i,j)); | |
| 748 if (tmp != 0.) | |
| 749 @{ | |
| 750 sm.data(ii) = tmp; | |
| 751 sm.ridx(ii) = i; | |
| 752 ii++; | |
| 753 @} | |
| 754 @} | |
| 755 sm.cidx(j+1) = ii; | |
| 756 @} | |
| 7081 | 757 sm.maybe_compress (); // If don't know a-priori |
| 758 // the final no of nz. | |
| 6569 | 759 @end example |
| 760 | |
| 6572 | 761 @noindent |
| 6569 | 762 which is probably the most efficient means of creating the sparse matrix. |
| 763 | |
| 764 Finally, it might sometimes arise that the amount of storage initially | |
| 6571 | 765 created is insufficient to completely store the sparse matrix. Therefore, |
| 6569 | 766 the method @code{change_capacity} exists to reallocate the sparse memory. |
| 6571 | 767 The above example would then be modified as |
| 6569 | 768 |
| 769 @example | |
| 6577 | 770 octave_value arg; |
| 771 @dots{} | |
| 772 int nz = 6, nr = 3, nc = 4; // Assume we know the max no nz | |
| 773 SparseMatrix sm (nr, nc, nz); | |
| 774 Matrix m = arg.matrix_value (); | |
| 6569 | 775 |
| 6577 | 776 int ii = 0; |
| 777 sm.cidx (0) = 0; | |
| 778 for (int j = 1; j < nc; j++) | |
| 779 @{ | |
| 780 for (int i = 0; i < nr; i++) | |
| 781 @{ | |
| 782 double tmp = foo (m(i,j)); | |
| 783 if (tmp != 0.) | |
| 784 @{ | |
| 785 if (ii == nz) | |
| 786 @{ | |
| 787 nz += 2; // Add 2 more elements | |
| 788 sm.change_capacity (nz); | |
| 789 @} | |
| 790 sm.data(ii) = tmp; | |
| 791 sm.ridx(ii) = i; | |
| 792 ii++; | |
| 793 @} | |
| 794 @} | |
| 795 sm.cidx(j+1) = ii; | |
| 796 @} | |
| 7081 | 797 sm.maybe_mutate (); // If don't know a-priori |
| 798 // the final no of nz. | |
| 6569 | 799 @end example |
| 800 | |
| 801 Note that both increasing and decreasing the number of non-zero elements in | |
| 6571 | 802 a sparse matrix is expensive, as it involves memory reallocation. Also as |
| 6569 | 803 parts of the matrix, though not its entirety, exist as the old and new copy |
| 6571 | 804 at the same time, additional memory is needed. Therefore if possible this |
| 6569 | 805 should be avoided. |
| 806 | |
| 6572 | 807 @node Using Sparse Matrices in Oct-Files |
| 6569 | 808 @subsubsection Using Sparse Matrices in Oct-Files |
| 809 | |
| 810 Most of the same operators and functions on sparse matrices that are | |
| 811 available from the Octave are equally available with oct-files. | |
| 812 The basic means of extracting a sparse matrix from an @code{octave_value} | |
| 813 and returning them as an @code{octave_value}, can be seen in the | |
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814 following example. |
| 6569 | 815 |
| 816 @example | |
| 6577 | 817 @group |
| 818 octave_value_list retval; | |
| 6569 | 819 |
| 6577 | 820 SparseMatrix sm = args(0).sparse_matrix_value (); |
| 7081 | 821 SparseComplexMatrix scm = |
| 822 args(1).sparse_complex_matrix_value (); | |
| 6577 | 823 SparseBoolMatrix sbm = args(2).sparse_bool_matrix_value (); |
| 824 @dots{} | |
| 825 retval(2) = sbm; | |
| 826 retval(1) = scm; | |
| 827 retval(0) = sm; | |
| 828 @end group | |
| 6569 | 829 @end example |
| 830 | |
| 831 The conversion to an octave-value is handled by the sparse | |
| 832 @code{octave_value} constructors, and so no special care is needed. | |
| 833 | |
| 834 @node Accessing Global Variables in Oct-Files | |
| 835 @subsection Accessing Global Variables in Oct-Files | |
| 836 | |
| 837 Global variables allow variables in the global scope to be | |
| 6571 | 838 accessed. Global variables can easily be accessed with oct-files using |
| 6569 | 839 the support functions @code{get_global_value} and |
| 6571 | 840 @code{set_global_value}. @code{get_global_value} takes two arguments, |
| 841 the first is a string representing the variable name to obtain. The | |
| 6569 | 842 second argument is a boolean argument specifying what to do in the case |
| 6571 | 843 that no global variable of the desired name is found. An example of the |
| 6569 | 844 use of these two functions is |
| 845 | |
| 9906 | 846 @example |
| 847 @EXAMPLEFILE(globaldemo.cc) | |
| 848 @end example | |
| 6569 | 849 |
| 850 An example of its use is | |
| 851 | |
| 852 @example | |
| 853 @group | |
| 854 global a b | |
| 855 b = 10; | |
| 856 globaldemo ("b") | |
| 857 @result{} 10 | |
| 858 globaldemo ("c") | |
| 859 @result{} "Global variable not found" | |
| 860 num2str (a) | |
| 861 @result{} 42 | |
| 862 @end group | |
| 863 @end example | |
| 864 | |
| 865 @node Calling Octave Functions from Oct-Files | |
| 866 @subsection Calling Octave Functions from Oct-Files | |
| 867 | |
| 868 There is often a need to be able to call another octave function from | |
| 869 within an oct-file, and there are many examples of such within octave | |
| 6571 | 870 itself. For example the @code{quad} function is an oct-file that |
| 6569 | 871 calculates the definite integral by quadrature over a user supplied |
| 872 function. | |
| 873 | |
| 6571 | 874 There are also many ways in which a function might be passed. It might |
| 875 be passed as one of | |
| 6569 | 876 |
| 877 @enumerate 1 | |
| 878 @item Function Handle | |
|
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879 |
| 6569 | 880 @item Anonymous Function Handle |
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881 |
| 6569 | 882 @item Inline Function |
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883 |
| 6569 | 884 @item String |
| 885 @end enumerate | |
| 886 | |
| 887 The example below demonstrates an example that accepts all four means of | |
| 6571 | 888 passing a function to an oct-file. |
| 6569 | 889 |
| 9906 | 890 @example |
| 891 @EXAMPLEFILE(funcdemo.cc) | |
| 892 @end example | |
| 6569 | 893 |
| 894 The first argument to this demonstration is the user supplied function | |
| 895 and the following arguments are all passed to the user function. | |
| 896 | |
| 897 @example | |
| 898 @group | |
| 6572 | 899 funcdemo (@@sin,1) |
| 6569 | 900 @result{} 0.84147 |
| 6572 | 901 funcdemo (@@(x) sin(x), 1) |
| 6569 | 902 @result{} 0.84147 |
| 6572 | 903 funcdemo (inline ("sin(x)"), 1) |
| 6569 | 904 @result{} 0.84147 |
| 6572 | 905 funcdemo ("sin",1) |
| 6569 | 906 @result{} 0.84147 |
| 907 funcdemo (@@atan2, 1, 1) | |
| 908 @result{} 0.78540 | |
| 909 @end group | |
| 910 @end example | |
| 911 | |
| 912 When the user function is passed as a string, the treatment of the | |
| 6571 | 913 function is different. In some cases it is necessary to always have the |
| 6572 | 914 user supplied function as an @code{octave_function} object. In that |
| 915 case the string argument can be used to create a temporary function like | |
| 6569 | 916 |
| 917 @example | |
| 918 @group | |
| 6577 | 919 std::octave fcn_name = unique_symbol_name ("__fcn__"); |
| 920 std::string fname = "function y = "; | |
| 921 fname.append (fcn_name); | |
| 922 fname.append ("(x) y = "); | |
| 923 fcn = extract_function (args(0), "funcdemo", fcn_name, | |
| 924 fname, "; endfunction"); | |
| 925 @dots{} | |
| 926 if (fcn_name.length ()) | |
| 927 clear_function (fcn_name); | |
| 6569 | 928 @end group |
| 929 @end example | |
| 930 | |
| 6571 | 931 There are two important things to know in this case. The number of input |
| 6569 | 932 arguments to the user function is fixed, and in the above is a single |
| 933 argument, and secondly to avoid leaving the temporary function in the | |
| 934 Octave symbol table it should be cleared after use. | |
| 935 | |
| 936 @node Calling External Code from Oct-Files | |
| 937 @subsection Calling External Code from Oct-Files | |
| 938 | |
| 939 Linking external C code to Octave is relatively simple, as the C | |
| 6571 | 940 functions can easily be called directly from C++. One possible issue is |
| 6569 | 941 the declarations of the external C functions might need to be explicitly |
| 6571 | 942 defined as C functions to the compiler. If the declarations of the |
| 6569 | 943 external C functions are in the header @code{foo.h}, then the manner in |
| 944 which to ensure that the C++ compiler treats these declarations as C | |
| 945 code is | |
| 946 | |
| 947 @example | |
| 948 @group | |
| 949 #ifdef __cplusplus | |
| 6571 | 950 extern "C" |
| 6569 | 951 @{ |
| 952 #endif | |
| 953 #include "foo.h" | |
| 954 #ifdef __cplusplus | |
| 955 @} /* end extern "C" */ | |
| 956 #endif | |
| 957 @end group | |
| 958 @end example | |
| 959 | |
| 6571 | 960 Calling Fortran code however can pose some difficulties. This is due to |
| 6569 | 961 differences in the manner in compilers treat the linking of Fortran code |
| 6571 | 962 with C or C++ code. Octave supplies a number of macros that allow |
| 6569 | 963 consistent behavior across a number of compilers. |
| 964 | |
| 965 The underlying Fortran code should use the @code{XSTOPX} function to | |
| 6571 | 966 replace the Fortran @code{STOP} function. @code{XSTOPX} uses the Octave |
|
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967 exception handler to treat failing cases in the Fortran code |
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968 explicitly. Note that Octave supplies its own replacement @sc{blas} |
| 6569 | 969 @code{XERBLA} function, which uses @code{XSTOPX}. |
| 970 | |
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971 If the underlying code calls @code{XSTOPX}, then the @w{@code{F77_XFCN}} |
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972 macro should be used to call the underlying Fortran function. The Fortran |
| 6569 | 973 exception state can then be checked with the global variable |
| 6572 | 974 @code{f77_exception_encountered}. If @code{XSTOPX} will not be called, |
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975 then the @w{@code{F77_FCN}} macro should be used instead to call the Fortran |
| 6569 | 976 code. |
| 977 | |
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978 There is no harm in using @w{@code{F77_XFCN}} in all cases, except that for |
| 6569 | 979 Fortran code that is short running and executes a large number of times, |
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980 there is potentially an overhead in doing so. However, if @w{@code{F77_FCN}} |
| 6569 | 981 is used with code that calls @code{XSTOP}, Octave can generate a |
| 982 segmentation fault. | |
| 983 | |
| 984 An example of the inclusion of a Fortran function in an oct-file is | |
| 985 given in the following example, where the C++ wrapper is | |
| 986 | |
| 9906 | 987 @example |
| 988 @EXAMPLEFILE(fortdemo.cc) | |
| 989 @end example | |
| 6569 | 990 |
| 6572 | 991 @noindent |
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992 and the Fortran function is |
| 6569 | 993 |
| 9906 | 994 @example |
| 995 @EXAMPLEFILE(fortsub.f) | |
| 996 @end example | |
| 6569 | 997 |
| 998 This example demonstrates most of the features needed to link to an | |
| 999 external Fortran function, including passing arrays and strings, as well | |
| 6571 | 1000 as exception handling. An example of the behavior of this function is |
| 6569 | 1001 |
| 1002 @example | |
| 1003 @group | |
| 6572 | 1004 [b, s] = fortdemo (1:3) |
| 6569 | 1005 @result{} |
| 1006 b = 1.00000 0.50000 0.33333 | |
| 1007 s = There are 3 values in the input vector | |
| 1008 [b, s] = fortdemo(0:3) | |
| 1009 error: fortsub:divide by zero | |
| 1010 error: exception encountered in Fortran subroutine fortsub_ | |
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1011 error: fortdemo: error in Fortran |
| 6569 | 1012 @end group |
| 1013 @end example | |
| 1014 | |
| 1015 @node Allocating Local Memory in Oct-Files | |
| 1016 @subsection Allocating Local Memory in Oct-Files | |
| 1017 | |
| 1018 Allocating memory within an oct-file might seem easy as the C++ | |
| 6571 | 1019 new/delete operators can be used. However, in that case care must be |
| 1020 taken to avoid memory leaks. The preferred manner in which to allocate | |
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1021 memory for use locally is to use the @w{@code{OCTAVE_LOCAL_BUFFER}} macro. |
| 6572 | 1022 An example of its use is |
| 6569 | 1023 |
| 1024 @example | |
| 1025 OCTAVE_LOCAL_BUFFER (double, tmp, len) | |
| 1026 @end example | |
| 1027 | |
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1028 @noindent |
| 6569 | 1029 that returns a pointer @code{tmp} of type @code{double *} of length |
| 1030 @code{len}. | |
| 1031 | |
| 1032 @node Input Parameter Checking in Oct-Files | |
| 1033 @subsection Input Parameter Checking in Oct-Files | |
| 1034 | |
| 6580 | 1035 As oct-files are compiled functions they have the possibility of causing |
| 7001 | 1036 Octave to abort abnormally. It is therefore important that |
| 1037 each and every function has the minimum of parameter | |
| 6580 | 1038 checking needed to ensure that Octave behaves well. |
| 1039 | |
| 1040 The minimum requirement, as previously discussed, is to check the number | |
| 1041 of input arguments before using them to avoid referencing a non existent | |
| 1042 argument. However, it some case this might not be sufficient as the | |
| 6593 | 1043 underlying code imposes further constraints. For example an external |
| 6580 | 1044 function call might be undefined if the input arguments are not |
| 6593 | 1045 integers, or if one of the arguments is zero. Therefore, oct-files often |
| 6580 | 1046 need additional input parameter checking. |
| 1047 | |
| 1048 There are several functions within Octave that might be useful for the | |
| 6593 | 1049 purposes of parameter checking. These include the methods of the |
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1050 octave_value class like @code{is_real_matrix}, etc., but equally include |
| 6593 | 1051 more specialized functions. Some of the more common ones are |
|
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1052 demonstrated in the following example. |
| 6580 | 1053 |
| 9906 | 1054 @example |
| 1055 @EXAMPLEFILE(paramdemo.cc) | |
| 1056 @end example | |
| 6580 | 1057 |
| 1058 @noindent | |
|
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1059 An example of its use is: |
| 6580 | 1060 |
| 1061 @example | |
| 1062 @group | |
| 1063 paramdemo ([1, 2, NaN, Inf]) | |
| 1064 @result{} Properties of input array: | |
| 1065 includes Inf or NaN values | |
| 1066 includes other values than 1 and 0 | |
| 1067 includes only int, Inf or NaN values | |
| 1068 @end group | |
| 1069 @end example | |
| 6569 | 1070 |
| 1071 @node Exception and Error Handling in Oct-Files | |
| 1072 @subsection Exception and Error Handling in Oct-Files | |
| 1073 | |
| 1074 Another important feature of Octave is its ability to react to the user | |
| 6571 | 1075 typing @kbd{Control-C} even during calculations. This ability is based on the |
| 6569 | 1076 C++ exception handler, where memory allocated by the C++ new/delete |
| 6571 | 1077 methods are automatically released when the exception is treated. When |
| 6569 | 1078 writing an oct-file, to allow Octave to treat the user typing @kbd{Control-C}, |
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1079 the @w{@code{OCTAVE_QUIT}} macro is supplied. For example: |
| 6569 | 1080 |
| 1081 @example | |
| 1082 @group | |
| 6577 | 1083 for (octave_idx_type i = 0; i < a.nelem (); i++) |
| 1084 @{ | |
| 1085 OCTAVE_QUIT; | |
| 1086 b.elem(i) = 2. * a.elem(i); | |
| 1087 @} | |
| 6569 | 1088 @end group |
| 1089 @end example | |
| 1090 | |
|
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1091 The presence of the @w{@code{OCTAVE_QUIT}} macro in the inner loop allows |
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1092 Octave to treat the user request with the @kbd{Control-C}. Without this macro, |
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1093 the user must either wait for the function to return before the interrupt is |
| 6569 | 1094 processed, or press @kbd{Control-C} three times to force Octave to exit. |
| 1095 | |
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1096 The @w{@code{OCTAVE_QUIT}} macro does impose a very small speed penalty, and so |
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1097 for loops that are known to be small it might not make sense to include |
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1098 @w{@code{OCTAVE_QUIT}}. |
| 6569 | 1099 |
| 1100 When creating an oct-file that uses an external libraries, the function | |
| 1101 might spend a significant portion of its time in the external | |
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1102 library. It is not generally possible to use the @w{@code{OCTAVE_QUIT}} macro |
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1103 in this case. The alternative in this case is |
| 6569 | 1104 |
| 1105 @example | |
| 1106 @group | |
| 6577 | 1107 BEGIN_INTERRUPT_IMMEDIATELY_IN_FOREIGN_CODE; |
| 1108 @dots{} some code that calls a "foreign" function @dots{} | |
| 1109 END_INTERRUPT_IMMEDIATELY_IN_FOREIGN_CODE; | |
| 6569 | 1110 @end group |
| 1111 @end example | |
| 1112 | |
| 1113 The disadvantage of this is that if the foreign code allocates any | |
| 1114 memory internally, then this memory might be lost during an interrupt, | |
| 6571 | 1115 without being deallocated. Therefore, ideally Octave itself should |
| 6569 | 1116 allocate any memory that is needed by the foreign code, with either the |
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1117 @nospell{fortran_vec} method or the @w{@code{OCTAVE_LOCAL_BUFFER}} macro. |
| 6569 | 1118 |
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1119 The Octave unwind_protect mechanism (@ref{The @code{unwind_protect} Statement}) |
| 6571 | 1120 can also be used in oct-files. In conjunction with the exception |
| 6569 | 1121 handling of Octave, it is important to enforce that certain code is run |
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1122 to allow variables, etc. to be restored even if an exception occurs. An |
| 6569 | 1123 example of the use of this mechanism is |
| 1124 | |
| 9906 | 1125 @example |
| 1126 @EXAMPLEFILE(unwinddemo.cc) | |
| 1127 @end example | |
| 6569 | 1128 |
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1129 As can be seen in the example: |
| 6569 | 1130 |
| 1131 @example | |
| 1132 @group | |
| 6572 | 1133 unwinddemo (1, 0) |
| 6569 | 1134 @result{} Inf |
| 1135 1 / 0 | |
| 1136 @result{} warning: division by zero | |
| 6593 | 1137 Inf |
| 6569 | 1138 @end group |
| 1139 @end example | |
| 1140 | |
| 1141 The division by zero (and in fact all warnings) is disabled in the | |
| 1142 @code{unwinddemo} function. | |
| 1143 | |
| 1144 @node Documentation and Test of Oct-Files | |
| 1145 @subsection Documentation and Test of Oct-Files | |
| 1146 | |
| 6580 | 1147 The documentation of an oct-file is the fourth string parameter of the |
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1148 @w{@code{DEFUN_DLD}} macro. This string can be formatted in the same manner |
| 6580 | 1149 as the help strings for user functions (@ref{Documentation Tips}), |
| 1150 however there are some issue that are particular to the formatting of | |
| 1151 help strings within oct-files. | |
| 1152 | |
| 1153 The major issue is that the help string will typically be longer than a | |
| 1154 single line of text, and so the formatting of long help strings need to | |
| 7001 | 1155 be taken into account. There are several manners in which to treat this |
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1156 issue, but the most common is illustrated in the following example, |
| 6580 | 1157 |
| 1158 @example | |
| 1159 @group | |
| 1160 DEFUN_DLD (do_what_i_want, args, nargout, | |
| 1161 "-*- texinfo -*-\n\ | |
| 1162 @@deftypefn @{Function File@} @{@} do_what_i_say (@@var@{n@})\n\ | |
| 7081 | 1163 A function that does what the user actually wants rather\n\ |
| 1164 than what they requested.\n\ | |
| 6580 | 1165 @@end deftypefn") |
| 1166 @{ | |
| 1167 @dots{} | |
| 1168 @} | |
| 1169 @end group | |
| 1170 @end example | |
| 1171 | |
| 1172 @noindent | |
| 1173 where, as can be seen, end line of text within the help string is | |
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1174 terminated by @code{\n\} which is an embedded new-line in the string |
| 6580 | 1175 together with a C++ string continuation character. Note that the final |
| 1176 @code{\} must be the last character on the line. | |
| 1177 | |
| 1178 Octave also includes the ability to embed the test and demonstration | |
| 1179 code for a function within the code itself (@ref{Test and Demo Functions}). | |
| 1180 This can be used from within oct-files (or in fact any file) with | |
| 1181 certain provisos. Firstly, the test and demo functions of Octave look | |
| 1182 for a @code{%!} as the first characters on a new-line to identify test | |
| 1183 and demonstration code. This is equally a requirement for | |
| 1184 oct-files. Furthermore the test and demonstration code must be included | |
| 1185 in a comment block of the compiled code to avoid it being interpreted by | |
| 6606 | 1186 the compiler. Finally, the Octave test and demonstration code must have |
| 6580 | 1187 access to the source code of the oct-file and not just the compiled code |
| 6606 | 1188 as the tests are stripped from the compiled code. An example in an |
| 6580 | 1189 oct-file might be |
| 1190 | |
| 1191 @example | |
| 1192 @group | |
| 1193 /* | |
| 1194 | |
| 1195 %!error (sin()) | |
| 1196 %!error (sin(1,1)) | |
| 1197 %!assert (sin([1,2]),[sin(1),sin(2)]) | |
| 1198 | |
| 1199 */ | |
| 1200 @end group | |
| 1201 @end example | |
| 6569 | 1202 |
| 6593 | 1203 @c @node Application Programming Interface for Oct-Files |
| 1204 @c @subsection Application Programming Interface for Oct-Files | |
| 1205 @c | |
| 1206 @c WRITE ME, using Coda section 1.3 as a starting point. | |
| 6569 | 1207 |
| 1208 @node Mex-Files | |
| 1209 @section Mex-Files | |
| 1210 @cindex mex-files | |
| 1211 @cindex mex | |
| 1212 | |
| 1213 Octave includes an interface to allow legacy mex-files to be compiled | |
| 6571 | 1214 and used with Octave. This interface can also be used to share code |
| 1215 between Octave and non Octave users. However, as mex-files expose the | |
| 6593 | 1216 internal API of an alternative product to Octave, and the internal |
| 6569 | 1217 structure of Octave is different to this product, a mex-file can never |
| 6571 | 1218 have the same performance in Octave as the equivalent oct-file. In |
| 6569 | 1219 particular to support the manner in which mex-files access the variables |
| 1220 passed to mex functions, there are a significant number of additional | |
| 6593 | 1221 copies of memory when calling or returning from a mex function. For |
| 1222 this reason, new code should be written using the oct-file interface | |
| 6569 | 1223 discussed above if possible. |
| 1224 | |
| 1225 @menu | |
| 6572 | 1226 * Getting Started with Mex-Files:: |
| 6580 | 1227 * Working with Matrices and Arrays in Mex-Files:: |
| 1228 * Character Strings in Mex-Files:: | |
| 1229 * Cell Arrays with Mex-Files:: | |
| 6572 | 1230 * Structures with Mex-Files:: |
| 1231 * Sparse Matrices with Mex-Files:: | |
| 6580 | 1232 * Calling Other Functions in Mex-Files:: |
| 6593 | 1233 @c * Application Programming Interface for Mex-Files:: |
| 6569 | 1234 @end menu |
| 1235 | |
| 1236 @node Getting Started with Mex-Files | |
| 1237 @subsection Getting Started with Mex-Files | |
| 1238 | |
| 1239 The basic command to build a mex-file is either @code{mkoctfile --mex} or | |
| 6571 | 1240 @code{mex}. The first can either be used from within Octave or from the |
| 8486 | 1241 command line. However, to avoid issues with the installation of other |
| 6569 | 1242 products, the use of the command @code{mex} is limited to within Octave. |
| 1243 | |
| 1244 @DOCSTRING(mex) | |
| 1245 | |
| 1246 @DOCSTRING(mexext) | |
| 1247 | |
| 1248 One important difference between the use of mex with other products and | |
| 1249 with Octave is that the header file "matrix.h" is implicitly included | |
| 6571 | 1250 through the inclusion of "mex.h". This is to avoid a conflict with the |
| 6569 | 1251 Octave file "Matrix.h" with operating systems and compilers that don't |
| 1252 distinguish between filenames in upper and lower case | |
| 1253 | |
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1254 Consider the short example: |
| 6569 | 1255 |
| 9906 | 1256 @example |
| 1257 @group | |
| 1258 @EXAMPLEFILE(firstmexdemo.c) | |
| 1259 @end group | |
| 1260 @end example | |
| 6569 | 1261 |
| 6593 | 1262 This simple example demonstrates the basics of writing a mex-file. The |
| 1263 entry point into the mex-file is defined by @code{mexFunction}. Note | |
| 6580 | 1264 that the function name is not explicitly included in the |
| 1265 @code{mexFunction} and so there can only be a single @code{mexFunction} | |
| 1266 entry point per-file. Also the name of the function is determined by the | |
| 1267 name of the mex-file itself. Therefore if the above function is in the | |
| 1268 file @file{firstmexdemo.c}, it can be compiled with | |
| 1269 | |
| 1270 @example | |
| 1271 mkoctfile --mex firstmexdemo.c | |
| 1272 @end example | |
| 1273 | |
| 1274 @noindent | |
| 1275 which creates a file @file{firstmexdemo.mex}. The function can then be run | |
| 1276 from Octave as | |
| 1277 | |
| 1278 @example | |
| 1279 @group | |
| 1280 firstmexdemo() | |
| 1281 @result{} 1.2346 | |
| 1282 @end group | |
| 1283 @end example | |
| 1284 | |
| 1285 It should be noted that the mex-file contains no help string for the | |
| 6593 | 1286 functions it contains. To document mex-files, there should exist an |
| 1287 m-file in the same directory as the mex-file itself. Taking the above as | |
| 6580 | 1288 an example, we would therefore have a file @file{firstmexdemo.m} that might |
| 1289 contain the text | |
| 1290 | |
| 1291 @example | |
| 1292 %FIRSTMEXDEMO Simple test of the functionality of a mex-file. | |
| 1293 @end example | |
| 1294 | |
| 1295 In this case, the function that will be executed within Octave will be | |
| 1296 given by the mex-file, while the help string will come from the | |
| 6593 | 1297 m-file. This can also be useful to allow a sample implementation of the |
| 6580 | 1298 mex-file within the Octave language itself for testing purposes. |
| 1299 | |
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1300 Although we cannot have multiple entry points into a single mex-file, |
| 6580 | 1301 we can use the @code{mexFunctionName} function to determine what name |
| 6593 | 1302 the mex-file was called with. This can be used to alter the behavior of |
| 1303 the mex-file based on the function name. For example if | |
| 6580 | 1304 |
| 9906 | 1305 @example |
| 1306 @group | |
| 1307 @EXAMPLEFILE(myfunc.c) | |
| 1308 @end group | |
| 1309 @end example | |
| 6580 | 1310 |
| 1311 @noindent | |
| 1312 is in file @file{myfunc.c}, and it is compiled with | |
| 1313 | |
| 1314 @example | |
| 1315 @group | |
| 1316 mkoctfile --mex myfunc.c | |
| 1317 ln -s myfunc.mex myfunc2.mex | |
| 1318 @end group | |
| 1319 @end example | |
| 1320 | |
| 1321 Then as can be seen by | |
| 1322 | |
| 1323 @example | |
| 1324 @group | |
| 1325 myfunc() | |
| 1326 @result{} You called function: myfunc | |
| 1327 This is the principal function | |
| 1328 myfunc2() | |
| 1329 @result{} You called function: myfunc2 | |
| 1330 @end group | |
| 1331 @end example | |
| 1332 | |
| 1333 @noindent | |
| 1334 the behavior of the mex-file can be altered depending on the functions | |
| 1335 name. | |
| 1336 | |
| 6593 | 1337 Allow the user should only include @code{mex.h} in their code, Octave |
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1338 declares additional functions, typedefs, etc., available to the user to |
| 6593 | 1339 write mex-files in the headers @code{mexproto.h} and @code{mxarray.h}. |
| 1340 | |
| 6580 | 1341 @node Working with Matrices and Arrays in Mex-Files |
| 1342 @subsection Working with Matrices and Arrays in Mex-Files | |
| 1343 | |
| 6593 | 1344 The basic mex type of all variables is @code{mxArray}. All variables, |
| 1345 such as matrices, cell arrays or structures are all stored in this basic | |
| 6580 | 1346 type, and this type serves basically the same purpose as the |
| 6593 | 1347 octave_value class in oct-files. That is it acts as a container for the |
| 6580 | 1348 more specialized types. |
| 1349 | |
| 6593 | 1350 The @code{mxArray} structure contains at a minimum, the variable it |
| 1351 represents name, its dimensions, its type and whether the variable is | |
| 1352 real or complex. It can however contain a number of additional fields | |
| 1353 depending on the type of the @code{mxArray}. There are a number of | |
| 1354 functions to create @code{mxArray} structures, including | |
| 1355 @code{mxCreateCellArray}, @code{mxCreateSparse} and the generic | |
| 1356 @code{mxCreateNumericArray}. | |
| 1357 | |
| 1358 The basic functions to access the data contained in an array is | |
| 1359 @code{mxGetPr}. As the mex interface assumes that the real and imaginary | |
| 6939 | 1360 parts of a complex array are stored separately, there is an equivalent |
| 6593 | 1361 function @code{mxGetPi} that get the imaginary part. Both of these |
| 1362 functions are for use only with double precision matrices. There also | |
| 1363 exists the generic function @code{mxGetData} and @code{mxGetImagData} | |
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1364 that perform the same operation on all matrix types. For example: |
| 6593 | 1365 |
| 1366 @example | |
| 1367 @group | |
| 1368 mxArray *m; | |
| 6686 | 1369 mwSize *dims; |
| 6593 | 1370 UINT32_T *pr; |
| 1371 | |
| 6686 | 1372 dims = (mwSize *) mxMalloc (2 * sizeof(mwSize)); |
| 6593 | 1373 dims[0] = 2; |
| 1374 dims[1] = 2; | |
| 1375 m = mxCreateNumericArray (2, dims, mxUINT32_CLASS, mxREAL); | |
| 1376 pr = = (UINT32_T *) mxGetData (m); | |
| 1377 @end group | |
| 1378 @end example | |
| 1379 | |
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1380 There are also the functions @code{mxSetPr}, etc., that perform the |
| 6593 | 1381 inverse, and set the data of an Array to use the block of memory pointed |
| 1382 to by the argument of @code{mxSetPr}. | |
| 1383 | |
| 6686 | 1384 Note the type @code{mwSize} used above, and @code{mwIndex} are defined |
| 1385 as the native precision of the indexing in Octave on the platform on | |
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1386 which the mex-file is built. This allows both 32- and 64-bit platforms |
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1387 to support mex-files. @code{mwSize} is used to define array dimension |
| 6686 | 1388 and maximum number or elements, while @code{mwIndex} is used to define |
| 1389 indexing into arrays. | |
| 1390 | |
| 6593 | 1391 An example that demonstration how to work with arbitrary real or complex |
| 1392 double precision arrays is given by the file @file{mypow2.c} as given | |
| 1393 below. | |
| 1394 | |
| 9906 | 1395 @example |
| 1396 @EXAMPLEFILE(mypow2.c) | |
| 1397 @end example | |
| 6593 | 1398 |
| 1399 @noindent | |
| 1400 with an example of its use | |
| 1401 | |
| 1402 @example | |
| 1403 @group | |
| 1404 b = randn(4,1) + 1i * randn(4,1); | |
| 1405 all(b.^2 == mypow2(b)) | |
| 1406 @result{} 1 | |
| 1407 @end group | |
| 1408 @end example | |
| 1409 | |
| 1410 | |
| 7096 | 1411 The example above uses the functions @code{mxGetDimensions}, |
| 1412 @code{mxGetNumberOfElements}, and @code{mxGetNumberOfDimensions} to work | |
| 1413 with the dimensions of multi-dimensional arrays. The functions | |
| 1414 @code{mxGetM}, and @code{mxGetN} are also available to find the number | |
| 1415 of rows and columns in a matrix. | |
| 6580 | 1416 |
| 1417 @node Character Strings in Mex-Files | |
| 1418 @subsection Character Strings in Mex-Files | |
| 1419 | |
| 6593 | 1420 As mex-files do not make the distinction between single and double |
| 1421 quoted strings within Octave, there is perhaps less complexity in the | |
| 1422 use of strings and character matrices in mex-files. An example of their | |
| 1423 use, that parallels the demo in @file{stringdemo.cc}, is given in the | |
| 1424 file @file{mystring.c}, as seen below. | |
| 1425 | |
| 9906 | 1426 @example |
| 1427 @EXAMPLEFILE(mystring.c) | |
| 1428 @end example | |
| 6593 | 1429 |
| 1430 @noindent | |
| 1431 An example of its expected output is | |
| 1432 | |
| 1433 @example | |
| 1434 @group | |
| 1435 mystring(["First String"; "Second String"]) | |
| 1436 @result{} s1 = Second String | |
| 1437 First String | |
| 1438 @end group | |
| 1439 @end example | |
| 1440 | |
| 7096 | 1441 Other functions in the mex interface for handling character strings are |
| 1442 @code{mxCreateString}, @code{mxArrayToString}, and | |
| 1443 @code{mxCreateCharMatrixFromStrings}. In a mex-file, a character string | |
| 1444 is considered to be a vector rather than a matrix. This is perhaps an | |
| 1445 arbitrary distinction as the data in the mxArray for the matrix is | |
| 1446 consecutive in any case. | |
| 6580 | 1447 |
| 1448 @node Cell Arrays with Mex-Files | |
| 1449 @subsection Cell Arrays with Mex-Files | |
| 6569 | 1450 |
| 6593 | 1451 We can perform exactly the same operations in Cell arrays in mex-files |
| 1452 as we can in oct-files. An example that reduplicates the functional of | |
| 1453 the @file{celldemo.cc} oct-file in a mex-file is given by | |
| 1454 @file{mycell.c} as below | |
| 1455 | |
| 9906 | 1456 @example |
| 1457 @group | |
| 1458 @EXAMPLEFILE(mycell.c) | |
| 1459 @end group | |
| 1460 @end example | |
| 6593 | 1461 |
| 1462 @noindent | |
| 1463 which as can be seen below has exactly the same behavior as the oct-file | |
| 1464 version. | |
| 1465 | |
| 1466 @example | |
| 1467 @group | |
| 1468 [b1, b2, b3] = mycell (@{1, [1, 2], "test"@}) | |
| 1469 @result{} | |
| 1470 b1 = 1 | |
| 1471 b2 = | |
| 1472 | |
| 1473 1 2 | |
| 1474 | |
| 1475 b3 = test | |
| 1476 @end group | |
| 1477 @end example | |
| 1478 | |
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1479 Note in the example the use of the @code{mxDuplicateArray} function. This |
| 6593 | 1480 is needed as the @code{mxArray} pointer returned by @code{mxGetCell} |
| 1481 might be deallocated. The inverse function to @code{mxGetCell} is | |
| 1482 @code{mcSetCell} and is defined as | |
| 1483 | |
| 1484 @example | |
| 1485 void mxSetCell (mxArray *ptr, int idx, mxArray *val); | |
| 1486 @end example | |
| 1487 | |
| 7007 | 1488 Finally, to create a cell array or matrix, the appropriate functions are |
| 6593 | 1489 |
| 1490 @example | |
| 1491 @group | |
| 1492 mxArray *mxCreateCellArray (int ndims, const int *dims); | |
| 1493 mxArray *mxCreateCellMatrix (int m, int n); | |
| 1494 @end group | |
| 1495 @end example | |
| 6569 | 1496 |
| 6572 | 1497 @node Structures with Mex-Files |
| 1498 @subsection Structures with Mex-Files | |
| 6569 | 1499 |
| 6593 | 1500 The basic function to create a structure in a mex-file is |
| 1501 @code{mxCreateStructMatrix}, which creates a structure array with a two | |
| 1502 dimensional matrix, or @code{mxCreateStructArray}. | |
| 1503 | |
| 1504 @example | |
| 1505 @group | |
| 7081 | 1506 mxArray *mxCreateStructArray (int ndims, int *dims, |
| 1507 int num_keys, | |
| 6593 | 1508 const char **keys); |
| 7081 | 1509 mxArray *mxCreateStructMatrix (int rows, int cols, |
| 1510 int num_keys, | |
| 6593 | 1511 const char **keys); |
| 1512 @end group | |
| 1513 @end example | |
| 1514 | |
| 1515 Accessing the fields of the structure can then be performed with the | |
| 1516 @code{mxGetField} and @code{mxSetField} or alternatively with the | |
| 1517 @code{mxGetFieldByNumber} and @code{mxSetFieldByNumber} functions. | |
| 1518 | |
| 1519 @example | |
| 1520 @group | |
| 7081 | 1521 mxArray *mxGetField (const mxArray *ptr, mwIndex index, |
| 1522 const char *key); | |
| 6593 | 1523 mxArray *mxGetFieldByNumber (const mxArray *ptr, |
| 6686 | 1524 mwIndex index, int key_num); |
| 1525 void mxSetField (mxArray *ptr, mwIndex index, | |
| 6593 | 1526 const char *key, mxArray *val); |
| 6686 | 1527 void mxSetFieldByNumber (mxArray *ptr, mwIndex index, |
| 6593 | 1528 int key_num, mxArray *val); |
| 1529 @end group | |
| 1530 @end example | |
| 1531 | |
| 1532 A difference between the oct-file interface to structures and the | |
| 1533 mex-file version is that the functions to operate on structures in | |
| 1534 mex-files directly include an @code{index} over the elements of the | |
| 1535 arrays of elements per @code{field}. Whereas the oct-file structure | |
| 1536 includes a Cell Array per field of the structure. | |
| 1537 | |
| 1538 An example that demonstrates the use of structures in mex-file can be | |
| 1539 found in the file @file{mystruct.c}, as seen below | |
| 6580 | 1540 |
| 9906 | 1541 @example |
| 1542 @EXAMPLEFILE(mystruct.c) | |
| 1543 @end example | |
| 6580 | 1544 |
| 6593 | 1545 An example of the behavior of this function within Octave is then |
| 1546 | |
| 1547 @example | |
| 7081 | 1548 a(1).f1 = "f11"; a(1).f2 = "f12"; |
| 1549 a(2).f1 = "f21"; a(2).f2 = "f22"; | |
| 6593 | 1550 b = mystruct(a) |
| 1551 @result{} field f1(0) = f11 | |
| 1552 field f1(1) = f21 | |
| 1553 field f2(0) = f12 | |
| 1554 field f2(1) = f22 | |
| 1555 b = | |
| 1556 @{ | |
| 1557 this = | |
| 1558 | |
| 1559 (, | |
| 1560 [1] = this1 | |
| 1561 [2] = this2 | |
| 1562 [3] = this3 | |
| 1563 [4] = this4 | |
| 1564 ,) | |
| 1565 | |
| 1566 that = | |
| 1567 | |
| 1568 (, | |
| 1569 [1] = that1 | |
| 1570 [2] = that2 | |
| 1571 [3] = that3 | |
| 1572 [4] = that4 | |
| 1573 ,) | |
| 1574 | |
| 1575 @} | |
| 1576 @end example | |
| 6569 | 1577 |
| 1578 @node Sparse Matrices with Mex-Files | |
| 1579 @subsection Sparse Matrices with Mex-Files | |
| 1580 | |
| 6593 | 1581 The Octave format for sparse matrices is identical to the mex format in |
| 7001 | 1582 that it is a compressed column sparse format. Also in both, sparse |
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1583 matrices are required to be two-dimensional. The only difference is that |
| 6939 | 1584 the real and imaginary parts of the matrix are stored separately. |
| 6593 | 1585 |
| 1586 The mex-file interface, as well as using @code{mxGetM}, @code{mxGetN}, | |
| 1587 @code{mxSetM}, @code{mxSetN}, @code{mxGetPr}, @code{mxGetPi}, | |
| 1588 @code{mxSetPr} and @code{mxSetPi}, the mex-file interface supplies the | |
| 1589 functions | |
| 1590 | |
| 1591 @example | |
| 1592 @group | |
| 6686 | 1593 mwIndex *mxGetIr (const mxArray *ptr); |
| 1594 mwIndex *mxGetJc (const mxArray *ptr); | |
| 1595 mwSize mxGetNzmax (const mxArray *ptr); | |
| 6593 | 1596 |
| 6686 | 1597 void mxSetIr (mxArray *ptr, mwIndex *ir); |
| 1598 void mxSetJc (mxArray *ptr, mwIndex *jc); | |
| 1599 void mxSetNzmax (mxArray *ptr, mwSize nzmax); | |
| 6593 | 1600 @end group |
| 1601 @end example | |
| 6580 | 1602 |
| 6593 | 1603 @noindent |
| 1604 @code{mxGetNzmax} gets the maximum number of elements that can be stored | |
| 1605 in the sparse matrix. This is not necessarily the number of non-zero | |
| 1606 elements in the sparse matrix. @code{mxGetJc} returns an array with one | |
| 1607 additional value than the number of columns in the sparse matrix. The | |
| 1608 difference between consecutive values of the array returned by | |
| 1609 @code{mxGetJc} define the number of non-zero elements in each column of | |
| 1610 the sparse matrix. Therefore | |
| 6580 | 1611 |
| 6593 | 1612 @example |
| 1613 @group | |
| 6686 | 1614 mwSize nz, n; |
| 1615 mwIndex *Jc; | |
| 6593 | 1616 mxArray *m; |
| 1617 @dots{} | |
| 1618 n = mxGetN (m); | |
| 1619 Jc = mxGetJc (m); | |
| 1620 nz = Jc[n]; | |
| 1621 @end group | |
| 1622 @end example | |
| 1623 | |
| 1624 @noindent | |
| 1625 returns the actual number of non-zero elements stored in the matrix in | |
| 1626 @code{nz}. As the arrays returned by @code{mxGetPr} and @code{mxGetPi} | |
| 1627 only contain the non-zero values of the matrix, we also need a pointer | |
| 1628 to the rows of the non-zero elements, and this is given by | |
| 1629 @code{mxGetIr}. A complete example of the use of sparse matrices in | |
| 1630 mex-files is given by the file @file{mysparse.c} as seen below | |
| 1631 | |
| 9906 | 1632 @example |
| 1633 @EXAMPLEFILE(mysparse.c) | |
| 1634 @end example | |
| 6569 | 1635 |
| 6580 | 1636 @node Calling Other Functions in Mex-Files |
| 1637 @subsection Calling Other Functions in Mex-Files | |
| 1638 | |
| 1639 It is also possible call other Octave functions from within a mex-file | |
| 6593 | 1640 using @code{mexCallMATLAB}. An example of the use of |
| 6580 | 1641 @code{mexCallMATLAB} can be see in the example below |
| 1642 | |
| 9906 | 1643 @example |
| 1644 @EXAMPLEFILE(myfeval.c) | |
| 1645 @end example | |
| 6580 | 1646 |
| 1647 If this code is in the file @file{myfeval.c}, and is compiled to | |
| 1648 @file{myfeval.mex}, then an example of its use is | |
| 6569 | 1649 |
| 6580 | 1650 @example |
| 1651 @group | |
| 1652 myfeval("sin", 1) | |
| 1653 a = myfeval("sin", 1) | |
| 1654 @result{} Hello, World! | |
| 1655 I have 2 inputs and 1 outputs | |
| 1656 I'm going to call the interpreter function sin | |
| 1657 a = 0.84147 | |
| 1658 @end group | |
| 1659 @end example | |
| 1660 | |
| 1661 Note that it is not possible to use function handles or inline functions | |
| 1662 within a mex-file. | |
| 1663 | |
| 6593 | 1664 @c @node Application Programming Interface for Mex-Files |
| 1665 @c @subsection Application Programming Interface for Mex-Files | |
| 1666 @c | |
| 1667 @c WRITE ME, refer to mex.h and mexproto.h | |
| 6569 | 1668 |
| 1669 @node Standalone Programs | |
| 1670 @section Standalone Programs | |
| 1671 | |
| 1672 The libraries Octave itself uses, can be utilized in standalone | |
| 6571 | 1673 applications. These applications then have access, for example, to the |
| 6569 | 1674 array and matrix classes as well as to all the Octave algorithms. The |
| 1675 following C++ program, uses class Matrix from liboctave.a or | |
| 1676 liboctave.so. | |
| 1677 | |
| 9906 | 1678 @example |
| 1679 @group | |
| 1680 @EXAMPLEFILE(standalone.cc) | |
| 1681 @end group | |
| 1682 @end example | |
| 6569 | 1683 |
| 6580 | 1684 @noindent |
| 6569 | 1685 mkoctfile can then be used to build a standalone application with a |
| 1686 command like | |
| 1687 | |
| 1688 @example | |
| 1689 @group | |
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1690 $ mkoctfile --link-stand-alone standalone.cc -o standalone |
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1691 $ ./standalone |
| 6569 | 1692 Hello Octave world! |
| 1693 11 12 | |
| 1694 21 22 | |
| 1695 $ | |
| 1696 @end group | |
| 1697 @end example | |
| 1698 | |
| 1699 Note that the application @code{hello} will be dynamically linked | |
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1700 against the octave libraries and any octave support libraries. The above |
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1701 allows the Octave math libraries to be used by an application. It does |
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1702 not however allow the script files, oct-files or builtin functions of |
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1703 Octave to be used by the application. To do that the Octave interpreter |
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1704 needs to be initialized first. An example of how to do this can then be |
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1705 seen in the code |
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1706 |
| 9906 | 1707 @example |
| 1708 @group | |
| 1709 @EXAMPLEFILE(embedded.cc) | |
| 1710 @end group | |
| 1711 @end example | |
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1712 |
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1713 @noindent |
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1714 which is compiled and run as before as a standalone application with |
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1715 |
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1716 @example |
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1717 @group |
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1718 $ mkoctfile --link-stand-alone embedded.cc -o embedded |
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1719 $ ./embedded |
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1720 GCD of [10, 15] is 5 |
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1721 $ |
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1722 @end group |
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1723 @end example |
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1724 |