1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332
|
# mlpack automatic bindings to other languages
mlpack has a system to automatically generate bindings to other languages, such
as Python and command-line programs, and it is extensible to other languages
with some amount of ease. The maintenance burden of this system is low, and it
is designed in such a way that the bindings produced are always up to date
across languages and up to date with the mlpack library itself.
This document describes the full functioning of the system, and is a good place
to start for someone who wishes to understand the system so that they can
contribute a new binding language, or someone who wants to understand so they
can adapt the system for use in their own project, or someone who is simply
curious enough to see how the sausage is made.
The document is split into several sections:
- [Introduction](#introduction)
- [Writing code that can be turned into a binding](#writing-code-that-can-be-turned-into-a-binding)
- [How to write mlpack bindings](#how-to-write-mlpack-bindings)
- [Structure of IO module and associated macros](#structure-of-io-module-and-associated-macros)
- [Command-line program bindings](#command-line-program-bindings)
- [Python bindings](#python-bindings)
- [Adding new binding types](#adding-new-binding-types)
## Introduction
C++ is not the most popular language on the planet, and it (unfortunately) can
scare many away with its ultra-verbose error messages, confusing template rules,
and complex metaprogramming techniques. Most practitioners of machine learning
tend to avoid writing native C++ and instead prefer other languages---probably
most notably Python.
In the case of Python, many projects will use tools like
[SWIG](https://www.swig.org) to automatically generate bindings, or they might
hand-write Cython. The same types of strategies may be used for other
languages; hand-written MEX files may be used for MATLAB, hand-written Rcpp
bindings might be used for R bindings, and so forth.
However, these approaches have a fundamental flaw: the hand-written bindings
must be maintained, and risk going out of date as the rest of the library
changes or new functionality is added. This incurs a maintenance burden: each
major change to the library means that someone must update the bindings and test
that they are still working. mlpack is not prepared to handle this maintenance
workload; therefore an alternate solution is needed.
At the time of the design of this system, mlpack shipped headers for a C++
library as well as many (~40) hand-written command-line programs that used the
`mlpack::IO` object to manage command-line arguments. These programs all had
similar structure, and could be logically split into three sections:
- parse the input options supplied by the user
- run the machine learning algorithm
- prepare the output to return to the user
The user might interface with this command-line program like the following:
```sh
$ mlpack_knn -r reference.csv -q query.csv -k 3 -d d.csv -n n.csv
```
That is, they would pass a number of input options---some were numeric values
(like `-k 3`); some were filenames (like `-r reference.csv`); and a few other
types also. Therefore, the first stage of the program---parsing input
options---would be handled by reading the command line and loading any input
matrices. Preparing the output, which usually consists of data matrices (i.e.
`-d d.csv`) involves saving the matrix returned by the algorithm to the user's
desired file.
Ideally, any binding to any language would have this same structure, and the
actual "run the machine learning algorithm" code could be identical. For
MATLAB, for instance, we would not need to read the file `reference.csv` but
instead the user would simply pass their data matrix as an argument. So each
input and output parameter would need to be handled differently, but the
algorithm could be run identically across all bindings.
Therefore, design of an automatically-generated binding system would simply
involve generating the boilerplate code necessary to parse input options for a
given language, and to return output options to a user.
## Writing code that can be turned into a binding
This section details what a binding file might actually look like. It is good
to have this API in mind when reading the following sections.
Each mlpack binding is typically contained in the `src/mlpack/methods/` folder
corresponding to a given machine learning algorithm, with the suffix
`_main.cpp`; so an example is `src/mlpack/methods/pca/pca_main.cpp`.
These files have roughly two parts:
- definition of the input and output parameters with `PARAM` macros and
documentation with `BINDING` macros
- implementation of `BINDING_FUNCTION()`, which is the actual machine learning
code
Here is a simple example file:
```c++
// This is a stripped version of mean_shift_main.cpp.
#include <mlpack/core.hpp>
// Define the name of the binding (as seen by the binding generation system).
#undef BINDING_NAME
#define BINDING_NAME mean_shift
#include <mlpack/core/util/mlpack_main.hpp>
#include <mlpack/core/kernels/gaussian_kernel.hpp>
#include "mean_shift.hpp"
using namespace mlpack;
using namespace mlpack::meanshift;
using namespace mlpack::kernel;
using namespace std;
// Define the help text for the program. The PRINT_PARAM_STRING() and
// PRINT_DATASET() macros are used to print the name of the parameter as seen in
// the binding type that is being used, and the PRINT_CALL() macro generates a
// sample invocation of the program in the language of the binding type that is
// being used. Note that the macros must have + on either side of them. We
// provide some extra references with the "SEE_ALSO()" macro, which is used to
// generate documentation for the website.
// Program Name.
BINDING_USER_NAME("Mean Shift Clustering");
// Short description.
BINDING_SHORT_DESC(
"A fast implementation of mean-shift clustering using dual-tree range "
"search. Given a dataset, this uses the mean shift algorithm to produce "
"and return a clustering of the data.");
// Long description.
BINDING_LONG_DESC(
"This program performs mean shift clustering on the given dataset, storing "
"the learned cluster assignments either as a column of labels in the input "
"dataset or separately."
"\n\n"
"The input dataset should be specified with the " +
PRINT_PARAM_STRING("input") + " parameter, and the radius used for search"
" can be specified with the " + PRINT_PARAM_STRING("radius") + " "
"parameter. The maximum number of iterations before algorithm termination "
"is controlled with the " + PRINT_PARAM_STRING("max_iterations") + " "
"parameter."
"\n\n"
"The output labels may be saved with the " + PRINT_PARAM_STRING("output") +
" output parameter and the centroids of each cluster may be saved with the"
" " + PRINT_PARAM_STRING("centroid") + " output parameter.");
// Example.
BINDING_EXAMPLE(
"For example, to run mean shift clustering on the dataset " +
PRINT_DATASET("data") + " and store the centroids to " +
PRINT_DATASET("centroids") + ", the following command may be used: "
"\n\n" +
PRINT_CALL("mean_shift", "input", "data", "centroid", "centroids"));
// See also...
BINDING_SEE_ALSO("@kmeans", "#kmeans");
BINDING_SEE_ALSO("@dbscan", "#dbscan");
BINDING_SEE_ALSO("Mean shift on Wikipedia",
"https://en.wikipedia.org/wiki/Mean_shift");
BINDING_SEE_ALSO("Mean Shift, Mode Seeking, and Clustering (pdf)",
"http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.510.1222"
"&rep=rep1&type=pdf");
BINDING_SEE_ALSO("mlpack::mean_shift::MeanShift C++ class documentation",
"@src/mlpack/methods/mean_shift/mean_shift.hpp");
// Define parameters for the executable.
// Required option: the user must give us a matrix.
PARAM_MATRIX_IN_REQ("input", "Input dataset to perform clustering on.", "i");
// Output options: the user can save the output matrix of labels and/or the
// centroids.
PARAM_UCOL_OUT("output", "Matrix to write output labels to.", "o");
PARAM_MATRIX_OUT("centroid", "If specified, the centroids of each cluster will "
"be written to the given matrix.", "C");
// Mean shift configuration options.
PARAM_INT_IN("max_iterations", "Maximum number of iterations before mean shift "
"terminates.", "m", 1000);
PARAM_DOUBLE_IN("radius", "If the distance between two centroids is less than "
"the given radius, one will be removed. A radius of 0 or less means an "
"estimate will be calculated and used for the radius.", "r", 0);
void BINDING_FUNCTION(util::Params& params, util::Timers& timers)
{
// Process the parameters that the user passed.
const double radius = params.Get<double>("radius");
const int maxIterations = params.Get<int>("max_iterations");
if (maxIterations < 0)
{
Log::Fatal << "Invalid value for maximum iterations (" << maxIterations <<
")! Must be greater than or equal to 0." << endl;
}
// Warn, if the user did not specify that they wanted any output.
if (!params.Has("output") && !params.Has("centroid"))
{
Log::Warn << "--output_file, --in_place, and --centroid_file are not set; "
<< "no results will be saved." << endl;
}
arma::mat dataset = std::move(params.Get<arma::mat>("input"));
arma::mat centroids;
arma::Col<size_t> assignments;
// Prepare and run the actual algorithm.
MeanShift<> meanShift(radius, maxIterations);
timers.Start("clustering");
Log::Info << "Performing mean shift clustering..." << endl;
meanShift.Cluster(dataset, assignments, centroids);
timers.Stop("clustering");
Log::Info << "Found " << centroids.n_cols << " centroids." << endl;
if (radius <= 0.0)
Log::Info << "Estimated radius was " << meanShift.Radius() << ".\n";
// Should we give the user the output matrix?
if (params.Has("output"))
params.Get<arma::Col<size_t>>("output") = std::move(assignments);
// Should we give the user the centroid matrix?
if (params.Has("centroid"))
params.Get<arma::mat>("centroid") = std::move(centroids);
}
```
We can see that we have defined the name of the binding with the `BINDING_NAME`
macro, and basic program information in the `BINDING_USER_NAME()`,
`BINDING_SHORT_DESC()`, `BINDING_LONG_DESC()`, `BINDING_EXAMPLE()` and
`BINDING_SEE_ALSO()` macros. This is, for instance, what is displayed to
describe the binding if the user passed the `--help` option for a command-line
program.
Then, we define five parameters, three input and two output, that define the
data and options that the mean shift clustering will function on. These
parameters are defined with the `PARAM` macros, of which there are many. The
names of these macros specify the type, whether the parameter is required, and
whether the parameter is input or output. Some examples:
- `PARAM_STRING_IN()` -- a string-type input parameter
- `PARAM_MATRIX_OUT()` -- a matrix-type output parameter
- `PARAM_DOUBLE_IN_REQ()` -- a required double-type input parameter
- `PARAM_UMATRIX_IN()` -- an unsigned matrix-type input parameter
- `PARAM_MODEL_IN()` -- a serializable model-type input parameter
Note that each of these macros may have slightly different syntax. See the
links above for further documentation.
In order to write a new binding, then, you simply must define `BINDING_NAME`,
then write `BINDING_USER_NAME()`, `BINDING_SHORT_DESC()`, `BINDING_LONG_DESC()`,
`BINDING_EXAMPLE()` and `BINDING_SEE_ALSO()` definitions of the program with
some documentation, define the input and output parameters as `PARAM` macros, and
then write a `BINDING_FUNCTION()` function that actually performs the
functionality of the binding.
Inside of `BINDING_FUNCTION(util::Params& params, util::Timers& timers)`:
- All input parameters are accessible through `params.Get<type>("name")`.
- All output parameters should be set by the end of the function with the
`params.Get<type>("name")` method.
- The `params.Has("name")` function will return `true` if the parameter
`"name"` was specified.
- Timers can be started and stopped with `timers.Start("timer_name")` and
`timers.Stop("timer_name")`.
Then, assuming that your program is saved in the file `program_name_main.cpp`,
generating bindings for other languages is a simple addition to the
`CMakeLists.txt` file in `src/mlpack/methods/CMakeLists.txt`:
```
add_all_bindings(program_dir program_name "category")
```
In this example, this will also add a Markdown binding, which will generate
documentation that is typically used to build the website. The `category`
parameter should be one of the categories in
`src/mlpack/bindings/Categories.cmake`.
## How to write mlpack bindings
This section describes the general structure of the automatic binding system and
how one might write a new binding for mlpack. After reading this section it
should be relatively clear how one could use the provided functionality in the
`Params` and `Timers` class along with CMake to add a binding for a new mlpack
machine learning method. If it is not clear, then the examples in the following
sections should clarify.
### Providing a name with `BINDING_NAME`
Every binding must have the macro `BINDING_NAME` defined, specifying a name
(without spaces, generally all lowercase) that will be used to represent the
binding. It is suggested to `#undef` any previous setting of `BINDING_NAME`
just to prevent any strange error messages in case it is already defined.
Here is an example that can be adapted:
```c++
#undef BINDING_NAME
#define BINDING_NAME my_binding_name
// BINDING_NAME should be defined before including mlpack_main.hpp!
#include <mlpack/core/util/mlpack_main.hpp>
```
If this macro is not defined, compilation of the binding will fail in many ways
with potentially obscure error messages! (Sorry that they are bad error
messages. The preprocessor doesn't give us too much to work with.)
### Documenting a program with macros
Any mlpack binding should be documented with the `BINDING_USER_NAME()`,
`BINDING_SHORT_DESC()`, `BINDING_LONG_DESC()`, `BINDING_EXAMPLE()` and
`BINDING_SEE_ALSO()` macros, which is available from the
`<mlpack/core/util/mlpack_main.hpp>` header. The macros are of the form
```c++
BINDING_USER_NAME("program name");
BINDING_SHORT_DESC("This is a short, two-sentence description of what the program does.");
BINDING_LONG_DESC("This is a long description of what the program does."
" It might be many lines long and have lots of details about different options.");
BINDING_EXAMPLE("This contains one example for this particular binding.\n" +
PROGRAM_CALL(...));
BINDING_EXAMPLE("This contains another example for this particular binding.\n" +
PROGRAM_CALL(...));
// There could be many of these "see alsos".
BINDING_SEE_ALSO("https://en.wikipedia.org/wiki/Machine_learning");
```
The short documentation should be two sentences indicating what the program
implements and does, and a quick overview of how it can be used and what it
should be used for. When writing new short documentation, it is a good idea to
take a look at the existing documentation to get an idea of the general format.
For the "see also" section, you can specify as many `SEE_ALSO()` calls as you
see fit. These are links used at the "see also" section of the website
documentation for each binding, and it's very important that relevant links are
provided (also to other bindings). See the `SEE_ALSO()` documentation for more
details.
Although it is possible to provide very short documentation, it is certainly
better to provide a long description including
- what the program does
- a basic overview of what input and output parameters the program has
- at least one example invocation
Examples are very important, and are probably what most users are going to
immediately search for, instead of taking a long time to read and carefully
consider all of the written documentation.
However, it is difficult to write language-agnostic documentation. For
instance, in a command-line program, an output parameter `--output_file` would
be specified on the command line as an input parameter, but in Python, the
output parameter 'output' would actually simply be returned from the call to the
Python function. Therefore, we must be careful how our documentation refers to
input and output parameters. The following general guidelines can help:
- Always refer to output parameters as "output parameters", which is a fairly
close term that can be interpreted to mean both "return values" for languages
like Python and MATLAB and also "arguments given on the command line" for
command line programs.
- Use the provided `PRINT_PARAM_STRING()` macro to print the names of
parameters. For instance, `PRINT_PARAM_STRING("shuffle")` will print
`--shuffle` for a command line program and `'shuffle'` for a Python
binding. The `PRINT_PARAM_STRING()` macro also takes into account the type
of the parameter.
- Use the provided `PRINT_DATASET()` and `PRINT_MODEL()` macro to introduce
example datasets or models, which can be useful when introducing an example
usage of the program. So you could write `"to run with a dataset " +
PRINT_DATASET("data") + "..."`.
- Use the provided `PRINT_CALL()` macro to print example invocations of the
program. The first argument is the name of the program, and then the
following arguments should be the name of a parameter followed by the value
of that parameter.
- Never mention files in the documentation---files are only relevant to
command-line programs. Similarly, avoid mentioning anything
language-specific.
- Remember that some languages give output through return values and some give
output using other input parameters. So the right verbiage to use is, e.g.,
`the results may be saved using the PRINT_PARAM_STRING("output") parameter`,
and ***not*** `the results are returned through the
PRINT_PARAM_STRING("output") parameter`.
Each of these macros (`PRINT_PARAM_STRING()`, `PRINT_DATASET()`,
`PRINT_MODEL()`, and `PRINT_CALL()`) provides different output depending on the
language. Below are some example of documentation strings and their outputs for
different languages. Note that the output might not be *exactly* as written or
formatted here, but the general gist should be the same.
*Input C++ (snippet):*
```c++
"The parameter " + PRINT_PARAM_STRING("shuffle") + ", if set, will shuffle "
"the data before learning."
```
*Command-line program output (snippet):*
```
The parameter '--shuffle', if set, will shuffle the data before learning.
```
*Python binding output (snippet):*
```
The parameter 'shuffle', if set, will shuffle the data before learning.
```
*Julia binding output (snippet):*
```
The parameter `shuffle`, if set, will shuffle the data before learning.
```
*Go binding output (snippet):*
```
The parameter "Shuffle", if set, will shuffle the data before learning.
```
Another example:
*Input C++ (snippet):*
```c++
"The output matrix can be saved with the " + PRINT_PARAM_STRING("output") +
" output parameter."
```
*Command-line program output (snippet):*
```
The output matrix can be saved with the '--output_file' output parameter.
```
*Python binding output (snippet):*
```
The output matrix can be saved with the 'output' output parameter.
```
*Julia binding output (snippet):*
```
The output matrix can be saved with the `output` output parameter.
```
*Go binding output (snippet):*
```
The output matrix can be saved with the "output" output parameter.
```
And another example:
*Input C++ (snippet):*
```c++
"For example, to train a model on the dataset " + PRINT_DATASET("x") + " and "
"save the output model to " + PRINT_MODEL("model") + ", the following command"
" can be used:"
"\n\n" +
PRINT_CALL("program", "input", "x", "output_model", "model")
```
*Command-line program output (snippet):*
```
For example, to train a model on the dataset 'x.csv' and save the output model
to 'model.bin', the following command can be used:
$ program --input_file x.csv --output_model_file model.bin
```
*Python binding output (snippet):*
```
For example, to train a model on the dataset 'x' and save the output model to
'model', the following command can be used:
>>> output = program(input=x)
>>> model = output['output_model']
```
*Julia binding output (snippet):*
```
For example, to train a model on the dataset `x` and save the output model to
`model`, the following command can be used:
julia> model = program(input=x)
```
*Go binding output (snippet):*
```
For example, to train a model on the dataset "x" and save the output model to
"model", the following command can be used:
// Initialize optional parameters for Program().
param := mlpack.ProgramOptions()
param.Input = x
model := mlpack.Program(param)
```
And finally, a full program example:
*Input C++ (full program, `random_numbers_main.cpp`):*
```c++
// Program Name.
BINDING_USER_NAME("Random Numbers");
// Short description.
BINDING_SHORT_DESC("An implementation of Random Numbers");
// Long description.
BINDING_LONG_DESC(
"This program generates random numbers with a "
"variety of nonsensical techniques and example parameters. The input "
"dataset, which will be ignored, can be specified with the " +
PRINT_PARAM_STRING("input") + " parameter. If you would like to subtract"
" values from each number, specify the " +
PRINT_PARAM_STRING("subtract") + " parameter. The number of random "
"numbers to generate is specified with the " +
PRINT_PARAM_STRING("num_values") + " parameter."
"\n\n"
"The output random numbers can be saved with the " +
PRINT_PARAM_STRING("output") + " output parameter. In addition, a "
"randomly generated linear regression model can be saved with the " +
PRINT_PARAM_STRING("output_model") + " output parameter.");
// Example.
BINDING_EXAMPLE(
"For example, to generate 100 random numbers with 3 subtracted from them "
"and save the output to " + PRINT_DATASET("rand") + " and the random "
"model to " + PRINT_MODEL("rand_lr") + ", use the following "
"command:"
"\n\n" +
PRINT_CALL("random_numbers", "num_values", 100, "subtract", 3, "output",
"rand", "output_model", "rand_lr"));
```
*Command line output*:
```
Random Numbers
This program generates random numbers with a variety of nonsensical
techniques and example parameters. The input dataset, which will be
ignored, can be specified with the '--input_file' parameter. If you would
like to subtract values from each number, specify the '--subtract'
parameter. The number of random numbers to generate is specified with the
'--num_values' parameter.
The output random numbers can be saved with the '--output_file' output
parameter. In addition, a randomly generated linear regression model can be
saved with the '--output_model_file' output parameter.
For example, to generate 100 random numbers with 3 subtracted from them and
save the output to 'rand.csv' and the random model to 'rand_lr.bin', use the
following command:
$ random_numbers --num_values 100 --subtract 3 --output_file rand.csv
--output_model_file rand_lr.bin
```
*Python binding output*:
```
Random Numbers
This program generates random numbers with a variety of nonsensical
techniques and example parameters. The input dataset, which will be
ignored, can be specified with the 'input' parameter. If you would like to
subtract values from each number, specify the 'subtract' parameter. The
number of random numbers to generate is specified with the 'num_values'
parameter.
The output random numbers can be saved with the 'output' output parameter.
In addition, a randomly generated linear regression model can be saved with
the 'output_model' output parameter.
For example, to generate 100 random numbers with 3 subtracted from them and
save the output to 'rand' and the random model to 'rand_lr', use the
following command:
>>> output = random_numbers(num_values=100, subtract=3)
>>> rand = output['output']
>>> rand_lr = output['output_model']
```
*Julia binding output:*
```
Random Numbers
This program generates random numbers with a variety of nonsensical
techniques and example parameters. The input dataset, which will be
ignored, can be specified with the `input` parameter. If you would like to
subtract values from each number, specify the `subtract` parameter. The
number of random numbers to generate is specified with the `num_values`
parameter.
The output random numbers can be saved with the `output` output parameter.
In addition, a randomly generated linear regression model can be saved with
the `output_model` output parameter.
For example, to generate 100 random numbers with 3 subtracted from them and
save the output to `rand` and the random model to `rand_lr`, use the
following command:
```julia
julia> rand, rand_lr = random_numbers(num_values=100, subtract=3)
```
```
*Go binding output:*
```
Random Numbers
This program generates random numbers with a variety of nonsensical
techniques and example parameters. The input dataset, which will be
ignored, can be specified with the "Input" parameter. If you would like to
subtract values from each number, specify the "Subtract" parameter. The
number of random numbers to generate is specified with the "NumValues"
parameter.
The output random numbers can be saved with the "output" output parameter.
In addition, a randomly generated linear regression model can be saved with
the "outputModel" output parameter.
For example, to generate 100 random numbers with 3 subtracted from them and
save the output to "rand" and the random model to "randLr", use the
following command:
// Initialize optional parameters for RandomNumbers().
param := mlpack.RandomNumbersOptions()
param.NumValues = 100
param.Subtract=3
rand, randLr := mlpack.RandomNumbers(param)
```
### Defining parameters for a program
There exist several macros that can be used after a `BINDING_LONG_DESC()` and
`BINDING_EXAMPLE()` definition to define the parameters that can be specified
for a given mlpack program. These macros all have the same general definition:
the name of the macro specifies the type of the parameter, whether or not the
parameter is required, and whether the parameter is an input or output
parameter. Then as arguments to the macros, the name, description, and
sometimes the single-character alias and the default value of the parameter.
To give a flavor of how these definitions look, the definition
```c++
PARAM_STRING_IN("algorithm", "The algorithm to use: 'svd' or 'blah'.", "a");
```
will define a string input parameter `algorithm` (referenced as `--algorithm`
from the command-line or `'algorithm'` from Python) with the description `The
algorithm to use: 'svd' or 'blah'.` The single-character alias `-a` can be used
from a command-line program (but means nothing in Python).
There are numerous different macros that can be used:
- `PARAM_FLAG()` - boolean flag parameter
- `PARAM_INT_IN()` - integer input parameter
- `PARAM_INT_OUT()` - integer output parameter
- `PARAM_DOUBLE_IN()` - double input parameter
- `PARAM_DOUBLE_OUT()` - double output parameter
- `PARAM_STRING_IN()` - string input parameter
- `PARAM_STRING_OUT()` - string output parameter
- `PARAM_MATRIX_IN()` - double-valued matrix (`arma::mat`) input parameter
- `PARAM_MATRIX_OUT()` - double-valued matrix (`arma::mat`) output parameter
- `PARAM_UMATRIX_IN()` - size_t-valued matrix (`arma::Mat<size_t>`) input
parameter
- `PARAM_UMATRIX_OUT()` - size_t-valued matrix (`arma::Mat<size_t>`) output
parameter
- `PARAM_TMATRIX_IN()` - transposed double-valued matrix (`arma::mat`) input
parameter
- `PARAM_TMATRIX_OUT()` - transposed double-valued matrix (`arma::mat`) output
parameter
- `PARAM_MATRIX_AND_INFO_IN()` - matrix with categoricals input parameter
(`std::tuple<data::DatasetInfo, arma::mat>`)
- `PARAM_COL_IN()` - double-valued column vector (`arma::vec`) input parameter
- `PARAM_COL_OUT()` - double-valued column vector (`arma::vec`) output
parameter
- `PARAM_UCOL_IN()` - size_t-valued column vector (`arma::Col<size_t>`) input
parameter
- `PARAM_UCOL_OUT()` - size_t-valued column vector (`arma::Col<size_t>`) output
parameter
- `PARAM_ROW_IN()` - double-valued row vector (`arma::rowvec`) input parameter
- `PARAM_ROW_OUT()` - double-valued row vector (`arma::rowvec`) output
parameter
- `PARAM_VECTOR_IN()` - `std::vector` input parameter
- `PARAM_VECTOR_OUT()` - `std::vector` output parameter
- `PARAM_MODEL_IN()` - serializable model input parameter
- `PARAM_MODEL_OUT()` - serializable model output parameter
And for input parameters, the parameter may also be required:
- `PARAM_INT_IN_REQ()`
- `PARAM_DOUBLE_IN_REQ()`
- `PARAM_STRING_IN_REQ()`
- `PARAM_MATRIX_IN_REQ()`
- `PARAM_UMATRIX_IN_REQ()`
- `PARAM_TMATRIX_IN_REQ()`
- `PARAM_VECTOR_IN_REQ()`
- `PARAM_MODEL_IN_REQ()`
See the source documentation for each macro to read further details. Note also
that each possible combination of `IN`, `OUT`, and `REQ` is not
available---output options cannot be required, and some combinations simply have
not been added because they have not been needed.
The `PARAM_MODEL_IN()` and `PARAM_MODEL_OUT()` macros are used to serialize
mlpack models. These could be used, for instance, to allow the user to save a
trained model (like a linear regression model) or load an input model. The
first parameter to the `PARAM_MODEL_IN()` or `PARAM_MODEL_OUT()` macro should be
the C++ type of the model to be serialized; this type *must* have a function
`template<typename Archive> void serialize(Archive&)` (i.e. the type must be
serializable via cereal). For example, to allow a user to specify an input
model of type `LinearRegression`, the follow definition could be used:
```c++
PARAM_MODEL_IN(LinearRegression, "input_model", "The input model to be used.",
"i");
```
Then, the user will be able to specify their model from the command-line as
`--input_model_file` and from Python using the `input_model` option to the
generated binding.
From the command line, matrix-type and model-type options (both input and
output) are loaded from or saved to the specified file. This means that `_file`
is appended to the name of the parameter; so if the parameter name is `data` and
it is of a matrix or model type, then the name that the user will specify on the
command line will be `--data_file`. This displayed parameter name change *only*
occurs with matrix and model type parameters for command-line programs.
The `PARAM_MATRIX_AND_INFO()` macro defines a categorical matrix parameter
(more specifically, a matrix type that can support categorical columns). From
the C++ program side, this means that the parameter type is
`std::tuple<data::DatasetInfo, arma::mat>`. From the user side, for a
command-line program, this means that the user will pass the filename of a
dataset that can have categorical features, such as an ARFF dataset. For a
Python program, the user may pass a Pandas matrix with categorical columns.
When the program is run, the input that the user gives will be processed and the
`data::DatasetInfo` object will be filled with the dimension types and the
`arma::mat` object will be filled with the data itself.
To give some examples, the parameter definitions from the example
`random_numbers` program in the previous section are shown below.
```c++
PARAM_MATRIX_IN("input", "The input matrix that will be ignored.", "i");
PARAM_DOUBLE_IN("subtract", "The value to subtract from each parameter.", "s",
0.0); // Default value of 0.0.
PARAM_INT_IN("num_samples", "The number of samples to generate.", "n", 100);
PARAM_MATRIX_OUT("output", "The output matrix of random samples.", "o");
PARAM_MODEL_OUT(LinearRegression, "output_model", "The randomly generated "
"linear regression output model.", "M");
```
Note that even the parameter documentation strings must be a little agnostic
to the binding type, because the command-line interface is so different from the
Python interface to the user.
### Using `Params` in a `BINDING_FUNCTION()` function
mlpack's `util::Params` class provides a unified abstract interface for getting
input from and providing output to users without needing to consider the
language (command-line, Python, MATLAB, etc.) that the user is running the
program from. This means that after the `BINDING_LONG_DESC()` and
`BINDING_EXAMPLE()` macros and the `PARAM_*()` macros have been defined, a
language-agnostic `void BINDING_FUNCTION(util::Params& params, util::Timers&
timers)` function can be written. This function then can perform the actual
computation that the entire program is meant to.
Inside of a `BINDING_FUNCTION()` function, the given `util::Params` object can
be used to access input parameters and set output parameters. There are two
main functions for this, plus a utility printing function:
- `params.Get<T>()` - get a reference to a parameter
- `params.Has()` - returns true if the user specified the parameter
- `params.GetPrintable<T>()` - returns a string representing the value of the
parameter
So, to print `hello` if the user specified the `print_hello` parameter, the
following code could be used:
```c++
if (params.Has("print_hello"))
std::cout << "Hello!" << std::endl;
else
std::cout << "No greetings for you!" << std::endl;
```
To access a string that a user passed in to the `string` parameter, the
following code could be used:
```c++
const std::string& str = params.Get<std::string>("string");
```
Matrix types are accessed in the same way:
```c++
arma::mat& matrix = params.Get<arma::mat>("matrix");
```
Similarly, model types can be accessed. If a `LinearRegression` model was
specified by the user as the parameter `model`, the following code can access
the model:
```c++
LinearRegression& lr = params.Get<LinearRegression>("model");
```
Matrices with categoricals are a little trickier to access since the C++
parameter type is `std::tuple<data::DatasetInfo, arma::mat>`. The example below
creates references to both the `DatasetInfo` and matrix objects, assuming the
user has passed a matrix with categoricals as the `matrix` parameter.
```c++
using namespace mlpack;
typename std::tuple<data::DatasetInfo, arma::mat> TupleType;
data::DatasetInfo& di = std::get<0>(params.Get<TupleType>("matrix"));
arma::mat& matrix = std::get<1>(params.Get<TupleType>("matrix"));
```
These two functions can be used to write an entire program. The third function,
`params.GetPrintable()`, can be used to help provide useful output in a
program. Typically, this function should be used if you want to provide some
kind of error message about a matrix or model parameter, but want to avoid
printing the matrix itself. For instance, printing a matrix parameter with
`params.GetPrintable()` will print the filename for a command-line binding or
the size of a matrix for a Python binding. `params.GetPrintable()` for a model
parameter will print the filename for the model for a command-line binding or a
simple string representing the type of the model for a Python binding.
Putting all of these ideas together, here is the `BINDING_FUNCTION()` function
that could be created for the `random_numbers` program from earlier sections.
```c++
// BINDING_NAME should be defined here: ...
#include <mlpack/core/util/mlpack_main.hpp>
// BINDING_USER_NAME(), BINDING_SHORT_DESC(), BINDING_LONG_DESC() ,
// BINDING_EXAMPLE(), BINDING_SEE_ALSO() and PARAM_*() definitions should go
// here: ...
using namespace mlpack;
void BINDING_FUNCTION(util::Params& params, util::Timers& timers)
{
// If the user passed an input matrix, tell them that we'll be ignoring it.
if (params.Has("input"))
{
// Print the filename the user passed, if a command-line binding, or the
// size of the matrix passed, if a Python binding.
Log::Warn << "The input matrix "
<< params.GetPrintable<arma::mat>("input") << " is ignored!"
<< std::endl;
}
// Get the number of samples and also the value we should subtract.
const size_t numSamples = (size_t) params.Get<int>("num_samples");
const double subtractValue = params.Get<double>("subtract");
// Create the random matrix (1-dimensional).
arma::mat output(1, numSamples, arma::fill::randu);
output -= subtractValue;
// Save the output matrix if the user wants.
if (params.Has("output"))
params.Get<arma::mat>("output") = std::move(output); // Avoid copy.
// Did the user request a random linear regression model?
if (params.Has("output_model"))
{
LinearRegression lr;
lr.Parameters().randu(10); // 10-dimensional (arbitrary).
lr.Lambda() = 0.0;
lr.Intercept() = false; // No intercept term.
params.Get<LinearRegression>("output_model") = std::move(lr);
}
}
```
### More documentation on using `util::Params`
More documentation for the `util::Params` class can either be found in the
source code for `util::Params`, or by reading the existing mlpack bindings.
These can be found in the `src/mlpack/methods/` folders, by finding the
`_main.cpp` files. For instance,
`src/mlpack/methods/neighbor_search/knn_main.cpp` is the k-nearest-neighbor
search program definition.
## Structure of IO module and associated macros
This section describes the internal functionality of the `IO` module, which
stores all known parameter sets, and the associated macros. If you are only
interested in writing mlpack programs, this section is probably not worth
reading.
There are eight main components involved with mlpack bindings:
- the `IO` module, a thread-safe singleton class that stores parameter
information
- the `BINDING_FUNCTION()` function that defines the functionality of the
binding
- the `BINDING_NAME()` macro that defines the binding name
- the `BINDING_SHORT_DESC()` macro that defines the short description
- the `BINDING_LONG_DESC()` macro that defines the long description
- (optional) the `BINDING_EXAMPLE()` macro that defines example usages
- (optional) the `BINDING_SEE_ALSO()` macro that defines "see also" links
- the `PARAM_*()` macros that define parameters for the binding
The `mlpack::IO` module is a singleton class that stores, at runtime, the
binding name, the documentation, and the parameter information and values for
any bindings available in the translation unit. When the binding is called, the
`mlpack::IO` class instantiates a `util::Params` and `util::Timers` object,
populating them with the correct options for the given binding, then calls
`BINDING_FUNCTION()` with those instantiated objects.
In order to do this, each parameter and the program documentation must make
themselves known to the IO singleton. This is accomplished by having the
`BINDING_USER_NAME()`, `BINDING_SHORT_DESC()`, `BINDING_LONG_DESC()`,
`BINDING_EXAMPLE()`, `BINDING_SEE_ALSO()` and `PARAM_*()` macros declare global
variables that, in their constructors, register themselves with the `IO`
singleton.
* The `BINDING_USER_NAME()` macro declares an object of type
`mlpack::util::BindingName`.
* The `BINDING_SHORT_DESC()` macro declares an object of type
`mlpack::util::ShortDescription`.
* The `BINDING_LONG_DESC()` macro declares an object of type
`mlpack::util::LongDescription`.
* The `BINDING_EXAMPLE()` macro declares an object of type
`mlpack::util::Example`.
* The `BINDING_SEE_ALSO()` macro declares an object of type
`mlpack::util::SeeAlso`.
* The `BindingName` class constructor calls `IO::AddBindingName()` in order
to register the given program name.
* The `ShortDescription` class constructor calls `IO::AddShortDescription()`
in order to register the given short description.
* The `LongDescription` class constructor calls `IO::AddLongDescription()` in
order to register the given long description.
* The `Example` class constructor calls `IO::AddExample()` in order to
register the given example.
* The `SeeAlso` class constructor calls `IO::AddSeeAlso()` in order to
register the given see-also link.
All of those macro calls use whatever the value of the `BINDING_NAME` macro is
at the time of instantiation. This is why it is important that `BINDING_NAME`
is set properly at the time `mlpack_main.hpp` is included and before any
options are defined.
The `PARAM_*()` macros declare an object that will, in its constructor, call
`IO::Add()` to register that parameter for the current binding (again specified
by the `BINDING_NAME` macro's value) with the IO singleton. The specific type
of that object will depend on the binding type being used.
The `IO::AddParameter()` function takes the name of the binding it is for and an
`mlpack::util::ParamData` object as its input. This `ParamData` object has a
number of fields that must be set to properly describe the parameter. Each of
the fields is documented and probably self-explanatory, but three fields deserve
further explanation:
- the `std::string tname` member is used to encode the true type of the
parameter---which is not known by the `IO` singleton at runtime. This should
be set to `TYPENAME(T)` where `T` is the type of the parameter.
- the `ANY value` member (where `ANY` is whatever type was chosen in case
`std::any` is not available) is used to hold the actual value of the
parameter. Typically this will simply be the parameter held by a `ANY`
object, but for some types it may be more complex. For instance, for a
command-line matrix option, the `value` parameter will actually hold a tuple
containing both the filename and the matrix itself.
- the `std::string cppType` should be a string containing the type as seen in
C++ code. Typically this can be encoded by stringifying a `PARAM_*()` macro
argument.
Thus, the global object defined by the `PARAM_*()` macro must turn its arguments
into a fully specified `ParamData` object and then call `IO::Add()` with it.
With different binding types, different behavior is often required for the
`params.Get<T>()`, `params.Has()`, and `params.GetPrintable<T>()` functions. In
order to handle this, the `IO` singleton also holds a function pointer map, so
that a given type of option can call specific functionality for a certain task.
Given a `util::Params` object (which can be obtained with
`IO::Parameters("binding_name")`), this function map is accessible as
`params.functionMap`, and is not meant to be used by users, but instead by
people writing binding types.
Each function in the map must have signature
```c++
void MapFunction(const util::ParamData& d,
const void* input,
void* output);
```
The use of `void` pointers allows any type to be specified as input or output to
the function without changing the signature for the map. The `IO` function map
is of type
```c++
std::map<std::string, std::map<std::string,
void (*)(const util::ParamData&, const void*, void*)>>
```
and the first map key is the typename (`tname`) of the parameter, and the second
map key is the string name of the function. For instance, calling
```c++
const util::ParamData& d = params.Parameters()["param"];
params.functionMap[d.tname]["GetParam"](d, input, output);
```
will call the `GetParam()` function for the type of the `"param"` parameter.
Examples are probably easiest to understand how this functionality works; see
the `params.Get<T>()` source to see how this might be used.
The `IO` singleton expects the following functions to be defined in the function
map for each type:
- `GetParam` -- return a pointer to the parameter in `output`.
- `GetPrintableParam` -- return a pointer to a string description of the
parameter in `output`.
If these functions are properly defined, then the `IO` module will work
correctly. Other functions may also be defined; these may be used by other
parts of the binding infrastructure for different languages.
## Command-line program bindings
This section describes the internal functionality of the command-line program
binding generator. If you are only interested in writing mlpack programs, this
section probably is not worth reading. This section is worth reading only if
you want to know the specifics of how the `BINDING_FUNCTION()` function and
macros get turned into a fully working command-line program.
The code for the command-line bindings is found in `src/mlpack/bindings/cli`.
### The `BINDING_FUNCTION()` definition
Any command-line program must be compiled with the `BINDING_TYPE` macro
set to the value `BINDING_TYPE_CLI`. This is handled by the CMake macro
`add_cli_executable()`.
When `BINDING_TYPE` is set to `BINDING_TYPE_CLI`, the following is set in
`src/mlpack/core/util/mlpack_main.hpp`, which must be included by every mlpack
binding:
- The options defined by `PARAM_*()` macros are of type
`mlpack::bindings::cli::CLIOption`.
- The parameter and value printing macros for `BINDING_LONG_DESC()`
and `BINDING_EXAMPLE()` are set:
* The `PRINT_PARAM_STRING()` macro is defined as
`mlpack::bindings::cli::ParamString()`.
* The `PRINT_DATASET()` macro is defined as
`mlpack::bindings::cli::PrintDataset()`.
* The `PRINT_MODEL()` macro is defined as
`mlpack::bindings::cli::PrintModel()`.
* The `PRINT_CALL()` macro is defined as
`mlpack::bindings::cli::ProgramCall()`.
- The function `int main()` is defined as:
```c++
int main(int argc, char** argv)
{
// Parse the command-line options; put them into CLI.
mlpack::util::Params params =
mlpack::bindings::cli::ParseCommandLine(argc, argv);
// Create a new timer object for this call.
mlpack::util::Timers timers;
timers.Enabled() = true;
mlpack::Timer::EnableTiming();
// A "total_time" timer is run by default for each mlpack program.
timers.Start("total_time");
BINDING_FUNCTION(params, timers);
timers.Stop("total_time");
// Print output options, print verbose information, save model parameters,
// clean up, and so forth.
mlpack::bindings::cli::EndProgram(params, timers);
}
```
Thus any mlpack command-line binding first processes the command-line arguments
with `mlpack::bindings::cli::ParseCommandLine()`, then runs the binding with
`BINDING_FUNCTION()`, then cleans up with `mlpack::bindings::cli::EndProgram()`.
The `ParseCommandLine()` function reads the input parameters and sets the
values in `IO`. For matrix-type and model-type parameters, this reads the
filenames from the command-line, but does not load the matrix or model. Instead
the matrix or model is loaded the first time it is accessed with
`params.Get<T>()`.
The `--help` parameter is handled by the `mlpack::bindings::cli::PrintHelp()`
function.
At the end of program execution, the `mlpack::bindings::cli::EndProgram()`
function is called. This writes any output matrix or model parameters to disk,
and prints the program parameters and timers if `--verbose` was given.
### Matrix and model parameter handling
For command line bindings, the matrix, model, and matrix with categorical type
parameters all require special handling, since it is not possible to pass a
matrix of any reasonable size or a model on the command line directly.
Therefore for a matrix or model parameter, the user specifies the file
containing that matrix or model parameter. If the parameter is an input
parameter, then the file is loaded when `params.Get<T>()` is called. If the
parameter is an output parameter, then the matrix or model is saved to the file
when `EndProgram()` is called.
The actual implementation of this is that the `ANY value` member of the
`ParamData` struct does not hold the model or the matrix, but instead a
`std::tuple` containing both the matrix or the model, and the filename
associated with that matrix or model.
This means that functions like `params.Get<T>()` and `params.GetPrintable<T>()`
(and all of the other associated functions in the function map) must have
special handling for matrix or model types. See those implementations for more
details---the special handling is enforced via SFINAE.
### Parsing the command line
The `ParseCommandLine()` function uses `CLI11` to read the values from the
command line into the `ParamData` structs held by the `IO` singleton.
In order to set up `CLI11`---and to keep its headers from needing to be included
by the rest of the library---the code loops over each parameter known by the
`IO` singleton and calls the `AddToPO` function from the function map. This in
turn calls the necessary functions to register a given parameter with `CLI11`,
and once all parameters have been registered, the facilities provided by `CLI11`
are used to parse the command line input properly.
## Python bindings
This section describes the internal functionality of the mlpack Python binding
generator. If you are only interested in writing new bindings or building the
bindings, this section is probably not worth reading. But if you are interested
in the internal working of the Python binding generator, then this section is
for you.
The Python bindings are significantly more complex than the command line
bindings because we cannot just compile directly to a finished product. Instead
we need a multi-stage compilation:
- We must generate a `setup.py` file that can be used to compile the bindings.
- We must generate the `.pyx` (Cython) bindings for each program.
- Then we must build each `.pyx` into a `.so` that is loadable from Python.
- We must also test the Python bindings.
This is done with a combination of C++ code to generate the `.pyx` bindings,
CMake to run the actual compilation and generate the `setup.py` file, some
utility Python functions, and tests written in both Python and C++. This code
is primarily contained in `src/mlpack/bindings/python/`.
### Passing matrices to/from Python
The standard Python matrix library is numpy, so mlpack bindings should accept
numpy matrices as input. Fortunately, numpy Cython bindings already exist,
which make it easy to convert from a numpy object to an Armadillo object without
copying any data. This code can be found in
`src/mlpack/bindings/python/mlpack/arma_numpy.pyx`, and is used by the Python
`params.Get<T>()` functionality.
mlpack also supports categorical matrices; in Python, the typical way of
representing matrices with categorical features is with Pandas. Therefore,
mlpack also accepts Pandas matrices, and if any of the Pandas matrix dimensions
are categorical, these are properly encoded. The function
`to_matrix_with_info()` from `mlpack/bindings/python/mlpack/matrix_utils.py` is
used to perform this conversion.
### Passing model parameters to/from Python
We use (or abuse) Cython functionality in order to give the user a model object
that they can use in their Python code. However, we do not want to (or have the
infrastructure to) write bindings for every method that a serializable model
class might support; therefore, we only desire to return a memory pointer to the
model to the user.
In this way, a user that receives a model from an output parameter can then
reuse the model as an input parameter to another binding (or the same binding).
To return a function pointer we have to define a Cython class in the following
way (this example is taken from the perceptron binding):
```py
cdef extern from "</home/ryan/src/mlpack-rc/src/mlpack/methods/perceptron/perceptron_main.cpp>" nogil:
cdef int mlpack_perceptron(Params, Timers) nogil except +RuntimeError
cdef cppclass PerceptronModel:
PerceptronModel() nogil
cdef class PerceptronModelType:
cdef PerceptronModel* modelptr
def __cinit__(self):
self.modelptr = new PerceptronModel()
def __dealloc__(self):
del self.modelptr
```
This class definition is automatically generated when the `.pyx` file is
automatically generated.
### CMake generation of `setup.py`
A boilerplate `setup.py` file can be found in
`src/mlpack/bindings/python/setup.py.in`. This will be configured by CMake to
produce the final `setup.py` file, but in order to do this, a list of the `.pyx`
files to be compiled must be gathered.
Therefore, the `add_python_binding()` macro is defined in
`src/mlpack/bindings/python/CMakeLists.txt`. This adds the given binding to the
`MLPACK_PYXS` variable, which is then inserted into `setup.py` as part of the
`configure_file()` step in `src/mlpack/CMakeLists.txt`.
### Generation of `.pyx` files
A binding named `program` is built into a program called
`generate_pyx_program` (this a CMake target, so you can build these
individually if you like). The file
`src/mlpack/bindings/python/generate_pyx.cpp.in` is configured by CMake to set
the name of the program and the `*_main.cpp` file to include correctly, then
the `mlpack::bindings::python::PrintPYX()` function is called by the program.
The `PrintPYX()` function uses the parameters that have been set in the `IO`
singleton by the `BINDING_USER_NAME()`, `BINDING_SHORT_DESC()`,
`BINDING_LONG_DESC()`, `BINDING_EXAMPLE()`, `BINDING_SEE_ALSO()` and `PARAM_*()`
macros in order to actually print a fully-working `.pyx` file that can be
compiled. The file has several sections:
- Python imports (numpy/pandas/cython/etc.)
- Cython imports of C++ utility functions and Armadillo functionality
- Cython imports of any necessary serializable model types
- Definitions of classes for serializable model types
- The binding function definition
- Documentation: input and output parameters
- The call to `BINDING_FUNCTION()`
- Handling of output functionality
- Return of output parameters
Any output parameters for Python bindings are returned in a dict containing
named elements.
### Building the `.pyx` files
After building the `generate_pyx_program` target, the `build_pyx_program` target
is built as a dependency of the `python` target. This simply takes the
generated `.pyx` file and uses Python setuptools to compile this to a Python
binding.
### Testing the Python bindings
In addition to the C++ tests we have implemented for each binding, we also have
tests from Python that ensure that we can successfully transfer parameter values
from Python to C++ and return output correctly.
The tests are in `src/mlpack/bindings/python/tests/` and test both the actual
bindings and also the auxiliary Python code included in
`src/mlpack/bindings/python/mlpack/`.
## Adding new binding types
Adding a new binding type to mlpack is fairly straightforward once the general
structure of the `IO` singleton and the function map that `IO` uses is
understood. For each different language that bindings are desired for, the
route to a solution will be particularly different---so it is hard to provide
any general guidance for how to make new bindings that will be applicable to
each language.
In general, the first thing to handle will be how matrices are passed back and
forth between the target language. Typically this might mean getting the memory
address of an input matrix and wrapping an `arma::mat` object around that memory
address. This can be handled in the `GetParam()` function that is part of the
`IO` singleton function map; see `get_param.hpp` for both the `IO` and Python
bindings for an example (in `src/mlpack/bindings/cli/` and
`src/mlpack/bindings/python/`).
Serialization of models is also a tricky consideration; in some languages you
will be able to pass a pointer to the model itself. This is generally
best---users should not expect to be able to manipulate the model in the target
language, but they should expect that they can pass a model back and forth
without paying a runtime penalty. So, for example, serializing a model using a
cereal text archive and then returning the string that represents the model
is not acceptable, because that string can be extremely large and the time it
takes to decode the model can be very large.
The strategy of generating a binding definition for the target language, like
what is done with Python, can be a useful strategy that should be considered.
If this is the route that is desired, a large amount of CMake boilerplate may be
necessary. The Python CMake configuration can be referred to as an example, but
probably a large amount of adaptation to other languages will be necessary.
Lastly, when adding a new language, make sure it works with the
Markdown documentation generator. In order to make this happen, you will need
to modify all of the `add_markdown_docs()` calls in
`src/mlpack/methods/CMakeLists.txt` to contain the name of the language you have
written a binding for. You will also need to modify every function in
`src/mlpack/bindings/markdown/print_doc_functions_impl.hpp` to correctly call
out to the corresponding function for the language that you have written
bindings for.
|