// doc/tutorial_code.dox

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/**
 \page tutorial_code Reading and modifying the code (1/2 hour)

  \ref tutorial "Up: Kaldi tutorial" <BR>
  \ref tutorial_running "Previous: Running the example scripts" <BR>


 While the triphone system build is running, we will take a little while to
 glance at some parts of the code.  The main thing you will get out of this
 section of the tutorial is some idea of how the code is organized and what the
 dependency structure is; and some experience with modifying and debugging the
 code.  If you want to understand it code in more depth, we advise you to follow the links
 on the \ref index "main documentation page", where we have more detailed documentation
 organized by topic.

 \section tutorial_code_utils Common utilities


 Go to the top-level directory (we called it kaldi-1) and then into
 src/.
 First look at the file base/kaldi-common.h (don't follow the links within
 this document; view it from the shell or from an editor).  This \#includes a number of
 things from the base/ directory that are used by almost every Kaldi program.  You
 can mostly guess from the filenames the types of things that are provided: things
 like error-logging macros, typedefs, math utility functions such as random number
 generation, and miscellaneous \#defines.  But this is a stripped-down set of
 utilities; in util/common-utils.h there is a more complete set, including
 command-line parsing and I/O functions that handle extended filenames such as
 pipes.  Take a few seconds to glance over util/common-utils.h and see what it
 \#includes.  The reason why
 we segregated a subset of utilities into the base/ directory is so that we could
 minimize the dependencies of the matrix/ directory (which is useful in
 itself);
 the matrix/ directory only depends on the base/ directory.  Look at matrix/Makefile
 and search for base/ to see how this is specified.  Looking at this type of rule
 in the Makefiles can give you some insight into the structure of the toolkit.


 \section tutorial_code_matrix Matrix library (and modifying and debugging code)

 Now look at the file matrix/matrix-lib.h.  See what files it includes.  This provides
 an overview of the kinds of things that are in the matrix library.  This library
 is basically a C++ wrapper for BLAS and LAPACK, if that means anything to you (if not,
 don't worry).  The files sp-matrix.h and tp-matrix.h relate to symmetric packed matrices and
 triangular packed matrices, respectively.  Quickly scan the file matrix/kaldi-matrix.h.
 This will give you some idea what the matrix code looks like.  It consists of
 a C++ class representing a matrix.  We provide a mini-tutorial on the matrix
 library \ref matrix "here", if you are interested.  You might notice what seems like
 a strange comment style in the code, with comments started by three slashes (///).
 These types of commends, and block comments that begin with \verbatim /**\endverbatim, are interpreted by the
 Doxygen software that automatically generates documentation.  It also generates the
 page you are reading right now (the source for this type of documentation
 is in src/doc/).

 At this point we would like you to modify the code and compile it.  We will be
 adding a test function to the file matrix/matrix-lib-test.cc.  As mentioned
 before, the test programs are designed to abort or exit with nonzero status if
 something is wrong.

 We will be adding a test routine for the function Vector::AddVec.  This function
 adds some constant times one vector, to another vector.  Read through the code
 below
 and try to understand as much of it as you can (be careful: we have deliberately
 inserted two errors into the code).  If you are not familiar with templates,
 understanding it may be difficult.  We have tried to avoid the use of templates as much as possible,
 so large parts of Kaldi are still understandable without knowing template progamming.
\verbatim
template<class Real>
void UnitTestAddVec() {
  // note: Real will be float or double when instantiated.
  int32 dim = 1 + Rand() % 10;
  Vector<Real> v(dim); w(dim); // two vectors the same size.
  v.SetRandn();
  w.SetRandn();
  Vector<Real> w2(w); // w2 is a copy of w.
  Real f = RandGauss();
  w.AddVec(f, v); // w <-- w + f v
  for (int32 i = 0; i < dim; i++) {
    Real a = w(i), b = f * w2(i) + v(i);
    AssertEqual(a, b); // will crash if not equal to within
    // a tolerance.
  }
}
\endverbatim
Add this code to the file matrix-lib-test.cc, just above the function
MatrixUnitTest().  Then, inside MatrixUnitTest(), add the line:
\verbatim
  UnitTestAddVec<Real>();
\endverbatim
It doesn't matter where in the function you add this.
Then type "make test".  There should be an error (a semicolon that should be
a comma); fix it and try again.
Now type "./matrix-lib-test".  This should crash with an assertion failure,
because there was another mistake in the unit-test code.  Next we will debug it.
Type
\verbatim
 gdb ./matrix-lib-test
\endverbatim
(if you are on cygwin, you should now type into the gdb prompt, "break __assert_func").
Type "r".  When it crashes, it calls abort(), which gets caught by the debugger.
Type "bt" to see the stack trace.  Nagivate up the stack by typing "up" until you are inside the
test function.  When you are at the right place you should see output like:
\verbatim
#5  0x080943cf in kaldi::UnitTestAddVec<float> () at matrix-lib-test.cc:2568
2568	    AssertEqual(a, b); // will crash if not equal to within
\endverbatim
If you go too far you can type "down".  Then type "p a" and "p b" to see the
values of a and b ("p" is short for "print").  Your screen should look someting like this:
\verbatim
(gdb) p a
$5 = -0.931363404
(gdb) p b
$6 = -0.270584524
(gdb)
\endverbatim
The exact values are, of course, random, and may be different for you.  Since
the numbers are considerably different, it's clear that it's not just a question
of the tolerances being wrong.  In general you can access any kind of expression
from the debugger using the "print" expression, but the parenthesis operator
(expressions like "v(i)") doesn't work, so to see the values inside the vectors
you have to enter expressions like the following:
\verbatim
(gdb) p v.data_[0]
$8 = 0.281656802
(gdb) p w.data_[0]
$9 = -0.931363404
(gdb) p w2.data_[0]
$10 = -1.07592916
(gdb)
\endverbatim
This may help you work out that the expression for "b" is wrong.  Fix it in the code, recompile, and run
again (you can just type "r" in the gdb prompt to rerun).  It should now run OK.  Force gdb to break into the
code at the point where it was previously failing, so you can check the values of the expressions again
and see that things are now working OK.  To get the debugger to break there you have to set a
breakpoint.  Work out the line number that the assertion was failing (somewhere in UnitTestAddVec()),
and type into gdb something like the following:
\verbatim
(gdb) b matrix-lib-test.cc:2568
Breakpoint 1 at 0x80943b4: file matrix-lib-test.cc, line 2568. (4 locations)
\endverbatim
Then run the program (type "r"), and when it breaks there, look at the values of the expressions
using "p" commands.  To continue, type "c".  It will keep stopping there since it was inside
a loop.  Type "d 1" to delete the breakpoint (assuming it was breakpoint number one),
and type "c" to continue.  The program should run to the end.  Type "q" to quit the debugger.
If you need to debug a program that takes command-line arguments, you can do it like:
\verbatim
 gdb --args kaldi-program arg1 arg2 ...
 (gdb) r
 ...
\endverbatim
or you can invoke gdb without arguments and then type "r arg1 arg2..." at the prompt.

When you are done, and it compiles, type
\verbatim
 git diff
\endverbatim
to see what changes you made.  If you are contributing to the Kaldi project and
planning to send us code in the near future, you
may want to commit them to a branch as described in the \tutorial_git, so that you
can generate a clean <a href="https://help.github.com/articles/using-pull-requests/">
GitHub pull request</a> later. We recommend that you familiarize
yourself with Git branches even if you are not contributing your changes
outright; Git is a powerful tool to maintain your local code changes as well as
those you may contribute.

\section tutorial_code_acoustic Acoustic modeling code

Next look at gmm/diag-gmm.h (this class stores a Gaussian Mixture Model).
The class DiagGmm may look a bit confusing as
it has many different accessor functions.  Search for "private" and look
at the class member variables (they always end with an underscore, as per
the Kaldi style).  This should make it clear how we store the GMM.
This is just a single GMM, not a whole collection of GMMs.
Look at gmm/am-diag-gmm.h; this class stores a collection of GMMs.
Notice that it does not inherit from anything.
Search for "private" and you can see the member variables (there
are only two of them).  You can understand from this how simple the
class is (everything else consists of various accessors and convenience
functions).  A natural question to ask is: where are the transitions,
where is the decision tree, and where is the HMM topology?  All of these
things are kept separate from the acoustic model, because it's likely
that researchers might want to replace the acoustic likelihoods while
keeping the rest of the system the same.  We'll come to this other stuff later.

\section tutorial_code_feat Feature extraction code

Next look at feat/feature-mfcc.h.  Focus on the MfccOptions struct.
The struct members give you some idea what kind of options are supported
in MFCC feature extraction.
Notice that some struct members are options structs themselves.
Look at the Register function.  This is standard in Kaldi options classes.
Then look at featbin/compute-mfcc-feats.cc (this is a command-line
program) and search for Register.
You can see where the Register function of the options struct is called.
To see a complete list of the options supported for MFCC feature extraction,
execute the program featbin/compute-mfcc-feats with no arguments.
Recall that you saw some of these options being registered in
the MfccOptions class, and others being registered in
featbin/compute-mfcc-feats.cc.  The way to specify options is --option=value.
Type
\verbatim
featbin/compute-mfcc-feats ark:/dev/null ark:/dev/null
\endverbatim
This should run successfuly, as it interprets /dev/null as an empty archive.
You can try setting the options using this example.  Try, for example,
\verbatim
featbin/compute-mfcc-feats --raw-energy=false ark:/dev/null ark:/dev/null
\endverbatim
The only useful information you get from this is that it doesn't crash; try
removing the "=" sign or abbreviating the option name or changing the
number of arguments, and see that it fails and prints a usage message.

\section tutorial_code_tree Acoustic decision-tree and HMM topology code

Next look at tree/build-tree.h.  Find the BuildTree function.  This is the main
top-level function for building the decision tree.  Notice that it returns a
pointer the type EventMap.  This is a type that stores a function from a set of
(key, value) pairs to an integer.  It's defined in tree/event-map.h.  The keys
and values are both integers, but the keys represent phonetic-context positions
(typically 0, 1 or 2) and the values represent phones.  There is also a special
key, -1, that roughly represents the position in the HMM.  Go to the experimental
directory (../egs/rm/s5), and we are going to look at how the tree is built.
The main input to the BuildTree function is of type BuildTreeStatsType,
which is a typedef as follows:
\verbatim
typedef vector<pair<EventType, Clusterable*> > BuildTreeStatsType;
\endverbatim
Here, EvenType is the following typedef:
\verbatim
typedef vector<pair<EventKeyType, EventValueType> > EventType;
\endverbatim
The EventType represents a set of (key,value) pairs, e.g. a typical one
would be { {-1, 1}, {0, 15}, {1, 21}, {2, 38} } which represents phone
21 with a left-context of phone 15, a right-context of phone 38, and
"pdf-class" 1 (which in the normal case means it's in state number 1, which
is the middle of three states).  The Clusterable* pointer is a pointer to
a virtual class which has a generic interface that supports operations like
adding statistics together and evaluating some kind of objective function
(e.g. a likelihood).  In the normal recipe, it actually points to a class
that contains sufficient statistics for estimating a diagonal Gaussian p.d.f..

Do
\verbatim
less exp/tri1/log/acc_tree.log
\endverbatim
There won't be much information in this file, but you can see the command
line.  This program accumulates the single-Gaussian statistics for each HMM-state
(actually, pdf-class) of each seen triphone context.
The <DFN>--ci-phones</DFN> options is so that it knows to avoid accumulating separate
statistics for distinct context of phones like silence that we don't want to be
context dependent (this is an optimization; it would work without this option).
The output of this program can be thought of as being of the type BuildTreeStatsType
discussed above, although in order to read it we have to know what concrete type it is.

Do
\verbatim
less exp/tri1/log/train_tree.log
\endverbatim
This program does the decision-tree clustering; it reads in the statistics
that were output by.  It is basically a wrapper for the BuildTree function discussed above.
The questions that it asks in the decision-tree clustering are automatically generated,
as you can see in the script steps/train_tri1.sh (look for the programs cluster-phones
and compile-questions).





Next look at hmm/hmm-topology.h.  The class HmmTopology defines a set of HMM
topologies for a number of phones.  In general each phone can have a different
topology.  The topology includes "default" transitions, used for initialization.
Look at the example topology in the extended comment at the top of the header.
There is a tag <PdfClass> (note: as with HTK text formats,
this file looks vaguely XML-like, but it is not really XML).
The <PdfClass> is always the same as the HMM-state (<State>) here; in
general, it doesn't have to be.  This is a mechanism to enforce tying of
distributions between distinct HMM states; it's possibly useful if you want to
5~create more interesting transition models.

  \ref tutorial "Up: Kaldi tutorial" <BR>
  \ref tutorial_running "Previous: Running the example scripts" <BR>
<P>
*/