PP(1) User Contributed Perl Documentation PP(1)NAMEPDL::PP - Generate PDL routines from concise descriptions
SYNOPSIS
e.g.
pp_def(
'sumover',
Pars => 'a(n); [o]b();',
Code => q{
double tmp=0;
loop(n) %{
tmp += $a();
%}
$b() = tmp;
},
);
pp_done();
FUNCTIONS
Here is a quick reference list of the functions provided by PDL::PP.
pp_add_boot
Add code to the BOOT section of generated XS file
pp_add_exported
Add functions to the list of exported functions
pp_add_isa
Add entries to the @ISA list
pp_addbegin
Sets code to be added at the top of the generate .pm file
pp_addhdr
Add code and includes to C section of the generated XS file
pp_addpm
Add code to the generated .pm file
pp_addxs
Add extra XS code to the generated XS file
pp_beginwrap
Add BEGIN-block wrapping to code for the generated .pm file
pp_bless
Sets the package to which the XS code is added (default is PDL)
pp_boundscheck
Control state of PDL bounds checking activity
pp_core_importList
Specify what is imported from PDL::Core
pp_def
Define a new PDL function
pp_deprecate_module
Add runtime and POD warnings about a module being deprecated
pp_done
Mark the end of PDL::PP definitions in the file
pp_export_nothing
Clear out the export list for your generated module
pp_line_numbers
Add line number information to simplify debugging of PDL::PP code
pp_setversion
Set the version for .pm and .xs files
OVERVIEW
Why do we need PP? Several reasons: firstly, we want to be able to
generate subroutine code for each of the PDL datatypes (PDL_Byte,
PDL_Short,. etc). AUTOMATICALLY. Secondly, when referring to slices
of PDL arrays in Perl (e.g. "$a->slice('0:10:2,:')" or other things
such as transposes) it is nice to be able to do this transparently and
to be able to do this 'in-place' - i.e, not to have to make a memory
copy of the section. PP handles all the necessary element and offset
arithmetic for you. There are also the notions of threading (repeated
calling of the same routine for multiple slices, see PDL::Indexing) and
dataflow (see PDL::Dataflow) which use of PP allows.
In much of what follows we will assume familiarity of the reader with
the concepts of implicit and explicit threading and index manipulations
within PDL. If you have not yet heard of these concepts or are not very
comfortable with them it is time to check PDL::Indexing.
As you may appreciate from its name PDL::PP is a Pre-Processor, i.e.
it expands code via substitutions to make real C-code. Technically, the
output is XS code (see perlxs) but that is very close to C.
So how do you use PP? Well for the most part you just write ordinary C
code except for special PP constructs which take the form:
$something(something else)
or:
PPfunction %{
<stuff>
%}
The most important PP construct is the form "$array()". Consider the
very simple PP function to sum the elements of a 1D vector (in fact
this is very similar to the actual code used by 'sumover'):
pp_def('sumit',
Pars => 'a(n); [o]b();',
Code => q{
double tmp;
tmp = 0;
loop(n) %{
tmp += $a();
%}
$b() = tmp;
}
);
What's going on? The "Pars =>" line is very important for PP - it
specifies all the arguments and their dimensionality. We call this the
signature of the PP function (compare also the explanations in
PDL::Indexing). In this case the routine takes a 1-D function as input
and returns a 0-D scalar as output. The "$a()" PP construct is used to
access elements of the array a(n) for you - PP fills in all the
required C code.
You will notice that we are using the "q{}" single-quote operator. This
is not an accident. You generally want to use single quotes to denote
your PP Code sections. PDL::PP uses "$var()" for its parsing and if you
don't use single quotes, Perl will try to interpolate "$var()". Also,
using the single quote "q" operator with curly braces makes it look
like you are creating a code block, which is What You Mean. (Perl is
smart enough to look for nested curly braces and not close the quote
until it finds the matching curly brace, so it's safe to have nested
blocks.) Under other circumstances, such as when you're stitching
together a Code block using string concatenations, it's often easiest
to use real single quotes as
Code => 'something'.$interpolatable.'somethingelse;'
In the simple case here where all elements are accessed the PP
construct "loop(n) %{ ... %}" is used to loop over all elements in
dimension "n". Note this feature of PP: ALL DIMENSIONS ARE SPECIFIED
BY NAME.
This is made clearer if we avoid the PP loop() construct and write the
loop explicitly using conventional C:
pp_def('sumit',
Pars => 'a(n); [o]b();',
Code => q{
int i,n_size;
double tmp;
n_size = $SIZE(n);
tmp = 0;
for(i=0; i<n_size; i++) {
tmp += $a(n=>i);
}
$b() = tmp;
},
);
which does the same as before, but is more long-winded. You can see to
get element "i" of a() we say "$a(n=>i)" - we are specifying the
dimension by name "n". In 2D we might say:
Pars=>'a(m,n);',
...
tmp += $a(m=>i,n=>j);
...
The syntax "m=>i" borrows from Perl hashes, which are in fact used in
the implementation of PP. One could also say "$a(n=>j,m=>i)" as order
is not important.
You can also see in the above example the use of another PP construct -
$SIZE(n) to get the length of the dimension "n".
It should, however, be noted that you shouldn't write an explicit
C-loop when you could have used the PP "loop" construct since PDL::PP
checks automatically the loop limits for you, usage of "loop" makes the
code more concise, etc. But there are certainly situations where you
need explicit control of the loop and now you know how to do it ;).
To revisit 'Why PP?' - the above code for sumit() will be generated for
each data-type. It will operate on slices of arrays 'in-place'. It will
thread automatically - e.g. if a 2D array is given it will be called
repeatedly for each 1D row (again check PDL::Indexing for the details
of threading). And then b() will be a 1D array of sums of each row.
We could call it with $a->xchg(0,1) to sum the columns instead. And
Dataflow tracing etc. will be available.
You can see PP saves the programmer from writing a lot of needlessly
repetitive C-code -- in our opinion this is one of the best features of
PDL making writing new C subroutines for PDL an amazingly concise
exercise. A second reason is the ability to make PP expand your concise
code definitions into different C code based on the needs of the
computer architecture in question. Imagine for example you are lucky to
have a supercomputer at your hands; in that case you want PDL::PP
certainly to generate code that takes advantage of the
vectorising/parallel computing features of your machine (this a project
for the future). In any case, the bottom line is that your unchanged
code should still expand to working XS code even if the internals of
PDL changed.
Also, because you are generating the code in an actual Perl script,
there are many fun things that you can do. Let's say that you need to
write both sumit (as above) and multit. With a little bit of
creativity, we can do
for({Name => 'sumit', Init => '0', Op => '+='},
{Name => 'multit', Init => '1', Op => '*='}) {
pp_def($_->{Name},
Pars => 'a(n); [o]b();',
Code => '
double tmp;
tmp = '.$_->{Init}.';
loop(n) %{
tmp '.$_->{Op}.' $a();
%}
$b() = tmp;
');
}
which defines both the functions easily. Now, if you later need to
change the signature or dimensionality or whatever, you only need to
change one place in your code. Yeah, sure, your editor does have 'cut
and paste' and 'search and replace' but it's still less bothersome and
definitely more difficult to forget just one place and have strange
bugs creep in. Also, adding 'orit' (bitwise or) later is a one-liner.
And remember, you really have Perl's full abilities with you - you can
very easily read any input file and make routines from the information
in that file. For simple cases like the above, the author (Tjl)
currently favors the hash syntax like the above - it's not too much
more characters than the corresponding array syntax but much easier to
understand and change.
We should mention here also the ability to get the pointer to the
beginning of the data in memory - a prerequisite for interfacing PDL to
some libraries. This is handled with the "$P(var)" directive, see
below.
When starting work on a new pp_def'ined function, if you make a
mistake, you will usually find a pile of compiler errors indicating
line numbers in the generated XS file. If you know how to read XS files
(or if you want to learn the hard way), you could open the generated XS
file and search for the line number with the error. However, a recent
addition to PDL::PP helps report the correct line number of your
errors: "pp_line_numbers". Working with the original summit example, if
you had a mis-spelling of tmp in your code, you could change the
(erroneos) code to something like this and the compiler would give you
much more useful information:
pp_def('sumit',
Pars => 'a(n); [o]b();',
Code => pp_line_numbers(__LINE__, q{
double tmp;
tmp = 0;
loop(n) %{
tmp += $a();
%}
$b() = rmp;
})
);
For the above situation, my compiler tells me:
...
test.pd:15: error: XrmpX undeclared (first use in this function)
...
In my example script (called test.pd), line 15 is exactly the line at
which I made my typo: "rmp" instead of "tmp".
So, after this quick overview of the general flavour of programming PDL
routines using PDL::PP let's summarise in which circumstances you
should actually use this preprocessor/precompiler. You should use
PDL::PP if you want to
· interface PDL to some external library
· write some algorithm that would be slow if coded in Perl (this is
not as often as you think; take a look at threading and dataflow
first).
· be a PDL developer (and even then it's not obligatory)
WARNING
Because of its architecture, PDL::PP can be both flexible and easy to
use on the one hand, yet exuberantly complicated at the same time.
Currently, part of the problem is that error messages are not very
informative and if something goes wrong, you'd better know what you are
doing and be able to hack your way through the internals (or be able to
figure out by trial and error what is wrong with your args to
"pp_def"). Although work is being done to produce better warnings, do
not be afraid to send your questions to the mailing list if you run
into trouble.
DESCRIPTION
Now that you have some idea how to use "pp_def" to define new PDL
functions it is time to explain the general syntax of "pp_def".
"pp_def" takes as arguments first the name of the function you are
defining and then a hash list that can contain various keys.
Based on these keys PP generates XS code and a .pm file. The function
"pp_done" (see example in the SYNOPSIS) is used to tell PDL::PP that
there are no more definitions in this file and it is time to generate
the .xs and
.pm file.
As a consequence, there may be several pp_def() calls inside a file (by
convention files with PP code have the extension .pd or .pp) but
generally only one pp_done().
There are two main different types of usage of pp_def(), the 'data
operation' and 'slice operation' prototypes.
The 'data operation' is used to take some data, mangle it and output
some other data; this includes for example the '+' operation, matrix
inverse, sumover etc and all the examples we have talked about in this
document so far. Implicit and explicit threading and the creation of
the result are taken care of automatically in those operations. You can
even do dataflow with "sumit", "sumover", etc (don't be dismayed if you
don't understand the concept of dataflow in PDL very well yet; it is
still very much experimental).
The 'slice operation' is a different kind of operation: in a slice
operation, you are not changing any data, you are defining
correspondences between different elements of two piddles (examples
include the index manipulation/slicing function definitions in the file
slices.pd that is part of the PDL distribution; but beware, this is not
introductory level stuff).
If PDL was compiled with support for bad values (i.e. "WITH_BADVAL =>
1"), then additional keys are required for "pp_def", as explained
below.
If you are just interested in communicating with some external library
(for example some linear algebra/matrix library), you'll usually want
the 'data operation' so we are going to discuss that first.
Data operation
A simple example
In the data operation, you must know what dimensions of data you need.
First, an example with scalars:
pp_def('add',
Pars => 'a(); b(); [o]c();',
Code => '$c() = $a() + $b();'
);
That looks a little strange but let's dissect it. The first line is
easy: we're defining a routine with the name 'add'. The second line
simply declares our parameters and the parentheses mean that they are
scalars. We call the string that defines our parameters and their
dimensionality the signature of that function. For its relevance with
regard to threading and index manipulations check the PDL::Indexing man
page.
The third line is the actual operation. You need to use the dollar
signs and parentheses to refer to your parameters (this will probably
change at some point in the future, once a good syntax is found).
These lines are all that is necessary to actually define the function
for PDL (well, actually it isn't; you additionally need to write a
Makefile.PL (see below) and build the module (something like 'perl
Makefile.PL; make'); but let's ignore that for the moment). So now you
can do
use MyModule;
$a = pdl 2,3,4;
$b = pdl 5;
$c = add($a,$b);
# or
add($a,$b,($c=null)); # Alternative form, useful if $c has been
# preset to something big, not useful here.
and have threading work correctly (the result is $c == [7 8 9]).
The Pars section: the signature of a PP function
Seeing the above example code you will most probably ask: what is this
strange "$c=null" syntax in the second call to our new "add" function?
If you take another look at the definition of "add" you will notice
that the third argument "c" is flagged with the qualifier "[o]" which
tells PDL::PP that this is an output argument. So the above call to add
means 'create a new $c from scratch with correct dimensions' - "null"
is a special token for 'empty piddle' (you might ask why we haven't
used the value "undef" to flag this instead of the PDL specific "null";
we are currently thinking about it ;).
[This should be explained in some other section of the manual as
well!!] The reason for having this syntax as an alternative is that if
you have really huge piddles, you can do
$c = PDL->null;
for(some long loop) {
# munge a,b
add($a,$b,$c);
# munge c, put something back to a,b
}
and avoid allocating and deallocating $c each time. It is allocated
once at the first add() and thereafter the memory stays until $c is
destroyed.
If you just say
$c = add($a,$b);
the code generated by PP will automatically fill in "$c=null" and
return the result. If you want to learn more about the reasons why
PDL::PP supports this style where output arguments are given as last
arguments check the PDL::Indexing man page.
"[o]" is not the only qualifier a pdl argument can have in the
signature. Another important qualifier is the "[t]" option which flags
a pdl as temporary. What does that mean? You tell PDL::PP that this
pdl is only used for temporary results in the course of the calculation
and you are not interested in its value after the computation has been
completed. But why should PDL::PP want to know about this in the first
place? The reason is closely related to the concepts of pdl auto
creation (you heard about that above) and implicit threading. If you
use implicit threading the dimensionality of automatically created pdls
is actually larger than that specified in the signature. With "[o]"
flagged pdls will be created so that they have the additional
dimensions as required by the number of implicit thread dimensions.
When creating a temporary pdl, however, it will always only be made big
enough so that it can hold the result for one iteration in a thread
loop, i.e. as large as required by the signature. So less memory is
wasted when you flag a pdl as temporary. Secondly, you can use output
auto creation with temporary pdls even when you are using explicit
threading which is forbidden for normal output pdls flagged with "[o]"
(see PDL::Indexing).
Here is an example where we use the [t] qualifier. We define the
function "callf" that calls a C routine "f" which needs a temporary
array of the same size and type as the array "a" (sorry about the
forward reference for $P; it's a pointer access, see below) :
pp_def('callf',
Pars => 'a(n); [t] tmp(n); [o] b()',
Code => 'int ns = $SIZE(n);
f($P(a),$P(b),$P(tmp),ns);
'
);
Argument dimensions and the signature
Now we have just talked about dimensions of pdls and the signature. How
are they related? Let's say that we want to add a scalar + the index
number to a vector:
pp_def('add2',
Pars => 'a(n); b(); [o]c(n);',
Code => 'loop(n) %{
$c() = $a() + $b() + n;
%}'
);
There are several points to notice here: first, the "Pars" argument now
contains the n arguments to show that we have a single dimensions in a
and c. It is important to note that dimensions are actual entities that
are accessed by name so this declares a and c to have the same first
dimensions. In most PP definitions the size of named dimensions will be
set from the respective dimensions of non-output pdls (those with no
"[o]" flag) but sometimes you might want to set the size of a named
dimension explicitly through an integer parameter. See below in the
description of the "OtherPars" section how that works.
Constant argument dimensions in the signature
Suppose you want an output piddle to be created automatically and you
know that on every call its dimension will have the same size (say 9)
regardless of the dimensions of the input piddles. In this case you use
the following syntax in the Pars section to specify the size of the
dimension:
' [o] y(n=9); '
As expected, extra dimensions required by threading will be created if
necessary. If you need to assign a named dimension according to a more
complicated formula (than a constant) you must use the "RedoDimsCode"
key described below.
Type conversions and the signature
The signature also determines the type conversions that will be
performed when a PP function is invoked. So what happens when we invoke
one of our previously defined functions with pdls of different type,
e.g.
add2($a,$b,($ret=null));
where $a is of type "PDL_Float" and $b of type "PDL_Short"? With the
signature as shown in the definition of "add2" above the datatype of
the operation (as determined at runtime) is that of the pdl with the
'highest' type (sequence is byte < short < ushort < long < float <
double). In the add2 example the datatype of the operation is float ($a
has that datatype). All pdl arguments are then type converted to that
datatype (they are not converted inplace but a copy with the right type
is created if a pdl argument doesn't have the type of the operation).
Null pdls don't contribute a type in the determination of the type of
the operation. However, they will be created with the datatype of the
operation; here, for example, $ret will be of type float. You should be
aware of these rules when calling PP functions with pdls of different
types to take the additional storage and runtime requirements into
account.
These type conversions are correct for most functions you normally
define with "pp_def". However, there are certain cases where slightly
modified type conversion behaviour is desired. For these cases
additional qualifiers in the signature can be used to specify the
desired properties with regard to type conversion. These qualifiers can
be combined with those we have encountered already (the creation
qualifiers "[o]" and "[t]"). Let's go through the list of qualifiers
that change type conversion behaviour.
The most important is the "int" qualifier which comes in handy when a
pdl argument represents indices into another pdl. Let's take a look at
an example from "PDL::Ufunc":
pp_def('maximum_ind',
Pars => 'a(n); int [o] b()',
Code => '$GENERIC() cur;
int curind;
loop(n) %{
if (!n || $a() > cur) {cur = $a(); curind = n;}
%}
$b() = curind;',
);
The function "maximum_ind" finds the index of the largest element of a
vector. If you look at the signature you notice that the output
argument "b" has been declared with the additional "int" qualifier.
This has the following consequences for type conversions: regardless of
the type of the input pdl "a" the output pdl "b" will be of type
"PDL_Long" which makes sense since "b" will represent an index into
"a". Furthermore, if you call the function with an existing output pdl
"b" its type will not influence the datatype of the operation (see
above). Hence, even if "a" is of a smaller type than "b" it will not be
converted to match the type of "b" but stays untouched, which saves
memory and CPU cycles and is the right thing to do when "b" represents
indices. Also note that you can use the 'int' qualifier together with
other qualifiers (the "[o]" and "[t]" qualifiers). Order is significant
-- type qualifiers precede creation qualifiers ("[o]" and "[t]").
The above example also demonstrates typical usage of the "$GENERIC()"
macro. It expands to the current type in a so called generic loop.
What is a generic loop? As you already heard a PP function has a
runtime datatype as determined by the type of the pdl arguments it has
been invoked with. The PP generated XS code for this function
therefore contains a switch like "switch (type) {case PDL_Byte: ...
case PDL_Double: ...}" that selects a case based on the runtime
datatype of the function (it's called a type ``loop'' because there is
a loop in PP code that generates the cases). In any case your code is
inserted once for each PDL type into this switch statement. The
"$GENERIC()" macro just expands to the respective type in each copy of
your parsed code in this "switch" statement, e.g., in the "case
PDL_Byte" section "cur" will expand to "PDL_Byte" and so on for the
other case statements. I guess you realise that this is a useful macro
to hold values of pdls in some code.
There are a couple of other qualifiers with similar effects as "int".
For your convenience there are the "float" and "double" qualifiers with
analogous consequences on type conversions as "int". Let's assume you
have a very large array for which you want to compute row and column
sums with an equivalent of the "sumover" function. However, with the
normal definition of "sumover" you might run into problems when your
data is, e.g. of type short. A call like
sumover($large_pdl,($sums = null));
will result in $sums be of type short and is therefore prone to
overflow errors if $large_pdl is a very large array. On the other hand
calling
@dims = $large_pdl->dims; shift @dims;
sumover($large_pdl,($sums = zeroes(double,@dims)));
is not a good alternative either. Now we don't have overflow problems
with $sums but at the expense of a type conversion of $large_pdl to
double, something bad if this is really a large pdl. That's where
"double" comes in handy:
pp_def('sumoverd',
Pars => 'a(n); double [o] b()',
Code => 'double tmp=0;
loop(n) %{ tmp += a(); %}
$b() = tmp;',
);
This gets us around the type conversion and overflow problems. Again,
analogous to the "int" qualifier "double" results in "b" always being
of type double regardless of the type of "a" without leading to a type
conversion of "a" as a side effect.
Finally, there are the "type+" qualifiers where type is one of "int" or
"float". What shall that mean. Let's illustrate the "int+" qualifier
with the actual definition of sumover:
pp_def('sumover',
Pars => 'a(n); int+ [o] b()',
Code => '$GENERIC(b) tmp=0;
loop(n) %{ tmp += a(); %}
$b() = tmp;',
);
As we had already seen for the "int", "float" and "double" qualifiers,
a pdl marked with a "type+" qualifier does not influence the datatype
of the pdl operation. Its meaning is "make this pdl at least of type
"type" or higher, as required by the type of the operation". In the
sumover example this means that when you call the function with an "a"
of type PDL_Short the output pdl will be of type PDL_Long (just as
would have been the case with the "int" qualifier). This again tries to
avoid overflow problems when using small datatypes (e.g. byte images).
However, when the datatype of the operation is higher than the type
specified in the "type+" qualifier "b" will be created with the
datatype of the operation, e.g. when "a" is of type double then "b"
will be double as well. We hope you agree that this is sensible
behaviour for "sumover". It should be obvious how the "float+"
qualifier works by analogy. It may become necessary to be able to
specify a set of alternative types for the parameters. However, this
will probably not be implemented until someone comes up with a
reasonable use for it.
Note that we now had to specify the $GENERIC macro with the name of the
pdl to derive the type from that argument. Why is that? If you
carefully followed our explanations you will have realised that in some
cases "b" will have a different type than the type of the operation.
Calling the '$GENERIC' macro with "b" as argument makes sure that the
type will always the same as that of "b" in that part of the generic
loop.
This is about all there is to say about the "Pars" section in a
"pp_def" call. You should remember that this section defines the
signature of a PP defined function, you can use several options to
qualify certain arguments as output and temporary args and all
dimensions that you can later refer to in the "Code" section are
defined by name.
It is important that you understand the meaning of the signature since
in the latest PDL versions you can use it to define threaded functions
from within Perl, i.e. what we call Perl level threading. Please check
PDL::Indexing for details.
The Code section
The "Code" section contains the actual XS code that will be in the
innermost part of a thread loop (if you don't know what a thread loop
is then you still haven't read PDL::Indexing; do it now ;) after any PP
macros (like $GENERIC) and PP functions have been expanded (like the
"loop" function we are going to explain next).
Let's quickly reiterate the "sumover" example:
pp_def('sumover',
Pars => 'a(n); int+ [o] b()',
Code => '$GENERIC(b) tmp=0;
loop(n) %{ tmp += a(); %}
$b() = tmp;',
);
The "loop" construct in the "Code" section also refers to the dimension
name so you don't need to specify any limits: the loop is correctly
sized and everything is done for you, again.
Next, there is the surprising fact that "$a()" and "$b()" do not
contain the index. This is not necessary because we're looping over n
and both variables know which dimensions they have so they
automatically know they're being looped over.
This feature comes in very handy in many places and makes for much
shorter code. Of course, there are times when you want to circumvent
this; here is a function which make a matrix symmetric and serves as an
example of how to code explicit looping:
pp_def('symm',
Pars => 'a(n,n); [o]c(n,n);',
Code => 'loop(n) %{
int n2;
for(n2=n; n2<$SIZE(n); n2++) {
$c(n0 => n, n1 => n2) =
$c(n0 => n2, n1 => n) =
$a(n0 => n, n1 => n2);
}
%}
'
);
Let's dissect what is happening. Firstly, what is this function
supposed to do? From its signature you see that it takes a 2D matrix
with equal numbers of columns and rows and outputs a matrix of the same
size. From a given input matrix $a it computes a symmetric output
matrix $c (symmetric in the matrix sense that A^T = A where ^T means
matrix transpose, or in PDL parlance $c == $c->xchg(0,1)). It does this
by using only the values on and below the diagonal of $a. In the output
matrix $c all values on and below the diagonal are the same as those in
$a while those above the diagonal are a mirror image of those below the
diagonal (above and below are here interpreted in the way that PDL
prints 2D pdls). If this explanation still sounds a bit strange just go
ahead, make a little file into which you write this definition, build
the new PDL extension (see section on Makefiles for PP code) and try it
out with a couple of examples.
Having explained what the function is supposed to do there are a couple
of points worth noting from the syntactical point of view. First, we
get the size of the dimension named "n" again by using the $SIZE macro.
Second, there are suddenly these funny "n0" and "n1" index names in the
code though the signature defines only the dimension "n". Why this? The
reason becomes clear when you note that both the first and second
dimension of $a and $b are named "n" in the signature of "symm". This
tells PDL::PP that the first and second dimension of these arguments
should have the same size. Otherwise the generated function will raise
a runtime error. However, now in an access to $a and $c PDL::PP cannot
figure out which index "n" refers to any more just from the name of the
index. Therefore, the indices with equal dimension names get numbered
from left to right starting at 0, e.g. in the above example "n0" refers
to the first dimension of $a and $c, "n1" to the second and so on.
In all examples so far, we have only used the "Pars" and "Code" members
of the hash that was passed to "pp_def". There are certainly other keys
that are recognised by PDL::PP and we will hear about some of them in
the course of this document. Find a (non-exhaustive) list of keys in
Appendix A. A list of macros and PPfunctions (we have only encountered
some of those in the examples above yet) that are expanded in values of
the hash argument to "pp_def" is summarised in Appendix B.
At this point, it might be appropriate to mention that PDL::PP is not a
completely static, well designed set of routines (as Tuomas puts it:
"stop thinking of PP as a set of routines carved in stone") but rather
a collection of things that the PDL::PP author (Tuomas J. Lukka)
considered he would have to write often into his PDL extension
routines. PP tries to be expandable so that in the future, as new needs
arise, new common code can be abstracted back into it. If you want to
learn more on why you might want to change PDL::PP and how to do it
check the section on PDL::PP internals.
Handling bad values
If you do not have bad-value support compiled into PDL you can ignore
this section and the related keys: "BadCode", "HandleBad", ... (try
printing out the value of $PDL::Bad::Status - if it equals 0 then move
straight on).
There are several keys and macros used when writing code to handle bad
values. The first one is the "HandleBad" key:
HandleBad => 0
This flags a pp-routine as NOT handling bad values. If this routine
is sent piddles with their "badflag" set, then a warning message is
printed to STDOUT and the piddles are processed as if the value
used to represent bad values is a valid number. The "badflag" value
is not propogated to the output piddles.
An example of when this is used is for FFT routines, which
generally do not have a way of ignoring part of the data.
HandleBad => 1
This causes PDL::PP to write extra code that ensures the BadCode
section is used, and that the "$ISBAD()" macro (and its brethren)
work.
HandleBad is not given
If any of the input piddles have their "badflag" set, then the
output piddles will have their "badflag" set, but any supplied
BadCode is ignored.
The value of "HandleBad" is used to define the contents of the "BadDoc"
key, if it is not given.
To handle bad values, code must be written somewhat differently; for
instance,
$c() = $a() + $b();
becomes something like
if ( $a() != BADVAL && $b() != BADVAL ) {
$c() = $a() + $b();
} else {
$c() = BADVAL;
}
However, we only want the second version if bad values are present in
the input piddles (and that bad-value support is wanted!) - otherwise
we actually want the original code. This is where the "BadCode" key
comes in; you use it to specify the code to execute if bad values may
be present, and PP uses both it and the "Code" section to create
something like:
if ( bad_values_are_present ) {
fancy_threadloop_stuff {
BadCode
}
} else {
fancy_threadloop_stuff {
Code
}
}
This approach means that there is virtually no overhead when bad values
are not present (i.e. the badflag routine returns 0).
The BadCode section can use the same macros and looping constructs as
the Code section. However, it wouldn't be much use without the
following additional macros:
$ISBAD(var)
To check whether a piddle's value is bad, use the $ISBAD macro:
if ( $ISBAD(a()) ) { printf("a() is bad\n"); }
You can also access given elements of a piddle:
if ( $ISBAD(a(n=>l)) ) { printf("element %d of a() is bad\n", l); }
$ISGOOD(var)
This is the opposite of the $ISBAD macro.
$SETBAD(var)
For when you want to set an element of a piddle bad.
$ISBADVAR(c_var,pdl)
If you have cached the value of a piddle "$a()" into a c-variable
("foo" say), then to check whether it is bad, use
"$ISBADVAR(foo,a)".
$ISGOODVAR(c_var,pdl)
As above, but this time checking that the cached value isn't bad.
$SETBADVAR(c_var,pdl)
To copy the bad value for a piddle into a c variable, use
"$SETBADVAR(foo,a)".
TODO: mention "$PPISBAD()" etc macros.
Using these macros, the above code could be specified as:
Code => '$c() = $a() + $b();',
BadCode => '
if ( $ISBAD(a()) || $ISBAD(b()) ) {
$SETBAD(c());
} else {
$c() = $a() + $b();
}',
Since this is Perl, TMTOWTDI, so you could also write:
BadCode => '
if ( $ISGOOD(a()) && $ISGOOD(b()) ) {
$c() = $a() + $b();
} else {
$SETBAD(c());
}',
If you want access to the value of the badflag for a given piddle, you
can use the "$PDLSTATExxxx()" macros:
$PDLSTATEISBAD(pdl)
$PDLSTATEISGOOD(pdl)
$PDLSTATESETBAD(pdl)
$PDLSTATESETGOOD(pdl)
TODO: mention the "FindBadStatusCode" and "CopyBadStatusCode" options
to "pp_def", as well as the "BadDoc" key.
Interfacing your own/library functions using PP
Now, consider the following: you have your own C function (that may in
fact be part of some library you want to interface to PDL) which takes
as arguments two pointers to vectors of double:
void myfunc(int n,double *v1,double *v2);
The correct way of defining the PDL function is
pp_def('myfunc',
Pars => 'a(n); [o]b(n);',
GenericTypes => ['D'],
Code => 'myfunc($SIZE(n),$P(a),$P(b));'
);
The "$P("par")" syntax returns a pointer to the first element and the
other elements are guaranteed to lie after that.
Notice that here it is possible to make many mistakes. First, $SIZE(n)
must be used instead of "n". Second, you shouldn't put any loops in
this code. Third, here we encounter a new hash key recognised by
PDL::PP : the "GenericTypes" declaration tells PDL::PP to ONLY GENERATE
THE TYPELOOP FOP THE LIST OF TYPES SPECIFIED. In this case "double".
This has two advantages. Firstly the size of the compiled code is
reduced vastly, secondly if non-double arguments are passed to
"myfunc()" PDL will automatically convert them to double before passing
to the external C routine and convert them back afterwards.
One can also use "Pars" to qualify the types of individual arguments.
Thus one could also write this as:
pp_def('myfunc',
Pars => 'double a(n); double [o]b(n);',
Code => 'myfunc($SIZE(n),$P(a),$P(b));'
);
The type specification in "Pars" exempts the argument from variation in
the typeloop - rather it is automatically converted too and from the
type specified. This is obviously useful in a more general example,
e.g.:
void myfunc(int n,float *v1,long *v2);
pp_def('myfunc',
Pars => 'float a(n); long [o]b(n);',
GenericTypes => ['F'],
Code => 'myfunc($SIZE(n),$P(a),$P(b));'
);
Note we still use "GenericTypes" to reduce the size of the type loop,
obviously PP could in principle spot this and do it automatically
though the code has yet to attain that level of sophistication!
Finally note when types are converted automatically one MUST use the
"[o]" qualifier for output variables or you hard one changes will get
optimised away by PP!
If you interface a large library you can automate the interfacing even
further. Perl can help you again(!) in doing this. In many libraries
you have certain calling conventions. This can be exploited. In short,
you can write a little parser (which is really not difficult in Perl)
that then generates the calls to "pp_def" from parsed descriptions of
the functions in that library. For an example, please check the Slatec
interface in the "Lib" tree of the PDL distribution. If you want to
check (during debugging) which calls to PP functions your Perl code
generated a little helper package comes in handy which replaces the PP
functions by identically named ones that dump their arguments to
stdout.
Just say
perl -MPDL::PP::Dump myfile.pd
to see the calls to "pp_def" and friends. Try it with ops.pd and
slatec.pd. If you're interested (or want to enhance it), the source is
in Basic/Gen/PP/Dump.pm
Other macros and functions in the Code section
Macros: So far we have encountered the $SIZE, $GENERIC and $P macros.
Now we are going to quickly explain the other macros that are expanded
in the "Code" section of PDL::PP along with examples of their usage.
$T The $T macro is used for type switches. This is very useful when you
have to use different external (e.g. library) functions depending on
the input type of arguments. The general syntax is
$Ttypeletters(type_alternatives)
where "typeletters" is a permutation of a subset of the letters
"BSULFD" which stand for Byte, Short, Ushort, etc. and
"type_alternatives" are the expansions when the type of the PP
operation is equal to that indicated by the respective letter. Let's
illustrate this incomprehensible description by an example. Assuming
you have two C functions with prototypes
void float_func(float *in, float *out);
void double_func(double *in, double *out);
which do basically the same thing but one accepts float and the
other double pointers. You could interface them to PDL by defining a
generic function "foofunc" (which will call the correct function
depending on the type of the transformation):
pp_def('foofunc',
Pars => ' a(n); [o] b();',
Code => ' $TFD(float_func,double_func) ($P(a),$P(b));'
GenericTypes => [qw(F D)],
);
Please note that you can't say
Code => ' $TFD(float,double)_func ($P(a),$P(b));'
since the $T macro expands with trailing spaces, analogously to C
preprocessor macros. The slightly longer form illustrated above is
correct. If you really want brevity, you can of course do
'$TBSULFD('.(join ',',map {"long_identifier_name_$_"}
qw/byt short unseigned lounge flotte dubble/).');'
$PP
The $PP macro is used for a so called physical pointer access. The
physical refers to some internal optimisations of PDL (for those who
are familiar with the PDL core we are talking about the vaffine
optimisations). This macro is mainly for internal use and you
shouldn't need to use it in any of your normal code.
$COMP (and the "OtherPars" section)
The $COMP macro is used to access non-pdl values in the code
section. Its name is derived from the implementation of
transformations in PDL. The variables you can refer to using $COMP
are members of the ``compiled'' structure that represents the PDL
transformation in question but does not yet contain any information
about dimensions (for further details check PDL::Internals).
However, you can treat $COMP just as a black box without knowing
anything about the implementation of transformations in PDL. So when
would you use this macro? Its main usage is to access values of
arguments that are declared in the "OtherPars" section of a "pp_def"
definition. But then you haven't heard about the "OtherPars" key
yet?! Let's have another example that illustrates typical usage of
both new features:
pp_def('pnmout',
Pars => 'a(m)',
OtherPars => "char* fd",
GenericTypes => [qw(B U S L)],
Code => 'PerlIO *fp;
IO *io;
io = GvIO(gv_fetchpv($COMP(fd),FALSE,SVt_PVIO));
if (!io || !(fp = IoIFP(io)))
croak("Can\'t figure out FP");
if (PerlIO_write(fp,$P(a),len) != len)
croak("Error writing pnm file");
');
This function is used to write data from a pdl to a file. The file
descriptor is passed as a string into this function. This parameter
does not go into the "Pars" section since it cannot be usefully
treated like a pdl but rather into the aptly named "OtherPars"
section. Parameters in the "OtherPars" section follow those in the
"Pars" section when invoking the function, i.e.
open FILE,">out.dat" or die "couldn't open out.dat";
pnmout($pdl,'FILE');
When you want to access this parameter inside the code section you
have to tell PP by using the $COMP macro, i.e. you write "$COMP(fd)"
as in the example. Otherwise PP wouldn't know that the "fd" you are
referring to is the same as that specified in the "OtherPars"
section.
Another use for the "OtherPars" section is to set a named dimension
in the signature. Let's have an example how that is done:
pp_def('setdim',
Pars => '[o] a(n)',
OtherPars => 'int ns => n',
Code => 'loop(n) %{ $a() = n; %}',
);
This says that the named dimension "n" will be initialised from the
value of the other parameter "ns" which is of integer type (I guess
you have realised that we use the "CType From => named_dim" syntax).
Now you can call this function in the usual way:
setdim(($a=null),5);
print $a;
[ 0 1 2 3 4 ]
Admittedly this function is not very useful but it demonstrates how
it works. If you call the function with an existing pdl and you
don't need to explicitly specify the size of "n" since PDL::PP can
figure it out from the dimensions of the non-null pdl. In that case
you just give the dimension parameter as "-1":
$a = hist($b);
setdim($a,-1);
That should do it.
The only PP function that we have used in the examples so far is
"loop". Additionally, there are currently two other functions which
are recognised in the "Code" section:
threadloop
As we heard above the signature of a PP defined function defines the
dimensions of all the pdl arguments involved in a primitive
operation. However, you often call the functions that you defined
with PP with pdls that have more dimensions than those specified in
the signature. In this case the primitive operation is performed on
all subslices of appropriate dimensionality in what is called a
thread loop (see also overview above and PDL::Indexing). Assuming you
have some notion of this concept you will probably appreciate that
the operation specified in the code section should be optimised since
this is the tightest loop inside a thread loop. However, if you
revisit the example where we define the "pnmout" function, you will
quickly realise that looking up the "IO" file descriptor in the inner
thread loop is not very efficient when writing a pdl with many rows.
A better approach would be to look up the "IO" descriptor once
outside the thread loop and use its value then inside the tightest
thread loop. This is exactly where the "threadloop" function comes in
handy. Here is an improved definition of "pnmout" which uses this
function:
pp_def('pnmout',
Pars => 'a(m)',
OtherPars => "char* fd",
GenericTypes => [qw(B U S L)],
Code => 'PerlIO *fp;
IO *io;
int len;
io = GvIO(gv_fetchpv($COMP(fd),FALSE,SVt_PVIO));
if (!io || !(fp = IoIFP(io)))
croak("Can\'t figure out FP");
len = $SIZE(m) * sizeof($GENERIC());
threadloop %{
if (PerlIO_write(fp,$P(a),len) != len)
croak("Error writing pnm file");
%}
');
This works as follows. Normally the C code you write inside the
"Code" section is placed inside a thread loop (i.e. PP generates the
appropriate wrapping XS code around it). However, when you explicitly
use the "threadloop" function, PDL::PP recognises this and doesn't
wrap your code with an additional thread loop. This has the effect
that code you write outside the thread loop is only executed once per
transformation and just the code with in the surrounding "%{ ... %}"
pair is placed within the tightest thread loop. This also comes in
handy when you want to perform a decision (or any other code,
especially CPU intensive code) only once per thread, i.e.
pp_addhdr('
#define RAW 0
#define ASCII 1
');
pp_def('do_raworascii',
Pars => 'a(); b(); [o]c()',
OtherPars => 'int mode',
Code => ' switch ($COMP(mode)) {
case RAW:
threadloop %{
/* do raw stuff */
%}
break;
case ASCII:
threadloop %{
/* do ASCII stuff */
%}
break;
default:
croak("unknown mode");
}'
);
types
The types function works similar to the $T macro. However, with the
"types" function the code in the following block (delimited by "%{"
and "%}" as usual) is executed for all those cases in which the
datatype of the operation is any of the types represented by the
letters in the argument to "type", e.g.
Code => '...
types(BSUL) %{
/* do integer type operation */
%}
types(FD) %{
/* do floating point operation */
%}
...'
The RedoDimsCode Section
The "RedoDimsCode" key is an optional key that is used to compute
dimensions of piddles at runtime in case the standard rules for
computing dimensions from the signature are not sufficient. The
contents of the "RedoDimsCode" entry is interpreted in the same way
that the Code section is interpreted-- i.e., PP macros are expanded and
the result is interpreted as C code. The purpose of the code is to set
the size of some dimensions that appear in the signature. Storage
allocation and threadloops and so forth will be set up as if the
computed dimension had appeared in the signature. In your code, you
first compute the desired size of a named dimension in the signature
according to your needs and then assign that value to it via the
$SIZE() macro.
As an example, consider the following situation. You are interfacing an
external library routine that requires an temporary array for workspace
to be passed as an argument. Two input data arrays that are passed are
p(m) and x(n). The output data array is y(n). The routine requires a
workspace array with a length of n+m*m, and you'd like the storage
created automatically just like it would be for any piddle flagged with
[t] or [o]. What you'd like is to say something like
pp_def( "myexternalfunc",
Pars => " p(m); x(n); [o] y; [t] work(n+m*m); ", ...
but that won't work, because PP can't interpret expressions with
arithmetic in the signature. Instead you write
pp_def( "myexternalfunc",
Pars => " p(m); x(n); [o] y; [t] work(wn); ",
RedoDimsCode => "
int im = $PDL(p)->dims[0];
int in = $PDL(x)->dims[0];
int min = in + im * im;
int inw = $PDL(work)->dims[0];
$SIZE(wn) = inw >= min ? inw : min; ",
Code => "
externalfunc($P(p),$P(x),$SIZE(m),$SIZE(n),$P(work));
";)
This code works as follows: The macro $PDL(p) expands to a pointer to
the pdl struct for the piddle p. You don't want a pointer to the data
( ie $P ) in this case, because you want to access the methods for the
piddle on the C level. You get the first dimension of each of the
piddles and store them in integers. Then you compute the minimum length
the work array can be. If the user sent a piddle "work" with sufficient
storage, then leave it alone. If the user sent, say a null pdl, or no
pdl at all, then the size of wn will be zero and you reset it to the
minimum value. Before the code in the Code section is executed PP will
create the proper storage for "work" if it does not exist. Note that
you only took the first dimension of "p" and "x" because the user may
have sent piddles with extra threading dimensions. Of course, the
temporary piddle "work" (note the [t] flag) should not be given any
thread dimensions anyway.
You can also use "RedoDimsCode" to set the dimension of a piddle
flagged with [o]. In this case you set the dimensions for the named
dimension in the signature using $SIZE() as in the preceeding example.
However, because the piddle is flagged with [o] instead of [t],
threading dimensions will be added if required just as if the size of
the dimension were computed from the signature according to the usual
rules. Here is an example from PDL::Math
pp_def("polyroots",
Pars => 'cr(n); ci(n); [o]rr(m); [o]ri(m);',
RedoDimsCode => 'int sn = $PDL(cr)->dims[0]; $SIZE(m) = sn-1;',
The input piddles are the real and imaginary parts of complex
coefficients of a polynomial. The output piddles are real and imaginary
parts of the roots. There are "n" roots to an "n"th order polynomial
and such a polynomial has "n+1" coefficients (the zeoreth through the
"n"th). In this example, threading will work correctly. That is, the
first dimension of the output piddle with have its dimension adjusted,
but other threading dimensions will be assigned just as if there were
no "RedoDimsCode".
Typemap handling in the "OtherPars" section
The "OtherPars" section discussed above is very often absolutely
crucial when you interface external libraries with PDL. However in many
cases the external libraries either use derived types or pointers of
various types.
The standard way to handle this in Perl is to use a "typemap" file.
This is discussed in some detail in perlxs in the standard Perl
documentation. In PP the functionality is very similar, so you can
create a "typemap" file in the directory where your PP file resides and
when it is built it is automatically read in to figure out the
appropriate translation between the C type and Perl's built-in type.
That said, there are a couple of important differences from the general
handling of types in XS. The first, and probably most important, is
that at the moment pointers to types are not allowed in the "OtherPars"
section. To get around this limitation you must use the "IV" type
(thanks to Judd Taylor for pointing out that this is necessary for
portability).
It is probably best to illustrate this with a couple of code-snippets:
For instance the "gsl_spline_init" function has the following C
declaration:
int gsl_spline_init(gsl_spline * spline,
const double xa[], const double ya[], size_t size);
Clearly the "xa" and "ya" arrays are candidates for being passed in as
piddles and the "size" argument is just the length of these piddles so
that can be handled by the "$SIZE()" macro in PP. The problem is the
pointer to the "gsl_spline" type. The natural solution would be to
write an "OtherPars" declaration of the form
OtherPars => 'gsl_spline *spl'
and write a short "typemap" file which handled this type. This does not
work at present however! So what you have to do is to go around the
problem slightly (and in some ways this is easier too!):
The solution is to declare "spline" in the "OtherPars" section using an
"Integer Value", "IV". This hides the nature of the variable from PP
and you then need to (well to avoid compiler warnings at least!)
perform a type cast when you use the variable in your code. Thus
"OtherPars" should take the form:
OtherPars => 'IV spl'
and when you use it in the code you will write
INT2PTR(gsl_spline *, $COMP(spl))
where the Perl API macro "INT2PTR" has been used to handle the pointer
cast to avoid compiler warnings and problems for machines with mixed
32bit and 64bit Perl configurations. Putting this together as Andres
Jordan has done (with the modification using "IV" by Judd Taylor) in
the "gsl_interp.pd" in the distribution source you get:
pp_def('init_meat',
Pars => 'double x(n); double y(n);',
OtherPars => 'IV spl',
Code =>'
gsl_spline_init,( INT2PTR(gsl_spline *, $COMP(spl)), $P(x),$P(y),$SIZE(n)));'
);
where I have removed a macro wrapper call, but that would obscure the
discussion.
The other minor difference as compared to the standard typemap handling
in Perl, is that the user cannot specify non-standard typemap locations
or typemap filenames using the "TYPEMAPS" option in MakeMaker... Thus
you can only use a file called "typemap" and/or the "IV" trick above.
Other useful PP keys in data operation definitions
You have already heard about the "OtherPars" key. Currently, there are
not many other keys for a data operation that will be useful in normal
(whatever that is) PP programming. In fact, it would be interesting to
hear about a case where you think you need more than what is provided
at the moment. Please speak up on one of the PDL mailing lists. Most
other keys recognised by "pp_def" are only really useful for what we
call slice operations (see also above).
One thing that is strongly being planned is variable number of
arguments, which will be a little tricky.
An incomplete list of the available keys:
Inplace
Setting this key marks the routine as working inplace - ie the
input and output piddles are the same. An example is
"$a->inplace->sqrt()" (or "sqrt(inplace($a))").
Inplace => 1
Use when the routine is a unary function, such as "sqrt".
Inplace => ['a']
If there are more than one input piddles, specify the name of
the one that can be changed inplace using an array reference.
Inplace => ['a','b']
If there are more than one output piddle, specify the name of
the input piddle and output piddle in a 2-element array
reference. This probably isn't needed, but left in for
completeness.
If bad values are being used, care must be taken to ensure the
propagation of the badflag when inplace is being used; consider
this excerpt from Basic/Bad/bad.pd:
pp_def('replacebad',HandleBad => 1,
Pars => 'a(); [o]b();',
OtherPars => 'double newval',
Inplace => 1,
CopyBadStatusCode =>
'/* propogate badflag if inplace AND it has changed */
if ( a == b && $ISPDLSTATEBAD(a) )
PDL->propogate_badflag( b, 0 );
/* always make sure the output is "good" */
$SETPDLSTATEGOOD(b);
',
...
Since this routine removes all bad values, then the output piddle
had its bad flag cleared. If run inplace (so "a == b"), then we
have to tell all the children of "a" that the bad flag has been
cleared (to save time we make sure that we call
"PDL->propogate_badgflag" only if the input piddle had its bad flag
set).
NOTE: one idea is that the documentation for the routine could be
automatically flagged to indicate that it can be executed inplace,
ie something similar to how "HandleBad" sets "BadDoc" if it's not
supplied (it's not an ideal solution).
Other PDL::PP functions to support concise package definition
So far, we have described the "pp_def" and "pp_done" functions. PDL::PP
exports a few other functions to aid you in writing concise PDL
extension package definitions.
pp_addhdr
Often when you interface library functions as in the above example you
have to include additional C include files. Since the XS file is
generated by PP we need some means to make PP insert the appropriate
include directives in the right place into the generated XS file. To
this end there is the "pp_addhdr" function. This is also the function
to use when you want to define some C functions for internal use by
some of the XS functions (which are mostly functions defined by
"pp_def"). By including these functions here you make sure that
PDL::PP inserts your code before the point where the actual XS module
section begins and will therefore be left untouched by xsubpp (cf.
perlxs and perlxstut man pages).
A typical call would be
pp_addhdr('
#include <unistd.h> /* we need defs of XXXX */
#include "libprotos.h" /* prototypes of library functions */
#include "mylocaldecs.h" /* Local decs */
static void do_the real_work(PDL_Byte * in, PDL_Byte * out, int n)
{
/* do some calculations with the data */
}
');
This ensures that all the constants and prototypes you need will be
properly included and that you can use the internal functions defined
here in the "pp_def"s, e.g.:
pp_def('barfoo',
Pars => ' a(n); [o] b(n)',
GenericTypes => ['B'],
Code => ' int ns = $SIZE(n);
do_the_real_work($P(a),$P(b),ns);
',
);
pp_addpm
In many cases the actual PP code (meaning the arguments to "pp_def"
calls) is only part of the package you are currently implementing.
Often there is additional Perl code and XS code you would normally have
written into the pm and XS files which are now automatically generated
by PP. So how to get this stuff into those dynamically generated files?
Fortunately, there are a couple of functions, generally called
"pp_addXXX" that assist you in doing this.
Let's assume you have additional Perl code that should go into the
generated pm-file. This is easily achieved with the "pp_addpm" command:
pp_addpm(<<'EOD');
=head1 NAME
PDL::Lib::Mylib -- a PDL interface to the Mylib library
=head1 DESCRIPTION
This package implements an interface to the Mylib package with full
threading and indexing support (see L<PDL::Indexing>).
=cut
use PGPLOT;
=head2 use_myfunc
this function applies the myfunc operation to all the
elements of the input pdl regardless of dimensions
and returns the sum of the result
=cut
sub use_myfunc {
my $pdl = shift;
myfunc($pdl->clump(-1),($res=null));
return $res->sum;
}
EOD
pp_add_exported
You have probably got the idea. In some cases you also want to export
your additional functions. To avoid getting into trouble with PP which
also messes around with the @EXPORT array you just tell PP to add your
functions to the list of exported functions:
pp_add_exported('use_myfunc gethynx');
pp_add_isa
The "pp_add_isa" command works like the the "pp_add_exported" function.
The arguments to "pp_add_isa" are added the @ISA list, e.g.
pp_add_isa(' Some::Other::Class ');
pp_bless
If your pp_def routines are to be used as object methods use "pp_bless"
to specify the package (i.e. class) to which your pp_defed methods will
be added. For example, "pp_bless('PDL::MyClass')". The default is "PDL"
if this is omitted.
pp_addxs
Sometimes you want to add extra XS code of your own (that is generally
not involved with any threading/indexing issues but supplies some other
functionality you want to access from the Perl side) to the generated
XS file, for example
pp_addxs('','
# Determine endianness of machine
int
isbigendian()
CODE:
unsigned short i;
PDL_Byte *b;
i = 42; b = (PDL_Byte*) (void*) &i;
if (*b == 42)
RETVAL = 0;
else if (*(b+1) == 42)
RETVAL = 1;
else
croak("Impossible - machine is neither big nor little endian!!\n");
OUTPUT:
RETVAL
');
Especially "pp_add_exported" and "pp_addxs" should be used with care.
PP uses PDL::Exporter, hence letting PP export your function means that
they get added to the standard list of function exported by default
(the list defined by the export tag ``:Func''). If you use "pp_addxs"
you shouldn't try to do anything that involves threading or indexing
directly. PP is much better at generating the appropriate code from
your definitions.
pp_add_boot
Finally, you may want to add some code to the BOOT section of the XS
file (if you don't know what that is check perlxs). This is easily done
with the "pp_add_boot" command:
pp_add_boot(<<EOB);
descrip = mylib_initialize(KEEP_OPEN);
if (descrip == NULL)
croak("Can't initialize library");
GlobalStruc->descrip = descrip;
GlobalStruc->maxfiles = 200;
EOB
pp_export_nothing
By default, PP.pm puts all subs defined using the pp_def function into
the output .pm file's EXPORT list. This can create problems if you are
creating a subclassed object where you don't want any methods exported.
(i.e. the methods will only be called using the $object->method
syntax).
For these cases you can call pp_export_nothing() to clear out the
export list. Example (At the end of the .pd file):
pp_export_nothing();
pp_done();
pp_core_importList
By default, PP.pm puts the 'use Core;' line into the output .pm file.
This imports Core's exported names into the current namespace, which
can create problems if you are over-riding one of Core's methods in the
current file. You end up getting messages like "Warning: sub sumover
redefined in file subclass.pm" when running the program.
For these cases the pp_core_importList can be used to change what is
imported from Core.pm. For example:
pp_core_importList('()')
This would result in
use Core();
being generated in the output .pm file. This would result in no names
being imported from Core.pm. Similarly, calling
pp_core_importList(' qw/ barf /')
would result in
use Core qw/ barf/;
being generated in the output .pm file. This would result in just
'barf' being imported from Core.pm.
pp_setversion
I am pretty sure that this allows you to simultaneously set the .pm and
.xs files' versions, thus avoiding unnecessary version-skew between the
two. To use this, simply have the following line at some point in your
.pd file:
pp_setversion('0.0.3');
However, don't use this if you use Module::Build::PDL. See that
module's documentation for details.
pp_deprecate_module
If a particular module is deemed obsolete, this function can be used to
mark it as deprecated. This has the effect of emitting a warning when a
user tries to "use" the module. The generated POD for this module also
carries a deprecation notice. The replacement module can be passed as
an argument like this:
pp_deprecate_module( infavor => "PDL::NewNonDeprecatedModule" );
Note that function affects only the runtime warning and the POD.
Making your PP function "private"
Let's say that you have a function in your module called PDL::foo that
uses the PP function "bar_pp" to do the heavy lifting. But you don't
want to advertise that "bar_pp" exists. To do this, you must move your
PP function to the top of your module file, then call
pp_export_nothing()
to clear the "EXPORT" list. To ensure that no documentation (even the
default PP docs) is generated, set
Doc => undef
and to prevent the function from being added to the symbol table, set
PMFunc => ''
in your pp_def declaration (see Image2D.pd for an example). This will
effectively make your PP function "private." However, it is always
accessible via PDL::bar_pp due to Perl's module design. But making it
private will cause the user to go very far out of his or her way to use
it, so he or she shoulders the consequences!
Slice operation
The slice operation section of this manual is provided using dataflow
and lazy evaluation: when you need it, ask Tjl to write it. a delivery
in a week from when I receive the email is 95% probable and two week
delivery is 99% probable.
And anyway, the slice operations require a much more intimate knowledge
of PDL internals than the data operations. Furthermore, the complexity
of the issues involved is considerably higher than that in the average
data operation. If you would like to convince yourself of this fact
take a look at the Basic/Slices/slices.pd file in the PDL distribution
:-). Nevertheless, functions generated using the slice operations are
at the heart of the index manipulation and dataflow capabilities of
PDL.
Also, there are a lot of dirty issues with virtual piddles and vaffines
which we shall entirely skip here.
Slices and bad values
Slice operations need to be able to handle bad values (if support is
compiled into PDL). The easiest thing to do is look at
Basic/Slices/slices.pd to see how this works.
Along with "BadCode", there are also the "BadBackCode" and
"BadRedoDimsCode" keys for "pp_def". However, any "EquivCPOffsCode"
should not need changing, since any changes are absorbed into the
definition of the "$EQUIVCPOFFS()" macro (i.e. it is handled
automatically by PDL::PP>.
A few notes on writing a slicing routine...
The following few paragraphs describe writing of a new slicing routine
('range'); any errors are CED's. (--CED 26-Aug-2002)
Handling of "warn" and "barf" in PP Code
For printing warning messages or aborting/dieing, you can call "warn"
or "barf" from PP code. However, you should be aware that these calls
have been redefined using C preprocessor macros to "PDL->barf" and
"PDL->warn". These redefinitions are in place to keep you from
inadvertently calling perl's "warn" or "barf" directly, which can cause
segfaults during pthreading (i.e. processor multi-threading).
PDL's own versions of "barf" and "warn" will queue-up warning or barf
messages until after pthreading is completed, and then call the perl
versions of these routines.
See PDL::ParallelCPU for more information on pthreading.
USEFUL ROUTINES
The PDL "Core" structure, defined in Basic/Core/pdlcore.h.PL, contains
pointers to a number of routines that may be useful to you. The
majority of these routines deal with manipulating piddles, but some are
more general:
PDL->qsort_B( PDL_Byte *xx, int a, int b )
Sort the array "xx" between the indices "a" and "b". There are
also versions for the other PDL datatypes, with postfix "_S", "_U",
"_L", "_F", and "_D". Any module using this must ensure that
"PDL::Ufunc" is loaded.
PDL->qsort_ind_B( PDL_Byte *xx, int *ix, int a, int b )
As for "PDL->qsort_B", but this time sorting the indices rather
than the data.
The routine "med2d" in Lib/Image2D/image2d.pd shows how such routines
are used.
MAKEFILES FOR PP FILES
If you are going to generate a package from your PP file (typical file
extensions are ".pd" or ".pp" for the files containing PP code) it is
easiest and safest to leave generation of the appropriate commands to
the Makefile. In the following we will outline the typical format of a
Perl Makefile to automatically build and install your package from a
description in a PP file. Most of the rules to build the xs, pm and
other required files from the PP file are already predefined in the
PDL::Core::Dev package. We just have to tell MakeMaker to use it.
In most cases you can define your Makefile like
# Makefile.PL for a package defined by PP code.
use PDL::Core::Dev; # Pick up development utilities
use ExtUtils::MakeMaker;
$package = ["mylib.pd",Mylib,PDL::Lib::Mylib];
%hash = pdlpp_stdargs($package);
$hash{OBJECT} .= ' additional_Ccode$(OBJ_EXT) ';
$hash{clean}->{FILES} .= ' todelete_Ccode$(OBJ_EXT) ';
$hash{'VERSION_FROM'} = 'mylib.pd';
WriteMakefile(%hash);
sub MY::postamble { pdlpp_postamble($package); }
Here, the list in $package is: first: PP source file name, then the
prefix for the produced files and finally the whole package name. You
can modify the hash in whatever way you like but it would be reasonable
to stay within some limits so that your package will continue to work
with later versions of PDL.
If you don't want to use prepackaged arguments, here is a generic
Makefile.PL that you can adapt for your own needs:
# Makefile.PL for a package defined by PP code.
use PDL::Core::Dev; # Pick up development utilities
use ExtUtils::MakeMaker;
WriteMakefile(
'NAME' => 'PDL::Lib::Mylib',
'VERSION_FROM' => 'mylib.pd',
'TYPEMAPS' => [&PDL_TYPEMAP()],
'OBJECT' => 'mylib$(OBJ_EXT) additional_Ccode$(OBJ_EXT)',
'PM' => { 'Mylib.pm' => '$(INST_LIBDIR)/Mylib.pm'},
'INC' => &PDL_INCLUDE(), # add include dirs as required by your lib
'LIBS' => [''], # add link directives as necessary
'clean' => {'FILES' =>
'Mylib.pm Mylib.xs Mylib$(OBJ_EXT)
additional_Ccode$(OBJ_EXT)'},
);
# Add genpp rule; this will invoke PDL::PP on our PP file
# the argument is an array reference where the array has three string elements:
# arg1: name of the source file that contains the PP code
# arg2: basename of the xs and pm files to be generated
# arg3: name of the package that is to be generated
sub MY::postamble { pdlpp_postamble(["mylib.pd",Mylib,PDL::Lib::Mylib]); }
To make life even easier PDL::Core::Dev defines the function
"pdlpp_stdargs" that returns a hash with default values that can be
passed (either directly or after appropriate modification) to a call to
WriteMakefile. Currently, "pdlpp_stdargs" returns a hash where the
keys are filled in as follows:
(
'NAME' => $mod,
'TYPEMAPS' => [&PDL_TYPEMAP()],
'OBJECT' => "$pref\$(OBJ_EXT)",
PM => {"$pref.pm" => "\$(INST_LIBDIR)/$pref.pm"},
MAN3PODS => {"$src" => "\$(INST_MAN3DIR)/$mod.\$(MAN3EXT)"},
'INC' => &PDL_INCLUDE(),
'LIBS' => [''],
'clean' => {'FILES' => "$pref.xs $pref.pm $pref\$(OBJ_EXT)"},
)
Here, $src is the name of the source file with PP code, $pref the
prefix for the generated .pm and .xs files and $mod the name of the
extension module to generate.
INTERNALS
The internals of the current version consist of a large table which
gives the rules according to which things are translated and the subs
which implement these rules.
Later on, it would be good to make the table modifiable by the user so
that different things may be tried.
[Meta comment: here will hopefully be more in the future; currently,
your best bet will be to read the source code :-( or ask on the list
(try the latter first) ]
Appendix A: Some keys recognised by PDL::PP
Unless otherwise specified, the arguments are strings. Keys marked with
(bad) are only used if bad-value support is compiled into PDL.
Pars
define the signature of your function
OtherPars
arguments which are not pdls. Default: nothing. This is a semi-
colon separated list of arguments, e.g., "OtherPars=>'int k; double
value; char* fd'". See $COMP(x) and also the same entry in Appendix
B.
Code
the actual code that implements the functionality; several PP
macros and PP functions are recognised in the string value
HandleBad (bad)
If set to 1, the routine is assumed to support bad values and the
code in the BadCode key is used if bad values are present; it also
sets things up so that the "$ISBAD()" etc macros can be used. If
set to 0, cause the routine to print a warning if any of the input
piddles have their bad flag set.
BadCode (bad)
Give the code to be used if bad values may be present in the input
piddles. Only used if "HandleBad => 1".
GenericTypes
An array reference. The array may contain any subset of the one-
character strings `B', `S', `U', `L', `Q', `F' and `D', which
specify which types your operation will accept. The meaning of each
type is:
B - signed byte (i.e. signed char)
S - signed short (two-byte integer)
U - unsigned short
L - signed long (four-byte integer, int on 32 bit systems)
Q - signed long long (eight byte integer)
F - float
D - double
This is very useful (and important!) when interfacing an external
library. Default: [qw/B S U L Q F D/]
Inplace
Mark a function as being able to work inplace.
Inplace => 1 if Pars => 'a(); [o]b();'
Inplace => ['a'] if Pars => 'a(); b(); [o]c();'
Inplace => ['a','b'] if Pars => 'a(); b(); [o]c(); [o]d();'
If bad values are being used, care must be taken to ensure the
propagation of the badflag when inplace is being used; for instance
see the code for "replacebad" in Basic/Bad/bad.pd.
Doc Used to specify a documentation string in Pod format. See PDL::Doc
for information on PDL documentation conventions. Note: in the
special case where the PP 'Doc' string is one line this is
implicitly used for the quick reference AND the documentation!
If the Doc field is omitted PP will generate default documentation
(after all it knows about the Signature).
If you really want the function NOT to be documented in any way at
this point (e.g. for an internal routine, or because you are doing
it elsewhere in the code) explicitly specify "Doc=>undef".
BadDoc (bad)
Contains the text returned by the "badinfo" command (in "perldl")
or the "-b" switch to the "pdldoc" shell script. In many cases, you
will not need to specify this, since the information can be
automatically created by PDL::PP. However, as befits computer-
generated text, it's rather stilted; it may be much better to do it
yourself!
NoPthread
Optional flag to indicate the PDL function should not use processor
threads (i.e. pthreads or POSIX threads) to split up work across
mutliple CPU cores. This option is typically set to 1 if the
underlying PDL function is not threadsafe. If this option isn't
present, then the function is assumed to be threadsafe. This option
only applies if PDL has been compiled with POSIX threads enabled.
PMCode
PDL functions allow you to pass in a piddle into which you want the
output saved. This is handy because you can allocate an output
piddle once and reuse it many times; the alternative would be for
PDL to create a new piddle each time, which may waste compute
cycles or, more likely, RAM. This added flexibility comes at the
cost of more complexity: PDL::PP has to write functions that are
smart enough to count the arguments passed to it and create new
piddles on the fly, but only if you want them.
PDL::PP is smart enough to do that, but there are restrictions on
argument order and the like. If you want a more flexible function,
you can write your own Perl-side wrapper and specify it in the
PMCode key. The string that you supply must (should) define a Perl
function with a name that matches what you gave to pp_def in the
first place. When you wish to eventually invoke the PP-generated
function, you will need to supply all piddles in the exact order
specified in the signature: output piddles are not optional, and
the PP-generated function will not return anything. The obfuscated
name that you will call is _<funcname>_int.
I believe this documentation needs further clarification, but this
will have to do. :-(
PMFunc
When pp_def generates functions, it typically defines them in the
PDL package. Then, in the .pm file that it generates for your
module, it typically adds a line that essentially copies that
function into your current package's symbol table with code that
looks like this:
*func_name = \&PDL::func_name;
It's a little bit smarter than that (it knows when to wrap that
sort of thing in a BEGIN block, for example, and if you specified
something different for pp_bless), but that's the gist of it. If
you don't care to import the function into your current package's
symbol table, you can specify
PMFunc => '',
PMFunc has no other side-effects, so you could use it to insert
arbitrary Perl code into your module if you like. However, you
should use pp_addpm if you want to add Perl code to your module.
Appendix B: PP macros and functions
Macros
Macros labeled by (bad) are only used if bad-value support is compiled
into PDL.
$variablename_from_sig()
access a pdl (by its name) that was specified in the signature
$COMP(x)
access a value in the private data structure of this
transformation (mainly used to use an argument that is specified
in the "OtherPars" section)
$SIZE(n)
replaced at runtime by the actual size of a named dimension (as
specified in the signature)
$GENERIC()
replaced by the C type that is equal to the runtime type of the
operation
$P(a) a pointer access to the PDL named "a" in the signature. Useful
for interfacing to C functions
$PP(a) a physical pointer access to pdl "a"; mainly for internal use
$TXXX(Alternative,Alternative)
expansion alternatives according to runtime type of operation,
where XXX is some string that is matched by "/[BSULFD+]/".
$PDL(a)
return a pointer to the pdl data structure (pdl *) of piddle "a"
$ISBAD(a()) (bad)
returns true if the value stored in "a()" equals the bad value
for this piddle. Requires "HandleBad" being set to 1.
$ISGOOD(a()) (bad)
returns true if the value stored in "a()" does not equal the bad
value for this piddle. Requires "HandleBad" being set to 1.
$SETBAD(a()) (bad)
Sets "a()" to equal the bad value for this piddle. Requires
"HandleBad" being set to 1.
functions
"loop(DIMS) %{ ... %}"
loop over named dimensions; limits are generated automatically by PP
"threadloop %{ ... %}"
enclose following code in a thread loop
"types(TYPES) %{ ... %}"
execute following code if type of operation is any of "TYPES"
Appendix C: Functions imported by PDL::PP
A number of functions are imported when you "use PDL::PP". These
include functions that control the generated C or XS code, functions
that control the generated Perl code, and functions that manipulate the
packages and symbol tables into which the code is created.
Generating C and XS Code
PDL::PP's main purpose is to make it easy for you to wrap the threading
engine around your own C code, but you can do some other things, too.
pp_def
Used to wrap the threading engine around your C code. Virtually all
of this document discusses the use of pp_def.
pp_done
Indicates you are done with PDL::PP and that it should generate its
.xs and .pm files based upon the other pp_* functions that you have
called. This function takes no arguments.
pp_addxs
This lets you add XS code to your .xs file. This is useful if you
want to create Perl-accessible functions that invoke C code but
cannot or should not invoke the threading engine. XS is the
standard means by which you wrap Perl-accessible C code. You can
learn more at perlxs.
pp_add_boot
This function adds whatever string you pass to the XS BOOT section.
The BOOT section is C code that gets called by Perl when your
module is loaded and is useful for automatic initialization. You
can learn more about XS and the BOOT section at perlxs.
pp_addhdr
Adds pure-C code to your XS file. XS files are structured such that
pure C code must come before XS specifications. This allows you to
specify such C code.
pp_boundscheck
PDL normally checks the bounds of your accesses before making them.
You can turn that on or off at runtime by setting
MyPackage::set_boundscheck. This function allows you to remove that
runtime flexibility and never do bounds checking. It also returns
the current boundschecking status if called without any argumens.
NOTE: I have not found anything about bounds checking in other
documentation. That needs to be addressed.
Generating Perl Code
Many functions imported when you use PDL::PP allow you to modify the
contents of the generated .pm file. In addition to pp_def and pp_done,
the role of these functions is primarily to add code to various parts
of your generated .pm file.
pp_addpm
Adds Perl code to the generated .pm file. PDL::PP actually keeps
track of three different sections of generated code: the Top, the
Middle, and the Bottom. You can add Perl code to the Middle section
using the one-argument form, where the argument is the Perl code
you want to supply. In the two-argument form, the first argument is
an anonymous hash with only one key that specifies where to put the
second argument, which is the string that you want to add to the
.pm file. The hash is one of these three:
{At => 'Top'}
{At => 'Middle'}
{At => 'Bot'}
For example:
pp_addpm({At => 'Bot'}, <<POD);
=head1 Some documentation
I know I'm typing this in the middle of my file, but it'll go at
the bottom.
=cut
POD
Warning: If, in the middle of your .pd file, you put documentation
meant for the bottom of your pod, you will thoroughly confuse CPAN.
On the other hand, if in the middle of your .pd fil, you add some
Perl code destined for the bottom or top of your .pm file, you only
have yourself to confuse. :-)
pp_beginwrap
Adds BEGIN-block wrapping. Certain declarations can be wrapped in
BEGIN blocks, though the default behavior is to have no such
wrapping.
pp_addbegin
Sets code to be added to the top of your .pm file, even above code
that you specify with "pp_addpm({At => 'Top'}, ...)". Unlike
pp_addpm, calling this overwrites whatever was there before.
Generally, you probably shouldn't use it.
Tracking Line Numbers
When you get compile errors, either from your C-like code or your Perl
code, it can help to make those errors back to the line numbers in the
source file at which the error occurred.
pp_line_numbers
Takes a line number and a (usually long) string of code. The line
number should indicate the line at which the quote begins. This is
usually Perl's "__LINE__" literal, unless you are using heredocs,
in which case it is "__LINE__ + 1". The returned string has #line
directives interspersed to help the compiler report errors on the
proper line.
Modifying the Symbol Table and Export Behavior
PDL::PP usually exports all functions generated using pp_def, and
usually installs them into the PDL symbol table. However, you can
modify this behavior with these functions.
pp_bless
Sets the package (symbol table) to which the XS code is added. The
default is PDL, which is generally what you want. If you use the
default blessing and you create a function myfunc, then you can do
the following:
$piddle->myfunc(<args>);
PDL::myfunc($piddle, <args>);
On the other hand, if you bless your functions into another
package, you cannot invoke them as PDL methods, and must invoke
them as:
MyPackage::myfunc($piddle, <args>);
Of course, you could always use the PMFunc key to add your function
to the PDL symbol table, but why do that?
pp_add_isa
Adds to the list of modules from which your module inherits. The
default list is
qw(PDL::Exporter DynaLoader)
pp_core_importlist
At the top of your generated .pm file is a line that looks like
this:
use PDL::Core;
You can modify that by specifying a string to pp_core_importlist.
For example,
pp_core_importlist('::Blarg');
will result in
use PDL::Core::Blarg;
You can use this, for example, to add a list of symbols to import
from PDL::Core. For example:
pp_core_importlist(" ':Internal'");
will lead to the following use statement:
use PDL::Core ':Internal';
pp_setversion
Sets your module's version. The version must be consistent between
the .xs and the .pm file, and is used to ensure that your Perl's
libraries do not suffer from version skew.
pp_add_exported
Adds to the export list whatever names you give it. Functions
created using pp_def are automatically added to the list. This
function is useful if you define any Perl functions using pp_addpm
or pp_addxs that you want exported as well.
pp_export_nothing
This resets the list of exported symbols to nothing. This is
probably better called "pp_export_clear", since you can add
exported symbols after calling "pp_export_nothing". When called
just before calling pp_done, this ensures that your module does not
export anything, for example, if you only want programmers to use
your functions as methods.
SEE ALSO
PDL
For the concepts of threading and slicing check PDL::Indexing.
PDL::Internals
PDL::BadValues for information on bad values
perlxs, perlxstut
CURRENTLY UNDOCUMENTED
$RESIZE()BUGS
Although PDL::PP is quite flexible and thoroughly used, there are
surely bugs. First amonth them: this documentation needs a thorough
revision.
AUTHORCopyright(C) 1997 Tuomas J. Lukka (lukka@fas.harvard.edu), Karl
Glaazebrook (kgb@aaocbn1.aao.GOV.AU) and Christian Soeller
(c.soeller@auckland.ac.nz). All rights reserved. Documentation updates
Copyright(C) 2011 David Mertens (dcmertens.perl@gmail.com). This
documentation is licensed under the same terms as Perl itself.
POD ERRORS
Hey! The above document had some coding errors, which are explained
below:
Around line 350:
Non-ASCII character seen before =encoding in 'XrmpX'. Assuming
UTF-8
perl v5.18.1 2013-10-07 PP(1)
