PDL::PP (1) - Linux Manuals
PDL::PP: Generate PDL routines from concise descriptions
NAME
PDL::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();
%}
$b() = tmp;
},
);
pp_done();
FUNCTIONS
Here is a quick reference list of the functions provided by PDL::PP.pp_add_boot
Add code to the BOOT section of generated XS filepp_add_exported
Add functions to the list of exported functionspp_add_isa
Add entries to the @ISA listpp_addbegin
Sets code to be added at the top of the generate .pm filepp_addhdr
Add code and includes to C section of the generated XS filepp_addpm
Add code to the generated .pm filepp_addxs
Add extra XS code to the generated XS filepp_beginwrap
Add BEGIN-block wrapping to code for the generated .pm filepp_bless
Sets the package to which the XS code is added (default is PDL)pp_boundscheck
Control state of PDL bounds checking activitypp_core_importList
Specify what is imported from PDL::Corepp_def
Define a new PDL functionpp_deprecate_module
Add runtime and POD warnings about a module being deprecatedpp_done
Mark the end of PDL::PP definitions in the filepp_export_nothing
Clear out the export list for your generated modulepp_line_numbers
Add line number information to simplify debugging of PDL::PP codepp_setversion
Set the version for .pm and .xs filesOVERVIEW
Why do we need PP? Several reasons: firstly, we want to be able to generate subroutine code for each of the PDL datatypes (PDL_Byte, PDL_Short,. etc). AUTOMATICALLY. Secondly, when referring to slices of PDL arrays in Perl (e.g. "$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
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.
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
and have threading work correctly (the result is $c == [7 8 9]).
[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
and avoid allocating and deallocating $c each time. It is allocated
once at the first add() and thereafter the memory stays until $c is
destroyed.
If you just say
the code generated by PP will automatically fill in "$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) :
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.
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.
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, $ret will be
of type float. You should be aware of these rules when calling PP functions
with pdls of different types to take the additional storage and runtime
requirements into account.
These type conversions are correct for most functions you normally define
with "pp_def". However, there are certain cases where slightly modified
type conversion behaviour is desired. For these cases additional qualifiers
in the signature can be used to specify the desired properties with regard
to type conversion. These qualifiers can be combined with those we have
encountered already (the creation qualifiers "[o]" and "[t]"). Let's
go through the list of qualifiers that change type conversion behaviour.
The most important is the "int" qualifier which comes in handy when a
pdl argument represents indices into another pdl. Let's take a look at
an example from "PDL::Ufunc":
The function "maximum_ind" finds the index of the largest element of
a vector. If you look at the signature you notice that the output
argument "b" has been declared with the additional "int" qualifier.
This has the following consequences for type conversions: regardless of
the type of the input pdl "a" the output pdl "b" will be of type
"PDL_Long" which makes sense since "b" will represent an index into
"a". Furthermore, if you call the function with an existing output
pdl "b" its type will not influence the datatype of the operation (see
above). Hence, even if "a" is of a smaller type than "b" it will not
be converted to match the type of "b" but stays untouched, which saves
memory and CPU cycles and is the right thing to do when "b" represents
indices. Also note that you can use the 'int' qualifier together with
other qualifiers (the "[o]" and "[t]" qualifiers). Order is significant ---
type qualifiers precede creation qualifiers ("[o]" and "[t]").
The above example also demonstrates typical usage of the "$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
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
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:
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:
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.
Let's quickly reiterate the "sumover" example:
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:
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.
There are several keys and macros used when writing code to handle
bad values. The first one is the "HandleBad" key:
An example of when this is used is for FFT routines, which generally
do not have a way of ignoring part of the data.
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,
becomes something like
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:
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:
You can also access given elements of a piddle:
TODO: mention "$PPISBAD()" etc macros.
Using these macros, the above code could be specified as:
Since this is Perl, TMTOWTDI, so you could also write:
If you want access to the value of the badflag for a given
piddle, you can use the "$PDLSTATExxxx()" macros:
TODO: mention the "FindBadStatusCode" and
"CopyBadStatusCode" options to "pp_def", as well as the
"BadDoc" key.
The correct way of defining the PDL function is
The "$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:
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.:
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
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
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
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):
Please note that you can't say
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
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.
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:
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:
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":
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:
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.
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
but that won't work, because PP can't interpret expressions with arithmetic
in the signature. Instead you write
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 $SIZE() as in
the preceeding example. However, because the piddle is
flagged with [o] instead of [t], threading dimensions will
be added if required just as if the size of the dimension
were computed from the signature according to the usual
rules. Here is an example from PDL::Math
The input piddles are the real and imaginary parts of
complex coefficients of a polynomial. The output piddles are
real and imaginary parts of the roots. There are "n" roots
to an "n"th order polynomial and such a polynomial has
"n+1" coefficients (the zeoreth through the "n"th). In
this example, threading will work correctly. That is, the
first dimension of the output piddle with have its dimension
adjusted, but other threading dimensions will be assigned
just as if there were no "RedoDimsCode".
The standard way to handle this in Perl is to use a "typemap" file.
This is discussed in some detail in perlxs in the standard
Perl documentation. In PP the functionality is very similar, so you can
create a "typemap" file in the directory where your PP file resides and
when it is built it is automatically read in to figure out the appropriate
translation between the C type and Perl's built-in type.
That said, there are a couple of important differences from the general
handling of types in XS. The first, and probably most important, is that
at the moment pointers to types are not allowed in the "OtherPars"
section. To get around this limitation you must use the "IV" type
(thanks to Judd Taylor for pointing out that this is necessary for
portability).
It is probably best to illustrate this with a couple of code-snippets:
For instance the "gsl_spline_init" function has the following C
declaration:
Clearly the "xa" and "ya" arrays are candidates for being passed
in as piddles and the "size" argument is just the length of these
piddles so that can be handled by the "$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
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:
and when you use it in the code you will write
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:
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.
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:
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:
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).
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
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_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_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_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_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
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_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_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:
This would result in
being generated in the output .pm file. This would result in no names being imported
from Core.pm. Similarly, calling
would result in
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:
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:
Note that function affects only the runtime warning and the POD.
to clear the "EXPORT" list. To ensure that no documentation (even the
default PP docs) is generated, set
and to prevent the function from being added to the symbol table, set
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!
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.
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>.
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.
The routine "med2d" in Lib/Image2D/image2d.pd shows how such routines are
used.
In most cases you can define your Makefile like
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:
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:
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.
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) ]
This is very useful (and important!) when interfacing an external library.
Default: [qw/B S U L Q F 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.
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".
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. :-(
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 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.
NOTE: I have not found anything about bounds checking in other documentation.
That needs to be addressed.
For example:
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. :-)
On the other hand, if you bless your functions into another package, you
cannot invoke them as PDL methods, and must invoke them as:
Of course, you could always use the PMFunc key to add your function to the
PDL symbol table, but why do that?
You can modify that by specifying a string to pp_core_importlist. For
example,
will result in
You can use this, for example, to add a list of symbols to import from
PDL::Core. For example:
will lead to the following use statement:
For the concepts of threading and slicing check PDL::Indexing.
PDL::Internals
PDL::BadValues for information on bad values
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();'
);
use MyModule;
$a = pdl 2,3,4;
$b = pdl 5;
$c = add($a,$b);
# or
add($a,$b,($c=null)); # Alternative form, useful if $c has been
# preset to something big, not useful here.
The Pars section: the signature of a PP function
Seeing the above example code you will most probably ask: what is this
strange "$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 ;).
$c = PDL->null;
for(some long loop) {
# munge a,b
add($a,$b,$c);
# munge c, put something back to a,b
}
$c = add($a,$b);
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() + $b() + n;
%}'
);
Constant argument dimensions in the signature
Suppose you want an output piddle to be created
automatically and you know that on every call its dimension
will have the same size (say 9) regardless of the dimensions
of the input piddles. In this case you use the following
syntax in the Pars section to specify the size of the dimension:
' [o] y(n=9); '
Type conversions and the signature
The signature also determines the type conversions that will be performed
when a PP function is invoked. So what happens when we invoke one of
our previously defined functions with pdls of different type, e.g.
add2($a,$b,($ret=null));
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;}
%}
$b() = curind;',
);
sumover($large_pdl,($sums = null));
@dims = $large_pdl->dims; shift @dims;
sumover($large_pdl,($sums = zeroes(double,@dims)));
pp_def('sumoverd',
Pars => 'a(n); double [o] b()',
Code => 'double tmp=0;
loop(n) %{ tmp += a(); %}
$b() = tmp;',
);
pp_def('sumover',
Pars => 'a(n); int+ [o] b()',
Code => '$GENERIC(b) tmp=0;
loop(n) %{ tmp += a(); %}
$b() = tmp;',
);
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 $GENERIC) and PP functions have been expanded (like the
"loop" function we are going to explain next).
pp_def('sumover',
Pars => 'a(n); int+ [o] b()',
Code => '$GENERIC(b) tmp=0;
loop(n) %{ tmp += a(); %}
$b() = tmp;',
);
pp_def('symm',
Pars => 'a(n,n); [o]c(n,n);',
Code => 'loop(n) %{
int n2;
for(n2=n; n2<$SIZE(n); n2++) {
$c(n0 => n, n1 => n2) =
$c(n0 => n2, n1 => n) =
$a(n0 => n, n1 => n2);
}
%}
'
);
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).
$c() = $a() + $b();
if ( $a() != BADVAL && $b() != BADVAL ) {
$c() = $a() + $b();
} else {
$c() = BADVAL;
}
if ( bad_values_are_present ) {
fancy_threadloop_stuff {
BadCode
}
} else {
fancy_threadloop_stuff {
Code
}
}
if ( $ISBAD(a()) ) { printf("a() is bad\n"); }
if ( $ISBAD(a(n=>l)) ) { printf("element %d of a() is bad\n", l); }
Code => '$c() = $a() + $b();',
BadCode => '
if ( $ISBAD(a()) || $ISBAD(b()) ) {
$SETBAD(c());
} else {
$c() = $a() + $b();
}',
BadCode => '
if ( $ISGOOD(a()) && $ISGOOD(b()) ) {
$c() = $a() + $b();
} else {
$SETBAD(c());
}',
Interfacing your own/library functions using PP
Now, consider the following: you have your own C function
(that may in fact be part of some library you want to interface to PDL)
which takes as arguments two pointers to vectors of double:
void myfunc(int n,double *v1,double *v2);
pp_def('myfunc',
Pars => 'a(n); [o]b(n);',
GenericTypes => ['D'],
Code => 'myfunc($SIZE(n),$P(a),$P(b));'
);
pp_def('myfunc',
Pars => 'double a(n); double [o]b(n);',
Code => 'myfunc($SIZE(n),$P(a),$P(b));'
);
void myfunc(int n,float *v1,long *v2);
pp_def('myfunc',
Pars => 'float a(n); long [o]b(n);',
GenericTypes => ['F'],
Code => 'myfunc($SIZE(n),$P(a),$P(b));'
);
perl -MPDL::PP::Dump myfile.pd
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.
$Ttypeletters(type_alternatives)
void float_func(float *in, float *out);
void double_func(double *in, double *out);
pp_def('foofunc',
Pars => ' a(n); [o] b();',
Code => ' $TFD(float_func,double_func) ($P(a),$P(b));'
GenericTypes => [qw(F D)],
);
Code => ' $TFD(float,double)_func ($P(a),$P(b));'
'$TBSULFD('.(join ',',map {"long_identifier_name_$_"}
qw/byt short unseigned lounge flotte dubble/).');'
pp_def('pnmout',
Pars => 'a(m)',
OtherPars => "char* fd",
GenericTypes => [qw(B U S L)],
Code => 'PerlIO *fp;
IO *io;
io = GvIO(gv_fetchpv($COMP(fd),FALSE,SVt_PVIO));
if (!io || !(fp = IoIFP(io)))
croak("Can\'t figure out FP");
if (PerlIO_write(fp,$P(a),len) != len)
croak("Error writing pnm file");
');
open FILE,">out.dat" or die "couldn't open out.dat";
pnmout($pdl,'FILE');
pp_def('setdim',
Pars => '[o] a(n)',
OtherPars => 'int ns => n',
Code => 'loop(n) %{ $a() = n; %}',
);
setdim(($a=null),5);
print $a;
[ 0 1 2 3 4 ]
$a = hist($b);
setdim($a,-1);
pp_def('pnmout',
Pars => 'a(m)',
OtherPars => "char* fd",
GenericTypes => [qw(B U S L)],
Code => 'PerlIO *fp;
IO *io;
int len;
io = GvIO(gv_fetchpv($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,$P(a),len) != len)
croak("Error writing pnm file");
%}
');
pp_addhdr('
#define RAW 0
#define ASCII 1
');
pp_def('do_raworascii',
Pars => 'a(); b(); [o]c()',
OtherPars => 'int mode',
Code => ' switch ($COMP(mode)) {
case RAW:
threadloop %{
/* do raw stuff */
%}
break;
case ASCII:
threadloop %{
/* do ASCII stuff */
%}
break;
default:
croak("unknown mode");
}'
);
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.
pp_def( "myexternalfunc",
Pars => " p(m); x(n); [o] y; [t] work(n+m*m); ", ...
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));
";)
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;',
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.
int gsl_spline_init(gsl_spline * spline,
const double xa[], const double ya[], size_t size);
OtherPars => 'gsl_spline *spl'
OtherPars => 'IV spl'
INT2PTR(gsl_spline *, $COMP(spl))
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)));'
);
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).
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);
',
...
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('
#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 */
}
');
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(<<'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('use_myfunc gethynx');
pp_add_isa(' Some::Other::Class ');
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
');
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();
pp_done();
pp_core_importList('()')
use Core();
pp_core_importList(' qw/ barf /')
use Core qw/ barf/;
pp_setversion('0.0.3');
pp_deprecate_module( infavor => "PDL::NewNonDeprecatedModule" );
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()
Doc => undef
PMFunc => ''
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.
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.
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).
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:
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.
# 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); }
# 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]); }
(
'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)"},
)
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.
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.
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
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();'
*func_name = \&PDL::func_name;
PMFunc => '',
Appendix B: PP macros and functions
Macros
Macros labeled by (bad) are only used if bad-value support is compiled into
PDL.
functions
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.
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.
{At => 'Top'}
{At => 'Middle'}
{At => 'Bot'}
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
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.
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.
$piddle->myfunc(<args>);
PDL::myfunc($piddle, <args>);
MyPackage::myfunc($piddle, <args>);
qw(PDL::Exporter DynaLoader)
use PDL::Core;
pp_core_importlist('::Blarg');
use PDL::Core::Blarg;
pp_core_importlist(" ':Internal'");
use PDL::Core ':Internal';
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.
AUTHOR
Copyright(C) 1997 Tuomas J. Lukka (lukka [at] fas.harvard.edu), Karl
Glaazebrook (kgb [at] aaocbn1.aao.GOV.AU) and Christian Soeller
(c.soeller [at] auckland.ac.nz). All rights reserved.
Documentation updates Copyright(C) 2011 David Mertens
(dcmertens.perl [at] 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:
SEE ALSO
PDL