PDL::API(3pm)

NAME
PDL::API - making ndarrays from Perl and C/XS code

SYNOPSIS
  use PDL;
  sub mkmyndarray {
   ...
  }

DESCRIPTION
A simple cookbook how to create ndarrays manually. It covers both the Perl and the C/XS level. Additionally, it describes the PDL core routines that can be accessed from other modules. These routines basically define the PDL API. If you need to access ndarrays from C/XS you probably need to know about these functions.

Also described is the new (as of PDL 2.058) access to PDL operations via C functions, which the XS functions now call.

  Creating an ndarray manually from Perl
Sometimes you want to create an ndarray manually from binary data. You can do that at the Perl level. Examples in the distribution include some of the IO routines. The code snippet below illustrates the required steps.

   use Carp;
   sub mkmyndarray {
     my $class = shift;
     my $pdl  = $class->new;
     $pdl->set_datatype($PDL_B);
     $pdl->setdims([1,3,4]);
     my $dref = $pdl->get_dataref();
     # read data directly from file
     open my $file, '<data.dat' or die "couldn't open data.dat";
     my $len = $pdl->nelems*PDL::Core::howbig($pdl->get_datatype);
     croak "couldn't read enough data" if
       read( $file, $$dref, $len) != $len;
     close $file;
     $pdl->upd_data();
     return $pdl;
   }

  Creating an ndarray in C
The following example creates an ndarray at the C level. We use the "Inline" module which is a good way to interface Perl and C, using the "with" capability in Inline 0.68+.

Note that to create a "scalar" ndarray (with no dimensions at all, and a single element), just pass a zero-length "dims" array, with "ndims" as zero.

   use PDL::LiteF;

   $x = myfloatseq(); # exercise our C ndarray constructor

   print $x->info,"\n";

   use Inline with => 'PDL';
   use Inline C;
   Inline->init; # useful if you want to be able to 'do'-load this script

   __DATA__

   __C__

   static pdl* new_pdl(int datatype, PDL_Indx dims[], int ndims)
   {
     pdl *p = PDL->pdlnew();
     if (!p) return p;
     pdl_error err = PDL->setdims(p, dims, ndims);  /* set dims */
     if (err.error) { PDL->destroy(p); return NULL; }
     p->datatype = datatype;         /* and data type */
     err = PDL->allocdata (p);       /* allocate the data chunk */
     if (err.error) { PDL->destroy(p); return NULL; }
     return p;
   }

   pdl* myfloatseq()
   {
     PDL_Indx dims[] = {5,5,5};
     pdl *p = new_pdl(PDL_F,dims,3);
     if (!p) return p;
     PDL_Float *dataf = (PDL_Float *) p->data;
     PDL_Indx i; /* dimensions might be 64bits */

     for (i=0;i<5*5*5;i++)
       dataf[i] = i; /* the data must be initialized ! */
     return p;
   }

  Wrapping your own data into an ndarray
Sometimes you obtain a chunk of data from another source, for example an image processing library, etc. All you want to do in that case is wrap your data into an ndarray struct at the C level. Examples using this approach can be found in the IO modules (where FastRaw and FlexRaw use it for mmapped access) and the Gimp Perl module (that uses it to wrap Gimp pixel regions into ndarrays). The following script demonstrates a simple example:

   use PDL::LiteF;
   use PDL::Core::Dev;

   $y = mkndarray();

   print $y->info,"\n";

   imag1 $y;

   use Inline with => 'PDL';
   use Inline C;
   Inline->init;

   __DATA__

   __C__

   /* wrap a user supplied chunk of data into an ndarray
    * You must specify the dimensions (dims,ndims) and
    * the datatype (constants for the datatypes are declared
    * in pdl.h; e.g. PDL_B for byte type, etc)
    *
    * when the created ndarray 'p' is destroyed on the
    * Perl side the function passed as the 'delete_magic'
    * parameter will be called with the pointer to the pdl structure
    * and the 'delparam' argument.
    * This gives you an opportunity to perform any clean up
    * that is necessary. For example, you might have to
    * explicitly call a function to free the resources
    * associated with your data pointer.
    * At the very least 'delete_magic' should zero the ndarray's data pointer:
    *
    *     void delete_mydata(pdl* pdl, int param)
    *     {
    *       pdl->data = 0;
    *     }
    *     pdl *p = pdl_wrap(mydata, PDL_B, dims, ndims, delete_mydata,0);
    *
    * pdl_wrap returns the pointer to the pdl
    * that was created.
    */
   typedef void (*DelMagic)(pdl *, int param);
   static void default_magic(pdl *p, int pa) { p->data = 0; }
   static pdl* pdl_wrap(void *data, int datatype, PDL_Indx dims[],
                        int ndims, DelMagic delete_magic, int delparam)
   {
     pdl* p = PDL->pdlnew(); /* get the empty container */
     if (!p) return p;
     pdl_error err = PDL->setdims(p, dims, ndims);  /* set dims */
     if (err.error) { PDL->destroy(p); return NULL; }
     p->datatype = datatype;     /* and data type */
     p->data = data;             /* point it to your data */
     /* make sure the core doesn't meddle with your data */
     p->state |= PDL_DONTTOUCHDATA | PDL_ALLOCATED;
     if (delete_magic != NULL)
       PDL->add_deletedata_magic(p, delete_magic, delparam);
     else
       PDL->add_deletedata_magic(p, default_magic, 0);
     return p;
   }

   #define SZ 256
   /* a really silly function that makes a ramp image
    * in reality this could be an opaque function
    * in some library that you are using
    */
   static PDL_Byte* mkramp(void)
   {
     PDL_Byte *data;
     int i; /* should use PDL_Indx to support 64bit pdl indexing */

     if ((data = malloc(SZ*SZ*sizeof(PDL_Byte))) == NULL)
       croak("mkramp: Couldn't allocate memory");
     for (i=0;i<SZ*SZ;i++)
       data[i] = i % SZ;

     return data;
   }

   /* this function takes care of the required clean-up */
   static void delete_myramp(pdl* p, int param)
   {
     if (p->data)
       free(p->data);
     p->data = 0;
   }

   pdl* mkndarray()
   {
     PDL_Indx dims[] = {SZ,SZ};
     pdl *p;

     p = pdl_wrap((void *) mkramp(), PDL_B, dims, 2,
                  delete_myramp,0); /* the delparam is abitrarily set to 0 */
     return p;
   }

IMPLEMENTATION DETAILS

  The Core struct -- getting at PDL core routines at runtime
PDL uses a technique similar to that employed by the Tk modules to let other modules use its core routines. A pointer to all shared core PDL routines is stored in the $PDL::SHARE variable. XS code should get hold of this pointer at boot time so that the rest of the C/XS code can then use that pointer for access at run time. This initial loading of the pointer is most easily achieved using the functions "PDL_AUTO_INCLUDE" and "PDL_BOOT" that are defined and exported by "PDL::Core::Dev". Typical usage with the Inline module has already been demonstrated:

   use Inline with => 'PDL';

In earlier versions of "Inline", this was achieved like this:

   use Inline C => Config =>
     INC           => &PDL_INCLUDE,
     TYPEMAPS      => &PDL_TYPEMAP,
     AUTO_INCLUDE  => &PDL_AUTO_INCLUDE, # declarations
     BOOT          => &PDL_BOOT;         # code for the XS boot section

The code returned by "PDL_AUTO_INCLUDE" makes sure that pdlcore.h is included and declares the static variables to hold the pointer to the "Core" struct. It looks something like this:

   print PDL_AUTO_INCLUDE;

 #include <pdlcore.h>
 static Core* PDL; /* Structure holds core C functions */

The code returned by "PDL_BOOT" retrieves the $PDL::SHARE variable and initializes the pointer to the "Core" struct. For those who know their way around the Perl API here is the code:

   perl_require_pv ("PDL/Core.pm"); /* make sure PDL::Core is loaded */
#ifndef aTHX_
#define aTHX_
#endif
   if (SvTRUE (ERRSV)) Perl_croak(aTHX_ "%s",SvPV_nolen (ERRSV));
   SV* CoreSV = perl_get_sv("PDL::SHARE",FALSE); /* var with core structure */
   if (!CoreSV)
     Perl_croak(aTHX_ "We require the PDL::Core module, which was not found");
   if (!(PDL = INT2PTR(Core*,SvIV( CoreSV )))) /* Core* value */
     Perl_croak(aTHX_ "Got NULL pointer for PDL");
   if (PDL->Version != PDL_CORE_VERSION)
     Perl_croak(aTHX_ "[PDL->Version: \%d PDL_CORE_VERSION: \%d XS_VERSION: \%s] The code needs to be recompiled against the newly installed PDL", PDL->Version, PDL_CORE_VERSION, XS_VERSION);

The "Core" struct contains version info to ensure that the structure defined in pdlcore.h really corresponds to the one obtained at runtime. The code above tests for this

   if (PDL->Version != PDL_CORE_VERSION)
     ....

For more information on the Core struct see PDL::Internals.

With these preparations your code can now access the core routines as already shown in some of the examples above, e.g.

  pdl *p = PDL->pdlnew();

By default the C variable named "PDL" is used to hold the pointer to the "Core" struct. If that is (for whichever reason) a problem you can explicitly specify a name for the variable with the "PDL_AUTO_INCLUDE" and the "PDL_BOOT" routines:

   use Inline C => Config =>
     INC           => &PDL_INCLUDE,
     TYPEMAPS      => &PDL_TYPEMAP,
     AUTO_INCLUDE  => &PDL_AUTO_INCLUDE 'PDL_Corep',
     BOOT          => &PDL_BOOT 'PDL_Corep';

Make sure you use the same identifier with "PDL_AUTO_INCLUDE" and "PDL_BOOT" and use that same identifier in your own code. E.g., continuing from the example above:

  pdl *p = PDL_Corep->pdlnew();

  Some selected core routines explained
The full definition of the "Core" struct can be found in the file pdlcore.h. In the following the most frequently used member functions of this struct are briefly explained.

•   "pdl *SvPDLV(SV *sv)"

•   "pdl *SetSV_PDL(SV *sv, pdl *it)"

•   "pdl *pdlnew()"

    "pdlnew" returns an empty pdl object that is initialised like a "null" but with no data. Example:

      pdl *p = PDL->pdlnew();
      if (!p) return p;
      pdl_error err = PDL->setdims(p, dims, ndims);  /* set dims */
      if (err.error) { PDL->destroy(p); return NULL; }
      p->datatype = PDL_B;

    Returns "NULL" if a problem occurred, so check for that.

•   "pdl *null()"

    Returns "NULL" if a problem occurred, so check for that.

•   "SV *copy(pdl* p, char* )"

•   "void *smalloc(STRLEN nbytes)"

•   "int howbig(int pdl_datatype)"

•   "pdl_error add_deletedata_magic(pdl *p, void (*func)(pdl*, int), int param)"

•   "pdl_error allocdata(pdl *p)"

•   "pdl_error make_physical(pdl *p)"

•   "pdl_error make_physdims(pdl *p)"

•   "pdl_error make_physvaffine(pdl *p)"

•   "void pdl_barf(const char* pat,...)" and "void pdl_warn(const char* pat,...)"

    These are C-code equivalents of "barf" and "warn". They include special handling of error or warning messages during pthreading (i.e. processor multi-threading) that defer the messages until after pthreading is completed. When pthreading is complete, perl's "barf" or "warn" is called with the deferred messages. This is needed to keep from calling perl's "barf" or "warn" during pthreading, which can cause segfaults.

    Note that "barf" and "warn" have been redefined (using c-preprocessor macros) in pdlcore.h to "PDL->barf" and "PDL->warn". This is to keep any XS or PP code from calling perl's "barf" or "warn" directly, which can cause segfaults during pthreading.

    See PDL::ParallelCPU for more information on pthreading.

    NB As of 2.064, it is highly recommended that you do not call "barf" at all in PP code, but instead use $CROAK(). This will return a "pdl_error" which will transparently be used to throw the correct exception in Perl code, but can be handled suitably by non-Perl callers.

•

      converttype

    Used by "set_datatype" to change an ndarray's type, converting and possibly re-allocating the data if a different size. If the ndarray's "badflag" was set, its "badvalue" will become the default for the new type. Bad values will still be bad. As of 2.093, will physicalise its ndarray.

•

      converttypei_new

    Affine transformation used only by "get_convertedpdl" to convert an ndarray's type. Not bad-value aware.

•

      get_convertedpdl

    Used by "convert" in PDL::Core.

•

      affine_new

    Creates a child vaffine ndarray from given parent ndarray, with given offs (starting point for that pthread in that ndarray), inclist and dims.

•

      make_trans_mutual

    Triggers the actual running of a previously-set-up "pdl_trans".

•

      get

    Get data at given coordinates.

•

      get_offs

    Get data at given offset.

•

      put_offs

    Put data at given offset.

•

      setdims_careful

    Despite the name, just calls "resize_defaultincs" then "reallocbroadcastids" with one.

•

      destroy

    Destroy ndarray.

•

      reallocdims

    Cause the ndarray to have given number of dimensions, destroying previous ones.

•

      reallocbroadcastids

    Reallocate n broadcastids. Set the new extra ones to the end.

•

      resize_defaultincs

    Recalculate default increments from "dims", and grow the PDL data.

  Handy macros from pdl.h
Some of the C API functions return "PDL_Anyval" C type which is a structure and therefore requires special handling.

You might want to use for example "get_pdl_badvalue" function:

 /* THIS DOES NOT WORK! (although it did in older PDL) */
 if( PDL->get_pdl_badvalue(a) == 0 )  { ... }

 /* THIS IS CORRECT */
 double bad_a;
 PDL_Anyval bv = PDL->get_pdl_badvalue(a);
 if (bv.type < 0) croak("error getting badvalue");
 ANYVAL_TO_CTYPE(bad_a, double, bv);
 if( bad_a == 0 ) { ... }

As of PDL 2.014, in pdl.h there are the following macros for handling PDL_Anyval from C code:

 ANYVAL_FROM_CTYPE(out_anyval, out_anyval_type, in_variable)
 ANYVAL_TO_CTYPE(out_variable, out_ctype, in_anyval)
 ANYVAL_EQ_ANYVAL(x, y) /* returns -1 on type error */

As of PDL 2.039 (returns -1 rather than croaking on failure as of 2.064) there is:

 ANYVAL_ISNAN(anyval)

As of PDL 2.040 (changed parameter list, also returns -1 rather than croaking on failure, in 2.064) - you need to check the badflag first:

 ANYVAL_ISBAD(in_anyval, badval)

e.g.

 int badflag = (x->state & PDL_BADVAL) > 0;
 PDL_Anyval badval = pdl_get_pdl_badvalue(x);
 if (badflag) {
   int isbad = ANYVAL_ISBAD(result, badval);
   if (isbad == -1) croak("ANYVAL_ISBAD error on types %d, %d", result.type, badval.type);
   if (isbad)
     RETVAL = newSVpvn( "BAD", 3 );
   else
     ANYVAL_TO_SV(RETVAL, result);
 } else
   ANYVAL_TO_SV(RETVAL, result);

As of PDL 2.058, there are:

  ANYVAL_FROM_CTYPE_OFFSET(result, datatype, x, ioff);
  ANYVAL_TO_CTYPE_OFFSET(x, ioff, datatype, value);

The latter dispatches on both the destination type and the input "anyval" type. They are intended for retrieving values from, and setting them within, ndarrays.

As of PDL 2.048, in pdlperl.h there are:

 ANYVAL_FROM_SV(out_anyval, in_SV, use_undefval, forced_type, warn_undef)
 ANYVAL_TO_SV(out_SV, in_anyval)

Because these are used in the PDL typemap, you will need to include pdlperl.h in any XS file with functions that take or return a "PDL_Anyval".

As of 2.083, "ANYVAL_TO_SV" assigns a value into the passed "SV*" using the Perl API, rather than assigning the given C value to having a newly-created "SV*", so the caller is responsible for memory-management.

PDL_GENERICSWITCH et al

As of 2.058, there is a mechanism to use pure C macros (without Perl generation) to do PDL type-generic operations, using the X macro <https://en.wikipedia.org/wiki/X_macro> concept. A simple(ish) example, that extracts the right "struct" member based on an ndarray's "type" variable (from "badvalue" in PDL::Bad):

  #define X(datatype, ctype, ppsym, ...) \
      *((ctype *)p->data) = PDL->bvals.ppsym;
      PDL_GENERICSWITCH(PDL_TYPELIST_ALL, type, X, croak("Not a known data type code=%d", type))
  #undef X

An example using a mapping from one ndarray type to another, with an outer and inner type, from the same function:

  #define X_OUTER(datatype, ctype, ppsym, ...) \
        ctype cnewval = val.value.ppsym;
  #define X_INNER(datatype, ctype, ppsym, ...) \
        PDL->bvals.ppsym = cnewval;
        PDL_GENERICSWITCH2(
          PDL_TYPELIST_ALL, val.type, X_OUTER, croak("Not a known data type code=%d", val.type),
          PDL_TYPELIST_ALL_, type, X_INNER, croak("Not a known data type code=%d", type))
  #undef X_OUTER
  #undef X_INNER

You will note the above examples simply hardcode external variable names, e.g. "cnewval", which they can afford to do as they are very local. In lambda calculus terms, those variables are not bound by the C macros.

Next is an example that does such lambda binding, adding "outany, inval," after the mandatory arguments to "PDL_GENERICSWITCH". The additional comma after "inval" is absolutely needed, so that when the arguments are expanded at the start of arguments to the "X macro" (here, "ANYVAL_FROM_CTYPE_X"), it's syntactically valid:

  #define ANYVAL_FROM_CTYPE_X(outany, inval, datatype, ctype, ppsym, ...) \
    (outany).type = datatype; (outany).value.ppsym = (inval);
  #define ANYVAL_FROM_CTYPE(outany,avtype,inval) \
    PDL_GENERICSWITCH(PDL_TYPELIST_ALL, avtype, ANYVAL_FROM_CTYPE_X, \
      outany.type = -1; outany.value.H = 0, \
      outany, inval, \
    )

A more complex example, implemented for 2.096, does away with the last Perl code generation for pdlperl.h, and unpacks the "switch" statement to use several "lister macros":

  #define ANYVAL_UNSIGNED_X(outsv, inany, sym, ctype, ppsym, ...) \
    sv_setuv(outsv, (UV)(inany.value.ppsym));
  #define ANYVAL_SIGNED_X(outsv, inany, sym, ctype, ppsym, ...) \
    sv_setiv(outsv, (IV)(inany.value.ppsym));
  #define ANYVAL_FLOATREAL_X(outsv, inany, sym, ctype, ppsym, ...) \
    sv_setnv(outsv, (NV)(inany.value.ppsym));
  #define ANYVAL_COMPLEX_X(outsv, inany, sym, ctype, ppsym, shortctype, defbval, realctype, convertfunc, floatsuffix, ...) \
    PDL_MAKE_PERL_COMPLEX(outsv, creal ## floatsuffix(inany.value.ppsym), cimag ## floatsuffix(inany.value.ppsym));
  #define ANYVAL_TO_SV(outsv,inany) do { switch (inany.type) { \
    PDL_TYPELIST_UNSIGNED(PDL_GENERICSWITCH_CASE, ANYVAL_UNSIGNED_X, (outsv,inany,),) \
    PDL_TYPELIST_SIGNED(PDL_GENERICSWITCH_CASE, ANYVAL_SIGNED_X, (outsv,inany,),) \
    PDL_TYPELIST_FLOATREAL(PDL_GENERICSWITCH_CASE, ANYVAL_FLOATREAL_X, (outsv,inany,),) \
    PDL_TYPELIST_COMPLEX(PDL_GENERICSWITCH_CASE, ANYVAL_COMPLEX_X, (outsv,inany,),) \
    default: outsv = &PL_sv_undef; \
    } \
   } while (0)

Points this author is noting while he still understands them (these macros are somewhat fiendish), having revisited them some months after creating this lambda-binding capability:

•   as with the last example, the "X macro" gets additional arguments at the start;

•   the "PDL_GENERICSWITCH_CASE" macro needs those wrapped in parentheses so the C preprocessor will treat them as one thing (the "PDL_GENERICSWITCH" system does this for you);

•   passing those on needs the additional "," at the end of that parenthesised group so that when it is prepended to the expansion of arguments in the no-extra-arguments case, chaos does not ensue.

  Access to PDL operations as C functions
As of 2.058, all PDL operations can be accessed from C code in a similar way to XS functions, since that is what the XS functions now call. Each module defines various C functions and data-structures for each operation, as needed to operate as a PDL transformation. The entry point from outside (and from XS functions) is a C function called "pdl_(operationname)_run", with a signature derived from its "Pars" and "OtherPars". E.g.

  # from PDL::Primitive
  pp_def('wtstat',
    Pars => 'a(n); wt(n); avg(); [o]b();',
    OtherPars => 'int deg',
    # ...
  );

has the C signature:

  void pdl_run_wtstat(pdl *a, pdl *wt, pdl *avg, pdl *b, int deg);

Not very surprisingly, all "pdl*" parameters must be initialised (at least to "PDL->null" status), and they are changed according to the operation's specification. This makes the XS "_(name)_int" non-varargs XS functions very thin layers over this.

SEE ALSO
PDL

Inline

BUGS
This manpage is still under development. Feedback and corrections are welcome.

COPYRIGHT
Copyright 2013 Chris Marshall (chm@cpan.org).

Copyright 2010 Christian Soeller (c.soeller@auckland.ac.nz). You can distribute and/or modify this document under the same terms as the current Perl license.

See: http://dev.perl.org/licenses/