pdl 1:2.007-2build1 / usr / lib / perl5 / PDL / FAQ.pod

=head1 NAME

PDL::FAQ - Frequently asked questions about PDL


=head1 VERSION

Current FAQ version:  1.004


=head1 DESCRIPTION

This is version 1.004 of the PDL FAQ, a collection of  frequently 
asked questions about PDL - the Perl Data Language.  




=head1 ABOUT THIS DOCUMENT


=head2 Q: 1.1    Where to find this document  


You can find the latest version of this document at 
L<http://pdl.perl.org/?docs=FAQ&title=Frequently%20Asked%20Questions> .


=head2 Q: 1.2    How to contribute to this document  


This is a considerably reworked version of the PDL FAQ. As
such many errors might have crept in and many updates might
not have made it in.  You are explicitly encouraged to let us
know about questions which you think should be answered in
this document but currently aren't.

Similarly, if you think parts of this document are
unclear, please tell the FAQ maintainer about it. Where
a specific answer is taken in full from someones posting
the authorship should be indicated, let the FAQ maintainer
know if it isn't. For more general information explicit
acknowledgment is not made in the text, but rather there
is an incomplete list of contributors at the end of this
document. Please contact the FAQ maintainer if you feel
hard done by.

Send your comments, additions, suggestions or corrections
to the PDL mailing list at perldl@jach.hawaii.edu. See Q: 3.2
below for instructions on how to join the mailing lists.




=head1 GENERAL QUESTIONS


=head2 Q: 2.1    What is PDL ?  


PDL stands for 
I<Perl Data  Language> . To say it with the words of Karl Glazebrook,
initiator of the PDL project:


    The PDL concept is to give standard perl5 the ability
    to COMPACTLY store and SPEEDILY manipulate the large
    N-dimensional data sets which are the bread and butter
    of scientific computing. e.g. $a=$b+$c can add two
    2048x2048 images in only a fraction of a second.


It provides tons of useful
functionality for scientific and numeric analysis.

For readers familiar with other scientific data evaluation packages it
may be helpful to add that PDL is in many respects similar to IDL,
MATLAB and similar packages. However, it tries to improve on a number
of issues which were perceived (by the authors of PDL) as shortcomings
of those existing packages.



=head2 Q: 2.2    Who supports PDL? Who develops it?  


PDL is supported by its users. General informal support for PDL
is provided through the PDL mailing list (perldl@jach.hawaii.edu ,
see below).

As a Perl extension (see Q: 2.5 below) it is devoted to the idea of free and
open development put forth by the Perl community. PDL was and is being
actively developed by a loosely knit group of people around the world who
coordinate their activities through the PDL development mailing list
(pdl-porters@jach.hawaii.edu , see Q: 3.2 below). If you would like to join in the
ongoing efforts to improve PDL please join this list.


=head2 Q: 2.3    Why yet another Data Language ?  


There are actually several reasons and everyone should decide for
himself which are the most important ones:

=over 4

=item *

PDL is "free software". The authors of PDL think
that this concept has several advantages: everyone has
access to the sources -> better debugging, easily
adaptable to your own needs, extensible for your purposes,
etc... In comparison with commercial packages such as MATLAB
and IDL this is of considerable importance for workers who
want to do some work at home and cannot afford the
considerable cost to buy commercial packages for personal
use.

=item *

PDL is based on a powerful and well designed scripting
language: Perl. In contrast to other scientific/numeric data
analysis languages it has been designed using the features of 
a proven language instead of having grown into existence from 
scratch. Defining the control structures while features were 
added during development leads to languages that often appear 
clumsy and badly planned for most existing packages with 
similar scope as PDL.

=item *

Using Perl as the basis a PDL programmer has all the
powerful features of Perl at his hand, right from the
start. This includes regular expressions, associative arrays
(hashes), well designed interfaces to the operating system,
network, etc. Experience has shown that even in mainly
numerically oriented programming it is often extremely handy
if you have easy access to powerful semi-numerical or
completely non-numerical functionality as well. For example,
you might want to offer the results of a complicated
computation as a server process to other processes on the
network, perhaps directly accepting input from other
processes on the network. Using Perl and existing Perl
extension packages things like this are no problem at all
(and it all will fit into your "PDL script").

=item *

Extremely easy extensibility and interoperability as PDL is
a Perl extension; development support for Perl extensions is
an integral part of Perl and there are already numerous
extensions to standard Perl freely available on the network.

=item *

Integral language features of Perl (regular expressions,
hashes, object modules) immensely facilitated development
and implementation of key concepts of PDL. One of the most
striking examples for this point is probably L<PDL::PP|PDL::PP> 
(see Q: 6.16 below), a code generator/parser/pre-processor that
generates PDL functions from concise descriptions.

=item *

None of the existing data languages follow the Perl language
rules, which the authors firmly believe in:

=over 4

=item *

TIMTOWTDI: There is more than one way to do it.
Minimalist languages are interesting for computer
scientists, but for users, a little bit of redundancy
makes things wildly easier to cope with and allows
individual programming styles - just as people speak in
different ways. For many people this will undoubtedly be
a reason to avoid PDL ;)

=item *

Simple things are simple, complicated things possible:
Things that are often done should be easy to do in the language,
whereas seldom done things shouldn't be too cumbersome.

=back

All existing languages violate at least one of these rules.

=item *

As a project for the future PDL should be able to use super
computer features, e.g. vector capabilities/parallel processing,
GPGPU acceleration. This will probably be achieved by having 
L<PDL::PP|PDL::PP> (see Q: 6.16 below) generate appropriate code
on such architectures to exploit these features.

=item *

[ fill in your personal 111 favourite reasons here...]

=back


=head2 Q: 2.4    What is PDL good for ?  


Just in case you do not yet know what the main features of PDL are and
what one could do with them, here is a (necessarily selective) list of
key features:

PDL is well suited for matrix computations, general handling
of multidimensional data, image processing, general scientific
computation, numerical applications. It supports I/O for many
popular image and data formats, 1D (line plots), 2D (images)
and 3D (volume visualization, surface plots via OpenGL - for
instance implemented using Mesa or video card OpenGL drivers),
graphics display capabilities and implements many numerical and
semi-numerical algorithms.

Through the powerful pre-processor it is also easy to interface Perl
to your favorite C routines, more of that further below.


=head2 Q: 2.5    What is the connection between PDL and Perl ?  


PDL is a Perl5 extension package. As such it needs an existing Perl5
installation (see below) to run. Furthermore, much of PDL is written in
Perl (+ some core functionality that is written in C). PDL programs
are (syntactically) just Perl scripts that happen to use some of the
functionality implemented by the package "PDL".


=head2 Q: 2.6    What do I need to run PDL on my machine ?  


Since PDL is just a Perl5 package you need first of
all an installation of Perl5 on your machine. As of this
writing PDL requires version 5.8 of perl, or higher.  More
information on where and how to get a Perl installation
can be found at the Perl home page L<http://www.perl.org>
and at many CPAN sites (if you do not know what I<CPAN>
is, check the answer to the next question).

To build PDL you also need a working C compiler, support
for Xsubs, and the package Extutils::MakeMaker. If you
don't have a compiler there might be a binary distribution
available, see "Binary distributions" below.

If you can (or cannot) get PDL working on a new (previously
unsupported) platform we would like to hear about it. Please,
report your success/failure to the PDL mailing list at 
perldl@jach.hawaii.edu . We will do our best to assist
you in porting PDL to a new system.


=head2 Q: 2.7    Where do I get it?  


PDL is available as source distribution in the 
I<Comprehensive Perl Archive Network> (or CPAN) and from the
sourceforge.net project page at L<https://sourceforge.net/projects/pdl/files/>.
The CPAN archives contains not only the PDL distribution but
also just about everything else that is Perl-related.  CPAN is
mirrored by dozens of sites all over the world.  The main site
is L<http://www.cpan.org>, and local CPAN sites (mirrors) can be
found there. Within CPAN you find the latest released version of
PDL in the directory /modules/by-module/PDL/. PDL's homepage is at
L<http://pdl.perl.org> and the latest version can also be downloaded
from there.


=head2 Q: 2.8    What do I have to pay to get PDL?  


We are delighted to be able to give you the nicest possible
answer on a question like this: PDL is *free software* and all
sources are publicly available. But still, there are some
copyrights to comply with. So please, try to be as nice as we
(the PDL authors) are and try to comply with them.

Oh, before you think it is *completely* free: you
have to invest some time to pull the distribution from the net,
compile and install it and (maybe) read the manuals.



=head1 GETTING HELP/MORE INFORMATION



=head2 Q: 3.1    Where can I get information on PDL?  


The complete PDL documentation is available with the PDL distribution.
Use the command C<perldoc PDL> to start learning about PDL.

The easiest way by far, however, to get familiar with PDL is to use
the PDL on-line help facility from within the PDL
shell, C<pdl2>  Just type C<pdl2> at your system prompt. Once you are inside the
C<pdl2> shell type C<help> .  Using the C<help> and C<apropos> commands
inside the shell you should be able to find the way round the
documentation.

Even better, you can immediately try your newly acquired
knowledge about PDL by issuing PDL/Perl commands directly at the command
line. To illustrate this process, here is the record of a typical
C<pdl2> session of a PDL beginner (lengthy output is only symbolically
reproduced in braces ( <... ...> ) ):

    unix> pdl2
    pdl> help
    < ... help output ... >
    pdl> help PDL::QuickStart
    < ... perldoc page ... >
    pdl> $a = pdl (1,5,7.3,1.0)
    pdl> $b = sequence float, 4, 4
    pdl> help inner
    < ... help on the 'inner' function ... >
    pdl> $c = inner $a, $b
    pdl> p $c
    [22.6 79.8 137 194.2]

For further sources of information that are accessible through the
Internet see next question.


=head2 Q: 3.2    Are there other PDL information sources on the Internet?  


First of all, for all purely Perl-related questions there are
tons of sources on the net. Good points to start are 
L<http://www.perl.com> and L<http://www.perl.org> .

The PDL home site can be accessed by pointing your web browser to 
L<http://pdl.perl.org> . It has tons of goodies for anyone interested in PDL:

=over 4

=item * 

PDL distributions 

=item * 

On-line documentation 

=item * 

Pointers to an HTML archive of the PDL mailing lists

=item * 

A list of platforms on which PDL has been successfully tested. 

=item * 

News about recently added features, ported libraries, etc.

=item * 

Name of the current pumpkin holders for the different PDL modules (if
you want to know what that means you better had a look at the web
pages).

=back

If you are interested in PDL in general you can join the PDL mailing
list perldl@jach.hawaii.edu. This is a forum to discuss programming
issues in PDL, report bugs, seek assistance with PDL related problems,
etc. To subscribe, fill out the form at
L<http://mailman.jach.hawaii.edu/mailman/listinfo/perldl> .

A searchable archive and a hypertext version of the traffic on this
list (1997-2004) can be found at
L<http://www.xray.mpe.mpg.de/mailing-lists/perldl/> . More recent
messages (since June 2005) can be found at
L<http://mailman.jach.hawaii.edu/mailman/listinfo/perldl> .

If you are interested in all the technical details of the ongoing PDL
development you can join the PDL developers mailing list
pdl-porters@jach.hawaii.edu . To subscribe, fill out the form at
L<http://mailman.jach.hawaii.edu/mailman/listinfo/pdl-porters> .

A searchable archive and a hypertext version
of the traffic on this list (1997-2004) can be found at 
L<http://www.xray.mpe.mpg.de/mailing-lists/pdl-porters/> . More recent messages 
(since June 2005) can be found at 
L<http://mailman.jach.hawaii.edu/mailman/listinfo/pdl-porters> .

Cross-posting between these lists should be avoided unless there is a
I<very> good reason for doing that.


=head2 Q: 3.3    What is the current version of PDL ?  


As of this writing (FAQ version 1.004 of 16 Sep 2013) the latest stable version
is 2.006.  The latest stable version should always be available from a CPAN
mirror site near you (see L<Question 2.7|"Q: 2.7    Where do I get it?"> for
info on where to get PDL).

The most current (possibly unstable) version of PDL can be obtained 
from the Git repository, see L<Question 4.10|"Q: 4.9    How do I get PDL via Git?">
and periodic CPAN developers releases of the Git code will be made for testing
purposes and more general availability.  The current post-PDL-2.006 developers
release of PDL is available as F<CHM/PDL-2.006_07.tar.gz> .


=head2 Q: 3.4    I want to contribute to the further development of PDL. How can I help?  


Two ways that you could help almost immediately are (1) participate
in CPAN Testers for PDL and related modules, and (2) proofreading and
clarifying the PDL documentation so that it is most useable for PDL
users, especially new users.

To participate in CPAN Testers and contribute test reports, the page
L<http://wiki.cpantesters.org/wiki/QuickStart> has instructions for
starting for either C<CPAN> or C<CPANPLUS> users.

If you have a certain project in mind you should check if somebody
else is already working on it or if you could benefit from existing
modules. Do so by posting your planned project to the PDL developers
mailing list at pdl-porters@jach.hawaii.edu . See the subscription
instructions in L<Question 3.2|"Q: 3.2 Are there other PDL information sources on the Internet?">.
We are always looking for people to write code and/or documentation ;).


=head2 Q: 3.5    I think I have found a bug in the current version of PDL. What shall I do?  


First, make sure that the bug/problem you came across has not already been
dealt with somewhere else in this FAQ.  Secondly, you can check the
searchable archive of the PDL mailing lists to find whether
this bug has already been discussed.  If you still haven't found
any explanations you can post a bug report to perldl@jach.hawaii.edu ,
or through the Bugs link on L<http://pdl.perl.org> .  See the F<BUGS>
file in the PDL distribution for what information to include.  If
you are unsure, discussions via the perldl mailing list can be
most helpful.



=head1 INSTALLATION



=head2 Q: 4.1    I have problems installing PDL. What shall I do?  


First make sure you have read the file F<INSTALL> in the distribution.
This contains a list of common problems which are unnecessary to repeat
here.

Next, check the file F<perldl.conf> to see if by editing the
configuration options in that file you will be able to successfully
build PDL. Some of the modules need additional software installed,
please refer to the file F<DEPENDENCIES> for further details. Make sure
to edit the location of these packages in perldl.conf if you have them
in non-standard locations.

N.B. Unix shell specific: If you would like to save an edited perldl.conf
for future builds just copy it as F<~/.perldl.conf> into your home directory
where it will be picked up automatically during the PDL build process.

Also, check for another, pre-existing version of PDL on the build
system.  Multiple PDL installs in the same PATH or @INC can cause
puzzling test or build failures.

If you still can't make it work properly please submit a bug
report including detailed information on the problems you
encountered to the perldl mailing list ( perldl@jach.hawaii.edu ,
see also above). Response is often rapid.


=head2 Q: 4.2    Are there configuration files for PDL I have to edit?  


Most users should not have to edit any configuration files manually.
However, in some cases you might have to supply some information
about awkwardly placed include files/libraries or you might want
to explicitly disable building some of the optional PDL modules.
Check the files F<INSTALL> and F<perldl.conf> for details.

If you had to manually edit F<perldl.conf> and are happy with the
results you can keep the file handy for future
reference. Place it in F<~/.perldl.conf> where it will be picked
up automatically or use C<perl Makefile.PL  PDLCONF=your_file_name>
next time you build PDL.


=head2 Q: 4.3    Do I need other software for successful operation?  


For the basic PDL functionality you don't need any
additional software.  However, some of the optional PDL
modules included in the distribution (notably most graphics
and some I/O modules) require certain other
libraries/programs to be installed. Check the file
F<DEPENDENCIES> in the distribution for details and directions
on how to get these.


=head2 Q: 4.4    How can I install PDL in a non-standard location?


To install PDL in a non-standard location, use the INSTALL_BASE
option in the C<perl Makefile.PL> configure step.  For example,
C<perl Makefile.PL INSTALL_BASE=/mydir/perl5> will configure PDL
to install into the tree rooted at C</mydir/perl5>.  For more
details see L<perlfaq8/"How do I keep my own module/library directory?">
and subsequent sections.  Another alternative is to use L<local::lib>
to do the heavy listing for the needed configuration.


=head2 Q: 4.5    How can I force a completely clean installation?


To guarantee a completely clean installation of PDL, you will need
to first delete the current installation files and folders.  These
will be all directories named C<PDL> in the Perl C<@INC> path,
files named C<*Pdlpp*> in any C<Inline> directories, and the 
programs C<pdl, pdldoc, pdl2, perldl, and pptemplate>.  Then just build
and install as usual.  This is much easier to keep track of if you
always install C<PDL> into a non-standard location.  See Q: 4.4 above.



=head1 BINARY DISTRIBUTIONS



=head2 Q: 4.5    What binary distributions are available?  


Information about binary distributions of PDL can be found on
L<http://pdl.perl.org> .  At present there are binary distributions 
of PDL for Linux (RedHat and Debian), FreeBSD, Mac OS X and Windows, 
though they might not be the most recent version.

If someone is interested in providing binary distributions for other 
architectures, that would be very welcome. Let us know on the 
pdl-porters@jach.hawaii.edu mailing list. Also check your Linux
distribution's package manager as many now include PDL.  PPMs
for win32 versions (both 32bit and 64bit) are also available.


=head2 Q: 4.6    Does PDL run on Linux? (And what about packages?)  


Yes, PDL does run on Linux and indeed much of the development
has been done under Linux. On L<http://pdl.perl.org> you can find 
links to packages for some of the major distributions. Also 
check your distribution's package manager (yum, apt, urpmi, ...)
as PDL is now found by many of these.


=head2 Q: 4.7    Does PDL run under Windows?  


PDL builds fine on Win32 using MinGW or Microsoft compilers.  See
the F<win32/INSTALL> file in the PDL source distribution for details.
Other compilers have not been tested--input is welcome.  There is
also a distribution of PDL through ActiveState's ppm, though it
might not always be the latest version.  PDL-2.006 builds out of
the box on Strawberry Perl and ActiveState Perl.



=head1 CVS, GIT, AND ON-GOING DEVELOPMENT



=head2 Q: 4.8    Can I get PDL via CVS?   


No.  PDL development was conducted with a CVS repository from December
1999 to April 2009.  In April 2009 the project switched to the
Git version control system (see L<http://git-scm.com>).


=head2 Q: 4.9    How do I get PDL via Git?


Assume you have Git installed on your system and want to download the
project source code into the directory C<PDL>. To get read-only access
to the repository, you type at the command line

   git clone git://git.code.sf.net/p/pdl/code pdl-code

For official PDL developers, to get read/write access to the repository
type at the command line

   git clone ssh://USERNAME@git.code.sf.net/p/pdl/code pdl-code


=head2 Q: 4.10   I had a problem with the Git version, how do I check if someone has submitted a patch?  


The Sourceforge system contains a patch-manager which contains patches
that have not yet been applied to the distribution. This can be
accessed via the Tickets menu at PDL's Sourceforge project page
L<http://sourceforge.net/projects/pdl> .

In addition, if you are not subscribing to the mailing list,
check the archive of the C<pdl-porters> and C<perldl> mailing lists.
See L<Question 3.2|"Q: 3.2 Are there other PDL information sources on the Internet?"> for details.


=head2 Q: 4.11   I have gotten developer access to Git, how do I upload my changes?


The first thing you should do is to read the Git documentation and
learn the basics about Git. There are many sources available online.
But here are the basics:

Before you upload your changes, commit them to YOUR repository

   git add <file1> <file2> ...
   git commit

or combine these two with 

   git commit -a

Then pull in any changes others have made

   git pull origin

Test the PDL before you push it to the main repository.  If the
code is broken for you, then it is most likely broken for others
and they won't be happy to have their recent PDL fail to build!
NOTE: git makes it very easy to maintain a separate branch of
development.  [ TBD, provide information on how ].

Then update the shared repository (at SF.net) with your changes

   git push origin master



=head1 PDL JARGON



=head2 Q: 5.1    What is threading (is PDL a newsreader) ?  


Unfortunately, in the context of PDL the term threading can have two
different (but related) meanings:

=over 4

=item *

When mentioned in the F<INSTALL> directions and possibly
during the build process we have the usual computer science
meaning of multi-threading in mind (useful mainly on
multiprocessor machines or clusters)

=item *

PDL threading of operations on piddles (as mentioned in the
indexing docs) is the iteration of a basic operation over
appropriate sub-slices of piddles, e.g. the inner product 
C<inner $a, $b> of a (3) pdl C<$a> and a (3,5,4) pdl 
C<$b> results in a (5,4) piddle where each
value is the result of an inner product of the (3) pdl with a
(3) sub-slice of the (3,5,4) piddle.  For details check
L<PDL::Indexing|PDL::Indexing> 

=back

PDL threading leads naturally to potentially parallel code
which can make use of multi threading on multiprocessor
machines/networks; there you have the connection between the
two types of use of the term. 


=head2 Q: 5.2    What is a piddle?  


Well, PDL scalar variables (which are instances of a particular class
of Perl objects, i.e. blessed thingies (see C<perldoc perlobj> )) are
in common PDL parlance often called I<piddles> (for example, check the
mailing list archives).  Err, clear?  If not, simply use the term
I<piddle> when you refer to a PDL variable (an instance of a PDL
object as you might remember) regardless of what actual data the PDL
variable contains.



=head1 TECHNICAL QUESTIONS



=head2 Q: 6.1    What is perldl?   What is pdl2?


Sometimes C<perldl> (C<pdl2>) is used as a synonym for PDL. Strictly
speaking, however, the name C<perldl> (C<pdl2>) is reserved for the
little shell that comes with the PDL distribution and is
supposed to be used for the interactive prototyping of PDL
scripts. For details check L<perldl> or L<pdl2>.


=head2 Q: 6.2    How do I get on-line help for PDL?  


Just type C<help> (shortcut = "?") at the C<pdl2> shell 
prompt and proceed from there. Another useful command 
is the C<apropos> (shortcut = "??") command.
Also try the C<demo> command in the C<perldl> or C<pdl2>
shell if you are new to PDL.



=head1 MANIPULATION OF PIDDLES



=head2 Q: 6.3    I want to access the third element of a pdl but $a[2] doesn't work ?!  


See answer to the next question why the normal Perl array syntax doesn't
work for piddles.


=head2 Q: 6.4    The docs say piddles are some kind of array. But why doesn't the Perl array syntax work with piddles then ?  


OK, you are right in a way. The docs say that piddles can be
thought of arrays.  More specifically, it says (
L<PDL::QuickStart|PDL::QuickStart> ):

    I find when using the Perl Data Language it is most useful
    to think of standard Perl @x variables as "lists" of generic
    "things" and PDL variables like $x as "arrays" which can be
    contained in lists or hashes.

So, while piddles can be thought of as some kind of
multi-dimensional array they are 
B< not> arrays in the Perl sense. Rather,
from the point of view of Perl they are some special class
(which is currently implemented as an opaque pointer to some
stuff in memory) and therefore need special functions (or
'methods' if you are using the OO version) to access
individual elements or a range of elements. The
functions/methods to check are 
C<at> / C<set> (see
L<the section 'Sections' in PDL::QuickStart|PDL::QuickStart/"Sections"> ) or the powerful 
C<slice> function and friends (see L<PDL::Slices|PDL::Slices> and 
L<PDL::Indexing|PDL::Indexing> and especially L<PDL::NiceSlice|PDL::NiceSlice> ).

Finally, to confuse you completely, you can have Perl arrays
of piddles, e.g. C<$spec[3]> can refer to a pdl representing ,e.g,
a spectrum, where C<$spec[3]> is the fourth element of the Perl
list (or array ;) C<@spec> .  This may be confusing but is 
very useful !


=head2 Q: 6.5    How do I concatenate piddles?  


Most people will try to form new piddles from old piddles
using some variation over the theme: 
C<$a =  pdl([$b, 0, 2])> , but this does not work. The way to
concatenate piddles is to use the function 
C<cat> (see also C<append> and C<glue>). Similarly you can split piddles
using the command C<dog> .


=head2 Q: 6.6    Sometimes I am getting these strange results when using inplace  operations?   


This question is related to the C<inplace> function. From the
documentation (see L<PDL::QuickStart>):

    Most functions, e.g. log(), return a result which is a
    transformation of their argument. This makes for good
    programming practice. However many operations can be done
    "in-place" and this may be required when large arrays are in
    use and memory is at a premium. For these circumstances the
    operator inplace() is provided which prevents the extra copy
    and allows the argument to be modified. e.g.:
    
    $x = log($array);          # $array unaffected
    log( inplace($bigarray) ); # $bigarray changed in situ

And also from the doc !!:

    Obviously when used with some functions which can not be
    applied in situ (e.g. convolve()) unexpected effects may
    occur!

=for comment Check the list of PDL functions at the end of PDL.pod which points out
C<inplace>-safe functions.  No longer in PDL.pod, need to fix!!


=head2 Q: 6.7    What is this strange usage of the string concatenation operator  C<.=>  in PDL scripts?  


See next question on assignment in PDL.


=head2 Q: 6.8    Why are there two different kinds of assignment in PDL ?  


This is caused by the fact that currently the assignment
operator C<=> allows only restricted
overloading. For some purposes of PDL it turned out to be
necessary to have more control over the overloading of an
assignment operator. Therefore, PDL peruses the operator 
C<.=> for certain types of assignments.


=head2 Q: 6.9    How do I set a set of values in a piddle?  


In Perl 5.6.7 and higher this assignment can be made
using lvalue subroutines:

    pdl> $a = sequence(5); p $a
    [0 1 2 3 4]
    pdl> $a->slice('1:2') .= pdl([5,6])
    pdl> p $a
    [0 5 6 3 4]

see L<PDL::Lvalue> for more info.  PDL also supports a more
matrix-like slice syntax via the L<PDL::NiceSlice|PDL::NiceSlice> module:

    pdl> $a(1:2) .= pdl([5,6])
    pdl> p $a
    [0 5 6 3 4]

With versions of Perl prior to 5.6.7 B<or when running under
the perl debugger> this has to be done using a temporary variable: 

    pdl> $a = sequence(5); p $a
    [0 1 2 3 4]
    pdl> $tmp = $a->slice('1:2'); p $tmp;
    [1 2]
    pdl> $tmp .= pdl([5, 6]);    # Note .= !!
    pdl> p $a
    [0 5 6 3 4]

This can also be made into one expression, which is often
seen in PDL code:

    pdl> ($tmp = $a->slice('1:2')) .= pdl([5,6])
    pdl> p $a
    [0 5 6 3 4]


=head2 Q: 6.10   Can I use a piddle in a conditional expression?  


Yes you can, but not in the way you probably tried first. It
is not possible to use a piddle directly in a conditional
expression since this is usually poorly defined. Instead PDL
has two very useful functions: 
C<any> and C<all> . Use these to test if any or
all elements in a piddle fulfills some criterion:

    pdl> $a=pdl ( 1, -2, 3);
    pdl> print '$a has at least one element < 0' if (any $a < 0);
    $a has at least one element < 0
    
    pdl> print '$a is not positive definite' unless (all $a > 0);
    $a is not positive definite


=head2 Q: 6.11   Logical operators and piddles -  '||' and '&&' don't work!  


It is a common problem that you try to make a mask array or something 
similar using a construct such as 

    $mask = which($piddle > 1 && $piddle < 2);   # incorrect

This B< does not> work! What you are looking for is the B< bitwise> 
logical operators '|' and '&' which work on an element-by-element
basis. So it is really very simple: Do not use logical operators on 
multi-element piddles since that really doesn't make sense, instead 
write the example as:

    $mask = which($piddle > 1 & $piddle < 2);

which works correctly.



=head1 ADVANCED TOPICS



=head2 Q: 6.12   What is a null pdl ?  


=for comment Is Q: 6.12 up-to-date with null and empty pdls?

C<null> is a special token for 'empty piddle'. A null pdl 
can be used to flag to a PDL function that it should create 
an appropriately sized and typed piddle. I<Null> piddles 
can be used in places where a PDL function expects an 
I<output> or I<temporary> argument. I<Output> and 
I<temporary> arguments are flagged in the
I<signature> of a PDL function with the C<[o]> and 
C<[t]> qualifiers (see next question if you don't know what 
the I<signature> of a PDL function is).  For example, you 
can invoke the C<sumover> function as follows:

    sumover $a, $b=null;

which is equivalent to

    $b = sumover $a;

If this seems still a bit murky check 
L<PDL::Indexing|PDL::Indexing> and 
L<PDL::PP|PDL::PP> for details about calling
conventions, the I<signature> and 
I<threading> (see also below).


=head2 Q: 6.13   What is the signature of a PDL function ?  


The I<signature> of a function is an important concept in PDL.
Many (but not all) PDL function have a I<signature> which 
specifies the arguments and their (minimal) dimensionality. As 
an example, look at the signature of the C<maximum> function:

    'a(n); [o] b;'

this says that C<maximum> takes two arguments, the first of which is
(at least) one-dimensional while the second one is zero-dimensional and
an I<output> argument (flagged by the C<[o]> qualifier). If the function
is called with piddles of higher dimension the function will be repeatedly
called with slices of these piddles of appropriate dimension(this is called 
I<threading> in PDL).

For details and further explanations consult 
L<PDL::Indexing|PDL::Indexing> and L<PDL::PP|PDL::PP> .


=head2 Q: 6.14   How can I subclass (inherit from) piddles?  


The short answer is: read L<PDL::Objects|PDL::Objects> (e.g. type 
C<help PDL::Objects> in the I<perldl> or I<pdl2> shell).

The longer answer (extracted from L<PDL::Objects|PDL::Objects> ): 
Since a PDL object is an opaque reference to a C struct, it is not 
possible to extend the PDL class by e.g. extra data via sub-classing 
(as you could do with a hash based Perl object).  To circumvent this 
problem PDL has built-in support to extend the PDL class via the 
I<has-a> relation for blessed hashes. You can get the I<HAS-A> to
behave like I<IS-A> simply in that you assign the PDL
object to the attribute named C<PDL> and
redefine the method initialize(). For example:

    package FOO;
    
    @FOO::ISA = qw(PDL);
    sub initialize {
       my $class = shift;
       my $self = {
          creation_time => time(),  # necessary extension :-)
          PDL => PDL->null,         # used to store PDL object
       };
       bless $self, $class;
    }

For another example check the script 
F<t/subclass.t> in the PDL distribution.


=head2 Q: 6.15   What on earth is this dataflow stuff ?  


Dataflow is an experimental project that you don't need to concern
yourself with (it should not interfere with your usual programming). 
However, if you want to know, have a look at 
L<PDL::Dataflow|PDL::Dataflow> . There
are applications which will benefit from this feature (and it is already
at work behind the scenes).


=head2 Q: 6.16   What is PDL::PP?  


Simple answer: PDL::PP is both a glue between external
libraries and PDL and a concise language for writing PDL
functions. 

Slightly longer answer: PDL::PP is used to compile very
concise definitions into XSUB routines implemented in C that
can easily be called from PDL and which automatically support
threading, dataflow and other things without you having to
worry about it. 

For further details check L<PDL::PP|PDL::PP> and the
section below on L<Extensions of PDL|"EXTENSIONS OF PDL">.


=head2 Q: 6.17   What happens when I have several references to the same PDL object in different variables (cloning, etc?) ?  


Piddles behave like Perl references in many respects. So when you say

    $a = pdl [0,1,2,3];
    $b = $a;

then both $b and $a point to the same object, e.g. then saying

    $b++;

will *not* create a copy of the original piddle but just increment in
place, of which you can convince yourself by saying

    print $a;
    [1 2 3 4]

This should not be mistaken for dataflow which connects several
*different* objects so that data changes are propagated between
the so linked piddles (though, under certain circumstances, dataflown
piddles can share physically the same data).

It is important to keep the "reference nature" of piddles in mind
when passing piddles into subroutines. If you modify the input
piddles you modify the original argument, I<not> a copy of it. This
is different from some other array processing languages but makes
for very efficient passing of piddles between subroutines. If you
do not want to modify the original argument but rather a copy
of it just create a copy explicitly (this example also demonstrates
how to properly check for an I<explicit> request to process
inplace, assuming your routine can work inplace):

    sub myfunc {
       my $pdl = shift;
       if ($pdl->is_inplace) {
          $pdl->set_inplace(0)
       } else {
          # modify a copy by default
          $pdl = $pdl->copy
       }
       $pdl->set(0,0);
       return $pdl;
    }



=head1 MISCELLANEOUS



=head2 Q: 6.18   What I/O formats are supported by PDL ?  


The current versions of PDL already support quite a number of different
I/O formats.  However, it is not always obvious which module implements
which formats.  To help you find the right module for the format you
require, here is a short list of the current list of I/O formats and
a hint in which module to find the implementation:

=over 4

=item *

A home brew fast raw (binary) I/O format for PDL is implemented by the
L<FastRaw|PDL::IO::FastRaw> module

=item *

The L<FlexRaw|PDL::IO::FlexRaw> module implements generic methods for
the input and output of `raw' data arrays.  In particular, it is
designed to read output from FORTRAN 77 UNFORMATTED files and the
low-level C C<write> function, even if the files are compressed or gzipped.

It is possible that the FastRaw functionality will be included in the
FlexRaw module at some time in the future.

=item *

FITS I/O is implemented by the C<wfits>/C<rfits> functions in L<PDL::IO::FITS|PDL::IO::FITS> .

=item *

ASCII file I/O in various formats can be achieved by using the 
C<rcols> and C<rgrep> functions, also in L<PDL::IO::Misc|PDL::IO::Misc> .

=item *

L<PDL::IO::Pic|PDL::IO::Pic> implements an interface to the
NetPBM/PBM+ filters to read/write several popular image formats; also
supported is output of image sequences as MPEG movies, animated GIFs
and a wide variety of other video formats.

=item *

On CPAN you can find the L<PDL::NetCDF|PDL::NetCDF> module that works with the current
released version of PDL 2.006.

=back

For further details consult the more detailed list in the L<PDL::IO|PDL::IO>
documentation or the documentation for the individual modules.


=head2 Q: 6.19   How can I stack a set of 2D arrays (images) into a 3D piddle?  


Assuming all arrays are of the same size and in some format recognized by
C<rpic> (see L<PDL::IO::Pic|PDL::IO::Pic> ) you could say:

    use PDL::IO::Pic;
    @names = qw/name1.tif .... nameN.tif/;  # some file names
    $dummy = PDL->rpic($names[0]);
    $cube = PDL->zeroes($dummy->type,$dummy->dims,$#names+1); # make 3D piddle
    for (0..$#names) {
        # this is the slice assignment
        ($tmp = $cube->slice(":,:,($_)")) .= PDL->rpic($names[$_]);
    }

or

    $cube(:,:,($_)) .= PDL->rpic($names[$_]);

for the slice assignment using the new L<PDL::NiceSlice|PDL::NiceSlice> syntax and Lvalue
assignments.

The for loop reads the actual images into a temporary 2D piddle whose
values are then assigned (using the overloaded C<.=> operator) to the
appropriate slices of the 3D piddle C<$cube> .


=head2 Q: 6.20   Where are test files for the graphics modules?  


This answer applies mainly to PDL::Graphics::TriD (PDL's device
independent 3D graphics model) which is the trickiest one in this
respect. You find some test scripts in Demos/TriD in the distribution.
There are also F<3dtest.pl> and F<line3d.pl> in the PDL/Example/TriD
directory.  After you have built PDL you can do:

    perl -Mblib Example/TriD/3dtest.pl

    perl -Mblib Example/TriD/line3d.pl

to try the two TriD test programs.  They only exercise one TriD function
each but their simplicity makes it easy to debug if needed with the
Perl debugger, see L<perldbug>.

The programs in the Demo directory can be run most easily from the
C<perldl> or C<pdl2> interactive shell:

    perl -Mblib perldl  or  perl -Mblib Perldl2/pdl2

followed by C<demo 3d> or C<demo 3d2> at the prompt.
C<demo> by itself will give you a list of the available PDL demos.

You can run the test scripts in the Demos/TriD directory manually
by changing to that directory and running

    perl -Mblib <testfile>


where C<< testfile >> ; should match the pattern C<test[3-9].p>
and watch the results. Some of the tests should bring up a window
where you can control (twiddle) the 3D objects with the mouse. Try using
mouse button 1 for turning the objects in 3D space, mouse button 3
to zoom in and out, and 'q' to advance to the next stage of the test.


=head2 Q: 6.21   What is TriD or PDL::TriD or PDL::Graphics::TriD?  


Questions like this should be a thing of the past with the PDL
on-line help system in place. Just try (after installation):

    un*x> pdl2
    pdl> apropos trid

Check the output for promising hits and then try to look up
some of them, e.g.

    pdl> help PDL::Graphics::TriD

Note that case matters with C<help> but not with C<apropos> .


=head2 Q: 6.22   PGPLOT does not write out PNG files.


There are a few sources of trouble with PGPLOT and PNG files. First,
when compiling the pgplot libraries, make sure you uncomment the PNG
entries in the F<drivers.list> file. Then when running 'make' you
probably got an error like

  C<make: *** No rule to make target `png.h', needed by `pndriv.o'.  Stop.>

To fix this, find the line in the 'makefile' that starts with
'pndriv.o:' (it's near the bottom). Change, for example, ./png.h to
/usr/include/png.h, if that is where your header files are (you do
have the libpng and libz devel packages, don't you?).  Do this for all
four entries on that line, then go back and run C<make>.

Second, if you already have the PGPLOT Perl module and PDL installed,
you probably tried to write out a PNG file and got fatal error message
like:

  C<undefined symbol: png_create_write_struct>

This is because the PGPLOT Perl module does not automatically link
against the png and z libraries. So when you are installing the PGPLOT
Perl module (version 2.19) from CPAN, don't do C<install PGPLOT>, but
just do C<get PGPLOT>. Then exit from CPAN and manually install
PGPLOT, calling the makefile thusly:

  C<perl Makefile.PL EXLIB=png,z EXDIR=/usr/lib>

assuming that there exist files such as /usr/lib/libpng.so.*,
/usr/lib/libz.so.*. Then do the standard C<make;make test;make
install;> sequence. Now you can write png files from PDL!



=head1 EXTENSIONS OF PDL



=head2 Q: 7.1    I am looking for a package to do XXX in PDL. Where shall I look for it?  


The first stop is again C<perldl> or C<pdl2> and the on-line help
or the PDL documentation. There is already a lot of functionality in
PDL which you might not be aware of.  The easiest way to look for
functionality is to use the C<apropos> command:

    pdl> apropos 'integral'
    ceil            Round to integral values in floating-point format
    floor           Round to integral values in floating-point format
    intover         Project via integral to N-1 dimensions
    rint            Round to integral values in floating-point format

Since the apropos command is no sophisticated search engine make
sure that you search on a couple of related topics and use short
phrases. 

However there is a good chance that what you need is not part
of the PDL distribution. You are then well advised to check
out L<http://pdl.perl.org> where there is a list of packages
using PDL. If that does not solve your problem, ask on the
mailing-list, if nothing else you might get assistance which
will let you interface your package with PDL yourself, see
also the next question.


=head2 Q: 7.2    Can I access my C/FORTRAN library routines in  PDL?  


Yes, you can, in fact it is very simple for many simple
applications. What you want is the PDL pre-processor PP
(L<PDL::PP|PDL::PP> ). This will allow you to make a 
simple interface to your C routine. 

The two functions you need to learn (at least first) are 
C<pp_def> which defines the calling interface to the function, 
specifying input and output parameters, and contains the code 
that links to the external library. The other command is 
C<pp_end> which finishes the PP definitions.  For details see
the L<PDL::PP|PDL::PP> man-page, but we also have a worked 
example here. 

    double eight_sum(int n)
    {
         int i;
         double sum, x;
    
         sum = 0.0; x=0.0;
         for (i=1; i<=n; i++) {
           x++;
           sum += x/((4.0*x*x-1.0)*(4.0*x*x-1.0));
         } 
         return 1.0/sum;
    }


We will here show you an example of how you interface C
code with PDL. This is the first example and will show
you how to approximate the number 8... 

The C code is shown above and is a simple function
returning a double, and expecting an integer - the number
of terms in the sum - as input. This function could be
defined in a library or, as we do here, as an inline
function.  

We will postpone the writing of the Makefile till
later. First we will construct the 
C<.pd> file. This is the file
containing PDL::PP code. We call this 
C<eight.pd> .

    # 
    # pp_def defines a PDL function. 
    #
    pp_addhdr (
    '
    double eight_sum(int n)
    {
      int i;
      double sum, x;
    
      sum = 0.0; x=0.0;
      for (i=1; i<=n; i++) {
       x++; 
       sum += x/((4.0*x*x-1.0)*(4.0*x*x-1.0));
      }
     return 1.0/sum; 
    
    }  
    '); 
    
    pp_def (
            'eight',
         Pars => 'int a(); double [o]b();',
            Code => '$b()=eight_sum($a());'
           );
    
    # Always make sure that you finish your PP declarations with
    # pp_done
    
    pp_done();

A peculiarity with our example is that we have included
the entire code with 
C<pp_addhdr> instead of linking it in. This is only for the purposes of
example, in a typical application you will use 
C<pp_addhdr> to include header
files. Note that the argument to 
C<pp_addhdr> is enclosed in quotes. 

What is most important in this example is however the
C<pp_def> command. The first
argument to this is the name of the new function 
I<eight > , then comes a hash which
the real meat:

=over 4

=item *

This gives the input parameters (here  C<a>) and the output parameters
(here  C<b>). The latter are indicated by the  C<[o]> specifier. Both
arguments can have a type specification as shown here. 

Many variations and further flexibility in the interface can be
specified. See C<perldoc PDL::PP> for details. 

=item *

This switch contains the code that should be
executed. As you can see this is a rather peculiar
mix of C and Perl, but essentially it is just as
you would write it in C, but the variables that
are passed from PDL are treated differently and
have to be referred to with a preceding '$'.

There are also simple macros to pass pointers to
data and to obtain the values of other Perl
quantities, see the manual page for further
details. 

=back

Finally note the call to  
C<pp_done()> at the end of the
file. This is necessary in all PP files. 

OK. So now we have a file with code that we dearly would
like to use in Perl via PDL. To do this we need to
compile the function, and to do that we need a
Makefile.

    use PDL::Core::Dev;
    use ExtUtils::MakeMaker;
    PDL::Core::Dev->import();
    
    $package = ["eight.pd",Eight,PDL::Eight];
    %hash = pdlpp_stdargs($package);
    
    WriteMakefile( %hash );
    
    sub MY::postamble {pdlpp_postamble($package)};

The code above should go in a file called Makefile.PL,
which should subsequently be called in  the standard
Perl way: 
C<perl Makefile.PL> .
This should give you a Makefile and running 
C<make> should compile the module for
you and 
C<make install> will
install it for you. 


=head2 Q: 7.3    How can I interface package XXX in PDL?  


This question is closely related to the previous one, and as
we said there, the 
L<PDL::PP|PDL::PP> pre-processor is the standard
way of interfacing external packages with PDL. The most usual
way to use PDL::PP is to write a short interface routine, see
the L<PDL::PP|PDL::PP> perldoc page and
the answer to the previous question for
examples. 

However it is also possible to interface a package to PDL by
re-writing your function in PDL::PP directly. This can be
convenient in certain situations, in particular if you have a
routine that expects a function as input and you would like to
pass the function a Perl function for convenience. 

The L<PDL::PP|PDL::PP> perldoc page is the main
source of information for writing PDL::PP extensions, but it
is very useful to look for files in the distribution of PDL as
many of the core functions are written in PDL::PP. Look for
files that end in C<.pd> which is the generally accepted 
suffix for PDL::PP files. But we also have a simple example here.

The following example will show you how to write a simple
function that automatically allows threading. To make this
concise the example is of an almost trivial function, but
the intention is to show the basics of writing a PDL::PP
interface. 

We will write a simple function that calculates the minimum,
maximum and average of a piddle. On my machine the resulting
function is 8 times faster than the built-in function 
C<stats> (of course the latter also
calculates the median). 

Let's jump straight in. Here is the code (from a file called
C<quickstats.pd> )

    #
    pp_def('quickstats',
         Pars => 'a(n); [o]avg(); [o]max(); [o]min()',
         Code => '$GENERIC(a) curmax, curmin;
                  $GENERIC(a) tmp=0;
                     loop(n) %{
                       tmp += $a();
                       if (!n || $a() > curmax) { curmax = $a();}
                       if (!n || $a() < curmin) { curmin = $a();}
                     %}
                     $avg() = tmp/$SIZE(n);
                  $max() = curmax;
                  $min() = curmin;
                    '
         );
    
    pp_done();

The above might look like a confusing mixture of C and
Perl, but behind the peculiar syntax lies a very
powerful language. Let us take it line by line.

The first line declares that we are starting the
definition of a PDL:PP function called
C<quickstats> .

The second line is very important as it specifies the
input and output parameters of the function.  
C<a(n)> tells us that there is one input
parameter that we will refer to as 
C<a> which is expected to be a vector of
length n (likewise matrices, both square and rectangular
would be written as 
C<a(n,n)> and
C<a(n,m)> respectively). To
indicate that something is an output parameter we put
C<[o]> in front of their names, so
referring back to the code we see that avg, max and min
are three output parameters, all of which are scalar
(since they have no dimensional size indicated.

The third line starts the code definition which is
essentially pure C but with a couple of convenient
functions. 
C<$GENERIC> is a
function that returns the C type of its argument - here
the input parameter a. Thus the first two lines of the
code section are variable declarations.

The 
C<loop(n)> construct is a
convenience function that loops over the dimension
called n in the parameter section. Inside this loop we
calculate the cumulative sum of the input vector and
keep track of the maximum and minimum values. Finally 
we assign the resulting values to the output
parameters. 

Finally we finish our function declaration with 
C<pp_done()> .

To compile our new function we need to create a Makefile,
which we will just list since its creation is discussed in
an earlier question. 

    use PDL::Core::Dev;
    use ExtUtils::MakeMaker;
    PDL::Core::Dev->import();
    
    $package = ["quickstats.pd",Quickstats,PDL::Quickstats];
    %hash = pdlpp_stdargs($package);
    
    WriteMakefile( %hash );
    
    sub MY::postamble {pdlpp_postamble($package)};


An example Makefile.PL

Our new statistic function should now compile using the
tried and tested Perl way: 
C<perl Makefile.PL; make> .

You should experiment with this function, changing the
calculations and input and output parameters. In conjunction
with the L<PDL::PP|PDL::PP> perldoc page this should allow you to quickly
write more advanced routines directly in PDL::PP.



=head1 BUGS


If you find any inaccuracies in this document (or dis-functional
URLs) please report to the perldl mailing list perldl@jach.hawaii.edu.



=head1 ACKNOWLEDGMENTS


Achim Bohnet (ach@mpe.mpg.de ) for suggesting CoolHTML as a
prettypodder (although we have switched to XML now) and various
other improvements. Suggestions for some questions were taken
from Perl FAQ and adapted for PDL.



=head1 CONTRIBUTORS


Many people have contributed or given feedback on the current
version of the FAQ, here is an incomplete list of individuals
whose contributions or posts to the mailing-list have improved
this FAQ at some point in time alphabetically listed by first
name: Christian Soeller, Chris Marshall, Doug Burke, Doug Hunt,
Frank Schmauder, Jarle Brinchmann, John Cerney, Karl Glazebrook,
Kurt Starsinic, Thomas Yengst, Tuomas J. Lukka.



=head1 AUTHOR AND COPYRIGHT


This document emerged from a joint effort of several PDL
developers (Karl Glazebrook, Tuomas J. Lukka, Christian
Soeller) to compile a list of the most frequently asked questions
about PDL with answers.  Permission is granted for verbatim
copying (and formatting) of this material as part of PDL.

Permission is explicitly not granted for distribution in book
or any corresponding form. Ask on the PDL mailing list
perldl@jach.hawaii.edu if some of the issues covered
in here are unclear.