Provided by: pdl_2.007-2build1_amd64 
NAME
PDL::FAQ - Frequently asked questions about PDL
VERSION
Current FAQ version: 1.004
DESCRIPTION
This is version 1.004 of the PDL FAQ, a collection of frequently asked questions about
PDL - the Perl Data Language.
ABOUT THIS DOCUMENT
Q: 1.1 Where to find this document
You can find the latest version of this document at
<http://pdl.perl.org/?docs=FAQ&title=Frequently%20Asked%20Questions> .
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.
GENERAL QUESTIONS
Q: 2.1 What is PDL ?
PDL stands for 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.
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.
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:
• 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.
• 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.
• 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").
• 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.
• 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 PDL::PP (see Q: 6.16 below), a
code generator/parser/pre-processor that generates PDL functions from concise
descriptions.
• None of the existing data languages follow the Perl language rules, which the authors
firmly believe in:
• 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 ;)
• 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.
All existing languages violate at least one of these rules.
• 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 PDL::PP (see Q: 6.16 below) generate appropriate code on such
architectures to exploit these features.
• [ fill in your personal 111 favourite reasons here...]
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.
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".
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
<http://www.perl.org> and at many CPAN sites (if you do not know what 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.
Q: 2.7 Where do I get it?
PDL is available as source distribution in the Comprehensive Perl Archive Network (or
CPAN) and from the sourceforge.net project page at
<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 <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
<http://pdl.perl.org> and the latest version can also be downloaded from there.
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.
GETTING HELP/MORE INFORMATION
Q: 3.1 Where can I get information on PDL?
The complete PDL documentation is available with the PDL distribution. Use the command
"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, "pdl2" Just type "pdl2" at your system prompt. Once
you are inside the "pdl2" shell type "help" . Using the "help" and "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 "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.
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 <http://www.perl.com> and <http://www.perl.org> .
The PDL home site can be accessed by pointing your web browser to <http://pdl.perl.org> .
It has tons of goodies for anyone interested in PDL:
• PDL distributions
• On-line documentation
• Pointers to an HTML archive of the PDL mailing lists
• A list of platforms on which PDL has been successfully tested.
• News about recently added features, ported libraries, etc.
• 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).
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
<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 <http://www.xray.mpe.mpg.de/mailing-lists/perldl/> . More recent messages
(since June 2005) can be found at <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 <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 <http://www.xray.mpe.mpg.de/mailing-lists/pdl-porters/> . More recent messages
(since June 2005) can be found at
<http://mailman.jach.hawaii.edu/mailman/listinfo/pdl-porters> .
Cross-posting between these lists should be avoided unless there is a very good reason for
doing that.
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
Question 2.7 for info on where to get PDL).
The most current (possibly unstable) version of PDL can be obtained from the Git
repository, see Question 4.10 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 CHM/PDL-2.006_07.tar.gz .
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
<http://wiki.cpantesters.org/wiki/QuickStart> has instructions for starting for either
"CPAN" or "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 Question 3.2. We are always looking for people to write code and/or
documentation ;).
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 <http://pdl.perl.org> . See the 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.
INSTALLATION
Q: 4.1 I have problems installing PDL. What shall I do?
First make sure you have read the file INSTALL in the distribution. This contains a list
of common problems which are unnecessary to repeat here.
Next, check the file 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 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 ~/.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.
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 INSTALL and perldl.conf for details.
If you had to manually edit perldl.conf and are happy with the results you can keep the
file handy for future reference. Place it in ~/.perldl.conf where it will be picked up
automatically or use "perl Makefile.PL PDLCONF=your_file_name" next time you build PDL.
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
DEPENDENCIES in the distribution for details and directions on how to get these.
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 "perl
Makefile.PL" configure step. For example, "perl Makefile.PL INSTALL_BASE=/mydir/perl5"
will configure PDL to install into the tree rooted at "/mydir/perl5". For more details
see "How do I keep my own module/library directory?" in perlfaq8 and subsequent sections.
Another alternative is to use local::lib to do the heavy listing for the needed
configuration.
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 "PDL" in the
Perl @INC path, files named "*Pdlpp*" in any "Inline" directories, and the programs "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 "PDL" into a non-standard location.
See Q: 4.4 above.
BINARY DISTRIBUTIONS
Q: 4.5 What binary distributions are available?
Information about binary distributions of PDL can be found on <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.
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 <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.
Q: 4.7 Does PDL run under Windows?
PDL builds fine on Win32 using MinGW or Microsoft compilers. See the 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.
CVS, GIT, AND ON-GOING DEVELOPMENT
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
<http://git-scm.com>).
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 "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
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 <http://sourceforge.net/projects/pdl> .
In addition, if you are not subscribing to the mailing list, check the archive of the
"pdl-porters" and "perldl" mailing lists. See Question 3.2 for details.
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
PDL JARGON
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:
• When mentioned in the 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)
• 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 "inner $a, $b" of a (3) pdl $a and a (3,5,4) pdl $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 PDL::Indexing
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.
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 "perldoc perlobj" )) are in common PDL parlance often called
piddles (for example, check the mailing list archives). Err, clear? If not, simply use
the term 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.
TECHNICAL QUESTIONS
Q: 6.1 What is perldl? What is pdl2?
Sometimes "perldl" ("pdl2") is used as a synonym for PDL. Strictly speaking, however, the
name "perldl" ("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 perldl or pdl2.
Q: 6.2 How do I get on-line help for PDL?
Just type "help" (shortcut = "?") at the "pdl2" shell prompt and proceed from there.
Another useful command is the "apropos" (shortcut = "??") command. Also try the "demo"
command in the "perldl" or "pdl2" shell if you are new to PDL.
MANIPULATION OF PIDDLES
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.
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 ( 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 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 "at" /
"set" (see the section 'Sections' in PDL::QuickStart ) or the powerful "slice" function
and friends (see PDL::Slices and PDL::Indexing and especially PDL::NiceSlice ).
Finally, to confuse you completely, you can have Perl arrays of piddles, e.g. $spec[3] can
refer to a pdl representing ,e.g, a spectrum, where $spec[3] is the fourth element of the
Perl list (or array ;) @spec . This may be confusing but is very useful !
Q: 6.5 How do I concatenate piddles?
Most people will try to form new piddles from old piddles using some variation over the
theme: "$a = pdl([$b, 0, 2])" , but this does not work. The way to concatenate piddles is
to use the function "cat" (see also "append" and "glue"). Similarly you can split piddles
using the command "dog" .
Q: 6.6 Sometimes I am getting these strange results when using inplace operations?
This question is related to the "inplace" function. From the documentation (see
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!
Q: 6.7 What is this strange usage of the string concatenation operator ".=" in PDL
scripts?
See next question on assignment in PDL.
Q: 6.8 Why are there two different kinds of assignment in PDL ?
This is caused by the fact that currently the assignment operator "=" 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 ".=" for certain types of assignments.
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 PDL::Lvalue for more info. PDL also supports a more matrix-like slice syntax via the
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 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]
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: "any" and "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
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 does not work! What you are looking for is the 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.
ADVANCED TOPICS
Q: 6.12 What is a null pdl ?
"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. Null piddles can
be used in places where a PDL function expects an output or temporary argument. Output and
temporary arguments are flagged in the signature of a PDL function with the "[o]" and
"[t]" qualifiers (see next question if you don't know what the signature of a PDL function
is). For example, you can invoke the "sumover" function as follows:
sumover $a, $b=null;
which is equivalent to
$b = sumover $a;
If this seems still a bit murky check PDL::Indexing and PDL::PP for details about calling
conventions, the signature and threading (see also below).
Q: 6.13 What is the signature of a PDL function ?
The signature of a function is an important concept in PDL. Many (but not all) PDL
function have a signature which specifies the arguments and their (minimal)
dimensionality. As an example, look at the signature of the "maximum" function:
'a(n); [o] b;'
this says that "maximum" takes two arguments, the first of which is (at least) one-
dimensional while the second one is zero-dimensional and an output argument (flagged by
the "[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 threading in PDL).
For details and further explanations consult PDL::Indexing and PDL::PP .
Q: 6.14 How can I subclass (inherit from) piddles?
The short answer is: read PDL::Objects (e.g. type "help PDL::Objects" in the perldl or
pdl2 shell).
The longer answer (extracted from 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 has-a relation for blessed
hashes. You can get the HAS-A to behave like IS-A simply in that you assign the PDL object
to the attribute named "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 t/subclass.t in the PDL distribution.
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 PDL::Dataflow . There are applications which will benefit from this feature (and
it is already at work behind the scenes).
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 PDL::PP and the section below on Extensions of PDL.
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, 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 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;
}
MISCELLANEOUS
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:
• A home brew fast raw (binary) I/O format for PDL is implemented by the FastRaw module
• The 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 "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.
• FITS I/O is implemented by the "wfits"/"rfits" functions in PDL::IO::FITS .
• ASCII file I/O in various formats can be achieved by using the "rcols" and "rgrep"
functions, also in PDL::IO::Misc .
• 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.
• On CPAN you can find the PDL::NetCDF module that works with the current released
version of PDL 2.006.
For further details consult the more detailed list in the PDL::IO documentation or the
documentation for the individual modules.
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 "rpic" (see
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 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 ".=" operator) to the appropriate slices of the 3D piddle
$cube .
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 3dtest.pl and 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 perldbug.
The programs in the Demo directory can be run most easily from the "perldl" or "pdl2"
interactive shell:
perl -Mblib perldl or perl -Mblib Perldl2/pdl2
followed by "demo 3d" or "demo 3d2" at the prompt. "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 "testfile" ; should match the pattern "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.
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 "help" but not with "apropos" .
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 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 "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 "install PGPLOT", but just do "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 "make;make test;make install;" sequence. Now you can write png files from
PDL!
EXTENSIONS OF PDL
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 "perldl" or "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 "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 <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.
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 (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 "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 "pp_end" which finishes
the PP definitions. For details see the 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 ".pd"
file. This is the file containing PDL::PP code. We call this "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($a());'
);
# Always make sure that you finish your PP declarations with
# pp_done
pp_done();
A peculiarity with our example is that we have included the entire code with "pp_addhdr"
instead of linking it in. This is only for the purposes of example, in a typical
application you will use "pp_addhdr" to include header files. Note that the argument to
"pp_addhdr" is enclosed in quotes.
What is most important in this example is however the "pp_def" command. The first argument
to this is the name of the new function eight , then comes a hash which the real meat:
• This gives the input parameters (here "a") and the output parameters (here "b"). The
latter are indicated by the "[o]" specifier. Both arguments can have a type
specification as shown here.
Many variations and further flexibility in the interface can be specified. See
"perldoc PDL::PP" for details.
• This switch contains the code that should be executed. As you can see this is a rather
peculiar mix of C and Perl, but essentially it is just as you would write it in C, but
the variables that are passed from PDL are treated differently and have to be referred
to with a preceding '$'.
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.
Finally note the call to "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($package)};
The code above should go in a file called Makefile.PL, which should subsequently be called
in the standard Perl way: "perl Makefile.PL" . This should give you a Makefile and
running "make" should compile the module for you and "make install" will install it for
you.
Q: 7.3 How can I interface package XXX in PDL?
This question is closely related to the previous one, and as we said there, the PDL::PP
pre-processor is the standard way of interfacing external packages with PDL. The most
usual way to use PDL::PP is to write a short interface routine, see the PDL::PP perldoc
page and the answer to the previous question for examples.
However it is also possible to interface a package to PDL by re-writing your function in
PDL::PP directly. This can be convenient in certain situations, in particular if you have
a routine that expects a function as input and you would like to pass the function a Perl
function for convenience.
The PDL::PP perldoc page is the main source of information for writing PDL::PP extensions,
but it is very useful to look for files in the distribution of PDL as many of the core
functions are written in PDL::PP. Look for files that end in ".pd" which is the generally
accepted suffix for PDL::PP files. But we also have a simple example here.
The following example will show you how to write a simple function that automatically
allows threading. To make this concise the example is of an almost trivial function, but
the intention is to show the basics of writing a PDL::PP interface.
We will write a simple function that calculates the minimum, maximum and average of a
piddle. On my machine the resulting function is 8 times faster than the built-in function
"stats" (of course the latter also calculates the median).
Let's jump straight in. Here is the code (from a file called "quickstats.pd" )
#
pp_def('quickstats',
Pars => 'a(n); [o]avg(); [o]max(); [o]min()',
Code => '$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
"quickstats" .
The second line is very important as it specifies the input and output parameters of the
function. a(n) tells us that there is one input parameter that we will refer to as "a"
which is expected to be a vector of length n (likewise matrices, both square and
rectangular would be written as "a(n,n)" and "a(n,m)" respectively). To indicate that
something is an output parameter we put "[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. $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 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 "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: "perl
Makefile.PL; make" .
You should experiment with this function, changing the calculations and input and output
parameters. In conjunction with the PDL::PP perldoc page this should allow you to quickly
write more advanced routines directly in PDL::PP.
BUGS
If you find any inaccuracies in this document (or dis-functional URLs) please report to
the perldl mailing list perldl@jach.hawaii.edu.
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.
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.
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.