Provided by: pdl_2.007-5_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.
perl v5.22.1 2013-09-21 FAQ(1p)