FAQ(1) User Contributed Perl Documentation FAQ(1)NAMEPDL::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 v5.18.1 2013-09-21 FAQ(1)
