PDL::IO - An overview of the modules in the PDL::IO namespace.
# At your system shell, type: perldoc PDL::IO
PDL contains many modules for displaying, loading, and saving data.
Perlish or Text-Based
A few IO modules provide Perl-inspired capabilities. These are PDL::IO::Dumper and PDL::IO::Storable. PDL::IO::Misc provides simpler routines for dealing with delimited files, though its capabilities are limited to tabular or at most 3-d data sets.
PDL has two modules that store their data in a raw binary format; they are PDL::IO::FastRaw and PDL::IO::FlexRaw. They are fast but the files they produce will not be readable across different architectures. These two modules are so similar that they could probably be combined.
At the moment, only PDL::IO::Browser provides data browsing functionality.
PDL has a handful of modules that will load images into piddles for you. They include PDL::IO::Dicom, PDL::IO::FITS, PDL::IO::GD, PDL::IO::Pic, and PDL::IO::Pnm. However, PDL::IO::FITS should also be considered something of a general data format.
Both PDL::IO::FastRaw and PDL::IO::FlexRaw provide for direct piddle-to-disk mapping, but they use PDL's underlying mmap functionality to do it, and that doesn't work for Windows. However, users of all operating systems can still use PDL::DiskCache, which can use any desired IO read/write functionality (though you may have to write a small wrapper function).
General Data Storage Formats
PDL has a number of modules that interface general data storage libraries. They include PDL::IO::HDF and PDL::IO::NDF (the latter is now a separate CPAN module). There is a PDL::IO::IDL, though at the moment it is not distributed with PDL. PDL::IO::FITS is something of a general data format, since piddle data can be stored to a FITS file without loss. PDL::IO::FlexRaw and PDL::IO::FastRaw read and write data identical C's low-level
writefunction and PDL::IO::FlexRaw can work with FORTRAN 77 UNFORMATTED files. FlexRaw and Storable provide general data storage capabilities. Finally, PDL can read Grib (weather-data) files using the CPAN module PDL::IO::Grib.
You can make an MPEG animation using PDL::IO::Pic's wmpeg function.
Here's a brief summary of all of the modules, in alphabetical order.
The DiskCache module allows you to tie a Perl array to a collection of files on your disk, which will be loaded into and out of memory as piddles. Although the module defaults to working with FITS files, it allows you to specify your own reading and writing functions. This allows you to vastly streamline your code by hiding the unnecessary details of loading and saving files.
If you find yourself writing scripts to procss many data files, especially if that data processing is not necessarily in sequential order, you should consider using PDL::DiskCache. To read more, check the PDL::DiskCache documentation.
The Browser module provides a text-based data browser for 2D data sets.
It uses the CURSES library to do the scrolling, so if your operating system does not have the cureses library, you won't be able to install this on your machine. (Note that the package containing the header files for the CURSES library may be called
libcurses or possibly
PDL::IO::Browser is not installed by default because it gives trouble on Mac OS X, and not enough is known to fix the problem. If you want to enable it, edit the perldl configuration file and rebuild PDL. To learn more about editing the configuration file, see the INSTALLATION section in the FAQ. (Also, if you are familiar with CURSES on Mac, your help would be much appreciated!)
To see if the module is installed on your machine (and to get more information about PDL::IO::Browser), follow this link or type at the system prompt:
If you want to get more information about PDL::IO::Browser and it's not installed on your system, I'm afraid you'll have to pick out the pod from the source file, which can be found online at http://pdl.git.sourceforge.net/git/gitweb.cgi?p=pdl/pdl;a=blob_plain;f=IO/Browser/browser.pd;hb=HEAD.
DICOM is an image format, and this module allows you to read image files with the DICOM file format. To read more, check the PDL::IO::Dicom documentation.
Provides functionality similar to Data::Dumper for piddles. Data::Dumper stringifies a data structure, creating a string that can be
evaled to reproduce the original data structure. It's also usually suitable for printing, to visualize the structure.
To read more, check the PDL::IO::Dumper documentation. See also PDL::IO::Storable for a more comprehensive structured data solution.
Very simple module for quickly writing, reading, and memory-mapping piddles to/from disk. It is fast to learn and fast to use, though you may be frustrated by its lack of options. To quote from the original POD:
"The binary files are in general NOT interchangeable between different architectures since the binary file is simply dumped from the memory region of the piddle. This is what makes the approach efficient."
This creates two files for every piddle saved - one that stores the raw data and another that stores the header file, which indicates the dimensions of the data stored in the raw file. Even if you save 1000 different piddles with the exact same dimensions, you will still need to write out a header file for each one. You cannot store multiple piddles in one file.
Note that at the time of writing, memory-mapping is not possible on Windows.
For more details, see PDL::IO::FastRaw. For a more flexible raw IO module, see PDL::IO::FlexRaw.
Allows basic reading and writing of FITS files. You can read more about FITS formatted files at http://fits.gsfc.nasa.gov/fits_intro.html and http://en.wikipedia.org/wiki/FITS. It is an image format commonly used in Astronomy.
This module may or may not be installed on your machine. To get more information, check online at http://pdl.sourceforge.net/PDLdocs/IO/FITS.html. To see if the module is installed on your machine, follow this link or type at the system prompt:
Somewhat smarter module (compared to FastRaw) for reading, writing, and memory mapping piddles to disk. In addition to everything that FastRaw can do, FlexRaw can also store multiple piddles in a single file, take user-specified headers (so you can use one header file for multiple files that have identical structure), and read compressed data. However, FlexRaw cannot memory-map compressed data, and just as with FastRaw, the format will not work across multiple architectures.
FlexRaw and FastRaw produce identical raw files and have essentially identical performance. Use whichever module seems to be more comfortable. I would generally recommend using FlexRaw over FastRaw, but the differences are minor for most uses.
Note that at the time of writing, memory-mapping is not possible on Windows.
For more details on FlexRaw, see PDL::IO::FlexRaw.
GD is a library for reading, creating, and writing bitmapped images, written in C. You can read more about the C-library here: http://www.libgd.org/.
In addition to reading and writing .png and .jpeg files, GD allows you to modify the bitmap by drawing rectangles, adding text, and probably much more. The documentation can be found here. As such, it should probably be not only considered an IO module, but a Graphics module as well.
This module provides PDL bindings for the GD library, which ought not be confused with the Perl bindings. The perl bindings were developed independently and can be found at GD, if you have Perl's GD bindings installed.
A CPAN module last updated in 2000 that allows you to read Grib files. GRIB is a data format commonly used in meteorology. In the off-chance that you have it installed, you should read PDL::IO::Grib's documentation.
Provides an interface to HDF4 and HDF5 file formats, which are kinda like cross-platform binary XML files. HDF stands for Heierarchicl Data Format. HDF was originally developed at the NCSA. To read more about HDF, see http://www.hdfgroup.org/. Note that HDF5 is not presently distributed with PDL, and neither HDF4 nor HDF5 will be installed unless you have the associated C libraries that these modules interface. Also note that the HDF5 library on CPAN is rather old and somebody from HDF contacted the mailing list in the Fall of 2009 to develop new and better HDF5 bindings for Perl.
Once upon a time, PDL had a module for reading IDL data files. Unfortunately, it cannot be distributed because the original author, Craig DeForest, signed the IDL license agreement and was unable to negotiate the administrative hurdles to get it published. However, it can be found in Sourceforge's CVS attic, and any PDL user who has not signed IDL's license agreement can fix it up and resubmit it.
Provides mostly text-based IO routines. Data input and output is restricted mostly to tabular (i.e. two-dimensional) data sets, though limited support is provided for 3d data sets.
Alternative text-based modules support higher dimensions, such as PDL::IO::Dumper and PDL::IO::Storable. Check the PDL::IO::Misc documentation for more details.
Starlink developed a file format for N-Dimensional data Files, which it cleverly dubbed NDF. If you work with these files, you're in luck! Check the PDL::IO::NDF documentation for more details.
Provides reading/writing of images to/from piddles, as well as creating MPEG animations! The module uses the netpbm library, so you will need that on your machine in order for this to work. To read more, see the PDL::IO::Pic documentation. Also look into the next module, as well as PDL::IO::GD.
Provides methods for reading and writing pnm files (of which pbm is but one). Check the PDL::IO::Pnm documentation for more details. Also check out the previous module and PDL::IO::GD.
Implements the relevant methods to be able to store and retrieve piddles via Storable. True, you can use many methods to save a single piddle. In contrast, this module is particularly useful if you need to save a complex Perl structure that contain piddles, such as an array of hashes, each of which contains piddles.
Check the PDL::IO::Storable documentation for more details. See also PDL::IO::Dumper for an alternative stringifier.
Copyright 2010 David Mertens (firstname.lastname@example.org). You can distribute and/or modify this document under the same terms as the current Perl license.