PDLA::IO - An overview of the modules in the PDLA::IO namespace.
# At your system shell, type: perldoc PDLA::IO
PDLA contains many modules for displaying, loading, and saving data.
Perlish or Text-Based
A few IO modules provide Perl-inspired capabilities. These are PDLA::IO::Dumper and PDLA::IO::Storable. PDLA::IO::Misc provides simpler routines for dealing with delimited files, though its capabilities are limited to tabular or at most 3-d data sets.
PDLA has two modules that store their data in a raw binary format; they are PDLA::IO::FastRaw and PDLA::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 PDLA::IO::Browser provides data browsing functionality.
PDLA has a handful of modules that will load images into piddles for you. They include PDLA::IO::Dicom, PDLA::IO::FITS, PDLA::IO::GD, PDLA::IO::Pic, and PDLA::IO::Pnm. However, PDLA::IO::FITS should also be considered something of a general data format.
Both PDLA::IO::FastRaw and PDLA::IO::FlexRaw provide for direct piddle-to-disk mapping, but they use PDLA's underlying mmap functionality to do it, and that doesn't work for Windows. However, users of all operating systems can still use PDLA::DiskCache, which can use any desired IO read/write functionality (though you may have to write a small wrapper function).
General Data Storage Formats
PDLA has a number of modules that interface general data storage libraries. They include PDLA::IO::HDF and PDLA::IO::NDF (the latter is now a separate CPAN module). There is a PDLA::IO::IDL, though at the moment it is not distributed with PDLA. PDLA::IO::FITS is something of a general data format, since piddle data can be stored to a FITS file without loss. PDLA::IO::FlexRaw and PDLA::IO::FastRaw read and write data identical C's low-level
writefunction and PDLA::IO::FlexRaw can work with FORTRAN 77 UNFORMATTED files. FlexRaw and Storable provide general data storage capabilities. Finally, PDLA can read Grib (weather-data) files using the CPAN module PDLA::IO::Grib.
You can make an MPEG animation using PDLA::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 PDLA::DiskCache. To read more, check the PDLA::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
PDLA::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 PDLA. 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 PDLA::IO::Browser), follow this link or type at the system prompt:
If you want to get more information about PDLA::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 https://github.com/PDLPorters/pdla-rest/blob/master/IO/Browser/browser.pd.
DICOM is an image format, and this module allows you to read image files with the DICOM file format. To read more, check the PDLA::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 PDLA::IO::Dumper documentation. See also PDLA::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 PDLA::IO::FastRaw. For a more flexible raw IO module, see PDLA::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.perl.org/?docs=IO/FITS&title=PDLA::IO::FITS. To see if the module is installed, look for PDLA::IO::FITS on your machine by typing 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 PDLA::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 PDLA 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 PDLA::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 PDLA, 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, PDLA 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 PDLA 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 PDLA::IO::Dumper and PDLA::IO::Storable. Check the PDLA::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 PDLA::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 PDLA::IO::Pic documentation. Also look into the next module, as well as PDLA::IO::GD.
Provides methods for reading and writing pnm files (of which pbm is but one). Check the PDLA::IO::Pnm documentation for more details. Also check out the previous module and PDLA::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 PDLA::IO::Storable documentation for more details. See also PDLA::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.