Mastering Perl for Bioinformatics [Electronic resources] نسخه متنی

8.1 Computer Graphics

Computer graphics
programming is a specialty within computer science, and it has its
own journals and conferences and laboratories. It encompasses just
about everything you can see on a computer, from the fonts with which
letters are drawn (both on the screen, and when computer typeset and
printed like this book), to elaborate images, animation, and the
special effects in movies.

Computer graphics images are represented as data in the computer;
they're usually organized in files, one per image,
although they can also be stored in a computer
program's memory, as I did when storing the graphics
for the Restrictionmap.pm module in a scalar
variable. Some kinds of animation store several images in one file,
but I won't cover those kinds of image files here.

For the purposes of this chapter, we won't be
digging into the details of how graphics files are designed; that
level of detail isn't possible in a single chapter.
Here, I'll just discuss the very basic information
you need to get started generating and displaying images for your web
site. I'm going to show you some easy (and
inexpensive) ways to generate graphics, enough to set your feet on
the right path. The modules I use have methods that handle the
details of reading and writing the different file formats, so you can
simply use the methods and ignore the details of the formats
themselves.

8.1.1 Basic Graphics Concepts

There are two things you need for computer
graphics: a program to create a graphics
file and the correct software and hardware to display the image.
These days, digital photography may be the source of digital images,
or a printed image may be entered into digital format by a scanning
device. As computer technology has developed, many graphics display
devices and file formats have seen some use and then virtually
disappeared as they are supplanted by other systems.[1]
However, even though there are many file formats that are currently
in use, a few standard formats are widely known and can be displayed
by most graphics display programs. The PNG and JPEG files I use here
are very commonly known.

[1] One of my first programming jobs was to write
vector graphics for a Tektronix
oscilloscope display. Vector graphics are specified by endpoints of
lines. Although such graphic programs are still in use, they are
almost always converted to raster graphics for display these days.
The same year, I wrote a large graphics program to write and play
computer music on a Blit terminala raster graphics display
that was the first to have modern-style simultaneously updated
windows. Both systems have faded away, but the software they were
written in was ported to other display devices.

Although I won't go into any detail about
graphics file formats, there are a few
basic facts you need to understand because you'll be
asked to specify some of these parameters when you use a graphics
library (such as GD.pm). For instance, in the Perl
code that follows, you'll see a method
colorAllocate that specifies and enters a color
into a color table. The few short comments that follow in this
section are meant to introduce these, and other common terms, and to
give brief definitions.

These days the standard graphics formats are mostly some variation of
a raster image, in which a rectangular image is
described by a two-dimensional matrix of pixel values. A
pixel
(short for "picture element") is
one glowing dot on your computer screen. These values can be
represented in different ways, from a simple 1 or 0 representing
black or white (called a
bitmap),
to a number representing various shades of grey, to various color
image schemes. A computer display may have different numbers of
pixels overall; for instance, the one I'm working on
now has 1024 horizontal and 768 vertical rows. Displays (or printers)
are also rated by how closely packed the pixels are, usually by
saying they have so many
DPI
or dots per inch.

Colors are typically represented in one of three ways:

RGB

Colors might be represented in the
RGB fashion by three
numbers indicating the values for the primary colors red, green, and
blue. All colors can be formed by mixing these values in different
quantities. A typical standard is 24-bit
color, also called
truecolor,
in which each of the three primary colors is represented by an 8-bit
value (256 possible values per primary color) for a total of over 16
million colors. This is well in excess of the 7 million colors most
humans can distinguish, and as a result, a 24-bit color scheme is
very popular, although many computer displays can handle only a
smaller number of colors.

Color table

Colors are also sometimes represented by a color table (also known as a
palette), which
uses 8 bits per color at each pixel, and uses the values as an index
into a 256-slot table for a total of 256 colors. In this way, the
image itself only needs to have 8 bits per color, instead of 24 bits,
so the image can be much smaller as data. The drawback, of course, is
that there are only 256 possible colors instead of 16 million; also,
an image needs a color table in addition to the pixel values. Still,
this scheme works quite well and is frequently used. Many computers
give you the option of displaying using a color table or using
truecolor.

CMYK

The third popular way to represent colors is the
CMYK color space, a
subtractive color scheme used mainly in high-quality printing. The
name CMYK comes from the colors cyan, magenta, yellow, and black,
which can be combined to represent the range of colors, similar to
the way that RGB does. I won't discuss this scheme
further here.

8.1.2 Graphics and File Formats

I'm going to generate
two kinds of graphics files in this chapter, PNG and JPEG. There are
also many different file formats for computer graphics. Some of these
different formats amount to little more than trivial variations in
the header section of the files; others represent quite different
ways of storing and displaying images on a computer screen.

PNG

Portable Network Graphic is a raster
format that has become especially popular since the late 1990s when
legal problems arose with the use of the very widely used GIF format.
PNG can be used to create indexed color images (via the color table
mentioned before) or to create 24-bit truecolor images. Because it
does not perform compression on the image data, PNG is good for
saving large images such as photographs because none of the
photographic data is lost saving it in PNG format. But because images
like photographs tend to be fairly large, and hence slow to display
over the Web, PNG is best used for generating and displaying simpler
graphics.

JPEG

Joint Photographic Experts Group is a
popular format for displaying images, especially such large images as
photographs. JPEG performs data compression, and although some
of the picture quality is lost, the result is usually a good quality
photographic image that is much smaller than the uncompressed
original image. This has led to JPEG being widely adopted on the Web,
where smaller picture sizes can dramatically improve the time it
takes to download and display an image. (Displaying a JPEG image also
requires decoding the compression, but that is a fairly fast
operation on modern computers compared with the time it often takes
to download a file.) However, the drawback to JPEG is exactly the
same as its advantage: the compression. If you have a JPEG image, and
want to do some editing of the digital image, you have to decode the
image to perform the edits and then recompress it. But once an image
is compressed, some of the original image data is lost. This
compression/decompression will cause the loss of image data to become
more apparent; several cycles of it can result in a noticeably poorer
quality image. So it's best to save the original
image in a noncompressed format, which can undergo editing without
major loss of quality, and then create JPEG images directly from an
uncompressed version.

GIF

An older file format which was standard on the Web and is still
widespread, GIF (Graphic Interchange Format), has fallen
afoul of some proprietary licensing issues; most Perl programmers
have shifted to the similar PNG format which is in the public domain.