Geology 300 Computer applications in Geology

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Geology 300 Computer applications in Geology
Instructor Rob Mellors
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The purpose of this class is 1) Learn some of
the commonly used software and programs in this
department. 2) Learn some statistics as applied
to geology and geophysics. Comments I do not
know all the menus and mouse button commands on
all the programs.
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What are we going to do?

• Learn basic programs (word, excel, Illustrator,
  PowerPoint)
• Learn basic programming and statistics.
• Basic geographical information systems and
  visualization.
• Learn some of the field equipment.
• Try to avoid sleeping.

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lab assignments due 1 week after
being assigned. 10 off for late assignments
will not be accepted more than one week late
without prior arrangement. 1 midterm (in
class and in lab) class - computer basics lab -
word, excel, mail, Netscape, PowerPoint, canvas
Grading See syllabus
Lab assignments are intended as both lab work and
homework! (they will likely require several hours
of work) The Department computer lab is available
at all times (with an access card)
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History 5000 B.C. abacus 1822 First
(Babbage's steam-powered mechanical computer),
punch cards 1940's World War II - large
electronic (tubes and resistors)
computers First electronic computers ,"machine
language" and basic design (CPU) 1950's Inven
tion and use of transistors and "assembly
language Use of Fortran programming in
seismology. 1960's Use of integrated circuit,
operating systems and higher-level languages
(FORTRAN) First computer generated map of
earthquakes 1970's First hand-calculators,
games (pong), and first "home" computers Inventio
n of Unix Arpanet developed and email
invented Landsat images used in geology
word-processors ----------------------------------
--------------------------------------------------
-------------- 1980's First PC (1981) First
Mac (1984) first use of mouse Widespread use
of email First internet worm
(1987) 1990s Web-pages Widespread use of
internet GIS popularity 2000s Wireless use
lots of spam and viruses google 2020 Skynet
rise of terminators end of mankind.
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• Computer hardware
• CPU
• memory
• motherboard and bus
• power supply
• monitor, video card
• hard drive
• ports (ethernet, parallel, serial, USB)
• CD, floppies, zips, etc.
• speakers
• keyboard and mouse

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Central Processing Unit (CPU) the brains- one
chip that contains all the transistors
used Various types - (PC), Complex Instruction
Set (CISC),Pentium RISC (Mac, Sun Unix),
Reduced Instruction Set different machine
languages 386 486 P1 P4
transistors 275,000 1,200,000 3,100,000 50
million Freq. (Mhz) 16-40 25-100 60-120 1000-30
00 MIPS 11.4 54 112 9000 Bits 32 32 32 32
address mem. 4GB 4GB 4GB 4GB mips millions
of instructions per second (related to
flops, floating-point operations per
second) clock speed controls how fast
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memory Read-only memory (ROM) - cannot be
altered - does the initial startup of a computer
(BIOS). Random-access memory (RAM) - chips that
the CPU puts information while operating -
different from disk drive. When you run a
program(s), it gets loaded into memory. When
handling memory chips,be very careful.
Each memory slot is a 0 or 1 and needs
an address. The more memory, the longer
the address and the bigger the bus.
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Motherboard part that all the others connect
to. bus - cables that connect all the parts of
the computer. Controls how fast the CPU can talk
to the memory.
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Other stuff video cards - controls monitor.
Sometimes part of the motherboard (onboard video)
or fits in AGP or PCI slot. AGP is
better. monitor - the thing you look at
keyboard and mouse disk drives printers modems
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Ports Connect computer to outside
world ethernet card connects to network each
card has specific address wireless uses
ethernet protocol usually serial - transmits one
bit at a time parallel - transmits several bits
at a time in parallel SCSI - small computer
interface used for disk drives, tape
drives fast, can connect up to 7 devices (why
7?) IDE - used for disk drives on PCs also
keyboard, mouse, etc
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Data storage devices - save data when computer is
turned off, usually as a magnetic spot (on or
off). Disk drives hard drives floppy drives,
CD, DVD Portable RAM Tapes DAT, Exabyte, 8
mm compressing all data storage devices can and
will fail - make copies (backup)of all
information - not a valid excuse for late
assignments.
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Disk drive data is stored on disks several
disks on one drive reformatting wipes it clean A
single file may be stored in several parts
(fragments). The address of the file has pointers
to all parts. When a files is deleted, only the
address is erased at the time. A directory (or
folder) is just a file with the addressesof
other files in it, i.e. cylinder 766, track
4,...
Cylinder (1 track per disk)
Direction of magnetic field defines bits
sector
0 1 0 1 1 1
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Monitors monochrome or color CRT or flat-screen
pixels (picture elements) resolution - usually
dimensions of screen in pixels (640x480,
1280x1024) CGA, VGA, SVGA may need a special
card flat screen LCD bits/pixel number of
colors 4 16 8 256 16 35,536 24 16,777,21
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Printers -differ in speed, resolution, and
cost dot matrix ink jets laser
printers plotters all require drivers -
programs that instruct the printer what to do.
Internal fonts - stored inside the printer, any
size other fonts may be bit-mapped and
not-scaled
R
R
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• Drivers
• Specific software programs that operates a
  specific piece of hardware.
• Customized for operating system and hardware.
• Common ones are often included in operating
  system (XP, linux)
• Less common ones arent
• Can be a major stumbling block for new (and
  especially cheap) hardware.

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• So how do it work ?
• power goes on
• ROM issues simple instructions, starting CPU
• The operating system gets loaded into RAM
  (memory).
• At every clock cycle, the CPU follows the
  instructions in memory.
• When you hit a key, (or move the mouse), that
  gets converted
• to numbers. These numbers get sent to the CPU
• if cntrl-alt-del ascii 13-17-127
• then execute commands 11000 through 11100
• sometimes others instructions get sent to the
  printer,
• monitor, etc. It may ask for instructions or data
  from
• another computer across the network.

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Printers require a driver program that tells
the printer what to do. The graphics must be
converted to a format that the printer
understands.
!PS-Adobe-3.0 EPSF-3.0 tells printer it is
PostScript produced by postscript psxy
/data/maps/world/magline.xy 1187 13 M go to
point (1187,13) 8 -4 D draw line 8 units up,
-4 over 5 -2 D draw line 5 units up, -2 over
showpage end drawing send paper out
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• Digital vs analog
• The real world is analog.
• Computers are digital.
• What does digital mean ?
• Information is encoded as numbers.
• This is how computers work. They manipulate
  numbers.
• The email you wrote this morning before class was
  send as a string of numbers.
• The word document is a string of numbers.
• The gif file you looked at is just numbers.
• The programs themselves that displayed the gif
  file
• and sent the email is a list of instructions
  encoded into
• numbers.
• Everything is numbers.

The secret to hacking is that these numbers
can be changed gt "if you know enough, you can
do anything"
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Binary numbers Yes or no in numbers - 0 is no,
1 is yes (1 electric current high or on, 0 means
electric current low or off) Decimal 0 1 2
3 4 5 6 7 8 9
10 Binary 0 1 10 11 100 101 110
111 1000 1001 1010 Each 0 or 1 is a "bit"
(binary digit). These bits are arranged in
groups into "bytes". 8 bits make one byte. 8
bits can be combined 256 ways, representing the
numbers 0 to ..? Note 28 256
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Integers whole numbers Usually two bytes (2)(8)
16 bits maximum value of 65536 216 or from
-32728 to 327728 -215 to 215 and using one
bit to denote positive or negative Sometimes
integers are saved using only one bytes 8
bits What is the maximum value?
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Floats what if we need decimals We could
assume a decimal point 00000001.00000001
1.1 it takes a lot of space for large numbers
Scientific notation uses 6.02 x 1036 in
decimal (base 10) notation Mantissa x
2exponent Exponentmantissa and assume a
decimal in the mantissa 0011000000000010 2
x 23 Floating point numbers take up more space
than integers (usually 4 bytes).
16 bit floating point number 4-bit exponent and
a 12-bit mantissa This is an approximation -
many numbers must be rounded-off. This
usually not a problem. For complex and longer
operations, round-off error is significant
(for example, in solving groundwater flow
equations for a large area or long time).
Double-precision allows 32 bits and therefore
may help. The exact way these numbers are
represented may vary slightly between machines,
for example Unix or PC windows
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An example of round-off error Value 102 should
be 0.01 0.01 0 But Excel says it
is 7.5x10-16 This is a small number but it
isnt zero. In most cases, not a big deal but
not always.
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Some big problems caused by small errors
1991 Patriot missile failed to destroy Scud
28 soldiers killed. Problem floating point
error in counting seconds after 100 hours of
operation. 1996 Ariane rocket failure ( 500
million US) Number needed to control direction of
rockets nozzles exceeded maximum value of a 16
bit integer (strictly speaking, not a round-off
error).
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Characters So how are letters represented ?
The obvious way is assign numbers (integers).
There are several ways of doing this - ASCII,
EBCDIC, and UNICODE. ASCII chart - works for
standard American English okay but not well for
other languages and not all for some some
(Arabic, Chinese, etc). Not only letters are
given numbers - a carriage return is given a
number. Different operating systems may use
different charts - PC's use EBCDIC, and Unix
uses ASCII. UNICODE is a newer standard.
So if you transfer a PC text file to a Unix
machine without some sort of conversion, it
will not look right.
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The ASCII chart (decimal,character) 0 NUL 1
SOH 2 STX 3 ETX 4 EOT 5 ENQ 6 ACK 7
BEL 8 BS 9 HT 10 NL 11 VT 12 NP 13
CR 14 SO 15 SI 16 DLE 17 DC1 18 DC2 19
DC3 20 DC4 21 NAK 22 SYN 23 ETB 24 CAN 25
EM 26 SUB 27 ESC 28 FS 29 GS 30 RS 31
US 32 SP 33 ! 34 " 35 36 37
38 39 ' 40 ( 41 ) 42 43
44 , 45 - 46 . 47 / 48 0 49
1 50 2 51 3 52 4 53 5 54 6 55 7
56 8 57 9 58 59 60 lt 61
62 gt 63 ? 64 _at_ 65 A 66 B 67 C
68 D 69 E 70 F 71 G 72 H 73 I
74 J 75 K 76 L 77 M 78 N 79 O
80 P 81 Q 82 R 83 S 84 T 85 U
86 V 87 W 88 X 89 Y 90 Z 91
92 \ 93 94 95 _ 96 97 a
98 b 99 c 100 d 101 e 102 f 103 g
104 h 105 i 106 j 107 k 108 l 109 m
110 n 111 o 112 p 113 q 114 r 115 s
116 t 117 u 118 v 119 w 120 x 121 y
122 z 123 124 125 126 127 DEL
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Files Most computers keep track of things by
grouping characters into files. A file is
generally a sequential list of characters with
an EOF (end-of-file) character at the end.
Again, this varies greatly between operating
systems. Usually, you run program files which
work with data files.
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Programs A program is a specialized type of
file that does something. It tells the computer
what to do at a very basic level. All programs
are written in some sort of computer language
(Fortran, C, etc) and then get converted into
"machine code by another program ( a
compiler) and what compiled the compiler .?.
In general, a program for one machine will not
work on another. Word for Windows 95 will not do
anything on a Mac or a Unix machine. (Java
programs are an exception) Scripts are text
files that tell programs what to do. We will
write matlab scripts this semester.
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Some examples.
Fortran code if (N .eq. M) then N M
1 endif C code if (N M) N M
1 Matlab if (N M) N M 1 end
An assembly language LDA N get n SUB
M subtract m JNZ NEXT test NM? ADD
C1 yes-add one STA N store result Machine
code - just bits.. 000010100 000100100 000001110
Question what do these do ?
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Images two ways to make a file of an
image raster bitmaps image divided up into a
grid of pixels - size doesnt vary with
complex pictures vector image
defined by x,y coordinates and lines

• 0 0 255 0 is white
• 0 155 0 255 is black
• 0 0

0,1
0,0 1,1 lineto
0,0
1,0
Converting a vector image to raster usually loses
resolution especially on fonts
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Operating systems What is an operating system ?
A way of organizing files and programs on a
computer. The most common ones are Windows,
Unix and Mac. Windows has various types NT,
Windows 95, and are based originally on DOS.
Unix has various types Linux, Solaris, etc.
Although the operating system generally follows
the machine type Windows on PC, Unix on
workstations, this is not always true. Linux
is Unix on a PC, for example. Operating
systems also define an interface - either
command use keyboard or graphical a mouse or
some combination.
Graphical interfaces are popular and easy to
learn but command interfaces are faster and
more powerful.
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Most operating systems have similar structures
files directories or folders and similar
types of commands. Listing files Unix ls
Dos dir Vax/vms dir Closing a window
Windows click in the upper left window Mac
click in the upper right. X-windows you
click ???.
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Networks Networks are how computers are linked
together. The "language" of the network is
called a protocol. The most common way a
computer is attached to a network is by an
Ethernet card or modem (sometimes wireless). All
the computers in the lab have Ethernet cards.
Outside, can be fiber or wireless or
whatever. So when you send that email message
(or login to another computer), all that
information is transmitted along that wire.
Suppose someone splices into that wire and copies
everything travelling along it ?
Routers control how networks are connected.
WAN - Wide Area Network LAN - Local Area Network
Modem - connects two computers over a
telephone line.
The Internet is network of networks.
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Internet The internet is a way of accessing
information on another computer that has been
made available. The address usually looks like
http//www.fubar.edu Domains are generally
.com, .edu., .gov but there are also others
(.mil or .org). Of course, a computer doesn't
use names - it uses numbers. So most of the
address is actually as string of numbers (the IP
number) 130.191.226.112 is an example - all
numbers are less than 256. Why ?
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Permissions Permissions are a way of
determining what users can do what to what
files. These are used only on machines with more
than one user. For example, the system
administrator might be able to delete everyone's
files while a single user might be able to
access only their own files. Commonly,
permissions are broken up into read-access,
write-access, or execute (run) access. So a
user might be able to read a file but not to edit
it (for example, a large database).
Permissions are often able to to broken up by
groups - the owner or world for example.
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• Viruses, worms, spyware
• These programs are written to deliberately cause
  problems, take over machines, or steal
  information.
• Usually, they are machine/operating system
  specific. A windows virus doesnt infect a Mac or
  Unix. So far.
• Currently, spread via a network connection.
• Also via email or clicking on the wrong web-page,
  or by transferring files from an infected
  machine.
• In rare cases, simply looking at the wrong
  web-page may contaminate your machine
  (drive-by).
• How to protect
• Use updated antivirus (especially on SDSU
  networks!)
• Try anti-spyware software.
• Be careful!
• (I would not type in personal information credit
  card s etc on lab machines)