Matlab Training Session 10: Loading Binary Data

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Matlab Training Session 10Loading Binary Data
Course Website http//www.queensu.ca/neurosci/Mat
lab Training Sessions.htm
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• Course Outline
• Term 1
• Introduction to Matlab and its Interface
• Fundamentals (Operators)
• Fundamentals (Flow)
• Importing Data
• Functions and M-Files
• Plotting (2D and 3D)
• Plotting (2D and 3D)
• Statistical Tools in Matlab
• Term 2
• 9. Term 1 review
• 10. Loading Binary Data
• Weeks 11-14 Topics Statistics, Creating Guis,
  Exponential curve fitting .

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• Week 5 Lecture Outline
• loading Binary Data
• A. Week 5 Review Importing Text Data
• B. Binary Encoding
• C. Binary Data Formats
• D. Exercise

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A. Week 5 Review Importing Text Data

• Basic issue
• How do we get data from other sources into Matlab
  so that we can play with it?
• Other Issues
• Where do we get the data?
• What types of data can we import?

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• Lots of options to load files
• load for basics
• fscanf for complex
• textread for any text
• xlsread for Excel worksheets

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load

• Command opens and imports data from a standard
  ASCII file into a matlab variable
• Usage var_name load(filename)
• Restrictions
• Data must be constantly sized
• Data must be ASCII
• No other characters

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load

• Works for simple and unstructured code
• Powerful and easy to use but limited
• Will likely force you to manually handle
  simplifying data which is prone to error
• More complex functions are more flexible

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File Handling

• f functions are associated with file opening,
  reading, manipulating, writing,
• Basic Functions of Interest for opening and
  reading generic files in matlab
• fopen
• fclose
• fseek/ftell/frewind
• fscanf
• fgetl

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fopen

• Opens a file object in matlab that points to the
  file of interest
• fid fopen(filepath)
• fid is an integer that represents the file
• Can open multiple files and matlab will assign
  unique fids

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fclose

• When you are done with a file, it is a good idea
  to close it especially if you are opening many
  files
• fclose(fid)

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What is a File?

• A specific organization of data
• In matlab it is identified with a fid
• Location is specified with a pointer that can be
  moved around

fid
file_name
Pointer
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Moving the Pointer

• We already know how to assign a fid (fopen)
• To find where the file is pointing
• x ftell(fid)
• To point somewhere else
• fseek(fid,offset,origin)
• Move pointer in file fid by offset relative to
  origin
• Origin can be beginning, current, end of file
• To point to the beginning
• frewind(fid)

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Getting Data

• Why move the pointer around?
• Get somewhere in the file from where you want
  data
• fscanf(fid,format,size)
• Format
• You have to tell matlab the type of data it
  should be expecting in the text file so that it
  can convert it
• d, f, c
• Size
• You can specify how to organize the imported data
• m,n import the data as m by n, n can be
  infinite
• Be careful because matlab will mangle your data
  and not tell you

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Getting Data

• fgetl returns the next line of the file as a
  character array
• You may need to convert these to numbers

gtgt fid1 fopen(test1.txt) gtgt a_str
fgetl(fid1) a_str 1 2 gtgt a_num
str2num(a_str) a_num 1 2
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B. Binary Encoding

• All data files are binary encoded
• ASCII text format is generally the easiest
  because it is relatively simple, easy to
  visualize in a text editor, and is a common
  output format
• BUT
• ASCII text is not the fastest or the most
  efficient way of encoding data
• Not all data files are ASCII!

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B. Binary Encoding

• Binary data consists of sequences of 0s and 1s
• 10101010101010101000010111110111101011
• Depending on the encoding used, individual
  meaningful values will occur every 4, 8, 16, 32
  or 64 bits
• For a tutorial on converting between binary and
  decimal numbers see http//www.rwc.uc.edu/koehle
  r/comath/11.html

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B. Binary Encoding

• Binary data consists of sequences of 0s and 1s
• 1010 1010 1010 1010 1000 0101 1111
• Depending on the encoding used, individual
  meaningful values will occur every 4, 8, 16 or 32
  bits

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B. Binary Encoding

• Binary data consists of sequences of 0s and 1s
• 10101010 10101010 10000101 11110111
• Depending on the encoding used, individual
  meaningful values will occur every 4, 8, 16 or 32
  bits

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B. Binary Encoding

• Binary data consists of sequences of 0s and 1s
• 1010101010101010 1000010111110111
• Depending on the encoding used, individual
  meaningful values will occur every 4, 8, 16 or 32
  bits

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B. Binary Encoding

• Each group of bits can represent a value,
  character, delimiter, command, instruction ect.
• Generally binary data is divided into 8 bit (1
  byte) segments
• 00000000 zero
• 11111111 255
• IT IS VERY IMPORTANT TO KNOW WHAT FORMAT THE DATA
  IS IN BEFORE YOU CAN READ IT!

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ASCII ENCODING

• ASCII American Standard Code for Information
  Interchange (1968).
• ASCII every character is coded by only seven
  bits of information. The eighth bit is ignored
  (it can be a zero or one).
• ASCII consists of 127 characters which include
  uppercase, lowercase, spaces and formatting
  characters
• See www.asciitable.com for the full ascii table

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ASCII vs Simple Binary Encoding

• ASCII requires 1 byte to be used for every
  character
• Data Table
• 105 124 27
• 101 102 111
• In ascii 1 byte is used for every character,
  space and carriage return 23 bytes
• If this was encoded in a simple 8 bit binary
  representation this would only use 11 bytes (1
  byte for every number and space)

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Binary Precision

• The number of bits used to represent a value
  determines how large or small that value can be
• 8 bits 0 to 256
• 16 bits 0 to 65536
• 32 bits 0 to 4.2950e009
• Precision also determines how many decimal places
  can be represented

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C. Binary Formats Integers and Characters
'schar' Signed character 8 bits 'uchar'
Unsigned character 8 bits 'int8' Integer 8
bits 'int16' Integer 16 bits 'int32'
Integer 32 bits 'int64' Integer 64
bits 'uint8' Unsigned integer 8 bits 'uint16'
Unsigned integer 16 bits 'uint32' Unsigned
integer 32 bits 'uint64' Unsigned integer 64
bits
The first bit denotes the sign if the integer
or character is signed.
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Readable Binary Data Formats Floating Point
Representation

• Used for numbers that require decimal
  representation (real numbers)
• Established by IEEE (Institute of Electrical and
  Electronics Engineers )
• Encoded in 32 (single precision) or 64 bits
  (double precision)
• Single precision(short) 32 bits 1 bit for the
  sign, 8 bits for the exponent, and 23 bits for
  the mantissa.
• Double precision(Long) Real 64 bits 1 bit for
  the sign, 11 bits for the exponent, and 52 bits
  for the mantissa.

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Readable Binary Data Formats Floating Point
Representation

• By default matlab stores all values with double
  precision
• The functions realmax and realmin return max and
  min value representations
• 'float32, single Floating-point 32 bits
• 'float64', 'double' Floating-point 64 bits

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Specifying Machine Formats

• The computer system used to record or save the
  binary data in unique addressing orders
• In order to load binary data from a particular
  system, Matlab needs to know the machine format
• You can use the fopen function to determine the
  machine format
• filename, mode, machineformat fopen(fid)

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Binary File Machine Formats
'ieee-be' or 'b IEEE floating point with
big-endian byte ordering'ieee-le' or 'l'
IEEE floating point with little-endian byte
ordering'ieee-be.l64' or 's IEEE floating
point with big-endian byte ordering
and 64-bit long data
type'ieee-le.l64' or 'a IEEE floating point
with little-endian byte ordering
and 64-bit long data
type'native' or 'n' Numeric format of
the machine on which MATLAB
is running (the default)'vaxd' or
'd' VAX D floating point and VAX
ordering'vaxg' or 'g' VAX G
floating point and VAX ordering
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Reading Binary Data

• The function fread() performs all binary data
  reading in matlab

Syntax A fread(fid) A fread(fid, count)
A fread(fid, count, precision) A fread(fid,
count, precision, skip) A fread(fid, count,
precision, skip, machineformat) A, count
fread(...)
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Reading Binary Data
Input Arguments Count
x read x elements
Inf read to end of file
m,n read
enough to fill a m by n matrix Precision
Specify input data format eg.
Int8, int16, short,
long see previous slides Skip
Skip specified
number of bits between
segments specified by the
Precision argument MachineFormat
Specify machine format 'ieee-be, 'ieee-le..
See
previous slides
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Exercise

• Load and plot position data saved in
  week10data.rob
• This file contains binary position data saved in
  32 bit floating point format precision
• Use the fopen function to determine the machine
  format
• hint fname, mode, mformat fopen(fid)
• 2. Load the data using the fread function
• 3. Plot the position
• 4. Try loading the data with an incorrect
  argument to see how this changes/corrupts the data

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Exercise Solution
fid fopen('week10data.rob','r') open file
for reading Determine file format fname,
mode, mformat fopen(fid) Format is
ieee-le Read binary data pos_data fread(fid,
inf, 'single', 'ieee-le') plot(pos_data) plot
position data fclose(fid) close file
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Getting Help

• Help and Documentation
• Digital
• Accessible Help from the Matlab Start Menu
• Updated online help from the Matlab Mathworks
  website
• http//www.mathworks.com/access/helpdesk/help/tech
  doc/matlab.html
• Matlab command prompt function lookup
• Built in Demos
• Websites
• Hard Copy
• Books, Guides, Reference
• The Student Edition of Matlab pub. Mathworks Inc.