final code? working on reports

This commit is contained in:
aj 2020-11-20 13:36:48 +00:00
parent ac791ce418
commit d93a980ed5
18 changed files with 1084 additions and 853 deletions

3
.gitignore vendored
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@ -1,2 +1,3 @@
obj_*
*~
*~
*#*

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@ -123,7 +123,7 @@ LatexCommand lstlistoflistings
\begin_inset CommandInset include
LatexCommand lstinputlisting
filename "../Coursework/coursework.c"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},caption={Main coursework program: 2 processes for reading and aggregating data}"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},otherkeywords={PROCESS_THREAD, PROCESS_BEGIN, PROCESS_END, etimer_set, process_alloc_event, initIO, getBuffer, PROCESS_WAIT_EVENT, PROCESS_WAIT_EVENT_UNTIL, leds_off, leds_on, getLight, printf, putFloat, putchar, process_post, etimer_reset, etimer_stop, handleSAXBufferRotation, handleSimpleBufferRotation, free, freeBuffer, calculateStdDev, handleFinalBuffer, ceil, normaliseBuffer, aggregateBuffer, printBuffer, stringifyBuffer, swapBufferMemory, malloc, calculateMean, valueToSAXChar, sqrt},caption={Main coursework program: 2 processes for reading and aggregating data}"
\end_inset
@ -141,7 +141,7 @@ lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentst
\begin_inset CommandInset include
LatexCommand lstinputlisting
filename "../Coursework/buffer.h"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},caption={Buffer header file: get, free and manipulate buffers}"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},otherkeywords={PROCESS_THREAD, PROCESS_BEGIN, PROCESS_END, etimer_set, process_alloc_event, initIO, getBuffer, PROCESS_WAIT_EVENT, PROCESS_WAIT_EVENT_UNTIL, leds_off, leds_on, getLight, printf, putFloat, putchar, process_post, etimer_reset, etimer_stop, handleSAXBufferRotation, handleSimpleBufferRotation, free, freeBuffer, calculateStdDev, handleFinalBuffer, ceil, normaliseBuffer, aggregateBuffer, printBuffer, stringifyBuffer, swapBufferMemory, malloc, calculateMean, valueToSAXChar, sqrt},caption={Buffer header file: get, free and manipulate buffers}"
\end_inset
@ -156,7 +156,7 @@ lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentst
\begin_inset CommandInset include
LatexCommand lstinputlisting
filename "../Coursework/sax.h"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},caption={SAX header file: z-normalise and stringify buffers}"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},otherkeywords={PROCESS_THREAD, PROCESS_BEGIN, PROCESS_END, etimer_set, process_alloc_event, initIO, getBuffer, PROCESS_WAIT_EVENT, PROCESS_WAIT_EVENT_UNTIL, leds_off, leds_on, getLight, printf, putFloat, putchar, process_post, etimer_reset, etimer_stop, handleSAXBufferRotation, handleSimpleBufferRotation, free, freeBuffer, calculateStdDev, handleFinalBuffer, ceil, normaliseBuffer, aggregateBuffer, printBuffer, stringifyBuffer, swapBufferMemory, malloc, calculateMean, valueToSAXChar, sqrt},caption={SAX header file: z-normalise and stringify buffers}"
\end_inset
@ -171,7 +171,7 @@ lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentst
\begin_inset CommandInset include
LatexCommand lstinputlisting
filename "../Coursework/math.h"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},caption={Math header file: mean, standard deviation, implementations of ceil, sqrt}"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},otherkeywords={PROCESS_THREAD, PROCESS_BEGIN, PROCESS_END, etimer_set, process_alloc_event, initIO, getBuffer, PROCESS_WAIT_EVENT, PROCESS_WAIT_EVENT_UNTIL, leds_off, leds_on, getLight, printf, putFloat, putchar, process_post, etimer_reset, etimer_stop, handleSAXBufferRotation, handleSimpleBufferRotation, free, freeBuffer, calculateStdDev, handleFinalBuffer, ceil, normaliseBuffer, aggregateBuffer, printBuffer, stringifyBuffer, swapBufferMemory, malloc, calculateMean, valueToSAXChar, sqrt},caption={Math header file: mean, standard deviation, implementations of ceil, sqrt}"
\end_inset
@ -186,7 +186,7 @@ lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentst
\begin_inset CommandInset include
LatexCommand lstinputlisting
filename "../Coursework/io.h"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},caption={IO header file: init function for starting sensors}"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},otherkeywords={PROCESS_THREAD, PROCESS_BEGIN, PROCESS_END, etimer_set, process_alloc_event, initIO, getBuffer, PROCESS_WAIT_EVENT, PROCESS_WAIT_EVENT_UNTIL, leds_off, leds_on, getLight, printf, putFloat, putchar, process_post, etimer_reset, etimer_stop, handleSAXBufferRotation, handleSimpleBufferRotation, free, freeBuffer, calculateStdDev, handleFinalBuffer, ceil, normaliseBuffer, aggregateBuffer, printBuffer, stringifyBuffer, swapBufferMemory, malloc, calculateMean, valueToSAXChar, sqrt},caption={IO header file: init function for starting sensors}"
\end_inset
@ -201,7 +201,7 @@ lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentst
\begin_inset CommandInset include
LatexCommand lstinputlisting
filename "../Coursework/util.h"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},caption={Other utilities: short and float printing functions from earlier labs}"
lstparams "breaklines=true,frame=tb,language=C,basicstyle={\\ttfamily},commentstyle={\\color{commentgreen}\\itshape},keywordstyle={\\color{blue}},emphstyle={\\color{red}},stringstyle={\\color{red}},identifierstyle={\\color{cyan}},otherkeywords={PROCESS_THREAD, PROCESS_BEGIN, PROCESS_END, etimer_set, process_alloc_event, initIO, getBuffer, PROCESS_WAIT_EVENT, PROCESS_WAIT_EVENT_UNTIL, leds_off, leds_on, getLight, printf, putFloat, putchar, process_post, etimer_reset, etimer_stop, handleSAXBufferRotation, handleSimpleBufferRotation, free, freeBuffer, calculateStdDev, handleFinalBuffer, ceil, normaliseBuffer, aggregateBuffer, printBuffer, stringifyBuffer, swapBufferMemory, malloc, calculateMean, valueToSAXChar, sqrt, putShort},caption={Other utilities: short and float printing functions from earlier labs}"
\end_inset

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@ -36,7 +36,7 @@ customHeadersFooters
\output_sync 0
\bibtex_command default
\index_command default
\paperfontsize default
\paperfontsize 10
\spacing single
\use_hyperref true
\pdf_title "IoT Aggregation Algorithm Coursework"
@ -117,21 +117,224 @@ Andy Pack / 6420013
Description
\end_layout
\begin_layout Standard
Symbolic Aggregation Approximation (SAX) was implemented as an in-network
data processing technique, compressing the representation while allowing
further processing on this symbolic string.
Figure
\begin_inset CommandInset ref
LatexCommand ref
reference "fig:Demonstration-of-SAX"
plural "false"
caps "false"
noprefix "false"
\end_inset
shows two rounds of SAX output following data collection, a window size
of 2 was used and an alphabet of length 4, i.e the characters
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
a
\end_layout
\end_inset
through
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
d
\end_layout
\end_inset
inclusive.
12 C
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
floats
\end_layout
\end_inset
total 48 bytes of data, this can be reduced by a factor of 4 using
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
char
\end_layout
\end_inset
representation instead, a window size of 2 halves the number of output
samples and lowers the required memory to just 6 bytes.
\end_layout
\begin_layout Section
Specification
\end_layout
\begin_layout Standard
SAX is implemented in two separate steps, that of transforming the time-series
into Piecewise Aggregate Approximation (PAA) representation and then representi
ng this numeric series with a symbolic alphabet.
\end_layout
\begin_layout Subsection
PAA
\end_layout
\begin_layout Standard
The standard deviation and mean of the data series were first calculated,
these are required for Z-normalisation.
This normalisation process takes a series of data and transforms it into
one with a mean of 0 and a standard deviation of 1.
This changes the context of the value from being measured in lux to being
a measure of a samples distance from the mean, 0, in standard deviations.
This allows comparison of different time-series.
\end_layout
\begin_layout Standard
Following Z-normalisation, the size of the series is reduced by applying
a windowing function.
This takes subsequent equally-sized groups of samples and reduces the group
to the mean of those values.
\end_layout
\begin_layout Standard
As a result of these two actions, the original time series has been reduced
to a given length of samples with a mean of 0 and standard deviation of
1.
\end_layout
\begin_layout Subsection
SAX
\end_layout
\begin_layout Standard
With the result of the above, the remaining step is to replace each sample
value with a symbol to represent it.
The amount of symbols to be used is given, each will represent the same
probability range when considering a Gaussian distribution of mean 0 and
standard deviation of 1.
This can be achieved by using standard deviation breakpoints defined such
that the area under Gaussian curve between breakpoints is the same.
\end_layout
\begin_layout Section
Implementation
\end_layout
\begin_layout Section
Output
\begin_layout Standard
The SAX functionality was added as an alternative buffer rotating mechanism
over the original 12-to-1/4-to-1/12-to-12 aggregation system.
The length of the output buffer is calculated such that it can be allocated.
From here the input buffer is Z-normalised using the
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
normaliseBuffer(buffer)
\end_layout
\end_inset
function from the
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
buffer.h
\end_layout
\end_inset
header.
This function iterates over each value in the buffer, subtracts the buffer's
mean and then divides by the standard deviation.
Following this, the buffer is aggregated using the same 4-to-1 aggregation
function
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
aggregateBuffer(bufferIn, bufferOut, groupSize)
\end_layout
\end_inset
as the group size is variable.
The output from this function represents the PAA form of the initial data
series.
\end_layout
\begin_layout Standard
This final buffer is handled using
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
handleFinalBuffer(buffer)
\end_layout
\end_inset
where a pre-processor directive checks whether SAX is being used.
If so the PAA buffer is
\emph on
stringified
\emph default
using
\begin_inset listings
lstparams "basicstyle={\ttfamily}"
inline true
status open
\begin_layout Plain Layout
stringifyBuffer(buffer)
\end_layout
\end_inset
which performs the SAX symbolic representation.
\end_layout
\begin_layout Standard
\begin_inset Float figure
placement h
wide false
sideways false
status open
@ -139,8 +342,8 @@ status open
\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename SaxBy2,10Break.png
width 100col%
filename SaxBy2,4Break.png
width 30col%
\end_inset
@ -152,7 +355,14 @@ status open
\begin_layout Plain Layout
Demonstration of SAX aggregation with window size of 2 and alphabet of length
10
4
\begin_inset CommandInset label
LatexCommand label
name "fig:Demonstration-of-SAX"
\end_inset
\end_layout
\end_inset

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@ -113,8 +113,31 @@ November 2020
Andy Pack / 6420013
\end_layout
\begin_layout Standard
\begin_inset FloatList figure
\end_inset
\end_layout
\begin_layout Standard
\begin_inset VSpace defskip
\end_inset
\end_layout
\begin_layout Standard
\emph on
Standard deviation thresholds of 400 for some activity and 1,000 for high
activity.
\end_layout
\begin_layout Standard
\begin_inset Float figure
placement bh
wide false
sideways false
status open
@ -122,8 +145,9 @@ status open
\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename NonSaxAggregate.png
width 100col%
filename 12to1.jpg
lyxscale 50
width 80col%
\end_inset
@ -134,7 +158,7 @@ status open
\begin_inset Caption Standard
\begin_layout Plain Layout
Demonstration of 4-into-1 aggregation taking place following moderate activity
Demonstration of 12-into-1 aggregation for little activity
\end_layout
\end_inset
@ -156,7 +180,8 @@ status open
\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename NonSaxWithRed.png
filename 12to3.jpg
lyxscale 50
width 100col%
\end_inset
@ -168,9 +193,7 @@ status open
\begin_inset Caption Standard
\begin_layout Plain Layout
Demonstration of both no aggregation for high activity (First output) and
tight 12-into-1 average for little activity (Last output), red LED on as
aggregation occurs
Demonstration of 4-into-1 aggregation for moderate activity
\end_layout
\end_inset
@ -192,7 +215,8 @@ status open
\begin_layout Plain Layout
\align center
\begin_inset Graphics
filename SaxBy2,10Break.png
filename 12to12.jpg
lyxscale 50
width 100col%
\end_inset
@ -204,8 +228,7 @@ status open
\begin_inset Caption Standard
\begin_layout Plain Layout
Demonstration of SAX aggregation with window size of 2 and alphabet of length
10
Demonstration of no aggregation for high activity
\end_layout
\end_inset

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@ -9,7 +9,7 @@
#define INITIAL_STATE true // whether begins running or not
#define SAX // use sax aggregation and transform instead of simple average aggregation
#define SAX_BREAKPOINTS 10 // number of characters to be used
#define SAX_BREAKPOINTS 4 // number of characters to be used
#include "contiki.h"
@ -35,15 +35,13 @@ PROCESS_THREAD(sensing_process, ev, data)
/*INIT*/
PROCESS_BEGIN();
static bool isRunning = INITIAL_STATE;
static struct etimer timer;
etimer_set(&timer, CLOCK_SECOND/READING_INTERVAL);
if(isRunning) etimer_set(&timer, CLOCK_SECOND/READING_INTERVAL); // start timer if running
event_buffer_full = process_alloc_event();
initIO();
static bool isRunning = INITIAL_STATE;
static Buffer buffer;
buffer = getBuffer(BUFFER_SIZE);
/*END INIT*/
@ -54,23 +52,20 @@ PROCESS_THREAD(sensing_process, ev, data)
PROCESS_WAIT_EVENT();
if (ev == PROCESS_EVENT_TIMER){
if (isRunning == true) {
leds_off(LEDS_RED);
float light_lx = getLight(); // GET
leds_off(LEDS_RED);
float light_lx = getLight(); // GET
buffer.items[counter] = light_lx; // STORE
printf("%2i/%i: ", counter + 1, buffer.length);putFloat(light_lx);putchar('\n'); // DISPLAY CURRENT VALUE
//printBuffer(buffer);putchar('\n'); // DISPLAY CURRENT BUFFER
counter++;
if(counter == buffer.length) // CHECK WHETHER FULL
{
process_post(&aggregator_process, event_buffer_full, &buffer); // pass buffer to processing thread
counter = 0;
buffer = getBuffer(BUFFER_SIZE); // get new buffer for next data, no freeing in this thread
}
buffer.items[counter] = light_lx; // STORE
printf("%2i/%i: ", counter + 1, buffer.length);putFloat(light_lx);putchar('\n'); // DISPLAY CURRENT VALUE
counter++;
if(counter == buffer.length) // CHECK WHETHER FULL
{
process_post(&aggregator_process, event_buffer_full, &buffer); // pass buffer to processing thread
counter = 0;
buffer = getBuffer(BUFFER_SIZE); // get new buffer for next data, no freeing in this thread
}
etimer_reset(&timer);
@ -82,12 +77,12 @@ PROCESS_THREAD(sensing_process, ev, data)
if (isRunning == true)
{
printf("Starting...\n");
etimer_set(&timer, CLOCK_SECOND/READING_INTERVAL);
}
else
{
printf("Stopping, clearing buffer...\n");
//freeBuffer(buffer);
//buffer = getBuffer(BUFFER_SIZE);
etimer_stop(&timer);
counter = 0; // just reset counter, used as index on buffer items, will overwrite
}
}
@ -158,10 +153,10 @@ handleSimpleBufferRotation(Buffer *inBufferPtr)
printf("Insignificant std. dev.: ");putFloat(sd.std);printf(", squashing buffer\n");
outBuffer = getBuffer(1); // CREATE OUTPUT BUFFER
outBuffer.items[0] = sd.mean;
}
outBuffer.stats = sd; // final compressed buffer has pointer to stats for uncompressed data in case of further interest
inBuffer.stats = sd;
outBuffer.stats = sd; // final compressed buffer has stats for uncompressed data in case of further interest
/*********************/
handleFinalBuffer(outBuffer); // PASS FINAL BUFFER

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@ -36,26 +36,25 @@
void
normaliseBuffer(Buffer bufferIn) // z normalise buffer for SAX
{
if(bufferIn.stats.std == 0) // error check
if(bufferIn.stats.std == 0) // error check, don't divide by 0
{
printf("Standard deviation of zero, unable to normalise\n");
return;
}
int i; // for group number
float *inputPtr = bufferIn.items; // cursor for full buffer
int i;
float *inputPtr = bufferIn.items; // cursor
for(i = 0; i < bufferIn.length; i++)
{
*inputPtr = (*inputPtr - bufferIn.stats.mean) / bufferIn.stats.std;
inputPtr++; // increment both cursors
inputPtr++;
}
}
char
valueToSAXChar(float inputValue)
{
float below, above;
{
int i;
for(i = 0; i < SAX_BREAKPOINTS; i++)
{
@ -69,7 +68,7 @@ valueToSAXChar(float inputValue)
}
else // in between check interval of two breakpoints
{
if(breakPoints[i - 1] < inputValue < breakPoints[i]) return SAX_CHAR_START + i;
if((breakPoints[i - 1] < inputValue) && (inputValue < breakPoints[i])) return SAX_CHAR_START + i;
}
}
return '0';
@ -78,7 +77,7 @@ valueToSAXChar(float inputValue)
char* // map buffer of normalised floats into SAX chars
stringifyBuffer(Buffer bufferIn)
{
char* outputString = (char*) malloc((bufferIn.length + 1) * sizeof(char));
char* outputString = (char*) malloc((bufferIn.length + 1) * sizeof(char)); // +1 for null terminator
int i;
for(i = 0; i < bufferIn.length; i++)

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@ -3,7 +3,7 @@
typedef unsigned short USHORT;
//print a unsigned short (as returned from rand) picewise char by char
//print a unsigned short picewise char by char
void
putShort(USHORT in)
{

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@ -2,3 +2,6 @@ IOT Labs
==========
Using Coniki and Cooja in C.
![4-into-1 aggregation](Coursework-Reports/12to3.jpg)
![SAX aggregation](Coursework-Reports/SaxBy2,4Break.png)