final code? working on reports

.gitignore

@@ -1,2 +1,3 @@
 obj_*
 *~
+*#*

Coursework-Reports/code.lyx

@@ -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
 

Coursework-Reports/report.lyx

@@ -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
+\begin_layout Standard
-Output
+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
+	filename SaxBy2,4Break.png
-	width 100col%
+	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

Coursework-Reports/screenshot.lyx

@@ -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
+	filename 12to1.jpg
-	width 100col%
+	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
+Demonstration of 4-into-1 aggregation for moderate activity
- tight 12-into-1 average for little activity (Last output), red LED on as
- aggregation occurs
 \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
+Demonstration of no aggregation for high activity
- 10
 \end_layout
 
 \end_inset

Coursework/coursework.c

@@ -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*/
@@ -54,7 +52,6 @@ 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
@@ -62,7 +59,6 @@ PROCESS_THREAD(sensing_process, ev, data)
             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
@@ -71,7 +67,6 @@ PROCESS_THREAD(sensing_process, ev, data)
                 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);
+                etimer_stop(&timer);
-                //buffer = getBuffer(BUFFER_SIZE);
                 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
+    outBuffer.stats = sd; // final compressed buffer has stats for uncompressed data in case of further interest
-    inBuffer.stats = sd;
     
     /*********************/
     handleFinalBuffer(outBuffer); // PASS FINAL BUFFER

Coursework/sax.h

@@ -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
+    int i;
-    float *inputPtr = bufferIn.items; // cursor for full buffer
+    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++)

Coursework/util.h

@@ -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) 
 {

README.md

@@ -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)