rename directory P5 -> p5.js; update report content

3 files changed, 61 insertions, 43 deletions

diff --git a/P5/light.js b/p5.js/light.js
index 20eb1c0..20eb1c0 100644
--- a/P5/light.js
+++ b/p5.js/light.js
diff --git a/ref.bib b/ref.bib
index ba6c3e1..ae942eb 100644
--- a/ref.bib
+++ b/ref.bib
@@ -139,6 +139,23 @@
   file        = {:GarciaHuertes2016 - The Use of Unio Tumidus for Detection of Water Pollution.pdf:PDF},
 }
 
+@Online{GeeksforGeeks2024,
+  date    = {2024-08-23},
+  editor  = {GeeksforGeeks},
+  title   = {Coupling in Java},
+  url     = {https://www.geeksforgeeks.org/coupling-in-java/},
+  urldate = {2025-04-19},
+}
+
+@Online{AccentSystems2021,
+  author  = {{Accent Systems}},
+  date    = {2021-07-06},
+  editor  = {{Accent Systems}},
+  title   = {What is Eddystone™?},
+  url     = {https://accent-systems.com/support/faq/what-is-eddystone/},
+  urldate = {2025-04-19},
+}
+
 @Comment{jabref-meta: databaseType:biblatex;}
 
 @Comment{jabref-meta: fileDirectory-jonas-bastian:/home/jonas/Projects/RUC/LIB/mussel;}
diff --git a/report.qmd b/report.qmd
index 966490d..847b26f 100644
--- a/report.qmd
+++ b/report.qmd
@@ -39,7 +39,6 @@ is illustration and demostration purposes.
 *TODO: come back and write about each step,
 OUR THREE REQUIRED COMPONENTS,and a conclusion*
 
-
 # Introduction - amal
 
 In Poland, several waterworks use biomonitoring systems
@@ -52,7 +51,6 @@ and have additionally made a p5.js program to simulate night and day,
 which influences the pseudomussels' behaviour (reaction).
 We have defined a research question to work around:
 
-
 **How do we simulate and visualise an existing biomonitoring technology
 for its core purpose**
 
@@ -140,12 +138,13 @@ but it is explicitly stated as "Not a part of the curicculum".
 Hence we have searched for external sources on API knowledge.
 
 We decided to implement a loosely coupled network design
-as in @GeeksForGeeks2024,
+as described e.g. in @GeeksforGeeks2024,
 to connect the different components
 and allow each of them to operate independently,
 whilst still being able to exchange data.
 We chose to use the BLE Beacon API --
-specifically the Eddystone protocol @accentSystems --
+specifically the Eddystone protocol
+as described e.g. in @AccentSystems2021 --
 and focused on TLM (telementry) frame type.
 The original purpose of of TLM
 is to transmit temperature and battery level,
@@ -156,10 +155,6 @@ of one of our android phones,
 indicating that any system supporting this API
 could interact with our sensors.
 
-*FIXME: add web link for @accentSystems above
-(that can be transformed into a biblatex reference)
-https://accent-systems.com/support/faq/what-is-eddystone/*
-
 ## Detecting stressful mussel behavior
 
 We wish to expound some of the ways
@@ -313,6 +308,13 @@ The sensor system is our beacon and it works like a lighthouse.
 It sends signals out to say "im here, i exist".
 Then Boom! a bluetooth connection is made.
 
+*TODO: "... connection is made" can mislead the reader
+into expecting a two-way connection
+which is not the case in our deliberately loose coupling.
+Probably better to phrase it like
+"...nearby Bluetooth receivers can capture the beacon message" --
+smooth and quiet, no "Boom!"*
+
 ```{.plantuml}
 !include Arduino/vote/vote.puml
 ```
@@ -332,36 +334,37 @@ whether used the guide from role 3 archetype
 (see course curriculum),
 and if it was helpful/right/wrong*
 
-We have chosen not to use AI in our project.
-This is mainly for imitation of the current technology
-and for scope purposes.
-Although, we have reflected upon how AI could be useful
-in an expansion of our prototype
-or hypothetically in an existing system.
-For an instance, in the future --
-when scientists have analysed and interpreted enough data
-to feed to a MLM --
-ai could be used for detecting subtle behavioral changes,
-that humans would otherwise miss,
-or spot patterns that further indicates pollution
-or predicts contamination or enviromental stress.
-
-*FIXME: the abbreviations AI and MLM must be introduced before used,
-and then used consistently (e.g. all caps or no caps)*
-
-It could also be put into perspective of surrounding cases,
-and through datacentric AI,
-it could be visualized like a weatherforecast on a dashboard.
-It could be based on patterns
-like "When x conditions rise, contamination tends to follow."
-
-*TODO: in above paragraph, "cases" intents to refer to ANT*
-
-This hypothesis would come at the cost of a lot of x,
-which would be a research question in itself.
-
-*FIXME: in above paragraph, "x" should say something
-about consuming a lot of space and resources*
+We have chosen not to involve generative artificial intelligence (AI)
+in this project,
+due to its scope of data collecting and processing
+from a source of simple imitations of living organisms.
+Related but different projects might sensibly involve AI,
+e.g. training an AI with sensor data from real living mussels,
+either unsupervised to aid in discovering behavioural patterns
+like CHIGA,
+Or in a future
+where a (non-AI) domain model for mussel behaviours is established,
+an AI could be trained supervised,
+i.e. generate an AI model supervised with the use of such domain model,
+e.g. to help calibrate sensors.
+
+This project succesfully demonstrates
+that a loosely coupled set of systems can mimic the systems in Poland
+where the behaviour of 8 mussels "vote" about the quality of water.
+The concrete output, however,
+do not reasonably reflect the logic of the Polish systems,
+because the mussel simulation is too simplistic in that
+a) mussel gape rhythm is simulated as simple linear movements
+rather than the steep S-shaped movements of real mussels,
+and consequently that b) voting is based on "is gape closed"
+rather than the -- with more realistic rhythm -- more telling
+"what is the CHIGA pattern",
+leading to our setup concluding "bad water quality" fairly randomly.
+That said, the code is structured so that it should only require
+minimal changes to change the evaluation logic
+given more realistic sensor data,
+mainly by rewriting the function `alignVotes()`
+(see @sec-vote in Appendix).
 
 # Conclusion - menna
 
@@ -377,19 +380,17 @@ about consuming a lot of space and resources*
 
 \appendix
 
-# Code
-
-## P5.js sketch `light.js` {.appendix}
+# P5.js sketch `light.js` {.appendix}
 
 ```{.js include="p5.js/light.js" code-line-numbers="true"}
 ```
 
-## Arduino sketch `sensor.js` {.appendix}
+# Arduino sketch `sensor.js` {.appendix}
 
 ```{.cpp include="Arduino/sensor/sensor.ino" code-line-numbers="true"}
 ```
 
-## Arduino sketch `vote.js` {.appendix}
+# Arduino sketch `vote.js` {#sec-vote .appendix}
 
 ```{.cpp include="Arduino/vote/vote.ino" code-line-numbers="true"}
 ```