As the revised diagram in Figure \ref{block_diagram_final.png} shows, to remove an extra layer of complexity it was decided to use a single device (the BeagleBone Black) to play the role of both the experiment server and the embedded device. From a software perspective, this eliminated the need for an entire layer of communication and synchronization. From a hardware perspective, use of the BeagleBone black instead of a Raspberry Pi removed the need to design or source analogue to digital conversion modules.
-Another major design change which occured quite early in the project is the switch from using multiple processes to running a single multithreaded process on the server. After performing some rudimentary testing (see Section \ref{Server Interface}) it became clear that a system of seperate programs would be difficult to implement and maintain. Threads are similar to processes but are able to directly share memory, with the result that much less synchronisation is required in order to transfer information.
+Another major design change which occurred quite early in the project is the switch from using multiple processes to running a single multithreaded process on the server. After performing some rudimentary testing (see Section \ref{Server Interface}) it became clear that a system of separate programs would be difficult to implement and maintain. Threads are similar to processes but are able to directly share memory, with the result that much less synchronisation is required in order to transfer information.
{\bf Note on filenames:} In the following, files and directories related to the server are located in the \href{https://github.com/szmoore/MCTX3420/tree/master/server}{server} directory, files related to the (currently used) GUI are in \href{https://github.com/szmoore/MCTX3420/tree/master/testing/MCTXWeb}{testing/MCTXWeb}, and files created for testing purposes are located in \href{https://github.com/szmoore/MCTX3420/tree/master/testing}{testing}.
\end{enumerate}
-In reality, threads do not run simultaneously; the operating system is responsible for sharing execution time between threads in the same way as it shares execution times between processes. Because the linux kernel is not deterministic, it is not possible to predict when a given thread is actually running. This renders it impossible to maintain a consistent sampling rate, and necessitates the use of time stamps whenever a data point is recorded.
+In reality, threads do not run simultaneously; the operating system is responsible for sharing execution time between threads in the same way as it shares execution times between processes. Because the Linux kernel is not deterministic, it is not possible to predict when a given thread is actually running. This renders it impossible to maintain a consistent sampling rate, and necessitates the use of time stamps whenever a data point is recorded.
Figure \ref{sample_rate_histogram.png} shows a distribution of times\footnote{The clock speed of the BeagleBone is between 200MHz and 700MHz (depends on power)\cite{cameon.net} which is fast enough to neglect the fact that recording the timestamp takes several CPU cycles} between samples for a test sensor with the software sampling as fast as possible. Note the logarithmic $t$ axis. Although context switching clearly causes the sample rate to vary (\textcolor{green}{green}), the actual process of reading an ADC (\textcolor{red}{red}) using \funct{ADC_Read} (\gitref{server}{bbb_pin.c}) is by far the greatest source of variation.
-It was not possible to obtain a real time linux kernel for the BeagleBone. In theory, real time variants of the linux kernel improve the reliability of sampling rates. However, testing on an amd64 laptop showed very little difference in the sampling time distribution when the real time linux kernel was used.
+It was not possible to obtain a real time Linux kernel for the BeagleBone. In theory, real time variants of the Linux kernel improve the reliability of sampling rates. However, testing on an amd64 laptop showed very little difference in the sampling time distribution when the real time Linux kernel was used.
\begin{figure}[H]
\subsection{Main Thread}\label{Main Thread}
-The main thread of the process is responsible for transfering data between the server and the client through the Hypertext Transmission Protocol (HTTP). A library called FastCGI is used to interface with an existing webserver called nginx\cite{nginx}. This configuration and the format of data transferred between the GUI and the server is discussed in more detail Section \ref{Communications}.
+The main thread of the process is responsible for transferring data between the server and the client through the Hypertext Transmission Protocol (HTTP). A library called FastCGI is used to interface with an existing webserver called nginx\cite{nginx}. This configuration and the format of data transferred between the GUI and the server is discussed in more detail Section \ref{Communications}.
-Essentially, the main thread of the process responds to HTTP requests. The GUI is designed to send requests periodically (eg: to update a graph) or when a user action is taken (eg: changing the pressure setting). When this is received, the main thread parses the request, the requested action is performed, and a response is sent. The GUI is then responsible for updating its appearance or alerting the user based on this response. Figure \ref{fastcgi-flow-chart.png} in Section \ref{API}gives an overview of this process.
+Essentially, the main thread of the process responds to HTTP requests. The GUI is designed to send requests periodically (e.g.: to update a graph) or when a user action is taken (e.g.: changing the pressure setting). When this is received, the main thread parses the request, the requested action is performed, and a response is sent. The GUI is then responsible for updating its appearance or alerting the user based on this response. Figure \ref{fastcgi-flow-chart.png} in Section \ref{API}gives an overview of this process.
\subsection{Sensor Threads}\label{Sensor Thread}
Figure \ref{sensor_thread.pdf} shows a flow chart for the thread controlling an individual sensor. This process is implemented by \verb/Sensor_Loop/ and associated helper functions.
-All sensors are treated as returning a single floating point number when read. A \type{DataPoint} consists of a time stamp and the sensor value. \type{DataPoint}s are continously saved to a binary file as long as the experiment is in process. An appropriate HTTP request (Section\ref{API}) will cause the main thread of the server program to respond with \type{DataPoint}s read back from the file. By using independent threads for reading data and transferring it to the GUI, the system does not rely on maintaining a consistent and synchronised network connection. This means that one the experiment is started with the desired parameters, a user can safely close the GUI or even shutdown their computer without impacting on the operation of the experiment.
+All sensors are treated as returning a single floating point number when read. A \type{DataPoint} consists of a time stamp and the sensor value. \type{DataPoint}s are continuously saved to a binary file as long as the experiment is in process. An appropriate HTTP request (Section\ref{API}) will cause the main thread of the server program to respond with \type{DataPoint}s read back from the file. By using independent threads for reading data and transferring it to the GUI, the system does not rely on maintaining a consistent and synchronised network connection. This means that one the experiment is started with the desired parameters, a user can safely close the GUI or even shutdown their computer without impacting on the operation of the experiment.
\subsection{Actuator Threads}\label{Actuator Thread}
-Actuators are controlled by threads in a similar way to sensors. Figure \ref{actuator_thread.pdf} shows a flow chart for these threads. This is implemented in \verb/Actuator_Loop/. Control over real hardware is seperated from the main logic in the same way as sensors (relevant files are in the \verb/actuators/ sub directory). The use of threads to control actuators gives similar advantages in terms of eliminating the need to syncronise the GUI and server software.
+Actuators are controlled by threads in a similar way to sensors. Figure \ref{actuator_thread.pdf} shows a flow chart for these threads. This is implemented in \verb/Actuator_Loop/. Control over real hardware is separated from the main logic in the same way as sensors (relevant files are in the \verb/actuators/ sub directory). The use of threads to control actuators gives similar advantages in terms of eliminating the need to synchronise the GUI and server software.
The actuator thread has been designed for flexibility in how exactly an actuator is controlled. Rather than specifying a single value, the main thread initialises a structure that determines the behaviour of the actuator over a period of time. The current structure represents a simple set of discrete linear changes in the actuator value. This means that a user does not need to specify every single value for the actuator. The Actuator thread stores a value every time the actuator is changed which can be requested in a similar way to sensor data.
\subsection{Data Storage and Retrieval}
-Each sensor or actuator thread stores data points in a seperate binary file identified by the name of the device. When the main thread receives an appropriate HTTP request, it will read data back from the binary file. To allow for selection of a range of data points from the file, a binary search has been implemented. Functions related to data storage and retrieval are located in the \gitref{server}{data.h} and \gitref{server}{data.c} source files.
+Each sensor or actuator thread stores data points in a separate binary file identified by the name of the device. When the main thread receives an appropriate HTTP request, it will read data back from the binary file. To allow for selection of a range of data points from the file, a binary search has been implemented. Functions related to data storage and retrieval are located in the \gitref{server}{data.h} and \gitref{server}{data.c} source files.
Several alternate means of data storage were considered for this project. Binary files were chosen because of the significant performance benefit after testing, and the ease with which data can be read from any location in file and converted directly into values. A downside of using binary files is that the server software must always be running in order to convert the data into a human readable format.
Given the inexperienced nature of the software team, the limited development time, and the unclear specifications, it is not wise to trust safety aspects of the system to software alone. It should also be mentioned that the correct functioning of the system is reliant not only upon the software written during this project, but also the many libraries which are used, and the operating system under which it runs. We found during development that many of the mechanisms for controlling BeagleBone hardware are unreliable and have unresolved issues; see the project wiki pages\cite{mctx3420_wiki} for more information. We attempted to incorporate safety mechanisms into the software wherever possible.
-Sensors and Actuators should define an initialisation and cleanup function. For an actuator (eg: the pressure regulator), the cleanup function must set the actuator to a predefined safe value (in the case of pressure, atmospheric pressure) before it can be deinitialised. In the case of a software error or user defined emergency, the \funct{Fatal} function can be called from any point in the software; this will lead to the cleanup functions of devices being called, which will in turn lead to the pressure being set to a safe value.
+Sensors and Actuators should define an initialisation and cleanup function. For an actuator (e.g.: the pressure regulator), the cleanup function must set the actuator to a predefined safe value (in the case of pressure, atmospheric pressure) before it can be uninitialised. In the case of a software error or user defined emergency, the \funct{Fatal} function can be called from any point in the software; this will lead to the cleanup functions of devices being called, which will in turn lead to the pressure being set to a safe value.
Sensors and Actuators are designed to include an optional \funct{sanity} function which will check a reading or setting is safe respectively. These checks occur whenever a sensor value is read or an actuator is about to be set. In the case of a sensor reading failing the sanity check, \funct{Fatal} is called immediately and the software shuts down the experiment. In the case of an actuator being set to an unsafe value the software will simply refuse to set the value.
\subsubsection{PWM Outputs}
-A single PWM output is used to control a pressure regulator (model: ). The electrical team constructed an RC filter circuit which effectively averages the PWM signal to produce an almost constant analogue output. The period of the PWM is $2\text{kHz}$. This actuator has been calibrated, which allows the user to input the pressure value in kPa rather than having to control the PWM duty cycle corretly.
+A single PWM output is used to control a pressure regulator (model: ). The electrical team constructed an RC filter circuit which effectively averages the PWM signal to produce an almost constant analogue output. The period of the PWM is $2\text{kHz}$. This actuator has been calibrated, which allows the user to input the pressure value in kPa rather than having to control the PWM duty cycle correctly.
\begin{figure}[H]
\item {\bf Unix style authentication}
- Unix like operating systems store a plain text file (/etc/shadow) of usernames and encrypted passwords. To check a password is valid, it is encrypted and then compared to the stored encrypted password. The actual password is never stored anywhere. The /etc/shadow file must be maintained by shell commands run directly from the beaglebone. Alternatively a web based system to upload a similar file may be created.
+ Unix like operating systems store a plain text file (/etc/shadow) of usernames and encrypted passwords. To check a password is valid, it is encrypted and then compared to the stored encrypted password. The actual password is never stored anywhere. The /etc/shadow file must be maintained by shell commands run directly from the BeagleBone. Alternatively a web based system to upload a similar file may be created.
\item {\bf Lightweight Directory Access Protocol (LDAP)}
LDAP is a widely used data base for storing user information. A central server is required to maintain the LDAP database; programs running on the same network can query the server for authentication purposes.
- The UWA user management system (pheme) employs an LDAP server for storing user information and passwords. The software has been designed so that it can interface with an LDAP server configured similarly to the server on UWA's network. Unfortunately we were unable to gain permission to query this server. However an alternative server could be setup to provide this authentication mechanism for our system.
+ The UWA user management system (Pheme) employs an LDAP server for storing user information and passwords. The software has been designed so that it can interface with an LDAP server configured similarly to the server on UWA's network. Unfortunately we were unable to gain permission to query this server. However an alternative server could be setup to provide this authentication mechanism for our system.
\item {\bf MySQL Database}
- MySQL is a popular and free database system that is widely used in web applications. The ability to search for a user in a MySQL database and check their encrypted password was added late in the design as an alternative to LDAP. There are several existing online user management systems which interface with a MySQL database, and so it is feasable to employ one of these to maintain a list of users authorised to access the experiment. UserCake is recommended, as it is both minimalistic and open source, so can be modified to suit future requirements. We have already begun integration of the UserCake system into the project, however a great deal of work is still required.
+ MySQL is a popular and free database system that is widely used in web applications. The ability to search for a user in a MySQL database and check their encrypted password was added late in the design as an alternative to LDAP. There are several existing online user management systems which interface with a MySQL database, and so it is feasible to employ one of these to maintain a list of users authorised to access the experiment. UserCake is recommended, as it is both minimalistic and open source, so can be modified to suit future requirements. We have already begun integration of the UserCake system into the project, however a great deal of work is still required.
MySQL and other databases are vulnerable to many different security issues which we did not have sufficient time to fully explore. Care should be taken to ensure that all these issues are addressed before deploying the system.
To generate the JSON response from the server program, \gitref{server}{fastcgi.c} contains a framework of helper functions. Most of the functions help to ensure that the generated output is in a valid JSON format, although only a subset of the JSON syntax is supported. Supporting the full syntax would overcomplicate writing the framework while being of little benefit. Modules can still respond with whatever format they like, using \funct{FCGI_JSONValue} (aka. \funct{FCGI_PrintRaw}), but lose the guarantee that the output will be in a valid JSON format.
-Additionally, not all responses are in the JSON format. In specific cases, some module handlers will respond in a more suitable format. For example, the image handler will return an image (using \funct{FCGI_WriteBinary}); it would make no sense to return anything else. On the other hand, the sensor and actuator modules will return data as tab-separated values, if the user specifically asks for it (eg: using \url{https://host/api/sensors?id=X&format=tsv})
+Additionally, not all responses are in the JSON format. In specific cases, some module handlers will respond in a more suitable format. For example, the image handler will return an image (using \funct{FCGI_WriteBinary}); it would make no sense to return anything else. On the other hand, the sensor and actuator modules will return data as tab-separated values, if the user specifically asks for it (e.g.: using \url{https://host/api/sensors?id=X&format=tsv})
\subsection{Server API - Cookies}\label{Cookies}
-The system makes use of HTTP cookies to keep track of who is logged in at any point. The cookie is a small token of information that gets sent by the server, which is then stored automatically by the web browser. The cookie then gets sent back automatically on subsequent requests to the server. If the cookie sent back matches what is expected, the user is ‘logged in'. Almost all web sites in existence that has some sort of login use cookies to keep track of this sort of information, so this method is standard practice.
-In the server code, this information is referred to as the ‘control key'. A control key is only provided to a user if they provide valid login credentials, and no one else is logged in at that time.
+The system makes use of HTTP cookies to keep track of who is logged in at any point. The cookie is a small token of information that gets sent by the server, which is then stored automatically by the web browser. The cookie then gets sent back automatically on subsequent requests to the server. If the cookie sent back matches what is expected, the user is `logged in'. Almost all web sites in existence that has some sort of login use cookies to keep track of this sort of information, so this method is standard practice.
+In the server code, this information is referred to as the `control key'. A control key is only provided to a user if they provide valid login credentials, and no one else is logged in at that time.
The control key used is the SHA-1 hash of some randomly generated data, in hexadecimal format. In essence, this is just a string of random numbers and letters that uniquely identifies the current user.
Getting the cameras to work on the BeagleBone was another major issue faced. After much testing, it was simply found that the cameras could only work on the latest version of the operating system. On anything else, only low resolution captures of around 352x288 pixels could be achieved.
-Finally, it should be noted that USB hotplugging does not work on the BeagleBone. This means that the cameras have to be plugged in before booting the BeagleBone. Upgrading to a newer kernel (when it exists) should solve this issue.
+Finally, it should be noted that USB hot-plugging does not work on the BeagleBone. This means that the cameras have to be plugged in before booting the BeagleBone. Upgrading to a newer kernel (when it exists) should solve this issue.
\subsection{Required software}
\subsection{Results}
-Figure \ref{image_in_api.png} shows an image obtained from one of two dilatometers used in the system setup with collaboration between all teams. The image is of a white lego tile attached to the can. This image was successfully streamed using the server software, and results of the dilatometer readings were monitored using the same software. Unfortunately we were unable to maintain a constant value for a stationary can, indicating that the algorithm needs further development. Due to a leak in the can seal we were unable to pressurize the can sufficiently to see a noticable change in the edge position.
+Figure \ref{image_in_api.png} shows an image obtained from one of two dilatometers used in the system setup with collaboration between all teams. The image is of a white Lego tile attached to the can. This image was successfully streamed using the server software, and results of the dilatometer readings were monitored using the same software. Unfortunately we were unable to maintain a constant value for a stationary can, indicating that the algorithm needs further development. Due to a leak in the can seal we were unable to pressurize the can sufficiently to see a noticeable change in the edge position.
\begin{figure}[H]
\centering
\includegraphics[width=0.6\textwidth]{figures/image_in_api.png}
- \caption{Microscope image of actual lego tile attached to can in experimental setup}
+ \caption{Microscope image of actual Lego tile attached to can in experimental setup}
\label{image_in_api.png}
\end{figure}
% BEGIN James' section
\subsection{Design Considerations}
-There are many considerations that are required to be taken into account for the successful creation of a Graphical User Interface (GUI) that allows Human Computer Interaction. A poorly design GUI can make a system difficult and frustrating to use. A GUI made with no considerations to the underlying software can make a system inoperable or block key features. Without a well designed GUI the Human Computer Interaction becomes difficult and discourages any interaction with the system at all.
+There are many considerations that are required to be taken into account for the successful creation of a Graphical User Interface (GUI) that allows Human Computer Interaction. A poorly designed GUI can make a system difficult and frustrating to use. A GUI made with no considerations to the underlying software can make a system inoperable or block key features. Without a well designed GUI the Human Computer Interaction becomes difficult and discourages any interaction with the system at all.
One of the key considerations made during the design of the GUI was the functionality it required. Originally this was limited to just allowing for simple control of the system including a start and stop and a display of system pressures however as the project progressed this was expanded to include a user login, limited admin functionality, graphing, image streaming and live server logs. The addition of these features came as a result of changing requirements from the initial brief as well as logical progression of the GUI's capabilities. This gradual progression represents a continual improvement in Human Computer interaction for the system.
Due to the limits of the Beagle Bone such as available memory and processing power it was important that the code, images and all libraries used were both small in size and efficient. This meant that careful consideration had to be made every time a library was considered for use. It also meant that where possible processing should be offloaded onto the client hardware rather than running on the server which already runs the server side code. This meant large libraries were ruled out and actions such as graphing were performed by the GUI on the client machine.
- The final consideration is extensibility. An extensible software base code allows easy addition of new features. A good extensible interface makes it a simple case of simply dropping the extra code in in order to add extra features whereas a GUI that doesn't take this into account can require deleting and recoding of large chunks of the previous code. This means that the interface code must be structured in a coherent way and all conform to a ``standard'' across the GUI. Code must be laid out in the same way from page to page and where possible sections of code facilitating specific goals should be removed from the main page code. The latter was achieved through the use of the \verb/.load()/ JavaScript function allowing whole widgets to be removed and placed in their own seperate files. This feature alone lets the developer add new widgets simply by creating a widget file conforming to the GUI's standard and then \verb/.load()/ it into the actual page.
+ The final consideration is extensibility. An extensible software base code allows easy addition of new features. A good extensible interface makes it a simple case of simply dropping the extra code in in order to add extra features whereas a GUI that doesn't take this into account can require deleting and recoding of large chunks of the previous code. This means that the interface code must be structured in a coherent way and all conform to a ``standard'' across the GUI. Code must be laid out in the same way from page to page and where possible sections of code facilitating specific goals should be removed from the main page code. The latter was achieved through the use of the \verb/.load()/ JavaScript function allowing whole widgets to be removed and placed in their own separate files. This feature alone lets the developer add new widgets simply by creating a widget file conforming to the GUI's standard and then \verb/.load()/ it into the actual page.
\subsection{Libraries used in GUI construction}
Flot\cite{flot} is a Javascript library designed for plotting and built for jQuery. This a lightweight easy to use library that allows easy production of attractive graphs. It also includes advanced support for interactive features and can support for $\text{IE} < 9$ . The Flot library provided an easy but powerful way to graph the data being sent by the server.
-\subsection{Libraries trialed but not used in GUI construction}
+\subsection{Libraries trialled but not used in GUI construction}
These are libraries that were looked at and considered for use in the GUI software but were decided to not be used in the final product.
\begin{figure}[H]
\centering
\includegraphics[width=0.8\textwidth]{figures/draftGUI.png}
- \caption{Draft GUI designed in Microsoft Powerpoint}
+ \caption{Draft GUI designed in Microsoft PowerPoint}
\label{draftGUI.png}
\end{figure}
\end{figure}
-This gui was running over a free domain name which allowed us to play with control and command.
+This GUI was running over a free domain name which allowed us to play with control and command.
\subsection{Iterations}
-After the basic testing of the initial GUIs we started playing with gui design ideas which would be aesthetic, easy to use and reflect on UWA in a positive way. To do this we looked into how professional websites were made by opening their source code and investigating techniques into layout, structure and style. Then we went away and completed some gui design trees, where there would be a clear flow between pages.
+After the basic testing of the initial GUIs we started playing with GUI design ideas which would be aesthetic, easy to use and reflect on UWA in a positive way. To do this we looked into how professional websites were made by opening their source code and investigating techniques into layout, structure and style. Then we went away and completed some GUI design trees, where there would be a clear flow between pages.
\subsection{Parallel GUI Design}
-During the GUI development phase, several GUIs were created. Some used graphical development software, while others used hard codded HTML, JavaScript, and CSS. Due to no organization within the group and a lack in communication a “final gui” was made by several of the team members. Some of theses are shown below.
+During the GUI development phase, several GUIs were created. Some used graphical development software, while others used hard codded HTML, JavaScript, and CSS. Due to no organization within the group and a lack in communication a ``final GUI'' was made by several of the team members. Some of theses are shown below.
\subsection{GUI Aesthetics}
-Once we had decided on our core GUI design, we decided that, although not yet complete we would get Adrain Keatings opinion on the GUI design. While the gui design was simple and functional Dr. Keating pointed out the design was bland. He encouraged us to release our artistic flair onto our GUI and make it more graphical and easy to use. Taking this into account we Began work on another final GUI designing almost from scratch. We kept our GUI design flow, and worked largely on the look and feel of the GUI rather the functionality the gui needed.
+Once we had decided on our core GUI design, we decided that, although not yet complete we would get Adrian Keating's opinion on the GUI design. While the GUI design was simple and functional Dr. Keating pointed out the design was bland. He encouraged us to release our artistic flair onto our GUI and make it more graphical and easy to use. Taking this into account we began work on another final GUI designing almost from scratch. We kept our GUI design flow, and worked largely on the look and feel of the GUI rather the functionality the GUI needed.
\subsection{HTML Structure}
-The way our GUI works, in a nutshell, is that we use Basic HTML code to lay out what the page needs, then we have CSS(Styles) on top which lays out and formats the basic HTML code. We the put JavaScript files into the HTML code so that graphs and images and be streamed. In out GUI we have chosen to use JQuery to ask the server for information from the client and jFlot for javascripts graphing functionality.
+The way our GUI works, in a nutshell, is that we use Basic HTML code to lay out what the page needs, then we have CSS(Styles) on top which lays out and formats the basic HTML code. We the put JavaScript files into the HTML code so that graphs and images and be streamed. In our GUI we have chosen to use JQuery to ask the server for information from the client and flot for graphing functionality.
\subsection{Graphical Development VS Hard Coding}
-From the Multiple GUI we had accidently created during the GUI design phase we noticed a large Varity in the styles of GUIs that came out (Which shouldn’t of happened) GUIs were created using HTML CSS and JavaScript being hard codded, from development software like Dreamweaver, and various java based development platforms.
+From the Multiple GUI we had accidentally created during the GUI design phase we noticed a large variety in the styles of GUIs that came out (Which shouldn't have happened) GUIs were created using HTML CSS and JavaScript being hard coded, from development software like Dreamweaver, and various Java based development platforms.
\subsection{Final Design}
\begin{figure}[H]
\centering
\includegraphics[width=0.8\textwidth]{figures/gui_pintest.png}
- \caption{The BBB Pin test page is for the software team only so that we can test and debug the experiment we errors are found in the gui or software. }
+ \caption{The BBB Pin test page is for the software team only so that we can test and debug the experiment we errors are found in the GUI or software. }
\end{figure}
\begin{figure}[H]
git.ucc.asn.au / matches / MCTX3420.git / blobdiff
UCC git Repository :: git.ucc.asn.au