Updated on May 20, 2011. The most recent version of this manual can be accessed here.
This document describes advanced details about internal BioEra architecture.
Pipes are the end points used to connect elements. There are many different pipe types (scalar, vector, object etc). Scalar stream value (up to 32 bit) can be considered as a vector with just one element. Object stream contains objects (e.g. texts) which are exchanged by reference (not by value like in other streams).
· Logical pipe is based on scalar pipe (they can be connected each to other). The 0 value is FALSE, and 1 is TRUE. This pipe operates on logical state rather than logical stream. This means, that logical elements usually send only the final logical value based on all available input.
· Complex pipe is compatible with vector pipe. Two complex vectors are stored in one: lower half part contains real fields and higher half part contains imaginary values. It is possible to use vector elements to process complex vectors.
· Matrix pipe is compatible with vector stream. Each matrix is stored as a vector, and matrix parameters (width, height) are stored in MatrixSignalParameters.
There are input pipes and output pipes. One output pipe can be connected to many input pipes. Input pipe is usually connected to only one output pipe. If input is connected to many outputs then it works as multiplexer, but without known order. Each input pipe has internal buffer.
Aside from streamed data, BioEra can also process vectors (one or two dimensional arrays) in real time. This is very unique feature not found in other software.
There are many uses of vector streams. One example is filtering. In conventional applications, input stream is being filtered with various types of digital filters. For example to get amplitude of a brainwave a filter is applied on the signal and the amplitude of the filtered output is measured. In BioEra signal can be first converted to vector (for example with FFT or Wavelet transform or any other), and then all further processing can be done on vectors. This allows build advanced protocols on FFT or wavelets.
One-dimensional vector streams have good support in BioEra. Matrix streams (two-dimensional) were added later have less support.
Each element in BioEra has special input/output (located at the bottom of each element) for special purpose. Usually they are connected to blue outputs/inputs of an element which allows such special functions e.g. PropertySetter.
BioEra supports traditional digital filters. There is one implementation which uses Fidlib.
BioEra Pro contains controls – advanced elements which let the user to modify current processing settings. They are put on Runtime window into toolbar, menu etc.
· ComboToolbarControl – combo component to select one value out of many.
· IconToolbarControl – icon that can be used as button to trigger action on current design.
· MenuList – automatically creates list of submenus, only one sub-menu can be chosen at a time.
· MenuItemControl, MenuItemList – creates a menu field which can then be used to trigger an action on current design.
BioEra Pro contains several interactors – advanced elements for operations and communication with system.
· KeyInteractor – keyboard activity can be generated here
· MouseInteractor - mouse activity (buttons and movement)
· SystemInteractor – to stop, start, pause, save etc.
· SystemEventSource – to receive various system events about start, stop, pause, resume, init, errors and others.
· ElementIntractor – various operations on single element (activate, deactivate, process)
· DesignInteractor – load another design
· CustomInteractor – load/save file path
· OSInfo – get the list of available drives or files in folder
· OSInteractor – execute external application
Information about signal parameters like rate, range or number of bits is provided on element level (as oppose to global level). An element can retrieve these values from other element connected to one of its inputs. An element can also modify its own values if necessarily. For example, if an FFT transform is being done 4 times per second, then it means that the output rate is 4, and this value is returned when rate value is requested.
Each element can provide status (being updated dynamically during processing). Status is located at the bottom of the element icon (on designer). At the moment status is represented as set of letters with different colors. The red letter X is generic for all elements, it means, that the element has been deactivated and is not processing data. Other letters are defined specifically for each element
and described with element information.
Some element properties contain a set of values. They are enclosed between "[" and "]" characters and are called array properties. Array properties use some characters exclusively, which can't then be used as content characters. Below is the list of characters along with meta values which can be used to encode (and then show) those special codes. Please note: <space> can be used only at the beginning or the end of the text (or alone).
BioEra is supposed to support all kinds of signals (not only neurofeedback). So there are many different signals and it is not possible to have just one measurement unit. That is why BioEra supports several scales. For example for EEG devices operate on uV (micro-volts), for EMG it is mV (mili-volts) etc. BioEra can operate on amplitude range, frequency domain and time domain.
Signal amplitude can be scaled on many ways. Often data that comes from input device is scaled in micro-volts. There are also other scales: digital and percentage. There are 6 possible amplitude scales available in BioEra at this moment:
· microvolt or uV – microvolt values starting from 0 and more
· digital or digi – digital values starting from 0 and more
· percent or % – percent values from 0 to 100
balanced microvolt or =uV – balanced microvolt values, any range is possible
(although usually they will be within max range)
balanced digital or =digi – balanced digital values, any range is possible
(although usually they will be within max range)
· balanced percent or =% – balanced percent values from -100 to 100
Note: there will be other scales added gradually here, e.g. radians, decibels. Mili-volts etc.
At this moment most EEG devices operate on micro-volts (or fraction of microvolt). Other biofeedback devices (like EMG or ECG) may use values of higher amplitudes.
Digital scale represents direct integer values being received from biofeedback device. BioEra operated on 32 bit numbers.
Percent scale is relative to full range allowed in an element. Range is from -100% to +100% for numbers symmetrical to zero, or from 0 to 100% for positive numbers.
Not implemented yet.
Sometimes input signal can be scaled with unusual units (for example Hertz or degrees). This is not yet fully implemented.
Time scales are at this moment presented usually in seconds. Eventually more units will be provided. Now the values are relative (since the recording start); eventually they will be option to show absolute times.
Not implemented yet.
It is implemented for all basic time units (seconds, minutes, milliseconds, hours, days).
This can be used when the rate of the input is constant.
Elements are processed in order; next element is being processed after previous element finished processing.
Elements are being processed in the same order as they were initialized. Elements that are closer to input (signal source) are initialized and processed first.
BioEra installation package includes all necessary drivers to access serial port on Windows. For further information about serial port installation or problems with serial port access see Sun’s site: http://java.sun.com/products/javacomm/downloads/index.html.
BioEra contains MIDI bank with basic instruments. Optionally to improve the quality of MIDI sounds it is possible to download deluxe sound bank from here. It contains about 400 instruments of the best sound quality. It can be installed either by following the instructions (coming with the installation file) or simply by unzipping and copying the soundbank.gm file into main BioEra folder.
If BioEra is started without command
line options, it will open with both designer and runtime windows (and the last
Command line syntax:
bioera.exe [-or|-op] [-diagnostic] [-log <filename>] [-start] [-root <folder_path>] [-logs <folder_path>] [-design <design_file.bpd>] [option_listed_below]
· -or: runtime mode only (no designer), runtime window is shown, and processing is started automatically after start.
· -op: processing mode, design is started automatically after start (no graphic windows). Please note, this option may not be reliable, it is not actively used
· -diagnostic: set diagnostic mode (printing messages on console).
· -cdiag – create diagnostic.zip file which can be sent by email for further analysis in case of a problem
· -log <filename>: text messages are saved to this file (and console)
· -start: processing is started automatically after start
· -stop: processing is not started automatically after start, useful with –or option which would normally start the design
· -root <folder_path>: path to BioEra folder, should be provided if started from a different folder.
· -logs <folder_path>: path to folder where logs are stored; default is bioerapro/logs.
· -design <filepath>: load a design from the file located at <filepath>
· -priorityNormal: BioEra starts with Normal program priority.
· -priorityAbove: BioEra starts with Above Normal program priority.
· -priorityHigh: BioEra starts with High priority.
· -dx – force to use DirectX graphic acceleration. By default, BioEra uses OpenGL library for 3D graphics. If OpenGl is not available, then it automatically switches to DirectX. But on some older computers OpenGl drivers may be improperly configured; in such case it will not be able to switch to DirectX by itself. This option forces it.
· -mxNNNN – set maximum memory, where NNNN is a number of Mega Bytes. The default value is 768MB.
· -mnNNNN – set minimum (start) memory, where NNNN is a number of Mega Bytes. The default value is 128MB.
· -jreXXX – set the java version used to run BioEra. Currently available options are -jre6, -jre7, -jre8 and –jre8_64. The -jre6 is default. See more info below.
The startup.cfg text file in config folder can be used to set the same options as on command line (listed above). If the same option is set both in startup.cfg and on command line, then the command line option takes precedence.
Each separate option in startup.cfg must be in its own line. That includes options which have an argument after a space, for example: “-design” and
“<filepath>” should be in separate lines.
Lines which start with ‘#’ are ignored (can be used for comments).
BioEra comes with several java versions. One of them can be selected at start using -jreXXX command line option (where the XXX is the jre version).
The -jre6, -jre7 and –jre8 are 32bit javas. The –jre8_64 is 64bit java.
Important note: when executed with 64bit java, some BioEra functionality is not available. Some known (but not all) limitations:
· SerialPort with javax.comm implementation option doesn’t work here. It works with the gnu.io option which should be used instead (but is not set as default). It can be also substituted with FTDISerialPort if connected to an FTDI device (this is the most recommended option in such case).
· Some devices do not work: JANDJ, Alpha64, Neurobit, Qpet, BrainMaster Atlantis, Alpha200, Alpha400, MitsarQEEG, Vilistus, NeurofieldQ20, Nia, Lightstone.
· VideoFilePlayer and DVDPlayer are slightly limited. Their functions to control brightness or contrast don’t work.
In most cases the 32bit java should be used. The 64bit option can be used only on 64bit Windows computers (most are). The 32bit java can be used on any Windows version starting from XP.
The 64bit version can be better (or necessary) in some cases:
· Large amount of memory is needed - for example to process lots of images, audio/video or very large designs.
· Custom code (in ExpressionEvaluator or CustomElement) accesses third party libraries which are 64bit only (for example deep neural network frameworks).
· Large designs can load much faster with 64bit java (than 32bit java); even 3 times faster by some reports.
An element is Synchronized, if
it sends out exactly the same number of samples as it received. For example:
all TimeTransform elements are synchronized, or Delay2. The importance of
synchronization is especially important with batch processing.
BioEra uses integer (scaled) numbers in all Scalar elements. Values in scalar pipes are also exchanged as integers. The primary reason is performance, especially on devices like PDA without coprocessor.
Float numbers are used in all Float elements and Float pipes. There is also an optional DoubleFloat type which can be used for ultra high precision at the cost of slower processing (lower performance).
Scalar numbers are exchanged as integers and scaled relative to the “Digital Max” and “Physical Max” which can be set individually for each element (can be viewed in Advanced Properties). The float value is calculated as: ScalarNumber * PhysicalMax / DigitalMax. For example - if the scalar number is 100, DigiMax=1000 and PhysMax=1, then the actual value is 0.1. The raw scalar number can be viewed on Console with Debugger element.
Because signal properties can be different in each element, then some elements (e.g. Threshold, BarDisplay) have options to “Rescale”. This option should be selected if DigitalMax/PhysicalMax ratio is different in the elements which are connected to inputs.
There is no scaling for Float numbers. If the above seems too complicated, you may want to try to use equivalent Float elements, which should behave the same, but have not been tested as well.
Some graphical components like toolbar have option to set custom border which is loaded from an image. Border can be either horizontal (image width is 1 pixel), or only vertical (image height is 1 pixel) or both. When border is painted the four quarters of border image are used for each border line, and four image corners for border corners. Border image can contain transparent pixels.
Example borders are in folder images/border.
Nested design can be added to existing design and behave like an element. It has inputs and outputs and properties.
Nested design is created and opened the same as normal design. It can contain special elements which customize its behavior.
The most important are: NestedInputs and NestedOutputs. You must have at least one of them (or both) in each nested design. They are used to define inputs/outputs which are used as interface to this nested design from main design.
Initially each input/output pipe on NestedInputs/NestedOutputs is black, this means their type is not defined so can be connected to any pipe. Once it has been connected, it automatically converts to compatible pipe. Note: only connected inputs/outputs are shown when this nested design is added to the main design.
NestedProperties is used to customize the behavior of the nested design. For more details, see the description of this element.
To add a nested design, you need first to add NestedDesign element. Then in properties set path to the nested design file.
One of the options in NestedProperties is ‘Charts are nested into one chart’. If this option is selected, then this nested design will expose only one chart to outside world. This chart will contain all internal charts. For more details, see the description of NestedProperties element.
Many elements allow set colors. Color
is usually selected in the Color Dialog. BioEra supports transparency whenever
· Four sliders show the current color selection. Sliders listed from top to bottom:
o Red – red component
o Green – red component
o Blue – red component
o Alpha – transparency component. The 0 value is full transparency and 255 means the color is opaque. Note: the 0 can mean also default value, see below.
· Fully transparent color – if selected, then the color is fully transparent. Can be used to “disable” some colors, e.g. name color set as transparent makes it invisible.
· Default color – if selected then this color is expected to have a default value. Default value depends on context, there is no general rule, usually this is a system color for this particular component (e.g. menu color the same as system menu color)
· Text field – it shows the color components in hexadecimal form. FF is maximum (equal to 255) value and 00 is minimal value. Note: alpha component is first, then red, green and blue.
Gradient color (for more information about this topic see here) allows convert a value into a color hue. For example, in Polygraph it is possible to fill the area under the trace using gradient color. Gradient color is loaded from an image file and can be custom created. Several gradient color images are under images/gradient folder.
Each output pipe of each element can have its own signal properties. The signal properties describe the signal which is being processed by this pipe. Different signal parameters occur when there are different signal sources, for example a few input devices, EEG and GSR at the same time.
To view Signal properties of an element, right click on the element, select Advanced Properties and select tab Signal properties.
· Rate – defines how many samples are exchanged per second.
· Digital min, Digial max – samples are usually exchanged as digital numbers. Those settings show its default range.
· Physical min, Physical max – corresponding physical values for the above digital numbers.
· Encoding – currently not used
· Physical unit – physical unit of the signal e.g. uV (microvolt) or Ohm or s.
· Vector length – used in vector pipes, defines the size of the vector
· Vector max, Vector min – defines the physical value of the vector at each side
· Vector unit – physical unit of the vector, e.g. this is Hz in the output of FFT.
· Vector fields descriptions – each field in a vector can contain a description
· Info – additional information
Almost everything in BioEra is created using Java. Java has been selected as the primary development platform for BioEra because:
· It is proven and reliable technology, used for instance by NASA on Mars.
· Java development is very effective for rapid improvements.
· Although the performance of Java can be sometimes less then C language (see performance chapter below), with JIT (Just in Time) virtual machine, the speed is reasonable in most cases. External C libraries (like numerical recipes) can be reused and included easily with JNI interface.
There are many additional components
which were created in C++ for best compatibility with Windows OS e.g. Video,
DVD and Flash players.
Java has a false reputation of being slower than other languages like C or C++. Do not believe it! That was the case with first versions of Java long time ago (10-15 years ago), but it has improved dramatically in recent versions because of the JIT compilers (which compile to native code on the fly). Due to the optimizations many functions are now faster than in native C programs, some are slower, overall performance is very comparable. There is many research done and published on Internet, e.g.:
BioEra supports various methods to allow interfacing with other applications and languages.
o CustomElement – allows interfacing with another java program. A custom element can be created that way and then added in Designer
o XmlNetServer – this interface uses plain Xml text and is language independent (can be used with any programming language)
o .NET SDK – an SDK for Microsoft .NET is provided and supported. It can be used from inside a CSharp or Visual Basic .NET application. C# example and source is provided which demonstrate how to receive data from BioEra (connecting to XmlNetServer). See picture. More info about SDK.
o ApplicationPlayer can be used to start and control an executable application.
o MIDI element can be used to play on external MIDI device like electric Piano.
o SerialPort element provides two way communications via serial port.
List of element names is shown on the “New element” dialog. There are 2 modes on this dialog:
o Categorized Elements - the names displayed on the list are simplified (for example they may be without some prefixes like: Scalar, or Float or F_). The category list is selected on the right panel if an element is selected and it does have more than one category.
o Elements – full names are shown on this list. There is no categorization in this case. Instead names can have prefixes like F_ D_ Float DoubleFloat Object etc.
The categorization is in order to simplify the selection and make it easier to find and add a new element. But in some cases it can be less clear how to find an element. The full list in Elements list mode is there to help in a case like that.
A full name of an element can be always viewed in its Properties, under Element tab there is Type field which contains full name. The full name is what identifies the element (and its type) and it is always unique.
Some full names start with one letter prefix. The prefix determines element category in this case:
Here is a list of all constant values available for each expression:
· In1 to In20 – input values
· Out1 to Out20 – output values
· LastIn1 to LastIn20 – previous input values
· PHYSICAL_TOP – equivalent to Physical Max (viewable advanced properties)
· PHYSICAL_BOTTOM – equivalent to Physical Min (viewable advanced properties)
· DIGITAL_TOP – equivalent to Digital Max (viewable advanced properties)
· DIGITAL_BOTTOM - equivalent to Digital Min (viewable advanced properties)
· PTDR – rescaling ratio (PhysicalMax / DigitalMax)
· SIGNAL_RATE – sample rate - equivalent to Rate (viewable advanced properties)
· VECTOR_MAX - equivalent to Vector Max (viewable advanced properties)
· VECTOR_MIN - equivalent to Vector Min (viewable advanced properties)
· VectorSize – maximum size of all input vectors. Only available in Vector expression evaluators.
· VectorIndex – current vector index. Only available in Vector expression evaluators.
· InVector1 to InVector20 – input vector variables. Only available in Vector expression evaluators.
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