Scratchpad for the realtime buffer interface
This page contains some loose ends and random pieces that don’t fit elsewhere.
- closing the loop lists some methods for interacting with, and controlling the external world (i.e. outside the analysis computer)
- pipeline contains example fMRI pipeline description
- Siemens fMRI also contains some fMRI details
Various notes and comments
Portability note: non-unix systems may not allow read()/write() on sockets, but recv()/send() are usually ok. This is true on Windows and OS/2, for example.
On a 32-bits Linux/RHEL4 machine (mentat068) I got the following error “libgcc_s.so.1 must be installed for pthread_cancel to work” Searching the internet did not give much helpfull suggestions, but using strace did help. It turned out that there was a version of libgcc_s on the LD_LIBRARY_PATH that was loaded prior to the system one. Changing it to first having /lib and then the rest solved it.
The following macro names are defined at compile time and may be handy for debuggin LINE Integer value representing the current line in the source code file being compiled. FILE A string literal containing the presumed name of the source file being compiled. DATE A string literal in the form “Mmm dd yyyy” containing the date in which the compilation process began. TIME A string literal in the form “hh:mm:ss” containing the time at which the compilation process began. __cplusplus An integer value. All C++ compilers have this constant defined to some value. If the compiler is fully compliant with the C++ standard its value is equal or greater than 199711L depending on the version of the standard they comply.
The threaded functions should be checked with http://en.wikipedia.org/wiki/Reentrant in mind
Suggestions for improvement
The suggested solution with different string results in letting the open_connection function guess (=parsing the string) which kind of connection is wanted. It is better to define a parameter which states which kind of connection is wanted, and then the string which must be used to open that connection. Another omission from the draft protocol is an outline of the commutation sequence. How is a connection initiated? Is a handshake required? Is authentication required?
Missing from the draft protocol is a explicit description of the transport mechanism: apparently it is based on TCP/IP over Ethernet. An explicit description of the transport mechanism of the packets would be helpful, including a discussion of the consequences of the physical transport layer (e..g 100Mbps, 1Gbps, 10Gbps, wifi) on the timing aspects of the buffer. Furthermore, the implementation is based on IPv4, what would be required to extend this to IPv6? Useful would be a discussion in which the different choices of the transport layer are discussed. Why not UDP over ethernet? Why not over communicate over RS-232 (serial), IEE-1394 (firewire), IEEE-802 (zigbee), X10, Bluetooth, or similar communication protocol.
It is unclear whether the TCP connection should remain open throughout the communication or whether it should be closed. It is just a mechanism for networked data exchange between processes running on different computers. It could be more compared to HTTP (see http://www.w3.org/Protocols/rfc2616/rfc2616.html). Some additional “meta” data can be transferred (with limitations).
Priorities of the buffer server
You should describe how you deal with the data in the buffer: is it stored on a hard drive or only in RAM? What happens, if the data rate is too high? What has priority: reading or writing the data? Is there a notion of fairness in server clients (against starvation)? Are there any guarantees for timeliness of responses?
An omission in the definition of the buffer is that it is not specified how much old data is to be maintained in RAM, nor is it possible to have clients influence that parameter.
In the reference implementation the data is stored in RAM. In case it were implemented on an embedded device, I could also imagine a two-tier storage (with the most recent data in RAM, slightly older data on SSD, and even older data getting dropped). Your question should be addressed in the documentation, and it should be clarified that it is a (large) ring-buffer.
A PUT_HDR reinitializes the buffer, similar to a FLUSH_HDR, FLUSH_DAT. Should be documented.
What is referred to as the “header” in the FieldTrip buffer can be thought of as all the fixed meta data. What is referred to as “events” in the fieldtrip buffer is can be thought of as time-varying meta-data. What remains is the data, which is the representation of a physical property that was measured (or computed from a measurement). But for example representing the volumetric data as separate slices does not fit well in the design. Different DICOM headers per slice does not fit. DICOM headers that change over time do not fit.
Het is aan de client om te controleren dat het aantal kanalen niet klopt na een PUT_HDR.
Only by looking in the message.h you get an idea what kind of chuck are already developed. Chunks are arbitrary binary blobs that can be stored on the server and hence be exchanged between one (acquisition) client and another (analysis) client without the server requiring any understanding of the blobs.
What are the chunk requirements? Does the extension of the protocol with another chunk require recompilation of the server? What are the chunk requirements? How should clients know how to interpret a chunk. How are chunk identified? How is chunk identity standardized between labs? Is it possible to store two chunks at the same time, and if so, how are they transmitted in a put and in a get request?
The chunks seem a logical extension of the header structure, as such it seems more logical to extend the GET and PUT commands with a GET_CHUNK and PUT_CHUNK, where the respective packet would contain the chunk type and length. Predefined chunks (such as Siemens, Nifti and CTF res4) can remain as they are, but would not be sent along with each GET_HDR. This removes the requirement to switch from the polling to the blocking-read operation as implemented with WAIT_DAT. See also the light-header proposal.
It would be nice to mention a list of some available chunks. For example, the gradiometer positions are not mentioned in that page.
We are missing discussion on multi-platform (Windows+Linux+macOS) issues, due to different resolutions available on each platform (http://msdn.microsoft.com/en-us/library/ms724397). In the situation where application and FieldTrip server are located on different PC’s, how is the time (roughly) synchronized? One solution could be to configure the NTP client on each PC to use the same (external) NTP server. In particular situations time information will certainly be useful. Regarding acquisition devices it remains difficult how to interpret the relation between buffer time and samples received. Why is time relevant? Probably to synchronize events and samples, or simultaneous recordings?
You should timestamp every event and data, but I would not use machine specific timing, but a global time. Otherwise it will be difficult to combine different modalities. Maybe you have two time stamp fields: one for the machine generating the data and one where the FieldTrip buffer is running.
We introduced the timestamp field, but sofar have not started using it. The time synchronisation of different computers is challenging. At the moment the data is implicitly timestamped by the sample number that depends on the acquisition computer. Events are presently timestamped using the sample number that relates the event to the acquired data. This time stamping is not explicitly addressed in the documentation.
It would be possible to (optionally) add an explicit timestamp channel in the continuous data stream. Ideally a timestamp would be assigned to every sample by the acquisition software. If the acquisition software does not assign timestamps, the buffer server could do it for the incoming data and for the incoming events.
Atomic PUT_DAT + PUT_EVT
Because TMSi frontend continuously samples all the channels, including the event channels, we suggest that an atomic put_dat and put_evt be made, in which in one call all data received from the frontend is stored in the FieldTrip buffer.
The proposed sequence of always first write events and then samples makes sense and should be preferred in non-atomic implementation, although something can be said to the approach of driving people into a guaranteed safe solution by combining both PUT_DAT and PUT_EVT operations.
Viewed from an online perspective, polling of events can already be achieved based on the nevents field returned by the header and assuming fifo behavior. In the offline case, adding index information to the events is useful since it reflects the incoming following order of events, which may differ from the ordering based on the sample field.
Homogeneous sample rate
The assumption here is that all channels have the same sampling frequency. TMSi has frontends where each channel can have a different sample rate. However, the samples of these channels are upscaled to the sample frequency of the fastest channel. Options to set the desired size of the buffers for both samples and events can be useful in case requesting events from far history or in case many events occur in a relatively short time interval. Also, prior information about the buffer sizes seems not available. This would be useful since in the current version such change is reflected in a sudden decrease in the number of samples.
Versions and compatibility
If the server needs to support all different versions of the protocol, the maintenance effort increases significantly. We suggest that server supports only the most recently released version of the protocol. Draft V2 mentions how to deal with a client and a server application that speak different implement of the protocol, but that description is rather limited. Is there a fallback mechanism in place to drop back to the highest common denominator as in RFB? Should backward compatibility be defined at the level of the protocol, or should it (optionally) be part of the reference implementation? Is this a requirement of the protocol? Although all available implementations for the various acquisition systems have been made based on the reference implementation, the protocol should outline the minimum requirements and the limitations that are imposed on any implementation.
A certification procedure should be considered, according to which a particular implementation can be certified as adhering to a particular version of the protocol. The reference implementation should contain an independent mechanism for verifying the compliance with particular versions of the protocol.
Doc and site
It is not clear from the page, how to call the functions in practice. For instance, if I want to use GET_HDR, what should I do? There should be some examples of different functions with some specified parameters as a guideline to be used.
Er moet een centrale tabel moeten hebben met alle constanten. Chunk information is hardly available. De pagina buffer_protocol zou alleen volgens mij alleen constanten moeten hebben die niet specifiek zijn voor de referentie implementatie.
FAQ: Combining modalities: Furthermore, they might require different numeric representations. Experimental settings that require this should use two buffers for the raw data and a single piece of real-time analysis software that reads from both and integrates the two (if desired). Writing two modalities into one buffer representation (e.g. fMRI and simultaneous EEG) is not supported. In general it is unlikely that the two modalities have the same sampling rate and are synchronized.
FAQ: The documentation should indeed make better clear that the data is not necessarily EEG or MEG channels, but that any set of N measurements of a physical parameter that pertains to the brain (be it EEG/MEG channels, optodes or voxels) that is sampled with a fixed dT between subsequent samples can be represented. Of course also a difference is that the sampling rate is rather different (about once per millisecond versus once per second), but that does not affect the core representation of the data.
FAQ: Does the extension of the protocol with another chunk require recompilation of the server?
FAQ: Buffer for volumetric data: The conceptual switch from EEG channel level data to volumetric data is to consider that (in BCI terminology) a feature vector is being sampled at a regular interval. The feature (or data vector) for MEG is 275x1 for the channels which have a spatial 3D location, the feature vector for MRI is for example (646432)x1 which is 1x131072 values that also have a 3D location. The location of the MRI voxel-level data vector can be mapped directly back on the volume by reshaping the vector for a single time point into a 64x64x32 array. A limitation that this touches upon (and that we should document) is that the data vector can not have a different length for different sample points.
FAQ: “Can I use the buffer to transfer XXX data over the network?”, where the answer would detail for different XXX what the data is that can be transferred and hence also what the information is that would consequently get lost in the transfer. Given that NIFTI is much more limited in what can be represented, it is possible to transfer NIFTI data without loss of information, whereas it is not possible to to transfer DICOM data. It is also not possible to transfer data from EEG and MEG systems without loss of information that in those systems is normally represent on disk.
FAQ: How is time synchronised?