HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc

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HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc

Rajah, Tim (NIH/CC/SURG) [E]

Hello Everyone,

I had posted earlier ago requesting any information on HDF based projects that were developed for Time-Series based storage of Physiological waveforms such as ECG etc.

 

I would really appreciate your help in this matter.


Thanks

Tim

 

Taimoore Rajah (Tim)

Biomedical Engineer

POIS–SIS IT Support Group|DPM IT & Medical Device Integration, HW & SW Support

Department of Perioperative Medicine (DPM)

National Institute of Health, Clinical Center

9000 Rockville Pike, MSC-1512

Building 10, Room 2C563

Bethesda, MD 20892-1512

Tel: O (301) 827-9402

Fax: (301) 480-1699

cid:image001.jpg@01CE56E6.8FCBD490

 


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Re: HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc

pierre.debuyl
Hi Tim,

I was curious about the topic too. From memory (earlier searches, a few years
ago), the was no standard for time series data.

By googling today, I find a few results

TsTables
http://andyfiedler.com/projects/tstables-store-high-frequency-data-with-pytables/

it is aimed at financial data series and is based on Pandas and PyTables. So, it
might no be very useful as a general purpose (i.e. usable by other software than
Python).

Modelica Association Time Series File Format
http://www.ep.liu.se/ecp/076/050/ecp12076050.pdf

Has been designed explicitly for generic time series data in the framework of
https://modelica.org/

NSDF
http://nsdf.readthedocs.org/en/latest/nsdf.html

Neuroscience Simulation Data Format, it seems a bit simpler in its definition
http://www.frontiersin.org/10.3389/conf.fninf.2014.18.00026/event_abstract

It is just a bunch of links, but I hope that it helps.

Regards,

Pierre

On Wed, Apr 08, 2015 at 01:24:50PM +0000, Rajah, Tim (NIH/CC/SURG) [E] wrote:
> Hello Everyone,
> I had posted earlier ago requesting any information on HDF based projects that were developed for Time-Series based storage of Physiological waveforms such as ECG etc.
>
> I would really appreciate your help in this matter.
>
> Thanks
> Tim
>

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Re: HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc

Mitchell, Scott - Exelis
I do quite a bit of heterogeneous sensor data in time series. A common time format would be nice. I ended up using Windows .NET DateTime.Ticks. Users complained that it was unreadable (shocking) and I had to add a parallel text string. Some of the sensors provide their own timestamp typically in Unix Time (plus milliseconds).

The timestamps are in dimension scales to the actual dataset. Dimension scales seem to be relatively unsupported... not by HDFView anyway. So they end up as a secondary, independent dataset. It works in my code though.


Scott

-----Original Message-----
From: Hdf-forum [mailto:[hidden email]] On Behalf Of Pierre de Buyl
Sent: Wednesday, April 08, 2015 3:27 PM
To: [hidden email]
Subject: Re: [Hdf-forum] HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc

Hi Tim,

I was curious about the topic too. From memory (earlier searches, a few years ago), the was no standard for time series data.

By googling today, I find a few results

TsTables
http://andyfiedler.com/projects/tstables-store-high-frequency-data-with-pytables/

it is aimed at financial data series and is based on Pandas and PyTables. So, it might no be very useful as a general purpose (i.e. usable by other software than Python).

Modelica Association Time Series File Format http://www.ep.liu.se/ecp/076/050/ecp12076050.pdf

Has been designed explicitly for generic time series data in the framework of https://modelica.org/

NSDF
http://nsdf.readthedocs.org/en/latest/nsdf.html

Neuroscience Simulation Data Format, it seems a bit simpler in its definition http://www.frontiersin.org/10.3389/conf.fninf.2014.18.00026/event_abstract

It is just a bunch of links, but I hope that it helps.

Regards,

Pierre

On Wed, Apr 08, 2015 at 01:24:50PM +0000, Rajah, Tim (NIH/CC/SURG) [E] wrote:
> Hello Everyone,
> I had posted earlier ago requesting any information on HDF based projects that were developed for Time-Series based storage of Physiological waveforms such as ECG etc.
>
> I would really appreciate your help in this matter.
>
> Thanks
> Tim
>

_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

________________________________

This e-mail and any files transmitted with it may be proprietary and are intended solely for the use of the individual or entity to whom they are addressed. If you have received this e-mail in error please notify the sender. Please note that any views or opinions presented in this e-mail are solely those of the author and do not necessarily represent those of Exelis Inc. The recipient should check this e-mail and any attachments for the presence of viruses. Exelis Inc. accepts no liability for any damage caused by any virus transmitted by this e-mail.

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Re: HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc

Rajah, Tim (NIH/CC/SURG) [E]
In reply to this post by Rajah, Tim (NIH/CC/SURG) [E]
Hello Scott and Pierre,
Thank you Pierre for the link that you sent earlier ago through the forum. I am currently going through them but really having difficulty to analyze if they have the correct setup for the physiological real-time waveforms that we want to collect, archive and then analyze for further analytics.

Does anyone or you guys perhaps have the Database Schema that if you don't mind sharing with me? I know a lot of groups who are looking for the same type of system but are having major difficulty finding a good fit for physiological waveforms. I looked at the www.physionet.org project but its more for static data instead of real-time. We really need to look into the database schema so as to understand how and what will be saved into the database.

Scott,
Can it be translated to the Linux OS platform? I thought .Net was not really meant for analyzing real-time data?

Thank you,
Kind regards
Tim
NIH




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Re: HDF Project for storing Time-Series storage of Physiological Waveforms - ECG etc

Pedro Vicente
In reply to this post by Mitchell, Scott - Exelis
Scott

>>> The timestamps are in dimension scales to the actual dataset. Dimension
>>> scales seem to be relatively unsupported... not by HDFView anyway.

HDF Explorer supports dimension scales. To see an example, please go to

http://www.space-research.org/

go to  menu "Online help" and search "HDF5 Dimension scales"

The example shows maps generated for a dataset that has 2 sets of dimension
scales attached. Choosing one set over the otther results in a different
map.

Direct link:

http://www.space-research.org/help/help.htm

more info

http://ftp.hdfgroup.org/HDF5/Tutor/h5dimscale.html



----------------------
Pedro Vicente
[hidden email]
http://www.space-research.org/




----- Original Message -----
From: "Mitchell, Scott - Exelis" <[hidden email]>
To: "HDF Users Discussion List" <[hidden email]>
Sent: Thursday, April 09, 2015 10:05 AM
Subject: Re: [Hdf-forum] HDF Project for storing Time-Series storage of
Physiological Waveforms - ECG etc


>I do quite a bit of heterogeneous sensor data in time series. A common time
>format would be nice. I ended up using Windows .NET DateTime.Ticks. Users
>complained that it was unreadable (shocking) and I had to add a parallel
>text string. Some of the sensors provide their own timestamp typically in
>Unix Time (plus milliseconds).
>
> The timestamps are in dimension scales to the actual dataset. Dimension
> scales seem to be relatively unsupported... not by HDFView anyway. So they
> end up as a secondary, independent dataset. It works in my code though.
>
>
> Scott
>
> -----Original Message-----
> From: Hdf-forum [mailto:[hidden email]] On Behalf Of
> Pierre de Buyl
> Sent: Wednesday, April 08, 2015 3:27 PM
> To: [hidden email]
> Subject: Re: [Hdf-forum] HDF Project for storing Time-Series storage of
> Physiological Waveforms - ECG etc
>
> Hi Tim,
>
> I was curious about the topic too. From memory (earlier searches, a few
> years ago), the was no standard for time series data.
>
> By googling today, I find a few results
>
> TsTables
> http://andyfiedler.com/projects/tstables-store-high-frequency-data-with-pytables/
>
> it is aimed at financial data series and is based on Pandas and PyTables.
> So, it might no be very useful as a general purpose (i.e. usable by other
> software than Python).
>
> Modelica Association Time Series File Format
> http://www.ep.liu.se/ecp/076/050/ecp12076050.pdf
>
> Has been designed explicitly for generic time series data in the framework
> of https://modelica.org/
>
> NSDF
> http://nsdf.readthedocs.org/en/latest/nsdf.html
>
> Neuroscience Simulation Data Format, it seems a bit simpler in its
> definition
> http://www.frontiersin.org/10.3389/conf.fninf.2014.18.00026/event_abstract
>
> It is just a bunch of links, but I hope that it helps.
>
> Regards,
>
> Pierre
>
> On Wed, Apr 08, 2015 at 01:24:50PM +0000, Rajah, Tim (NIH/CC/SURG) [E]
> wrote:
>> Hello Everyone,
>> I had posted earlier ago requesting any information on HDF based projects
>> that were developed for Time-Series based storage of Physiological
>> waveforms such as ECG etc.
>>
>> I would really appreciate your help in this matter.
>>
>> Thanks
>> Tim
>>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
> ________________________________
>
> This e-mail and any files transmitted with it may be proprietary and are
> intended solely for the use of the individual or entity to whom they are
> addressed. If you have received this e-mail in error please notify the
> sender. Please note that any views or opinions presented in this e-mail
> are solely those of the author and do not necessarily represent those of
> Exelis Inc. The recipient should check this e-mail and any attachments for
> the presence of viruses. Exelis Inc. accepts no liability for any damage
> caused by any virus transmitted by this e-mail.
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> [hidden email]
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
>


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