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Open Source Instruments Forum Message boards for technical support and customer questions. 2024-08-13T20:26:39-05:00 https://opensourceinstruments.com:443/Forums/feed.php?f=3 2024-08-13T20:26:39-05:00 2024-08-13T20:26:39-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=129#p129 <![CDATA[Telemetry • Re: Convert multiple files within one folder]]>
> It seems to work, but quite slowly.

I have an NDF file containing 14 telemetry signals, each at 256 SPS. I make a 128-s export of all channels to a single EDF file. I start with a 1-s playback interval, with the Value vs. Time (VT) and Amplitude vs. Frequency (AF) plots enabled. The export takes 19 s. Now I increase the playback interval to 8 s. The export takes 5 s. Now I disable the VT and AF plots. The export takes 4 s.

What playback interval are you using? Do you have the VT and AF plots enabled?

With the correct playback interval, you should be able to export 14 channels of 256 SPS at a rate of one one-hour archive every two minutes. You should be able to export 4 weeks of recordings from 14 animals in less than one day. I'm running on a 1-GHz MacBook Air. On a 3-GHz desktop PC, I expect the export to be twice as fast.

> Is there any chance that you would have a few lines of code to open ndf files and metadata in Matlab?

Reliable reconstruction of the signal, where we reject interference messages, fill in missing messages, and remove glitches, takes hundreds of lines of code. I don't have Matlab code to do the job. My hope is that you can get the exporter to run fast enough.

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Tue Aug 13, 2024 9:26 pm

]]> 2024-08-12T03:01:56-05:00 2024-08-12T03:01:56-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=128#p128 <![CDATA[Telemetry • Re: Convert multiple files within one folder]]>
Thanks a lot for for the update. It seems to work, but quite slowly. Based on a few files, I calculated that it would takes days, if not weeks, to convert all my data. Is there any chance that you would have a few lines of code to open ndf files and metadata in Matlab? That would be extremely useful.

Thanks,
Best
Laurent

Statistics: Posted by Laurent — Mon Aug 12, 2024 4:01 am

]]> 2024-08-01T08:37:01-05:00 2024-08-01T08:37:01-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=30&p=127#p127 <![CDATA[Telemetry • Re: reading NDF files in python]]>
I apologize for missing some of your previous posts; I hadn't realized there was a second page for the discussion... It turns out most of my questions had already been answered!

1) We are missing 1-second intervals as the Neurorecorder synchronizes with the computer, but the file names and lengths are consistent. Do you agree that this is the correct behavior?
I do agree that this is the correct behavior.

2) Please try the Exporter in Neuroplayer 171 and let me know if it eliminates overlap and correctly names the export files.
Thank you for addressing the issue we discussed in this update. I will provide feedback as soon as I have tested this new version.

3) Do you really mean 10.6.10?
I hadn’t seen the post mentioning version LWDAQ 10.6.11, so we installed the previous version. We will migrate to the new version as soon as possible.

4) I tested 10.6.11 with hour-long archives and 8-second intervals. It did not produce extra files for me. If you are using 10.6.11 and still see this error, please let me know. I may need more samples of your hour-long files. Does this problem occur with every archive, or only some?
I will test version 10.6.11 and check if the error persists.

Thank you very much for your help. We are grateful.

Best wishes,
Raphaël

Statistics: Posted by Raphaël Nunes — Thu Aug 01, 2024 9:37 am

]]> 2024-07-29T11:33:27-05:00 2024-07-29T11:33:27-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=30&p=126#p126 <![CDATA[Telemetry • Re: reading NDF files in python]]>
I am sorry to hear that you are still having problems with the exporter.

> We have installed the latest version of LWDAQ (10.6.10) on our new recording machine.

The latest version is LWDAQ 10.6.11. Do you really mean 10.6.10? You can download 10.6.11 from here:



or here:



> 2) The 8-second overlap still exists when exporting files with an 8-second processing interval.

I tested 10.6.11 with hour-long archives and 8-second intervals. For me it did not produce these extra files. If you are using 10.6.11 and you still see this error, then I will test again. I may need some more samples of your hour-long files. Does this problem occur with every archive, or only with some archives?

> 3) When exporting in EDF format with the latest version of Neuroplayer, the exported files use "cnt" as units instead of mVs (millivolts).

That's because you lost your Exporter settings when you updated your LWDAQ. You need to set up the conversion between "cnt" (sixteen-bit analog to digital converter counts) to mVs using the EDF setup button. See the EDF section here:



You can read the EDF header from one of your older files with the Read button in the EDF Setup Panel.

> Additionally, we are not familiar with the "cnt" unit and cannot convert it to mVs.

The A3047A1B transmitters you are using have three voltage inputs with dynamic range 60 mV, 120 mV and 120 mV. This range is asymmetric about zero volts. For 60-mV, the input range is -36 mV to +24 mV. For the 120 mV, it is -72 mV to +48 mV. In the EDF setup, you set the units to "mV" and you set "min" and "max" to the two range limits. The temperature sensor entry allows you to convert the digitized temperature sensor output into centigrade, like this:



Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Mon Jul 29, 2024 12:33 pm

]]> 2024-07-29T10:42:51-05:00 2024-07-29T10:42:51-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=30&p=125#p125 <![CDATA[Telemetry • Re: reading NDF files in python]]>
Thank you again for your help.

We have installed the latest version of LWDAQ (10.6.10) on our new recording machine. After using this new machine to record and export the signals, here are some observations:

1) Although the Neuroplayer no longer crashes, it now creates two files when exporting: one containing the full 3600 seconds and another with only the last 8 seconds.

2) The 8-second overlap still exists when exporting files with an 8-second processing interval.

3) When exporting in EDF format with the latest version of Neuroplayer, the exported files use "cnt" as units instead of mVs (millivolts). This is problematic for us because we built our processing scripts based on the previously used mVs units. Additionally, we are not familiar with the "cnt" unit and cannot convert it to mVs. Is there a way to modify the export unit in version 10.6.10 of Neuroplayer? This would be very useful to us.

Best wishes,
Raphaël

Statistics: Posted by Raphaël Nunes — Mon Jul 29, 2024 11:42 am

]]> 2024-07-22T12:34:31-05:00 2024-07-22T12:34:31-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=124#p124 <![CDATA[Telemetry • Re: Convert multiple files within one folder]]>
We just released LWDAQ 10.6.11 with Neuroplayer 171 and Neurorecorder 168. You can pull from our Git repository:



Or download and unzip our new archive:



Please try the Exporter in the Neuroplayer 171 and let me know if it assigns the correct names to the export files.

When you make more recordings, please note that the default behavior of the Neurorecorder 168 is "free-running" rather than "re-synchronizing". The Synchronization box will be un-checked. We discuss the two synchronization strategies here:



If you use the free-running strategy, your one-hour NDF files will have names separated by 3600 s, except for occasional differences of 3599 s or 3601 s as the computer and telemetry receiver clocks drift apart. With the free-running strategy, you will not lose one second of data every hour.

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Mon Jul 22, 2024 1:34 pm

]]> 2024-07-22T12:30:13-05:00 2024-07-22T12:30:13-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=30&p=123#p123 <![CDATA[Telemetry • Re: reading NDF files in python]]>
Thank you for your patience. We just released LWDAQ 10.6.11 with Neuroplayer 171 and Neurorecorder 168. You can pull from our Git repository:



Or download and unzip our new archive:



The default behavior of the Neurorecorder is now "free-running" rather than "re-synchronizing". The Synchronization box will be un-checked. We discuss the two synchronization strategies here:



Please try the Exporter in the Neuroplayer 171 and let me know if it eliminates overlap and assigns the correct names to the export files.

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Mon Jul 22, 2024 1:30 pm

]]> 2024-07-21T04:49:10-05:00 2024-07-21T04:49:10-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=122#p122 <![CDATA[Telemetry • Re: Convert multiple files within one folder]]> Best,
LS

Statistics: Posted by Laurent — Sun Jul 21, 2024 5:49 am

]]> 2024-07-19T08:56:58-05:00 2024-07-19T08:56:58-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=121#p121 <![CDATA[Telemetry • Re: Convert multiple files within one folder]]>
> However, the exported files do not have the same name as the original ones.

Indeed, they do not. This is exactly the problem that we are working on in Neuroplayer 171. If you look at the earlier topic on this message board, "reading NDF files in python", you will see Raphael explaining how the files don't have the same names AND they contain overlapping data. The beginning of one file is a copy of the last few seconds at the end of the previous file. This overlap is a serious problem, and that is what we are fixing in Neuroplayewr 171. In addition to fixing that serious problem, we have set up the Exporter so that, when the export file is supposed to have the same length as the original NDF file, the export file will always have the same name as the NDF file.

I am trying to break Neuroarchiver 171 now with Exporter tests. When I am convinced that I cannot break it, I will release LWDAQ 10.6.11 with Neuroarchiver 171 and ask you to test it.

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Fri Jul 19, 2024 9:56 am

]]> 2024-07-19T05:13:27-05:00 2024-07-19T05:13:27-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=120#p120 <![CDATA[Telemetry • Re: Convert multiple files within one folder]]>
Thank you for your prompt answer.
I followed your explanations step-by-step. However, the exported files do not have the same name as the original ones. Actually the first file is correct (M1717677796 becomes E1717677796) but then there are slight changes (e.g., the second file M1717681397 becomes E1717681395). Note that I set the duration to 3600 since I want to export the entire length of my files.

If alternatively you have some lines of codes that simply convert the entirety of .ndf into .edf, I could maybe run a .tcl script (if that is easier) ?

Thanks again for your help,
Best
Laurent

Statistics: Posted by Laurent — Fri Jul 19, 2024 6:13 am

]]> 2024-07-18T11:41:22-05:00 2024-07-18T11:41:22-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=119#p119 <![CDATA[Telemetry • Re: Convert multiple files within one folder]]>
Yes, you can export all files in a directory automatically. See "repetitions" in the Exporter manual:



You can export to one big file, or many smaller files. I will summarize the procedure for you here.

In the Neuroplayer, select the directory containing your NDF files. The Neuroplayer's "directory tree" is now the directory you selected as well as all subdirectories. The Neuroplayer will be searching the directory tree for NDF files. Press First to make sure you have selected the first file in this directory.

Open The Exporter. Define your export. Suppose you have 1000 one-hour NDF files and you want to export to 24-hour EDF files. Set the duration to 24*60*60, press "Archive Beginning". In the "Repetitions" box, enter "*". After every export, the Exporter will start another export. Please try this and let me know if it works.

Before you proceed with exporting thousands of files, I recommend that you wait one more day until I have released Neuroplayer 171 with LWDAQ 10.6.11. Earlier Neuroplayers failed to calculate the start time of repeated exports correctly. The result is overlap between export files. I am currently working with another group to fix this problem.

I will let you know when Neuroplayer 171 is ready. I would like it very much if you could try Neuroplayer 171 on your data and let me know if it behaves well.

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Thu Jul 18, 2024 12:41 pm

]]> 2024-07-18T08:52:10-05:00 2024-07-18T08:52:10-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=31&p=118#p118 <![CDATA[Telemetry • Convert multiple files within one folder]]>
I’m using the LWDAQ software and need to convert > 1000 files from ndf to edf format. I see that LWDAQ can do this, but I cannot find a way to just enter the directory and let LWDAQ process each file successively. Is this possible?

Thanks for your help,
Best

Statistics: Posted by Laurent — Thu Jul 18, 2024 9:52 am

]]> 2024-07-17T16:17:55-05:00 2024-07-17T16:17:55-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=30&p=117#p117 <![CDATA[Telemetry • Re: reading NDF files in python]]>
Returning to this behavior:

> Once the conversion to EDF is complete:
> “M1702291203.ndf” has been converted to “E1702291203.edf”
> “M1702294804.ndf” has been converted to “E1702294795.edf”

I am able to reproduce this behavior easily. I am recording 60-s files with synchronization at the start of each new file. I am exporting 60-s files, starting with the first file. I see the following conversions:

M1721250458.ndf -> M1721250458.edf
M1721250519.ndf -> E1721250516.edf
M1721250580.ndf -> E1721250575.edf
M1721250641.ndf -> E1721250634.edf

The problem arises when the file and the export length are the same. There is a logical error in my code for this particular situation. I believe the correct behavior should be:

M1721250458.ndf -> M1721250458.edf
M1721250519.ndf -> M1721250519.edf
M1721250580.ndf -> M1721250580.edf
M1721250641.ndf -> M1721250641.edf

Here we are missing 1-s intervals as the Neurorecorder synchronizes with the computer, but the file names are the same and all the files are the same length. Do you agree that this is the correct behavior?

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Wed Jul 17, 2024 5:17 pm

]]> 2024-07-16T15:23:55-05:00 2024-07-16T15:23:55-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=30&p=116#p116 <![CDATA[Telemetry • Re: reading NDF files in python]]>
I have just exported all four of the files you sent me, no crash or freeze or stop, no error message. I'm using LWDAQ 10.6.10, Neuroplayer 170. The metadata in your NDF files says, "Creator: Neurorecorder 162, LWDAQ_10.5.2." The LWDAQ GitLog has the following entry just before the release of LWDAQ 10.5.4:

commit a188b7552d0c1ed4f3fd01708d6eb1b623f918f6
Author: Kevan Hashemi <hashemi@opensourceinstruments.com>
Date: Mon Feb 27 17:32:23 2023 -0500
Fixed Neuroexporter freeze bug in Windows.

A "freeze" bug is different from a "crash" bug. But we did a lot of work on the Neuroexporter between 10.5.3 and 10.5.4. I suggest you try upgrading your LWDAQ. If you are using our GitHub repository (link below), just do "git pull" to get the latest pre-release version.



If you install using our multi-platform ZIP archive, use this link to get LWDAQ 10.6.10:



Please try the new version and see if it can export without stopping.

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Tue Jul 16, 2024 4:23 pm

]]> 2024-07-16T12:08:44-05:00 2024-07-16T12:08:44-05:00 https://opensourceinstruments.com:443/Forums/viewtopic.php?t=30&p=115#p115 <![CDATA[Telemetry • Re: reading NDF files in python]]>
Thank you for your detailed explanation of the problems with overlap between export files.

> Once the conversion to EDF is complete:
> “M1702291203.ndf” has been converted to “E1702291203.edf”
> “M1702294804.ndf” has been converted to “E1702294795.edf”

This does not look right to me. That's not what I wanted the Exporter to do. There may be something unusual about your NDF file that is causing the Exporter to behave badly. I will start by fixing the bug in the Exporter that causes the Exporter to crash the Neuroplayer. After that, I will look at why the Exporter is creating these overlaps.

Right now, I think that both the problems you are having with the Exporter are due to problems in our Exporter code. Which is good news, in a way, because we can fix problems in our code. In the meantime, thank you for your patience, and thank you for answering all my questions.

Best Wishes, Kevan

Statistics: Posted by Kevan Hashemi — Tue Jul 16, 2024 1:08 pm

]]>