Problem using SpinnakerCapture

[Spark Zhu]

Bonsai Users/Developers,

 

       Hi!  I am trying to interface Bonsai with a point Gray black fly camera https://www.ptgrey.com/blackfly-s-usb3-vision-cameras.  My task is to do simultaneous ephys recording and imaging similar to this project: https://groups.google.com/forum/#!topic/bonsai-users/286lNUqacG8.   I was able to run the camera with pointGray's Spinnaker View software itself, but when I loaded the SpinnakerCapture Source node to the bonsai and tried to right click it to output timestamp and videos, I got the following error. All related screenshot and error message details have been attached. What would you suggest me to try under this situation, Thanks!

[Gonçalo Lopes]

Hi Spark and welcome to the forums!

Can you provide the version of the Spinnaker software you are using? It is possible that there is a mismatch between the version Bonsai is trying to load and the latest Spinnaker drivers.

On 8 December 2017 at 16:13, Spark Zhu <1213...@gmail.com> wrote:

Bonsai Users/Developers,

 

       Hi!  I am trying to interface Bonsai with a point Gray black fly camera https://www.ptgrey.com/blackfly-s-usb3-vision-cameras.  My task is to do simultaneous ephys recording and imaging similar to this project: https://groups.google.com/forum/#!topic/bonsai-users/286lNUqacG8.   I was able to run the camera with pointGray's Spinnaker View software itself, but when I loaded the SpinnakerCapture Source node to the bonsai and tried to right click it to output timestamp and videos, I got the following error. All related screenshot and error message details have been attached. What would you suggest me to try under this situation, Thanks!

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[Spark Zhu]

Thanks for your prompt reply!  I have a bonsai 2.3.1 and a Spinnaker 1.8.0.64. Hope that helps! 

On Friday, December 8, 2017 at 6:30:27 PM UTC-6, goncaloclopes wrote:

Hi Spark and welcome to the forums!

Can you provide the version of the Spinnaker software you are using? It is possible that there is a mismatch between the version Bonsai is trying to load and the latest Spinnaker drivers.

On 8 December 2017 at 16:13, Spark Zhu <1213...@gmail.com> wrote:

Bonsai Users/Developers,

 

       Hi!  I am trying to interface Bonsai with a point Gray black fly camera https://www.ptgrey.com/blackfly-s-usb3-vision-cameras.  My task is to do simultaneous ephys recording and imaging similar to this project: https://groups.google.com/forum/#!topic/bonsai-users/286lNUqacG8.   I was able to run the camera with pointGray's Spinnaker View software itself, but when I loaded the SpinnakerCapture Source node to the bonsai and tried to right click it to output timestamp and videos, I got the following error. All related screenshot and error message details have been attached. What would you suggest me to try under this situation, Thanks!

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[Gonçalo Lopes]

Hi Spark,

I am attaching a preview of an updated version of the Spinnaker package referencing the latest available version.

You can find instructions to installing custom packages here:

https://bitbucket.org/horizongir/bonsai/wiki/InstallCustomPackageTutorial

Don't forget to turn on "Include Prerelease" so you can see the experimental package.

Let me know if this helps.

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[Spark Zhu]

Hi goncaloclopes! I tried your new package, it could load normally and allow me to add the member selection node, I added source.Image as well as videoWriter after Spinnaker. However, when I click on the source.Image while the workflow ran, it was a completely dark screen, so did the saved video. When I open the camera with the SpinView software that came with the pointGray BFS camera, it had no problem showing what it saw. Any chance you know what might have happened? Thanks! 

[Gonçalo Lopes]

Hi Spark,

This is strange. If you right-click on the image node while it is running and select Show Visualizer > ObjectTextVisualizer does it show you the correct image resolution? I'm just trying to understand if there is any communication happening between the node and the camera at all.

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[joshua.m...@gmail.com]

Hi Goncalo,

I seem to be seeing a very similar problem with my new blackfly S camera even after downloading the updated spinnaker package you posted - when I right click on the node I see this message and when I tell it to run I see this one. I'm running Bonsai 2.3.0 and Spinnaker/Spinview  1.10.0.31, so I'm wondering whether this has to do with the updated version of spinnaker. I've emailed FLIR asking for the version that Spark was using but they haven't gotten back to me - any ideas to try in the meantime?

Thanks,
Josh

[Gonçalo Lopes]

Hey Josh,

It seems like the spinnaker native DLLs keep changing their binary layout every time they update their drivers. This will be very annoying as it will require rebuilding the library for every single release they make (which is quite often unfortunately)... I am a bit in crunch mode these days trying to push the release of Bonsai 2.4, so I'm trying to minimize library updates for a bit until it's out.

The two possible workarounds for now are:
 1)  downgrade the Spinnaker driver to the right version

 2)  recompile the Bonsai.Spinnaker package targeting the newer driver (source code is here).

I will try to get to it as soon as I have some extra time.

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[Torben Ott]

Hi Goncalo & Josh,

I have the same issue using Bonsai & Spinnaker 1.10.0.31. I haven't figured out how to get an older version of Spinnaker - maybe you found out, Josh, or do you have another solution?

PointGrey just sent me a new firmware release for testing, in which ChunkData (eg GPIO status) is supposed to be embedded finally in the image metadata (there has been a discussion about one year ago, which seems to be gone) and I wanted to test it.

Thanks!

Torben

[joshua.m...@gmail.com]

Hey Torben,

I contacted Flir about this and they sent me these links for the old versions of Spinnaker: 

64bit: https://flir.box.com/s/xuy7o55hpbr1dewlfrwmxnijnys485af
32bit: https://flir.box.com/s/ndtmxz49mvf1ta0tbk3417iarizpjxbm

While very kind of them, unfortunately installing this still doesn't fix the issue with the Bonsai/Spinnaker interface - it only brings you to the next issue that Spark mentioned in his later comment, where you can play the node but the video window only displays a black screen. For me, it seems to have the correct video resolution in the information window but there is no video feed. Haven't found a way around this, except to use a webcam for live acquisition and triggering stimuli, and then the PointGrey camera for posthoc analysis of the same trials which is not ideal. Let me know if you are able to find a solution!

Josh

[Gonçalo Lopes]

Hi everyone,

I have just updated a new version of the Bonsai.Spinnaker package (0.2.0) that hopefully fixes these problems.

Let me know how it goes and whether there are any pending issues.

I don't have Spinnaker cameras on me to test things at the moment, so there may be some trial and error involved.

Hope this helps.

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[joshua.m...@gmail.com]

Hey Goncalo,

Thank you for the update! Just tested out the new version, but unfortunately I'm not seeing any change in the behavior of the node with the Spinnaker 1.8 build - it still shows just a black screen with correct resolution but no image. Please let me know if there's anything at all I can do to help you with diagnostics since you don't have access to a Spinnaker camera!

Josh

[Stefano Zucca]

Hi Goncalo,

I am having problems using the spinnaker function. I have downloaded the last version of Bonsai (2.3.1) and the last version of Spinnaker Library (0.2.0) updated 24/5/18.

I am running Bonsai on Windows 10 and I am using the latest version of SpinView (1.10.0.31). When I try to start a workflow with the Spinnaker Capture function I receive the following error:  "A procedure imported by 'SpinnakerNET_v120.dll' could not be loaded.'

I am using a BlackFly S camera to aquire the image.

Do you have any suggestion? Are there any other information I could provide that might help you in figuring out what is going on?

Thanks for you help,

Stefano

[Stefano Zucca]

Just a small update:

I tried with the old version of Spinnaker (1.8.0) and it worked perfectly with the new update of Spinnaker Library. It seems to be a problem only with the new version!

Stefano

[Torben Ott]

I got Spinnaker/Bonsai/GPIO states (in chunk data) to work with the following setup:

- Spinnaker 1.8 (does NOT work with 1.10) from Josh's post (64bit https://flir.box.com/s/xuy7o55hpbr1dewlfrwmxnijnys485af)

- beta firmware I received after contacting PointGrey https://www.dropbox.com/s/6du5077rk77vnzz/PGR_318390.zip?dl=0

- newest Bonsai package updates (6/6/18)

- in Spinview activate chunk mode active and select Exposure End Line Status All and chunk enable

then use Spinnaker Capture and Source.ChunkData.ExposureEndLineStatusAll (LineStatusAll does not work - also does not seem to be uncluded in SpinView)

[Gonçalo Lopes]

Hi Torben,

Thanks for the awesome step-by-step, this will be very useful :)

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[Josset Nicolas]

Thanks for the step by step!

I don't know if it is just me but I cannot access the spinnaker 1.8 version, could anyone post a new link?

thanks!!

[joshua.m...@gmail.com]

It looks like the link they provided has gone dead! I still have the 64 bit version of 1.8 saved which you can access here:

https://drive.google.com/file/d/1ZczV_-RRIpb8fFu1tX4njmzAvaysc7_i/view?usp=sharing

Anybody who needs the 32 bit version should contact FLIR and ask them for a link!

[Andrew Hardaway]

Hi Torben and others,

This is a really helpful guide to connecting the BlackFly S with Bonsai. Can you post a new dropbox or drive link to the beta firmware? The link above isn't working anymore. Also, can you expand on how to select the Exposure End Line Status in Spinview with a screenshot?

I got Bonsai to stop giving me errors, but I still can't visualize the feed even though data is still being received.

Thanks!

Andrew

[Virginia Rutten]

Hi Goncalo, Torben and co,

Thanks for all the useful instructions.

I'm having issues enabling Bonsai to access the frames of a BlackFlyS camera.

So far what I have:

- Spinnaker 1.8 (working well)

- Bonsai 2.3.1

- I can create a "Spinnaker node", without Bonsai complaining but when I look at either the Source.Image or Source.Chunk.ExposureEndLineStatusAll, the camera window appears black/not changing or returns 0's.

You mentioned that we should:

- in Spinview activate chunk mode active and select Exposure End Line Status All and chunk enable

I have:
    chunk mode: active 
    chunk: enable

however the: 

    Line Status section in Digital IO Control won't let me change the settings - telling me that I need to enable something else to be able to change (though the software doesn't say what...)

finally:
 "select Exposure End"
is this referring to the "Event Control" section?
   Event Selector: Exposure End

If you have a second could also explain what these features/why they are necessary?

Any advice hugely welcomed,

Best,

Ginny

On Wednesday, June 6, 2018 at 12:30:30 PM UTC-4, Torben Ott wrote:

[Virginia Rutten]

To add a picture of the section which doesn't allow me to select it.

[Andrew Hardaway]

Hey Virginia,

I'm having virtually identical issues that you are having right now. I talked to FLIR technical support today and they were able to track the ticket from Torben's request above so that I can be sure I'm using the same firmware (attached to this message). I can't speak to the Spinview issues, but I'll let you know if this works for me tomorrow with the firmware update. 

best,

Andrew

[Andrew Hardaway]

Hi everyone,

I'm having the same issues that others at the top of this thread have described. Have tried following some of the suggestions, but to no avail. Gonna give a breakdown here so maybe people can offer up suggestions.

OS: Windows 10 64 bit

Camera: BFS-U3-13Y3C-C (FLIR retrieved the firmware from Torben's ticket above - see message to Virginia, not sure if this firmware is appropriate for my model camera but have also tried latest firmware specifically for my model with no luck)

Bonsai: 2.3.1(64) (have also tried running in 32 bit mode with same issue)

Spinnaker: 1.8.064(Full SDK installation)

In Spinnaker I set Chunk Mode to Active, Chunk Selector to ExposureEndLineStatusAll via dropdown menu, and checked the box for Chunk Enable. See image for this attached.

In Bonsai I have a simple video recording layout using the Spinnaker Capture Source. The program runs with no errors. Initially I had errors described above which were fixed by downgrading from Spinnaker 1.10. Bonsai is clearly receiving data and reads the image at the appropriate resolution in Source.Image or Video Capture. I can see incoming data in ChunkData and Chunkdata.ExposureEndLineStatusAll (reading a steady value of 12).

Thanks for any helpful feedback! I'm new to Bonsai.

Andrew

[Josset Nicolas]

I don't want to pollute the discussion, but I just want to add that I still have the same problem, 

I have switched to a pseye for now but would prefer using the blackfly in the near future!

Any input would be appreciated :) 

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[Gonçalo Lopes]

Hi everyone,

Unfortunately I don't have a blackfly camera with me at the moment. It is a bit hard to debug this at the driver level without actually having the hardware.

I don't mind trying to recompile the Spinnaker package to target the latest SDK version, if that would help.

Would be good to hear back from technical support about the compatibility issues.

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[Andrew Hardaway]

Hi Goncalo,

Thanks for your reply. For what its worth, in my discussions with FLIR tech support they said the latest version of the firmware should include the update that Torben said worked for him above. I can provide a link later but it is too large to attach. I'm happy to try a new install of Spinnaker SDK 1.10 and a package update on your end if you have time. Cheers

Andrew

On Wed, Oct 10, 2018 at 11:38 AM Andrew Hardaway <harda...@gmail.com> wrote:

Hi Goncalo,

Thanks for your reply. For what its worth, in my discussions with FLIR tech support they said the latest version of the firmware should include the update that Torben said worked for him above. Its attached here in case its getting lost in the discussion. I'm happy to try a new install of Spinnaker SDK 1.10 and a package update on your end if you have time. Cheers

Andrew

--

Andrew Hardaway
Research Assistant Professor
University of North Carolina at Chapel Hill

--

Andrew Hardaway
Research Assistant Professor
University of North Carolina at Chapel Hill

[Virginia Rutten]

 

Hi all,

I'm still having issues - if anyone has solved the problem please do post your breakthrough/updates! :) 

Looking forward to getting back in sync with Bonsai,

Best,

Ginny

[Andrew Hardaway]

Hi Goncalo et al.

I'm getting some help from FLIR tech support, but at a road block as I don't technically grasp how Bonsai is triggering the hardware through Spinnaker and the Spinnaker.capture package. Can you explain? Sorry if this is in another thread, but didn't see it in my cursory search. Thanks!

Andrew 

[Gonçalo Lopes]

Hi Andrew,

All the code is open-source here, if it helps to diagnose the Spinnaker issues:

https://bitbucket.org/horizongir/bonsai.spinnaker

Specifically this file:

https://bitbucket.org/horizongir/bonsai.spinnaker/src/20ad5b67c188eec57261be59c69ce52551bb7860/Bonsai.Spinnaker/SpinnakerCapture.cs

But basically, the only thing the code does is access the Spinnaker SDK directly. I don't try to do anything in particular, simply directly accessing the Chunk Data through their APIs based on the examples they provide.

Of course, it is possible that something is not being properly configured, especially if firmware updates and API has been changing significantly. I'm sorry I am having trouble recently to find the time to recompile the code for the latest SDK, will try to do that as soon as possible.

It is really unfortunate that I don't have any access to Spinnaker cameras at the moment. I have to admit my experience of dealing with hardware is that things go much slower without having access to the devices themselves, because you can't debug the problems properly, run the SDK examples to see if they work, etc, etc.

Let me know if there is anything I can do to help debug the situation, apart from recompiling the package, which I will get to ASAP.

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[Andrew Hardaway]

Hey guys,

The FLIR tech support and I are still trying some different things that you can alter in Spinview to get Bonsai to read the stream. Its not a total fix(as I would like color movies), but I am able to see a black/white video stream if you change one setting.

Go to Spinview -> Image Format Control ->   Pixel Format dropdown menu -> select Mono8. I tried the other settings and still just got a black screen. This may be a suitable workaround for some who don't care about color.

My other settings - 

Blackfly S UF3-U3-13YC3 connected

Windows 10 64

Bonsai 2.3.1

Spinnaker  1.8.0.64

I'll let you know if I have more updates.

Andrew

[Virginia Rutten]

Hi Andrew,

Thanks a lot for the update!

It's really very helpful.

Do keep us informed if you crack the colour issue.

best,

V

[Josset Nicolas]

Hi everyone!

Thanks for the update! I still can't see anything in Mono8 but that may be have to do with my bonsai inexperience, could you send us the workflow you are using?

Thanks a lot!

Nicolas

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[Andrew Hardaway]

Hi Nicolas,

Sorry for the delay. Here is the very simple Bonsai layout that is working with the Mono8 workaround and my settings above.

Andrew 

[Alessandro Di Filippo]

Hi, thank you Andrew.

I tried the suggested fix and it also works for me.

These are my specifics:

- Blackfly S BFS-U3-31S4-C

- Windows 10 64

- Bonsai 2.3.1

- Spinnaker  1.8.0.64

Anyway, here at my lab people are using different coloured marker for animal head tracking, and that is obviously not possible with only Mono8 video.

I'm currently trying to find another solution, using ArUco markers.

[Gonçalo Lopes]

Hi Alessandro et al,

Just to let you know I have updated today the Spinnaker API to work with the latest drivers (1.20.0+). Unfortunately most compatibility issues come from the fact that FLIR keeps changing the DLL names with new driver releases (SpinnakerNET_v120, SpinnakerNET_v140, etc...).

If you update to the new package version (0.3.0) it is therefore critical that you also update the Spinnaker drivers to their latest version.

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[Gonçalo Lopes]

Also, I took the liberty of enabling all available metadata chunks in the SpinnakerCapture node by default, which means that it should now be possible to read available image metadata, such as timestamp, frame counter, etc...

[Alessandro Di Filippo]

This is great news!
Thank you for your effort, the metadata information could be really useful for my project.

By the way, after updating everything, I tried again using SpinnakerCapture by setting my camera (Blackfly S BFS-U3-31S4C) in SpinView to something different from Mono8.

Sadly, it didn't work.

Can you please explain to me why only Mono8 is working with this model?

[Gonçalo Lopes]

Hi Alessandro,

Unfortunately I don't have a Blackfly S color camera with me that I could use to debug this. It's very hard to maintain these packages without access to hardware where you can test it, which is why the Spinnaker interface has been evolving so slowly (basically whenever I can have access to an actual camera for 20 minutes). I may have access to one next week, and will update here what I find.

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[Alessandro Di Filippo]

No problem, thank you, Goncalo.

Just tell me whether I can help you with anything regarding this, like getting in touch with the people at PointGrey asking them for a specific issue.

[Gonçalo Lopes]

No worries, will do. I'm confident it will work out as soon as I have access to the color camera. Will let you know how it goes.

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[Gonçalo Lopes]

Hi Alessandro et al,

I have replaced the 0.3.0 version of the NuGet package. If you can uninstall and reinstall the package, the color decoding should now work. It will be really useful if whoever can try it now does so, while I have the camera with me. I have about a week to fix any pending issues with Spinnaker, so feel free to report them here.

[Alessandro Di Filippo]

Hello Goncalo,

I will try it tomorrow afternoon, I will write to you as soon as I see how it goes.

Thank you for your help!

[Alessandro Di Filippo]

Hi Goncalo,

I just tried what you told me: I uninstalled the Spinnaker Nuget, and installed the new version...and it worked!

I tried setting the camera at BayerGB8 and everything was fine and colorful.

Really, thank you for your help.

[Gonçalo Lopes]

Good to hear, thanks for the heads-up!

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[Gonçalo Lopes]

Hi Andrew, Torben, and others who have managed to sample from ChunkData using Bonsai.Spinnaker.

In the last few days I had the chance to play around with a new Blackfly S model BFS-U3-04S2C, and to my surprise FLIR indeed seems to have removed the ChunkSelector ExposureEndLineStatusAll from the Spinview dropdowns, which means there is currently no way to sample the GPIO lines from the newer Blackfly S cameras.

Can anyone confirm that this is indeed the case? I have also emailed PointGrey/FLIR support but I also wanted to confirm who in the community is affected by this. Has anyone succeeded in reverting firmware / drivers to resolve this?

At this point, until the issue is solved, I have no option other than to strongly recommend that new users interested in precise sychronization of external signals to video data should NOT to buy any Blackfly S or other Spinnaker cameras without previously inquiring with PointGrey / FLIR that the camera you are buying supports this specific event.

There is currently no other known way of precisely synchronizing external events to frame acquisition, other than triggering the camera externally, or routing a camera strobe signal to an external DAQ.

I will provide new updates on this thread as we learn more about the situation.

[Alessandro Di Filippo]

Hello Goncalo, 

I cannot help you on the specific issue, because I'm using an external trigger to synchronise the camera, but if you need any support in pushing the issue with FLIR people, I will gladly help.

[Andrew Hardaway]

Hey Goncalo,

Thanks so much for helping us troubleshoot these cameras and Spinnaker Capture. I am using Spinview 1.8.0.64 and it still shows up as an option. I am not syncing external devices to video info right now, but would be good to do in the future. Let me know what else I can do to help out. I haven't tried the new spinnaker.capture module yet as the Mono8 work around was fine for what I needed. What should we bother FLIR about? 

Best,

Andrew

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[Gonçalo Lopes]

Hey Andrew,

Thanks for chipping in, it's reassuring to hear that you still see the Exposure End Line Status All option. I am currently trying out another Blackfly S, BFS-U3-04S2C, and that option is missing from the chunk selector entirely. This seems to be more of a firmware issue, as it happens with both SpinView 1.8.0.64 and with the latest 1.20.0.15.

So the suggestion seems to be that some cameras allow for reporting line status on exposure end, and some others don't.

Can you let us know what is the camera model and firmware version? That way I can include it in the report to FLIR and also start collecting a list of what cameras are compatible with this.

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[Andrew Hardaway]

Sure. I think is everything.

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[Amina Kinkhabwala]

I can try to test that today since I am playing with camera settings. I also agree that I'm happy to complain to FLIR if it helps. 

I send the camera strobe signal (exposure active) through the open ephys analog input and have no trouble with synchrony with this method.

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[Gonçalo Lopes]

Hey Amina, that's reassuring to know that the strobe signals still work. I am trying to go over the list of features from FlyCapture2 and trying to figure out how to port everything to the Spinnaker interface, so it's also good to know how the terminology changes.

Andrew, that's interesting, it looks like you have a more up-to-date firmware, although I'm not sure how these version numbers transfer across variations of Blackfly S (i.e. 13Y3C versus 04S2C). I will compile all this into the support ticket  and will share the answers in this thread (or create a new pinned one once we have some conclusions).

Thanks everyone!

To view this discussion on the web visit https://groups.google.com/d/msgid/bonsai-users/CAPuiM9tiJjajXVVO%3DKW_E6oEXeq_GRRZGqTdAiny5ri-MaPkrQ%40mail.gmail.com.

[Amina Kinkhabwala]

Hey Goncalo, 

I spoke too soon. When I run the camera in Spinview I can see the strobe signal. When I run my Bonsai code (2.4 preview) I do NOT see the camera output signal. I will try to revert to Bonsai 2.3 and get back to you.

[Andrew Hardaway]

Hi Goncalo,

Not relevant to the ExposureEndlinestatus issue, but after upgrading to the latest Spinnaker Capture package and the latest version of Spinnaker I was able to record and visualize movies in Bonsai without the Mono8 workaround from before. So that's something. Thank you very much for repackaging it.

best,

Andrew

To view this discussion on the web visit https://groups.google.com/d/msgid/bonsai-users/CAPuiM9u%2BOMGm%3Ds6BN7JO6GuL%2BpY5Qq%3D6t8DfsJxo%3DMSS39L9Sw%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.

--

Andrew Hardaway
Research Assistant Professor
University of North Carolina at Chapel Hill

[Amina Kinkhabwala]

Hey Goncalo,

I have everything up and running with the latest Spinnaker (1.20) and Bonsai with the new February update of the Spinnaker package. Looks like I can see my camera signal while opening in Bonsai and in Spinview. 

One problem I have which is purely a Camera software issue is that I set the "Acquisition Frame Rate" to the highest value and the actual frame frame ("Processed FPS") ends up being a bit slower. The problem is that the camera output signal is set to be the "Acquisition Frame Rate" but what Bonsai sees is the "Processed Frame Rate".  I can slow down the "Acquisition Frame Rate" until it meets the processed frame rate and then my Camera digital output strobe signal is correct. This isn't a perfect fix since it slows down my frame rate. I was on the phone with FLIR and they recommended trying the latest software but this is a bug that is still present in Spinnaker 1.20.

Just a heads up if you also send a camera output signal for synchronization.

To view this discussion on the web visit https://groups.google.com/d/msgid/bonsai-users/CAPvW33pEmT%2BX%2B_8CDayzGdMqXcbYe_8t1xMY%3DJcU-tmwMDQdcA%40mail.gmail.com.

[Gonçalo Lopes]

Hi Amina,

Thanks for the hint, that is good to know (and a bit weird, yeah). I'm sure this will help me when I hit this issue later on.

This thread has been really useful by the way: literally 2 days ago I was googling the internet about these issues and the only place that was giving me any kind of meaningful information on this was this thread, which is kind of impressive!

Re. the frame rate issue: this might be because the package is doing the debayering in order to reconstruct the RGB color image by default (that is the "processing", even on SpinView). Can you try setting the ColorProcessing property to NoColorProcessing and see if that helps with the frame rate? You will get a grayscale bayer image, but it should give you faster frame rates.

Nothing pressing, just curious if that is where the performance hit is coming from.

[Amina Kinkhabwala]

Hey Goncalo,

For my timing issue, it is a problem within the Spinview software independent of running Bonsai. I did notice the ColorProcessing node, if you want me to try something specific with it I can, but my Bonsai data stream runs fast enough that I haven't had problems. If I do have a problem I will let you know.

One thing that I'm unsure about is why my video recording does not record the entire experiment. My fish escaped halfway through the recording according to the Bonsai tracking but the video showed the fish always there. Just wondering if there are some settings that might have it not write to disk after some amount of time. The issue is not skipping frames, but not recording for the entire time to the end. 

To view this discussion on the web visit https://groups.google.com/d/msgid/bonsai-users/CAGV1SGLRjd04BJo9exLsdsdX4xQcDK55JYZkfPEMiRR_GyByfw%40mail.gmail.com.

[Gonçalo Lopes]

Hi Amina,

 

You are using Bonsai 2.4-preview, right? There was an issue in a recent preview version where videos were not being closed properly. This has since been fixed, so if you download a fresh preview, this should be resolved.

 

Hope this helps!

To view this discussion on the web visit https://groups.google.com/d/msgid/bonsai-users/CAPuiM9vE4_fo%2BGROmywYvekocqBF2%3DaxQwZLTxqWNqM%3DwwkGjA%40mail.gmail.com.

[Torben Ott]

sorry- i didn't follow this thread anymore.

Just an update on which new configuration works for me (after a few things have been updated):

- Blackfly S BFS-U3-13Y3M-C

- Beta firmware I received from PT in summer 2018 (not sure if they finally have a proper release of that? PT's download website still lists 1/18/2017 as date!); download from my dropbox here: https://www.dropbox.com/s/88izglavwhimzds/PGR_318390.zip?dl=0

- Spinnaker software v1.20 (current online version as of 3/2019)

- Bonsai with all updates (3/2019) specifically Spinnaker module v 0.3.0 that expects the new Spinnaker version (thanks Goncalo for updating)

In SpinView, chunk mode is enabled and I do have the selection 'Exposure End Line Status All', which I can use to read out GPIO states in Bonsai.

[Michael Hendricks]

Hi all, I've looked at the history on this and wondering if anyone else is having issues persist with latest Spinnaker / Bonsai.

Blackly S BFS-U3-13Y3M-C USB3, Monochrome
Spinnaker 1.25.0.52 
Bonsai 2.4.0

Bonsai.Spinnaker 0.4.0

No image from source node and Bonsai crashes on stop. 

[Gonçalo Lopes]

Hi Michael,

I have just updated the Spinnaker package to 0.5.0, which brings compatibility with the latest Spinnaker 1.25.0.52, updates all the bonsai package icons and improves color mode compatibility.

A word of warning: Spinnaker SDK releases from FLIR are NOT backwards compatible, so if you update your Bonsai package to 0.5.0, you WILL have to use the 1.25.0.52 release.

Until FLIR changes their build pipeline to make their releases backwards compatible, I have decided to start adding the required driver version to the bonsai package description. That way users can always check which exact version they need from now on.

Also conveniently FLIR now has an archive of all driver versions up on their website, so makes it easier to keep your machine compatible.

Hope this helps.

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[Michael Hendricks]

Thanks! I called FLIR and complained about the back-compatibility issue, maybe if enough other people do they'll stop it. 

On Thursday, October 31, 2019 at 9:05:14 PM UTC-4, goncaloclopes wrote:

Hi Michael,

I have just updated the Spinnaker package to 0.5.0, which brings compatibility with the latest Spinnaker 1.25.0.52, updates all the bonsai package icons and improves color mode compatibility.

A word of warning: Spinnaker SDK releases from FLIR are NOT backwards compatible, so if you update your Bonsai package to 0.5.0, you WILL have to use the 1.25.0.52 release.

Until FLIR changes their build pipeline to make their releases backwards compatible, I have decided to start adding the required driver version to the bonsai package description. That way users can always check which exact version they need from now on.

Also conveniently FLIR now has an archive of all driver versions up on their website, so makes it easier to keep your machine compatible.

Hope this helps.

On Wed, 16 Oct 2019 at 14:46, Michael Hendricks <s.michae...@gmail.com> wrote:

Hi all, I've looked at the history on this and wondering if anyone else is having issues persist with latest Spinnaker / Bonsai.

Blackly S BFS-U3-13Y3M-C USB3, Monochrome
Spinnaker 1.25.0.52 
Bonsai 2.4.0

Bonsai.Spinnaker 0.4.0

No image from source node and Bonsai crashes on stop. 

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[Masayoshi Murakami]

Hi Gonçalo and all,

I am having a problem reading the "line status all" of blackfly camera using Bonsai.

(It seems that it's been solved already, but I can't make it work...)

In SpinView I can see the "line status all" changing its value. 

But I cannot see the ChunkData.LineStatusAll (or ChunkData.ExposureEndLineStatusAll) changing in Bonsai. 

It stays 0 all the time.

Does anyone know how to solve this problem? 

Should I use an older version of Bonsai and Spinnaker SDK?

In SpinView, I don't see "Exposure End Line Status All" or "Line Status All" in a list of items under Chunk Data Control.

Maybe this is the problem??? Do I need to change the firmware of the camera somehow?  

I am using:

Bonsai 2.4.0

Spinnaker Library 0.6.0

SpinView 1.29.0.5

BlackFly S (BFS-U3-16S2M)

Thanks,

Masa

[Gonçalo Lopes]

Hi Masa,

The fix to reading the line status does indeed require a firmware update.

Are you using the latest firmware from Spinnaker? I got an email from them saying that they released the fix at the end of March 2020, but I can't seem to find it again on their website and the link they sent me is not valid anymore.

What is the firmware version installed in your camera? Maybe you can email them for the link to the latest updates?

Hope this helps!

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[Masayoshi Murakami]

Thanks Gonçalo,

A firmware version of my camera is 1707.0.125.0.

I bought the camera a while ago, so probably older than a version with the fix.

I cannot find the newest firmware in their website either.

I will contact them.

Masa

[ott.t...@gmail.com]

I don't know if this is still relevant - I hadn't checked this thread in a long time.

I needed to add more Blackly S BFS-U3-13Y3M-C USB3 cameras to our setup so I encountered this again. Even the newest firmware on their website still does not support including LineStatus in the frame's chunk data (incredible!) 

So here is a repaired link to the beta firmware I'm using: https://www.dropbox.com/s/ydexiy6iler3vh6/PGR_318390.zip?dl=0

I'm using this together with SpinView 1.20.0.15 and Bonsai's Spinnaker Capture module. In the SpinView software you need to activate chunk data and ExposureEndLineStatusAll, which you can then use in Bonsai and it works reliably on our end.

Torben

[Gonçalo Lopes]

Thanks Torben for the link to the beta firmware!

It is indeed annoying that FLIR does not seem to include this by default. My experience has been that they add it on demand if you ask them, but they basically seem to be doing it on a case-by-case basis for each individual camera model, and often don't actually include it in the official distribution. Hopefully if enough people voice their need they would understand the importance of this feature.

To view this discussion on the web visit https://groups.google.com/d/msgid/bonsai-users/577a13ce-2b2d-4436-ba31-dfd96a2fb962n%40googlegroups.com.

[Amina Kinkhabwala]

Hi! I just updated from 2.4 to 2.6 Bonsai and adding the Spinnaker package but am not seeing it in Bonsai.  Am I missing something? When I load old experiments I ran with Spinnaker packages they also do not show up in this latest Bonsai version.

[Amina Kinkhabwala]

In case this helps anyone, I had not used Bonsai in 2 years and last had Bonsai 2.4 working with Spinnaker. Updating to 2.6 I had to install the 1.29.0.5 Spinnaker SDK (somehow I had a 1.20. version). Now I can see the Spinnaker options in the "Source" list and only immediately after installing the 1.29.0.5.  I'm mentioning this because I had everything working just fine in Bonsai 2.4.  Maybe this will help someone else that wandered away from Bonsai for awhile and came back =).

[Gonçalo Lopes]

Hi Amina,

Thanks for the update. Indeed, unfortunately the Spinnaker SDK releases are not backwards compatible, so you will need the exact match for the nodes to show up. As a reference, I have been including which version is required in the package description in the package manager, so you can check there for any changes.

Glad to hear things were sorted,

To view this discussion on the web visit https://groups.google.com/d/msgid/bonsai-users/b00796e9-f6a7-4471-83e7-853523559f57n%40googlegroups.com.

[Liad Baruchin]

Hi, Sanna,

Can you get to something similar to the screen shown below?

If you can that would let you see the image.

On Wednesday, 10 November 2021 at 17:01:35 UTC s.t...@ucl.ac.uk wrote:

Hi everyone,

I am new to Bonsai and am having trouble viewing any output from my FLIR camera. When running the workflow (photo attached), I receive no error messages; however, the window displaying the camera's view doesn't pop up whatsoever... I just hit start, it runs, and nothing happens. 

For reference, I am using: 

-FLIR camera BFS-U3-16S2M-CS with a computar lens

-FLIR firmware 1707.0.125.0

-Bonsai 2.6.3

-SpinView 1.29.0.5 (full SDK installation)

-Bonsai.Spinnaker 0.7.0 (this package description states that Spinnaker SDK version 1.29.0.5 is required, which is what I'm using)

I can view what the camera sees within SpinView no problem, and I am sure to quit SpinView every time when attempting to run the Bonsai workflow. The only node I have in the workflow is Spinnaker Capture. NoColorProcessing is chosen from the drop-down ColorProcessing, the index is set at 0 and the serial number is entered. I was advised that I may have to input camera properties, but don't see a way to save this from SpinView in a file format compatible with Bonsai. Within SpinView, as reccomended by this thread, I checked the pixel format, chunk mode and chunk enable, which were all already set to the parameters suggested here as default settings (i.e., mono8, activated and check-marked, respectively). I didn't see an option to choose ExposureEndLineStatusAll via the drop down menu, so I just selected "exposure". 

Firstly, Does anyone know how to input the camera properties into Bonsai with the versions I am using? I'm not able to add them manually within Bonsai as the "..." icon within the Misc box doesn't show for me after clicking on the Spinnaker Capture node. 

Secondly, do I need another node/connection, or should the window with the camera's view pop up automatically with the one spinnaker capture node? I have the Bonsai.Design.ObjectTextVisualizer enabled already. 

Thank you for your time and I would appreciate any advice saving me from a downwards spiral into Bonsai's roots! 

Sanna 

[Sanna Titus]

Hi, thanks for your response. Adding member selector and double clicking that node while the code was running actually ended up working perfectly - thank you so much!!

[Liad Baruchin]

Perfect. Happy to hear :)

[kapil...@gmail.com]

Cant control the FPS of video captured in rFLIR cam, is there a way, The video write node is set to 30 but getting recordings around 66FPS. Any solution would help.thanks

Best,

Kapil