MMCorePy import crash kernel

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MMCorePy import crash kernel

William Magrini
Hi,
I'm a new user of MicroManager and I would like to use Python. The thing is that when I run the command import MMCorePy into python shell, it crashes and restarts.
I precise that I have Python 2.7.16 installed with the last version of numpy and MicroManger version is 1.4.22
If someone has a solution for me it would be great !
Regards,
William


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Re: MMCorePy import crash kernel

StevenF
Hey William,

I have used Micromanager's MMCorePy quite a lot but without any error logs
or things of this kind i think it's gonna be very hard for anyone to help
find where the issue comes from!

I think you should definitively try a nightly version from the gamma or beta
branch as i think there has been some improvements made to the MMCorePy
since 1.4.22

more info on this page : https://micro-manager.org/wiki/Version_2.0

I personally have been using python 3.6 and a beta version of micromanager
without having any particular issues if you want to consider this as a
possible solution!

this version of the beta is use :
https://valelab4.ucsf.edu/~MM/nightlyBuilds/2.0.0-beta/Windows/MMSetup_64bit_2.0.0-beta3_20171106.exe

the compatible python 3.6 version of MMCorePy :
https://github.com/zfphil/micro-manager-python3

Hopefully these tips or alternate solutions can be of assistance!

Cheers,

Steven



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Re: MMCorePy import crash kernel

William Magrini
Thank you Steven,
I tried your solution and it worked. I’ll continue using this.
Regards,
William



> Le 22 mars 2019 à 13:22, StevenF <[hidden email]> a écrit :
>
> Hey William,
>
> I have used Micromanager's MMCorePy quite a lot but without any error logs
> or things of this kind i think it's gonna be very hard for anyone to help
> find where the issue comes from!
>
> I think you should definitively try a nightly version from the gamma or beta
> branch as i think there has been some improvements made to the MMCorePy
> since 1.4.22
>
> more info on this page : https://micro-manager.org/wiki/Version_2.0
>
> I personally have been using python 3.6 and a beta version of micromanager
> without having any particular issues if you want to consider this as a
> possible solution!
>
> this version of the beta is use :
> https://valelab4.ucsf.edu/~MM/nightlyBuilds/2.0.0-beta/Windows/MMSetup_64bit_2.0.0-beta3_20171106.exe
>
> the compatible python 3.6 version of MMCorePy :
> https://github.com/zfphil/micro-manager-python3
>
> Hopefully these tips or alternate solutions can be of assistance!
>
> Cheers,
>
> Steven
>
>
>
> --
> Sent from: http://micro-manager.3463995.n2.nabble.com/
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general



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Re: MMCorePy import crash kernel

UF_Microfluidics
In reply to this post by StevenF
StevenF wrote

> Hey William,
>
> I have used Micromanager's MMCorePy quite a lot but without any error logs
> or things of this kind i think it's gonna be very hard for anyone to help
> find where the issue comes from!
>
> I think you should definitively try a nightly version from the gamma or
> beta
> branch as i think there has been some improvements made to the MMCorePy
> since 1.4.22
>
> more info on this page : https://micro-manager.org/wiki/Version_2.0
>
> I personally have been using python 3.6 and a beta version of micromanager
> without having any particular issues if you want to consider this as a
> possible solution!
>
> this version of the beta is use :
> https://valelab4.ucsf.edu/~MM/nightlyBuilds/2.0.0-beta/Windows/MMSetup_64bit_2.0.0-beta3_20171106.exe
>
> the compatible python 3.6 version of MMCorePy :
> https://github.com/zfphil/micro-manager-python3
>
> Hopefully these tips or alternate solutions can be of assistance!
>
> Cheers,
>
> Steven
>
>
>
> --
> Sent from: http://micro-manager.3463995.n2.nabble.com/
>
>
> _______________________________________________
> micro-manager-general mailing list

> micro-manager-general@.sourceforge

> https://lists.sourceforge.net/lists/listinfo/micro-manager-general

Hi Steven,

I'm experiencing the same issue importing MMCorePy as William, and I'm
trying to use your solution, which the github readme says to open the
Micro-manager.sln. The thing is though, I don't have any .sln files in my
build, is that the important part of the workaround? Because I tried adding
new files and using python 3.6.8 but now I get a "ModuleNotFoundError"
instead.

Thanks,
Alex



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Re: MMCorePy import crash kernel

William Magrini
Hi Alex,

For my problem, I didn't have to compile from the sources. I just downloaded the 2.0.0-beta version of MM :
https://valelab4.ucsf.edu/~MM/nightlyBuilds/2.0.0-beta/Windows/MMSetup_64bit_2.0.0-beta3_20171106.exe

Then I followed the Installation part of the instructions in the GitHub page :
https://github.com/zfphil/micro-manager-python3

The thing is that I use anaconda, so I don't know if that makes a difference.

But if you want to compile, you need to use this as a source :
https://github.com/micro-manager/micro-manager
Then the micromanager.sln file is present.
Regards,
William

----- Mail original -----
De: "UF_Microfluidics" <[hidden email]>
À: "micro-manager-general" <[hidden email]>
Envoyé: Vendredi 14 Juin 2019 18:11:26
Objet: Re: [micro-manager-general] MMCorePy import crash kernel

StevenF wrote

> Hey William,
>
> I have used Micromanager's MMCorePy quite a lot but without any error logs
> or things of this kind i think it's gonna be very hard for anyone to help
> find where the issue comes from!
>
> I think you should definitively try a nightly version from the gamma or
> beta
> branch as i think there has been some improvements made to the MMCorePy
> since 1.4.22
>
> more info on this page : https://micro-manager.org/wiki/Version_2.0
>
> I personally have been using python 3.6 and a beta version of micromanager
> without having any particular issues if you want to consider this as a
> possible solution!
>
> this version of the beta is use :
> https://valelab4.ucsf.edu/~MM/nightlyBuilds/2.0.0-beta/Windows/MMSetup_64bit_2.0.0-beta3_20171106.exe
>
> the compatible python 3.6 version of MMCorePy :
> https://github.com/zfphil/micro-manager-python3
>
> Hopefully these tips or alternate solutions can be of assistance!
>
> Cheers,
>
> Steven
>
>
>
> --
> Sent from: http://micro-manager.3463995.n2.nabble.com/
>
>
> _______________________________________________
> micro-manager-general mailing list

> micro-manager-general@.sourceforge

> https://lists.sourceforge.net/lists/listinfo/micro-manager-general

Hi Steven,

I'm experiencing the same issue importing MMCorePy as William, and I'm
trying to use your solution, which the github readme says to open the
Micro-manager.sln. The thing is though, I don't have any .sln files in my
build, is that the important part of the workaround? Because I tried adding
new files and using python 3.6.8 but now I get a "ModuleNotFoundError"
instead.

Thanks,
Alex



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Re: MMCorePy import crash kernel

StevenF
In reply to this post by UF_Microfluidics
UF_Microfluidics wrote

> Hi Steven,
>
> I'm experiencing the same issue importing MMCorePy as William, and I'm
> trying to use your solution, which the github readme says to open the
> Micro-manager.sln. The thing is though, I don't have any .sln files in my
> build, is that the important part of the workaround? Because I tried
> adding
> new files and using python 3.6.8 but now I get a "ModuleNotFoundError"
> instead.
>
> Thanks,
> Alex

Hey Alex so if you don't want to go through the hassle of doing the
compilation yourself you don't need the whole micromanager.sln all you need
to do is download all the files in the MMCorePy folder from the github and
then copy paste them in the version of micromanager i linked which you
should have installed. You then should be able to use the Python library in
3.6!
Don't forget to make sure once all this is done to have the micromanager
folder in the PYTHONPATH otherwise python will not be able to find the
MMCorePy library.

hope this helps,

cheers,

Steven




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Re: MMCorePy import crash kernel

UF_Microfluidics
In reply to this post by William Magrini
Hi William and Steven,

As per your instructions, I redownloaded the beta version, put those
MMCorePy files into the folder, then followed the installation instructions
on the github page and it works now! I think I was focusing on the compiling
too much and didn't even get to the jupyter script part, which was I think
the primary missing piece.

Thanks so much for your help,
Alex



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