Question about save SPRING file

Question

Question about save SPRING file

njumay opened this issue 6 years ago · 7 comments

I am learning the SPRING Viewer by repeating the code of tutorial pbmc 4K.
I have some trouble with the last step(Save SPRING files).
I got the error : TypeError: 1386 is not JSON serializable(https://github.com/njumay/SPRING/blob/master/spring_example_pbmc4k.ipynb).
I do not kown how to solve this problem.
I hope someone can help me. Thanks a lot.

Answer 1 · 2019-06-19T14:37:49.000Z

Hello, Did you change the notebook at all from the original? Also what version of python and OS are you using?

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On Wed, Jun 19, 2019 at 9:12 AM njumay ***@***.***> wrote: I am learning the SPRING Viewer by repeating the code of tutorial pbmc 4K. I have some trouble with the last step(Save SPRING files). I got the error : TypeError: 1386 is not JSON serializable( https://github.com/njumay/SPRING/blob/master/spring_example_pbmc4k.ipynb). I do not kown how to solve this problem. I hope someone can help me. Thanks a lot. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#14?email_source=notifications&email_token=ABO45MSM7J74VFNTPLHHBWDP3IWELA5CNFSM4HZJPB72YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G2MTXEA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABO45MVBMYNMP2J75WEISL3P3IWELANCNFSM4HZJPB7Q> .

Answer 2 · 2019-06-19T14:41:49.000Z

I did not change anything in the notebook. And i run this notebook on python2.7 installing in Windows10.

Answer 3 · 2019-06-21T14:44:00.000Z

Hi, Can you identity the datatype of the int that is giving the problem in json? Alternatively, can you send me a screenshot of the full traceback of the error? Then I can give you an updated noteook which would identify the problem

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On Wed, Jun 19, 2019 at 10:41 AM njumay ***@***.***> wrote: I did not change anything in the notebook. And i run this notebook on python2.7 installing in Windows10. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#14?email_source=notifications&email_token=ABO45MVZBYX5SYXAZPN7QFTP3JAS5A5CNFSM4HZJPB72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYCC6TY#issuecomment-503590735>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABO45MTR5KRUAGA45BUTOBDP3JAS5ANCNFSM4HZJPB7Q> .

Answer 4 · 2019-06-23T07:04:09.000Z

Did you mean the feedback, when I ran the notebook? Since it is a little long, I upload the files to github. And this is the URL: https://github.com/njumay/SPRING/blob/master/spring_example_pbmc4k.ipynb .

Answer 5 · 2019-06-27T17:40:36.000Z

Could you add the the following line below line 632 of spring_helpers.py and send the output? for k,v in color_stats.items(): print(k,v,[type(vv) for vv in v])

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On Sun, Jun 23, 2019 at 3:04 AM njumay ***@***.***> wrote: Did you mean the feedback, when I ran the notebook? Since it is a little long, I upload the files to github. And this is the URL: https://github.com/njumay/SPRING/blob/master/spring_example_pbmc4k.ipynb . — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#14?email_source=notifications&email_token=ABO45MS6MQNQODRFUUTF3GTP34N6TA5CNFSM4HZJPB72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODYKYEFI#issuecomment-504726037>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABO45MRFPNPJAICON7GHFADP34N6TANCNFSM4HZJPB7Q> .

Answer 6 · 2020-10-08T03:25:43.000Z

Hi!

Thanks for the generating this software!

Is this problem solved? I am still facing the same error and this is the output after adding the line

Thanks!
Justine

Answer 7 · 2020-10-08T08:36:32.000Z

Hi!

Fixed problem by adding this line after line 632

color_stats = {k:[int(i) for i in v] for k,v in color_stats.items()}

also removed .decode('utf-8') from a couple of lines

Thanks!!