Error on running analysis (too many indices for array: array is 1-dimensional, but 2 were indexed)

[sameerbau]

Traceback (most recent call last):
  File "/home/LAB/Desktop/GEMspa/main_gui.py", line 584, in on_go
    traj_an.calculate_msd_and_diffusion()
  File "/home/LAB/Desktop/GEMspa/trajectory_analysis.py", line 2140, in calculate_msd_and_diffusion
    msd_diff_obj.calculate_ensemble_average()
  File "/home/LAB/Desktop/GEMspa/msd_diffusion.py", line 388, in calculate_ensemble_average
    valid_tracks = self.msd_tracks[np.where(self.msd_tracks[:, self.msd_len_col] >= (self.min_track_len_ensemble - 1))]
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

Hello,

I'm getting the above error upon running some of the files. It works when I remove the file from the list. Any inputs would be greatly welcome.

Regards Sameer

[snkeegan]

Hi Sameer,

I think I have a fix for this. Would you mind providing a the file that causes the error so I can validate the fix? You can email me at @.***

Thanks!

Sarah

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From: sameerbau @.***> Sent: Tuesday, January 18, 2022 11:26:43 PM To: liamholtlab/GEMspa Cc: Subscribed Subject: [liamholtlab/GEMspa] Error on running analysis (too many indices for array: array is 1-dimensional, but 2 were indexed) (Issue #3)

[EXTERNAL]

Traceback (most recent call last): File "/home/LAB/Desktop/GEMspa/main_gui.py", line 584, in on_go traj_an.calculate_msd_and_diffusion() File "/home/LAB/Desktop/GEMspa/trajectory_analysis.py", line 2140, in calculate_msd_and_diffusion msd_diff_obj.calculate_ensemble_average() File "/home/LAB/Desktop/GEMspa/msd_diffusion.py", line 388, in calculate_ensemble_average valid_tracks = self.msd_tracks[np.where(self.msd_tracks[:, self.msd_len_col] >= (self.min_track_len_ensemble - 1))] IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

Hello,

I'm getting the above error upon running some of the files. It works when I remove the file from the list. Any inputs would be greatly welcome.

Regards Sameer

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/liamholtlab/GEMspa/issues/3__;!!MXfaZl3l!OFv6psmQ__XBqPblwr0-SdQL9ty0E4T_RIFV8l5I7f1zSZiFToEVas96Lsu7m9_t8eTlrg$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAV5H5RMAJ2XX6GOM52TAR3UWY4QHANCNFSM5MI4HMIA__;!!MXfaZl3l!OFv6psmQ__XBqPblwr0-SdQL9ty0E4T_RIFV8l5I7f1zSZiFToEVas96Lsu7m99JCC1k0Q$. Triage notifications on the go with GitHub Mobile for iOShttps://urldefense.com/v3/__https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675__;!!MXfaZl3l!OFv6psmQ__XBqPblwr0-SdQL9ty0E4T_RIFV8l5I7f1zSZiFToEVas96Lsu7m9_zjbJZ6A$ or Androidhttps://urldefense.com/v3/__https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign*3Dnotification-email*26utm_medium*3Demail*26utm_source*3Dgithub__;JSUlJSU!!MXfaZl3l!OFv6psmQ__XBqPblwr0-SdQL9ty0E4T_RIFV8l5I7f1zSZiFToEVas96Lsu7m99OPak56w$. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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[sameerbau]

https://drive.google.com/drive/folders/1jm3BDiGJJ8ANYbXaTfYpI1DiajVEanyn?usp=sharing

Let me know if you are able to reproduce the error

[snkeegan]

I have added a fix for this issue. Please download the latest code from the main branch.

[sameerbau]

Works! Thank you!