issue with 1D interpolation function

[alexisfaure77]

Dear,

I first would thank you for your wonderfull pipeline. I have run it recently on one miniscope video and it have work well. However, to day after, trying the same video, it give me following error that seems to be link to basic matlab function rather than toolboxes. I am very new in Matlab and I hope that my question will not be too trivial.

Thank you

Alexis FAURE

Here the log of error

Warning: Name is nonexistent or not a directory: C:\Users\afaure\AppData\Local\Temp\Editor_qekiv Warning: "C:\Work Alexis\Recherche\endoscopie\MIN1PIPE-master" using the Custom Working Folder preference could not be accessed. Using "C:\Users\afaure\Documents\MATLAB" as the initial working folder instead.

min1pipe Downloading CVX Begin collecting datasets info Warning: AVIINFO will be removed in a future release. Use VIDEOREADER instead. In aviinfo (line 74) In data_cat (line 60) In min1pipe (line 84) Done collecting datasets info, time: 1.6748 Begin data cat 100 200 300 400 500 Done data cat, time: 4.1977 Begin dirts clean #1/1 batch Starting parallel pool (parpool) using the 'local' profile ... Connected to the parallel pool (number of workers: 4). Done frame #100/500 Done frame #200/500 Done frame #300/500 Done frame #400/500 Done frame #500/500 Done dirts clean #1/1 batch Begin anisotropic diffusion #1/1 batch done frame #200/500 done frame #100/500 done frame #300/500 done frame #400/500 done frame #500/500 Done anisotropic diffusion #1/1 batch Begin background removal #1/1 batch Done frame #100/500 Done frame #200/500 Done frame #400/500 Done frame #300/500 Done frame #500/500 Done background removal #1/1 batch Begin saving Ydebg #1/1 batch Done saving Ydebg #1/1 batch Elapsed time is 50.154272 seconds. Done neural enhancing, time 50.4222 Done noise suppression, time 1.4847 GPU Device available but outdated. Begin initial computation of translation score computed score of frame #200/500 computed score of frame #250/500 computed score of frame #50/500 computed score of frame #100/500 computed score of frame #150/500 computed score of frame #300/500 computed score of frame #350/500 computed score of frame #400/500 computed score of frame #500/500 computed score of frame #450/500 Done initialization, 6.6461 seconds Begin intra-section Done intra_section # 18/92, batch 1/1 Done intra_section # 27/92, batch 1/1 Done intra_section # 9/92, batch 1/1 Done intra_section # 36/92, batch 1/1 Done intra_section # 54/92, batch 1/1 Done intra_section # 81/92, batch 1/1 Done intra_section # 72/92, batch 1/1 Done intra_section # 63/92, batch 1/1 Done intra_section # 45/92, batch 1/1 Done intra_section # 90/92, batch 1/1 Done intra-section, 46.7725 seconds Begin nonstable-section Done nonstable-LogDemons section # 10/48 Done nonstable-LogDemons section # 15/48 Done nonstable-LogDemons section # 5/48 Done nonstable-LogDemons section # 20/48 Done nonstable-LogDemons section # 25/48 Done nonstable-LogDemons section # 56/48 Done nonstable-LogDemons section # 61/48 Done nonstable-LogDemons section # 71/48 Done nonstable-LogDemons section # 66/48 Done nonstable-section, 167.8896 seconds Begin inter-section ... Done data prep Done loop #1/3 Done loop #2/3 Done loop #3/3 Done inter-section, 417.6008 seconds Begin final computation of translation score computed score of frame #200/500 computed score of frame #50/500 computed score of frame #250/500 computed score of frame #100/500 computed score of frame #300/500 computed score of frame #150/500 computed score of frame #350/500 computed score of frame #400/500 computed score of frame #450/500 computed score of frame #500/500 Done frame reg, total time: 426.6846 seconds Warning: Ignoring the version specified. The version flag is not required when using the '-append' flag. In min1pipe (line 115) Done noise suppression, time 10.3753 Estimating the noise power for each pixel from a simple PSD estimate... done Done randomized seeds init Elapsed time is 1.280880 seconds. Done coarse selection, 2.0814 seconds Done refinement, 2.7068 seconds Done #3/28 Done #6/28 Done #9/28 Done #3/28 Done #6/28 Done #9/28 Done #12/28 Done #15/28 Done #18/28 Done pix select, time: 7.4459 seconds Done init, use 0.10131 seconds Done BPDN, use 5.654 seconds Done postprocessing, use 6.7172 seconds Done refine roi, total time: 6.7175 seconds 2 out of 28 components updated 6 out of 28 components updated 11 out of 28 components updated 28 out of 28 components updated 1 out of 28 components updated 4 out of 28 components updated 12 out of 28 components updated 28 out of 28 components updated Done refine sig, 1.0509 seconds Done merge roi, 0.28087 seconds Done init, use 0.063251 seconds Done BPDN, use 4.2518 seconds Done postprocessing, use 5.0142 seconds Done refine roi, total time: 5.0146 seconds 1 out of 28 components updated 6 out of 28 components updated 12 out of 28 components updated 28 out of 28 components updated Done refine sig, 21.1915 seconds Error using interp1>reshapeAndSortXandV (line 438) X must be a vector.

Error in interp1 (line 128) [X,V,orig_size_v] = reshapeAndSortXandV(X,V);

Error in get_trans_score (line 91) acorr(idss) = interp1(ids, acorr(ids), idss, 'pchip', 'extrap');

Error in logdemons_unit (line 52) sco = get_trans_score(cat(3, imref, imcur), [], [], [], mq, maskc);

Error in min1pipe (line 179) [img, sx, sy] = logdemons_unit(imref, imcur);

[JinghaoLu]

Hi Alexis, thanks for the question. You are right, this does not seem to be toolbox related. I would suggest setting a breakpoint at for example line 29 in function get_trans_score, and then see what causes the loop (line 36-86) to throw an error so that it runs into line 88+, the makeup interpolation part. You can set the breakpoint and rerun the code, with all the selections to be "N" (no need to rerun the most part of the algorithm). Or since this is just a video of 500 frames, you can send it to me then I can take a look at what is wrong.

[alexisfaure77]

Dear,

Thank you for your quick response. We debug this with a colleague and it seems that it was licence issue.

Error was not that clear, but it seems to be only an absence of image processing toolbox licence (because we share licence at institute) that cause the bug.

If this was not eventually the case, I would comme back to you

Thank you again

Alexis

De: "JinghaoLu" notifications@github.com À: "JinghaoLu/MIN1PIPE" MIN1PIPE@noreply.github.com Cc: "Alexis Faure" alexis.faure@universite-paris-saclay.fr, "Author" author@noreply.github.com Envoyé: Vendredi 22 Janvier 2021 16:25:42 Objet: Re: [JinghaoLu/MIN1PIPE] issue with 1D interpolation function (#50)

Hi Alexis, thanks for the question. You are right, this does not seem to be toolbox related. I would suggest setting a breakpoint at for example line 29 in function get_trans_score, and then see what causes the loop (line 36-86) to throw an error so that it runs into line 88+, the makeup interpolation part. You can set the breakpoint and rerun the code, with all the selections to be "N" (no need to rerun the most part of the algorithm). Or since this is just a video of 500 frames, you can send it to me then I can take a look at what is wrong.

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Alexis FAURE

Institut des Neurosciences Paris-Saclay (NeuroPSI) UMR9197 Université Paris-Saclay / CNRS

Cognitive & Network Neuroscience (CNN)

Neurobiology of Decision-making team

Université Paris-Sud, building 446 or 430

91405 Orsay, France

Phone: 01 69 15 68 30

http://neuro-psi.cnrs.fr/spip.php?article133