Issue while importing h5 files..

[Marcelobot]

Hello,

My issue seem quite similar to this one: https://github.com/sgoldenlab/simba/issues/66

I cannot import h5 Files into my created SimBA project while i recieve the following in the Terminal:

What does taht actually mean "Cannot locate video oxt10_190728_165111_s_TRIMMcroppedDLC_dlcrnetms5_Full_Videos_David_MA_1Nov25shuffle1_50000_bx.h5 in mp4 or avi format"

The Video has definitely been stored correctly only a few clicks before. Ive checked the videoname - its the same as in the h5 file.. Ive also tried less complicated and short names like "animal_1" but the problem is the same..

What can i do? Have to present results on monday :S

But thank you for your support! Cheers :-)

[sronilsson]

Hi @Marcelobot!

This, I think, was addressed in a recent update, and was due to DLC changing the filename conventions a bit. Can you make sure you are running the most recent version of SimBA and try again?

I think the most recent version is 0.88.1. So run `pip install simba-uw-tf-dev==0.88.1" and let me know if that fixes it?

[Marcelobot]

Thank you very much for your immediate answer - appreciate it!

It worked out, ive quickly tried out all nessesary options and its looking good - except: feature extraction throws me an error: "Pose-estimation body part setting for feature extraction: 16 0 Extracting features from 1 files... Processing "oxt10_190728_165111_s_TRIMMcropped". Fps: 29.0. mm/ppx: 0.8162450612408017 Evaluating convex hulls... ("qhull precision warning: \nThe initial hull is narrow (cosine of min. angle is 1.0000000000000000).\nIs the input lower dimensional (e.g., on a plane in 3-d)? Qhull may\nproduce a wide facet. Options 'QbB' (scale to unit box) or 'Qbb' (scale\nlast coordinate) may remove this warning. Use 'Pp' to skip this warning.\nSee 'Limitations' in qh-impre.htm.\nQH6114 qhull precision error: initial simplex is not convex. Distance=0\n\nWhile executing: | qhull i Qt\nOptions selected for Qhull 2015.2.r 2016/01/18:\n run-id 1895525931 incidence Qtriangulate _pre-merge _zero-centrum\n _max-width 2e+02 Error-roundoff 1.7e-13 _one-merge 8.7e-13\n _near-inside 4.4e-12 Visible-distance 3.5e-13 U-coplanar-distance 3.5e-13\n Width-outside 7e-13 _wide-facet 2.1e-12 _narrow-hull 0\n\nprecision problems (corrected unless 'Q0' or an error)\n 1 flipped facets\n\nThe input to qhull appears to be less than 2 dimensional, or a\ncomputation has overflowed.\n\nQhull could not construct a clearly convex simplex from points:\n- p2(v2): 0 0\n- p1(v1): 1.6e+02 2e+02\n- p0(v0): 0 0\n\nThe center point is coplanar with a facet, or a vertex is coplanar\nwith a neighboring facet. The maximum round off error for\ncomputing distances is 1.7e-13. The center point, facets and distances\nto the center point are as follows:\n\ncenter point 54 68\n\nfacet p1 p0 distance= -7.1e-15\nfacet p2 p0 distance= -86\nfacet p2 p1 distance= -7.1e-15\n\nThese points either have a maximum or minimum x-coordinate, or\nthey maximize the determinant for k coordinates. Trial points\nare first selected from points that maximize a coordinate.\n\nThe min and max coordinates for each dimension are:\n 0: 0 162 difference= 162\n 1: 0 204 difference= 204\n\nIf the input should be full dimensional, you have several options that\nmay determine an initial simplex:\n - use 'QJ' to joggle the input and make it full dimensional\n - use 'QbB' to scale the points to the unit cube\n - use 'QR0' to randomly rotate the input for different maximum points\n - use 'Qs' to search all points for the initial simplex\n - use 'En' to specify a maximum roundoff error less than 1.7e-13.\n - trace execution with 'T3' to see the determinant for each point.\n\nIf the input is lower dimensional:\n - use 'QJ' to joggle the input and make it full dimensional\n - use 'Qbk:0Bk:0' to delete coordinate k from the input. You should\n pick the coordinate with the least range. The hull will have the\n correct topology.\n - determine the flat containing the points, rotate the points\n into a coordinate plane, and delete the other coordinates.\n - add one or more points to make the input full dimensional.\n", 'occurred at index 2657') ERROR: For more information, go to https://github.com/sgoldenlab/simba/blob/SimBA_no_TF/docs/FAQ.md#i-get-a-qhull-eg-qh6154-or-6013-error-when-extracting-the-features"

Do you have any idea?

Cheers!

[Marcelobot]

Following the mentioned link within the Error there is written, that it could happen, when an animal is missing for a few seconds.

Can i fix it by using the "interpolation" when importing tracking files?

Cheers

[Marcelobot]

Even the last mentioned ERROR is fixed now - Ive quickly fixed it by using the interpolation function.

More sustainable Ill try to even more improve the labeling perfomance of my DLC project.

Thanks - can be closed :)

All the best!

[Marcelobot]

Hello im Sorry but its just one week later and I recieve again that error while importing H5 files..

Tomorrow again I have to present results.. Would be great If you could give me a quick advice - ive followed your last advice and updated Simba to version 0.88.1 - is there a newer Version? Is may an Update again the solution?

Cheers! Just a quick answer please :)