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🐜🐀🐒🚶 A toolkit for robust markerless 3D pose estimation

Home Page: http://anipose.org

License: BSD 2-Clause "Simplified" License

Python 64.66% Shell 0.03% HTML 5.33% JavaScript 26.63% CSS 3.34%

3d-tracking 2d-tracking calibration deeplabcut deep-learning anipose animals 3d markerless

anipose's Introduction

Anipose

Anipose is an open-source toolkit for robust, markerless 3D pose estimation of animal behavior from multiple camera views. It leverages the machine learning toolbox DeepLabCut to track keypoints in 2D, then triangulates across camera views to estimate 3D pose.

Check out the Anipose paper for more information.

The name Anipose comes from Animal Pose, but it also sounds like "any pose".

Documentation

Up to date documentation may be found at anipose.org .

Demos

Videos of flies by Evyn Dickinson (slowed 5x), Tuthill Lab

Videos of hand by Katie Rupp

References

Here are some references for DeepLabCut and other things this project relies upon:

Mathis et al, 2018, "DeepLabCut: markerless pose estimation of user-defined body parts with deep learning"
Romero-Ramirez et al, 2018, "Speeded up detection of squared fiducial markers"

anipose's People

Contributors

Stargazers

Watchers

anipose's Issues

label-3d Version Conflict

Hi guys,
After anipose analyze, filter, calibrate and triangulate I wanted to label 2d and 3d videos. 2d videos worked fine, but label-3d seemed to have a pkg_resource.ContextualVersionConflict with pyface.
Downgrading from pyface==7.0.1 to pyface==6.1.2 solved the problem, and 3d video looks great.
Thank you for these awesome tools.

Error with Calibration: TypeError: 'NoneType' object is not subscriptable

Hi,

I am having a problem with calibration and attached the output of anipose calibrate below:
Thank you

D:\workspac_deepcut\local_DLC\FN 10-02-2020 - Short Clip-Chrissy-2020-10-08\videos\anipose_test\test1\calibration\TEST5-20201117T115653-115904_cam5.mp4
100%|████████████████████████████| 3960/3960 [00:35<00:00, 112.75it/s]
841 boards detected
defaultdict(<class 'int'>, {})
Traceback (most recent call last):
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\rahmank\AppData\Local\Continuum\anaconda3\envs\anipose\Scripts\anipose.exe_main.py", line 7, in
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 829, in call
return self.main(*args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 782, in main
rv = self.invoke(ctx)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 610, in invoke
return callback(*args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\decorators.py", line 73, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 610, in invoke
return callback(*args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\anipose.py", line 115, in calibrate
calibrate_all(config)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\common.py", line 168, in fun
return process_all(config, process_session, **args)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\common.py", line 125, in process_all
output[()] = process_session(config, pipeline_prefix, **args)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\calibrate.py", line 187, in process_session
verbose=True)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\aniposelib\cameras.py", line 1560, in calibrate_rows
rvecs, tvecs = get_initial_extrinsics(rtvecs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\aniposelib\utils.py", line 173, in get_initial_extrinsics
pairs = find_calibration_pairs(graph, source=0)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\aniposelib\utils.py", line 156, in find_calibration_pairs
for new in graph[item]:
TypeError: 'NoneType' object is not subscriptable

anipose calibrate - error: input matrix must be 1x3, 3x1 or 3x3 in function cvRodigrues2

Describe the bug
When trying 'anipose calibrate' on my movies I get the error message 'input matrix must be 1x3, 3x1 or 3x3 in function cvRodigrues2'.
I use three calibration movies cropped from one camera view. Two views are cropped and flipped since they're via mirrors, the center is only cropped.

I have the feeling this is an opencv version issue, but I'm really not sure.

Another issue is the low number of detected boards. I will take new movies with more boards, but I hope to first solve this issue. (Except of course when this is potentially an issue of low number of boars)

Error:

(DLC-GPU) D:\DLC\Trial_Loes_mirrors>anipose calibrate
Calibrating...
D:\DLC\Trial_Loes_mirrors\experiment 200526
D:\DLC\Trial_Loes_mirrors\experiment 200526\calibration\calibration.toml
defaultdict(<class 'int'>,
            {('A', 'B'): 54,
             ('B', 'A'): 54,
             ('B', 'C'): 73,
             ('C', 'B'): 73})
c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\numpy\core\fromnumeric.py:3118: RuntimeWarning: Mean of empty slice.
  out=out, **kwargs)
c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\numpy\core\_methods.py:85: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\Anaconda3\envs\DLC-GPU\Scripts\anipose.exe\__main__.py",
line 7, in <module>
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\click\core.py",
line 829, in __call__
    return self.main(*args, **kwargs)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\click\core.py",
line 782, in main
    rv = self.invoke(ctx)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\click\core.py",
line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\click\core.py",
line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\click\core.py",
line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\click\decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\click\core.py",
line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\anipose\anipose.py", line 115, in calibrate
    calibrate_all(config)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\anipose\common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\anipose\common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\anipose\calibrate.py", line 187, in process_session
    verbose=True)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\aniposelib\cameras.py", line 1560, in calibrate_rows
    rvecs, tvecs = get_initial_extrinsics(rtvecs)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\aniposelib\utils.py", line 174, in get_initial_extrinsics
    extrinsics = compute_camera_matrices(rtvecs, pairs)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\aniposelib\utils.py", line 167, in compute_camera_matrices
    ext = get_transform(rtvecs, b, a)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\aniposelib\utils.py", line 78, in get_transform
    M_mean = mean_transform_robust(L, M_mean, error=0.1)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\aniposelib\utils.py", line 60, in mean_transform_robust
    return mean_transform(M_list_robust)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\aniposelib\utils.py", line 48, in mean_transform
    return make_M(rvec, tvec)
  File "c:\programdata\anaconda3\envs\dlc-gpu\lib\site-packages\aniposelib\utils.py", line 11, in make_M
    rotmat, _ = cv2.Rodrigues(rvec)
cv2.error: OpenCV(3.4.9) C:\projects\opencv-python\opencv\modules\calib3d\src\calibration.cpp:292: error: (-201:Incorrect size of input array) Input matrix must
 be 1x3, 3x1 or 3x3 in function 'cvRodrigues2'

Desktop (please complete the following information):

OS: Win7 (SP1) 64bits
ipython 7.13.0
conda 4.8.2
opencv 3.4.9
anipose 0.8.1
Xeon W2123
32 GB
RTX2080Ti

the use of separate trained networks for each camera

Hello,
I looked at the data set; ‘anipose-shared: hand-demo’ of the anipose tutorial (great, thank you for this!) and I noticed one network was trained on all views/cameras. I was wondering if it is also possible to use separate trained networks for each camera?
Best regards,
Maud

numba.core.errors.ConstantInferenceError: Failed in nopython mode pipeline

Describe the bug

(anipose) anipose[0]$  anipose calibrate
Calibrating...
/home/jon/data/2020-08_large-3d-maze/2020-08-19_3d-camera-calibration/anipose/dlc-hand
/home/jon/data/2020-08_large-3d-maze/2020-08-19_3d-camera-calibration/anipose/calibration/calibration.toml
/home/jon/data/2020-08_large-3d-maze/2020-08-19_3d-camera-calibration/anipose/calibration/cam-0_2020-08-20T15_56_14.avi
100%|█████████████████████████████| 9471/9471 [05:07<00:00, 30.80it/s]
6930 boards detected
/home/jon/data/2020-08_large-3d-maze/2020-08-19_3d-camera-calibration/anipose/calibration/cam-1_2020-08-20T15_56_14.avi
100%|█████████████████████████████| 9471/9471 [05:14<00:00, 30.11it/s]
6996 boards detected
/home/jon/data/2020-08_large-3d-maze/2020-08-19_3d-camera-calibration/anipose/calibration/cam-2_2020-08-20T15_56_14.avi
100%|█████████████████████████████| 9470/9470 [05:29<00:00, 28.72it/s]
7090 boards detected
/home/jon/data/2020-08_large-3d-maze/2020-08-19_3d-camera-calibration/anipose/calibration/cam-3_2020-08-20T15_56_14.avi
100%|█████████████████████████████| 9471/9471 [05:33<00:00, 28.38it/s]
7392 boards detected
/home/jon/data/2020-08_large-3d-maze/2020-08-19_3d-camera-calibration/anipose/calibration/cam-4_2020-08-20T15_56_14.avi
100%|█████████████████████████████| 9470/9470 [05:49<00:00, 27.09it/s]
8372 boards detected
defaultdict(<class 'int'>,
            {('0', '1'): 5885,
             ('0', '2'): 5681,
             ('0', '3'): 6490,
             ('0', '4'): 6768,
             ('1', '0'): 5885,
             ('1', '2'): 6042,
             ('1', '3'): 6255,
             ('1', '4'): 6854,
             ('2', '0'): 5681,
             ('2', '1'): 6042,
             ('2', '3'): 6257,
             ('2', '4'): 6976,
             ('3', '0'): 6490,
             ('3', '1'): 6255,
             ('3', '2'): 6257,
             ('3', '4'): 7315,
             ('4', '0'): 6768,
             ('4', '1'): 6854,
             ('4', '2'): 6976,
             ('4', '3'): 7315})
Traceback (most recent call last):
  File "/home/jon/anaconda3/envs/anipose/bin/anipose", line 33, in <module>
    sys.exit(load_entry_point('anipose', 'console_scripts', 'anipose')())
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/anipose.py", line 115, in calibrate
    calibrate_all(config)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/calibrate.py", line 187, in process_session
    verbose=True)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 1564, in calibrate_rows
    error = self.bundle_adjust_iter(imgp, extra, verbose=verbose, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 681, in bundle_adjust_iter
    error = self.average_error(p2ds, median=True)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 1528, in average_error
    errors = self.reprojection_error(p3ds, p2ds, mean=True)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/numba/core/dispatcher.py", line 427, in _compile_for_args
    error_rewrite(e, 'constant_inference')
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/numba/core/dispatcher.py", line 358, in error_rewrite
    reraise(type(e), e, None)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/numba/core/utils.py", line 80, in reraise
    raise value.with_traceback(tb)
numba.core.errors.ConstantInferenceError: Failed in nopython mode pipeline (step: nopython rewrites)
Constant inference not possible for: getattr(value=$const92.1, attr=format)

File "../../../../anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 632:
    def reprojection_error(self, p3ds, p2ds, mean=False):
        <source elided>
            "shapes of 2D and 3D points are not consistent: " \
            "2D={}, 3D={}".format(p2ds.shape, p3ds.shape)
            ^


File "../../../../anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 632:
    def reprojection_error(self, p3ds, p2ds, mean=False):
        <source elided>
            "shapes of 2D and 3D points are not consistent: " \
            "2D={}, 3D={}".format(p2ds.shape, p3ds.shape)

Seems to be another issue with numba (or use of numba), like my last submitted issue.

Desktop (please complete the following information):

OS: Ubuntu 18.04

calibration_init.toml not found?

Hi, I'm trying to setup anipose for tracking, and I run into an issue when using "anipose calibrate" - it can't find the calibration_init.toml file. I could not find an example of such a file in the repository, what is it's exact role?

Thanks

How can i fix the error about OpenGL.

When i run command 'anipose label-3d', i encountered an error that cannot create GLX context.

My development environment is as follow.
OS: Ubuntu 16.04
GPU: RTX 2080 Ti
I'm using 'ssh -Y remoteserver' in terminal

please let me know if you need more information about my environment.

Triangulation

Hello,
A few weeks ago, i was asking about the triangulation method you were using. To which you answered using RANSAC and least-means-square method (i suppose it's getting the point minimising the reprojections?).

I tried to look again into your code and the function called when the ransac flag is set (triangulate_ransac) does seem to only reformat the entry. Also in your function (triangulate_simple) you are using the svd method to solve the triangulation, though my mathematical background isn't advanced enough to be sure of what is beeing done exactly. Is that triangulating optimaly given all the cameras intrinsic and extrinsic matrix and the 2d points for each one?

Could you give me some explaination of the strategy beeing used there ?

I did try to use your pipeline in order to triangulate from multiple cameras. I annotated 51 frames on 5 cameras using deeplabcut. The triangulation from 5 of the cameras with reprojection onto the others helped me annotating 51 frames for a total 11 cameras. (which have been calibrated with the charuco method which led to weird intrinsec parameters, though they were the best qualitative reprojection i could see while proceding on a few reprojections of the pattern using opencv triangulation (by pair)). The reprojection was quite impressive and most of the time, only a few modifications were required.

After proceding to the few corrections of the annotations, i wanted to proceed on triangulating then reprojecting every view together in order to train a robust network using deeplabcut.

Unfortunnately, results are quite random and i have absolutely no idea how to fix it.
https://www.pixenli.com/image/lzSAoGAq

I'll let you the anipose pipeline i used to triangulate and the results i got.
https://we.tl/t-MsJF3ki9sG

Though the triangulation with five cameras (1,2,7,9,12) was working pretty well and was computed in less than 4 seconds, the calibration with 11 cameras took arround 4 minutes on the same computer.

PS: the camera 5 has been erased as the camera was never able to see the hand on the videos i have, the configuration file has been adapted consequently.

Thank you a lot for you work once again !

EDIT
I continued my research in order to isolate the problem. There seem to be an issue when using up to 10 cameras, it seems to work fine :
Exemple using : cam [1,2,3,4,6,7,8,9,10,12] and [1,2,3,4,6,7,8,9,11,12]

Though as soon as i'm using 11 cameras together, the results became messy and is not usable at all

How to set reference plane in 3d video

I am running a project with several sessions to triangulate human faces, and the final 3d videos (and combined videos) are upside down, and also inconsistently rotated between session, although 2d videos have all the same orientation.
Is there any setting in label_videos_3d.py or label_combined.py to set specific markers or even a specific plane in the 3D space to rotate the final 3d videos to a common orientation?

Converting calibration from Simi

How to convert Simi calibration to Anipose or anipose-lib?

This is a continuation of the issue initially posted by @SjoerdBruijn at #15 (comment)

calibration charuco

Hello again!

i was able to try to use a set of 12 videos from 12 cameras disposed arround a cube. As Charuco is robust to occlusion, i tried to calibrate all the cameras directly, though i came some issue:

I'm getting the following output (for the sake of simplicity, i just putted a few cameras):

[cam_0]
name = "1"
size = [ 1920, 1080,]
matrix = [ [ 1352.881831286193, 0.0, 959.5,], [ 0.0, 1352.881831286193, 539.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ 0.06123193869724274, 0.0, 0.0, 0.0, 0.0,]
rotation = [ -0.9187013796846374, -0.1314637697651443, -0.01424130024745966,]
translation = [ -5.619613368346561, -657.6452591254599, -581.905597021176,]


[cam_4]
name = "2"
size = [ 1920, 1080,]
matrix = [ [ 1438.070128521826, 0.0, 959.5,], [ 0.0, 1438.070128521826, 539.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ 0.2796506087772396, 0.0, 0.0, 0.0, 0.0,]
rotation = [ -0.7143773130873536, 1.382841802203809, 0.4807818109132332,]
translation = [ -675.5911522271351, -558.2044612932817, 62.95864975515903,]

[cam_10]
name = "8"
size = [ 1920, 1080,]
matrix = [ [ 1145.838629150258, 0.0, 959.5,], [ 0.0, 1145.838629150258, 539.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ 0.07663770925150003, 0.0, 0.0, 0.0, 0.0,]
rotation = [ 0.1836874264634381, 0.3578359386120759, 0.6576390160822976,]
translation = [ -442.3095802361823, 29.51957730274389, -757.8845126085191,]

As you can see, the intrinsic parameter have a wide variation especially for the focal. I was wondering if by any chance, there is a way to impose those intrinsic parameters? I'm using intel realsense and i can get the intrinsic parameters by some other way.

Once again, thank you a lot for you time !

Error during calibration

Hi,

when using anipose calibrate I get following error. "detections.pickle" file is created in calibration folder. When I use anipose label-3d after this it shows message "Labeling videos in 3D..." but nothing happens. Nothing is created and there is no error message.

(dlc-windowsGPUclone) D:\Anipose\Test>anipose calibrate Calibrating... D:\Anipose\Test\Iteration1\calibration\calibration.toml Traceback (most recent call last): File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\ProgramData\Anaconda3\envs\dlc-windowsGPUclone\Scripts\anipose.exe\__main__.py", line 9, in <module> File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\click\core.py", line 764, in __call__ return self.main(*args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\click\core.py", line 717, in main rv = self.invoke(ctx) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\click\core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\click\core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\click\core.py", line 555, in invoke return callback(*args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\click\decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\click\core.py", line 555, in invoke return callback(*args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\anipose\anipose.py", line 105, in calibrate calibrate_all(config) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\anipose\common.py", line 165, in fun return process_all(config, process_session, **args) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\anipose\common.py", line 150, in process_all output[past_folders] = process_session(config, path, **args) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\anipose\calibrate.py", line 182, in process_session n_samp_iter=100, n_samp_full=2000) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\calligator\cameras.py", line 1544, in calibrate_rows all_rows[i] = board.estimate_pose_rows(cam, row) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\calligator\boards.py", line 333, in estimate_pose_rows row['ids']) File "c:\programdata\anaconda3\envs\dlc-windowsgpuclone\lib\site-packages\calligator\boards.py", line 611, in estimate_pose_points corners, ids, self.board, K, D) TypeError: Required argument 'rvec' (pos 6) not found

DeepLabCut/Anipose conda env. MacOS [feature request and errors]?

Is your feature request related to a problem? Please describe.

on MacOS, Catalina
conda env with deeplabcut and calligator installed as follows:

DLC-calligator.yaml

# DLC-calligator.yaml 
#
# install: conda env create -f DLC-calligator.yaml 
# update:  conda env update -f DLC-calligator.yaml 

name: DLC-calligator
dependencies:
  - python=3.7
  - pip
  - jupyter
  - nb_conda
  - tensorflow==1.13.1
  - wxpython
  - Shapely
  - pip:
    - deeplabcut
    - calligator

Error:
When trying to install anipose with pip inside this env, there are issues with installing lapsolver:

mwmathis@Mackenzies-MacBook-Pro Desktop % pip install anipose
Collecting anipose
  Using cached anipose-0.6.6-py3-none-any.whl (54 kB)
Collecting scikit-video
  Using cached scikit_video-1.1.11-py2.py3-none-any.whl (2.3 MB)
Requirement already satisfied: calligator>=0.3.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (0.3.2)
Requirement already satisfied: opencv-python in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (3.4.9.31)
Requirement already satisfied: scipy in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (1.4.1)
Requirement already satisfied: tqdm in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (4.43.0)
Requirement already satisfied: pandas in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (1.0.1)
Requirement already satisfied: click in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (7.0)
Requirement already satisfied: toml in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (0.10.0)
Requirement already satisfied: numpy in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (1.16.4)
Requirement already satisfied: deeplabcut>=2.0.4.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from anipose) (2.1.6.2)
Collecting lapsolver>=1.0.2
  Using cached lapsolver-1.1.0.tar.gz (261 kB)
Requirement already satisfied: pillow in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from scikit-video->anipose) (7.0.0)
Requirement already satisfied: numba in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from calligator>=0.3.2->anipose) (0.48.0)
Requirement already satisfied: opencv-contrib-python~=3.4 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from calligator>=0.3.2->anipose) (3.4.9.31)
Requirement already satisfied: python-dateutil>=2.6.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from pandas->anipose) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from pandas->anipose) (2019.3)
Requirement already satisfied: scikit-learn in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.22.2.post1)
Requirement already satisfied: tensorpack>=0.9.7.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.9.9)
Requirement already satisfied: six in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (1.14.0)
Requirement already satisfied: setuptools in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (45.2.0.post20200210)
Requirement already satisfied: chardet in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (3.0.4)
Requirement already satisfied: ipython in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (7.12.0)
Requirement already satisfied: wheel in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.34.2)
Requirement already satisfied: ruamel.yaml~=0.15 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.16.10)
Requirement already satisfied: easydict in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (1.9)
Requirement already satisfied: moviepy in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (1.0.1)
Requirement already satisfied: h5py~=2.7 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (2.10.0)
Requirement already satisfied: tables in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (3.6.1)
Requirement already satisfied: scikit-image in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.16.2)
Requirement already satisfied: patsy in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.5.1)
Requirement already satisfied: statsmodels in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.11.1)
Requirement already satisfied: certifi in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (2019.11.28)
Requirement already satisfied: imgaug in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.4.0)
Requirement already satisfied: pyyaml>=5.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (5.3)
Requirement already satisfied: requests in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (2.23.0)
Requirement already satisfied: matplotlib==3.0.3 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (3.0.3)
Requirement already satisfied: ipython-genutils in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (0.2.0)
Requirement already satisfied: intel-openmp in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from deeplabcut>=2.0.4.1->anipose) (2019.0)
Requirement already satisfied: llvmlite<0.32.0,>=0.31.0dev0 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from numba->calligator>=0.3.2->anipose) (0.31.0)
Requirement already satisfied: joblib>=0.11 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from scikit-learn->deeplabcut>=2.0.4.1->anipose) (0.14.1)
Requirement already satisfied: tabulate>=0.7.7 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut>=2.0.4.1->anipose) (0.8.6)
Requirement already satisfied: psutil>=5 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut>=2.0.4.1->anipose) (5.7.0)
Requirement already satisfied: msgpack>=0.5.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut>=2.0.4.1->anipose) (1.0.0)
Requirement already satisfied: pyzmq>=16 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut>=2.0.4.1->anipose) (18.1.1)
Requirement already satisfied: termcolor>=1.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut>=2.0.4.1->anipose) (1.1.0)
Requirement already satisfied: msgpack-numpy>=0.4.4.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from tensorpack>=0.9.7.1->deeplabcut>=2.0.4.1->anipose) (0.4.4.3)
Requirement already satisfied: traitlets>=4.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (4.3.3)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (3.0.3)
Requirement already satisfied: jedi>=0.10 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (0.16.0)
Requirement already satisfied: backcall in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (0.1.0)
Requirement already satisfied: pickleshare in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (0.7.5)
Requirement already satisfied: appnope; sys_platform == "darwin" in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (0.1.0)
Requirement already satisfied: decorator in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (4.4.1)
Requirement already satisfied: pexpect; sys_platform != "win32" in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (4.8.0)
Requirement already satisfied: pygments in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ipython->deeplabcut>=2.0.4.1->anipose) (2.5.2)
Requirement already satisfied: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9" in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from ruamel.yaml~=0.15->deeplabcut>=2.0.4.1->anipose) (0.2.0)
Requirement already satisfied: proglog<=1.0.0 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from moviepy->deeplabcut>=2.0.4.1->anipose) (0.1.9)
Requirement already satisfied: imageio<3.0,>=2.5; python_version >= "3.4" in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from moviepy->deeplabcut>=2.0.4.1->anipose) (2.8.0)
Requirement already satisfied: imageio-ffmpeg>=0.2.0; python_version >= "3.4" in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from moviepy->deeplabcut>=2.0.4.1->anipose) (0.4.1)
Requirement already satisfied: numexpr>=2.6.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from tables->deeplabcut>=2.0.4.1->anipose) (2.7.1)
Requirement already satisfied: networkx>=2.0 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from scikit-image->deeplabcut>=2.0.4.1->anipose) (2.4)
Requirement already satisfied: PyWavelets>=0.4.0 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from scikit-image->deeplabcut>=2.0.4.1->anipose) (1.1.1)
Requirement already satisfied: Shapely in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from imgaug->deeplabcut>=2.0.4.1->anipose) (1.6.4.post2)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from requests->deeplabcut>=2.0.4.1->anipose) (1.25.8)
Requirement already satisfied: idna<3,>=2.5 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from requests->deeplabcut>=2.0.4.1->anipose) (2.9)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from matplotlib==3.0.3->deeplabcut>=2.0.4.1->anipose) (1.1.0)
Requirement already satisfied: cycler>=0.10 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from matplotlib==3.0.3->deeplabcut>=2.0.4.1->anipose) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from matplotlib==3.0.3->deeplabcut>=2.0.4.1->anipose) (2.4.6)
Requirement already satisfied: wcwidth in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->deeplabcut>=2.0.4.1->anipose) (0.1.8)
Requirement already satisfied: parso>=0.5.2 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from jedi>=0.10->ipython->deeplabcut>=2.0.4.1->anipose) (0.6.1)
Requirement already satisfied: ptyprocess>=0.5 in /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages (from pexpect; sys_platform != "win32"->ipython->deeplabcut>=2.0.4.1->anipose) (0.6.0)
Building wheels for collected packages: lapsolver
  Building wheel for lapsolver (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py'"'"'; __file__='"'"'/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-wheel-2gzfjn4b
       cwd: /private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/
  Complete output (77 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-x86_64-3.7
  creating build/lib.macosx-10.9-x86_64-3.7/lapsolver
  copying lapsolver/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver
  creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
  copying lapsolver/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
  copying lapsolver/tests/test_files.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
  copying lapsolver/tests/test_dense.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
  running egg_info
  writing lapsolver.egg-info/PKG-INFO
  writing dependency_links to lapsolver.egg-info/dependency_links.txt
  writing top-level names to lapsolver.egg-info/top_level.txt
  reading manifest file 'lapsolver.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  writing manifest file 'lapsolver.egg-info/SOURCES.txt'
  creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/data
  creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs0.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs1.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs10.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs2.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs3.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs4.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs5.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs6.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs7.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs8.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  copying lapsolver/data/dense/costs9.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
  creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/etc
  copying lapsolver/etc/benchmark-dtype-int.png -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/etc
  copying lapsolver/etc/benchmark-dtype-numpy.float32.png -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/etc
  running build_ext
  Traceback (most recent call last):
    File "/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py", line 22, in run
      out = subprocess.check_output(['cmake', '--version'])
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 411, in check_output
      **kwargs).stdout
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 488, in run
      with Popen(*popenargs, **kwargs) as process:
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 800, in __init__
      restore_signals, start_new_session)
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 1551, in _execute_child
      raise child_exception_type(errno_num, err_msg, err_filename)
  FileNotFoundError: [Errno 2] No such file or directory: 'cmake': 'cmake'
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py", line 88, in <module>
      keywords='hungarian munkres kuhn linear-sum-assignment bipartite-graph lap'
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages/setuptools/__init__.py", line 144, in setup
      return distutils.core.setup(**attrs)
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/core.py", line 148, in setup
      dist.run_commands()
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 966, in run_commands
      self.run_command(cmd)
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 223, in run
      self.run_command('build')
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/command/build.py", line 135, in run
      self.run_command(cmd_name)
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/cmd.py", line 313, in run_command
      self.distribution.run_command(command)
    File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 985, in run_command
      cmd_obj.run()
    File "/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py", line 25, in run
      ", ".join(e.name for e in self.extensions))
  RuntimeError: CMake must be installed to build the following extensions: lapsolverc
  ----------------------------------------
  ERROR: Failed building wheel for lapsolver
  Running setup.py clean for lapsolver
Failed to build lapsolver
Installing collected packages: scikit-video, lapsolver, anipose
    Running setup.py install for lapsolver ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py'"'"'; __file__='"'"'/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-record-ppsvuzrf/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/include/python3.7m/lapsolver
         cwd: /private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/
    Complete output (79 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.7
    creating build/lib.macosx-10.9-x86_64-3.7/lapsolver
    copying lapsolver/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver
    creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
    copying lapsolver/tests/__init__.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
    copying lapsolver/tests/test_files.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
    copying lapsolver/tests/test_dense.py -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/tests
    running egg_info
    writing lapsolver.egg-info/PKG-INFO
    writing dependency_links to lapsolver.egg-info/dependency_links.txt
    writing top-level names to lapsolver.egg-info/top_level.txt
    reading manifest file 'lapsolver.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'lapsolver.egg-info/SOURCES.txt'
    creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/data
    creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs0.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs1.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs10.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs2.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs3.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs4.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs5.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs6.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs7.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs8.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    copying lapsolver/data/dense/costs9.npz -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/data/dense
    creating build/lib.macosx-10.9-x86_64-3.7/lapsolver/etc
    copying lapsolver/etc/benchmark-dtype-int.png -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/etc
    copying lapsolver/etc/benchmark-dtype-numpy.float32.png -> build/lib.macosx-10.9-x86_64-3.7/lapsolver/etc
    running build_ext
    Traceback (most recent call last):
      File "/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py", line 22, in run
        out = subprocess.check_output(['cmake', '--version'])
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 411, in check_output
        **kwargs).stdout
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 488, in run
        with Popen(*popenargs, **kwargs) as process:
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 800, in __init__
        restore_signals, start_new_session)
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/subprocess.py", line 1551, in _execute_child
        raise child_exception_type(errno_num, err_msg, err_filename)
    FileNotFoundError: [Errno 2] No such file or directory: 'cmake': 'cmake'
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py", line 88, in <module>
        keywords='hungarian munkres kuhn linear-sum-assignment bipartite-graph lap'
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages/setuptools/__init__.py", line 144, in setup
        return distutils.core.setup(**attrs)
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run
        return orig.install.run(self)
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/command/install.py", line 545, in run
        self.run_command('build')
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/Users/mwmathis/opt/anaconda3/envs/DLC-anipose/lib/python3.7/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py", line 25, in run
        ", ".join(e.name for e in self.extensions))
    RuntimeError: CMake must be installed to build the following extensions: lapsolverc
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py'"'"'; __file__='"'"'/private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-install-_qt4q6_o/lapsolver/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/ct/4w_vk2wn10xb_xj2fm7d6vqc0000gn/T/pip-record-ppsvuzrf/install-record.txt --single-version-externally-managed --compile --install-headers /Users/mwmathis/opt/anaconda3/envs/DLC-anipose/include/python3.7m/lapsolver Check the logs for full command output.
(DLC-anipose) mwmathis@Mackenzies-MacBook-Pro Desktop %

I also noticed that there is a bit of an issue with the 3 packages, such that order of operation matters a bit, which is suboptimal: can anipose be pinged to 'opencv-python~=3.4'?
DLC setup requires: 'opencv-python~=3.4'
calligator requires: 'opencv-python~=3.4', 'opencv-contrib-python~=3.4'
anipose just has: 'opencv-python'

calibration-errors results in "Import error cannot import name 'get_board_type'"

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[ENH] ffmpeg + opencv wrapper image processing scripts

I made some image processing scripts to take a raw video with claps in it and synchronize several cameras based on the audio. I'm not sure if there is a better way to do it, but the documentation starts at three synchronized videos so I thought those might be useful to getting unedited video into the anipose format.

Also is anyone maintaining this repository? @lambdaloop @katierupp @tuthill-lab

Triangulation method

Hello,

First of all, thank your for your incredible work. I was looking into your triangulation method though i couldn't really understand it... Could you describe the method you are using to triangulate with multiple views ? Are you using some RANSAC for filtering some bad tracking ?

Thank you a lot for your time

calibration target

Hello!

I have a quick question not regarding the code base, so I apologize if the GitHub issues section is an inappropriate place for me to ask--but I thought a lot of people might find this question relevant, and there seems to be a lot of traction here.

I noticed in your wonderful and detailed preprint that the ChArUco board was manufactured by Applied Image Inc to a very precise level. I was wondering if you guys had any luck with a homemade ChArUco target--e.g. something you might print out and then tape to a little piece of acrylic. Or was purchasing a custom manufactured board necessary?

Back when I was playing around with Anipose (5 months ago now ...) I noticed I was getting pretty good 2D labels from DeepLabCut, but my 3D model looked absolutely horrendous. I suspected it likely had to do with poor triangulation, which might ultimately have been caused by a less than ideal calibration target? My calibration target was relatively janky--I printed it on a sheet of paper and taped it flat to a small piece of acrylic. I then manually waved it about in front of my cameras. My use case is similar, in scale, to yours--the movements of very tiny insects (not flies though).

Do you think such scales necessitate precision-manufactured ChArUco boards?

Thanks!

Notebook not finding cv2

Hi guys,
I'm just testing out anipose, but on a machine without GPU support (so analysis would take forever). So I decided to try the notebook on Google Colab to make use of their GPU acceleration; I've added a few lines in the top, uninstalling opencv-python and installing aniposelib (and for good measure making sure that the opecv-contrib-python is indeed installed), but would think it possible to continue from there.

But I am for some reason getting an error stating that cv2 cannot be found.

Entire error message here:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-3657c5a7600f> in <module>()
      1 import numpy as np
----> 2 from aniposelib.boards import CharucoBoard, Checkerboard
      3 from aniposelib.cameras import Camera, CameraGroup
      4 from aniposelib.utils import load_pose2d_fnames

3 frames
/usr/lib/python3.6/imp.py in find_module(name, path)
    295         break  # Break out of outer loop when breaking out of inner loop.
    296     else:
--> 297         raise ImportError(_ERR_MSG.format(name), name=name)
    298 
    299     encoding = None

ImportError: No module named 'cv2'

I did also notice that the notebook uses Python3.6, but in the docs the conda environment uses 3.7. I don't know if that's valuable, but might be worth checking up.

Thanks for all your work on making anipose, I look very much forward to trying it out in the wild!

Issue installing anipose

Windows 10
Using Anaconda

When I open a terminal in Anaconda to install anipose through pip install i get the following error

ERROR: Command errored out with exit status 1:
command: 'C:\Users\Milestone\Anaconda3\envs\anipose\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\MILEST~~1\AppData\Local\Temp\pip-install-xhsfiply\tables\setup.py'"'"'; file='"'"'C:\Users\MILEST~~1\AppData\Local\Temp\pip-install-xhsfiply\tables\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
cwd: C:\Users\MILEST1\AppData\Local\Temp\pip-install-xhsfiply\tables
Complete output (11 lines):
* Using Python 3.7.4 (default, Aug 9 2019, 18:34:13) [MSC v.1915 64 bit (AMD64)]
* USE_PKGCONFIG: False
* Found HDF5 using system PATH ('C:\Users\Milestone\Anaconda3\Library\bin')
* Found conda env: C:\Users\Milestone\Anaconda3\envs\anipose
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\MILEST1\AppData\Local\Temp\pip-install-xhsfiply\tables\setup.py", line 597, in
hdf5_version = get_hdf5_version(hdf5_header)
File "C:\Users\MILEST~1\AppData\Local\Temp\pip-install-xhsfiply\tables\setup.py", line 350, in get_hdf5_version
major_version = int(re.split("\s*", line)[2])
ValueError: invalid literal for int() with base 10: 'd'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I have tried to update pip but didn't work. Any idea what is happening?

Computer force close remotely

Hi,

Thanks for your great work.

I am using a Ubuntu machine remotely. Currently, I stuck on the tutorial "https://anipose.readthedocs.io/en/latest/tutorial.html", where I run "anipose analyze", it will make my computer force shutdown, so I have to call my friend to go to the lab and open it again.
(anipose) robot1@yifu-x99:~/Shukai/hand-demo-unfilled$ anipose analyze
Analyzing videos...
/mnt/uhdd/shukai/hand-demo-unfilled/2019-08-02/pose-2d/2019-08-02-vid01-camA.h5
WARNING:tensorflow:From /home/robot1/anaconda3/envs/anipose/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
WARNING:tensorflow:From /home/robot1/anaconda3/envs/anipose/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py:263: colocate_with (from tensorflow.python.framework.ops) is deprecated and will be removed in a future version.
Instructions for updating:
Colocations handled automatically by placer.
OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info
OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 0-15
OMP: Info #156: KMP_AFFINITY: 16 available OS procs
OMP: Info #157: KMP_AFFINITY: Uniform topology
OMP: Info #179: KMP_AFFINITY: 1 packages x 8 cores/pkg x 2 threads/core (8 total cores)
OMP: Info #214: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 core 0 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 0 core 0 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 0 core 1 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 0 core 1 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 0 core 2 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 0 core 2 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 0 core 3 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 0 core 3 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 0 core 4 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 12 maps to package 0 core 4 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 0 core 5 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 13 maps to package 0 core 5 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 0 core 6 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 14 maps to package 0 core 6 thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 0 core 7 thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 15 maps to package 0 core 7 thread 1
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18697 thread 0 bound to OS proc set 0
WARNING:tensorflow:From /home/robot1/anaconda3/envs/anipose/lib/python3.7/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
WARNING:tensorflow:From /home/robot1/anaconda3/envs/anipose/lib/python3.7/site-packages/tensorflow/python/training/saver.py:1266: checkpoint_exists (from tensorflow.python.training.checkpoint_management) is deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
0%| | 0/4395 [00:00<?, ?it/s]OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18767 thread 1 bound to OS proc set 1
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18835 thread 2 bound to OS proc set 2
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18836 thread 3 bound to OS proc set 3
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18837 thread 4 bound to OS proc set 4
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18838 thread 5 bound to OS proc set 5
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18839 thread 6 bound to OS proc set 6
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18840 thread 7 bound to OS proc set 7
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18841 thread 8 bound to OS proc set 8
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18842 thread 9 bound to OS proc set 9
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18843 thread 10 bound to OS proc set 10
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18844 thread 11 bound to OS proc set 11
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18845 thread 12 bound to OS proc set 12
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18846 thread 13 bound to OS proc set 13
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18847 thread 14 bound to OS proc set 14
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18848 thread 15 bound to OS proc set 15
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18849 thread 16 bound to OS proc set 0
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18768 thread 17 bound to OS proc set 1
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18850 thread 18 bound to OS proc set 2
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18851 thread 19 bound to OS proc set 3
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18852 thread 20 bound to OS proc set 4
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18853 thread 21 bound to OS proc set 5
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18854 thread 22 bound to OS proc set 6
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18855 thread 23 bound to OS proc set 7
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18856 thread 24 bound to OS proc set 8
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18857 thread 25 bound to OS proc set 9
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18858 thread 26 bound to OS proc set 10
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18859 thread 27 bound to OS proc set 11
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18860 thread 28 bound to OS proc set 12
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18862 thread 30 bound to OS proc set 14
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18861 thread 29 bound to OS proc set 13
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18863 thread 31 bound to OS proc set 15
OMP: Info #250: KMP_AFFINITY: pid 18697 tid 18864 thread 32 bound to OS proc set 0
18%|██████████▋ | 774/4395 [03:26<16:55, 3.57it/s]

It will stuck here, and no matter I use either remote viewer, such as VNC or teamviewer, or run fully on SSH in terminal.

I know it is a tricky problem, any help would be appreciated. If you need further information, I would reply shortly.

Easy entry point for DLC users

Is your feature request related to a problem? Please describe.
Hi @lambdaloop! Thanks for this great package. We are hoping to have better integration with DLC users to DLC (see here: https://github.com/AlexEMG/DeepLabCut/blob/master/docs/Overviewof3D.md#more-than-2-camera-support)

One issue our users are having is an "easy entry" point. Right now, your docs are for setting up 2D then 3D tracking, but many users have the 2D done, and some images they want to calibrate. I really like the merger of DLC + anipose/calligator, so I want to help/ask to make this more seamless.

My understanding of the workflow for you is it requires users to use your file structure, which is a bit rigid. Would it be possible to make docs such that a user could jump in at this point: https://github.com/lambdaloop/anipose/blob/master/docs/github/start_3d.md#calibration-marker-configuration // https://anipose.readthedocs.io/en/latest/tutorial.html#calibrating-the-cameras

i.e. minimally, now after the 3d set up there is no link to your nice "readthedocs.io" demo (https://anipose.readthedocs.io/en/latest/tutorial.html#calibrating-the-cameras)

i.e. a more optimal solution would be: a simple Jupyter Notebook demo such that the person can navigate to their DLC project folder and then set up a simple config file for your system, then be able to run:

anipose calibrate
anipose triangulate
anipose label-3d

Also, for each of these functions, there is (at least I cannot find) any easy to read docstrings. For example, it is not clear what each function requires. (What file type, format, etc is points?)

triangulate(points, undistort=True, progress=False)
Given an CxNx2 array, this returns an Nx3 array of points, where N is the number of points and C is the number of cameras

Describe the solution you'd like
Ideally, one could come in and use your functions (i.e. inhttps://github.com/lambdaloop/calligator, some below) with a clear entry point. i.e.

import anipose (or calligator directly?)

the use your functions: https://calligator.readthedocs.io/en/latest/api.html#module-calligator.boards
anipose calibrate

then your triangulation functions:

anipose triangulate

triangulate(points, undistort=True, progress=False)
Given an CxNx2 array, this returns an Nx3 array of points, where N is the number of points and C is the number of cameras

triangulate_possible(points, undistort=True, min_cams=2, progress=False, threshold=0.5)
Given an CxNxPx2 array, this returns an Nx3 array of points by triangulating all possible points and picking the ones with best reprojection error where: C: number of cameras N: number of points P: number of possible options per point

triangulate_ransac(points, undistort=True, min_cams=2, progress=False)
Given an CxNx2 array, this returns an Nx3 array of points, where N is the number of points and C is the number of cameras

reprojection_error
Given an Nx3 array of 3D points and an CxNx2 array of 2D points, where N is the number of points and C is the number of cameras, this returns an CxNx2 array of errors. Optionally mean=True, this averages the errors and returns array of length N of errors

bundle_adjust_iter(p2ds, extra=None, n_iters=10, start_mu=15, end_mu=1, max_nfev=200, ftol=0.0001, n_samp_iter=100, n_samp_full=1000, error_threshold=0.3, verbose=False)
Given an CxNx2 array of 2D points, where N is the number of points and C is the number of cameras, this performs iterative bundle adjustsment to fine-tune the parameters of the cameras. That is, it performs bundle adjustment multiple times, adjusting the weights given to points to reduce the influence of outliers. This is inspired by the algorithm for Fast Global Registration by Zhou, Park, and Koltun

bundle_adjust(p2ds, extra=None, loss='linear', threshold=50, ftol=0.0001, max_nfev=1000, weights=None, start_params=None, verbose=True)
Given an CxNx2 array of 2D points, where N is the number of points and C is the number of cameras, this performs bundle adjustsment to fine-tune the parameters of the cameras

Describe alternatives you've considered
We have considered making DLC n-camera support, but we would rather not :)

Additional context
Right now the documentation is making this hard for us to guide users

Cheers,
DLC hackathon subgroup "3d, yeah!"

Documentation Errors

While I was trying to use anipose for 3D calibration purposes, I came across a couple things in the current documentation that could be changed to prevent confusion for future users.

In start_3d.md, under the [https://github.com/lambdaloop/anipose/blob/master/docs/start_3d.md#drawing-the-calibration-board(url),
anipose draw_calibration is actually anipose draw-calibration
Also if we're doing 3D projects, turns out because the minimum number of folders are 2 (calibration and videos-raw), I had to set nesting=2 in the config.toml file or none of the code even executes.
If the GPU is being used by something else, like a Jupyter Notebook environment which was idling with DeepLabCut, it threw the following error and stopped me from using anipose.

019-10-29 20:57:14.464694: E tensorflow/stream_executor/cuda/cuda_dnn.cc:334] Could not create cudnn handle: CUDNN_STATUS_ALLOC_FAILED
2019-10-29 20:57:14.467602: E tensorflow/stream_executor/cuda/cuda_dnn.cc:334] Could not create cudnn handle: CUDNN_STATUS_ALLOC_FAILED
Traceback (most recent call last):
File "c:\programdata\anaconda3\envs\dlc_gpu\lib\site-packages\tensorflow\python\client\session.py", line 1334, in _do_call
return fn(*args)
File "c:\programdata\anaconda3\envs\dlc_gpu\lib\site-packages\tensorflow\python\client\session.py", line 1319, in _run_fn
options, feed_dict, fetch_list, target_list, run_metadata)
File "c:\programdata\anaconda3\envs\dlc_gpu\lib\site-packages\tensorflow\python\client\session.py", line 1407, in _call_tf_sessionrun
run_metadata)
tensorflow.python.framework.errors_impl.UnknownError: Failed to get convolution algorithm. This is probably because cuDNN failed to initialize, so try looking to see if a warning log message was printed above.
[[{{node resnet_v1_50/conv1/Conv2D}}]]
[[{{node concat_1}}]]

Thank you for your work!

Is it possible to combine with grid search and cross validation in Anipose toolbox?

Actually, I'm struggling to motion tracking using Anipose toolbox.
Even though I completed all steps, results are not good. so, I'm trying to change the parameters.
below the picture is the what i want to change the parameters.

I read the document in anipose's docs page(https://anipose.readthedocs.io/en/latest/params.html). but I don't understand what they mean.
and even I can understand, I'm likely to find the optimal parameter.
so, I'm trying to combine with gird search and cross validation in Anipose toolbox.

please give me some advice for me. thank you!

Consider using a conda config file for installation

Currently instructions indicate that deeplabcut should be installed as a pip dependency but don't go into how to get a CPU or GPU dlc version. DLC solved this by just making conda config files for both options. I've pasted a conda specification file that I used to install a anipose-modified GPU DLC installation. Might be useful to supply this (along with CPU version that I didn't make) for easy install.

# FIRST: INSTALL CORRECT DRIVER for GPU, see https://stackoverflow.com/questions/30820513/what-is-the-correct-version-of-cuda-for-my-nvidia-driver/30820690
#
# install: conda env create -f anipose.yaml 
# update:  conda env update -f anipose.yaml 
name: anipose
dependencies:
  - python=3.7
  - pip
  - tensorflow-gpu==1.13.1
  - cudnn=7
  - wxpython
  - jupyter
  - nb_conda
  - Shapely
  - ffmpeg
  - mayavi
  - pip:
    - deeplabcut
    - anipose

error during calibration

Hello,
I am using Ubuntu 18.04 and a charuco board to calibrate. I am getting the following error when running anipose calibrate:

(dlc-anipose) hank-x299@hank-x299:~/src/dlc-utils/examples/beetlepose$ anipose calibrate
Calibrating...
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor/calibration/calibration.toml
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor/calibration/dal_liom_guid_18475996_2020_02_13_20_25_06.mp4
100%|██████████████████████████| 30033/30033 [01:46<00:00, 281.65it/s]
15051 boards detected
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor/calibration/dal_liom_guid_18475997_2020_02_13_20_25_08.mp4
100%|██████████████████████████| 30033/30033 [00:43<00:00, 694.39it/s]
879 boards detected
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor/calibration/dal_liom_guid_19061101_2020_02_13_20_25_09.mp4
100%|██████████████████████████| 30033/30033 [00:58<00:00, 512.92it/s]
3818 boards detected
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor/calibration/dal_liom_guid_19061600_2020_02_13_20_25_10.mp4
100%|██████████████████████████| 30033/30033 [00:49<00:00, 604.37it/s]
2022 boards detected
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor/calibration/dal_liom_guid_19061602_2020_02_13_20_25_11.mp4
100%|██████████████████████████| 30033/30033 [00:49<00:00, 603.06it/s]
2297 boards detected
defaultdict(<class 'int'>,
            {('18475996', '19061101'): 6,
             ('18475996', '19061600'): 38,
             ('19061101', '18475996'): 6,
             ('19061600', '18475996'): 38})
Traceback (most recent call last):
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/bin/anipose", line 11, in <module>
    load_entry_point('anipose', 'console_scripts', 'anipose')()
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/decorators.py", line 64, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/hank-x299/src/anipose/anipose/anipose.py", line 115, in calibrate
    calibrate_all(config)
  File "/home/hank-x299/src/anipose/anipose/common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "/home/hank-x299/src/anipose/anipose/common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "/home/hank-x299/src/anipose/anipose/calibrate.py", line 186, in process_session
    n_samp_iter=100, n_samp_full=2000)
  File "/home/hank-x299/src/calligator/calligator/cameras.py", line 1555, in calibrate_rows
    rvecs, tvecs = get_initial_extrinsics(rtvecs)
  File "/home/hank-x299/src/calligator/calligator/utils.py", line 173, in get_initial_extrinsics
    pairs = find_calibration_pairs(graph, source=0)
  File "/home/hank-x299/src/calligator/calligator/utils.py", line 156, in find_calibration_pairs
    for new in graph[item]:
TypeError: 'NoneType' object is not subscriptable

My config.toml file has the following:

[calibration]
# checkerboard / charuco / aruco
board_type = "charuco"

# width and height of grid
board_size = [4, 4]

# number of bits in the markers, if aruco/charuco
board_marker_bits = 4

# number of markers in dictionary, if aruco/charuco
board_marker_dict_number = 50

# length of marker side
# board_marker_length = 0.7 # mm
board_marker_length = 1.4 # mm

# If charuco or checkerboard, square side length
# board_square_side_length = 1.0 # mm
board_square_side_length = 2.0 # mm

[manual_verification]
# true / false
manually_verify = false

Any advice addressing this error is appreciated!
Thanks!

[DOC] Installation on Ubuntu 18.04 package conflicts

When installing on Ubuntu 18.04, if opencv-python is already installed then when opencv-contrib-python is installed, aruco and the rest of the development open-cv modules are not installed due to the package conflict. This could be documented in the installation possibly.

3D coordinates

I encounter problems with retrieving reliable 3D coordinates of markers which are visible in a different amount of cameras.
For example:
6 markers (marker 1-6) are visible in the same cameras (let's say camera 1 and 2, with likelihood > 0.95), when visualizing the 3D coordinates of these markers, these look reliable. However, when marker 7 is visible in camera 1 and 2 (likelihood > 0.95) for a certain amount of time, this marker location seems reliable when comparing the location of marker 1-6 and marker 7. But when marker 7 becomes visible in camera 1, 2 and 3 (likelihood > 0.95) later on, this marker shifts away from the other markers (marker 1-6). The location of marker 7 is not longer logical when comparing this location to the location of marker 1-6.

Would you have a suggestion to solve this?

I already applied the 'filter' to only use 2D coordinates of markers with a high likelihood (> 0.95)
to determine the 3Dcoordinates.
Does it has something to do with filtering? Is there some more documentation about the different 2D/3D filter options? or does it has something to do with the calibration?

I added a zip folder with the calibration.toml, config.toml, pose-2d and pose-3d excels of sample data
Maud.zip

Good detections but bad calibration

Apologies if this has been addressed before, I had a look through the existing issues and nothing quite match.

Basically, the first few times I used anipose it worked great. Since then, however, more often than not I get bizarre results out of the calibration. Manually verifying the marker detections, they're usually >99% correct. The reprojection error is low, often <1. But when I check the calibration parameters, they don't make sense, e.g. the "cameras"* are both within a couple millimeters of the world origin and pointing in virtually the same direction. This in turn leads to implausible triangulation, i.e. the mouse that I'm tracking is either microscopic or several meters tall.

Am I doing something wrong? Or have I run into a pathological case for anipose's camera calibration algorithm? Calibration videos are here and here. Attached are the project config, the calibration target, the detections file, the resultant calibration file. I've tried things like turning fisheye on or off, turning ransac on and off, and changing the camera used for alignment, and get basically the same results each time.

*I'm actually using a single camera with a prism and a pair of mirrors to get two views of the subject. Could it be that anipose's camera calibration just doesn't work in this case? It does get it right (or at least comes up with a plausible solution) sometimes though.

Thanks in advance for your help and thanks for anipose in general, when I can get it to work it's great! Please let me know if you need any more info.

Calibration error

Hi,

I encounter a problem when a want to calibrate my cameras.
Videos containing checkerboard are analyzed and boards are detected but then an error occurs (cv2.error).

I tried to downgrade the opencv version to 3.4 as you mentioned in a previous issue but the same error message appears.

C:\Users\ormen\Desktop\anipose\Patient1\Nothing\calibration\Cam1_Calibration_1_10-29-19_11-29-34.avi
100%|█████████████████████████████| 1482/1482 [01:52<00:00, 13.23it/s]
1346 boards detected
C:\Users\ormen\Desktop\anipose\Patient1\Nothing\calibration\Cam2_Calibration_1_10-29-19_11-29-34.avi
100%|█████████████████████████████| 1482/1482 [01:20<00:00, 18.51it/s]
1394 boards detected
Traceback (most recent call last):
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\ormen\Anaconda3\envs\dlc-windowsGPU\Scripts\anipose.exe_main.py", line 9, in
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 764, in call
return self.main(*args, **kwargs)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 717, in main
rv = self.invoke(ctx)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 555, in invoke
return callback(*args, **kwargs)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\decorators.py", line 64, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 555, in invoke
return callback(*args, **kwargs)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\anipose.py", line 108, in calibrate
calibrate_all(config)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\common.py", line 168, in fun
return process_all(config, process_session, **args)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\common.py", line 153, in process_all
output[past_folders] = process_session(config, path, **args)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\calibrate.py", line 183, in process_session
n_samp_iter=100, n_samp_full=2000)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\calligator\cameras.py", line 1546, in calibrate_rows
all_rows[i] = board.estimate_pose_rows(cam, row)
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\calligator\boards.py", line 333, in estimate_pose_rows
row['ids'])
File "c:\users\ormen\anaconda3\envs\dlc-windowsgpu\lib\site-packages\calligator\boards.py", line 465, in estimate_pose_points
reprojectionError=30)
cv2.error: OpenCV(3.4.7) C:\projects\opencv-python\opencv\modules\calib3d\src\solvepnp.cpp:216: error: (-215:Assertion failed) npoints >= 4 && npoints == std::max(ipoints.checkVector(2, CV_32F), ipoints.checkVector(2, CV_64F)) in function 'cv::solvePnPRansac'

Do you have an idea what can be the problem?

Best,

Camera offset

Hi,

I decided to 'crop' my 3 cameras views (same camera and lenses) and I set exactly the same offset to each camera.
Should I precise the offset in my config.toml file if I redo the calibration?
Since the offset is exactly the same in each camera I guess that it's like having the full view of each camera or am I wrong?

Best,

error during calibration

Hi,

Using windows 10, installed anipose today from "pip install anipose"
While trying to use anipose calibrate I get this error,

(dlc-windowsGPU) C:\deeplabcut\anipose3d recon>anipose calibrate
Calibrating...
C:\deeplabcut\anipose3d recon\session1\calibration\calibration.toml
C:\deeplabcut\anipose3d recon\session1\calibration\cam1cut.avi
100%|█████████████████████████████| 1056/1056 [00:19<00:00, 53.65it/s]
1056 boards detected
C:\deeplabcut\anipose3d recon\session1\calibration\cam2cut.avi
100%|█████████████████████████████| 1056/1056 [00:21<00:00, 50.00it/s]
1056 boards detected
defaultdict(<class 'int'>, {})
Traceback (most recent call last):
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\User\Anaconda3\envs\dlc-windowsGPU\Scripts\anipose.exe_main.py", line 9, in
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 764, in call
return self.main(*args, **kwargs)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 717, in main
rv = self.invoke(ctx)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 555, in invoke
return callback(*args, **kwargs)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\decorators.py", line 64, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 555, in invoke
return callback(*args, **kwargs)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\anipose.py", line 109, in calibrate
calibrate_all(config)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\common.py", line 168, in fun
return process_all(config, process_session, **args)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\common.py", line 153, in process_all
output[past_folders] = process_session(config, path, **args)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\calibrate.py", line 184, in process_session
n_samp_iter=100, n_samp_full=2000)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\calligator\cameras.py", line 1555, in calibrate_rows
rvecs, tvecs = get_initial_extrinsics(rtvecs)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\calligator\utils.py", line 174, in get_initial_extrinsics
extrinsics = compute_camera_matrices(rtvecs, pairs)
File "c:\users\user\anaconda3\envs\dlc-windowsgpu\lib\site-packages\calligator\utils.py", line 164, in compute_camera_matrices
source = pairs[0][0]
IndexError: list index out of range

a pickle file is created.
Thank you.

cristian

TypeError: init() got an unexpected keyword argument 'manually_verify'

Hello,

I came across a weird problem. When trying to draw calibration board or calibrate cameras I get the following error:

(dlc-windowsgpu) C:\Kalibracja_3D>anipose draw-calibration Drawing calibration board... Traceback (most recent call last): File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\ProgramData\Anaconda3\envs\dlc-windowsgpu\Scripts\anipose.exe\__main__.py", line 7, in <module> File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 764, in __call__ return self.main(*args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 717, in main rv = self.invoke(ctx) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 1137, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 555, in invoke return callback(*args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\click\core.py", line 555, in invoke return callback(*args, **kwargs) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\anipose.py", line 273, in draw_calibration img = get_calibration_board_image(config) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\common.py", line 224, in get_calibration_board_image board = get_calibration_board(config) File "c:\programdata\anaconda3\envs\dlc-windowsgpu\lib\site-packages\anipose\common.py", line 207, in get_calibration_board manually_verify=manually_verify) TypeError: __init__() got an unexpected keyword argument 'manually_verify'

When this part is added into the config file (either true or false) I get the same error.
[manual_verification] manually_verify = true

It's probably something mundane, but I cannot solve this issue on my own.

Konrad

calibration-errors results in "Import error cannot import name 'get_board_type'"

Describe the bug
calibration-errors results in "Import error cannot import name 'get_board_type'"

When i checked the calibration_errors.py file I saw that of all the imports from commons, get_board_type is the only function which is missing from the commons.py file

Screenshots

[BUG] Calibration Squares not the same size as demo

When I print out the calibration.png from here https://drive.google.com/drive/u/1/folders/18qGbHyiSJ2au9sFXScZ63EZ83PtC1-ld, it measures 28 mm instead of 25 mm in as in the toml config file. This is likely because it doesn't have the margins that are shown in the calibration clipboard videos.

DLT algorithm needs at least 6 points

Hello!

i just came accross an issue:

Describe the bug

DLT algorithm needs at least 6 points for pose estimation from 3D-2D point correspondences. (expected: 'count >= 6'), where

'count' is 5
must be greater than or equal to
'6' is 6

To Reproduce
I just used anipose calibration. I did exactly the same operations for several other groups of videos while everything went smooth.

Expected behavior
getting the calibration.toml file

here is a full log of what i obtained:

Calibrating...
/home/imagedpt/Documents/CN/Projets/Pipeline_pose_estimation/Anipose/calibration
/home/imagedpt/Documents/CN/Projets/Pipeline_pose_estimation/Anipose/calibration/calibration.toml
/home/imagedpt/Documents/CN/Projets/Pipeline_pose_estimation/Anipose/calibration/calib5_bigpat_30fps_cam11.avi
100%|███████████████████████████████| 937/937 [02:04<00:00,  7.55it/s]
306 boards detected
/home/imagedpt/Documents/CN/Projets/Pipeline_pose_estimation/Anipose/calibration/calib5_bigpat_30fps_cam12.avi
100%|███████████████████████████████| 937/937 [03:43<00:00,  4.19it/s]
518 boards detected
/home/imagedpt/Documents/CN/Projets/Pipeline_pose_estimation/Anipose/calibration/calib5_bigpat_30fps_cam5.avi
100%|███████████████████████████████| 937/937 [02:42<00:00,  5.78it/s]
870 boards detected
/home/imagedpt/Documents/CN/Projets/Pipeline_pose_estimation/Anipose/calibration/calib5_bigpat_30fps_cam8.avi
100%|███████████████████████████████| 937/937 [02:21<00:00,  6.61it/s]
902 boards detected
Traceback (most recent call last):
  File "/home/imagedpt/.virtualenvs/anipose_test/bin/anipose", line 8, in <module>
    sys.exit(cli())
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/anipose/anipose.py", line 115, in calibrate
    calibrate_all(config)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/anipose/common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/anipose/common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/anipose/calibrate.py", line 186, in process_session
    n_samp_iter=100, n_samp_full=2000)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/calligator/cameras.py", line 1551, in calibrate_rows
    all_rows[i] = board.estimate_pose_rows(cam, row)
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/calligator/boards.py", line 343, in estimate_pose_rows
    row['ids'])
  File "/home/imagedpt/.virtualenvs/anipose_test/lib/python3.6/site-packages/calligator/boards.py", line 504, in estimate_pose_points
    reprojectionError=30)
cv2.error: OpenCV(3.4.9) /io/opencv/modules/calib3d/src/calibration.cpp:1097: error: (-2:Unspecified error) in function 'void cvFindExtrinsicCameraParams2(const CvMat*, const CvMat*, const CvMat*, const CvMat*, CvMat*, CvMat*, int)'
> DLT algorithm needs at least 6 points for pose estimation from 3D-2D point correspondences. (expected: 'count >= 6'), where
>     'count' is 5
> must be greater than or equal to
>     '6' is 6
(anipose_test)

i'm using this configuration :

[calibration]
# checkerboard / charuco / aruco
board_type = "checkerboard"

# width and height of grid
board_size = [9, 6]

# number of bits in the markers, if aruco/charuco
# board_marker_bits = 4

# number of markers in dictionary, if aruco/charuco
# board_marker_dict_number = 50

# length of marker side
# board_marker_length = 33 # mm

# If aruco, length of marker separation
# board_marker_separation_length = 1 # mm

# If charuco or checkerboard, square side length
board_square_side_length = 33 # mm
animal_calibration = false
fisheye = false

[triangulation]
triangulate = true
# cam_regex = '-cam([1-12])'
cam_regex = 'cam([0-9]*)'
ransac = true
optim = true
constraints = [
   ["base", "MCP1"], ["MCP1", "PIP1"], ["PIP1", "tip1"],
   ["base", "MCP2"], ["MCP2", "PIP2"], ["PIP2", "DIP2"], ["DIP2", "tip2"],
   ["base", "MCP3"], ["MCP3", "PIP3"], ["PIP3", "DIP3"], ["DIP3", "tip3"],
   ["base", "MCP4"], ["MCP4", "PIP4"], ["PIP4", "DIP4"], ["DIP4", "tip4"],
   ["base", "MCP5"], ["MCP5", "PIP5"], ["PIP5", "DIP5"], ["DIP5", "tip5"]
]
scale_smooth = 25
scale_length = 10
scale_length_weak = 2
reproj_error_threshold = 3
score_threshold = 0.6
n_deriv_smooth = 2

As the video i'm using contains faces of people that i cannot provide, i won't be able to send the videos used... though i can provide the pickle file : https://we.tl/t-RbrtQPrGcE

Once again, thank you a lot for you work,

Anipose analyze has ImportError

Describe the bug
When I run anipose analyze I get: ImportError: cannot import name 'aruco'
Installing opencv-python~=3.4 and opencv-contrib-python~=3.4doesn't do anything because it's already installed. Uninstalling and reinstalling does not work either.

To Reproduce
Steps to reproduce the behavior:

Install DeepLabCut and anipose in a new conda environment
Run anipose analyze

Expected behavior
It's expected to analyze the videos based on the config.toml file.

Desktop (please complete the following information):

OS: Ubuntu 18.04

Additional context
Full traceback:

anipose analyze
Traceback (most recent call last):
  File "/home/ml/anaconda3/envs/anipose/bin/anipose", line 8, in <module>
    sys.exit(cli())
  File "/home/ml/.local/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/ml/.local/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/ml/.local/lib/python3.6/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/ml/.local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/ml/.local/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/ml/.local/lib/python3.6/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/ml/.local/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/ml/anaconda3/envs/anipose/lib/python3.6/site-packages/anipose/anipose.py", line 135, in analyze
    from .pose_videos import pose_videos_all
  File "/home/ml/anaconda3/envs/anipose/lib/python3.6/site-packages/anipose/pose_videos.py", line 11, in <module>
    from .common import natural_keys, make_process_fun
  File "/home/ml/anaconda3/envs/anipose/lib/python3.6/site-packages/anipose/common.py", line 10, in <module>
    from aniposelib.boards import CharucoBoard, Checkerboard
  File "/home/ml/anaconda3/envs/anipose/lib/python3.6/site-packages/aniposelib/__init__.py", line 6, in <module>
    from . import boards, cameras, utils
  File "/home/ml/anaconda3/envs/anipose/lib/python3.6/site-packages/aniposelib/boards.py", line 2, in <module>
    from cv2 import aruco
ImportError: cannot import name 'aruco'

Good detections but calibration routine crashes

Hi,

I'm using 5 cameras and the standard charuco board for camera calibration. This results in 100's of detections per camera and anipose-calibrate makes it to the point where it saves detections.pickle. However, during the actual model estimation step, it crashes with the following

Calibrating...
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/calibration.toml
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-0_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [02:45<00:00, 42.51it/s]
4676 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-1_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:04<00:00, 38.08it/s]
5149 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-2_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:12<00:00, 36.55it/s]
5403 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-3_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:01<00:00, 38.74it/s]
5122 boards detected
/media/jon/Ephys Data Buffe/mouse_young_b/2020-09-03_mouse-young_b/calibration/cam-4_2020-09-03T18_15_36.avi
100%|█████████████████████████████| 7043/7043 [03:02<00:00, 38.49it/s]
6628 boards detected
defaultdict(<class 'int'>, {('1', '4'): 4900, ('4', '1'): 4900})
Traceback (most recent call last):
  File "/home/jon/anaconda3/envs/anipose/bin/anipose", line 8, in <module>
    sys.exit(cli())
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/anipose.py", line 314, in run_data
    calibrate_all(config)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/calibrate.py", line 203, in process_session
    verbose=True)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 1563, in calibrate_rows
    rvecs, tvecs = get_initial_extrinsics(rtvecs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/utils.py", line 173, in get_initial_extrinsics
    pairs = find_calibration_pairs(graph, source=0)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/utils.py", line 156, in find_calibration_pairs
    for new in graph[item]:
TypeError: 'NoneType' object is not subscriptable

I've attached my detections.pickle in case there is evidence of what corner case I've reached here...

detections.zip

ValueError: Only one of 'nopython' or 'forceobj' can be True

Describe the bug

(anipose) hand-demo-unfilled[0]$ anipose analyze
Traceback (most recent call last):
  File "/home/jon/anaconda3/envs/anipose/bin/anipose", line 8, in <module>
    sys.exit(cli())
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/anipose.py", line 135, in analyze
    from .pose_videos import pose_videos_all
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/pose_videos.py", line 11, in <module>
    from .common import natural_keys, make_process_fun
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/anipose/common.py", line 10, in <module>
    from aniposelib.boards import CharucoBoard, Checkerboard
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/__init__.py", line 6, in <module>
    from . import boards, cameras, utils
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 428, in <module>
    class CameraGroup:
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/aniposelib/cameras.py", line 616, in CameraGroup
    @jit(nopython=True, parallel=True, forceobj=True)
  File "/home/jon/anaconda3/envs/anipose/lib/python3.7/site-packages/numba/core/decorators.py", line 147, in jit
    raise ValueError("Only one of 'nopython' or 'forceobj' can be True.")
ValueError: Only one of 'nopython' or 'forceobj' can be True.
(anipose) hand-demo-unfilled[0]$

To Reproduce
Steps to reproduce the behavior:
Install via instructions on docs website
Download the hand-demo-unfilled data set
Call anipose analyze on the hand-demo-unfilled data set

Desktop (please complete the following information):

OS: Ubuntu 18.04

Filtering tutorial/instructions suggestions

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

What is the offset threshold parameter? Your description is a bit vague. Is this a standard deviation threshold, for example?
If I wanted to conduct my own comparisons of various filters what is the best way to do this?
Random question: after triangulation are outputs automatically converted into real space (mm for example rather than pixels?)
Random suggestion: offer an option to define points in space to establish a ground plane. I, for example, work in an arena and have trained my network to identify corners of the arena. It would be nice to have coordinates automatically rotated accordingly.

Describe the solution you'd like

Descriptions of config parameters that are better suited for someone who is not familiar with the package.
Suggestions for how to deploy different filters, how to modify filtering parameters, and how to use outputs that have been filtered with different parameters for comparisons. Thanks!

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

triangulation error

Hello @lambdaloop ,
I am trying to run anipose triangulate but I appear to be getting a shape error like so:

(anipose-2d-viz) hank-x299@hank-x299:/mnt/2TB/Dropbox/datasets/for_anipose/dalotiapose$ anipose triangulate
Triangulating points...
/mnt/2TB/Dropbox/datasets/for_anipose/dalotiapose/test_6_no_motor/pose-3d/dal_liom__2020_02_06_15_59_43.csv
Traceback (most recent call last):
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/bin/anipose", line 11, in <module>
    load_entry_point('anipose', 'console_scripts', 'anipose')()
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/click/decorators.py", line 64, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/hank-x299/src/anipose/anipose/anipose.py", line 158, in triangulate
    triangulate_all(config)
  File "/home/hank-x299/src/anipose/anipose/common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "/home/hank-x299/src/anipose/anipose/common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "/home/hank-x299/src/anipose/anipose/triangulate.py", line 328, in process_session
    fname_dict, output_fname)
  File "/home/hank-x299/src/anipose/anipose/triangulate.py", line 237, in triangulate
    points_3d = cgroup.triangulate(points_2d, progress=True)
  File "/home/hank-x299/src/calligator/calligator/cameras.py", line 470, in triangulate
    len(self.cameras), points.shape
AssertionError: Invalid points shape, first dim should be equal to number of cameras (4), but shape is (1, 8016, 2)

Why might my first dim not match my number of cameras? The output calibration.toml file from anipose calibrate is as follows:

[cam_0]
name = "18475997"
size = [ 720, 540,]
matrix = [ [ 1.579937897350622e-9, 0.0, 359.5,], [ 0.0, 1.579937897350622e-9, 269.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ -3.144523897087529e-6, 0.0, 0.0, 0.0, 0.0,]
rotation = [ 0.00414603630815267, 0.1219035008662274, -0.2865174292114367,]
translation = [ 27691.78492496907, 18857.25662426044, -0.05080337727313677,]

[cam_1]
name = "19061101"
size = [ 720, 540,]
matrix = [ [ 3940085.308362053, 0.0, 359.5,], [ 0.0, 3940085.308362053, 269.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ -2074.529286566875, 0.0, 0.0, 0.0, 0.0,]
rotation = [ 17557.08058349543, -737.7576224740999, -327.2018426416136,]
translation = [ 2016808012.038999, -253530721.0348125, 280339008.100099,]

[cam_2]
name = "19061600"
size = [ 720, 540,]
matrix = [ [ -166371.7609030413, 0.0, 359.5,], [ 0.0, -166371.7609030413, 269.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ 26.6270212226631, 0.0, 0.0, 0.0, 0.0,]
rotation = [ 5.110329415919487, 3.386310472928838, -6.314679086461423,]
translation = [ 43310.79681988942, 47221.44031715184, 1046.281440359661,]

[cam_3]
name = "19061602"
size = [ 720, 540,]
matrix = [ [ 3477688.138059122, 0.0, 359.5,], [ 0.0, 3477688.138059122, 269.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ -52.13839237435668, 0.0, 0.0, 0.0, 0.0,]
rotation = [ -3.878485957787288, 5.094652480771372, -14.79670715654272,]
translation = [ -99616.9443827019, -84179.57879928176, 9541.193737878069,]

[metadata]
adjusted = false
error = 1.312791890549888e+17

Thanks!

Calibration - anipose not detecting checkerboard pattern #SOLVED

Hi,

whenever I run anipose calibrate I end up with 0 detected checkerboard patterns. I tried different calibration videos and different config.toml settings.

I use a 11x8 checkerboard with a square side length of 25mm. So far I did the following:
set board_size to [11,8] or [275, 200]. I used the latter cause of the documentation saying the units should be consistent.
Anyway, using [11,8] or [275,200] with board_square_side_length = 25 always leads to zero detected checkerboards.
I also tried all above combinations with board_marker_length = 25, though I think that this code is not necessary when using checkerboards.

My folder structure is as followed:

rect_check--2020-09-16    (DLC model folder)
rect_check          (anipose project folder)
|  config.toml
|  calibration
|     --- calib_left.avi
|     --- calib_right.avi
|  pose-2d
|  videos_raw
|     --- 011_left.avi
|     --- 011_right.avi
|     --- 012_left.avi
|     --- 012_right.avi ...

and I use nesting = 1.
I attached the config.toml.

config.zip

Calibration Video Suggestion

Hi,

I was wondering if the board needs to be in videos in all of the cameras all the time.
My setup has 4 cameras in 4 corners of a square area. So, it is not possible to have the boards projected on all the cameras for calibration.

I was also wondering if this is leading me to the error below:

D:\workspac_deepcut\local_DLC\FN 10-02-2020 - Short Clip-Chrissy-2020-10-08\videos\anipose_test\test1\calibration\calibrate1_cam2.mp4
99%|███████████████████████████▋| 3917/3960 [01:30<00:00, 356.40it/s][h264 @ 000002b22675ca80] Invalid NAL unit size (19244 > 789).
[h264 @ 000002b22675ca80] Error splitting the input into NAL units.
99%|████████████████████████████▊| 3934/3960 [01:30<00:00, 43.41it/s]
562 boards detected
D:\workspac_deepcut\local_DLC\FN 10-02-2020 - Short Clip-Chrissy-2020-10-08\videos\anipose_test\test1\calibration\calibrate1_cam5.mp4
100%|█████████████████████████████| 3960/3960 [01:00<00:00, 65.21it/s]
435 boards detected
defaultdict(<class 'int'>, {('2', '5'): 1, ('5', '2'): 1})
Traceback (most recent call last):
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\rahmank\AppData\Local\Continuum\anaconda3\envs\anipose\Scripts\anipose.exe_main.py", line 7, in
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 829, in call
return self.main(*args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 782, in main
rv = self.invoke(ctx)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 610, in invoke
return callback(*args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\decorators.py", line 73, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 610, in invoke
return callback(*args, **kwargs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\anipose.py", line 115, in calibrate
calibrate_all(config)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\common.py", line 168, in fun
return process_all(config, process_session, **args)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\common.py", line 125, in process_all
output[()] = process_session(config, pipeline_prefix, **args)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\anipose\calibrate.py", line 187, in process_session
verbose=True)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\aniposelib\cameras.py", line 1560, in calibrate_rows
rvecs, tvecs = get_initial_extrinsics(rtvecs)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\aniposelib\utils.py", line 173, in get_initial_extrinsics
pairs = find_calibration_pairs(graph, source=0)
File "c:\users\rahmank\appdata\local\continuum\anaconda3\envs\anipose\lib\site-packages\aniposelib\utils.py", line 156, in find_calibration_pairs
for new in graph[item]:
TypeError: 'NoneType' object is not subscriptable

My config toml is given below:

project = 'anipose_test'

model_folder = '../../../'

nesting = 0
video_extension = 'mp4'

[manual_verification]

true / false

manually_verify = true

[calibration]

checkerboard / charuco / aruco

board_type = "charuco"

width and height of grid

board_size = [10, 7]

number of bits in the markers, if aruco/charuco

board_marker_bits = 4

number of markers in dictionary, if aruco/charuco

board_marker_dict_number = 50

length of marker side

board_marker_length = 18.75 # mm

If aruco, length of marker separation

board_marker_separation_length = 1 # mm

If charuco or checkerboard, square side length

board_square_side_length = 25 # mm

animal_calibration = false

fisheye = true

[labeling]
scheme = [

]

[triangulation]
triangulate = true
cam_regex = '_cam([0-9])'
cam_align = "1"
ransac = true
optim = true
constraints = [

]
scale_smooth = 25
scale_length = 10
scale_length_weak = 2
reproj_error_threshold = 3
score_threshold = 0.6
n_deriv_smooth = 2

Settings for a threshold filter

Removes data outside threshold (probably errors in tracking), and interpolates

[filter]
enabled = true
medfilt = 9 # length of median filter
offset_threshold = 25 # offset from median filter to count as jump
score_threshold = 0.8 # score below which to count as bad
spline = true # interpolate using cubic spline instead of linear

Thank you for your help.

error during calibration

Hello,
I've been having an issue running the anipose calibrate command. I am using a Conda environment that can run DeepLabCut, on Ubuntu 18.04. When trying to run anipose calibrate I get the following error:

(dlc-anipose) hank-x299@hank-x299:~/src/dlc-utils/examples/beetlepose$ anipose calibrate
Calibrating...
/home/hank-x299/src/dlc-utils/examples/beetlepose/test_1_no_motor
Traceback (most recent call last):
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/bin/anipose", line 11, in <module>
    load_entry_point('anipose', 'console_scripts', 'anipose')()
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/decorators.py", line 64, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/hank-x299/anaconda3/envs/dlc-anipose/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/hank-x299/src/anipose/anipose/anipose.py", line 115, in calibrate
    calibrate_all(config)
  File "/home/hank-x299/src/anipose/anipose/common.py", line 168, in fun
    return process_all(config, process_session, **args)
  File "/home/hank-x299/src/anipose/anipose/common.py", line 153, in process_all
    output[past_folders] = process_session(config, path, **args)
  File "/home/hank-x299/src/anipose/anipose/calibrate.py", line 126, in process_session
    name = get_cam_name(config, vid)
  File "/home/hank-x299/src/anipose/anipose/common.py", line 72, in get_cam_name
    name = match.groups()[0]
IndexError: tuple index out of range

My file structure is as follows:

(dlc-anipose) hank-x299@hank-x299:~/src/dlc-utils/examples/beetlepose$ tree
.
├── config.toml
└── test_1_no_motor
    ├── calibration
    │   ├── dal_liom_guid_18475996_2020_02_06_23_26_17.mp4
    │   ├── dal_liom_guid_18475997_2020_02_06_23_26_18.mp4
    │   ├── dal_liom_guid_19061101_2020_02_06_23_26_20.mp4
    │   ├── dal_liom_guid_19061600_2020_02_06_23_26_22.mp4
    │   └── dal_liom_guid_19061602_2020_02_06_23_26_23.mp4
    └── videos-raw
        ├── dal_liom_guid_18475996_2020_02_06_11_22_17.mp4
        ├── dal_liom_guid_18475997_2020_02_06_11_22_02.mp4
        ├── dal_liom_guid_19061101_2020_02_06_11_21_52.mp4
        ├── dal_liom_guid_19061600_2020_02_06_11_21_40.mp4
        └── dal_liom_guid_19061602_2020_02_06_11_21_26.mp4

My config.toml file looks like so:

project = "beetlepose"
path = "/home/hank-x299/src/dlc-utils/examples/beetlepose"

nesting = 1

video_extension = "mp4"

# regex matches 8-digits proceeding a "_":
[triangulation]
cam_regex = "guid_[0-9]{8}"

[calibration]
# checkerboard / charuco / aruco
board_type = "checkerboard"

# width and height of grid
board_size = [6, 6]

# length of marker side
board_marker_length = 0.3 # mm

# If charuco or checkerboard, square side length
board_square_side_length = 0.3 # mm

animal_calibration = true

Given the above, why might I be getting IndexError: tuple index out of range?
Thanks!

Error in pose estimation from trained DLC Model

Encountered an error while running anipose analyze on a new config.toml with a working DeepLabCut config.yaml

Had no trouble running deeplabcut.analyze_videos() in the same folder.

[DOC] Installation opencv-python and opencv-contrib-python

anipose filter-3d issue

Hello,

I'm having some issues trying to execute anipose filter-3d. I consistently get a numpy error like so:

(anipose-2d-viz) hank-x299@hank-x299:/mnt/2TB/Dropbox/datasets/for_anipose/dalotiapose$ anipose filter-3d
Filtering tracked points...
/mnt/2TB/Dropbox/datasets/for_anipose/dalotiapose/test_1_no_motor/pose-3d-filtered/dal_liom__2020_02_06_11_21.csv
/home/hank-x299/anaconda3/envs/anipose-2d-viz/lib/python3.6/site-packages/numpy/lib/function_base.py:3405: RuntimeWarning: Invalid value encountered in median
  r = func(a, **kwargs)

I am using numpy==1.16.4. My 2D-tracking after filtering looks good, and my calibration.toml file is like so:

[cam_0]
name = "18475997"
size = [ 720, 540,]
matrix = [ [ 9.638756622617622, 0.0, 359.5,], [ 0.0, 9.638756622617622, 269.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ 0.002321125597023245, 0.0, 0.0, 0.0, 0.0,]
rotation = [ 0.07377960282678943, 0.00883013460354334, -0.04760874463639168,]
translation = [ -0.2786317828208055, 0.3293169341307745, -0.03600747822987863,]

[cam_1]
name = "19061101"
size = [ 720, 540,]
matrix = [ [ 24.96617363229602, 0.0, 359.5,], [ 0.0, 24.96617363229602, 269.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ 0.0003751601954273957, 0.0, 0.0, 0.0, 0.0,]
rotation = [ -0.07387913606012508, 0.01903475208959475, 0.1710721036246948,]
translation = [ -1.384724062163185, 0.1546314401368329, 0.05040677950337349,]

[cam_2]
name = "19061600"
size = [ 720, 540,]
matrix = [ [ 9.670335210422285, 0.0, 359.5,], [ 0.0, 9.670335210422285, 269.5,], [ 0.0, 0.0, 1.0,],]
distortions = [ 0.003562620248271928, 0.0, 0.0, 0.0, 0.0,]
rotation = [ 0.1284161881272207, 0.003714826710541101, -0.1994563425933652,]
translation = [ -0.2258772873279897, 0.3692173507505997, -0.01727518616371634,]

[metadata]
adjusted = false
error = 1.931100687210916

My filter in the config.toml file consists of the default values included in the repo:

# Settings for a threshold filter
# Removes data outside threshold (probably errors in tracking), and interpolates
[filter]
enabled = true
medfilt = 13 # length of median filter
offset_threshold = 25 # offset from median filter to count as jump
score_threshold = 0.8 # score below which to count as bad
spline = true # interpolate using cubic spline instead of linear

Why might I be getting the above error?
Thank you!

draw-calibration / anipose analyze not working

Hi folks,

this is kind of a follow up of issue #46. After solving the issue of 0 detected calibration patterns / checkerboards, I encountered two more issues:

draw-calibration ending with an error (see output 1 below)
anipose analyze running for 1-2s before stopping without error and/or output (see output 2 below)

Output 1 / draw-calibration

(anipose-conrad) C:\Conrad\AniPose\rect_check--unfilled>anipose draw-calibration
Drawing calibration board...
Traceback (most recent call last):
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\bknUser\anaconda3\envs\anipose-conrad\Scripts\anipose.exe\__main__.py", line 7, in <module>
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\click\core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\click\core.py", line 782, in main
    rv = self.invoke(ctx)
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\click\core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\click\core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\click\decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\users\bknuser\anaconda3\envs\anipose-conrad\lib\site-packages\anipose\anipose.py", line 287, in draw_calibration
    cv2.imwrite('calibration.png', img)
cv2.error: OpenCV(3.4.11) C:\Users\appveyor\AppData\Local\Temp\1\pip-req-build-lw30ardm\opencv\modules\imgcodecs\src\loadsave.cpp:759: error: (-215:Assertion failed) !_img.empty() in function 'cv::imwrite'

Output 2 - anipose analyze

(anipose-conrad) C:\Conrad\AniPose\rect_check--unfilled>anipose analyze
Analyzing videos...

(anipose-conrad) C:\Conrad\AniPose\rect_check--unfilled>

A few infos of my setup:
OS: Win10 Pro, 1903, System Build: 18362.1082
CPU: Core i7-9750H
GPU: RTX 2070 Max-Q
GPU driver: 442.23 DCH

Installed python libraries and versions: see conda list output.txt
conda list output.txt

For an overview of the anipose projects folder and file structure: see tree output anipose dir.txt
tree output anipose dir.txt

For the DLC and anipose config files see config_files.zip
config_files.zip

You'll also find the calibration toml and pickle attached:
calibration.zip

I really want to use anipose for cheap in the field human reach motion tracking but don't really know what else to do. Any hint as to where the problem could originate is much appreciated.

Cheers,
Conrad

Documentation improvements for filters

Is your feature request related to a problem? Please describe.
I'd like to use filtering (2D as well as 3D with distance constraints) but the description of the filter parameters is insufficient. While it is clear how to enable filters and what general kind of operation they will perform, I cannot find accurate descriptions of the filter parameters.

Describe the solution you'd like
Please clarify these points in the documentation:

What happens when a point is considered erroneous? Is this a requirement for a point to be corrected by a filter or do filters apply to all points in general?
How do scale_smooth an scale_length work exactly?
- What kind of smoothing is applied and what exactly does scale_smooth mean? Is it smoothing kernel width, shape, ...?
- How does scale_length work? I assume, if some constrained joint suddenly moves far away from its (by constraint) expected position, this somehow moves it back. How does scale_length specify this behaviour? Is it a maximum percentage, the constraint can get longer before action is taken, or is it the strength with which a constraint "pulls" on a joint, ...?
Looking through the source code I find other parameters like scale_length_weak, n_deriv_smooth, reproj_error_threshold which also contribute to the optimization but are not mentioned at all in the docs. Please clarify what they mean.

Additional context
Maybe it's just me not finding these descriptions but I have looked here (parameter list) and here (tutorial). As well as in the source code here (anipose) and here (optimization function in aniposelib) which also gives no comments / explanation.

Question: GPU Usage

I'm currently running through the tutorial in a "clean" environment on a computer that successfully runs DeepLabCut (in a different environment) with the GPU. Does the Anipose environment use the GPU by default or does the installation require the DLC GPU installation with Anipose on top?

label-2d problems

Hello,
I ran the anipose label-2d on raw videos that are either .mp4 or .avi. For both cases, the output labelled video is black, and no images can be seen. What might the issue be?
Thanks!

lambdaloop / anipose Goto Github PK

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true / false

checkerboard / charuco / aruco

width and height of grid

number of bits in the markers, if aruco/charuco

number of markers in dictionary, if aruco/charuco

length of marker side

If aruco, length of marker separation

board_marker_separation_length = 1 # mm

If charuco or checkerboard, square side length

Settings for a threshold filter

Removes data outside threshold (probably errors in tracking), and interpolates

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