Could not run anipose with the toml file #140
Description
Hi all,
I am currently trying to integrate frames from 4 cameras to have a 3d posture estimation of my animals. I have problems when trying to run the anipose analyze command.
The below is the config file that I use and the error message.
project = "BRYE203c"
# path = "/nemo/lab/iacarusof/home/users/yangy1/anipose"
path = 'E:\anipose'
# model_folder = "/nemo/lab/iacarusof/home/shared/DeepLabCut/BRYE203c_4_cameras-YY-2024-06-14"
model_folder = 'Z:\home\shared\DeepLabCut\BRYE203c_4_cameras-YY-2024-06-14'
nesting = 0
video_extension = 'avi'
[pipeline]
videos_raw = "240524" # change this if you'd like to change name of "videos-raw" folder
[calibration]
# checkerboard / charuco / aruco
board_type = "charuco"
# width and height of grid, in squares
board_size = [6, 8]
# number of bits in the markers, if aruco/charuco
board_marker_bits = 6
# number of markers in dictionary, if aruco/charuco
board_marker_dict_number = 250
# length of marker side
board_marker_length = 15 # mm
# If charuco or checkerboard, square side length
board_square_side_length = 30 # mm
[manual_verification]
# true / false
manually_verify = true
animal_calibration = false
# calibration_init = 'calibration_init.toml'
[filter]
enabled = true
medfilt = 13
offset_threshold = 25
score_threshold = 0.8
spline = true
[labeling]
scheme = [
['Snout', 'Right_Ear'],
['Snout', 'Left_Ear'],
['Snout', 'Neck'],
['Neck', 'Shoulder'],
['Shoulder', 'Hip'],
['Hip', 'Tail_Base'],
['Tail_Base', 'Tail_End'],
['Left_Ear', 'Neck'],
['Right_Ear', 'Neck'],
['Left_Ear', 'Right_Ear'],
['Prey', 'Prey_Dup_bar'],
['Left_Screen', 'Right_Screen'],
['Left_Corridor', 'Right_Corridor']
]
[triangulation]
cam_regex = r'BRYE203c_\d{6}_(\w+?)\d+\.avi'
axes = [
["x", "Left_Corridor", "Right_Corridor"],
["z", "Prey", "Prey_Dup_bar"]
]
reference_point = "Left_Corridor"
cam_align = "TOP"
(anipose) E:\anipose>anipose calibrate
Traceback (most recent call last):
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\toml\decoder.py", line 512, in loads
multibackslash)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\toml\decoder.py", line 778, in load_line
value, vtype = self.load_value(pair[1], strictly_valid)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\toml\decoder.py", line 910, in load_value
raise ValueError("This float doesn't have a leading "
ValueError: This float doesn't have a leading digit
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\Scripts\anipose.exe\__main__.py", line 7, in <module>
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1078, in main
rv = self.invoke(ctx)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1685, in invoke
super().invoke(ctx)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\click\core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\click\decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\anipose\anipose.py", line 113, in cli
ctx.obj = load_config(config)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\anipose\anipose.py", line 81, in load_config
config = toml.load(fname)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\toml\decoder.py", line 134, in load
return loads(ffile.read(), _dict, decoder)
File "C:\Users\yangy1\AppData\Local\anaconda3\envs\anipose\lib\site-packages\toml\decoder.py", line 514, in loads
raise TomlDecodeError(str(err), original, pos)
toml.decoder.TomlDecodeError: This float doesn't have a leading digit (line 62 column 1 char 1481)
Does anyone what would cause this problem?
Thanks!
Yi