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... uses the dorsal contour in place of the skeleton, because of an error in calculating the skeleton from the contour. If we replace the above with:
'skeleton': bw.h_skeleton} # DEBUG
We get this error:
RUNNING TEST WCON demo.py:
Traceback (most recent call last):
File "../open_worm_analysis_toolbox/prefeatures/basic_worm.py", line 447, in h_skeleton
return self._h_skeleton
AttributeError: 'BasicWorm' object has no attribute '_h_skeleton'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "WCON demo.py", line 83, in <module>
w = schafer_to_WCON(schafer_bw_file_path)
File "WCON demo.py", line 52, in schafer_to_WCON
'skeleton': bw.h_skeleton} # DEBUG
File "../open_worm_analysis_toolbox/prefeatures/basic_worm.py", line 452, in h_skeleton
self.h_ventral_contour, self.h_dorsal_contour)[1]
File "../open_worm_analysis_toolbox/prefeatures/pre_features.py", line 96, in compute_skeleton_and_widths
frames_to_plot=[])
File "../open_worm_analysis_toolbox/prefeatures/skeleton_calculator1.py", line 124, in compute_skeleton_and_widths
polyorder=SMOOTHING_ORDER)
File "/home/ubuntu/miniconda3/lib/python3.5/site-packages/scipy/signal/_savitzky_golay.py", line 344, in savgol_filter
_fit_edges_polyfit(x, window_length, polyorder, deriv, delta, axis, y)
File "/home/ubuntu/miniconda3/lib/python3.5/site-packages/scipy/signal/_savitzky_golay.py", line 222, in _fit_edges_polyfit
polyorder, deriv, delta, y)
File "/home/ubuntu/miniconda3/lib/python3.5/site-packages/scipy/signal/_savitzky_golay.py", line 180, in _fit_edge
x_edge = axis_slice(x, start=window_start, stop=window_stop, axis=axis)
File "/home/ubuntu/miniconda3/lib/python3.5/site-packages/scipy/signal/_arraytools.py", line 45, in axis_slice
b = a[a_slice]
IndexError: invalid slice
@JimHokanson does this error ring any bells for you? Otherwise I will investigate. Thanks
The text was updated successfully, but these errors were encountered:
Line 52 of
WCON demo.py
:... uses the dorsal contour in place of the skeleton, because of an error in calculating the skeleton from the contour. If we replace the above with:
We get this error:
@JimHokanson does this error ring any bells for you? Otherwise I will investigate. Thanks
The text was updated successfully, but these errors were encountered: