Error calculating skeleton from contour

Line 52 of WCON demo.py:

'skeleton': bw.h_dorsal_contour}  # DEBUG

... 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

openworm / open-worm-analysis-toolbox

Error calculating skeleton from contour #185