replace non interpolated values by last valid value; change lxml version; fixed interpolation message
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davidpagnon
parent
9a60007a5a
commit
de14598a42
@ -97,7 +97,7 @@ def interpolate_zeros_nans(col, *args):
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f_interp = interpolate.interp1d(idx_good, col[idx_good], kind=kind, fill_value='extrapolate', bounds_error=False)
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col_interp = np.where(mask, col, f_interp(col.index)) #replace at false index with interpolated values
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# Reintroduce nans if lenght of sequence > N
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# Reintroduce nans if length of sequence > N
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idx_notgood = np.where(~mask)[0]
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gaps = np.where(np.diff(idx_notgood) > 1)[0] + 1 # where the indices of true are not contiguous
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sequences = np.split(idx_notgood, gaps)
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@ -321,6 +321,7 @@ def recap_triangulate(config, error, nb_cams_excluded, keypoints_names, cam_excl
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likelihood_threshold = config.get('triangulation').get('likelihood_threshold_triangulation')
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show_interp_indices = config.get('triangulation').get('show_interp_indices')
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interpolation_kind = config.get('triangulation').get('interpolation')
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interp_gap_smaller_than = config.get('triangulation').get('interp_if_gap_smaller_than')
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make_c3d = config.get('triangulation').get('make_c3d')
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handle_LR_swap = config.get('triangulation').get('handle_LR_swap')
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undistort_points = config.get('triangulation').get('undistort_points')
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@ -343,14 +344,14 @@ def recap_triangulate(config, error, nb_cams_excluded, keypoints_names, cam_excl
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logging.info(f'Mean reprojection error for {name} is {mean_error_keypoint_px} px (~ {mean_error_keypoint_m} m), reached with {mean_cam_excluded_keypoint} excluded cameras. ')
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if show_interp_indices:
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if interpolation_kind != 'none':
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if len(list(interp_frames[n][idx])) ==0:
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if len(list(interp_frames[n][idx])) == 0 and len(list(non_interp_frames[n][idx])) == 0:
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logging.info(f' No frames needed to be interpolated.')
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else:
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if len(list(interp_frames[n][idx]))>0:
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interp_str = str(interp_frames[n][idx]).replace(":", " to ").replace("'", "").replace("]", "").replace("[", "")
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logging.info(f' Frames {interp_str} were interpolated.')
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if len(list(non_interp_frames[n][idx]))>0:
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noninterp_str = str(non_interp_frames[n][idx]).replace(":", " to ").replace("'", "").replace("]", "").replace("[", "")
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logging.info(f' Frames {non_interp_frames[n][idx]} could not be interpolated: consider adjusting thresholds.')
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logging.info(f' Frames {noninterp_str} were not interpolated.')
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else:
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logging.info(f' No frames were interpolated because \'interpolation_kind\' was set to none. ')
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@ -360,6 +361,8 @@ def recap_triangulate(config, error, nb_cams_excluded, keypoints_names, cam_excl
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logging.info(f'\n--> Mean reprojection error for all points on all frames is {mean_error_px} px, which roughly corresponds to {mean_error_mm} mm. ')
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logging.info(f'Cameras were excluded if likelihood was below {likelihood_threshold} and if the reprojection error was above {error_threshold_triangulation} px.')
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if interpolation_kind != 'none':
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logging.info(f'Gaps were interpolated with {interpolation_kind} method if smaller than {interp_gap_smaller_than} frames.')
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logging.info(f'In average, {mean_cam_excluded} cameras had to be excluded to reach these thresholds.')
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cam_excluded_count[n] = {i: v for i, v in zip(cam_names, cam_excluded_count[n].values())}
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@ -707,7 +710,6 @@ def triangulate_all(config):
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show_interp_indices = config.get('triangulation').get('show_interp_indices')
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undistort_points = config.get('triangulation').get('undistort_points')
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make_c3d = config.get('triangulation').get('make_c3d')
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frame_rate = config.get('project').get('frame_rate')
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calib_dir = [os.path.join(session_dir, c) for c in os.listdir(session_dir) if 'calib' in c.lower()][0]
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try:
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@ -803,7 +805,6 @@ def triangulate_all(config):
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# Q_old = Q except when it has nan, otherwise it takes the Q_old value
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nan_mask = np.isnan(Q)
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Q_old = np.where(nan_mask, Q_old, Q)
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error_old, nb_cams_excluded_old, id_excluded_cams_old = error.copy(), nb_cams_excluded.copy(), id_excluded_cams.copy()
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Q = [[] for n in range(nb_persons_to_detect)]
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error = [[] for n in range(nb_persons_to_detect)]
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nb_cams_excluded = [[] for n in range(nb_persons_to_detect)]
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@ -908,7 +909,10 @@ def triangulate_all(config):
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Q_tot[n] = Q_tot[n].apply(interpolate_zeros_nans, axis=0, args = [interp_gap_smaller_than, interpolation_kind])
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except:
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logging.info(f'Interpolation was not possible for person {n}. This means that not enough points are available, which is often due to a bad calibration.')
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# Q_tot.replace(np.nan, 0, inplace=True)
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# Fill non-interpolated values with last valid one
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for n in range(nb_persons_to_detect):
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Q_tot[n] = Q_tot[n].ffill(axis=0).bfill(axis=0)
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# Q_tot[n].replace(np.nan, 0, inplace=True)
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# Create TRC file
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trc_paths = [make_trc(config, Q_tot[n], keypoints_names, f_range, id_person=n) for n in range(len(Q_tot))]
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