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added facial tremor variable

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This commit is contained in:
Ubuntu
2020-12-01 19:54:35 +00:00
parent 4cacbb8b37
commit 9a751ca434
9 changed files with 78 additions and 59 deletions
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2
dbm_lib/dbm_features/raw_features/movement/__init__.py
View File

@@ -13,4 +13,4 @@ import os
DBMLIB_PATH = os.path.dirname(__file__)
DBMLIB_VTREMOR_LIB = os.path.abspath(os.path.join(DBMLIB_PATH,
'../../../../resources/libraries/voice_tremor.praat'))
DBMLIB_FTREMOR_CONFIG = os.path.abspath(os.path.join(DBMLIB_PATH, '../resources/features/facial/config.json'))
DBMLIB_FTREMOR_CONFIG = os.path.abspath(os.path.join(DBMLIB_PATH, '../../../../resources/features/facial/config.json'))

43
dbm_lib/dbm_features/raw_features/movement/facial_tremor.py
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@@ -25,7 +25,7 @@ def compute_features(out_dir, df_of, r_config):
Returns: features in vector format
"""
config = json.loads(open(DBMLIB_FTREMOR_CONFIG,'r').read())
logger.info('json file read')
pattern_x = re.compile("l\d+_x")
pattern_y = re.compile("l\d+_y")
@@ -40,7 +40,7 @@ def compute_features(out_dir, df_of, r_config):
df_of= df_of[(df_of[landmark_columns]!= 0).any(axis=1)]
df_of.reset_index(inplace=True)
num_frames = len(df)
num_frames = len(df_of)
logger.info("Number of frames to be processed: {}".format(str(num_frames)))
landmarks = config['landmarks']
@@ -104,7 +104,7 @@ def compute_features(out_dir, df_of, r_config):
for i, landmark in enumerate(landmarks):
fac_features_dict['fac_features_mean_{}'.format(landmark)] = [fac_features2[i]]
raw_variable_map = 'fac_tremor_median_{}'.format(landmark)
fac_features_dict[r_config.raw_feature[raw_variable_map]] = [fac_features1[i]]
fac_features_dict[r_config.base_raw['raw_feature'][raw_variable_map]] = [fac_features1[i]]
fac_features_dict['fac_disp_median_{}'.format(landmark)] = [fac_disp_median[i]]
fac_features_dict['fac_corr_{}'.format(landmark)] = [fac_corr[i]]
@@ -123,7 +123,7 @@ def empty_frame(landmarks, r_config, error_reason):
fac_features_dict = {}
for i, landmark in enumerate(landmarks):
raw_variable_map = 'fac_tremor_median_{}'.format(landmark)
fac_features_dict[r_config.raw_feature[raw_variable_map]] = [np.nan]
fac_features_dict[r_config.base_raw['raw_feature'][raw_variable_map]] = [np.nan]
fac_features_dict['fac_features_mean_{}'.format(landmark)] = [np.nan]
fac_features_dict['fac_disp_median_{}'.format(landmark)] = [np.nan]
@@ -133,27 +133,32 @@ def empty_frame(landmarks, r_config, error_reason):
empty_frame = pd.DataFrame.from_dict(fac_features_dict)
return empty_frame
def fac_tremor_process(video_uri,out_dir,r_config, model_output=False):
def fac_tremor_process(video_uri, out_dir, r_config, model_output=False):
"""
processing input videos
"""
try:
logger.info('filtering path: ',video_uri,out_dir)
input_loc, out_loc, fl_name = ut.filter_path(video_uri, out_dir)
of_csv_path = glob.glob(join(out_loc, fl_name + '_OF_video_features/*.csv'))
# try:
input_loc, out_loc, fl_name = ut.filter_path(video_uri, out_dir)
of_csv_path = glob.glob(join(out_loc, fl_name + '_OF_video_features/*.csv'))
if len(of_csv_path)>0:
of_csv = of_csv_path[0]
df_of = pd.read_csv(of_csv, error_bad_lines=False)
if len(of_csv_path)>0:
of_csv = of_csv_path[0]
df_of = pd.read_csv(of_csv, error_bad_lines=False)
logger.info('Processing Output file {} '.format(os.path.join(out_loc, fl_name)))
logger.info('Processing Output file {} '.format(os.path.join(out_loc, fl_name)))
feats = compute_features(of_csv_path , df_of, r_config)
if model_output:
result = score(feats, r_config)
feats = pd.concat([feats, result], axis=1)
feats = compute_features(of_csv_path , df_of, r_config)
# if model_output:
# result = score(feats, r_config)
# feats = pd.concat([feats, result], axis=1)
ut.save_output(feats, out_loc, fl_name, ft_dir, csv_ext)
ut.output_audio_feature(feats, new_out_base_dir, '/'+fac_dir, fac_ext)
except Exception as e:
# except Exception as e:
logger.error('Failed to process video file')

5
dbm_lib/dbm_features/raw_features/movement/head_motion.py
View File

@@ -179,11 +179,12 @@ def run_head_movement(video_uri, out_dir, r_config):
out_dir: (str) Output directory for processed output; r_config: raw variable config object
"""
try:
#filtering path to generate input & output path
input_loc, out_loc, fl_name = ut.filter_path(video_uri, out_dir)
of_csv_path = glob.glob(join(out_loc, fl_name + '_OF_features/*.csv'))
if len(of_csv_path)>0:
of_csv = of_csv_path[0]
@@ -192,4 +193,4 @@ def run_head_movement(video_uri, out_dir, r_config):
logger.info('Processing Output file {} '.format(os.path.join(out_loc, fl_name)))
calc_head_mov(video_uri, df_of, out_loc, fl_name, r_config)
except Exception as e:
logger.error('Failed to process video file')
logger.error('Failed to process video file')

6
dbm_lib/dbm_features/raw_features/movement/voice_tremor.py
View File

@@ -47,7 +47,7 @@ def prepare_vtrem_output(audio_file, out_loc, r_config, fl_name):
df_tremor = tremor_praat(audio_file, r_config)
df_tremor[r_config.err_reason] = 'Pass'# will replace with threshold in future release
logger.info('Processing Output file {} '.format(out_loc))
logger.info('Processing Output file {} '.format(os.path.join(out_loc, fl_name)))
ut.save_output(df_tremor, out_loc, fl_name, vt_dir, csv_ext)
def prepare_empty_vt(out_loc, fl_name, r_config, error_txt):
@@ -61,7 +61,7 @@ def prepare_empty_vt(out_loc, fl_name, r_config, error_txt):
out_val = [[np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, error_txt]]
df_tremor = pd.DataFrame(out_val, columns = cols)
logger.info('Saving Output file {} '.format(out_loc))
logger.info('Saving Output file {} '.format(os.path.join(out_loc, fl_name)))
ut.save_output(df_tremor, out_loc, fl_name, vt_dir, csv_ext)
def run_vtremor(video_uri, out_dir, r_config):
@@ -74,9 +74,9 @@ def run_vtremor(video_uri, out_dir, r_config):
out_dir: (str) Output directory for processed output
"""
try:
input_loc, out_loc, fl_name = ut.filter_path(video_uri, out_dir)
aud_filter = glob.glob(join(input_loc, fl_name + '.wav'))
if len(aud_filter)>0:
audio_file = aud_filter[0]

13
dbm_lib/dbm_features/raw_features/video/open_face_process.py
View File

@@ -15,7 +15,7 @@ from dbm_lib.dbm_features.raw_features.util import util as ut
logging.basicConfig(level=logging.INFO)
logger=logging.getLogger()
def batch_open_face(filepaths,video_url, input_dir, out_dir, of_path,video_tracking=False):
def batch_open_face(filepaths,video_url, input_dir, out_dir, of_path, video_tracking=False):
""" Computes open_face features for the files in filepaths
Args:
@@ -31,21 +31,22 @@ def batch_open_face(filepaths,video_url, input_dir, out_dir, of_path,video_track
Returns:
--------
(itreable[str]) list of .csv files
"""
"""
if video_tracking:
suffix = '_OF_video_features/'
suffix = '_OF_video_features'
else:
suffix = '_OF_features'
csv_files = []
for fp in filepaths:
try:
_, out_loc, fl_name = ut.filter_path(video_url, out_dir)
full_f_name = fl_name + suffix
output_directory = os.path.join(out_loc, full_f_name)
if not os.path.isdir(output_directory):
os.mkdir(output_directory)
csv_files.append(ut.compute_open_face_features(fp,output_directory,of_path))
except Exception as e:
@@ -69,7 +70,7 @@ def process_open_face(video_uri, input_dir, out_dir, of_path, dbm_group,video_tr
return
filepaths = [video_uri]
csv_filepaths = batch_open_face(filepaths, video_uri, input_dir, out_dir, of_path,video_tracking)
csv_filepaths = batch_open_face(filepaths, video_uri, input_dir, out_dir, of_path, video_tracking)
except Exception as e:
logger.error('Failed to process video file')