def run_compute_feature_images(yamlfile):
yparams = YamlParams(filename=yamlfile)
params = yparams.get_params()
# Logger stuff
yparams.set_indent(1)
yparams.startlogger(filename=params['resultfolder'] +
'compute_feature_images.log',
type='w',
name='ComputeFeatureImages')
try:
# experiment_parser(yparams, compute_feature_images, 'compute_feature_images')
experiment_parser(yparams, compute_feature_images_multi,
'compute_feature_images')
# compute_feature_images(yparams)
yparams.logging('')
yparams.stoplogger()
except:
raise
yparams.errout('Unexpected error')
def run_random_forest(yamlfile,
logging=True,
make_only_feature_array=False,
debug=False,
write=True):
yparams = YamlParams(filename=yamlfile)
params = yparams.get_params()
# Logger stuff
yparams.set_indent(1)
yparams.startlogger(filename=params['resultfolder'] + 'random_forest.log',
type='w',
name='RandomForest')
try:
random_forest(yparams, debug)
yparams.logging('')
yparams.stoplogger()
except:
raise
yparams.errout('Unexpected error')
def run_compute_paths(yamlfile, logging=True):
yparams = YamlParams(filename=yamlfile)
params = yparams.get_params()
# Logger stuff
yparams.set_indent(1)
yparams.startlogger(filename=params['resultfolder'] + 'compute_paths.log',
type='w',
name='ComputePaths')
try:
compute_paths(yparams)
yparams.logging('')
yparams.stoplogger()
except:
yparams.errout('Unexpected error')
def run_find_border_contacts(yamlfile, logging=True):
yparams = YamlParams(filename=yamlfile)
params = yparams.get_params()
# Logger stuff
yparams.set_indent(1)
yparams.startlogger(filename=params['resultfolder'] +
'find_border_contacts.log',
type='w',
name='FindBorderContacts')
try:
find_border_contacts(yparams)
yparams.logging('')
yparams.stoplogger()
except:
yparams.errout('Unexpected error')
def run_remove_small_objects(yamlfile):
yparams = YamlParams(filename=yamlfile)
params = yparams.get_params()
# Logger stuff
yparams.set_indent(1)
yparams.startlogger(filename=params['resultfolder'] +
'remove_small_objects.log',
type='w',
name='RemoveSmallObjects')
try:
remove_small_objects(yparams)
yparams.logging('')
yparams.stoplogger()
except:
yparams.errout('Unexpected error')
if params['run_remove_small_objects']:
yaml.logging('Removing small objects ...')
run_remove_small_objects(paramfile_rso)
if params['run_merge_adjacent_objects']:
yaml.logging('Merging adjacent objects ...')
run_merge_adjacent_objects(paramfile_mao)
if params['run_compute_feature_images']:
yaml.logging('Computing feature images ...')
run_compute_feature_images(paramfile_cfi)
if params['run_find_border_contacts']:
yaml.logging('Finding border contacts ...')
run_find_border_contacts(paramfile_fbc)
if params['run_compute_paths']:
yaml.logging('Calculating paths ...')
run_compute_paths(paramfile_pth)
if params['run_features_of_paths']:
yaml.logging('Extracting features along paths ...')
run_features_of_paths(paramfile_fop)
if params['run_random_forest']:
yaml.logging('Running random forst on paths ...')
run_random_forest(paramfile_rdf)
# _________________________________________________________________________________________
yaml.stoplogger()
