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')
yamlfile = args.ParameterFile
resultfolder = None
if args.ResultFolder is not None:
resultfolder = args.ResultFolder[0]
if resultfolder is not None:
replace('./parameters.yml', '^resultfolder: .*$',
"resultfolder: {}".format(resultfolder))
replace('./parameters.yml', '^intermedfolder: .*$',
'intermedfolder: {}{}'.format(resultfolder, 'intermed/'))
replace('./parameters.yml', '^scriptsfolder: .*$',
'scriptsfolder: {}{}'.format(resultfolder, 'scripts/'))
if not os.path.exists(resultfolder):
os.makedirs(resultfolder)
yaml = YamlParams(filename=yamlfile)
params = yaml.get_params()
yaml.startlogger(filename=params['resultfolder'] + 'pipeline.log',
type='w',
name='Pipeline')
yaml.logging('Starting script with:')
yaml.logging(' ParameterFile = {}\n', yamlfile)
# Create folder for scripts
if not os.path.exists(params['scriptsfolder']):
os.makedirs(params['scriptsfolder'])
else:
if params['overwriteresults']:
yaml.logging(
