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 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( 'Warning: Scriptsfolder already exists and content will be overwritten...\n' ) else: raise IOError('Error: Scriptsfolder already exists!')