def run_paths_of_merges(yamlfile, logging=True): ipl = IPL(yaml=yamlfile) ipl.set_indent(1) params = rdict(data=ipl.get_params()) if logging: ipl.startlogger(filename=params['resultfolder'] + 'paths_of_merges.log', type='w', name='PathsOfMerges') else: ipl.startlogger() try: # # Copy the script file and the parameters to the scriptsfolder # copy(inspect.stack()[0][1], params['scriptsfolder']) # copy(yamlfile, params['scriptsfolder'] + 'paths_of_merges.parameters.yml') # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) paths_of_merges(ipl, params['debug']) # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile']) ipl.logging('') ipl.stoplogger() except: ipl.errout('Unexpected error')
def run_find_border_contacts(yamlfile, logging=True): ipl = IPL(yaml=yamlfile) ipl.set_indent(1) params = rdict(data=ipl.get_params()) if logging: ipl.startlogger(filename=params['resultfolder'] + 'find_border_contacts.log', type='w', name='FindBorderContacts') else: ipl.startlogger() try: # # Copy the script file and the parameters to the scriptsfolder # copy(inspect.stack()[0][1], params['scriptsfolder']) # copy(yamlfile, params['scriptsfolder'] + 'find_border_contacts.parameters.yml') # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) find_border_contacts(ipl) # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile']) ipl.logging('') ipl.stoplogger() except: ipl.errout('Unexpected error')
def run_compute_feature_images(yamlfile): ipl = IPL(yaml=yamlfile) ipl.set_indent(1) params = rdict(data=ipl.get_params()) ipl.startlogger(filename=params['resultfolder'] + 'compute_feature_images.log', type='w', name='ComputeFeatureImages') try: # # Copy the script file and the parameters to the scriptsfolder # copy(inspect.stack()[0][1], params['scriptsfolder']) # copy(yamlfile, params['scriptsfolder'] + 'compute_feature_images.parameters.yml') # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) compute_feature_images(ipl) # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile']) ipl.logging('') ipl.stoplogger() except: ipl.errout('Unexpected error')
def run_remove_small_objects(yamlfile): ipl = IPL( yaml=yamlfile, yamlspec={'path': 'datafolder', 'filename': 'labelsfile', 'skeys': 'labelsname'}, recursive_search=True, nodata=True ) # Set indentation of the logging ipl.set_indent(1) params = ipl.get_params() ipl.startlogger(filename=params['resultfolder'] + 'remove_small_objects.log', type='w', name='RemoveSmallObjects') try: # # Copy the script file and the parameters to the scriptsfolder # copy(inspect.stack()[0][1], params['scriptsfolder']) # copy(yamlfile, params['scriptsfolder'] + 'remove_small_objects.parameters.yml') ipl.logging('\nipl datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) remove_small_objects(ipl) ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile']) ipl.logging('') ipl.stoplogger() except: ipl.errout('Unexpected error')
def run_random_forest(yamlfile, logging=True, make_only_feature_array=False, debug=False, write=True): ipl = IPL(yaml=yamlfile) ipl.set_indent(1) params = rdict(data=ipl.get_params()) if logging: ipl.startlogger(filename=params['resultfolder'] + 'random_forest.log', type='w', name='RandomForest') else: ipl.startlogger() try: # # Copy the script file and the parameters to the scriptsfolder # copy(inspect.stack()[0][1], params['scriptsfolder']) # copy(yamlfile, params['scriptsfolder'] + 'random_forest.parameters.yml') # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) if make_only_feature_array: make_feature_arrays(ipl) else: result = IPL() result['result'], result['evaluation'] = random_forest(ipl, debug=debug) # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) if write: result.write(filepath=params['resultfolder'] + params['resultsfile']) ipl.logging('') ipl.stoplogger() except: ipl.errout('Unexpected error')
def run_remove_small_objects(yamlfile): ipl = IPL(yaml=yamlfile, yamlspec={ 'path': 'datafolder', 'filename': 'labelsfile', 'skeys': 'labelsname' }, recursive_search=True, nodata=True) # Set indentation of the logging ipl.set_indent(1) params = ipl.get_params() ipl.startlogger(filename=params['resultfolder'] + 'remove_small_objects.log', type='w', name='RemoveSmallObjects') try: # # Copy the script file and the parameters to the scriptsfolder # copy(inspect.stack()[0][1], params['scriptsfolder']) # copy(yamlfile, params['scriptsfolder'] + 'remove_small_objects.parameters.yml') ipl.logging('\nipl datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) remove_small_objects(ipl) ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) # ipl.write(filepath=params['intermedfolder'] + params['largeobjfile']) ipl.logging('') ipl.stoplogger() except: ipl.errout('Unexpected error')
def run_random_forest(yamlfile, logging=True, make_only_feature_array=False, debug=False, write=True): ipl = IPL(yaml=yamlfile) ipl.set_indent(1) params = rdict(data=ipl.get_params()) if logging: ipl.startlogger(filename=params['resultfolder'] + 'random_forest.log', type='w', name='RandomForest') else: ipl.startlogger() try: # # Copy the script file and the parameters to the scriptsfolder # copy(inspect.stack()[0][1], params['scriptsfolder']) # copy(yamlfile, params['scriptsfolder'] + 'random_forest.parameters.yml') # ipl.logging('\nInitial datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) if make_only_feature_array: make_feature_arrays(ipl) else: result = IPL() result['result'], result['evaluation'] = random_forest(ipl, debug=debug) # ipl.logging('\nFinal datastructure: \n\n{}', ipl.datastructure2string(maxdepth=3)) if write: result.write(filepath=params['resultfolder'] + params['resultsfile']) ipl.logging('') ipl.stoplogger() except: ipl.errout('Unexpected error')