def make_lawn_measurements(experiment_root, annotations, remake_lawns=False):
if not (pathlib.Path(experiment_root) / 'derived_data' /
'lawn_masks').exists() or remake_lawns:
process_data.annotate(experiment_root,
position_annotators=[process_data.annotate_lawn])
measures = [process_data.LawnMeasurements()]
measurement_name = 'lawn_measures'
process_data.measure_worms(experiment_root, annotations, measures,
measurement_name)
def make_gfp_measurements(experiment_root,
annotations,
fl_measurement_name='gfp',
adult_only=True):
measures = [process_data.FluorMeasurements(fl_measurement_name)]
measurement_name = 'fluorescence_measures'
if adult_only:
annotations = load_data.filter_annotations(
annotations, elegant_filters.filter_by_stage('adult')).copy()
process_data.measure_worms(experiment_root, annotations, measures,
measurement_name)
def make_multipass_measurements(experiment_root, annotations, adult_only=True):
experiment_metadata = load_data.read_metadata(experiment_root)
microns_per_pixel = 1.3 * 5 / (experiment_metadata['objective'] *
experiment_metadata['optocoupler'])
measures = [MultipassPoseMeasurements(microns_per_pixel=microns_per_pixel)]
measurement_name = 'multipass_measures'
if adult_only:
annotations = load_data.filter_annotations(
annotations, elegant_filters.filter_by_stage('adult')).copy()
process_data.measure_worms(experiment_root, annotations, measures,
measurement_name)
def make_mask_measurements(experiment_root, annotations=None, adult_only=True):
#process_data.annotate(experiment_root, annotators=[annotate_timepoints]) # Why?
experiment_metadata = load_data.read_metadata(experiment_root)
microns_per_pixel = 1.3 * 5 / (experiment_metadata['objective'] *
experiment_metadata['optocoupler'])
measures = [MaskPoseMeasurements(microns_per_pixel=microns_per_pixel)]
measurement_name = 'mask_measures'
if annotations is None:
annotations = load_data.read_annotations(experiment_root)
annotations = load_data.filter_annotations(annotations,
filter_excluded)
annotations = load_data.filter_annotations(
annotations, elegant_filters.filter_living_timepoints)
if adult_only:
annotations = load_data.filter_annotations(
annotations, elegant_filters.filter_by_stage('adult'))
process_data.measure_worms(experiment_root, annotations, measures,
measurement_name)
def make_basic_measurements(experiment_root, annotations):
measures = [process_data.BasicMeasurements()]
measurement_name = 'core_measures'
process_data.measure_worms(experiment_root, annotations, measures,
measurement_name)