def get_apartment_info(experiment_config_path, output_dir, keys):
"""Get apartment data for a specific set of "keys"
Args:
experiment_config_path: Path to experiment configuration
(e.g. /lab/repos/celldom/config/experiment/experiment_example_01.yaml)
output_dir: Path to output directory; this is the `output_dir` given to `run_processor`
(e.g. /lab/data/celldom/output/20180820-G3-full)
keys: One or more key string(s) representing apartment address in the form experimental condition fields +
apartment number + street number (':' delimited); Examples:
- gravity:White:3:Control:01:70
- gravity:Pink:3:0.5uM:27:02
- gravity:Blue:3:Control:04:04
"""
if isinstance(keys, str):
keys = [keys]
store = cytometry.get_readonly_datastore(output_dir)
config = experiment_config.ExperimentConfig(celldom.read_config(experiment_config_path))
df = store.get('apartment').reset_index(drop=True)
raw_files_map = store.get('acquisition').set_index('acq_id')['raw_image_path']
key_fields = config.experimental_condition_fields + ['apt_num', 'st_num']
df['key'] = df[key_fields].apply(lambda r: ':'.join(r.values.astype(str)), axis=1)
df['raw_image_path'] = df['acq_id'].map(raw_files_map)
return df[df['key'].isin(keys)].sort_values(['key', 'acq_datetime'])
def __init__(self, conf):
# Load configuration if provided as path instead of deserialized object
if isinstance(conf, str):
conf = celldom.read_config(conf)
self.conf = conf
self._chip_config = None
self._analysis_config = None
self._validate()
def _get_config(self, typ):
if typ not in self.conf:
raise ValueError('Experiment configuration does not have required property "{}"'.format(typ))
res = None
if 'path' in self.conf[typ]:
res = celldom.read_config(self.conf[typ]['path'])
elif 'name' in self.conf[typ]:
res = celldom.get_config(typ, self.conf[typ]['name'])
if res is None:
raise ValueError(
'{} configuration "{}" does not have one of "path" or "name"'
.format(typ.title(), self.conf[typ])
)
return res
def __init__(self, conf):
# Load configuration if provided as path instead of deserialized object
if isinstance(conf, str):
conf = celldom.read_config(conf)
self.conf = conf
def initialize(exp_config_path, output_dir):
global CONFIG
exp_config = experiment_config.ExperimentConfig(
celldom.read_config(exp_config_path))
CONFIG = AppConfig(Experiment(exp_config, output_dir))