def add_entity(self, domain, **kwargs):
''' Add a new Entity to tracking. '''
# Set the entity's mapping func if one was specified
map_func = kwargs.get('map_func', None)
if map_func is not None and not callable(kwargs['map_func']):
if self.entity_mapper is None:
raise ValueError("Mapping function '%s' specified for Entity "
"'%s', but no entity mapper was passed when "
"initializing the current Layout. Please make"
" sure the 'entity_mapper' argument is set." %
(map_func, kwargs['name']))
map_func = getattr(self.entity_mapper, kwargs['map_func'])
kwargs['map_func'] = map_func
ent = Entity(domain=domain, **kwargs)
domain.add_entity(ent)
if ent.mandatory:
self.mandatory.add(ent.id)
if ent.directory is not None:
ent.directory = ent.directory.replace('{{root}}', self.root)
self.entities[ent.id] = ent
for alias in ent.aliases:
self.entities[alias] = ent
if self.dynamic_getters:
func = partial(getattr(self, 'get'),
target=ent.name,
return_type='id')
func_name = inflect.engine().plural(ent.name)
setattr(self, 'get_%s' % func_name, func)
def add_entity(self, **kwargs):
# Set up the entities we need to track
ent = Entity(**kwargs)
if ent.mandatory:
self.mandatory.add(ent.name)
if ent.directory is not None:
ent.directory = ent.directory.replace('{{root}}', self.root)
self.entities[ent.name] = ent
if self.dynamic_getters:
func = partial(getattr(self, 'get'), target=ent.name,
return_type='id')
func_name = inflect.engine().plural(ent.name)
setattr(self, 'get_%s' % func_name, func)
def add_derivatives(self, path, **kwargs):
''' Add BIDS-Derivatives datasets to tracking.
Args:
path (str, list): One or more paths to BIDS-Derivatives datasets.
Each path can point to either a derivatives/ directory
containing one more more pipeline directories, or to a single
pipeline directory (e.g., derivatives/fmriprep).
kwargs (dict): Optional keyword arguments to pass on to
BIDSLayout() when initializing each of the derivative datasets.
'''
paths = listify(path)
deriv_dirs = []
# Collect all paths that contain a dataset_description.json
def check_for_description(dir):
dd = os.path.join(dir, 'dataset_description.json')
return os.path.exists(dd)
for p in paths:
p = os.path.abspath(p)
if os.path.exists(p):
if check_for_description(p):
deriv_dirs.append(p)
else:
subdirs = [
d for d in os.listdir(p)
if os.path.isdir(os.path.join(p, d))
]
for sd in subdirs:
sd = os.path.join(p, sd)
if check_for_description(sd):
deriv_dirs.append(sd)
local_entities = set(ent.name for ent in self.entities.values())
for deriv in deriv_dirs:
dd = os.path.join(deriv, 'dataset_description.json')
with open(dd, 'r', encoding='utf-8') as ddfd:
description = json.load(ddfd)
pipeline_name = description.get('PipelineDescription',
{}).get('Name', None)
if pipeline_name is None:
raise ValueError("Every valid BIDS-derivatives dataset must "
"have a PipelineDescription.Name field set "
"inside dataset_description.json.")
if pipeline_name in self.derivatives:
raise ValueError("Pipeline name '%s' has already been added "
"to this BIDSLayout. Every added pipeline "
"must have a unique name!")
# Default config and sources values
kwargs['config'] = kwargs.get('config') or ['bids', 'derivatives']
kwargs['sources'] = kwargs.get('sources') or self
self.derivatives[pipeline_name] = BIDSLayout(deriv, **kwargs)
# Propagate derivative entities into top-level dynamic getters
deriv_entities = set(
ent.name
for ent in self.derivatives[pipeline_name].entities.values())
for deriv_ent in deriv_entities - local_entities:
local_entities.add(deriv_ent)
getter = 'get_' + inflect.engine().plural(deriv_ent)
if not hasattr(self, getter):
func = partial(self.get,
target=deriv_ent,
return_type='id')
setattr(self, getter, func)