def input_tree(self):
sessions = []
visit_ids = set()
for subj_id, visits in list(self.PROJECT_STRUCTURE.items()):
for visit_id, filesets in list(visits.items()):
sessions.append(
Session(subj_id,
visit_id,
filesets=[
Fileset(d,
text_format,
subject_id=subj_id,
visit_id=visit_id,
from_study=((self.STUDY_NAME
if d != 'one' else None)))
for d in filesets
]))
visit_ids.add(visit_id)
subjects = [
Subject(i, sessions=[s for s in sessions if s.subject_id == i])
for i in self.PROJECT_STRUCTURE
]
visits = [
Visit(i, sessions=[s for s in sessions if s.visit == i])
for i in visit_ids
]
return Tree(subjects=subjects, visits=visits)
def input_tree(self):
fields = [
Field(name='acquired_field1',
value=1,
dtype=int, frequency='per_session',
subject_id='0', visit_id='0'),
Field(name='acquired_field1',
value=2,
dtype=int, frequency='per_session',
subject_id='0', visit_id='1'),
Field(name='acquired_field1',
value=3,
dtype=int, frequency='per_session',
subject_id='1', visit_id='0'),
Field(name='acquired_field1',
value=4,
dtype=int, frequency='per_session',
subject_id='1', visit_id='1'),
Field(name='acquired_field2',
value=10,
dtype=int, frequency='per_session',
subject_id='0', visit_id='0'),
Field(name='acquired_field2',
value=20,
dtype=int, frequency='per_session',
subject_id='0', visit_id='1'),
Field(name='acquired_field2',
value=30,
dtype=int, frequency='per_session',
subject_id='1', visit_id='0')]
return Tree.construct(self.dataset.repository, fields=fields)
def input_tree(self):
sessions = []
for subj_id in self.SUBJECT_IDS:
for visit_id in self.VISIT_IDS:
sessions.append(
Session(subj_id,
visit_id,
filesets=[
Fileset('one_input',
text_format,
subject_id=subj_id,
visit_id=visit_id),
Fileset('ten_input',
text_format,
subject_id=subj_id,
visit_id=visit_id)
]))
subjects = [
Subject(i, sessions=[s for s in sessions if s.subject_id == i])
for i in self.SUBJECT_IDS
]
visits = [
Visit(i, sessions=[s for s in sessions if s.visit == i])
for i in self.VISIT_IDS
]
return Tree(subjects=subjects, visits=visits)
def input_tree(self):
fields = []
for subj_i in range(self.NUM_SUBJECTS):
for visit_i in range(self.NUM_VISITS):
fields.append(
Field(name='acquired_field1', value=visit_i + subj_i * 10,
dtype=int, frequency='per_session',
subject_id=str(subj_i), visit_id=str(visit_i)))
return Tree.construct(self.dataset.repository, fields=fields)
def input_tree(self):
filesets = []
for subj_id, visit_ids in list(self.PROJECT_STRUCTURE.items()):
for visit_id, fileset_names in list(visit_ids.items()):
# Create filesets
for name in fileset_names:
from_analysis = self.STUDY_NAME if name != 'one' else None
filesets.append(
Fileset(name,
text_format,
subject_id=subj_id,
visit_id=visit_id,
from_analysis=from_analysis))
return Tree.construct(self.dataset.repository, filesets=filesets)
def input_tree(self):
filesets = []
for subj_id in self.SUBJECT_IDS:
for visit_id in self.VISIT_IDS:
filesets.append(
Fileset('one_input',
text_format,
subject_id=subj_id,
visit_id=visit_id))
filesets.append(
Fileset('ten_input',
text_format,
subject_id=subj_id,
visit_id=visit_id))
return Tree.construct(self.dataset.repository, filesets=filesets)
def get_tree(self, dataset, sync_with_repo=False):
filesets = [
# Subject1
Fileset('ones', text_format,
frequency='per_subject',
subject_id='subject1',
resource_name='text',
dataset=dataset),
Fileset('tens', text_format,
frequency='per_subject',
subject_id='subject1',
resource_name='text',
dataset=dataset),
# subject1/visit1
Fileset('hundreds', text_format,
subject_id='subject1', visit_id='visit1',
resource_name='text',
dataset=dataset),
Fileset('ones', text_format,
subject_id='subject1', visit_id='visit1',
resource_name='text',
dataset=dataset),
Fileset('tens', text_format,
subject_id='subject1', visit_id='visit1',
resource_name='text',
dataset=dataset),
Fileset('with_header', text_format,
frequency='per_session',
subject_id='subject1', visit_id='visit1',
resource_name='text',
dataset=dataset),
# subject1/visit2
Fileset('ones', text_format,
subject_id='subject1', visit_id='visit2',
resource_name='text',
dataset=dataset),
Fileset('tens', text_format,
subject_id='subject1', visit_id='visit2',
resource_name='text',
dataset=dataset),
# Subject 2
Fileset('ones', text_format,
frequency='per_subject',
subject_id='subject2',
resource_name='text',
dataset=dataset),
Fileset('tens', text_format,
frequency='per_subject',
subject_id='subject2',
resource_name='text',
dataset=dataset),
# subject2/visit1
Fileset('ones', text_format,
subject_id='subject2', visit_id='visit1',
resource_name='text',
dataset=dataset),
Fileset('tens', text_format,
subject_id='subject2', visit_id='visit1',
resource_name='text',
dataset=dataset),
# subject2/visit2
Fileset('ones', text_format,
subject_id='subject2', visit_id='visit2',
resource_name='text',
dataset=dataset),
Fileset('tens', text_format,
subject_id='subject2', visit_id='visit2',
resource_name='text',
dataset=dataset),
# Visit 1
Fileset('ones', text_format,
frequency='per_visit',
visit_id='visit1',
resource_name='text',
dataset=dataset),
# Analysis
Fileset('ones', text_format,
frequency='per_dataset',
resource_name='text',
dataset=dataset)]
fields = [
# Subject 2
Field('e', value=3.33333,
frequency='per_subject',
subject_id='subject2',
dataset=dataset),
# subject2/visit2
Field('a', value=22,
subject_id='subject2', visit_id='visit2',
dataset=dataset),
Field('b', value=220,
subject_id='subject2', visit_id='visit2',
dataset=dataset),
Field('c', value='buggy',
subject_id='subject2', visit_id='visit2',
dataset=dataset),
# Subject1
Field('e', value=4.44444,
frequency='per_subject',
subject_id='subject1',
dataset=dataset),
# subject1/visit1
Field('a', value=1,
subject_id='subject1', visit_id='visit1',
dataset=dataset),
Field('b', value=10,
subject_id='subject1', visit_id='visit1',
dataset=dataset),
Field('d', value=42.42,
subject_id='subject1', visit_id='visit1',
dataset=dataset),
# subject1/visit2
Field('a', value=2,
subject_id='subject1', visit_id='visit2',
dataset=dataset),
Field('c', value='van',
subject_id='subject1', visit_id='visit2',
dataset=dataset),
# Visit 1
Field('f', value='dog',
frequency='per_visit',
visit_id='visit1',
dataset=dataset),
# Visit 2
Field('f', value='cat',
frequency='per_visit',
visit_id='visit2',
dataset=dataset),
# Analysis
Field('g', value=100,
frequency='per_dataset',
dataset=dataset)]
# Set URI and IDs if necessary for repository type
if sync_with_repo:
for fileset in filesets:
fileset.get()
for field in fields:
field.get()
tree = Tree.construct(self.dataset, filesets, fields)
return tree
def get_tree(self, repository, set_ids=False):
sessions = [
Session('subject1',
'visit1',
filesets=[
Fileset('hundreds',
text_format,
subject_id='subject1',
visit_id='visit1',
repository=repository),
Fileset('ones',
text_format,
subject_id='subject1',
visit_id='visit1',
repository=repository),
Fileset('tens',
text_format,
subject_id='subject1',
visit_id='visit1',
repository=repository)
],
fields=[
Field('a',
value=1,
subject_id='subject1',
visit_id='visit1',
repository=repository),
Field('b',
value=10,
subject_id='subject1',
visit_id='visit1',
repository=repository),
Field('d',
value=42.42,
subject_id='subject1',
visit_id='visit1',
repository=repository)
]),
Session('subject1',
'visit2',
filesets=[
Fileset('ones',
text_format,
subject_id='subject1',
visit_id='visit2',
repository=repository),
Fileset('tens',
text_format,
subject_id='subject1',
visit_id='visit2',
repository=repository)
],
fields=[
Field('a',
value=2,
subject_id='subject1',
visit_id='visit2',
repository=repository),
Field('c',
value='van',
subject_id='subject1',
visit_id='visit2',
repository=repository)
]),
Session('subject2',
'visit1',
filesets=[
Fileset('ones',
text_format,
subject_id='subject2',
visit_id='visit1',
repository=repository),
Fileset('tens',
text_format,
subject_id='subject2',
visit_id='visit1',
repository=repository)
],
fields=[]),
Session('subject2',
'visit2',
filesets=[
Fileset('ones',
text_format,
subject_id='subject2',
visit_id='visit2',
repository=repository),
Fileset('tens',
text_format,
subject_id='subject2',
visit_id='visit2',
repository=repository)
],
fields=[
Field('a',
value=22,
subject_id='subject2',
visit_id='visit2',
repository=repository),
Field('b',
value=220,
subject_id='subject2',
visit_id='visit2',
repository=repository),
Field('c',
value='buggy',
subject_id='subject2',
visit_id='visit2',
repository=repository)
])
]
project = Tree(
subjects=[
Subject('subject1',
sessions=[
s for s in sessions if s.subject_id == 'subject1'
],
filesets=[
Fileset('ones',
text_format,
frequency='per_subject',
subject_id='subject1',
repository=repository),
Fileset('tens',
text_format,
frequency='per_subject',
subject_id='subject1',
repository=repository)
],
fields=[
Field('e',
value=4.44444,
frequency='per_subject',
subject_id='subject1',
repository=repository)
]),
Subject('subject2',
sessions=[
s for s in sessions if s.subject_id == 'subject2'
],
filesets=[
Fileset('ones',
text_format,
frequency='per_subject',
subject_id='subject2',
repository=repository),
Fileset('tens',
text_format,
frequency='per_subject',
subject_id='subject2',
repository=repository)
],
fields=[
Field('e',
value=3.33333,
frequency='per_subject',
subject_id='subject2',
repository=repository)
])
],
visits=[
Visit('visit1',
sessions=[s for s in sessions if s.visit_id == 'visit1'],
filesets=[
Fileset('ones',
text_format,
frequency='per_visit',
visit_id='visit1',
repository=repository)
],
fields=[
Field('f',
value='dog',
frequency='per_visit',
visit_id='visit1',
repository=repository)
]),
Visit('visit2',
sessions=[s for s in sessions if s.visit_id == 'visit2'],
filesets=[],
fields=[
Field('f',
value='cat',
frequency='per_visit',
visit_id='visit2',
repository=repository)
])
],
filesets=[
Fileset('ones',
text_format,
frequency='per_study',
repository=repository)
],
fields=[
Field('g',
value=100,
frequency='per_study',
repository=repository)
])
if set_ids: # For xnat repository
for fileset in project.filesets:
fileset._id = fileset.name
for visit in project.visits:
for fileset in visit.filesets:
fileset._id = fileset.name
for subject in project.subjects:
for fileset in subject.filesets:
fileset._id = fileset.name
for session in subject.sessions:
for fileset in session.filesets:
fileset._id = fileset.name
return project