def test_local_sublist_regexp_match(self):
'''
Method to test that the subject list builder includes only
desired sites from S3
Parameters
----------
self : BuildSublistTestCase
a unittest.TestCase-inherited class
'''
# Import packages
import os
from CPAC.utils import test_init
# Init variables
data_config_dict = self.data_config_dict
subs_match_regex = [
'0010042', '0010064', '0010128', '0021019', '0023008', '0023008',
'0023012', '0027011', '0027018', '0027034', '0027037', '1019436',
'1206380', '1418396'
]
# Copy original inputs to all same folder with
# {participant}_{series} in filenames
base_dir = test_init.return_resource_subfolder('input_reorg_files')
# Set up local templates
anat_template = os.path.join(
base_dir,
'[si]?*{site}_mprage_sub{participant}_sess{session}_ser_{series}.nii.gz'
)
func_template = os.path.join(
base_dir,
'?[si]*{site}_rest_sub{participant}_sess{session}_ser_{series}.nii.gz'
)
# Add include sites to data config dictionary
data_config_dict['anatomicalTemplate'] = anat_template
data_config_dict['functionalTemplate'] = func_template
# Return found filepaths from subject list
filepaths = self._return_sublist_filepaths(data_config_dict)
# And check them
properly_filtered, filter_msg = \
self._check_filepaths(filepaths, subs_match_regex, include=True)
# Assert resulting list is properly filtered
self.assertTrue(properly_filtered, msg=filter_msg)
def test_local_sublist_regexp_match(self):
'''
Method to test that the subject list builder includes only
desired sites from S3
Parameters
----------
self : BuildSublistTestCase
a unittest.TestCase-inherited class
'''
# Import packages
import os
from CPAC.utils import test_init
# Init variables
data_config_dict = self.data_config_dict
subs_match_regex = ['0010042', '0010064', '0010128', '0021019', '0023008',
'0023008', '0023012', '0027011', '0027018',
'0027034', '0027037', '1019436', '1206380', '1418396']
# Copy original inputs to all same folder with
# {participant}_{series} in filenames
base_dir = test_init.return_resource_subfolder('input_reorg_files')
# Set up local templates
anat_template = os.path.join(base_dir,
'[si]?*{site}_mprage_sub{participant}_sess{session}_ser_{series}.nii.gz')
func_template = os.path.join(base_dir,
'?[si]*{site}_rest_sub{participant}_sess{session}_ser_{series}.nii.gz')
# Add include sites to data config dictionary
data_config_dict['anatomicalTemplate'] = anat_template
data_config_dict['functionalTemplate'] = func_template
# Return found filepaths from subject list
filepaths = self._return_sublist_filepaths(data_config_dict)
# And check them
properly_filtered, filter_msg = \
self._check_filepaths(filepaths, subs_match_regex, include=True)
# Assert resulting list is properly filtered
self.assertTrue(properly_filtered, msg=filter_msg)
def test_local_sublist_exclude_subs(self):
'''
Method to test that the subject list builder excludes only
non-desired subjects from S3
Parameters
----------
self : BuildSublistTestCase
a unittest.TestCase-inherited class
'''
# Import packages
import os
from CPAC.utils import test_init
# Init variables
data_config_dict = self.data_config_dict
exclude_subs = ['0010042', '0010064', '0010128']
base_dir = test_init.return_resource_subfolder('input')
# Set up local templates
anat_template = os.path.join(base_dir,
'{site}/{participant}/{session}/{series}/'\
'mprage.nii.gz')
func_template = os.path.join(base_dir,
'{site}/{participant}/{session}/{series}/'\
'rest.nii.gz')
# Add include sites to data config dictionary
data_config_dict['anatomicalTemplate'] = anat_template
data_config_dict['functionalTemplate'] = func_template
data_config_dict['exclusionSubjectList'] = exclude_subs
# Return found filepaths from subject list
filepaths = self._return_sublist_filepaths(data_config_dict)
# And check them
properly_filtered, filter_msg = \
self._check_filepaths(filepaths, exclude_subs, include=False)
# Assert resulting list is properly filtered
self.assertTrue(properly_filtered, msg=filter_msg)
def test_ambiguous_template(self):
'''
Function that tests the subject list cannot be built properly
with an over-ambiguous path template
Parameters
----------
self : BuildSublistTestCase
a unittest.TestCase-inherited class
'''
# Import packages
import os
from CPAC.utils import build_sublist, test_init
# Init variables
# Init variables
data_config_dict = self.data_config_dict
# Copy original inputs to all same folder with
# {participant}_{series} in filenames
base_dir = test_init.return_resource_subfolder('input_reorg_files')
# Set up local templates
anat_template = os.path.join(base_dir,
'{site}_mprage_{participant}_{session}_{series}.nii.gz')
func_template = os.path.join(base_dir,
'{site}_rest_{participant}_{session}_{series}.nii.gz')
# Add include sites to data config dictionary
data_config_dict['anatomicalTemplate'] = anat_template
data_config_dict['functionalTemplate'] = func_template
# Build subject list
try:
self._return_sublist_filepaths(data_config_dict)
except Exception as exc:
self.assertIsInstance(exc, Exception)
def setUp(self):
'''
Method to instantiate the TestCase
Parameters
----------
self : DatSinkTestCase
a unittest.TestCase-inherited class
Returns
-------
None
this function does not return any values, but populates the
instance attributes for:
self.base_dir : string
filepath to base directory of DataSink
self.creds_path : string
filepath to AWS keys credentials file
self.data_sink : nipype DataSink object
object from nipype.interfaces.io.DataSink()
self.ds_node : nipype Node object
object from nipype.pipeline.engine.Node()
self.in_file : string
filepath to nifti file to use as test input to datasink
'''
# Import packages
import os
import sys
import tempfile
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from CPAC.utils import test_init
# Init variables
try:
input_dir = test_init.return_resource_subfolder('input')
subj_id = test_init.return_test_subj()
creds_path = test_init.return_aws_creds()
bucket_name = test_init.default_bucket_name()
except Exception as exc:
print 'Unable to locate testing resources.\nError: %s' % exc
sys.exit()
# Datasink parameters
base_dir = tempfile.mkdtemp()
# Get the input file as an anatomical scan from th e CPAC_RESOURCES
in_file = os.path.join(input_dir, 'site_1', subj_id, 'session_1',
'anat_1', 'mprage.nii.gz')
# Init the datasinks
data_sink = nio.DataSink()
ds_node = pe.Node(nio.DataSink(), name='sinker_0')
# Add instance variables to TestCase
self.base_dir = base_dir
self.bucket_name = bucket_name
self.creds_path = creds_path
self.data_sink = data_sink
self.ds_node = ds_node
self.in_file = in_file
def setUp(self):
'''
Method to instantiate the TestCase
Parameters
----------
self : DatSinkTestCase
a unittest.TestCase-inherited class
Returns
-------
None
this function does not return any values, but populates the
instance attributes for:
self.base_dir : string
filepath to base directory of DataSink
self.creds_path : string
filepath to AWS keys credentials file
self.data_sink : nipype DataSink object
object from nipype.interfaces.io.DataSink()
self.ds_node : nipype Node object
object from nipype.pipeline.engine.Node()
self.in_file : string
filepath to nifti file to use as test input to datasink
'''
# Import packages
import os
import sys
import tempfile
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from CPAC.utils import test_init
# Init variables
try:
input_dir = test_init.return_resource_subfolder('input')
subj_id = test_init.return_test_subj()
creds_path = test_init.return_aws_creds()
bucket_name = test_init.default_bucket_name()
except Exception as exc:
print 'Unable to locate testing resources.\nError: %s' % exc
sys.exit()
# Datasink parameters
base_dir = tempfile.mkdtemp()
# Get the input file as an anatomical scan from th e CPAC_RESOURCES
in_file = os.path.join(input_dir, 'site_1', subj_id, 'session_1',
'anat_1', 'mprage.nii.gz')
# Init the datasinks
data_sink = nio.DataSink()
ds_node = pe.Node(nio.DataSink(), name='sinker_0')
# Add instance variables to TestCase
self.base_dir = base_dir
self.bucket_name = bucket_name
self.creds_path = creds_path
self.data_sink = data_sink
self.ds_node = ds_node
self.in_file = in_file
