def run_suite(show_list=False, pipeline_filter=''):
import os
import pkg_resources as p
import CPAC.pipeline.cpac_runner as cpac_runner
test_config_dir = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs"))
data_test = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs",
"data-test_S3-ADHD200_1.yml"))
data_test_no_scan_param = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs",
"data-test_S3-ADHD200_no-params.yml"))
data_test_fmap = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs",
"data-test_S3-NKI-RS_fmap.yml"))
if show_list:
print("")
print("Availables pipelines:")
no_params = False
for config_file in os.listdir(test_config_dir):
if config_file.startswith('pipe-test_'):
if pipeline_filter not in config_file:
continue
if show_list:
print("- " + config_file[len('pipe-test_'):])
continue
pipe = os.path.join(test_config_dir, config_file)
if 'DistCorr' in pipe:
data = data_test_fmap
elif not no_params:
data = data_test_no_scan_param
no_params = True
else:
data = data_test
# run
cpac_runner.run(pipe, data)
if show_list:
print("")
def run(data_config, pipe_config=None):
if not pipe_config:
import os
import pkg_resources as p
pipe_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"pipeline_config_template.yml"))
if data_config == 'ADHD200':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-ADHD200.yml"))
if data_config == 'ADHD200_2':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-ADHD200_only2.yml"))
if data_config == 'ABIDE':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-ABIDE.yml"))
if data_config == 'NKI-RS':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-NKI-RocklandSample.yml"))
import CPAC.pipeline.cpac_runner as cpac_runner
cpac_runner.run(pipe_config, data_config)
def run_suite():
import os
import pkg_resources as p
import CPAC.pipeline.cpac_runner as cpac_runner
test_config_dir = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs"))
data_test = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs",
"data-test_S3-ADHD200_1.yml"))
data_test_no_scan_param = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs",
"data-test_S3-ADHD200_no-params.yml"))
data_test_fmap = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs", "test_configs",
"data-test_S3-NKI-RS_fmap.yml"))
no_params = False
for config_file in os.listdir(test_config_dir):
if 'pipe-test' in config_file:
pipe = os.path.join(test_config_dir, config_file)
if 'DistCorr' in pipe:
data = data_test_fmap
elif not no_params:
data = data_test_no_scan_param
no_params = True
else:
data = data_test
# run
cpac_runner.run(pipe, data)
def cpac_cli(config, subs, pipe):
#extract_data.run(args.config_file)
#config = yaml.load(open(args.config_file,'r'))
#subject_list_file = os.path.join(config.get('outputSubjectListLocation'),args.sub_list)
run(config, subs, pipe)
def run(data_config,
pipe_config=None,
num_cores=None,
ndmg_mode=False,
debug=False):
if not pipe_config:
import os
import pkg_resources as p
pipe_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"pipeline_config_template.yml"))
if pipe_config == 'benchmark-ants':
import os
import pkg_resources as p
pipe_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"pipeline_config_benchmark-ANTS.yml"))
if pipe_config == 'benchmark-fnirt':
import os
import pkg_resources as p
pipe_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"pipeline_config_benchmark-FNIRT.yml"))
if pipe_config == 'anat-only':
import os
import pkg_resources as p
pipe_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"pipeline_config_anat-only.yml"))
if data_config == 'benchmark-data':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_cpac_benchmark.yml"))
if data_config == 'ADHD200':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-ADHD200.yml"))
if data_config == 'ADHD200_2':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-ADHD200_only2.yml"))
if data_config == 'ABIDE':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-ABIDE.yml"))
if data_config == 'NKI-RS':
import os
import pkg_resources as p
data_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"data_config_S3-BIDS-NKI-RocklandSample.yml"))
if ndmg_mode:
import os
import pkg_resources as p
pipe_config = \
p.resource_filename("CPAC",
os.path.join("resources",
"configs",
"pipeline_config_ndmg.yml"))
import CPAC.pipeline.cpac_runner as cpac_runner
cpac_runner.run(pipe_config,
data_config,
num_subs_at_once=num_cores,
debug=debug)
