def set_analysis_parameters(self):
subjectname = "sujet02"
groupname = "group1"
tests_dir = os.environ.get('BRAINVISA_TEST_RUN_DATA_DIR')
if not tests_dir:
raise RuntimeError('BRAINVISA_TEST_RUN_DATA_DIR is not set')
tests_dir = os.path.join(tests_dir, 'tmp_tests_brainvisa')
filename = os.path.join(tests_dir, 'data_unprocessed', subjectname,
'anatomy', subjectname + ".ima")
subject = Subject(subjectname, groupname, filename)
self.analysis.set_parameters(subject=subject)
from capsul.api import get_process_instance
import_step = get_process_instance(
'morphologist.capsul.import_t1_mri.ImportT1Mri')
import_step.input = subject.filename
import_step.output \
= self.analysis.pipeline.t1mri
import_step.referential = self.analysis.pipeline.t1mri_referential
pipeline_tools.create_output_directories(import_step)
self.analysis.clear_results()
def set_analysis_parameters(self):
subjectname = "sujet02"
groupname = "group1"
test_dir = os.environ.get("BRAINVISA_TESTS_DIR")
if not test_dir:
raise RuntimeError("BRAINVISA_TESTS_DIR is not set")
test_dir = os.path.join(test_dir, "tmp_tests_brainvisa")
filename = os.path.join(test_dir, "data_unprocessed", subjectname, "anatomy", subjectname + ".ima")
subject = Subject(subjectname, groupname, filename)
self.analysis.set_parameters(subject=subject)
from capsul.process import get_process_instance
import_step = get_process_instance("morphologist.capsul.import_t1_mri.ImportT1Mri")
import_step.input = subject.filename
import_step.output = self.analysis.pipeline.process.t1mri
import_step.referential = (
self.analysis.pipeline.process.PrepareSubject_TalairachFromNormalization_source_referential
)
pipeline_tools.create_output_directories(import_step)
self.analysis.clear_results()
def import_data(self, subject):
import_step = self.study.get_process_instance(
'morphologist.capsul.import_t1_mri.ImportT1Mri')
import_step.input = subject.filename
import_step.output = self.pipeline.t1mri
import_step.referential = self.pipeline.t1mri_referential
pipeline_tools.create_output_directories(import_step)
import_step() # run
return import_step.output
def import_data(self, subject):
from capsul.process import get_process_instance
import_step = get_process_instance(
'morphologist.capsul.import_t1_mri.ImportT1Mri')
import_step.input = subject.filename
import_step.output \
= self.pipeline.process.t1mri
import_step.referential = self.pipeline.process. \
PrepareSubject_TalairachFromNormalization_source_referential
pipeline_tools.create_output_directories(import_step)
import_step() # run
return import_step.output
