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