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Commit 975cc6b3 authored by Constantin Pape's avatar Constantin Pape
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Add simpler check for registration wrapper

parent 0af98c8a
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1 merge request!6Add python scripts to run registration on the cluster
......@@ -8,6 +8,42 @@ sys.path.insert(0, '../..')
from scripts.extension.registration import ApplyRegistrationLocal
def check_wrapper_simple():
in_path = '/g/almf/software/elastix-test/muscles.tif'
tmp_folder = '/g/kreshuk/pape/Work/my_projects/dev-platy/test/registration/tmp_registration_simple'
out_path = os.path.join(tmp_folder, 'out')
in_list = [in_path]
out_list = [out_path]
in_file = './in_list.json'
with open(in_file, 'w') as f:
json.dump(in_list, f)
out_file = './out_list.json'
with open(out_file, 'w') as f:
json.dump(out_list, f)
task = ApplyRegistrationLocal
conf_dir = './configs'
os.makedirs(conf_dir, exist_ok=True)
global_conf = task.default_global_config()
shebang = '/g/kreshuk/pape/Work/software/conda/miniconda3/envs/cluster_env37/bin/python'
global_conf.update({'shebang': shebang})
with open(os.path.join(conf_dir, 'global.config'), 'w') as f:
json.dump(global_conf, f)
trafo = '/g/almf/software/elastix-test/TransformParameters.RotationPreAlign.0.txt'
t = task(tmp_folder=tmp_folder, config_dir=conf_dir, max_jobs=1,
input_path_file=in_file, output_path_file=out_file, transformation_file=trafo)
ret = luigi.build([t], local_scheduler=True)
assert ret
expected_out_xml = out_path + '.xml'
assert os.path.exists(expected_out_xml), expected_out_xml
expected_out_h5 = out_path + '.h5'
assert os.path.exists(expected_out_h5), expected_out_h5
def check_wrapper():
in_path = os.path.join('/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/9.9.9/images/ProSPr',
'Stomach_forRegistration.tif')
......@@ -43,4 +79,5 @@ def check_wrapper():
assert os.path.exists(expected_out), expected_out
check_wrapper()
# check_wrapper()
check_wrapper_simple()
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