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import sys, shutil, json
from os import path as opath
from tempfile import mkdtemp
from glob import glob
import numpy as np
from . import test_dir, src_dir
from dcmstack import dcmstack_cli, nitool_cli
test_data = {}
def setup_module():
input_dir = mkdtemp(prefix='dcmstack_cli_test_in')
data_dir = opath.join(test_dir,
'data',
'dcmstack',
'2D_16Echo_qT2')
fns = ('TE_20_SlcPos_-33.707626341697.dcm',
'TE_20_SlcPos_-23.207628249046.dcm',
'TE_40_SlcPos_-33.707626341697.dcm',
'TE_40_SlcPos_-23.207628249046.dcm',
)
for fn in fns:
shutil.copyfile(opath.join(data_dir, fn), opath.join(input_dir, fn))
test_data['base_dir'] = input_dir
def teardown_module():
shutil.rmtree(test_data['base_dir'])
del test_data['base_dir']
def make_niftis(out_dir, extra_args=tuple()):
'''Helper function runs dcmstack and returns any Nifti files
'''
assert len(glob(opath.join(out_dir, '*.nii*'))) == 0
args = ['dcmstack', test_data['base_dir'], '--dest-dir', out_dir]
args.extend(extra_args)
dcmstack_cli.main(args)
return glob(opath.join(out_dir, '*.nii*'))
class CliTest(object):
def setup_method(self):
self.out_dir = mkdtemp(prefix='dcmstack_cli_test_out')
def teardown_method(self):
shutil.rmtree(self.out_dir)
class TestDcmstackCli(CliTest):
def test_basic(self):
nii_paths = make_niftis(self.out_dir)
assert len(nii_paths) == 1
def test_embed(self):
nii_paths = make_niftis(self.out_dir, ['--embed'])
assert len(nii_paths) == 1
class TestNitoolCli(CliTest):
def test_basic(self):
nii_path = make_niftis(self.out_dir, ['--embed'])[0]
json_path = opath.join(self.out_dir, 'meta.json')
nitool_cli.main(['nitool', 'dump', nii_path, json_path])
with open(json_path) as fp:
meta = json.load(fp)
print(json.dumps(meta, indent=4))
assert('dcmmeta_version' in meta)
assert('dcmmeta_affine' in meta)
assert('dcmmeta_reorient_transform' in meta)
assert meta['dcmmeta_shape'] == [192, 192, 2, 2]
assert meta['dcmmeta_slice_dim'] == 2
assert meta['global']['const']['Rows'] == 192
assert meta['global']['const']['Columns'] == 192
assert(np.allclose(meta['time']['samples']['EchoTime'], [20.0, 40.0]))
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