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"""
Tests for dcmstack.extract
"""
import sys, warnings
from os import path
import pytest
from nibabel.nicom import csareader
try:
import pydicom
except ImportError:
import dicom as pydicom
from . import test_dir, src_dir
with warnings.catch_warnings():
warnings.simplefilter('ignore')
from dcmstack import extract
class TestCsa(object):
def setup_method(self, method):
data_fn = path.join(test_dir, 'data', 'extract', 'csa_test.dcm')
self.data = pydicom.read_file(data_fn)
def teardown_method(self, method):
del self.data
def test_simplify(self):
assert extract.simplify_csa_dict(None) == None
csa_dict = csareader.read(self.data[pydicom.tag.Tag(0x29, 0x1010)].value)
simp_dict = extract.simplify_csa_dict(csa_dict)
for tag in csa_dict['tags']:
items = csa_dict['tags'][tag]['items']
if len(items) == 0:
assert(not tag in simp_dict)
elif len(items) == 1:
assert simp_dict[tag] == items[0]
else:
assert simp_dict[tag] == items
def test_csa_image_trans(self):
csa_dict = extract.csa_series_trans_func(self.data[(0x29, 0x1010)])
assert csa_dict["EchoLinePosition"] == 64
def test_parse_phx_line(self):
assert(extract._parse_phoenix_line("") is None)
assert(extract._parse_phoenix_line("#test = 2") is None)
assert extract._parse_phoenix_line('test = "" 2 ""') == ('test', ' 2 ')
assert extract._parse_phoenix_line('test = "" #2 ""'), ('test', ' #2 ')
assert extract._parse_phoenix_line('test = "" 2 ""#=') == ('test', ' 2 ')
assert extract._parse_phoenix_line("test = 2#") == ('test', 2)
assert extract._parse_phoenix_line("test = 0x2") == ('test', 2)
assert extract._parse_phoenix_line("test = 2.") == ('test', 2.0)
with pytest.raises(extract.PhoenixParseError):
extract._parse_phoenix_line('test = blah')
with pytest.raises(extract.PhoenixParseError):
extract._parse_phoenix_line('==')
with pytest.raises(extract.PhoenixParseError):
extract._parse_phoenix_line('test')
with pytest.raises(extract.PhoenixParseError):
extract._parse_phoenix_line('test = "" 2 ""3')
def test_csa_series_trans(self):
csa_dict = extract.csa_series_trans_func(self.data[(0x29, 0x1020)])
assert csa_dict['MrPhoenixProtocol.sEFISPEC.bEFIDataValid'] == 1
class TestMetaExtractor(object):
def setup_method(self, method):
data_fn = path.join(test_dir, 'data', 'extract', 'csa_test.dcm')
self.data = pydicom.read_file(data_fn)
def teardown_method(self,method):
del self.data
def test_get_elem_key(self):
ignore_rules = (extract.ignore_pixel_data,)
extractor = extract.MetaExtractor(ignore_rules=ignore_rules)
for elem in self.data:
key = extractor._get_elem_key(elem)
assert(key.strip() != '')
assert(key[0].isalpha())
assert(key[-1].isalnum())
def test_get_elem_value(self):
ignore_rules = (extract.ignore_pixel_data,)
extractor = extract.MetaExtractor(ignore_rules=ignore_rules)
for elem in self.data:
value = extractor._get_elem_value(elem)
if elem.VM > 1:
assert(isinstance(value, list))
if elem.VR in list(extract.unpack_vr_map) + ['DS', 'IS']:
if elem.VM == 1:
assert(not isinstance(value, str))
else:
assert(not any(isinstance(val, str) for val in value))
def test_dup_trans(self):
translators = [extract.csa_image_trans, extract.csa_image_trans]
extractor = extract.MetaExtractor(translators=translators)
with pytest.raises(ValueError):
extractor(self.data)
def test_reloc_private(self):
extractor = extract.MetaExtractor()
self.data[(0x29, 0x10)].tag = pydicom.tag.Tag((0x29, 0x20))
self.data[(0x29, 0x1010)].tag = pydicom.tag.Tag((0x29, 0x2010))
self.data[(0x29, 0x1020)].tag = pydicom.tag.Tag((0x29, 0x2020))
meta_dict = extractor(self.data)
assert meta_dict["CsaImage.EchoLinePosition"] == 64
assert meta_dict['CsaSeries.MrPhoenixProtocol.sEFISPEC.bEFIDataValid'] == 1
def test_non_reloc_private(self):
extractor = extract.MetaExtractor()
meta_dict = extractor(self.data)
assert meta_dict["CsaImage.EchoLinePosition"] == 64
assert meta_dict['CsaSeries.MrPhoenixProtocol.sEFISPEC.bEFIDataValid'] == 1
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