def test_split_pattern(self):
"""Test the split_pattern property."""
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
self.assertEqual(wrapper.split_pattern(), 'S%s_C%c_Z%z_T%t')
self.assertEqual(wrapper.split_pattern(win32=True),
'S%%s_C%%c_Z%%z_T%%t')
def test_metadata_from_fname(self):
"""Test the metadata_from_fname function."""
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
meta_data = wrapper.metadata_from_fname("S1_C2_Z3_T4.tif", md5_hexdigest="dummy")
self.assertEqual(meta_data["filename"], "S1_C2_Z3_T4.tif")
self.assertEqual(meta_data["md5_hexdigest"], "dummy")
self.assertEqual(meta_data["series"], 1)
self.assertEqual(meta_data["channel"], 2)
self.assertEqual(meta_data["zslice"], 3)
self.assertEqual(meta_data["timepoint"], 4)
meta_data = wrapper.metadata_from_fname('S83_C4_Z5_T6.tif', md5_hexdigest="dummy")
self.assertEqual(meta_data["series"], 83)
def test_metadata_from_fname(self):
"""Test the metadata_from_fname function."""
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
meta_data = wrapper.metadata_from_fname("S1_C2_Z3_T4.tif",
md5_hexdigest="dummy")
self.assertEqual(meta_data["filename"], "S1_C2_Z3_T4.tif")
self.assertEqual(meta_data["md5_hexdigest"], "dummy")
self.assertEqual(meta_data["series"], 1)
self.assertEqual(meta_data["channel"], 2)
self.assertEqual(meta_data["zslice"], 3)
self.assertEqual(meta_data["timepoint"], 4)
meta_data = wrapper.metadata_from_fname('S83_C4_Z5_T6.tif',
md5_hexdigest="dummy")
self.assertEqual(meta_data["series"], 83)
def test_run_command_linux(self):
"""Test the run_command function."""
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
sys.platform = 'linux2'
cmd = wrapper.run_command('test.lif')
self.assertEqual(
cmd, ['bfconvert', '-nolookup', 'test.lif', 'S%s_C%c_Z%z_T%t.tif'])
cmd = wrapper.run_command('test.lif',
output_dir=os.path.join('/', 'tmp'))
self.assertEqual(cmd, [
'bfconvert', '-nolookup', 'test.lif',
os.path.join('/', 'tmp', 'S%s_C%c_Z%z_T%t.tif')
])
def test_run_command_windows(self):
"""Test the run_command function."""
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
sys.platform = 'win32'
cmd = wrapper.run_command('test.lif')
self.assertEqual(cmd, ['bfconvert.bat',
'-nolookup',
'test.lif',
'S%%s_C%%c_Z%%z_T%%t.tif'])
cmd = wrapper.run_command('test.lif', output_dir=os.path.join('/', 'tmp'))
self.assertEqual(cmd, ['bfconvert.bat',
'-nolookup',
'test.lif',
os.path.join('/', 'tmp', 'S%%s_C%%c_Z%%z_T%%t.tif')])
def test_manifest(self):
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
with patch('os.listdir', return_value=[]):
entry = Mock()
entry.directory = 'dummy'
self.assertEqual(wrapper.manifest(entry), [])
with patch('os.listdir', return_value=['S1_C2_Z3_T4.tif']), \
patch('jicbioimage.core.io._md5_hexdigest_from_file', return_value="dummy_hexdigest"):
entry = Mock()
entry.directory = 'dummy'
self.assertEqual(wrapper.manifest(entry),
[{"filename": 'S1_C2_Z3_T4.tif',
"md5_hexdigest": "dummy_hexdigest",
"series": 1,
"channel": 2,
"zslice": 3,
"timepoint": 4}])
def test_manifest(self):
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
with patch('os.listdir', return_value=[]):
entry = Mock()
entry.directory = 'dummy'
self.assertEqual(wrapper.manifest(entry), [])
with patch('os.listdir', return_value=['S1_C2_Z3_T4.tif']), \
patch('jicbioimage.core.io._md5_hexdigest_from_file', return_value="dummy_hexdigest"):
entry = Mock()
entry.directory = 'dummy'
self.assertEqual(wrapper.manifest(entry), [{
"filename": 'S1_C2_Z3_T4.tif',
"md5_hexdigest": "dummy_hexdigest",
"series": 1,
"channel": 2,
"zslice": 3,
"timepoint": 4
}])
def test_split_order(self):
"""Test the split_order attribute."""
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
self.assertEqual(wrapper._split_order, ['s', 'c', 'z', 't'])
def test_backend_attribute(self):
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
self.assertEqual(wrapper.backend, 'backend')
def test_split_pattern(self):
"""Test the split_pattern property."""
from jicbioimage.core.io import BFConvertWrapper
wrapper = BFConvertWrapper('backend')
self.assertEqual(wrapper.split_pattern(), 'S%s_C%c_Z%z_T%t')
self.assertEqual(wrapper.split_pattern(win32=True), 'S%%s_C%%c_Z%%z_T%%t')
