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_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')