def run(self):
log = logging.getLogger(".".join([__name__, self.__class__.__name__]))
log.addFilter(logconfig.ThreadContextFilter())
try:
total_start = time.time()
parser_manager = ParserManager()
script_path = os.path.dirname(os.path.abspath(__file__))
parser_manager.set_script_path(script_path)
parser_manager.build_parser()
logconfig.set_additional_handler(
parser_manager.get_log_file_path())
config_directory = parser_manager.get_config_dir()
log.info('used config directory: ' + config_directory +
', path to script: ' + script_path)
scale_override = parser_manager.get_scale_override()
to_json_flag = parser_manager.get_to_json()
service = CrystalMatch(config_directory,
scale_override=scale_override)
service_results = service.perform_match(parser_manager)
total_time = time.time() - total_start
service_results.log_final_result(total_time)
service_results.print_results(to_json_flag)
except IOError as e:
log.error(e)
def test_get_config_returns_CrystalMatch_when_config_directory_is_not_specified_and_running_from_egg(self):
pm = ParserManager()
path = "site-packages/CrystalMatch-v1.0.0-py2.7.egg/CrystalMatch/"
pm.set_script_path(path)
pm.get_args = Mock(return_value=Mock(config=None))
config_dir = pm.get_config_dir()
self.assertTrue(".CrystalMatch" in config_dir)
default_config_dir = abspath(join(pm.get_script_path(), 'config'))
self.assertEqual(config_dir, default_config_dir)
def test_get_log_file_dir_returns_CrystalMatch_when_log_parameter_not_set_and_running_form_egg(self):
pm = ParserManager()
path = "site-packages/CrystalMatch-v1.0.0-py2.7.egg/CrystalMatch/"
pm.set_script_path(path)
pm.get_args = Mock(return_value=Mock(log=None, config="test_config"))
log_dir = pm._get_log_file_dir()
self.assertTrue(".CrystalMatch" in log_dir)
default_log_dir = abspath(join(pm.get_script_path(), 'logs'))
self.assertEqual(log_dir, default_log_dir)
def tearDownClass(self):
pm = ParserManager()
pm.set_script_path('test')
pm.get_args = Mock(return_value=Mock(output=None, log=None, config="test_config"))
default_log_path = pm._get_log_file_dir()
config = pm.get_config_dir()
default_script_path = pm.DEFAULT_SCRIPT_PATH
try:
shutil.rmtree(default_log_path)
shutil.rmtree(config)
shutil.rmtree(default_script_path)
except:
pass
def setUp(self):
self.pm = ParserManager()
path = join(dirname(abspath(__file__)), '..')
self.pm.set_script_path(path)
class TestParserManager(unittest.TestCase):
def setUp(self):
self.pm = ParserManager()
path = join(dirname(abspath(__file__)), '..')
self.pm.set_script_path(path)
def tearDown(self):
# make sure the default destination does not contain processed file
self.pm.get_args = Mock(return_value=Mock(output=None, log=None, config="test_config"))
default_path = self.pm.get_out_file_path()
try:
remove(default_path)
except:
pass
@classmethod
def tearDownClass(self):
pm = ParserManager()
pm.set_script_path('test')
pm.get_args = Mock(return_value=Mock(output=None, log=None, config="test_config"))
default_log_path = pm._get_log_file_dir()
config = pm.get_config_dir()
default_script_path = pm.DEFAULT_SCRIPT_PATH
try:
shutil.rmtree(default_log_path)
shutil.rmtree(config)
shutil.rmtree(default_script_path)
except:
pass
def test_build_parer_creates_parser_object(self):
self.assertIsNone(self.pm.parser)
self.pm.build_parser()
self.assertIsNotNone(self.pm.parser)
def test_get_config_returns_default_config_directory_when_config_directory_is_not_specified(self):
self.pm.get_args = Mock(return_value=Mock(config=None)) #!! return value has to be a mock with particular parameters
config_dir = self.pm.get_config_dir()
default_config_dir = abspath(join(self.pm.get_script_path(), 'config'))
self.assertEqual(config_dir, default_config_dir)
def test_get_config_returns_whatever_is_specified_as_config(self):
test_string = 'ble'
self.pm.get_args = Mock(return_value=Mock(config=test_string))
self.assertIn(test_string, self.pm.get_config_dir())
def test_get_scale_override_returns_None_if_not_set(self):
self.pm.get_args = Mock(return_value=Mock(scale=None))
self.assertIsNone(self.pm.get_scale_override())
def test_get_scale_override_returns_scale_when_set_correctly(self):
correct_scale = "2.0:3.0"
self.pm.get_args = Mock(return_value=Mock(scale=correct_scale))
self.assertEqual(self.pm.get_scale_override(), (float(2),float(3)))
def test_get_scale_override_raises_assertion_error_when_scale_element_divided_by_coma(self):
bad_scale = "20,3"
self.pm.get_args = Mock(return_value=Mock(scale=bad_scale))
with (self.assertRaises(AssertionError)):
self.pm.get_scale_override()
def test_get_scale_override_raises_assertion_error_when_only_one_element(self):
bad_scale = ":3"
self.pm.get_args = Mock(return_value=Mock(scale=bad_scale))
with (self.assertRaises(ValueError)):
self.pm.get_scale_override()
def test_parse_selected_point_returns_empty_array_when_no_points_specified(self):
self.pm.get_args = Mock(return_value=Mock(selected_points=None))
self.assertEqual(self.pm.parse_selected_points_from_args(), [])
def test_parse_selected_point_ignores_point_with_invalid_format(self):
points_invalid_format = "2:4 4:5"
self.pm.get_args = Mock(return_value=Mock(selected_points=points_invalid_format))
self.assertEqual(self.pm.parse_selected_points_from_args(),[])
def test_parse_selected_points_creates_list_of_points_when_the_format_is_valid(self):
valid_format = ['1800,1690']
self.pm.get_args = Mock(return_value=Mock(selected_points=valid_format))
points = self.pm.parse_selected_points_from_args()
self.assertEqual(len(points), 1)
def test_get_focused_image_returns_an_instance_of_image_when_single_image_path_is_passed(self):
path = 'system-tests/resources/stacking/ideal.tif'
self.pm.get_args = Mock(return_value=Mock(beamline_stack_path=path))
im = self.pm.get_focused_image()
self.assertIsInstance(im, Image)
tulp = (0, 0)
self.assertGreater(im.size(), tulp)
def test_get_focused_image_returns_an_instance_of_image_when_directory_path_is_passed(self):
path = 'system-tests/resources/stacking/levels'
self.pm.get_args = Mock(return_value=Mock(beamline_stack_path=path, config="test_config"))
im = self.pm.get_focused_image()
self.assertIsInstance(im, Image)
tulp = (0, 0)
self.assertGreater(im.size(), tulp)
def test_sort_files_according_to_names(self):
path = 'system-tests/resources/stacking/levels'
files = ParserManager._sort_files_according_to_names(path)
self.assertIn('FL0', files[0].name)
self.assertIn('FL10', files[-1].name)
def test_get_focused_image_path_when_beamline_image_path_points_to_file(self):
path = 'system-tests/resources/stacking/ideal.tif'
self.pm.get_args = Mock(return_value=Mock(beamline_stack_path=path))
result_path = self.pm.get_focused_image_path()
self.assertIn('ideal.tif', result_path)
def test_get_focused_image_path_when_beamline_image_path_points_to_dictionary_and_file_saved(self):
path = 'levels'
self.pm.get_args = Mock(return_value=Mock(beamline_stack_path=path, output=None, log=None, config="test_config"))
self.pm._check_is_file = Mock() # mute check_is_file
result_path = self.pm.get_focused_image_path()
self.assertIn('processed.tif', result_path)#def when output and log are none
def test_get_focused_image_path_throws_exp_when_beamline_image_path_points_to_dictionary_and_file_not_saved(self):
path = 'levels'
self.pm.get_args = Mock(
return_value=Mock(beamline_stack_path=path, output=None, log=None, config="test_config"))
with (self.assertRaises(SystemExit)):
self.pm.get_focused_image_path()
def test_get_focused_image_path_beamline_image_path_points_to_nonexisting_file(self):
path = 'ideal_gost.tif'
self.pm.get_args = Mock(return_value=Mock(beamline_stack_path=path))
with (self.assertRaises(SystemExit)):
self.pm.get_focused_image_path()
def test_save_function_saves_image_in_a_default_destination(self):
self.pm.get_args = Mock(return_value=Mock(output=None, log=None, config="test_config"))
default_path = self.pm.get_out_file_path()
self.assertFalse(isfile(default_path))
self.pm.save_focused_image(Image(np.zeros((3, 3),dtype=np.uint8)))
self.assertTrue(isfile(default_path))
def test_get_out_file_path_returns_path_to_output_file_called_processed(self):
self.pm.get_args = Mock(return_value=Mock(output=None, log=None, config="test_config"))
path = self.pm.get_out_file_path()
head, tail = split(path)
self.assertEqual(tail, self.pm.FOCUSED_IMAGE_NAME)
def test_log_file_path_returns_path_to_log_file_called_log(self):
self.pm.get_args = Mock(return_value=Mock(output=None, log=None, config="test_config"))
path = self.pm.get_log_file_path()
head, tail = split(path)
self.assertEqual(tail, self.pm.LOG_FILE_NAME)
def test_get_log_file_dir_returnes_defualt_when_log_parameter_not_set(self):
self.pm.get_args = Mock(return_value=Mock(log=None, config="test_config"))
log_dir = self.pm._get_log_file_dir()
default_log_dir = abspath(join(self.pm.get_script_path(), 'logs'))
self.assertEqual(log_dir, default_log_dir)
def test_get_log_file_dir_uses_location_specified_by_parameter_log(self):
self.pm.get_args = Mock(return_value=Mock(log='test_dir', config="test_config"))
log_dir = self.pm._get_log_file_dir()
head, tail = split(log_dir)
self.assertEqual(tail, 'test_dir')
self.assertEqual(abspath('.'), head )
def test_get_output_dir_uses_location_specified_by_parameter_output(self):
self.pm.get_args = Mock(return_value=Mock(output='out_dir'))
out_dir = self.pm._get_output_dir()
head, tail = split(out_dir)
self.assertEqual(tail, 'out_dir')
self.assertEqual(abspath('.'), head)
def test_get_output_dir_is_log_file_dir_if_parameter_out_not_specified(self):
self.pm.get_args = Mock(return_value=Mock(output=None, log='hoho'))
out_dir = self.pm._get_output_dir()
log_file_dir = self.pm._get_log_file_dir()
head, tail = split(out_dir)
self.assertEqual(tail, 'hoho')
self.assertEqual(out_dir, log_file_dir)
def test_check_is_file_raises_system_exit_when_no_file(self):
with (self.assertRaises(SystemExit)):
self.pm._check_is_file('nofile.tif')
def test_check_make_dirs_creates_new_directory_if_does_not_exist(self):
self.pm.get_args = Mock()
try:
rmdir('new')
except: pass
self.pm._check_make_dirs('new')
self.assertTrue(exists('new'))
rmdir('new')
self.assertFalse(exists('new'))
def test_if_egg_use_home_creates_new_directory(self):
path = abspath("site-packages/CrystalMatch-v1.0.0-py2.7.egg/CrystalMatch/")
new_path = self.pm._if_egg_use_home(path)
self.assertTrue(exists(new_path))
self.assertTrue(".CrystalMatch" in new_path)
def test_get_log_file_dir_returns_CrystalMatch_when_log_parameter_not_set_and_running_form_egg(self):
pm = ParserManager()
path = "site-packages/CrystalMatch-v1.0.0-py2.7.egg/CrystalMatch/"
pm.set_script_path(path)
pm.get_args = Mock(return_value=Mock(log=None, config="test_config"))
log_dir = pm._get_log_file_dir()
self.assertTrue(".CrystalMatch" in log_dir)
default_log_dir = abspath(join(pm.get_script_path(), 'logs'))
self.assertEqual(log_dir, default_log_dir)
def test_get_config_returns_CrystalMatch_when_config_directory_is_not_specified_and_running_from_egg(self):
pm = ParserManager()
path = "site-packages/CrystalMatch-v1.0.0-py2.7.egg/CrystalMatch/"
pm.set_script_path(path)
pm.get_args = Mock(return_value=Mock(config=None))
config_dir = pm.get_config_dir()
self.assertTrue(".CrystalMatch" in config_dir)
default_config_dir = abspath(join(pm.get_script_path(), 'config'))
self.assertEqual(config_dir, default_config_dir)
def test_sort_files_according_to_names(self):
path = 'system-tests/resources/stacking/levels'
files = ParserManager._sort_files_according_to_names(path)
self.assertIn('FL0', files[0].name)
self.assertIn('FL10', files[-1].name)