def perform_match(self, parser_manager):
"""
Perform image alignment and crystal matching returning a results object.
:param .
:return: ServiceResult object.
"""
log = logging.getLogger(".".join([__name__, self.__class__.__name__]))
log.addFilter(logconfig.ThreadContextFilter())
extra = self._config_align.all_to_json()
extra.update(self._config_crystal.all_to_json())
log = logging.LoggerAdapter(log, extra)
log.info("Matching Started")
log.debug(extra)
input_poi = parser_manager.parse_selected_points_from_args()
beamline_image = parser_manager.get_focused_image()
parser_manager.save_focused_image(beamline_image)
focused_image_path = parser_manager.get_focused_image_path()
formulatrix_image_path = parser_manager.get_formulatrix_image_path()
job_id = parser_manager.get_job_id()
# Create the images
image1 = Image.from_file(formulatrix_image_path)
image2 = beamline_image
# Create results object
service_result = ServiceResult(job_id, formulatrix_image_path,
focused_image_path)
# Perform alignment
try:
aligned_images, scaled_poi = self._perform_alignment(
image1, image2, input_poi)
service_result.set_image_alignment_results(aligned_images)
# Perform Crystal Matching - only proceed if we have a valid alignment
if aligned_images.alignment_status_code(
) == ALIGNED_IMAGE_STATUS_OK:
match_results = self._perform_matching(aligned_images,
scaled_poi,
parser_manager)
service_result.append_crystal_matching_results(match_results)
except Exception as e:
if sys.version_info[0] < 3:
log.error("ERROR: " + e.message)
else:
log.error("ERROR: " + str(e))
service_result.set_err_state(e)
return service_result
def test_exit_code_in_std_out_with_error(self, mock_print):
# Set up mock for successful image alignment
status = ALIGNED_IMAGE_STATUS_OK
confidence = 9.8
transform = (1.0, Point(3.0, 4.0))
mock_aligned_image = self.mock_aligned_images(confidence, status, transform)
result = ServiceResult("job-id", "fomulatrix", "beamline")
result.set_image_alignment_results(mock_aligned_image)
# Throw an exception and print results
e = Exception("test exception")
result.set_err_state(e)
result.print_results(False)
# Test for exit status of -1 with err message
mock_print.assert_has_calls([call('exit_code:-1, test exception')])
def test_exit_code_in_json_output_with_error(self):
# Set up mock for successful image alignment
status = ALIGNED_IMAGE_STATUS_OK
confidence = 9.8
transform = (1.0, Point(3.0, 4.0))
mock_aligned_image = self.mock_aligned_images(confidence, status, transform)
result = ServiceResult("job-id", "fomulatrix", "beamline")
result.set_image_alignment_results(mock_aligned_image)
# Throw an exception and print results
e = Exception("test exception")
result.set_err_state(e)
json_obj = result.print_results(jason_output = True)
# Test for exit status of -1 in JSON object
self.failUnlessEqual(-1, json_obj['exit_code']['code'])
self.failUnlessEqual('test exception', json_obj['exit_code']['err_msg'])