def test_append_multiple_crystal_match_results(self, mock_print):
# Setup - create mock result
result = ServiceResult("job-id", "fomulatrix", "beamline")
# Set 1
new_positions = [Point(100, 100)]
deltas = [Point(3, 4)]
mean_errors = ["0.45"]
status_codes = [CRYSTAL_MATCH_STATUS_OK]
mock_match_results = self.mock_crystal_matcher_results(deltas, mean_errors, new_positions, status_codes)
result.append_crystal_matching_results(mock_match_results)
# Set 2
new_positions = [Point(123, 456), Point(654, 321)]
deltas = [Point(1, 2), Point(7, 8)]
mean_errors = ["4.56", "65.4"]
status_codes = [CRYSTAL_MATCH_STATUS_OK, CRYSTAL_MATCH_STATUS_FAIL]
mock_match_results = self.mock_crystal_matcher_results(deltas, mean_errors, new_positions, status_codes)
result.append_crystal_matching_results(mock_match_results)
result.print_results(False)
# Test
mock_print.assert_has_calls([
call("\nlocation ; transform ; status ; mean error"),
call("poi:(100.00, 100.00) z: 0 ; (3.00, 4.00) ; 1, OK ; 0.45"),
call("poi:(123.00, 456.00) z: 0 ; (1.00, 2.00) ; 1, OK ; 4.56"),
call("poi:(654.00, 321.00) z: 0 ; (7.00, 8.00) ; 0, FAIL ; 65.4"),
])
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_failed_crystal_match_result_prints_correctly(self, mock_print):
# Setup - create mock result
result = ServiceResult("job-id", "fomulatrix", "beamline")
new_positions = [Point(654, 321)]
deltas = [Point(7, 8)]
mean_errors = ["65.4"]
status_codes = [CRYSTAL_MATCH_STATUS_FAIL]
mock_match_results = self.mock_crystal_matcher_results(deltas, mean_errors, new_positions, status_codes)
result.append_crystal_matching_results(mock_match_results)
result.print_results(False)
# Test
mock_print.assert_has_calls([
call("\nlocation ; transform ; status ; mean error"),
call("poi:(654.00, 321.00) z: 0 ; (7.00, 8.00) ; 0, FAIL ; 65.4"),
])
def test_append_single_crystal_match_result(self, mock_print):
# Setup - create mock result
new_positions = [Point(100, 100)]
deltas = [Point(3, 4)]
mean_errors = ["0.45"]
status_codes = [CRYSTAL_MATCH_STATUS_OK]
mock_match_results = self.mock_crystal_matcher_results(deltas, mean_errors, new_positions, status_codes)
# Run
result = ServiceResult("job-id", "fomulatrix", "beamline")
result.append_crystal_matching_results(mock_match_results)
result.print_results(False)
# Test
mock_print.assert_has_calls([
call("\nlocation ; transform ; status ; mean error"),
call("poi:(100.00, 100.00) z: 0 ; (3.00, 4.00) ; 1, OK ; 0.45")
])