def test_output_prints_correctly_with_no_crystal_match_results(self, mock_print):
result = ServiceResult("job-id", "fomulatrix", "beamline")
result.print_results(False)
# Test for presence of poi: objects in output
output = self.get_output(mock_print)
self.failIf("poi:" in output)
def test_job_id_and_image_paths_printed_correctly_for_file(self, mock_print):
result = ServiceResult("", "test/file/path/fomulatrix", "test/file/path/beamline/test.tif")
result.print_results(False)
mock_print.assert_any_call('input_image:"' + abspath('test/file/path/fomulatrix') + '"')
mock_print.assert_any_call('output_image:"' + abspath('test/file/path/beamline/test.tif') + '"')
output = self.get_output(mock_print)
self.failIf("job_id" in output)
def test_add_image_alignment_results(self):
mock_aligned_image = Mock(spec_set=[
"alignment_status_code", "overlap_metric", "pixel_offset",
"get_alignment_transform"
])
mock_aligned_image.get_alignment_transform = MagicMock(
return_value=(1.0, Point(0, 0)))
result = ServiceResult("job-id", "fomulatrix", "beamline")
result.set_image_alignment_results(mock_aligned_image)
def test_print_without_alignment_results_shows_default_values(self, mock_print):
Mock(spec_set=["alignment_status_code", "overlap_metric", "pixel_offset", "get_alignment_transform"])
result = ServiceResult("job-id","fomulatrix","beamline")
result.print_results(False)
# Test output
mock_print.assert_has_calls([
call('align_transform:1.0, (0.00, 0.00)'),
call('align_status:-1, NOT SET'),
call('align_error:0.0')
])
def test_exit_code_in_json_output_success(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)
json_obj = result.print_results(jason_output = True)
# Test for exit status of -1 in JSON object
self.failUnlessEqual(0, json_obj['exit_code']['code'])
self.failIf('err_msg' in json_obj['exit_code'].keys())
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_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_std_out_success(self, mock_print):
# Set up mock for successful image match
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)
result.print_results(False)
# Test for exit status present in output
mock_print.assert_has_calls([call('exit_code:0')])
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'])
def test_image_alignment_results_print_for_success_case(self, mock_print):
# Set up mock for successful image match
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)
result.print_results(False)
# Test output
mock_print.assert_has_calls([
call("align_transform:" + str(transform[0]) + ", " + str(transform[1])),
call("align_status:1, OK"),
call("align_error:9.8")])
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_image_alignment_results_print_for_failure_case(self, mock_print):
# Set up mock for successful image match
status = ALIGNED_IMAGE_STATUS_FAIL
confidence = 0.0
transform = (1.0, Point(0, 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)
result.print_results(False)
# Test output
mock_print.assert_has_calls([
call("align_transform:1.0, (0.00, 0.00)"),
call("align_status:0, FAIL"),
call("align_error:0.0")])
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")
])
def test_exit_code_starting_state_is_negative_1(self, mock_print):
result = ServiceResult("job-id", "fomulatrix", "beamline")
result.print_results(False)
mock_print.assert_has_calls([call('exit_code:-1')])