def setUp(self): AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \ FromFileOriginalFileProvider original_files = list() # Create our container images and an original file image map images = list() n_images = 0 for row in range(16): for column in range(24): well = WellI(n_images, True) well.column = rint(column) well.row = rint(row) well_sample = WellSampleI(n_images, True) well_sample.well = well image = ImageI(n_images, True) image.addWellSample(well_sample) images.append(image) original_file_image_map = dict() # Our required original file format format = rstring('Companion/MIAS') # Create original file representing the log file o = OriginalFileI(1, True) o.name = rstring(self.LOG_FILE) o.path = rstring(os.path.join(self.ROOT, self.LOG_FILE)) o.mimetype = format original_files.append(o) # [1] = o original_file_image_map[1] = images[0] # Create original file representing the result file o = OriginalFileI(2, True) o.name = rstring(self.RESULT_FILE) o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE)) o.mimetype = format original_files.append(o) # [2] = o original_file_image_map[2] = images[0] sf = TestingServiceFactory() self.analysis_ctx = MIASPlateAnalysisCtx(images, original_files, original_file_image_map, 1, sf)
def setUp(self): AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \ FromFileOriginalFileProvider original_files = list() # Create our container images and an original file image map images = list() n_images = 0 for row in range(16): for column in range(24): well = WellI(n_images, True) well.column = rint(column) well.row = rint(row) well_sample = WellSampleI(n_images, True) well_sample.well = well image = ImageI(n_images, True) image.addWellSample(well_sample) images.append(image) original_file_image_map = dict() # Our required original file format format = rstring('Companion/MIAS') # Create original file representing the log file o = OriginalFileI(1L, True) o.name = rstring(self.LOG_FILE) o.path = rstring(os.path.join(self.ROOT, self.LOG_FILE)) o.mimetype = format original_files.append(o) # [1L] = o original_file_image_map[1L] = images[0] # Create original file representing the result file o = OriginalFileI(2L, True) o.name = rstring(self.RESULT_FILE) o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE)) o.mimetype = format original_files.append(o) # [2L] = o original_file_image_map[2L] = images[0] sf = TestingServiceFactory() self.analysis_ctx = MIASPlateAnalysisCtx( images, original_files, original_file_image_map, 1L, sf)
class MIASParseRoiTest(unittest.TestCase): LOG_FILE = "NEOlog2008-09-18-14h37m07s.txt" RESULT_FILE = "Well0001_mode1_z000_t000_detail_2008-09-18-10h48m54s.txt" ROOT = "/Users/callan/testimages/siRNA_PRIM1_03102008/"\ "001-365700055641/results/" def setUp(self): AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \ FromFileOriginalFileProvider original_files = list() # Create our container images and an original file image map images = list() n_images = 0 for row in range(16): for column in range(24): well = WellI(n_images, True) well.column = rint(column) well.row = rint(row) well_sample = WellSampleI(n_images, True) well_sample.well = well image = ImageI(n_images, True) image.addWellSample(well_sample) images.append(image) original_file_image_map = dict() # Our required original file format format = rstring('Companion/MIAS') # Create original file representing the log file o = OriginalFileI(1, True) o.name = rstring(self.LOG_FILE) o.path = rstring(os.path.join(self.ROOT, self.LOG_FILE)) o.mimetype = format original_files.append(o) # [1] = o original_file_image_map[1] = images[0] # Create original file representing the result file o = OriginalFileI(2, True) o.name = rstring(self.RESULT_FILE) o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE)) o.mimetype = format original_files.append(o) # [2] = o original_file_image_map[2] = images[0] sf = TestingServiceFactory() self.analysis_ctx = MIASPlateAnalysisCtx(images, original_files, original_file_image_map, 1, sf) def test_get_measurement_ctx(self): ctx = self.analysis_ctx.get_measurement_ctx(0) self.assertNotEqual(None, ctx) def test_get_columns(self): ctx = self.analysis_ctx.get_measurement_ctx(0) columns = ctx.parse() self.assertNotEqual(None, columns) self.assertEqual(9, len(columns)) self.assertEqual('Image', columns[0].name) self.assertEqual('ROI', columns[1].name) self.assertEqual('Label', columns[2].name) self.assertEqual('Row', columns[3].name) self.assertEqual('Col', columns[4].name) self.assertEqual('Nucleus Area', columns[5].name) self.assertEqual('Cell Diam.', columns[6].name) self.assertEqual('Cell Type', columns[7].name) self.assertEqual('Mean Nucleus Intens.', columns[8].name) for column in columns: if column.name == "ROI": continue self.assertEqual(173, len(column.values))
class MIASParseRoiTest(unittest.TestCase): LOG_FILE = "NEOlog2008-09-18-14h37m07s.txt" RESULT_FILE = "Well0001_mode1_z000_t000_detail_2008-09-18-10h48m54s.txt" ROOT = "/Users/callan/testimages/siRNA_PRIM1_03102008/"\ "001-365700055641/results/" def setUp(self): AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \ FromFileOriginalFileProvider original_files = list() # Create our container images and an original file image map images = list() n_images = 0 for row in range(16): for column in range(24): well = WellI(n_images, True) well.column = rint(column) well.row = rint(row) well_sample = WellSampleI(n_images, True) well_sample.well = well image = ImageI(n_images, True) image.addWellSample(well_sample) images.append(image) original_file_image_map = dict() # Our required original file format format = rstring('Companion/MIAS') # Create original file representing the log file o = OriginalFileI(1L, True) o.name = rstring(self.LOG_FILE) o.path = rstring(os.path.join(self.ROOT, self.LOG_FILE)) o.mimetype = format original_files.append(o) # [1L] = o original_file_image_map[1L] = images[0] # Create original file representing the result file o = OriginalFileI(2L, True) o.name = rstring(self.RESULT_FILE) o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE)) o.mimetype = format original_files.append(o) # [2L] = o original_file_image_map[2L] = images[0] sf = TestingServiceFactory() self.analysis_ctx = MIASPlateAnalysisCtx( images, original_files, original_file_image_map, 1L, sf) def test_get_measurement_ctx(self): ctx = self.analysis_ctx.get_measurement_ctx(0) self.assertNotEqual(None, ctx) def test_get_columns(self): ctx = self.analysis_ctx.get_measurement_ctx(0) columns = ctx.parse() self.assertNotEqual(None, columns) self.assertEqual(9, len(columns)) self.assertEqual('Image', columns[0].name) self.assertEqual('ROI', columns[1].name) self.assertEqual('Label', columns[2].name) self.assertEqual('Row', columns[3].name) self.assertEqual('Col', columns[4].name) self.assertEqual('Nucleus Area', columns[5].name) self.assertEqual('Cell Diam.', columns[6].name) self.assertEqual('Cell Type', columns[7].name) self.assertEqual('Mean Nucleus Intens.', columns[8].name) for column in columns: if column.name == "ROI": continue self.assertEqual(173, len(column.values))