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))
