def test_decode_barcode_8_ok(self):
""" Should decode valid codewords w/o error """
self.assertEqual(decode_barcode_8(self.valid_bc_1), (self.valid_bc_1, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_2), (self.valid_bc_2, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_3), (self.valid_bc_3, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_4), (self.valid_bc_4, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_5), (self.valid_bc_5, 0))
def test_decode_barcode_8_ok(self):
""" Should decode valid codewords w/o error """
self.assertEqual(decode_barcode_8(self.valid_bc_1),
(self.valid_bc_1, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_2),
(self.valid_bc_2, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_3),
(self.valid_bc_3, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_4),
(self.valid_bc_4, 0))
self.assertEqual(decode_barcode_8(self.valid_bc_5),
(self.valid_bc_5, 0))
def attempt_bc_correction(curr_bc,
all_bcs,
barcode_type = "golay_12"):
""" Gets corrected barcode and number of errors
curr_bc: current barcode sequence to attempt correction with
all_bcs: List of all barcode sequences.
barcode_type: Specified barcode, can be golay_12, hamming_8,
variable_length, or an integer specifying length.
"""
# First check for exact matches
corrected_bc = get_exact_bc_matches(curr_bc, all_bcs)
if corrected_bc:
return corrected_bc, 0
if barcode_type == "golay_12":
corrected_bc, num_errors = decode_golay_12(curr_bc)
elif barcode_type == "hamming_8":
corrected_bc, num_errors = decode_barcode_8(curr_bc)
elif barcode_type == 0:
corrected_bc, num_errors = ('', 0)
else:
corrected_bc, num_errors = correct_barcode(curr_bc, all_bcs)
return corrected_bc, num_errors
def attempt_bc_correction(curr_bc,
all_bcs,
barcode_type = "golay_12"):
""" Gets corrected barcode and number of errors
curr_bc: current barcode sequence to attempt correction with
all_bcs: List of all barcode sequences.
barcode_type: Specified barcode, can be golay_12, hamming_8,
variable_length, or an integer specifying length.
"""
# First check for exact matches
corrected_bc = get_exact_bc_matches(curr_bc, all_bcs)
if corrected_bc:
return corrected_bc, 0
if barcode_type == "golay_12":
corrected_bc, num_errors = decode_golay_12(curr_bc)
elif barcode_type == "hamming_8":
corrected_bc, num_errors = decode_barcode_8(curr_bc)
elif barcode_type == 0:
corrected_bc, num_errors = ('', 0)
else:
corrected_bc, num_errors = correct_barcode(curr_bc, all_bcs)
return corrected_bc, num_errors
def test_decode_barcode_8_one_error(self):
""" Should correct single bit errors w/o error """
self.assertEqual(decode_barcode_8(self.single_error_1), (self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_2), (self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_3), (self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_4), (self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_5), (self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_6), (self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_7), (self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_8), (self.single_error_ref, 0.5))
def test_decode_barcode_8_one_error(self):
""" Should correct single bit errors w/o error """
self.assertEqual(decode_barcode_8(self.single_error_1),
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_2),
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_3),
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_4),
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_5),
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_6),
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_7),
(self.single_error_ref, 0.5))
self.assertEqual(decode_barcode_8(self.single_error_8),
(self.single_error_ref, 0.5))
def test_decode_barcode_8_two_error(self):
""" Should raise error when double error detected """
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
def test_decode_barcode_8_two_error(self):
""" Should raise error when double error detected """
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
self.assertEqual(decode_barcode_8(self.double_error_1), (None, 1))
## in versions 1.2.0 through 1.3.*, and a try/except to handle errors from
## versions 1.4.0 or later.
numpy_version = re.split("[^\d]", numpy_version)
numpy_version = tuple([int(i) for i in numpy_version if i.isdigit()])
if numpy_version < (1,3,0):
numpy_histogram = histogram
def histogram(a, bins=10, range=None, normed=False, weights=None):
return numpy_histogram(a,bins=bins,range=range,\
normed=normed,weights=weights,new=True)
# Supported barcode types - need to adapt these functions to ignore list
# of valid barcodes that the generic decoder requires
BARCODE_TYPES = {
"golay_12":(12, lambda bc, bcodes: decode_golay_12(bc)),
"hamming_8":(8, lambda bc, bcodes: decode_barcode_8(bc)),
# The decode function for variable length barcode does nothing -
# it's just provided to comply with the interface of the other
# barcode types. The returned barcode is always the same as the
# one passed in, and the number of mismatches is always 0. The
# length is None, corresponding to variable length.
"variable_length":(None, lambda bc, bcodes: (bc, 0))}
def get_infile(filename):
"""Returns filehandle, allowing gzip input."""
if filename.endswith(".gz"):
fin = GzipFile(filename, "rb")
else:
fin = open(filename, "U")
return fin
