def write_bits_to_file(path, matrix, bit_size, need_logs=False):
monitor = Monitor()
with open(path, "wb+") as file:
if need_logs:
print("Write file from binary matrix: " + path)
byte_size = int(bit_size / 8)
# Change bit to byte (8 -> 1), and write a file as bytes
bit_index = 0
temp_byte = 0
for row in range(len(matrix)):
for col in range(len(matrix[0])):
bit_index += 1
temp_byte *= 2
temp_byte += matrix[row][col]
if bit_index == 8:
if byte_size > 0:
file.write(struct.pack("B", int(temp_byte)))
bit_index = 0
temp_byte = 0
byte_size -= 1
if need_logs:
monitor.output(row + 1, len(matrix))
return True
def read_bits_from_file(path, segment_length=120, need_logs=False):
monitor = Monitor()
with open(path, mode="rb") as file:
if need_logs:
print("Read binary matrix from file: " + path)
size = os.path.getsize(path)
if segment_length > 0:
# Set init storage matrix
matrix = [[0 for _ in range(segment_length)]
for _ in range(math.ceil(size * 8 / segment_length))]
row = 0
col = 0
for byte_index in range(size):
# Read a file as bytes
one_byte = file.read(1)
element = list(
map(
int,
list(
str(bin(struct.unpack(
"B", one_byte)[0]))[2:].zfill(8))))
for bit_index in range(8):
matrix[row][col] = element[bit_index]
col += 1
if col == segment_length:
col = 0
row += 1
if need_logs:
monitor.output(byte_index + 1, size)
else:
matrix = []
for byte_index in range(size):
# Read a file as bytes
one_byte = file.read(1)
matrix += list(
map(
int,
list(
str(bin(struct.unpack(
"B", one_byte)[0]))[2:].zfill(8))))
matrix = [matrix]
if int(len(str(bin(len(matrix)))) - 2) * 4 > segment_length:
if need_logs:
warn(
"The proportion of index in whole sequence may be high. \n"
"It is recommended to increase the length of output DNA sequences "
"or to divide the file into more segment pools")
return matrix, size * 8
def write_dna_file(path, dna_sequences, need_logs=False):
monitor = Monitor()
with open(path, "w") as file:
if need_logs:
print("Write DNA sequences to file: " + path)
for index, dna_sequence in enumerate(dna_sequences):
file.write("".join(dna_sequence) + "\n")
if need_logs:
monitor.output(index + 1, len(dna_sequences))
return True
def connect_all(bit_segments, need_logs=False):
index_binary_length = int(len(str(bin(len(bit_segments)))) - 2)
if need_logs:
print("Add index in the binary matrix.")
monitor = Monitor()
connected_bit_segments = []
for row in range(len(bit_segments)):
connected_bit_segments.append(
connect(row, bit_segments[row], index_binary_length))
if need_logs:
monitor.output(row + 1, len(bit_segments))
return connected_bit_segments, index_binary_length
def write_bits_to_str(matrix, bit_size, need_logs=False):
if need_logs:
print("Write binary matrix to string.")
monitor = Monitor()
temp_list = []
for index, row in enumerate(matrix):
temp_list += row
if need_logs:
monitor.output(index, len(matrix))
temp_list = temp_list[:bit_size]
values = []
for index in range(0, len(temp_list), 8):
values.append(
int("".join(list(map(str, temp_list[index:index + 8]))), 2))
return str(bytes(values), encoding="utf8")
def divide_all(bit_segments, need_logs=False):
index_binary_length = int(len(str(bin(len(bit_segments)))) - 2)
if need_logs:
print("Divide index and data from binary matrix.")
monitor = Monitor()
indices = []
divided_matrix = []
for row in range(len(bit_segments)):
index, data = divide(bit_segments[row], index_binary_length)
indices.append(index)
divided_matrix.append(data)
if need_logs:
monitor.output(row + 1, len(bit_segments))
return indices, divided_matrix
def sort_order(indices, bit_segments, need_logs=False):
monitor = Monitor()
if need_logs:
print("Restore data order according to index.")
sorted_bit_segments = []
for index in range(max(indices) + 1):
if index in indices:
sorted_bit_segments.append(bit_segments[indices.index(index)])
else:
sorted_bit_segments.append(
[0 for _ in range(len(bit_segments[0]))])
if need_logs:
monitor.output(index + 1, max(indices) + 1)
return sorted_bit_segments
def write_bits_to_file(path, matrix, bit_size, need_logs=True):
monitor = Monitor()
with open(path, "wb+") as file:
if need_logs:
print("Write file from binary matrix: " + path)
matrix = array(matrix).reshape(-1)
for position in range(0, bit_size, 8):
file.write(
struct.pack(
"B",
int("".join(list(map(str, matrix[position:position + 8]))),
2)))
if need_logs:
monitor.output(int(position / 8 + 1), int(bit_size / 8))
return True
def read_dna_file(path, need_logs=True):
monitor = Monitor()
dna_sequences = []
with open(path, "r") as file:
if need_logs:
print("Read DNA sequences from file: " + path)
# Read current file by line
lines = file.readlines()
for index, line in enumerate(lines):
dna_sequences.append(list(line.replace("\n", "")))
if need_logs:
monitor.output(index + 1, len(lines))
return dna_sequences
def read_bits_from_str(string, segment_length=120, need_logs=False):
monitor = Monitor()
if need_logs:
print("Read binary matrix from string: " + string)
data = []
for value in bytes(string, encoding="utf8"):
data += list(map(int, list(str(bin(value))[2:].zfill(8))))
matrix = []
for index in range(0, len(data), segment_length):
if index + segment_length < len(data):
matrix.append(data[index:index + segment_length])
else:
matrix.append(data[index:] + [0] *
(segment_length - len(data[index:])))
if need_logs:
monitor.output(max(index + segment_length, len(data)), len(data))
return matrix, len(data)
def read_bits_from_file(path, segment_length=120, need_logs=True):
monitor = Monitor()
if need_logs:
print("Read binary matrix from file: " + path)
matrix, values = [], fromfile(file=path, dtype=uint8)
for current, value in enumerate(values):
matrix += list(map(int, list(str(bin(value))[2:].zfill(8))))
if need_logs:
monitor.output(current + 1, len(values))
if len(matrix) % segment_length != 0:
matrix += [0] * (segment_length - len(matrix) % segment_length)
matrix = array(matrix)
matrix = matrix.reshape(int(len(matrix) / segment_length), segment_length)
if need_logs:
print(
"There are " + str(len(values) * 8) +
" bits in the inputted file. " +
"Please keep this information in mind if you do not consider storing the model in serialization!"
)
return matrix.tolist(), len(values) * 8
class AbstractCodingAlgorithm(object):
def __init__(self, need_logs):
self.bit_size = None
self.need_logs = need_logs
self.monitor = Monitor()
self.segment_length = None
def __init_check__(self):
raise NotImplementedError("\"init_check\" interface needs to be implemented!")
def silicon_to_carbon(self, bit_segments, bit_size):
for bit_segment in bit_segments:
if type(bit_segment) != list or type(bit_segment[0]) != int:
raise ValueError("The dimension of bit matrix can only be 2!")
self.bit_size = bit_size
self.segment_length = len(bit_segments[0])
start_time = datetime.now()
if self.need_logs:
print("Encode bit segments to DNA sequences by coding scheme.")
self.monitor.restore()
dna_sequences = self.encode(bit_segments)
self.monitor.restore()
encoding_runtime = (datetime.now() - start_time).total_seconds()
nucleotide_count = 0
for dna_sequence in dna_sequences:
nucleotide_count += len(dna_sequence)
information_density = bit_size / nucleotide_count
return {"dna": dna_sequences, "i": information_density, "t": encoding_runtime}
def carbon_to_silicon(self, dna_sequences):
for dna_sequence in dna_sequences:
if type(dna_sequence) != list or type(dna_sequence[0]) != str:
raise ValueError("The dimension of nucleotide matrix can only be 2!")
start_time = datetime.now()
if self.need_logs:
print("Decode DNA sequences to bit segments by coding scheme.")
self.monitor.restore()
bit_segments = self.decode(dna_sequences)
self.monitor.restore()
for segment_index, bit_segment in enumerate(bit_segments):
if len(bit_segment) != self.segment_length:
bit_segments[segment_index] = bit_segment[: self.segment_length]
decoding_runtime = (datetime.now() - start_time).total_seconds()
return {"bit": bit_segments, "s": self.bit_size, "t": decoding_runtime}
def encode(self, bit_segments):
raise NotImplementedError("\"decode\" interface needs to be implemented!")
def decode(self, dna_sequences):
raise NotImplementedError("\"decode\" interface needs to be implemented!")
def __init__(self, need_logs):
self.need_logs = need_logs
self.segment_lengths = []
self.monitor = Monitor()
class AbstractErrorCorrectionCode(object):
def __init__(self, need_logs):
self.need_logs = need_logs
self.segment_lengths = []
self.monitor = Monitor()
def insert(self, bit_segments):
if self.need_logs:
print("Insert the error-correction code to the bit segments.")
self.segment_lengths = []
verified_bit_segments = []
if type(bit_segments) == list and type(bit_segments[0]) == list:
for index, bit_segment in enumerate(bit_segments):
self.segment_lengths.append(len(bit_segment))
verified_bit_segments.append(self.insert_one(bit_segment))
if self.need_logs:
self.monitor.output(index + 1, len(bit_segments))
elif type(bit_segments) == list and type(bit_segments[0]) == int:
self.segment_lengths = [len(bit_segments)]
verified_bit_segments = self.insert_one(bit_segments)
else:
raise ValueError("The matrix must be 1-dimensional or 2-dimensional, and the value is of type \"int\".")
self.monitor.restore()
return verified_bit_segments, len(verified_bit_segments[0]) - len(bit_segments[0])
def remove(self, verified_bit_segments):
if self.need_logs:
print("Check and remove the error-correction code from the bit segments.")
bit_segments = []
error_bit_segments = []
error_indices = []
if type(verified_bit_segments) == list and type(verified_bit_segments[0]) == list:
error_rate = 0
for index, verified_bit_segment in enumerate(verified_bit_segments):
if verified_bit_segment is not None:
output = self.remove_one(verified_bit_segment)
data, data_type = output.get("data"), output.get("type")
if data_type and len(data) >= self.segment_lengths[index]:
bit_segments.append(data[len(data) - self.segment_lengths[index]:])
else:
error_rate += 1
error_indices.append(index)
error_bit_segments.append(data)
else:
error_rate += 1
error_indices.append(index)
error_bit_segments.append(None)
if self.need_logs:
self.monitor.output(index + 1, len(verified_bit_segments))
error_rate /= len(verified_bit_segments)
elif type(verified_bit_segments) == list and type(verified_bit_segments[0]) == int:
output = self.remove_one(verified_bit_segments[0])
data, data_type = output.get("data"), output.get("type")
if data_type:
error_rate = 0
bit_segments = [data[len(data) - self.segment_lengths[0]:]]
else:
error_rate = 1
error_indices.append(0)
error_bit_segments.append(data)
else:
raise ValueError("The matrix must be 1-dimensional or 2-dimensional, and the value is of type \"int\".")
self.monitor.restore()
return {"bit": bit_segments, "e_r": error_rate, "e_i": error_indices, "e_bit": error_bit_segments}
def insert_one(self, input_list):
raise NotImplementedError("\"insert_one\" interface needs to be implemented!")
def remove_one(self, input_list):
raise NotImplementedError("\"remove_one\" interface needs to be implemented!")
class AbstractErrorCorrectionCode(object):
def __init__(self, need_logs):
self.need_logs = need_logs
self.segment_length = None
self.monitor = Monitor()
def insert(self, bit_segments):
if self.need_logs:
print("Insert the error-correction code to the bit segments.")
verified_bit_segments = []
if type(bit_segments) == list and type(bit_segments[0]) == list:
self.segment_length = len(bit_segments[0])
for index, bit_segment in enumerate(bit_segments):
verified_bit_segments.append(self.insert_one(bit_segment))
if self.need_logs:
self.monitor.output(index + 1, len(bit_segments))
elif type(bit_segments) == list and type(bit_segments[0]) == int:
self.segment_length = len(bit_segments)
verified_bit_segments = self.insert_one(bit_segments)
else:
raise ValueError(
"The matrix must be 1-dimensional or 2-dimensional, and the value is of type \"int\"."
)
if self.need_logs:
print(
"The error-correction code automatically records the original length ("
+ str(self.segment_length) +
") of each binary segment, which provide more information when an error really occurs."
)
print("We recommend you save this code through serialized object!")
print(
"Generally, ignoring it during decoding does not cause more problems."
)
return verified_bit_segments, len(verified_bit_segments[0]) - len(
bit_segments[0])
def remove(self, verified_bit_segments):
if self.need_logs:
print(
"Check and remove the error-correction code from the bit segments."
)
bit_segments = []
error_bit_segments = []
error_indices = []
if type(verified_bit_segments) == list and type(
verified_bit_segments[0]) == list:
error_rate = 0
for index, verified_bit_segment in enumerate(
verified_bit_segments):
if verified_bit_segment is not None:
output = self.remove_one(verified_bit_segment)
data, data_type = output.get("data"), output.get("type")
if data_type:
if self.segment_length is not None:
bit_segments.append(data[len(data) -
self.segment_length:])
else:
bit_segments.append(data)
else:
error_rate += 1
error_indices.append(index)
error_bit_segments.append(data)
else:
error_rate += 1
error_indices.append(index)
error_bit_segments.append(None)
if self.need_logs:
self.monitor.output(index + 1, len(verified_bit_segments))
error_rate /= len(verified_bit_segments)
elif type(verified_bit_segments) == list and type(
verified_bit_segments[0]) == int:
output = self.remove_one(verified_bit_segments[0])
data, data_type = output.get("data"), output.get("type")
if data_type:
error_rate = 0
if self.segment_length is not None:
bit_segments = data[len(data) - self.segment_length:]
else:
bit_segments = data
else:
error_rate = 1
error_indices.append(0)
error_bit_segments.append(data)
else:
raise ValueError(
"The matrix must be 1-dimensional or 2-dimensional, and the value is of type \"int\"."
)
return {
"bit": bit_segments,
"e_r": error_rate,
"e_i": error_indices,
"e_bit": error_bit_segments
}
def insert_one(self, input_list):
raise NotImplementedError(
"\"insert_one\" interface needs to be implemented!")
def remove_one(self, input_list):
raise NotImplementedError(
"\"remove_one\" interface needs to be implemented!")
def __init__(self, need_logs):
self.bit_size = None
self.need_logs = need_logs
self.monitor = Monitor()
self.segment_length = None
def __init__(self, **info):
self.need_logs = info["need_logs"] if "need_logs" in info else False
self.monitor = Monitor()
self.records = {}