def readHuffTable(f):
huffTable = {}
buffer = ''
bufferSize = 0
# Get the number of codewords
(numCodewords, buffer, bufferSize) = bits.getVarBits(f, 32, buffer, bufferSize)
numCodewords = int(numCodewords, 2)
# Keep reading codewords
while numCodewords > 0:
# Get the key
(key, buffer, bufferSize) = bits.getVarBits(f, 32, buffer, bufferSize)
key= int(key, 2)
# Get the codeword length
(codewordLen, buffer, bufferSize) = bits.getVarBits(f, 8, buffer, bufferSize)
codewordLen = int(codewordLen, 2)
(codeword, buffer, bufferSize) = bits.getVarBits(f, codewordLen, buffer, bufferSize)
huffTable[codeword] = key
numCodewords -= 1
return huffTable
def readHuffTable2(f):
huffTable = {}
buffer = ''
bufferSize = 0
# Get the number of codewords
(numCodewords, buffer, bufferSize) = bits.getVarBits(f, 32, buffer, bufferSize)
numCodewords = int(numCodewords, 2)
# Keep reading codewords
while numCodewords > 0:
# Get the key
stop = 0
key = ''
while stop == 0:
# First get 1 bit
(temp, buffer, bufferSize) = bits.getVarBits(f, 1, buffer, bufferSize)
# If first bit is a 0, then get one more bit
if (temp == '0'):
currbp = '0'
(temp, buffer, bufferSize) = bits.getVarBits(f, 1, buffer, bufferSize)
currbp += temp
if currbp == '00':
key += 'A'
else:
key += 'C'
# Otherwise, get two bits
else:
currbp = '1'
(temp, buffer, bufferSize) = bits.getVarBits(f, 2, buffer, bufferSize)
currbp += temp
if (currbp == '100'):
key += 'G'
elif (currbp == '101'):
key += 'T'
elif (currbp == '110'):
key += 'N'
else:
stop = 1
# Get the codeword length
(codewordLen, buffer, bufferSize) = bits.getVarBits(f, 8, buffer, bufferSize)
codewordLen = int(codewordLen, 2)
(codeword, buffer, bufferSize) = bits.getVarBits(f, codewordLen, buffer, bufferSize)
huffTable[codeword] = key
numCodewords -= 1
return huffTable
def readGolombCodedHuffTable(f):
huffTable = {}
buffer = ''
bufferSize = 0
# Get the number of codewords
(numCodewords, buffer, bufferSize) = bits.getVarBits(f, tableSize, buffer, bufferSize)
numCodewords = int(numCodewords, 2)
# Get the number of consecutive keys
(sparseStart, buffer, bufferSize) = bits.getVarBits(f, denseSize, buffer, bufferSize)
sparseStart = int(sparseStart, 2)
# Get count for the Golomb code (count is the first number in the dense region: usually 0)
(count, buffer, bufferSize) = bits.getVarBits(f, countSize, buffer, bufferSize)
count = int(count, 2)
# Get M for the Golomb code
(M, buffer, bufferSize) = bits.getVarBits(f, MSize, buffer, bufferSize)
M = int(M, 2)
# Calculate the length of the remainder part
MLen = int(math.ceil(math.log(M,2)))
ind = 0
currKey = 0
prevKey = 0
# Keep reading codewords
for ind in xrange(numCodewords):
# The key's not specified if we're in the dense region
if ind < sparseStart:
currKey = count + ind
else:
# Decode by Golomb
# Get the quotient
quotient = 0
(currBit, buffer, bufferSize) = bits.getVarBits(f, 1, buffer, bufferSize)
while (currBit == '1'):
(currBit, buffer, bufferSize) = bits.getVarBits(f, 1, buffer, bufferSize)
quotient = quotient + 1
# Get the remainder
(remainder, buffer, bufferSize) = bits.getVarBits(f, MLen, buffer, bufferSize)
remainder = int(remainder, 2)
# Get the delta between the previous key and the current key
delta = quotient*M + remainder + 1
# Now get the actual key
currKey = prevKey + delta
# Update previous key (needed when we're in the sparse region)
prevKey = currKey
# Get the codeword length
(codewordLen, buffer, bufferSize) = bits.getVarBits(f, lenSize, buffer, bufferSize)
codewordLen = int(codewordLen, 2)
# Get the codeword
(codeword, buffer, bufferSize) = bits.getVarBits(f, codewordLen, buffer, bufferSize)
huffTable[codeword] = currKey
return huffTable