use numba to speed up binary processing - numba

Question

I have a binary file containing information of different types. I know the types and have written a parsing script to extract the information:
import numba as nb
import numpy as np
def fread(fid, nelements, dtype):
if dtype is np.str:
dt = np.uint8 # WARNING: assuming 8-bit ASCII for np.str!
else:
dt = dtype
data_array = np.fromfile(fid, dt, nelements)
data_array.shape = (nelements, 1)
return data_array
fid = open('./binary_information.bts', 'rb');
nffc = 3
fileFmt = 'int16'
nz = fread( fid, 1, np.int32); # the number of grid points vertically, INT(4)
ny = fread( fid, 1, np.int32); # the number of grid points laterally, INT(4)
nPts = ny*nz;
nv = nffc*nPts; # the size of one time step
velocity = np.zeros([int(s) for s in (nt,nffc,ny,nz)])
for it in range(1, nt):
ip = 1
v_cnt = fread( fid, int(nv), fileFmt )
for iz in range(1, nz):
for iy in range(1, ny):
for k in range(1, nffc):
velocity[it,k,iy,iz] = ( v_cnt[ip] - Voffset[k])/Vslope[k]
ip = ip + 1
My for loop takes a large amount of time. I want to speed it up with numba. I tried to do this, and got a weird error, posted below. Is there any way I can speed up this reading process with numba? What went wrong here? Why is it raising this range issue?
#nb.jit(nopython=True)
def main(velocity, v_cnt):
ip = 1
for iz in xrange(1, nz):
for iy in xrange(1, ny):
for k in xrange(1, nffc):
velocity[it,k,iy,iz] = ( v_cnt[ip] - Voffset[k])/Vslope[k]
ip = ip + 1
return velocity
for it in range(nt):
ip = 0
v_cnt = fread( fid, int(nv), fileFmt )
velocity = main(velocity, v_cnt)
Traceback (most recent call last):
File "bts_read.py", line 66, in <module>
velocity = main(velocity, v_cnt)
File "/usr/local/lib/python2.7/site-packages/numba/dispatcher.py", line 330, in _compile_for_args
raise e
numba.errors.TypingError: Caused By:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 235, in run
stage()
File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 449, in stage_nopython_frontend
self.locals)
File "/usr/local/lib/python2.7/site-packages/numba/compiler.py", line 805, in type_inference_stage
infer.propagate()
File "/usr/local/lib/python2.7/site-packages/numba/typeinfer.py", line 767, in propagate
raise errors[0]
TypingError: Invalid usage of Function(<built-in function range>) with parameters (int64, readonly array(int32, 2d, C))
Known signatures:
* (int32,) -> range_state_int32
* (int32, int32) -> range_state_int32
* (int32, int32, int32) -> range_state_int32
* (int64,) -> range_state_int64
* (int64, int64) -> range_state_int64
* (int64, int64, int64) -> range_state_int64
* (uint64,) -> range_state_uint64
* (uint64, uint64) -> range_state_uint64
* (uint64, uint64, uint64) -> range_state_uint64
File "bts_read.py", line 56
[1] During: resolving callee type: Function(<built-in function range>)
[2] During: typing of call at bts_read.py (56)
Failed at nopython (nopython frontend)
Invalid usage of Function(<built-in function range>) with parameters (int64, readonly array(int32, 2d, C))
Known signatures:
* (int32,) -> range_state_int32
* (int32, int32) -> range_state_int32
* (int32, int32, int32) -> range_state_int32
* (int64,) -> range_state_int64
* (int64, int64) -> range_state_int64
* (int64, int64, int64) -> range_state_int64
* (uint64,) -> range_state_uint64
* (uint64, uint64) -> range_state_uint64
* (uint64, uint64, uint64) -> range_state_uint64
File "bts_read.py", line 56
[1] During: resolving callee type: Function(<built-in function range>)
[2] During: typing of call at bts_read.py (56)