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jcdoming
jcdoming

Reputation: 361

Reading several arrays in a binary file with numpy

I'm trying to read a binary file which is composed by several matrices of float numbers separated by a single int. The code in Matlab to achieve this is the following:

fid1=fopen(fname1,'r');
for i=1:xx
    Rstart= fread(fid1,1,'int32');        #read blank at the begining
    ZZ1 = fread(fid1,[Nx Ny],'real*4');   #read z
    Rend  = fread(fid1,1,'int32');        #read blank at the end
end

As you can see, each matrix size is Nx by Ny. Rstart and Rend are just dummy values. ZZ1 is the matrix I'm interested in.

I am trying to do the same in python, doing the following:

Rstart = np.fromfile(fname1,dtype='int32',count=1)
ZZ1 = np.fromfile(fname1,dtype='float32',count=Ny1*Nx1).reshape(Ny1,Nx1)
Rend = np.fromfile(fname1,dtype='int32',count=1)

Then, I have to iterate to read the subsequent matrices, but the function np.fromfile doesn't retain the pointer in the file.

Another option:

with open(fname1,'r') as f:
   ZZ1=np.memmap(f, dtype='float32', mode='r', offset = 4,shape=(Ny1,Nx1))
   plt.pcolor(ZZ1)

This works fine for the first array, but doesn't read the next matrices. Any idea how can I do this?

I searched for similar questions but didn't find a suitable answer.

Thanks

Upvotes: 0

Views: 345

Answers (2)

Eelco Hoogendoorn
Eelco Hoogendoorn

Reputation: 10759

The cleanest way to read all your matrices in a single vectorized statement is to use a struct array:

dtype = [('start', np.int32), ('ZZ', np.float32, (Ny1, Nx1)), ('end', np.int32)]
with open(fname1, 'rb') as fh:
    data = np.fromfile(fh, dtype)
print(data['ZZ'])

Upvotes: 2

jcdoming
jcdoming

Reputation: 361

There are 2 solutions for this problem.

The first one:

for i in range(x):
    ZZ1=np.memmap(fname1, dtype='float32', mode='r', offset = 4+8*i+(Nx1*Ny1)*4*i,shape=(Ny1,Nx1))

Where i is the array you want to get.

The second one:

fid=open('fname','rb')
for i in range(x):
    Rstart = np.fromfile(fid,dtype='int32',count=1)
    ZZ1 = np.fromfile(fid,dtype='float32',count=Ny1*Nx1).reshape(Ny1,Nx1)
    Rend = np.fromfile(fid,dtype='int32',count=1)

So as morningsun points out, np.fromfile can receive a file object as an argument and keep track of the pointer. Notice that you must open the file in binary mode 'rb'.

Upvotes: 1

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