Hi,
I'm saving a large batch of data using savemat and although I get no errors, the files produced are not readable for either matlab or scipy. Is there a limit on file size? Thanks, Michal _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
Hi,
On Mon, Aug 19, 2013 at 7:44 AM, Michal Romaniuk <[hidden email]> wrote: > Hi, > > I'm saving a large batch of data using savemat and although I get no > errors, the files produced are not readable for either matlab or scipy. > Is there a limit on file size? Ah - yes there is - the individual matrices in the mat file cannot be larger than 4GB. Is it possible you hit this limit? Sorry, I only realized this when Richard Llewellyn pointed this out a couple of weeks ago on the list: http://scipy-user.10969.n7.nabble.com/SciPy-User-scipy-io-loadmat-throws-TypeError-with-large-files-td18558.html The current scipy code has an error message for matrices that are too large. Cheers, Matthew _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
Hi,
With some further work, I found that the file produced by SciPy isn't actually correct. Matlab can read it but at some point in the array the rest of the data is just zeros. I'm surprised that SciPy doesn't throw an error when writing data that is too big... Are there any good alternatives to .mat files? (Preferably something that Matlab could read too.) PyTables? The data consists of one large array (around 9GB), one list containing a few smaller arrays, and a few other arrays and scalars. Thanks, Michal > Hi, > >> Hi, >> >> On Mon, Aug 19, 2013 at 7:44 AM, Michal Romaniuk >> <[hidden email]> wrote: >>> Hi, >>> >>> I'm saving a large batch of data using savemat and although I get no >>> errors, the files produced are not readable for either matlab or scipy. >>> Is there a limit on file size? >> >> Ah - yes there is - the individual matrices in the mat file cannot be >> larger than 4GB. Is it possible you hit this limit? >> >> Sorry, I only realized this when Richard Llewellyn pointed this out a >> couple of weeks ago on the list: >> >> http://scipy-user.10969.n7.nabble.com/SciPy-User-scipy-io-loadmat-throws-TypeError-with-large-files-td18558.html >> >> The current scipy code has an error message for matrices that are too large. >> >> Cheers, >> >> Matthew > > Well, I managed to work around the problem to some extent by setting > do_compression=True. Now Matlab can read those files (so they must be > valid to some extent) but SciPy can't (even though they were written > with SciPy). > > I get this error: > > > PATH/lib/python2.6/site-packages/scipy/io/matlab/mio.pyc in > loadmat(file_name, mdict, appendmat, **kwargs) > 173 variable_names = kwargs.pop('variable_names', None) > 174 MR = mat_reader_factory(file_name, appendmat, **kwargs) > --> 175 matfile_dict = MR.get_variables(variable_names) > 176 if mdict is not None: > 177 mdict.update(matfile_dict) > > PATH/lib/python2.6/site-packages/scipy/io/matlab/mio5.pyc in > get_variables(self, variable_names) > 290 continue > 291 try: > --> 292 res = self.read_var_array(hdr, process) > 293 except MatReadError, err: > 294 warnings.warn( > > PATH/lib/python2.6/site-packages/scipy/io/matlab/mio5.pyc in > read_var_array(self, header, process) > 253 `process`. > 254 ''' > --> 255 return self._matrix_reader.array_from_header(header, > process) > 256 > 257 def get_variables(self, variable_names=None): > > PATH/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so in > scipy.io.matlab.mio5_utils.VarReader5.array_from_header > (scipy/io/matlab/mio5_utils.c:5401)() > > PATH/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so in > scipy.io.matlab.mio5_utils.VarReader5.array_from_header > (scipy/io/matlab/mio5_utils.c:4849)() > > PATH/lib/python2.6/site-packages/scipy/io/matlab/mio5_utils.so in > scipy.io.matlab.mio5_utils.VarReader5.read_real_complex > (scipy/io/matlab/mio5_utils.c:5602)() > > ValueError: total size of new array must be unchanged > > > > The size of the main array is about 9 GB before compression, but the > compressed files are less than 500 MB and closer to 400 MB. There are > some other arrays in the file too but they are much smaller. > > Any ideas on how I could get SciPy to read this data back? Right now I > can only think of storing the data in single precision format... > > Thanks, > Michal _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
20.08.2013 20:33, Michal Romaniuk kirjoitti:
[clip] > Are there any good alternatives to .mat files? (Preferably > something that Matlab could read too.) PyTables? > > The data consists of one large array (around 9GB), one list > containing a few smaller arrays, and a few other arrays and > scalars. Use HDF5 --- both Matlab and Python can work with it. On the Python side use either h5py or PyTables, depending on which one you like more. As you found out, the .mat file format simply does not support data bigger than 4 GB. The development version of Scipy (to be 0.13.0) should throw a warning AFAIK. -- Pauli Virtanen _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
In reply to this post by Michal Romaniuk
Hi,
On Tue, Aug 20, 2013 at 10:33 AM, Michal Romaniuk <[hidden email]> wrote: > Hi, > > With some further work, I found that the file produced by SciPy isn't > actually correct. Matlab can read it but at some point in the array the > rest of the data is just zeros. I'm surprised that SciPy doesn't throw > an error when writing data that is too big... Yes, that was a bug. It should be fixed in the current code and the next release. The problem is that there is a length-of-array entry in the matfile that is a uint32, so there is no way of storing matrices longer than 4GB. Because I hadn't considered the case of very large matrices, this length value was silently overflowing, so the pointer to the next matrix in the mat file will be garbage, and the effect is unpredictable. > Are there any good alternatives to .mat files? (Preferably something > that Matlab could read too.) PyTables? I have no experience with matlab hdf5 (7.3) format - but I guess that is a reasonable option > The data consists of one large array (around 9GB), one list containing a > few smaller arrays, and a few other arrays and scalars. I guess you could save everything but the large array in a mat file, and save the large array as simple binary data? Cheers, Matthew _______________________________________________ SciPy-User mailing list [hidden email] http://mail.scipy.org/mailman/listinfo/scipy-user |
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