scipy.io.loadmat() excessively slow (regression)
Affects | Status | Importance | Assigned to | Milestone | |
---|---|---|---|---|---|
python-scipy (Ubuntu) |
Fix Released
|
Undecided
|
Rick McBride |
Bug Description
Binary package hint: python-scipy
Recent ubuntus (at least from 9.04 till lucid) provide scipy v0.7.0 (python-scipy) which has an important regression problem for the function scipy.io.loadmat(). The loadmat() imports data from Matlab format (".mat") files into NumPy arrays, a task which is very popular among scipy users. Note that there is no alternative to using this function if you need to work with Matlab files.
Scipy v0.7.0 introduced a severe regression problem in that function which became excessively slow, like requiring tens of minutes instead of ten seconds to load files. The result is that the loadmat() function is unusable in SciPy v0.7.0.
This bug has been tracked and solved by SciPy developers nearly one year ago with very simple patch. Details here, with a test case and thorough discussion:
http://
The very simple patch is here:
http://
it modifies few lines of gzipstreams.py which lies here:
/usr/share/
Note that within the discussion's thread there more than one patch was proposed, but the only correct one is the last proposed, which the above link refers to.
I am attaching the same patch here for your convenience.
Please apply it or upgrade python-scipy package to a more recent SciPy version.
Thanks.
Related branches
- Ubuntu branches: Pending requested
-
Diff: 111 lines (+60/-3)5 files modifieddebian/changelog (+6/-0)
debian/control (+4/-3)
debian/patches/10_scipy_gzipstreams_patch.dpatch (+48/-0)
debian/patches/series (+1/-0)
debian/source/format (+1/-0)
tags: | added: patch |
Changed in python-scipy (Ubuntu): | |
status: | In Progress → Fix Committed |
tags: | added: patch-accepted-debian patch-accepted-upstream |
I have a branch of the UDD branch for this waiting to be proposed when Maverick Meerkat opens up.