FAQs and Known IssuesΒΆ
Q: How can I open and inspect an HDF5 file created by pypet?
Q: My program does not terminate (i.e. it does not crash but runs forever) when I use pypet in multiprocessing mode in combination with matplotlib and savefig!?
A: Matplotlib uses numpy for linear algebra operations, these operations are often necessary when plotting. So, to solve the issues take a look at the next question.
Q: My program does not terminate (i.e. it does not crash but runs forever) when I use pypet in multiprocessing mode in combination with numpy and linalg.inv or some similar function!?
A: Numpy uses openBLAS (http://www.openblas.net/) to solve linear algebra operations. Yet, there are many issues with openBLAS and multiprocessing. To resolve this set the environment variable OPENBLAS_NUM_THREADS=1.
Q: GitPython does not work. If I specify my repository git_repository='./myrepo', pypet crashes with an AttributeError: 'Repo' object has no attribute 'index'. What should I do?
A: You probably have an older version of GitPython (likely 0.1.7), install a newer one. If pip install GitPython still downloads the old version, try pip install --pre GitPython or if you simply want to upgrade use pip install --upgrade --pre GitPython.
Q: If I create and environment in an IPython console everything becomes gibberish!?
A: Pypet will redirect STDOUT and STDERROR to files. Unfortunately, this messes with the IPython console. To avoid this simply disable logging of these two streams setting the log_stdout to False: env = Environment( ..., log_stdout=False, ...).
Q: I have large data sets that are not stored if I use multiprocessing and the lock wrapping!?
A: Probably, you use an older HDF5 version (< 1.8.7) that does not allow simultaneous openings of a single HDF5 file. Either install a newer version or switch to queue wrapping.
Q: My program crashes with TypeError: [..] dtype: float64 its type is <class 'pandas.core.series.Series'>.!?
A: You are using pandas version 0.13.x. Unfortunately, pandas performs some unwanted upcasting that cannot be handled by pypet (see https://github.com/pydata/pandas/issues/6526/). This unwanted upcasting did not happen in previous pandas versions and will be, or more precisely, has already been removed in the next pandas version. So either downgrade pandas to version 0.12.0 or upgrade to 0.14.1.
Q: My program crashes if I try to store a Trajectory containing an ArrayParameter!?
A: Look at the previous answer, you are using pandas 0.13.x, please up or downgrade your pandas package.
Q: Why can I no longer decide on the search strategy and what happened to v_check_uniqueness?
A: Both of them have been removed because they lead to inconsistencies. The child nodes of a particular group are not ordered, so tree traversal happens arbitrarily. Thus, if you search for two nodes with the same name and same depth in the tree, the search result also becomes arbitrary. Thus, pypet will now always check if your search yields a unique result up to a particular depth. Accordingly, v_check_uniqueness is rendered obsolete. Likewise is depth first search because this automatic checking only works with breadth first tree traversal. Sorry for any inconvenience caused by this API change.