How to read HDF5 attributes (metadata) with Python and h5py Question: I have a HDF5 file with multiple folders inside. Each folder has attributes added (some call attributes "metadata"). I know how to access the keys inside a folder, but I don’t know how to pull the attributes with Python’s h5py package. Here are attributes …
How to store and load a Python dictionary with HDF5 Question: I’m having issues loading (I think storing is working – a file is being created and contains data) a dictionary (string key and array/list value) from a HDF5 file. I’m receiving the following error: ValueError: malformed node or string: < HDF5 dataset “dataset_1”: shape …
Is there in python a single function that shows the full structure of a .hdf5 file? Question: When opening a .hdf5 file, one can explore the levels, keys and names of the file in different ways. I wonder if there is a way or a function that displays all the available paths to explore in …
Missing optional dependency 'tables'. In pandas to_hdf Question: following code is giving me error. import pandas as pd df = pd.DataFrame({‘a’ : [1,2,3]}) df.to_hdf(‘temp.h5′, key=’df’, mode=’w’) This is giving me error. Missing optional dependency ‘tables’. Use pip or conda to install tables. I already tried ImportError HDFStore requires PyTables No module named tables. Still the …
How to append data to one specific dataset in a hdf5 file with h5py Question: I am looking for a possibility to append data to an existing dataset inside a .h5 file using Python (h5py). A short intro to my project: I try to train a CNN using medical image data. Because of the huge …
Warning! ***HDF5 library version mismatched error*** python pandas windows Question: I’m using pandas/python to save a DataFrame in a HDFStore format. When I apply the my_data_frame.to_hdf(arguments…) command I have an error message:Warning! ***HDF5 library version mismatched error *** and my program is stopped. I’m working on Windows 7 (64bits), using Python 3.5.2 :: Anaconda 4.1.1 …
which is faster for load: pickle or hdf5 in python Question: Given a 1.5 Gb list of pandas dataframes, which format is fastest for loading compressed data: pickle (via cPickle), hdf5, or something else in Python? I only care about fastest speed to load the data into memory I don’t care about dumping the data, …
install HDF5 and pytables in ubuntu Question: I am trying to install tables package in Ubuntu 14.04 but sems like it is complaining. I am trying to install it using PyCharm and its package installer, however seems like it is complaining about HDF5 package. However, seems like I cannnot find any hdf5 package to install …
How to read HDF5 files in Python Question: I am trying to read data from hdf5 file in Python. I can read the hdf5 file using h5py, but I cannot figure out how to access data within the file. My code import h5py import numpy as np f1 = h5py.File(file_name,’r+’) This works and the file …
Is there an analysis speed or memory usage advantage to using HDF5 for large array storage (instead of flat binary files)? Question: I am processing large 3D arrays, which I often need to slice in various ways to do a variety of data analysis. A typical “cube” can be ~100GB (and will likely get larger …
