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Questions - h5py

HDF5 makes a problem after brew update & upgrade

I'm M1 user and coding on python 3.9.10 up to now. I try updating lib. with homebrew, especially for python 3.9.12 and HDF5. Also I reinstalled h5py. Here I tried. brew update & upgrade brew reins...
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navian

python

homebrew

hdf5

h5py

Votes: 0

Answers: 2

Latest Answer

The following worked for me. First, uninstall h5py and hdf5 (also deleted my pip cache, but not sure how relevant this is). Then just run > brew install hdf5 > export HDF5_DIR="$(brew --pre...
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Sito

h5py extremely slow writing

After preparing data from a dataset, I want to save the prepared data using h5py. The data is a float32 numpy array of shape (16813, 60, 44, 257). Preparing the data is very fast, only a few seconds t...
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frankatank

python

linux

h5py

Votes: 0

Answers: 1

Latest Answer

If you implement chunking correctly, writing this much data should be "relatively fast" (minutes, not hours). Without chunking, this could take a very long time. To demonstrate how to use ch...
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kcw78

Spyder won't import h5py, but iPython console will. Why is that?

I am trying to open a .h5 file that contains data I need to plot, and I want to do this with Spyder (on macOS Big Sur). I have installed h5py through pip and here is what happens: If I open an iPython...
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vlabadaboum

python

spyder

h5py

Votes: 0

Answers: 1

Latest Answer

This is a result of Apple delivering Macs with Python installed. They think they are doing you a favor. Instead, they just complicate your life (especially if you want to use Conda Python.) For refere...
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kcw78

Converting .h5/.hic file to .csv/.json

I want to convert .h5/.hic files to .csv/.json format. I found this https://pypi.org/project/h5json/ and their GitHub page https://github.com/HDFGroup/hdf5-json to convert to json from h5. I was succe...
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Deep

python

json

h5py

Votes: 0

Answers: 1

Latest Answer

A possible solution is pandas, see the official guide. Here an example: import pandas as pd df = pd.DataFrame({"x": list(range(5)), "y": list(range(5))}) df.to_hdf("tab.h5&qu...
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Andrea Di Iura

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