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Questions tagged [h5py]

h5py is a NumPy-compatible Python module for handling The Hierarchical Data Format (HDF5) files.

h5py is a NumPy-compatible Python module for handling The Hierarchical Data Format (HDF5) files.

Main features

  • Free (BSD licensed)
  • limited dependencies (Python, NumPy, HDF5 libs.)
  • includes both a low level c-like HDF5 interface and a high level Python/NumPy style interface
  • directly interact with datasets using NumPy metaphors, such as slicing
  • datatypes specified using standard NumPy dtype objects

Some links to get started

1301 questions
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Reading files with .h5 format and using it in dataset

I have two folders( one for train and one for test) and each one has around 10 files in h5 format. I want to read them and use them in a dataset. I have a function to read them, but I don't know how I can use it to read the file in my class. def…
Aysan
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Unable to open .hdf file using h5py in Python

OSError: Unable to open file (file signature not found) I feel that the problem is .hdf file as I don't have .h5 or .hdf5 file. So how to I open .hdf in python?
Aniket
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What is the easiest way to load hdf5 chunks to a single variable in python?

Now I have a bunch of hdf5 chunks, their structures are all the same. And I would load them as a whole in python, is there any easiest way? (For now, I'd have to use for loop to load them file by file and then concatenate together, but I believe…
Hangci Du
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Generator function with h5py doesn't close properly

I am trying to create a generator function to train my machine learning model and yield some images. Basically it goes like that (the minimum to reproduce the error on my side): def generator(hdf5_path: str, primary_keys: list): while True: …
Unic0
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HDF5 file to dictionary

I've a hdf5 file in the below format. {...} represent groups and some have subgroups. download the file with the below link https://drive.google.com/file/d/1f6a0XEPGE4aSEKODVbJ1Q9AUw24Bt9_2/view?usp=sharing {'A': np.array(...), …
Arunakiri Venkatachalam
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How to load a keras model file to OpenCV code?

I've created a traffic sign classification model. I need to use it in OpenCV for Video traffic sign detection. How can I do that using a .h5 file Thanks in advance!
Hussein Jammal
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What is the purpose of optimizer's state_dict in PyToch Big Graph's embedding dataset?

The documentation for PyTorch Big Graph (PBG) states that "An additional dataset may exist, optimizer/state_dict, which contains the binary blob (obtained through torch.save()) of the state dict of the model’s optimizer." When inspecting this…
user876901
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write HDF h5 dataset (via h5py) which is a mix of string and numpy list

I have the following two datasets (I have several of these tuples): filename_string: "something" filename_list: [1,2,3,4,5] # this is a numpy array. Id like to know how to write this in a compact format via h5py. The goal is to have the end user…
JohnJ
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Is there a way to save each HDF5 data set as a .csv column?

I'm struggling with a H5 file to extract and save data as a multi column csv. as shown in the picture the structure of h5 file consisted of main groups (Genotypes, Positions, and taxa). The main group, Genotypes contains more than 1500 subgroups…
Pouya M. Noparvar
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Broadcast error HDF5: Can't broadcast (3, 2048, 1, 1) -> (4, 2048, 1, 1)

I have received the following error: TypeError: Can't broadcast (3, 2048, 1, 1) -> (4, 2048, 1, 1) I am extracting features and placing them into a hdf5 dataset like this: array_40 = hdf5_file.create_dataset( …
Ze0ruso
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AttributeError: type object 'h5py.h5r.Reference' has no attribute '__reduce_cython__'

I am using python 3.6,Tensorflow 1.3, Keras 2.1.2 I was importing Resnet50 and I got this error"ImportError: load_model requires h5py" so I used conda install h5py but then I got this error knowing that the installed version of h5py is 2.9.0enter…
Menna T-Allah Magdy
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how to display elements of arrays in a .mat file in python

This is the first time that I try to work with ".mat" files. I am going to use the data of a ".mat" file, but the elements of the arrays can not be opened. Can any one help me? Since the "*.mat" file is > 7.3, I can not use Scipy.io import numpy as…
Haj Nasser
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OSError: No such file or directory

When I try to open .h5 file, it shows the following error Traceback (most recent call last): File "C:\Users\VW3ZTWS\PycharmProjects\Data_Collection_and_learnings\venv\lib\site-packages\IPython\core\interactiveshell.py", line 2869, in run_code …
Mari
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importing illustris hdf5 file into numpy array using h5py

I am working on importing a rather large hdf5 file of illustris galaxy simulation code using h5py. I have the file displayed here if anyone wants to see - it is 1.96 GB. https://drive.google.com/file/d/0B1Kj475OJBnuaFBIS2FhTFpvNkk/view?usp=sharing I…
W. Ojanen
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How to query a PyTables frame_table saved via a Pandas Dataframe?

I have the following pandas dataframe: import pandas as pd df = pd.read_table('fname.dat') So, I create/ open an existing HDFStore file: store = pd.HDFStore('store.h5') To index a subset of columns, I simply use store.append('key_name', df,…
ShanZhengYang
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