https://github.com/alisiahkoohi/h5utils

h5utils: Some basic tools for interfacing with h5py
https://github.com/alisiahkoohi/h5utils

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h5utils: Some basic tools for interfacing with h5py

• Host: GitHub
• URL: https://github.com/alisiahkoohi/h5utils
• Owner: alisiahkoohi
• License: mit
• Created: 2024-07-17T17:43:21.000Z (5 months ago)
• Default Branch: main
• Last Pushed: 2024-07-19T17:16:06.000Z (5 months ago)
• Last Synced: 2024-10-30T06:05:35.588Z (about 2 months ago)
• Language: Python
• Homepage:
• Size: 8.79 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
h5utils: Some basic tools for interfacing with h5py


## Installation

Run the command below to install the package to be used in your Python environment.

```bash

pip install git+https://github.com/alisiahkoohi/h5utils

```

For further development and to run the examples, clone the repository

and install the package in editable mode.

```bash

git clone ttps://github.com/alisiahkoohi/h5utils

cd h5utils/

pip install -e .

```

## Usage

The package provides the following functions:

- `write_data_and_label(file_path, dataset_name, data_array, label_array)`: Writes data and label to an HDF5 file.

- `print_hdf5_structure(group, indent=2)`: Recursively prints the structure of an HDF5 file.

To write data and labels to an HDF5 file:

```python

from h5utils import write_data_and_label, datadir

# Path to the HDF5 file and dataset name.

file_path = os.path.join(datadir('example_directory'), 'example.h5')

dataset_name = 'example_dataset'

# Example data array.

data = np.random.rand(10, 3, 256, 256).astype(np.float32)

# Example label strings for each element (10 in total).

label = np.array([f"label_{i}" for i in range(data.shape[0])], dtype='S')

# Write the data and label to the HDF5 file.

write_data_and_label(file_path, dataset_name, data, label)

```

To print the structure of an HDF5 file:

```python

import h5py

from h5utils import print_hdf5_structure, datadir

# Path to the HDF5 file.

file_path = os.path.join(datadir('example_directory'), 'example.h5')

with h5py.File(file_path, 'r') as file:

    print_hdf5_structure(file)

```

Replace `file_path` with the path to the HDF5 file you want to inspect.

`datadir` is a helper function that returns the absolute path to the

`data` directory located in the repository.

## Examples

The `examples/` directory contains a Python script that demonstrates how

to use the package to write a JPEG image and its label to an HDF5 file

and then read the data back.

```bash

python examples/write_jpg_to_h5.py

```

## Questions

Please contact [email protected] for questions.

## Author

Ali Siahkoohi