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HDF5 to TIFF Conversion and RSM Visualization

This repository contains scripts to process HDF5 data files, convert them into TIFF format, and visualize data using reciprocal space mapping (RSM).

Features

  1. HDF5 to TIFF Conversion:

    • Reads HDF5 files containing scientific data.
    • Extracts datasets and saves them as TIFF files for further analysis or visualization.

  2. Reciprocal Space Mapping (RSM):

    • Visualizes data from reciprocal space to real space using the rsm function.
    • Provides 3D and 2D projection plots to analyze diffraction patterns.

Requirements

Ensure you have the following Python libraries installed:

  • numpy
  • h5py
  • tifffile
  • matplotlib
  • pyvista
  • imageio

Install dependencies using pip:

pip install numpy h5py tifffile matplotlib pyvista imageio

Usage

HDF5 to TIFF Conversion

  1. Set the input directory containing .h5 or .hdf5 files.
  2. Specify the output directory for saving the converted TIFF files.
  3. Run the script: 
    python hdf5_to_tiff.py

Example:

input_directory = "/path/to/input/hdf5_files"
output_directory = "/path/to/output/tiff_files"

# Ensure the output directory exists
if not os.path.exists(output_directory):
    os.makedirs(output_directory)

# Convert HDF5 to TIFF
from hdf2tiff import hdf2tiff
input_directory = "/nsls2/data/staff/xyang4/data_cs/ca3ir4sn13/setup_6oct23/"
output_directory = "/nsls2/data/staff/xyang4/data_cs/ca3ir4sn13/setup_6oct23_tiff_0910_tmp/"
hdf2tiff(input_directory, output_directory)

Reciprocal Space Mapping (RSM)

The rsm function visualizes TIFF data from reciprocal space. It generates:

  • A 3D isosurface plot for the reciprocal space.
  • A 2D projection plot for specific data planes.

Parameters:

  • path: Directory containing TIFF files.
  • fnamepng: Output prefix for saved visualization images.
  • cmap: Colormap for rendering.
  • op: Opacity for the 3D plot.
  • md, nd: Dead pixel coordinates (optional).
  • el, az: Camera elevation and azimuth for 3D visualization.

Example:

from rsm_visualization import rsm

# Visualize the TIFF files from reciprocal space to real space
input_tiff_path = "/path/to/tiff/files"
output_visual_prefix = "visualization_output"

rsm(input_tiff_path, output_visual_prefix, cmap='viridis', el=30, az=45)

Output

  1. TIFF Files:

    • Saved in the specified output directory with meaningful names derived from the HDF5 dataset.

  2. RSM Visualizations:

    • 3D Isosurface plot: <output_prefix>_3D.png
    • 2D Projection plot: <output_prefix>_2D.png

License

This project is distributed under the MIT License. See the LICENSE file for more details.

Contact

For questions, suggestions, or contributions, feel free to open an issue or contact the author.