Tools for High Energy Diffraction Microscopy (HEDM) analysis
Project description
HEDM Pre-processing
This Python package provides tools for pre-processing data for High Energy Diffraction Microscopy (HEDM) analysis.
Features
- Conversion between different file formats (.ge, .tiff, .hdf5)
- Background subtraction
- Processing with ilastik
- Conversion to HEDM formats
Installation
Before installing this package, you need to install hexrd first. Follow the link for the guide, https://github.com/HEXRD/hexrd.
Then you need to downgrade numpy to version: numpy-1.22.4:
pip install numpy==1.22.4
Use pip to install this package:
pip install hedm_pre
Usage
The package provides several classes, including FileConverter
, Standardize_format
, Subtract_background
, Process_with_ilastik
, and Convert_to_hedm_formats
.
Each class can be instantiated with a dictionary of parameters and then the convert
method can be called to perform the operation.
Here is a basic example:
from hedm_pre import FileConverter
params = {
'input_file': 'input.tif',
'output_file': 'output.h5',
'bgsub': True,
...
}
converter = FileConverter(**params)
converter.convert()
For more detailed usage, please refer to the source code and comments.
License hedm_pre is distributed under the terms of the BSD 3-Clause license. All new contributions must be made under this license.
Contact For any question, please contact ytian37@jhu.edu.
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