SciAnalysis is a set of Python scripts for batch processing of image data, including x-ray scattering detector images. The code was written primarily by Kevin Yager.
http://gisaxs.com/index.php/SciAnalysis
An under-developing GPT-based Agent for answering questions on SciAnalysis (Siyu Wu):
https://chatgpt.com/g/g-67b88a7cbd9c81919e3141a64d11cf5f-scianalysis-agent
INSTALL:
- python setup.py develop
OR, simply download the package and see examples/beamlines/NSLSII_11BM_CMS/UShell/SciAnalysis_jn.ipynb for tutorial.
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SciAnalysis is a Python-based framework for batch processing of X-ray scattering data and other image-based scientific analyses. Developed primarily by Kevin G. Yager and maintained by the Center for Functional Nanomaterials at Brookhaven National Laboratory, SciAnalysis provides tools for automated data reduction, calibration, and visualization.
- Supports multiple data formats including
.tiff,.h5, and other standard scientific formats. - Built-in protocols for data analysis such as circular averaging, sector averaging, and line cuts.
- Calibration tools for detector alignment, beam center correction, and energy calibration.
- Customizable processing pipelines to extend analysis for specific experiments.
- Integration with beamline workflows for automated processing of large datasets.
- Download and install Python from python.org.
- Ensure you check 'Add Python to PATH' during installation.
- Verify installation:
python --version
- Download and install Git from gitforwindows.org.
- Verify installation:
git --version
cd Desktop
git clone https://github.com/CFN-SoftBio/SciAnalysis.git
cd SciAnalysispip install -r requirements.txt
python setup.py installpython -c "import SciAnalysis; print(SciAnalysis.__version__)"SciAnalysis is organized into several modules:
SciAnalysis/
├── Base.py # Core utilities
├── Data.py # Data processing classes
├── Fit.py # Curve fitting utilities
├── IO_HDF.py # HDF5 file I/O handling
├── XSAnalysis/ # X-ray scattering analysis
│ ├── Data.py # Handles scattering image data
│ ├── Protocols.py # Analysis protocols
│ ├── masks/ # Detector masks
└── examples/ # Sample scripts for running analyses
- Handles 1D data such as line cuts.
- Example usage:
from SciAnalysis.XSAnalysis.Data import DataLine data = DataLine.load('datafile.dat')
- Processes 2D scattering images.
- Example:
from SciAnalysis.XSAnalysis.Data import Data2DScattering image_data = Data2DScattering('sample.tiff')
- Used for setting beam center, detector distance, and masking.
- Example:
from SciAnalysis.XSAnalysis.Tools import Calibration calib = Calibration(wavelength_A=0.770088) calib.set_image_size(981, height=1043) calib.set_pixel_size(pixel_size_um=172.0) calib.set_beam_position(391, 549)
- Defines analysis routines for scattering experiments.
- Example:
from SciAnalysis.XSAnalysis import Protocols load_args = {'calibration': calib, 'mask': mask} run_args = {'verbosity': 3} process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args) image_data = process.load('sample.tiff') process.run([image_data], [Protocols.circular_average()], output_dir='output/')
from SciAnalysis.XSAnalysis.Data import Data2DScattering
image_data = Data2DScattering('sample.tiff')
image_data.plot(show=True)from SciAnalysis.XSAnalysis.Tools import Calibration
calib = Calibration(wavelength_A=0.770088)
calib.set_image_size(981, height=1043)
calib.set_pixel_size(pixel_size_um=172.0)
calib.set_beam_position(391, 549)from SciAnalysis.XSAnalysis import Protocols
load_args = {'calibration': calib, 'mask': mask}
run_args = {'verbosity': 3}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
image_data = process.load('sample.tiff')
process.run([image_data], [Protocols.circular_average()], output_dir='output/').png: Plots of processed data.dat: Data tables of extracted results.xml: Metadata and fitted parameters
| Error | Solution |
|---|---|
ModuleNotFoundError: No module named 'SciAnalysis' |
Ensure installation was successful and SciAnalysis is in PYTHONPATH. |
ImportError: No module named 'matplotlib' |
Run pip install matplotlib. |
FileNotFoundError: No such file or directory |
Check the path of input files. |
- Fork the repository on GitHub.
- Make changes and submit a pull request.
- Follow PEP8 style guidelines.
SciAnalysis is open-source and licensed under Brookhaven Science Associates License.
This README file was generated by GPT models. While efforts have been made to ensure accuracy, ChatGPT can make mistakes. Please verify important information and refer to official SciAnalysis documentation or consult experts for critical use cases.
For issues, contact the maintainers via GitHub Issues.