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CodeFactor Documentation Status

SASNets

SASNets is a Python program for determining the shape that a SANS (Small Angle Neutron Scattering) dataset of Q and I(Q) comes from. It currently contains two nets: a traditional MLP of 9 layers, and a 1D convolutional network of 11 layers.

SASNets makes use of datafiles generated by a fork of SASModels, found at pkienzle/sasmodels.

Basic flow:

# Grab sasnets repo, and sasmodels repo to generate data.
git clone https://github.com/scattering/sasnets
git clone https://github.com/pkienzle/sasmodels

# Create the conda environment.
# ... probably missing some packages here...
conda create -n sasnets python numpy scipy matplotlib scikit-learn pandas
conda activate sasnets
pip install columnize # ... for pretty output columns [optional]

# Add tensorflow or tensorflow-gpu, depending on whether you have nvidia
# hardware (and drivers for cuda 10.0 for tensorflow 2.x).
#conda install -y tensorflow-gpu
conda install -y tensorflow

# Need sasmodels for data generation. This requires pycuda, pyopencl
# or a C compiler to run.
conda install -y pybind11 appdirs decorator mako
pip install pyopencl
#pip install pycuda
#pip install tinycc  # small C compiler for windows, if you need it.

# Work from the sasnets directory
cd sasnets

# Generate the table "train" in sasnets.db.  In this case we are
# only selecting the different types of sphere models.
bin/sasgen --count=2000 --mono=true *sphere | tee generate.log
# Use 'all' for the full dataset (600 MB at 2000 items per model).

# Train on the dataset (you will want to use more epochs...)
bin/sasnet -v --epochs=10

# Show training results
bin/sasanal
# Show dendrogram
bin/sasanal -c

On windows, use python bin/sasgen, etc.