Merge pull request #40 from aajayi-21/mainfunction

stretchednmfapp.py

Author: sbillinge

diffpy/snmf/stretchednmfapp.py

@@ -0,0 +1,39 @@
+import numpy as np
+import argparse
+from pathlib import Path
+from diffpy.snmf.subroutines import lift_data, initialize_components
+from diffpy.snmf.containers import ComponentSignal
+from diffpy.snmf.io import load_input_signals, initialize_variables
+
+ALLOWED_DATA_TYPES = ['powder_diffraction', 'pd', 'pair_distribution_function', 'pdf']
+
+
+def create_parser():
+    parser = argparse.ArgumentParser(
+        prog="stretched_nmf",
+        description="Stretched Nonnegative Matrix Factorization"
+    )
+    parser.add_argument('-i', '--input-directory', type=str, default=None,
+                        help="Directory containing experimental data. Defaults to current working directory.")
+    parser.add_argument('-o', '--output-directory', type=str,
+                        help="The directory where the results will be written. Defaults to '<input_directory>/snmf_results'.")
+    parser.add_argument('t', '--data-type', type=str, default=None, choices=ALLOWED_DATA_TYPES,
+                        help="The type of the experimental data.")
+    parser.add_argument('-l', '--lift-factor', type=float, default=1,
+                        help="The lifting factor. Data will be lifted by lifted_data = data + abs(min(data) * lift). Default is 1.")
+    parser.add_argument('number-of-components', type=int,
+                        help="The number of component signals for the NMF decomposition. Must be an integer greater than 0")
+    parser.add_argument('-v', '--version', action='version', help='Print the software version number')
+    args = parser.parse_args()
+    return args
+
+
+def main():
+    args = create_parser()
+    if args.input_directory is None:
+        args.input_directory = Path.cwd()
+    grid, input_data = load_input_signals(args.input_directory)
+    lifted_input_data = lift_data(input_data, args.lift_factor)
+    variables = initialize_variables(lifted_input_data, args.number_of_components, args.data_type)
+    components = initialize_components(variables['number_of_components'], variables['number_of_signals'], grid)
+    return components