renamed parameters and added output directory parameter. Added functionality for getting data type from file extension

Author: aajayi-21

Diff for: diffpy/snmf/io.py

@@ -101,8 +101,10 @@ def load_input_signals(file_path=None):
     values_list = []
     grid_list = []
     current_grid = []
+    file_extension = ""
     for item in directory_path.iterdir():
         if item.is_file():
+            file_extension = Path(item).suffix
             data = loadData(item.resolve())
             if len(current_grid) != 0 and (current_grid != data[:, 0]).any():
                 print(f"{item.name} was ignored as it is not on a compatible grid.")
@@ -115,4 +117,10 @@ def load_input_signals(file_path=None):
     grid_array = np.column_stack(grid_list)
     grid_vector = np.unique(grid_array, axis=1)
     values_array = np.column_stack(values_list)
-    return grid_vector, values_array
+    if file_extension in {'.gr','.chi'}:
+        data_type = 'pdf'
+    elif file_extension in {'iq','.xy','.xye','.xrd'}:
+        data_type = 'xrd'
+    else:
+        data_type = None
+    return grid_vector, values_array,data_type

Diff for: diffpy/snmf/stretchednmfapp.py

@@ -10,22 +10,28 @@ def create_parser():
         description="Stretched Nonnegative Matrix Factorization"
     )
     parser.add_argument('-v', '--version', action='version', help='Print the software version number')
-    parser.add_argument('-d', '--directory', type=str,
-                        help="Directory containing experimental data. Ensure it is in quotations or apostrophes.")
-
-    parser.add_argument('component_number', type=int,
+    parser.add_argument('-i', '--input-directory', type=str,
+                        help="Directory containing experimental data. Has a default value of None which sets the input as your current working directory.")
+    parser.add_argument('-o', '--output-directory', type=str,
+                        help="The directory where the results will be dumped. Default behavior will create a new directory named 'smnf_results' inside the input directory.")
+    parser.add_argument('-t', '--data-type', type=str, choices=['xrd', 'pdf'],
+                        help="The type of the experimental data.")
+    parser.add_argument('components', type=int,
                         help="The number of component signals to obtain from experimental "
                              "data. Must be an integer greater than 0.")
-    parser.add_argument('data_type', type=str, choices=['xrd', 'pdf'], help="The type of the experimental data.")
     args = parser.parse_args()
     return args
 
 
 def main():
     args = create_parser()
 
-    grid, data_input = load_input_signals(args.directory)
-    variables = initialize_variables(data_input, args.component_number, args.data_type)
+    grid, data_input, data_type = load_input_signals(args.input_directory)
+    if args.data_type is not None:
+        variables = initialize_variables(data_input, args.components, args.data_type)
+    else:
+        variables = initialize_variables(data_input, args.components, data_type)
+
     if variables["data_type"] == 'pdf':
         lifted_data = data_input - np.ndarray.min(data_input[:])
     maxiter = 300