Changes to read .xy files

Author: Filippo Ballerini

src/diffpy/snmf/io.py

@@ -99,22 +99,45 @@ def load_input_signals(file_path=None):
         directory_path = Path.cwd()
     else:
         directory_path = Path(file_path)
+        if not directory_path.is_dir():
+            raise ValueError(f"The provided file_path '{file_path}' is not a valid directory.")
 
     values_list = []
     grid_list = []
-    current_grid = []
+    #current_grid = []
+    current_grid = None  # Initialize as None
     for item in directory_path.iterdir():
         if item.is_file():
-            data = loadData(item.resolve())
-            if current_grid and current_grid != data[:, 0]:
-                print(f"{item.name} was ignored as it is not on a compatible grid.")
-                continue
+            data = loadData(item.resolve())  # Assuming loadData reads the XY data correctly
+            x_values = data[:, 0]  # First column as X values
+            y_values = data[:, 1]  # Second column as Y values
+
+            #data = loadData(item.resolve())
+            #if current_grid is not None and not np.array_equal(current_grid, data[:, 0]):
+                #print(f"{item.name} was ignored as it is not on a compatible grid.")
+                #continue
+            #if current_grid is not None and not np.array_equal(current_grid, x_values):
+                #print(f"{item.name} was ignored as it is not on a compatible grid.")
+            if current_grid is not None:
+                if not np.array_equal(current_grid, x_values):
+                    print(f"{item.name} has incompatible grid: {x_values}")
+                    continue
             else:
-                grid_list.append(data[:, 0])
-                current_grid = grid_list[-1]
-                values_list.append(data[:, 1])
-
-    grid_array = np.column_stack(grid_list)
-    grid_vector = np.unique(grid_array, axis=1)
+                #grid_list.append(data[:, 0])
+                #current_grid = grid_list[-1]
+                #values_list.append(data[:, 1])
+                current_grid = x_values  # Update the current grid
+                values_list.append(y_values)  # Store the Y values
+
+    if not grid_list:
+        print("No compatible grid found.")
+        return None, None
+    
+    # Stack Y values and create a unique grid array
     values_array = np.column_stack(values_list)
+
+    #grid_array = np.column_stack(grid_list)
+    #grid_vector = np.unique(grid_array, axis=1)
+    #values_array = np.column_stack(values_list)
+    print(f"Grid vector shape: {grid_vector.shape}, Values array shape: {values_array.shape}")
     return grid_vector, values_array

src/diffpy/snmf/stretchednmfapp.py

@@ -40,7 +40,8 @@ def create_parser():
         help="The lifting factor. Data will be lifted by lifted_data = data + abs(min(data) * lift). Default 1.",
     )
     parser.add_argument(
-        "number-of-components",
+        "-n",
+        "--number-of-components",
         type=int,
         help="The number of component signals for the NMF decomposition. Must be an integer greater than 0",
     )
@@ -54,6 +55,9 @@ def main():
     if args.input_directory is None:
         args.input_directory = Path.cwd()
     grid, input_data = load_input_signals(args.input_directory)
+    if input_data is None:
+        print("No valid input data found. Please check your input directory.")
+        return
     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)