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README.rst

@@ -45,6 +45,8 @@ on the independent variable axis. For example, for powder diffraction data taken
 chemical phases where the measurements were done at different temperatures and the materials were undergoing thermal
 expansion.
 
+I think it is not very clear here what the package does and how it can be used to solve the example problem. You are talking about VT-PXRD experiment of samples with different phases which undergo a termal expansion, so a modification of unit cell parameters, each phase independently with respect to the other in the same sample?
+
 For more information about the diffpy.snmf library, please consult our `online documentation <https://diffpy.github.io/diffpy.snmf>`_.
 
 Citation

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_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
 
-    grid_array = np.column_stack(grid_list)
-    grid_vector = np.unique(grid_array, axis=1)
+    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)

src/diffpy/snmf/subroutines.py

@@ -112,9 +112,9 @@ def construct_component_matrix(components):
 def construct_weight_matrix(components):
     """Constructs the weights matrix.
 
-    Constructs a Ķ x M matrix where K is the number of components and M is the
+    Constructs a K x M matrix where K is the number of components and M is the
     number of signals. Each element is the stretching factor for a specific
-    weights for a specific signal from the data input.
+    weight factor for a specific signal from the data input.
 
     Parameters
     ----------
@@ -359,10 +359,10 @@ def update_weights_matrix(
       The length of the experimental signal patterns
 
     stretching_factor_matrix: 2d array like
-      The matrx containing the stretching factors of the calculated component signals. Has dimensions K x M
+      The matrix containing the stretching factors of the calculated component signals. Has dimensions K x M
       where K is the number of component signals and M is the number of XRD/PDF patterns.
 
-    component_matrix: 2d array lik
+    component_matrix: 2d array like
       The matrix containing the unstretched calculated component signals. Has dimensions N x K where N is the
       length of the signals and K is the number of component signals.