Merge pull request #38 from aajayi-21/construct_stretching

function construct_stretching_matrix

Author: sbillinge

diffpy/snmf/subroutines.py

@@ -25,7 +25,7 @@ def initialize_components(number_of_components, number_of_signals, grid_vector):
         raise ValueError(f"Number of components = {number_of_components}. Number_of_components must be >= 1.")
     components = list()
     for component in range(number_of_components):
-        component = ComponentSignal(grid_vector,number_of_signals,component)
+        component = ComponentSignal(grid_vector, number_of_signals, component)
         components.append(component)
     return tuple(components)
 
@@ -54,6 +54,36 @@ def lift_data(data_input, lift=1):
     return data_input + np.abs(np.min(data_input) * lift)
 
 
+def construct_stretching_matrix(components, number_of_components, number_of_signals):
+    """Constructs the stretching factor matrix
+
+    Parameters
+    ----------
+    components: tuple of ComponentSignal objects
+       The tuple containing the component signals in ComponentSignal objects.
+    number_of_signals: int
+      The number of signals in the data provided by the user.
+
+    Returns
+    -------
+    2d array
+      The matrix containing the stretching factors for the component signals for each of the signals in the raw data.
+      Has dimensions `component_signal` x `number_of_signals`
+
+    """
+    if (len(components)) == 0:
+        raise ValueError(f"Number of components = {number_of_components}. Number_of_components must be >= 1.")
+    number_of_components = len(components)
+    
+    if number_of_signals <= 0:
+        raise ValueError(f"Number of signals = {number_of_signals}. Number_of_signals must be >= 1.")
+        
+    stretching_factor_matrix = np.zeros((number_of_components, number_of_signals))
+    for i, component in enumerate(components):
+        stretching_factor_matrix[i] = component.stretching_factors
+    return stretching_factor_matrix
+
+
 def initialize_arrays(number_of_components, number_of_moments, signal_length):
     """Generates the initial guesses for the weight, stretching, and component matrices
 

diffpy/snmf/tests/test_subroutines.py

@@ -1,7 +1,8 @@
 import pytest
 import numpy as np
+from diffpy.snmf.containers import ComponentSignal
 from diffpy.snmf.subroutines import objective_function, get_stretched_component, reconstruct_data, get_residual_matrix, \
-    update_weights_matrix, initialize_arrays, lift_data, initialize_components
+    update_weights_matrix, initialize_arrays, lift_data, initialize_components, construct_stretching_matrix
 
 to = [
     ([[[1, 2], [3, 4]], [[5, 6], [7, 8]], 1e11, [[1, 2], [3, 4]], [[1, 2], [3, 4]], 1], 2.574e14),
@@ -161,3 +162,27 @@ def test_initialize_components(tcc):
     assert len(actual) == tcc[0]
     assert len(actual[0].weights) == tcc[1]
     assert (actual[0].grid == np.array(tcc[2])).all()
+
+tcso =[([ComponentSignal([0,.5,1,1.5],20,0)],1,20),
+       ([ComponentSignal([0,.5,1,1.5],20,0)],4,20),
+       # ([ComponentSignal([0,.5,1,1.5],20,0)],0,20), # Raises an exception
+       # ([ComponentSignal([0,.5,1,1.5],20,0)],-2,20), # Raises an exception
+       # ([ComponentSignal([0,.5,1,1.5],20,0)],1,0), # Raises an Exception
+       # ([ComponentSignal([0,.5,1,1.5],20,0)],1,-3), # Raises an exception
+       ([ComponentSignal([0,.5,1,1.5],20,0),ComponentSignal([0,.5,1,1.5],20,1)],2,20),
+       ([ComponentSignal([0,.5,1,1.5],20,0),ComponentSignal([0,.5,1,21.5],20,1)],2,20),
+       ([ComponentSignal([0,1,1.5],20,0),ComponentSignal([0,.5,1,21.5],20,1)],2,20),
+       # ([ComponentSignal([0,.5,1,1.5],20,0),ComponentSignal([0,.5,1,1.5],20,1)],1,-3), # Negative signal length. Raises an exception
+       #([],1,20), # Empty components. Raises an Exception
+       #([],-1,20), # Empty components with negative number of components. Raises an exception
+       #([],0,20), # Empty components with zero number of components. Raises an exception
+       #([],1,0), # Empty components with zero signal length. Raises an exception.
+       #([],-1,-2), # Empty components with negative number of components and signal length Raises an exception.
+
+]
+@pytest.mark.parametrize('tcso',tcso)
+def test_construct_stretching_matrix(tcso):
+    actual = construct_stretching_matrix(tcso[0],tcso[1],tcso[2])
+    for component in tcso[0]:
+        np.testing.assert_allclose(actual[component.id,:], component.stretching_factors)
+        #assert actual[component.id, :] == component.stretching_factors