Merge pull request #126 from Arun-Niranjan/improvement/refactor-get-m…

…odel-dimensions-and-add-unit-test

Refactor get model dimensions from labels

.gitignore

@@ -7,4 +7,5 @@ __pycache__
 .ipynb_checkpoints/
 .pytest_cache
 env/
-pymdp.egg-info
+pymdp.egg-info
+inferactively_pymdp.egg-info

pymdp/utils.py

@@ -16,6 +16,27 @@
 
 EPS_VAL = 1e-16 # global constant for use in norm_dist()
 
+class Dimensions(object):
+    """
+    The Dimensions class stores all data related to the size and shape of a model.
+    """
+    def __init__(
+        self,
+        num_observations=None,
+        num_observation_modalities=0,
+        num_states=None,
+        num_state_factors=0,
+        num_controls=None,
+        num_control_factors=0,
+    ):
+        self.num_observations=num_observations
+        self.num_observation_modalities=num_observation_modalities
+        self.num_states=num_states
+        self.num_state_factors=num_state_factors
+        self.num_controls=num_controls
+        self.num_control_factors=num_control_factors
+
+
 def sample(probabilities):
     probabilities = probabilities.squeeze() if len(probabilities) > 1 else probabilities
     sample_onehot = np.random.multinomial(1, probabilities)
@@ -196,22 +217,22 @@ def get_model_dimensions(A=None, B=None):
 def get_model_dimensions_from_labels(model_labels):
 
     modalities = model_labels['observations']
-    num_modalities = len(modalities.keys())
-    num_obs = [len(modalities[modality]) for modality in modalities.keys()]
-
     factors = model_labels['states']
-    num_factors = len(factors.keys())
-    num_states = [len(factors[factor]) for factor in factors.keys()]
 
-    if 'actions' in model_labels.keys():
+    res = Dimensions(
+        num_observations=[len(modalities[modality]) for modality in modalities.keys()],
+        num_observation_modalities=len(modalities.keys()),
+        num_states=[len(factors[factor]) for factor in factors.keys()],
+        num_state_factors=len(factors.keys()),
+    )
 
+    if 'actions' in model_labels.keys():
         controls = model_labels['actions']
-        num_control_fac = len(controls.keys())
-        num_controls = [len(controls[cfac]) for cfac in controls.keys()]
+        res.num_controls=[len(controls[cfac]) for cfac in controls.keys()]
+        res.num_control_factors=len(controls.keys())
+
+    return res
 
-        return num_obs, num_modalities, num_states, num_factors, num_controls, num_control_fac
-    else:
-        return num_obs, num_modalities, num_states, num_factors
 
 
 def norm_dist(dist):
@@ -449,21 +470,18 @@ def construct_full_a(A_reduced, original_factor_idx, num_states):
 
 def create_A_matrix_stub(model_labels):
 
-    num_obs, _, num_states, _= get_model_dimensions_from_labels(model_labels)
+    dimensions = get_model_dimensions_from_labels(model_labels)
 
     obs_labels, state_labels = model_labels['observations'], model_labels['states']
 
     state_combinations = pd.MultiIndex.from_product(list(state_labels.values()), names=list(state_labels.keys()))
-    num_state_combos = np.prod(num_states)
-    # num_rows = (np.array(num_obs) * num_state_combos).sum()
-    num_rows = sum(num_obs)
+    num_rows = sum(dimensions.num_observations)
 
     cell_values = np.zeros((num_rows, len(state_combinations)))
 
     obs_combinations = []
     for modality in obs_labels.keys():
         levels_to_combine = [[modality]] + [obs_labels[modality]]
-        # obs_combinations += num_state_combos * list(itertools.product(*levels_to_combine))
         obs_combinations += list(itertools.product(*levels_to_combine))
 
 
@@ -475,7 +493,7 @@ def create_A_matrix_stub(model_labels):
 
 def create_B_matrix_stubs(model_labels):
 
-    _, _, num_states, _, num_controls, _ = get_model_dimensions_from_labels(model_labels)
+    dimensions = get_model_dimensions_from_labels(model_labels)
 
     state_labels = model_labels['states']
     action_labels = model_labels['actions']
@@ -489,9 +507,9 @@ def create_B_matrix_stubs(model_labels):
 
         prev_state_action_combos = pd.MultiIndex.from_product(factor_list, names=[factor, list(action_labels.keys())[f_idx]])
 
-        num_state_action_combos = num_states[f_idx] * num_controls[f_idx]
+        num_state_action_combos = dimensions.num_states[f_idx] * dimensions.num_controls[f_idx]
 
-        num_rows = num_states[f_idx]
+        num_rows = dimensions.num_states[f_idx]
 
         cell_values = np.zeros((num_rows, num_state_action_combos))
 
@@ -544,13 +562,12 @@ def convert_A_stub_to_ndarray(A_stub, model_labels):
     This function converts a multi-index pandas dataframe `A_stub` into an object array of different
     A matrices, one per observation modality. 
     """
+    dimensions = get_model_dimensions_from_labels(model_labels)
 
-    num_obs, num_modalities, num_states, num_factors = get_model_dimensions_from_labels(model_labels)
-
-    A = obj_array(num_modalities)
+    A = obj_array(dimensions.num_observation_modalities)
 
     for g, modality_name in enumerate(model_labels['observations'].keys()):
-        A[g] = A_stub.loc[modality_name].to_numpy().reshape(num_obs[g], *num_states)
+        A[g] = A_stub.loc[modality_name].to_numpy().reshape(dimensions.num_observations[g], *dimensions.num_states)
         assert (A[g].sum(axis=0) == 1.0).all(), 'A matrix not normalized! Check your initialization....\n'
 
     return A
@@ -561,13 +578,13 @@ def convert_B_stubs_to_ndarray(B_stubs, model_labels):
     of different B matrices, one per hidden state factor
     """
 
-    _, _, num_states, num_factors, num_controls, num_control_fac  = get_model_dimensions_from_labels(model_labels)
+    dimensions  = get_model_dimensions_from_labels(model_labels)
 
-    B = obj_array(num_factors)
+    B = obj_array(dimensions.num_control_factors)
 
     for f, factor_name in enumerate(B_stubs.keys()):
 
-        B[f] = B_stubs[factor_name].to_numpy().reshape(num_states[f], num_states[f], num_controls[f])
+        B[f] = B_stubs[factor_name].to_numpy().reshape(dimensions.num_states[f], dimensions.num_states[f], dimensions.num_controls[f])
         assert (B[f].sum(axis=0) == 1.0).all(), 'B matrix not normalized! Check your initialization....\n'
 
     return B

test/test_wrappers.py

@@ -1,15 +1,11 @@
 import os
 import unittest
 from pathlib import Path
-import shutil
-import tempfile
 
-import numpy as np
-import itertools
 import pandas as pd
 from pandas.testing import assert_frame_equal
 
-from pymdp.utils import create_A_matrix_stub, read_A_matrix, create_B_matrix_stubs, read_B_matrices
+from pymdp.utils import Dimensions, get_model_dimensions_from_labels, create_A_matrix_stub, read_A_matrix, create_B_matrix_stubs, read_B_matrices
 
 tmp_path = Path('tmp_dir')
 
@@ -18,11 +14,62 @@
 
 class TestWrappers(unittest.TestCase):
 
+    def test_get_model_dimensions_from_labels(self):
+        """
+        Tests model dimension extraction from labels including observations, states and actions.
+        """
+        model_labels = {
+            "observations": {
+                "species_observation": [
+                    "absent",
+                    "present",
+                ],
+                "budget_observation": [
+                    "high",
+                    "medium",
+                    "low",
+                ],
+            },
+            "states": {
+                "species_state": [
+                    "extant",
+                    "extinct",
+                ],
+            },
+            "actions": {
+                "conservation_action": [
+                    "manage",
+                    "survey",
+                    "stop",
+                ],
+            },
+        }
+
+        want = Dimensions(
+            num_observations=[2, 3],
+            num_observation_modalities=2,
+            num_states=[2],
+            num_state_factors=1,
+            num_controls=[3],
+            num_control_factors=1,
+        )
+
+        got = get_model_dimensions_from_labels(model_labels)
+
+        self.assertEqual(want.num_observations, got.num_observations)
+        self.assertEqual(want.num_observation_modalities, got.num_observation_modalities)
+        self.assertEqual(want.num_states, got.num_states)
+        self.assertEqual(want.num_state_factors, got.num_state_factors)
+        self.assertEqual(want.num_controls, got.num_controls)
+        self.assertEqual(want.num_control_factors, got.num_control_factors)
+
     def test_A_matrix_stub(self):
         """
         This tests the construction of a 2-modality, 2-hidden state factor pandas MultiIndex dataframe using 
         the `model_labels` dictionary, which contains the modality- and factor-specific levels, labeled with string
-        identifiers
+        identifiers.
+
+        Note: actions are ignored when creating an A matrix stub
         """
 
         model_labels = {
@@ -41,6 +88,9 @@ def test_A_matrix_stub(self):
                 "weather_state": ["raining", "clear"],
                 "sprinkler_state": ["on", "off"],
             },
+            "actions": {
+                "actions": ["something", "nothing"],
+            }
         }
 
         num_hidden_state_factors = len(model_labels["states"])