Add test for s2c mode

notebooks/scratch.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -11,6 +11,28 @@
     "a = [np.random.randint(0, 10, size=(3,2)) for _ in range(10)]\n",
     "b = [np.random.randint(0, 10, size=(3,2)) for _ in range(10)]"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "a = np.array([1,2,3,4])\n",
+    "b = np.array([4,6,7,8])\n",
+    "np.intersect1d(a, b).size"
+   ]
   }
  ],
  "metadata": {

test.py

@@ -3,7 +3,8 @@
 import glob
 import numpy as np
 
-from test_utils.dataloader import get_dataloader, yield_data_from_tensorflow_dataloader, yield_data_from_pytorch_dataloader
+from test_utils.dataloader import get_dataloader, yield_data_from_tensorflow_dataloader, yield_data_from_pytorch_dataloader, \
+    s2c_row_inds
 
 
 #def test_model():
@@ -16,6 +17,9 @@
 
 # Test for correct shape
 def test_correct_shape():
+    """
+    A function to test if the batch yielded by both Tensorflow and Pytorch has the same shape
+    """
     experiment_config_path = "/users/ngun7t/Documents/cellbox-jun-6/configs_dev/Example.random_partition.json"
     tensorflow_dataloader_list = get_dataloader(experiment_config_path, tensorflow_code=True)
     pytorch_dataloader_list = get_dataloader(experiment_config_path, tensorflow_code=False)
@@ -44,8 +48,43 @@ def test_correct_shape():
 
 
 # Test for correct input
+def test_single_to_combo():
+    """
+    A function to test if pytorch and tensorflow dataloaders yield the correct rows in the dataset for s2c experiment
+    """
+    experiment_config_path = "/users/ngun7t/Documents/cellbox-jun-6/configs_dev/Example.single_to_combo.json"
+    loo_label_dir = "/users/ngun7t/Documents/cellbox-jun-6/data/loo_label.csv"
+    tensorflow_dataloader_list = get_dataloader(experiment_config_path, tensorflow_code=True)
+    pytorch_dataloader_list = get_dataloader(experiment_config_path, tensorflow_code=False)
 
+    # Get the row index that contains single drugs
+    rows_with_single_drugs, rows_with_multiple_drugs = s2c_row_inds(loo_label_dir)
 
+    # Code to extract the shape of each yield
+    for tf_dict, torch_dict in zip(tensorflow_dataloader_list, pytorch_dataloader_list):
+        tf_train_pert, tf_train_expr = yield_data_from_tensorflow_dataloader(
+            dataloader=tf_dict["iter_train"],
+            feed_dict=tf_dict["feed_dict"]
+        )
+        torch_train_pert, torch_train_expr = yield_data_from_pytorch_dataloader(
+            dataloader=torch_dict["iter_train"]
+        )
+        # Assert that the count of batches obtained is equal
+        assert len(tf_train_pert) == len(torch_train_pert), "Length of number of arrays yield for train pert not equal"
+        assert len(tf_train_expr) == len(torch_train_expr), "Length of number of arrays yield for train expr not equal"
+
+        # Assert that the shape of each batch is equal, and also it contains the correct row index
+        for tf_arr, torch_arr in zip(tf_train_pert, torch_train_pert):
+            assert tf_arr.shape == np.array(torch_arr).shape, f"For pert batches, shape of tf batch = {tf_arr.shape} is not equal to shape of torch batch = {np.array(torch_arr).shape}"
+            assert np.intersect1d(tf_arr[:, -1], rows_with_multiple_drugs).size == 0, f"batches for tf train set contains data rows that has multiple drugs in s2c mode"
+            assert np.intersect1d(torch_arr[:, -1], rows_with_multiple_drugs).size == 0, f"batches for torch train set contains data rows that has multiple drugs in s2c mode"
+
+        # Assert that the shape of each batch is equal
+        for tf_arr, torch_arr in zip(tf_train_expr, torch_train_expr):
+            assert tf_arr.shape == np.array(torch_arr).shape, f"For expr batches, shape of tf batch = {tf_arr.shape} is not equal to shape of torch batch = {np.array(torch_arr).shape}"
+            assert np.intersect1d(tf_arr[:, -1], rows_with_multiple_drugs).size == 0, f"batches for tf train set contains data rows that has multiple drugs in s2c mode"
+            assert np.intersect1d(torch_arr[:, -1], rows_with_multiple_drugs).size == 0, f"batches for torch train set contains data rows that has multiple drugs in s2c mode"
+
 
 if __name__ == '__main__':
 

test_utils/dataloader.py

@@ -136,4 +136,15 @@ def yield_data_from_pytorch_dataloader(dataloader):
     for pert, expr in dataloader:
         items_pert.append(pert)
         items_expr.append(expr)
-    return items_pert, items_expr
+    return items_pert, items_expr
+
+
+def s2c_row_inds(loo_label_dir):
+    """
+    Identify the rows of the dataset that only has one drug.
+    The information is stored in the loo_label file
+    """
+    loo_label = pd.read_csv(loo_label_dir, header=None)
+    rows_with_single_drugs = loo_label.index[(loo_label[[0, 1]] == 0).any(axis=1)].tolist()
+    rows_with_multiple_drugs = list(set(list(range(loo_label.shape[0]))) - set(rows_with_single_drugs))
+    return rows_with_single_drugs, rows_with_multiple_drugs