Merge pull request #81 from jodreen/master

[WIP] tests for preprocess

code/stat159lambda/config.py

@@ -5,6 +5,9 @@
 # Python specific constants
 path_to_file = os.path.realpath(__file__)
 
+# if os.environ.get('TEST') and os.environ['TEST'] == 1:
+    # REPO_HOME_PATH = re.sub(r'/code/stat159lambda/config.py(c)*', '/testing', path_to_file)
+# else:
 REPO_HOME_PATH = re.sub(r'/code/stat159lambda/config.py(c)*', '', path_to_file)
 
 USE_CACHED_DATA = os.environ.get('STAT159_CACHED_DATA', 'True') == 'True'
@@ -23,4 +26,4 @@
 
 SUBJECTS = [1, 2, 3, 5, 6]
 
-RUN_DIVISIONS = [447,  880, 1310, 1790, 2244, 2675, 3209, 3543]
+RUN_DIVISIONS = [447,  880, 1310, 1790, 2244, 2675, 3209, 3543]

code/stat159lambda/linear_modeling/tests/test_linear_modeling.py

@@ -2,73 +2,62 @@
 Test linear_modeling.py module
 
 Run with:
-	nosetests test_linear_modeling.py
+    nosetests test_linear_modeling.py
 """
 
 # Python 3 compatibility
 from __future__ import absolute_import, division, print_function
 import numpy as np
 import matplotlib.pyplot as plt
 import numpy.linalg as npl
-from scipy.stats import t as t_dist
-
-from stat159lambda.linear_modeling import linear_modeling
+from stat159lambda.linear_modeling import linear_modeling as lm
 from numpy.testing import assert_equal, assert_almost_equal
 
-# Make an X, y
-X = np.ones((4, 2))
-X[:, 0] = np.array([4, 8, 2, 9])
-data = np.array([[[1, 0, 7, 0], [1, 0, 4, 4], [3, 7, 9, 7]]])
-
-# def test_get_design_matrix():
-# not done writing this function, need to wait
-
-# def test_plot_design_matrix():
-# not sure how to test plots
-
 
-def test_get_betas_Y():
-    actual = linear_modeling.get_betas_Y(X, data)[0]
-    expected = np.array([[-0.85496183, -0.11450382, -0.01526718],
-                         [6.91603053, 2.90839695, 6.58778626]])
-    assert_almost_equal(expected, actual)
-    actual = linear_modeling.get_betas_Y(X, data)[1]
-    expected = np.array([[1, 1, 3], [0, 0, 7], [7, 4, 9], [0, 4, 7]])
-    assert_almost_equal(expected, actual)
+# def setup_test():
+#     data = np.array([[1, 0, 7, 8, 0], [1, 0, 4, 10, 4], [3, 7, 10, 1, 12
+#                                                          ], [3, 7, 10, 1, 12],
+#                      [3, 7, 10, 1, 12], [3, 0, 7, 4, 12], [3, 0, 7, 4, 12]])
+#     ve = lm.VoxelExtractor(0, 'day-night', data=data)
+#     return ve
 
 
-def test_get_betas_4d():
-    actual = linear_modeling.get_betas_4d(
-        linear_modeling.get_betas_Y(X, data)[0], data)
-    expected = np.array([[[-0.85496183, 6.91603053], [-0.11450382, 2.90839695],
-                          [-0.01526718, 6.58778626]]])
-    assert_almost_equal(expected, actual)
+# def test_get_betas_Y():
+#     ve = setup_test()
+#     actual = linear_modeling.get_betas_Y(X, data)[0]
+#     expected = np.array([[-0.85496183, -0.11450382, -0.01526718],
+#                          [6.91603053, 2.90839695, 6.58778626]])
+#     assert_almost_equal(expected, actual)
+#     actual = linear_modeling.get_betas_Y(X, data)[1]
+#     expected = np.array([[1, 1, 3], [0, 0, 7], [7, 4, 9], [0, 4, 7]])
+#     assert_almost_equal(expected, actual)
 
-# def test_plot_betas():
-#    assert_array_equal(mock_imshow.call_args
-#    n_trs =
 
+# def test_get_betas_4d():
+#     actual = linear_modeling.get_betas_4d(
+#         linear_modeling.get_betas_Y(X, data)[0], data)
+#     expected = np.array([[[-0.85496183, 6.91603053], [-0.11450382, 2.90839695],
+#                           [-0.01526718, 6.58778626]]])
+#     assert_almost_equal(expected, actual)
 
-def test_t_stat():
-    actual = linear_modeling.t_stat(
-        linear_modeling.get_betas_Y(X, data)[1], X, [0, 1])
-    expected = np.array([2.7475368, 1.04410995, 1.90484058])
-    assert_almost_equal(expected, actual)
 
+# def test_t_stat():
+#     actual = linear_modeling.t_stat(
+#         linear_modeling.get_betas_Y(X, data)[1], X, [0, 1])
+#     expected = np.array([2.7475368, 1.04410995, 1.90484058])
+#     assert_almost_equal(expected, actual)
 
-def test_get_top_32():
-    a = np.array([6, 4, 1, 2, 8, 8, 1, 9, 5, 2, 1, 9, 5, 4, 3, 6, 5, 3, 5, 8])
-    assert_equal(linear_modeling.get_top_32(a, .2), [11, 7, 19, 4])
-    actual = linear_modeling.get_top_32(
-        linear_modeling.t_stat(
-            linear_modeling.get_betas_Y(X, data)[1], X, [0, 1]), .5)
-    expected = np.array([0, 2])
-    assert_almost_equal(actual, expected)
 
+# def test_get_top_32():
+#     a = np.array([6, 4, 1, 2, 8, 8, 1, 9, 5, 2, 1, 9, 5, 4, 3, 6, 5, 3, 5, 8])
+#     assert_equal(linear_modeling.get_top_32(a, .2), [11, 7, 19, 4])
+#     actual = linear_modeling.get_top_32(
+#         linear_modeling.t_stat(
+#             linear_modeling.get_betas_Y(X, data)[1], X, [0, 1]), .5)
+#     expected = np.array([0, 2])
+#     assert_almost_equal(actual, expected)
 
-def test_get_index_4d():
-    actual = linear_modeling.get_index_4d([0, 2], data)
-    assert_equal(list(actual), [(0, 0), (0, 2)])
 
-    # def test_plot_single_voxel():
-    # 	not sure how to test plots
+# def test_get_index_4d():
+#     actual = linear_modeling.get_index_4d([0, 2], data)
+#     assert_equal(list(actual), [(0, 0), (0, 2)])

code/stat159lambda/preprocess/tests/test_preprocess.py

@@ -0,0 +1,81 @@
+from __future__ import absolute_import
+from stat159lambda.preprocess import preprocess
+from stat159lambda.config import REPO_HOME_PATH
+from stat159lambda.utils import data_path as dp
+import numpy as np
+import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
+from numpy.testing import assert_array_equal, assert_almost_equal, assert_array_almost_equal
+import unittest
+import imp
+import os.path
+
+try:
+    from mock import patch
+except:
+    from unittest.mock import patch
+
+
+class ConcatenateRunsTestCase(unittest.TestCase):
+    @patch.object(np, 'save')
+    @patch.object(dp, 'get_concatenated_path')
+    @patch.object(dp, 'get_raw_path')
+    def test_concatenate_runs(self, mock_raw, mock_con, mock_np):
+        if os.path.isfile('{0}/testing/test_concatenate.nii'.format(REPO_HOME_PATH)):
+            os.remove('{0}/testing/test_concatenate.nii'.format(REPO_HOME_PATH))
+        mock_raw.return_value = '{0}/testing/test_raw.nii'.format(REPO_HOME_PATH)
+        mock_con.return_value = '{0}/testing/test_concatenate.nii'.format(REPO_HOME_PATH)
+        preprocess.concatenate_runs(1)
+        assert mock_np.call_args[0][0] == '{0}/testing/test_concatenate.nii'.format(REPO_HOME_PATH)
+
+    @patch.object(np, 'save')
+    @patch.object(dp, 'get_smoothed_path')
+    def test_reshape_smoothed_to_2d(self, mock_smooth, mock_np):
+        mock_smooth.return_value = '{0}/testing/test_smoothed_fake.npy'.format(REPO_HOME_PATH)
+        # Checking that a value error is raised if the smoothed data does not exist
+        self.assertRaises(ValueError, preprocess.reshape_smoothed_to_2d, 2, 2)
+        mock_smooth.return_value = '{0}/testing/test_smoothed.npy'.format(REPO_HOME_PATH)
+        preprocess.reshape_smoothed_to_2d(1, 1)
+        # Checking that data is saved if smoothed data exists and is not yet flattened
+        assert mock_np.call_args[0][0] == '{0}/testing/test_smoothed_2d.npy'.format(REPO_HOME_PATH)
+        preprocess.reshape_smoothed_to_2d(1, 1)
+
+    @patch.object(np, 'load')
+    @patch.object(np, 'save')
+    @patch.object(dp, 'get_raw_path')
+    def test_get_affine(self, mock_raw, mock_np_save, mock_np_load):
+        mock_raw.return_value = '{0}/testing/test_raw.nii'.format(REPO_HOME_PATH)
+        preprocess.get_affine()
+        assert mock_np_save.call_args[0][0] == '{0}/data/affine.npy'.format(REPO_HOME_PATH)
+
+    @patch.object(preprocess, 'apply_gaussian_smooth')
+    @patch.object(np, 'load')
+    @patch.object(dp, 'get_concatenated_path')
+    @patch.object(dp, 'get_smoothed_path')
+    def test_gaussian_smooth_subj(self, mock_smooth, mock_con, mock_np_load, mock_apply_gaussian):
+        if os.path.isfile('{0}/testing/test_smoothed_fake.npy'.format(REPO_HOME_PATH)):
+            os.remove('{0}/testing/test_smoothed_fake.npy'.format(REPO_HOME_PATH))
+        mock_smooth.return_value = '{0}/testing/test_smoothed_fake.npy'.format(REPO_HOME_PATH)
+        mock_con.return_value = '{0}/testing/test_concatenate.nii'.format(REPO_HOME_PATH)
+        mock_apply_gaussian.return_value
+        preprocess.gaussian_smooth_subj(1, 1)
+        assert mock_np_load.call_args[0][0] == '{0}/testing/test_concatenate.nii'.format(REPO_HOME_PATH)
+
+    def test_convert_fwhm_to_sigma(self):
+        assert_almost_equal(preprocess.convert_fwhm_to_sigma(2), 0.849321800288)
+
+    def test_get_voxel_lengths(self):
+        affine = np.array([[1, 2, 4, 5], [1, 2, 3, 4], [2, 3, 5, 6]])
+        voxel_len = preprocess.get_voxel_lengths(affine)
+        assert voxel_len.size == 3
+        assert_array_almost_equal(voxel_len, [2.44948974, 4.12310563, 7.07106781])
+
+    @patch.object(preprocess, 'get_affine')
+    @patch.object(preprocess, 'get_voxel_lengths')
+    @patch.object(preprocess, 'convert_fwhm_to_sigma')
+    def test_convert_fwhm_mm_to_sd_voxel(self, mock_convert, mock_voxel_len, mock_affine):
+        mock_affine.return_value = 1
+        mock_convert.return_value = 4
+        mock_voxel_len.return_value = 2
+        assert preprocess.convert_fwhm_mm_to_sd_voxel(4) == 2