Merge pull request #469 from MouseLand/test-separation

Test type separation

tests/conftest.py

@@ -6,7 +6,7 @@
 
 @pytest.fixture()
 def data_dir():
-    return Path(__file__).parent.parent.joinpath('data/test_data')
+    return Path('data/test_data')
 
 
 @pytest.fixture()

tests/regression/test_io_pipeline.py

@@ -0,0 +1,36 @@
+
+
+import numpy as np
+from pathlib import Path
+from tifffile import imread
+from suite2p import io
+
+from utils import get_binary_file_data
+
+
+def test_tiff_reconstruction_from_binary_file(test_ops):
+    """
+    Tests to see if tif generated by tiff_to_binary and write_tiff matches test tif.
+    """
+    test_ops['tiff_list'] = ['input.tif']
+    op = io.tiff_to_binary(test_ops)[0]
+    output_data = get_binary_file_data(op)
+    # Make sure data in matrix is nonnegative
+    assert np.all(output_data >= 0)
+    fname = io.generate_tiff_filename(
+        functional_chan=op['functional_chan'],
+        align_by_chan=op['align_by_chan'],
+        save_path=op['save_path'],
+        k=0,
+        ichan=True
+    )
+    io.save_tiff(output_data, fname=fname)
+    reconstructed_tiff_data = imread(
+        str(Path(test_ops['save_path0']).joinpath('suite2p', 'plane0', 'reg_tif', 'file000_chan0.tif'))
+    )
+    # Compare to our test data
+    prior_data = imread(
+        str(Path(test_ops['data_path'][0]).joinpath('1plane1chan', 'suite2p', 'test_write_tiff.tif'))
+    )
+    assert np.array_equal(reconstructed_tiff_data, prior_data)
+

tests/test_modules/test_registration_module.py → tests/regression/test_registration_pipeline.py

@@ -5,7 +5,7 @@
 import numpy as np
 from pathlib import Path
 from tifffile import imread
-from suite2p.registration import bidiphase, utils, register_binary, get_pc_metrics
+from suite2p.registration import register_binary
 
 
 def prepare_for_registration(op, input_file_name, dimensions):
@@ -95,58 +95,3 @@ def test_register_binary_rigid_registration_only(test_ops):
     assert num_col_lines == 16
     assert num_row_lines == 16
 
-
-def test_spatial_smooth_has_not_regressed_during_refactor():
-    frames = np.ones((2, 3, 3))
-    smoothed = utils.spatial_smooth(frames, 2)
-    expected = np.array([
-        [[1.  , 1.  , 0.5 ],
-         [1.  , 1.  , 0.5 ],
-         [0.5 , 0.5 , 0.25]],
-
-        [[1.  , 1.  , 0.5 ],
-         [1.  , 1.  , 0.5 ],
-         [0.5 , 0.5 , 0.25]]], dtype=np.float32)
-    assert np.allclose(smoothed, expected)
-
-
-def test_positive_bidiphase_shift_shifts_every_other_line():
-    orig = np.array([
-        [[1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7]]
-    ])
-    expected = np.array([
-        [[1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 1, 2, 3, 4, 5],
-         [1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 1, 2, 3, 4, 5],
-         [1, 2, 3, 4, 5, 6, 7]]
-    ])
-
-    shifted = orig.copy()
-    bidiphase.shift(shifted, 2)
-    assert np.allclose(shifted, expected)
-
-
-def test_negative_bidiphase_shift_shifts_every_other_line():
-    orig = np.array([
-        [[1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7]]
-    ])
-    expected = np.array([
-        [[1, 2, 3, 4, 5, 6, 7],
-         [3, 4, 5, 6, 7, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7],
-         [3, 4, 5, 6, 7, 6, 7],
-         [1, 2, 3, 4, 5, 6, 7]]
-    ])
-
-    shifted = orig.copy()
-    bidiphase.shift(shifted, -2)
-    assert np.allclose(shifted, expected)

tests/test_modules/test_io_module.py → tests/test_io.py

@@ -4,18 +4,12 @@
 
 import numpy as np
 from pathlib import Path
-from tifffile import imread
 from suite2p import io
 from pytest import fixture
 
+from utils import get_binary_file_data
+
 
-def get_binary_file_data(op):
-    # Read in binary file's contents as int16 np array
-    binary_file_data = np.fromfile(
-        str(Path(op['save_path0']).joinpath('suite2p', 'plane0', 'data.bin')),
-        np.int16
-    )
-    return np.reshape(binary_file_data, (-1, op['Ly'], op['Lx']))
 
 
 @fixture()
@@ -27,32 +21,6 @@ def binfile1500(test_ops):
         yield bin_file
 
 
-def test_tiff_reconstruction_from_binary_file(test_ops):
-    """
-    Tests to see if tif generated by tiff_to_binary and write_tiff matches test tif.
-    """
-    test_ops['tiff_list'] = ['input.tif']
-    op = io.tiff_to_binary(test_ops)[0]
-    output_data = get_binary_file_data(op)
-    # Make sure data in matrix is nonnegative
-    assert np.all(output_data >= 0)
-    fname = io.generate_tiff_filename(
-        functional_chan=op['functional_chan'],
-        align_by_chan=op['align_by_chan'],
-        save_path=op['save_path'],
-        k=0,
-        ichan=True
-    )
-    io.save_tiff(output_data, fname=fname)
-    reconstructed_tiff_data = imread(
-        str(Path(test_ops['save_path0']).joinpath('suite2p', 'plane0', 'reg_tif', 'file000_chan0.tif'))
-    )
-    # Compare to our test data
-    prior_data = imread(
-        str(Path(test_ops['data_path'][0]).joinpath('1plane1chan', 'suite2p', 'test_write_tiff.tif'))
-    )
-    assert np.array_equal(reconstructed_tiff_data, prior_data)
-
 
 def test_h5_to_binary_produces_nonnegative_output_data(test_ops):
     test_ops['h5py'] = Path(test_ops['data_path'][0]).joinpath('input.h5')

tests/test_registration.py

@@ -0,0 +1,58 @@
+import numpy as np
+from suite2p.registration import bidiphase, utils
+
+
+def test_spatial_smooth_has_not_regressed_during_refactor():
+    frames = np.ones((2, 3, 3))
+    smoothed = utils.spatial_smooth(frames, 2)
+    expected = np.array([
+        [[1.  , 1.  , 0.5 ],
+         [1.  , 1.  , 0.5 ],
+         [0.5 , 0.5 , 0.25]],
+
+        [[1.  , 1.  , 0.5 ],
+         [1.  , 1.  , 0.5 ],
+         [0.5 , 0.5 , 0.25]]], dtype=np.float32)
+    assert np.allclose(smoothed, expected)
+
+
+def test_positive_bidiphase_shift_shifts_every_other_line():
+    orig = np.array([
+        [[1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7]]
+    ])
+    expected = np.array([
+        [[1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 1, 2, 3, 4, 5],
+         [1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 1, 2, 3, 4, 5],
+         [1, 2, 3, 4, 5, 6, 7]]
+    ])
+
+    shifted = orig.copy()
+    bidiphase.shift(shifted, 2)
+    assert np.allclose(shifted, expected)
+
+
+def test_negative_bidiphase_shift_shifts_every_other_line():
+    orig = np.array([
+        [[1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7]]
+    ])
+    expected = np.array([
+        [[1, 2, 3, 4, 5, 6, 7],
+         [3, 4, 5, 6, 7, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7],
+         [3, 4, 5, 6, 7, 6, 7],
+         [1, 2, 3, 4, 5, 6, 7]]
+    ])
+
+    shifted = orig.copy()
+    bidiphase.shift(shifted, -2)
+    assert np.allclose(shifted, expected)

tests/utils.py

@@ -9,14 +9,19 @@
 r_tol, a_tol = 1e-4, 5e-2
 
 
-def get_plane_dir(op, plane):
-    suite_dir = Path(op['save_path0']).joinpath('suite2p')
-    suite_dir.mkdir(exist_ok=True)
-    plane_dir = Path(op['save_path0']).joinpath('suite2p').joinpath('plane{}'.format(plane))
-    plane_dir.mkdir(exist_ok=True)
+def get_plane_dir(op, plane, mkdir=True):
+    plane_dir = Path(op['save_path0']).joinpath('suite2p/plane{}'.format(plane))
+    if mkdir:
+        plane_dir.mkdir(exist_ok=True, parents=True)
     return plane_dir
 
 
+def get_binary_file_data(op):
+    # Read in binary file's contents as int16 np array
+    mov = np.fromfile(str(Path(op['save_path0']).joinpath('suite2p/plane0/data.bin')), np.int16)
+    return mov.reshape(-1, op['Ly'], op['Lx'])
+
+
 def write_data_to_binary(binary_path, data_path):
     input_data = np.load(data_path)
     with open(binary_path, 'wb') as f:
@@ -25,8 +30,8 @@ def write_data_to_binary(binary_path, data_path):
 
 
 def check_lists_of_arr_all_close(list1, list2):
-    for i in range(len(list1)):
-        assert np.allclose(list1[i], list2[i], rtol=r_tol, atol=a_tol)
+    for l1, l2 in zip(list1, list2):
+        assert np.allclose(l1, l2, rtol=r_tol, atol=a_tol)
 
 
 def check_dict_dicts_all_close(first_dict, second_dict):
@@ -50,9 +55,9 @@ def get_list_of_test_data(outputs_to_check, test_data_dir, nplanes, nchannels, a
                 np.concatenate([imread(tif) for tif in glob.glob(str(test_plane_dir.joinpath(output)) + '/*.tif')])
             )
         else:
-            test_data_list.append(np.load(
-                str(test_plane_dir.joinpath("{}.npy".format(output))), allow_pickle=True
-            ))
+            test_data_list.append(
+                np.load(str(test_plane_dir.joinpath("{}.npy".format(output))), allow_pickle=True)
+            )
     return test_data_list