Merge pull request #374 from dhruvm9/main

Decoder with TsdFrame

pynapple/process/decoding.py

@@ -22,8 +22,9 @@ def decode_1d(tuning_curves, group, ep, bin_size, time_units="s", feature=None):
     tuning_curves : pandas.DataFrame
         Each column is the tuning curve of one neuron relative to the feature.
         Index should be the center of the bin.
-    group : TsGroup or dict of Ts/Tsd object.
+    group : TsGroup, TsdFrame or dict of Ts/Tsd object.
         A group of neurons with the same index as tuning curves column names.
+        You may also pass a TsdFrame with smoothed rates (recommended).
     ep : IntervalSet
         The epoch on which decoding is computed
     bin_size : float
@@ -48,21 +49,35 @@ def decode_1d(tuning_curves, group, ep, bin_size, time_units="s", feature=None):
         If different size of neurons for tuning_curves and group.
         If indexes don't match between tuning_curves and group.
     """
-    if isinstance(group, dict):
-        newgroup = nap.TsGroup(group, time_support=ep)
+    if isinstance(group, nap.TsdFrame):
+        newgroup = group.restrict(ep)
+
+        if tuning_curves.shape[1] != newgroup.shape[1]:
+            raise RuntimeError("Different shapes for tuning_curves and group")
+
+        if not np.all(tuning_curves.columns.values == np.array(newgroup.columns)):
+            raise RuntimeError("Different indices for tuning curves and group keys")
+
+        count = group
+
     elif isinstance(group, nap.TsGroup):
         newgroup = group.restrict(ep)
-    else:
-        raise RuntimeError("Unknown format for group")
 
-    if tuning_curves.shape[1] != len(newgroup):
-        raise RuntimeError("Different shapes for tuning_curves and group")
+        if tuning_curves.shape[1] != len(newgroup):
+            raise RuntimeError("Different shapes for tuning_curves and group")
 
-    if not np.all(tuning_curves.columns.values == np.array(newgroup.keys())):
-        raise RuntimeError("Difference indexes for tuning curves and group keys")
+        if not np.all(tuning_curves.columns.values == np.array(newgroup.keys())):
+            raise RuntimeError("Different indices for tuning curves and group keys")
 
-    # Bin spikes
-    count = newgroup.count(bin_size, ep, time_units)
+        # Bin spikes
+        count = newgroup.count(bin_size, ep, time_units)
+
+    elif isinstance(group, dict):
+        newgroup = nap.TsGroup(group, time_support=ep)
+        count = newgroup.count(bin_size, ep, time_units)
+
+    else:
+        raise RuntimeError("Unknown format for group")
 
     # Occupancy
     if feature is None:
@@ -122,9 +137,10 @@ def decode_2d(tuning_curves, group, ep, bin_size, xy, time_units="s", features=N
     Parameters
     ----------
     tuning_curves : dict
-        Dictionnay of 2d tuning curves (one for each neuron).
-    group : TsGroup or dict of Ts/Tsd object.
+        Dictionary of 2d tuning curves (one for each neuron).
+    group : TsGroup, TsdFrame or dict of Ts/Tsd object.
         A group of neurons with the same keys as tuning_curves dictionary.
+        You may also pass a TsdFrame with smoothed rates (recommended).
     ep : IntervalSet
         The epoch on which decoding is computed
     bin_size : float
@@ -153,27 +169,40 @@ def decode_2d(tuning_curves, group, ep, bin_size, xy, time_units="s", features=N
 
     """
 
-    if type(group) is dict:
-        newgroup = nap.TsGroup(group, time_support=ep)
-        numcells = len(newgroup)
+    if type(group) is nap.TsdFrame:
+        newgroup = group.restrict(ep)
+        numcells = newgroup.shape[1]
+
+        if len(tuning_curves) != numcells:
+            raise RuntimeError("Different shapes for tuning_curves and group")
+
+        if not np.all(
+            np.array(list(tuning_curves.keys())) == np.array(newgroup.columns)
+        ):
+            raise RuntimeError("Different indices for tuning curves and group keys")
+
+        count = group
+
     elif type(group) is nap.TsGroup:
         newgroup = group.restrict(ep)
         numcells = len(newgroup)
-    else:
-        raise RuntimeError("Unknown format for group")
 
-    if len(tuning_curves) != numcells:
-        raise RuntimeError("Different shapes for tuning_curves and group")
+        if len(tuning_curves) != numcells:
+            raise RuntimeError("Different shapes for tuning_curves and group")
 
-    if not np.all(np.array(list(tuning_curves.keys())) == np.array(newgroup.keys())):
-        raise RuntimeError("Difference indexes for tuning curves and group keys")
+        if not np.all(
+            np.array(list(tuning_curves.keys())) == np.array(newgroup.keys())
+        ):
+            raise RuntimeError("Different indices for tuning curves and group keys")
 
-    # Bin spikes
-    # if type(newgroup) is not nap.TsdFrame:
-    count = newgroup.count(bin_size, ep, time_units)
-    # else:
-    #     #Spikes already "binned" with continuous TsdFrame input
-    #     count = newgroup
+        count = newgroup.count(bin_size, ep, time_units)
+
+    elif type(group) is dict:
+        newgroup = nap.TsGroup(group, time_support=ep)
+        count = newgroup.count(bin_size, ep, time_units)
+
+    else:
+        raise RuntimeError("Unknown format for group")
 
     indexes = list(tuning_curves.keys())
 
@@ -199,9 +228,7 @@ def decode_2d(tuning_curves, group, ep, bin_size, xy, time_units="s", features=N
     tc = np.array([tuning_curves[i] for i in tuning_curves.keys()])
     tc = tc.reshape(tc.shape[0], np.prod(tc.shape[1:]))
     tc = tc.T
-
     ct = count.values
-
     bin_size_s = nap.TsIndex.format_timestamps(
         np.array([bin_size], dtype=np.float64), time_units
     )[0]

tests/test_decoding.py

@@ -26,7 +26,6 @@ def get_testing_set_1d():
 def test_decode_1d():
     feature, group, tc, ep = get_testing_set_1d()
     decoded, proba = nap.decode_1d(tc, group, ep, bin_size=1)
-
     assert isinstance(decoded, nap.Tsd)
     assert isinstance(proba, nap.TsdFrame)
     np.testing.assert_array_almost_equal(feature.values, decoded.values)
@@ -37,11 +36,10 @@ def test_decode_1d():
     tmp[0:50, 1] = 0.0
     np.testing.assert_array_almost_equal(proba.values, tmp)
 
-def test_decode_1d_with_dict():
+def test_decode_1d_with_TsdFrame():
     feature, group, tc, ep = get_testing_set_1d()
-    group = dict(group)
-    decoded, proba = nap.decode_1d(tc, group, ep, bin_size=1)
-
+    count = group.count(bin_size=1, ep = ep)
+    decoded, proba = nap.decode_1d(tc, count, ep, bin_size=1)
     assert isinstance(decoded, nap.Tsd)
     assert isinstance(proba, nap.TsdFrame)
     np.testing.assert_array_almost_equal(feature.values, decoded.values)
@@ -65,6 +63,21 @@ def test_decode_1d_with_feature():
     tmp[50:, 0] = 0.0
     tmp[0:50, 1] = 0.0
     np.testing.assert_array_almost_equal(proba.values, tmp)
+
+def test_decode_1d_with_dict():
+    feature, group, tc, ep = get_testing_set_1d()
+    group = dict(group)
+    decoded, proba = nap.decode_1d(tc, group, ep, bin_size=1, feature=feature)
+    np.testing.assert_array_almost_equal(feature.values, decoded.values)
+    assert isinstance(decoded, nap.Tsd)
+    assert isinstance(proba, nap.TsdFrame)
+    np.testing.assert_array_almost_equal(feature.values, decoded.values)
+    assert len(decoded) == 100
+    assert len(proba) == 100
+    tmp = np.ones((100, 2))
+    tmp[50:, 0] = 0.0
+    tmp[0:50, 1] = 0.0
+    np.testing.assert_array_almost_equal(proba.values, tmp)
 
 def test_decode_1d_with_wrong_feature():
     feature, group, tc, ep = get_testing_set_1d()
@@ -94,7 +107,7 @@ def test_decoded_1d_raise_errors():
     tc.columns = [0, 2]
     with pytest.raises(Exception) as e_info:
         nap.decode_1d(tc, group, ep, 1)
-    assert str(e_info.value) == "Difference indexes for tuning curves and group keys"
+    assert str(e_info.value) == "Different indices for tuning curves and group keys"
 
 
 def get_testing_set_2d():
@@ -137,6 +150,26 @@ def test_decode_2d():
     tmp[51:100:2, 1] = 1
     np.testing.assert_array_almost_equal(proba[:, :, 1], tmp)
 
+def test_decode_2d_with_TsdFrame():
+    features, group, tc, ep, xy = get_testing_set_2d()
+    count = group.count(bin_size=1, ep = ep)
+    decoded, proba = nap.decode_2d(tc, count, ep, 1, xy)
+
+    assert isinstance(decoded, nap.TsdFrame)
+    assert isinstance(proba, np.ndarray)
+    np.testing.assert_array_almost_equal(features.values, decoded.values)
+    assert len(decoded) == 100
+    assert len(proba) == 100
+    tmp = np.zeros((100, 2))
+    tmp[0:50:2, 0] = 1
+    tmp[50:100:2, 1] = 1
+    np.testing.assert_array_almost_equal(proba[:, :, 0], tmp)
+
+    tmp = np.zeros((100, 2))
+    tmp[1:50:2, 0] = 1
+    tmp[51:100:2, 1] = 1
+    np.testing.assert_array_almost_equal(proba[:, :, 1], tmp)
+
 def test_decode_2d_with_dict():
     features, group, tc, ep, xy = get_testing_set_2d()
     group = dict(group)
@@ -186,4 +219,4 @@ def test_decoded_2d_raise_errors():
     tc = {k: tc[i] for k, i in zip(np.arange(0, 40, 10), tc.keys())}
     with pytest.raises(Exception) as e_info:
         nap.decode_2d(tc, group, ep, 1, xy)
-    assert str(e_info.value) == "Difference indexes for tuning curves and group keys"
+    assert str(e_info.value) == "Different indices for tuning curves and group keys"