217 not all the eeg channels are turning up on the expression plot

kymata-toolbox-data/sensor_locations/EEG-layout-channel-mappings.yaml

@@ -1,4 +1,4 @@
-EEG001: 'P09'
+EEG001: 'PO9'
 EEG002: 'FPz'
 EEG003: 'PO10'
 EEG004: 'AF7'
@@ -23,10 +23,10 @@ EEG023: 'FCZ'
 EEG024: 'FC2'
 EEG025: 'FC4'
 EEG026: 'FC6'
-EEG027: 'FC8'
+EEG027: 'FT8'
 EEG030: 'T7'
-EEG031: 'С5'
-EEG032: 'С3'
+EEG031: 'C5'
+EEG032: 'C3'
 EEG033: 'C1'
 EEG034: 'CZ'
 EEG035: 'C2'
@@ -40,8 +40,8 @@ EEG043: 'CP3'
 EEG044: 'CP1'
 EEG045: 'CPZ'
 EEG046: 'CP2'
-EEG047: 'СР4'
-EEG048: 'СР6'
+EEG047: 'CP4'
+EEG048: 'CP6'
 EEG049: 'TP8'
 EEG050: 'TP10'
 EEG052: 'P7'
@@ -55,10 +55,10 @@ EEG059: 'P6'
 EEG060: 'P8'
 EEG062: 'PO7'
 EEG063: 'PO3'
-EEG064: 'P0Z'
-EEG018: 'P04'
-EEG028: 'P08'
+EEG064: 'POZ'
+EEG018: 'PO4'
+EEG028: 'PO8'
 EEG029: 'O1'
 EEG039: 'OZ'
 EEG051: 'O2'
-EEG061: 'IZ'
+EEG061: 'IZ'

kymata/config/dataset4.yaml

@@ -2,7 +2,7 @@
 # Config file for Kymata Dataset 4.00
 
 # General
-data_location: "cbu-local"                # local | cbu | cbu-local
+data_location: "local"                # local | cbu | cbu-local
 dataset_directory_name: "dataset_4-english-narratives"
 mri_structurals_directory: "raw_mri_structurals"
 

kymata/plot/layouts.py

@@ -35,6 +35,10 @@ def get_meg_sensor_xy() -> dict[str, Point2d]:
 
 
 def get_eeg_sensor_xy() -> dict[str, Point2d]:
+    with Path(Path(__file__).parent.parent.parent, "kymata-toolbox-data", "sensor_locations",
+              "EEG-layout-channel-mappings.yaml").open("r") as eeg_name_mapping_file:
+        mapping = yaml.safe_load(eeg_name_mapping_file)
+    mapping = {k.upper(): v.upper() for k, v in mapping.items()}
     d = dict()
     with Path(Path(__file__).parent.parent.parent, "kymata-toolbox-data", "sensor_locations",
               "EEG1005.lay").open("r") as layout_file:
@@ -44,19 +48,11 @@ def get_eeg_sensor_xy() -> dict[str, Point2d]:
             y = float(parts[2])
             name = parts[-1].upper()
             d[name] = Point2d(x, y)
-    # Get name mapping
-    with Path(Path(__file__).parent.parent.parent, "kymata-toolbox-data", "sensor_locations",
-              "EEG-layout-channel-mappings.yaml").open("r") as eeg_name_mapping_file:
-        mapping = yaml.safe_load(eeg_name_mapping_file)
-    mapping = {k.upper(): v.upper() for k, v in mapping.items()}
-    inverted_mapping = {v: k for k, v in mapping.items()}
-    # Apply name mapping
-    new_d = {
-        inverted_mapping[name]: point
-        for name, point in d.items()
-        if name in inverted_mapping.keys()
+    our_sensor_d = {
+        our_name: d[their_name]
+        for our_name, their_name in mapping.items()
     }
-    return new_d
+    return our_sensor_d
 
 
 def plot_eeg_sensor_positions(raw_fif: Raw):

kymata/plot/plot.py

@@ -50,7 +50,7 @@ class AxisAssignment(NamedTuple):
     axis_channels: list
 
 
-_left_right_sensors: tuple[AxisAssignment, AxisAssignment] = (
+sensor_left_right_assignment: tuple[AxisAssignment, AxisAssignment] = (
     AxisAssignment(axis_name="left",
                    axis_channels=[
                        sensor
@@ -179,7 +179,7 @@ def expression_plot(
         # We have a special case with paired sensor data, in that some sensors need to appear
         # on both sides of the midline.
         if paired_axes and isinstance(expression_set, SensorExpressionSet):
-            assign_left_right_channels = _left_right_sensors
+            assign_left_right_channels = sensor_left_right_assignment
             # Some points will be plotted on one axis, filled, some on both, empty
             top_chans = set(assign_left_right_channels[0].axis_channels)
             bottom_chans = set(assign_left_right_channels[1].axis_channels)

tests/test_iterables.py

@@ -1,18 +1,32 @@
+import pytest
+
 from kymata.entities.iterables import all_equal
 
 
-def test_all_0s_are_equal():
-    all_zeros = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-    assert all_equal(all_zeros)
+@pytest.fixture
+def all_0s():
+    return [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
+
+
+@pytest.fixture
+def all_0s_and_a_1():
+    return [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]
+
+
+@pytest.fixture
+def all_nones():
+    return [None, None, None, None, None, None, None, None]
+
+
+def test_all_0s_are_equal(all_0s):
+    assert all_equal(all_0s)
 
 
-def test_0s_and_a_1_are_not_equal():
-    all_zeros_and_a_one = [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]
-    assert not all_equal(all_zeros_and_a_one)
+def test_0s_and_a_1_are_not_equal(all_0s_and_a_1):
+    assert not all_equal(all_0s_and_a_1)
 
 
-def test_all_nones_are_equal():
-    all_nones = [None, None, None, None, None, None, None, None]
+def test_all_nones_are_equal(all_nones):
     assert all_equal(all_nones)