Fix compute_scores to handle protocol names with '.' (#166)

bluepyemodel/emodel_pipeline/plotting_utils.py

@@ -32,6 +32,9 @@
 from bluepyemodel.evaluation.protocols import ThresholdBasedProtocol
 from bluepyemodel.evaluation.recordings import FixedDtRecordingCustom
 from bluepyemodel.evaluation.recordings import FixedDtRecordingStimulus
+from bluepyemodel.tools.utils import get_curr_name
+from bluepyemodel.tools.utils import get_loc_name
+from bluepyemodel.tools.utils import get_protocol_name
 
 logger = logging.getLogger("__main__")
 
@@ -379,12 +382,7 @@ def get_simulated_FI_curve_for_plotting(evaluator, responses, prot_name):
     simulated_amp = []
     for val in values:
         if prot_name.lower() in val.lower():
-            # val is e.g. IV_40.soma.maximum_voltage_from_voltagebase
-            n = val.split(".")
-            # case where protocol has '.' in its name, e.g. IV_40.0
-            if len(n) == 4 and n[1].isdigit():
-                n = [".".join(n[:2]), n[2], n[3]]
-            protocol_name = n[0]
+            protocol_name = get_protocol_name(val)
             amp_temp = float(protocol_name.split("_")[-1])
             if "mean_frequency" in val:
                 simulated_freq.append(values[val])
@@ -593,17 +591,11 @@ def get_ordered_currentscape_keys(keys):
 
     ordered_keys = {}
     for name in keys:
-        n = name.split(".")
-        # case where protocol has '.' in its name, e.g. IV_-100.0
-        if len(n) == 4 and n[1].isdigit():
-            n = [".".join(n[:2]), n[2], n[3]]
-        prot_name = n[0]
+        prot_name = get_protocol_name(name)
         # prot_name can be e.g. RMPProtocol, or RMPProtocol_apical055
         if not any(to_skip_ in prot_name for to_skip_ in to_skip):
-            if len(n) != 3:
-                raise ValueError(f"Expected 3 elements in {n}")
-            loc_name = n[1]
-            curr_name = n[2]
+            loc_name = get_loc_name(name)
+            curr_name = get_curr_name(name)
 
             if prot_name not in ordered_keys:
                 ordered_keys[prot_name] = {}

bluepyemodel/tools/utils.py

@@ -256,10 +256,119 @@ def get_amplitude_from_feature_key(feat_key):
     Args:
         feat_key (str): feature key, e.g. IV_40.soma.maximum_voltage_from_voltagebase
     """
-    n = feat_key.split(".")
-    # case where protocol has '.' in its name, e.g. IV_40.0
-    if len(n) == 4 and n[1].isdigit():
-        n = [".".join(n[:2]), n[2], n[3]]
-    protocol_name = n[0]
+    protocol_name = get_protocol_name(feat_key)
 
     return float(protocol_name.split("_")[-1])
+
+
+def parse_feature_name_parts(feature_name):
+    """
+    Splits the feature name into its respective parts,
+    handling cases where the protocol name contains a dot.
+
+    This function works with both a full feature name string (e.g., "IV_40.0.soma.v.voltage_base")
+    and a response key (e.g., "IV_40.0.soma.v"). It splits the input into a list of parts,
+    combining the first two parts if the protocol name contains a dot and is followed by
+    a numeric component.
+
+    Args:
+        feature_name (str): The full feature name string or response key to be parsed.
+
+    Returns:
+        list: A list of strings representing the correctly parsed parts of the feature name.
+
+    Examples:
+        >>> parse_feature_name_parts("IV_40.0.soma.v.voltage_base")
+        ['IV_40.0', 'soma', 'v', 'voltage_base']
+
+        >>> parse_feature_name_parts("IV_40.0.soma.v")
+        ['IV_40.0', 'soma', 'v']
+    """
+    parts = feature_name.split(".")
+    if len(parts) > 1 and parts[1].isdigit():
+        return [".".join(parts[:2])] + parts[2:]
+    return parts
+
+
+def get_protocol_name(feature_name):
+    """
+    Extracts the protocol name from the feature name or response key.
+
+    This function works with both a full feature name string (e.g., "IV_40.0.soma.v.voltage_base")
+    and a response key (e.g., "IV_40.0.soma.v"). It returns the first part of the input, which is
+    the protocol name, correctly handling cases where the protocol contains a dot.
+
+    Args:
+        feature_name (str): The full feature name string or response key.
+
+    Returns:
+        str: The protocol name part of the feature name.
+
+    Examples:
+        >>> get_protocol_name("IV_40.0.soma.v.voltage_base")
+        'IV_40.0'
+
+        >>> get_protocol_name("IV_40.0.soma.v")
+        'IV_40.0'
+    """
+    return parse_feature_name_parts(feature_name)[0]
+
+
+def get_loc_name(feature_name):
+    """
+    Extracts the location name from the feature name or response key.
+
+    This function works with both a full feature name string (e.g., "IV_40.0.soma.v.voltage_base")
+    and a response key (e.g., "IV_40.0.soma.v"). It returns the second part of the input, which is
+    the location name, correctly handling cases where the protocol contains a dot.
+
+    Args:
+        feature_name (str): The full feature name string or response key.
+
+    Returns:
+        str: The location name part of the feature name.
+
+    Raises:
+        IndexError: If the location name cannot be determined from the input.
+
+    Examples:
+        >>> get_loc_name("IV_40.0.soma.v.voltage_base")
+        'soma'
+
+        >>> get_loc_name("IV_40.0.soma.v")
+        'soma'
+    """
+    parts = parse_feature_name_parts(feature_name)
+    if len(parts) < 2:
+        raise IndexError("Location name not found in the feature name.")
+    return parts[1]
+
+
+def get_curr_name(feature_name):
+    """
+    Extracts the current name from the feature name or response key.
+
+    This function works with both a full feature name string (e.g., "IV_40.0.soma.v.voltage_base")
+    and a response key (e.g., "IV_40.0.soma.v"). It returns the third part of the input, which is
+    the current name, correctly handling cases where the protocol contains a dot.
+
+    Args:
+        feature_name (str): The full feature name string or response key.
+
+    Returns:
+        str: The current name part of the feature name.
+
+    Raises:
+        IndexError: If the current name cannot be determined from the input.
+
+    Examples:
+        >>> get_curr_name("IV_40.0.soma.v.voltage_base")
+        'v'
+
+        >>> get_curr_name("IV_40.0.soma.v")
+        'v'
+    """
+    parts = parse_feature_name_parts(feature_name)
+    if len(parts) < 3:
+        raise IndexError("Current name not found in the feature name.")
+    return parts[2]

bluepyemodel/validation/validation.py

@@ -25,6 +25,7 @@
 from bluepyemodel.evaluation.evaluation import compute_responses
 from bluepyemodel.evaluation.evaluation import get_evaluator_from_access_point
 from bluepyemodel.tools.utils import are_same_protocol
+from bluepyemodel.tools.utils import get_protocol_name
 from bluepyemodel.validation import validation_functions
 
 logger = logging.getLogger(__name__)
@@ -76,7 +77,7 @@ def compute_scores(model, validation_protocols):
 
     scores = model.evaluator.fitness_calculator.calculate_scores(model.responses)
     for feature_name in scores:
-        protocol_name = feature_name.split(".")[0]
+        protocol_name = get_protocol_name(feature_name)
         if any(are_same_protocol(p, protocol_name) for p in validation_protocols):
             model.scores_validation[feature_name] = scores[feature_name]
         else:

tests/unit_tests/test_tools.py

@@ -20,6 +20,9 @@
 from bluepyemodel.tools.utils import are_same_protocol
 from bluepyemodel.tools.utils import format_protocol_name_to_list
 from bluepyemodel.tools.utils import select_rec_for_thumbnail
+from bluepyemodel.tools.utils import get_protocol_name
+from bluepyemodel.tools.utils import get_loc_name
+from bluepyemodel.tools.utils import get_curr_name
 from tests.utils import DATA
 
 
@@ -136,3 +139,70 @@ def test_select_rec_for_thumbnail():
     assert (
         select_rec_for_thumbnail(rec_names, thumbnail_rec="sAHP_20.soma.v") == "IDrest_130.soma.v"
     )
+
+
+def test_get_protocol_name():
+    # feature keys
+    feature_name = "IV_40.0.soma.v.voltage_base"
+    assert get_protocol_name(feature_name) == "IV_40.0"
+
+    feature_name = "IV_40.soma.v.voltage_base"
+    assert get_protocol_name(feature_name) == "IV_40"
+
+    feature_name = "ProtocolA.1.soma.v.some_feature"
+    assert get_protocol_name(feature_name) == "ProtocolA.1"
+
+    # response keys
+    feature_name = "IV_40.0.soma.v"
+    assert get_protocol_name(feature_name) == "IV_40.0"
+
+    feature_name = "IV_40.soma.v"
+    assert get_protocol_name(feature_name) == "IV_40"
+
+    feature_name = "ProtocolA.1.soma.v"
+    assert get_protocol_name(feature_name) == "ProtocolA.1"
+
+
+def test_get_loc_name():
+    # feature keys
+    feature_name = "IV_40.0.soma.v.voltage_base"
+    assert get_loc_name(feature_name) == "soma"
+
+    feature_name = "IV_40.soma.v.voltage_base"
+    assert get_loc_name(feature_name) == "soma"
+
+    feature_name = "IV_40.0"
+    with pytest.raises(IndexError, match="Location name not found in the feature name."):
+        get_loc_name(feature_name)
+
+    # response keys
+    feature_name = "IV_40.0.soma.v"
+    assert get_loc_name(feature_name) == "soma"
+
+    feature_name = "IV_40.soma.v"
+    assert get_loc_name(feature_name) == "soma"
+
+    feature_name = "ProtocolA.1.soma.v"
+    assert get_loc_name(feature_name) == "soma"
+
+def test_get_curr_name():
+    # feature keys
+    feature_name = "IV_40.0.soma.v.voltage_base"
+    assert get_curr_name(feature_name) == "v"
+
+    feature_name = "IV_40.soma.v.voltage_base"
+    assert get_curr_name(feature_name) == "v"
+
+    feature_name = "IV_40.0.soma"
+    with pytest.raises(IndexError, match="Current name not found in the feature name."):
+        get_curr_name(feature_name)
+
+    # response keys
+    feature_name = "IV_40.0.soma.v"
+    assert get_curr_name(feature_name) == "v"
+
+    feature_name = "IV_40.soma.v"
+    assert get_curr_name(feature_name) == "v"
+
+    feature_name = "ProtocolA.1.soma.v"
+    assert get_curr_name(feature_name) == "v"