aind-dynamic-foraging-basic-analysis 0.3.39__tar.gz → 0.3.41__tar.gz

{aind_dynamic_foraging_basic_analysis-0.3.39 → aind_dynamic_foraging_basic_analysis-0.3.41}/.github/workflows/tag_and_publish.yml

@@ -62,9 +62,9 @@ jobs:
         add: '["README.md"]'
   tag:
     needs: update_badges
-    uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
+    uses: AllenNeuralDynamics/.github/.github/workflows/release-bump-version.yml@main
     secrets:
-      SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
+      repo-token: ${{ secrets.SERVICE_TOKEN }}
   publish:
     needs: tag
     if: true

{aind_dynamic_foraging_basic_analysis-0.3.39 → aind_dynamic_foraging_basic_analysis-0.3.41}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aind-dynamic-foraging-basic-analysis
-Version: 0.3.39
+Version: 0.3.41
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT

{aind_dynamic_foraging_basic_analysis-0.3.39 → aind_dynamic_foraging_basic_analysis-0.3.41}/src/aind_dynamic_foraging_basic_analysis/__init__.py

@@ -1,6 +1,6 @@
 """Init package"""
 
-__version__ = "0.3.39"
+__version__ = "0.3.41"
 
 from .metrics.foraging_efficiency import compute_foraging_efficiency  # noqa: F401
 from .plot.plot_foraging_session import plot_foraging_session  # noqa: F401

aind_dynamic_foraging_basic_analysis-0.3.41/src/aind_dynamic_foraging_basic_analysis/metrics/session_metrics.py

@@ -0,0 +1,156 @@
+"""
+Tools for computing per session metrics
+compute_auroc: compute auroc for one NWB given alignments
+compute_auroc_multi: compute auroc for multiple NWB given alignments
+
+"""
+
+from sklearn.metrics import roc_auc_score
+from aind_dynamic_foraging_basic_analysis.plot import plot_fip as pf
+import warnings
+import pandas as pd
+import numpy as np
+
+
+def compute_auroc(nwb, alignment_times, labels, channel, tw, bin_size=0.25, data_col="data_z"):
+    """
+    Compute the time-resolved area under the ROC curve (auROC) for a single NWB session.
+
+    Parameters
+    - nwb: object
+        NWB session object expected to contain a DataFrame `df_fip` with
+        FIP data and a `session_id`.
+    - alignment_times: array-like, shape (n_trials,)
+        Times to align trials to (seconds), given in session time
+    - labels: array-like, shape (n_trials,)
+        Binary labels (0/1) for each alignment time. Must have same
+        length as alignment_times.
+    - channel: str
+        Channel name to select from `nwb.df_fip.event`.
+    - tw: tuple (start, end)
+        Time window (seconds) around the alignment to compute auROC over
+        (centered bins will be between tw[0] and tw[1]).
+    - bin_size: float, optional
+        Width (seconds) of each time bin used to aggregate values
+        before computing auROC. Default 0.25s.
+    - data_col: str, optional
+        Column name in the FIP data to use for values (default is z-scored data, 'data_z').
+
+    Returns
+    - pandas.DataFrame
+        DataFrame with columns:
+          - 'bin_center': center time of each bin (seconds)
+          - 'auc': auROC value for that bin (NaN when computation failed)
+        If the requested channel is not present in the NWB,
+        returns an empty DataFrame with those columns.
+
+    Notes
+    - alignment_times and labels are sorted together before computing PSTHs.
+    - Trials with NaNs in the aggregated bin are dropped;
+       event_numbers that contain any NaNs across bins are removed.
+    """
+    if len(labels) != len(alignment_times):
+        raise Exception("Alignment times must have same number of labels ")
+
+    if np.unique(labels).size > 2:
+        raise Exception("Labels must be binary for auROC computation")
+
+    if channel not in nwb.df_fip.event.unique():
+        warnings.warn("No channel found in this NWB, returning empty DataFrame")
+        return pd.DataFrame(columns=["bin_center", "auc"])
+
+    # sort labels and alignment times
+    sorted_indices = np.argsort(alignment_times)
+    alignment_times = alignment_times[sorted_indices]
+    labels = labels[sorted_indices]
+
+    tw_for_center_bin = [tw[0] - bin_size / 2, tw[1] + bin_size / 2]
+
+    # get alignments
+    aligns = pf.fip_psth_inner_compute(
+        nwb, alignment_times, channel, average=False, tw=tw_for_center_bin, data_column=data_col
+    )
+    n_centers = int(round((tw[1] - tw[0]) / bin_size)) + 1
+
+    # bin the time values into discrete bins and compute bin centers
+    left0 = tw_for_center_bin[0]
+    edges = left0 + np.arange(n_centers + 1) * bin_size
+    aligns["time_bin"] = pd.cut(aligns["time"], bins=edges, right=False, include_lowest=True)
+    aligns["bin_center"] = aligns["time_bin"].apply(
+        lambda iv: (iv.left + float(bin_size) / 2.0) if pd.notnull(iv) else np.nan
+    )
+
+    aligns = aligns.dropna(subset=["bin_center", data_col]).copy()
+
+    # average by bin_centers
+    agg_align = (
+        aligns.groupby(["bin_center", "event_number"], observed=True)[data_col]
+        .mean()
+        .unstack(["event_number"])
+    )
+    # drop any event_number with nan values for any bin_centers.
+    agg_align = agg_align.dropna(how="any", axis=1)
+
+    # calculate auROC
+    aucs = []
+    labels_valid = labels[agg_align.columns.values]
+    for bin_center, row in agg_align.iterrows():
+        try:
+            auc_val = roc_auc_score(labels_valid, row.values)
+        except Exception:
+            auc_val = np.nan
+        aucs.append(auc_val)
+
+    curr_auc_df = pd.DataFrame(
+        {"bin_center": agg_align.index.values, "auc": np.asarray(aucs, dtype=float)}
+    )
+
+    return curr_auc_df
+
+
+def compute_auroc_multi(nwb_list, alignment_times_list, label_list, channel, tw, bin_size=0.25):
+    """
+    Compute auROC across multiple NWB sessions and return a session x time-bin table.
+
+    Parameters
+    - nwb_list: sequence of NWB objects
+        Each element should provide FIP data and a `session_id`.
+    - alignment_times_list: sequence of array-like
+        Per-session alignment times; must be same length as nwb_list.
+    - label_list: sequence of array-like
+        Per-session labels corresponding to alignment times; must be same length as nwb_list.
+    - channel: str
+        Channel name to use in each NWB.
+    - tw: tuple (start, end)
+        Time window (seconds) around alignments to compute auROC over.
+    - bin_size: float, optional
+        Time bin width for aggregation (default 0.25s).
+
+    Returns
+    - pandas.DataFrame
+        Concatenated DataFrame where each row is a session (index = session_id)
+        and each column is a bin_center; cell values are the auROC for that session
+        and bin. If no sessions produced results, an empty DataFrame is returned.
+    """
+
+    if len(nwb_list) != len(alignment_times_list) or len(nwb_list) != len(label_list):
+        raise ValueError("nwb_list, alignment_times_list, label_list must have the same length")
+
+    # across sessions, should alway use z-scored data to compare
+    data_col = "data_z"
+
+    auc_df_list = []
+    for nwb, align_times, labels in zip(nwb_list, alignment_times_list, label_list):
+        auc_df = compute_auroc(nwb, align_times, labels, channel, tw, bin_size, data_col)
+        if auc_df.empty:
+            continue
+        auc_df["session_id"] = nwb.session_id
+        # pivot to single-row DataFrame: index=session_id, columns=bin_center, values=auc
+        row = auc_df.pivot(index="session_id", columns="bin_center", values="auc")
+        auc_df_list.append(row)
+
+    if len(auc_df_list) == 0:
+        return pd.DataFrame()
+
+    # Concatenate all DataFrames in the list
+    return pd.concat(auc_df_list, axis=0)

{aind_dynamic_foraging_basic_analysis-0.3.39 → aind_dynamic_foraging_basic_analysis-0.3.41}/src/aind_dynamic_foraging_basic_analysis.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aind-dynamic-foraging-basic-analysis
-Version: 0.3.39
+Version: 0.3.41
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT

{aind_dynamic_foraging_basic_analysis-0.3.39 → aind_dynamic_foraging_basic_analysis-0.3.41}/src/aind_dynamic_foraging_basic_analysis.egg-info/SOURCES.txt

@@ -28,6 +28,7 @@ src/aind_dynamic_foraging_basic_analysis/licks/lick_analysis.py
 src/aind_dynamic_foraging_basic_analysis/licks/plot_interlick_interval.py
 src/aind_dynamic_foraging_basic_analysis/metrics/event_rate.py
 src/aind_dynamic_foraging_basic_analysis/metrics/foraging_efficiency.py
+src/aind_dynamic_foraging_basic_analysis/metrics/session_metrics.py
 src/aind_dynamic_foraging_basic_analysis/metrics/snr_kurtosis.py
 src/aind_dynamic_foraging_basic_analysis/metrics/trial_metrics.py
 src/aind_dynamic_foraging_basic_analysis/plot/plot_fip.py