bmtool 0.7.1.6__py3-none-any.whl → 0.7.2__py3-none-any.whl

bmtool/bmplot/spikes.py

@@ -20,6 +20,7 @@ def raster(
     tstart: Optional[float] = None,
     tstop: Optional[float] = None,
     color_map: Optional[Dict[str, str]] = None,
+    dot_size: Optional[float] = 0.3,
 ) -> Axes:
     """
     Plots a raster plot of neural spikes, with different colors for each population.
@@ -40,6 +41,8 @@ def raster(
         Stop time for filtering spikes; only spikes with timestamps less than `tstop` will be plotted.
     color_map : dict, optional
         Dictionary specifying colors for each population. Keys should be population names, and values should be color values.
+    dot_size: float, optional
+        Size of the dot to display on the scatterplot
 
     Returns:
     -------
@@ -53,6 +56,7 @@ def raster(
     - If `color_map` is provided, it should contain colors for all unique `pop_name` values in `spikes_df`.
     """
     # Initialize axes if none provided
+    sns.set_style("whitegrid")
     if ax is None:
         _, ax = plt.subplots(1, 1)
 
@@ -102,15 +106,17 @@ def raster(
             raise ValueError(f"color_map is missing colors for populations: {missing_colors}")
 
     # Plot each population with its specified or generated color
+    legend_handles = []
     for pop_name, group in spikes_df.groupby(groupby):
-        ax.scatter(
-            group["timestamps"], group["node_ids"], label=pop_name, color=color_map[pop_name], s=0.5
-        )
+        ax.scatter(group["timestamps"], group["node_ids"], color=color_map[pop_name], s=dot_size)
+        # Dummy scatter for consistent legend appearance
+        handle = ax.scatter([], [], color=color_map[pop_name], label=pop_name, s=20)
+        legend_handles.append(handle)
 
     # Label axes
     ax.set_xlabel("Time")
     ax.set_ylabel("Node ID")
-    ax.legend(title="Population", loc="upper right", framealpha=0.9, markerfirst=False)
+    ax.legend(handles=legend_handles, title="Population", loc="upper right", framealpha=0.9)
 
     return ax
 
@@ -142,6 +148,7 @@ def plot_firing_rate_pop_stats(
         Axes with the bar plot.
     """
     # Ensure groupby is a list for consistent handling
+    sns.set_style("whitegrid")
     if isinstance(groupby, str):
         groupby = [groupby]
 
@@ -234,6 +241,7 @@ def plot_firing_rate_distribution(
     matplotlib.axes.Axes
         Axes with the selected plot type(s) overlayed.
     """
+    sns.set_style("whitegrid")
     # Ensure groupby is a list for consistent handling
     if isinstance(groupby, str):
         groupby = [groupby]
@@ -287,8 +295,9 @@ def plot_firing_rate_distribution(
                 y="firing_rate",
                 ax=ax,
                 palette=color_map,
-                inner="quartile",
+                inner="box",
                 alpha=0.4,
+                cut=0,  # This prevents the KDE from extending beyond the data range
             )
         elif pt == "swarm":
             sns.swarmplot(
@@ -308,3 +317,107 @@ def plot_firing_rate_distribution(
     ax.grid(axis="y", linestyle="--", alpha=0.7)
 
     return ax
+
+
+def plot_firing_rate_vs_node_attribute(
+    individual_stats: Optional[pd.DataFrame] = None,
+    config: Optional[str] = None,
+    nodes: Optional[pd.DataFrame] = None,
+    groupby: Optional[str] = None,
+    network_name: Optional[str] = None,
+    attribute: Optional[str] = None,
+    figsize=(12, 8),
+    dot_size: float = 3,
+) -> plt.Figure:
+    """
+    Plot firing rate vs node attribute for each group in separate subplots.
+
+    Parameters
+    ----------
+    individual_stats : pd.DataFrame, optional
+        DataFrame containing individual cell firing rates from compute_firing_rate_stats
+    config : str, optional
+        Path to configuration file for loading node data
+    nodes : pd.DataFrame, optional
+        Pre-loaded node data as alternative to loading from config
+    groupby : str, optional
+        Column name in individual_stats to group plots by
+    network_name : str, optional
+        Name of network to load from config file
+    attribute : str, optional
+        Node attribute column name to plot against firing rate
+    figsize : tuple[int, int], optional
+        Figure dimensions (width, height) in inches
+    dot_size : float, optional
+        Size of scatter plot points
+
+    Returns
+    -------
+    matplotlib.figure.Figure
+        Figure containing the subplots
+
+    Raises
+    ------
+    ValueError
+        If neither config nor nodes is provided
+        If network_name is missing when using config
+        If attribute is not found in nodes DataFrame
+        If node_ids column is missing
+        If nodes index is not unique
+    """
+    # Input validation
+    if config is None and nodes is None:
+        raise ValueError("Must provide either config or nodes")
+    if config is not None and nodes is None:
+        if network_name is None:
+            raise ValueError("network_name required when using config")
+        nodes = load_nodes_from_config(config)
+    if attribute not in nodes.columns:
+        raise ValueError(f"Attribute '{attribute}' not found in nodes DataFrame")
+
+    # Extract node attribute data
+    node_attribute = nodes[attribute]
+
+    # Validate data structure
+    if "node_ids" not in individual_stats.columns:
+        raise ValueError("individual_stats missing required 'node_ids' column")
+    if not nodes.index.is_unique:
+        raise ValueError("nodes DataFrame must have unique index for merging")
+
+    # Merge firing rate data with node attributes
+    merged_df = individual_stats.merge(
+        node_attribute, left_on="node_ids", right_index=True, how="left"
+    )
+
+    # Setup subplot layout
+    max_groups = 15  # Maximum number of subplots to avoid overcrowding
+    unique_groups = merged_df[groupby].unique()
+    n_groups = min(len(unique_groups), max_groups)
+
+    if len(unique_groups) > max_groups:
+        print(f"Warning: Limiting display to {max_groups} groups out of {len(unique_groups)}")
+        unique_groups = unique_groups[:max_groups]
+
+    n_cols = min(3, n_groups)
+    n_rows = (n_groups + n_cols - 1) // n_cols
+
+    # Create subplots
+    fig, axes = plt.subplots(n_rows, n_cols, figsize=figsize)
+    if n_groups == 1:
+        axes = np.array([axes])
+    axes = axes.flatten()
+
+    # Plot each group
+    for i, group in enumerate(unique_groups):
+        group_df = merged_df[merged_df[groupby] == group]
+        axes[i].scatter(group_df["firing_rate"], group_df[attribute], s=dot_size)
+        axes[i].set_xlabel("Firing Rate (Hz)")
+        axes[i].set_ylabel(attribute)
+        axes[i].set_title(f"{groupby}: {group}")
+
+    # Hide unused subplots
+    for j in range(i + 1, len(axes)):
+        axes[j].set_visible(False)
+
+    plt.tight_layout()
+    plt.show()

bmtool/synapses.py

@@ -18,15 +18,18 @@ from scipy.optimize import curve_fit, minimize, minimize_scalar
 from scipy.signal import find_peaks
 from tqdm.notebook import tqdm
 
+from bmtool.util.util import load_templates_from_config
+
 
 class SynapseTuner:
     def __init__(
         self,
-        mechanisms_dir: str,
-        templates_dir: str,
-        conn_type_settings: dict,
-        connection: str,
-        general_settings: dict,
+        mechanisms_dir: str = None,
+        templates_dir: str = None,
+        config: str = None,
+        conn_type_settings: dict = None,
+        connection: str = None,
+        general_settings: dict = None,
         json_folder_path: str = None,
         current_name: str = "i",
         other_vars_to_record: list = None,
@@ -57,8 +60,18 @@ class SynapseTuner:
             List of synaptic variables you would like sliders set up for the STP sliders method by default will use all parameters in spec_syn_param.
 
         """
-        neuron.load_mechanisms(mechanisms_dir)
-        h.load_file(templates_dir)
+        if config is None and (mechanisms_dir is None or templates_dir is None):
+            raise ValueError(
+                "Either a config file or both mechanisms_dir and templates_dir must be provided."
+            )
+
+        if config is None:
+            neuron.load_mechanisms(mechanisms_dir)
+            h.load_file(templates_dir)
+        else:
+            # loads both mech and templates
+            load_templates_from_config(config)
+
         self.conn_type_settings = conn_type_settings
         if json_folder_path:
             print(f"updating settings from json path {json_folder_path}")
@@ -939,10 +952,11 @@ class SynapseTuner:
 class GapJunctionTuner:
     def __init__(
         self,
-        mechanisms_dir: str,
-        templates_dir: str,
-        general_settings: dict,
-        conn_type_settings: dict,
+        mechanisms_dir: str = None,
+        templates_dir: str = None,
+        config: str = None,
+        general_settings: dict = None,
+        conn_type_settings: dict = None,
     ):
         """
         Initialize the GapJunctionTuner class.
@@ -953,13 +967,24 @@ class GapJunctionTuner:
             Directory path containing the compiled mod files needed for NEURON mechanisms.
         templates_dir : str
             Directory path containing cell template files (.hoc or .py) loaded into NEURON.
+        config : str
+            Path to a BMTK config.json file. Can be used to load mechanisms, templates, and other settings.
         general_settings : dict
             General settings dictionary including parameters like simulation time step, duration, and temperature.
         conn_type_settings : dict
             A dictionary containing connection-specific settings for gap junctions.
         """
-        neuron.load_mechanisms(mechanisms_dir)
-        h.load_file(templates_dir)
+        if config is None and (mechanisms_dir is None or templates_dir is None):
+            raise ValueError(
+                "Either a config file or both mechanisms_dir and templates_dir must be provided."
+            )
+
+        if config is None:
+            neuron.load_mechanisms(mechanisms_dir)
+            h.load_file(templates_dir)
+        else:
+            # this will load both mechs and templates
+            load_templates_from_config(config)
 
         self.general_settings = general_settings
         self.conn_type_settings = conn_type_settings
@@ -1049,7 +1074,6 @@ class GapJunctionTuner:
         plt.xlabel("Time (ms)")
         plt.ylabel("Membrane Voltage (mV)")
         plt.legend()
-        plt.show()
 
     def coupling_coefficient(self, t, v1, v2, t_start, t_end, dt=h.dt):
         """
@@ -1085,28 +1109,55 @@ class GapJunctionTuner:
 
     def InteractiveTuner(self):
         w_run = widgets.Button(description="Run", icon="history", button_style="primary")
-        values = [i * 10**-4 for i in range(1, 101)]  # From 1e-4 to 1e-2
+        values = [i * 10**-4 for i in range(1, 1001)]  # From 1e-4 to 1e-1
 
         # Create the SelectionSlider widget with appropriate formatting
-        resistance = widgets.SelectionSlider(
-            options=[("%g" % i, i) for i in values],  # Use scientific notation for display
-            value=10**-3,  # Default value
+        resistance = widgets.FloatLogSlider(
+            value=0.001,
+            base=10,
+            min=-4,  # max exponent of base
+            max=-1,  # min exponent of base
+            step=0.1,  # exponent step
             description="Resistance: ",
             continuous_update=True,
         )
 
         ui = VBox([w_run, resistance])
+
+        # Create an output widget to control what gets cleared
+        output = widgets.Output()
+
         display(ui)
+        display(output)
 
         def on_button(*args):
-            clear_output()
-            display(ui)
-            resistance_for_gap = resistance.value
-            self.model(resistance_for_gap)
-            self.plot_model()
-            cc = self.coupling_coefficient(self.t_vec, self.soma_v_1, self.soma_v_2, 500, 1000)
-            print(f"coupling_coefficient is {cc:0.4f}")
+            with output:
+                # Clear only the output widget, not the entire cell
+                output.clear_output(wait=True)
+
+                resistance_for_gap = resistance.value
+                print(f"Running simulation with resistance: {resistance_for_gap}")
+
+                try:
+                    self.model(resistance_for_gap)
+                    self.plot_model()
+
+                    # Convert NEURON vectors to numpy arrays
+                    t_array = np.array(self.t_vec)
+                    v1_array = np.array(self.soma_v_1)
+                    v2_array = np.array(self.soma_v_2)
+
+                    cc = self.coupling_coefficient(t_array, v1_array, v2_array, 500, 1000)
+                    print(f"coupling_coefficient is {cc:0.4f}")
+                    plt.show()
+
+                except Exception as e:
+                    print(f"Error during simulation or analysis: {e}")
+                    import traceback
+
+                    traceback.print_exc()
 
+        # Run once initially
         on_button()
         w_run.on_click(on_button)
 

bmtool/util/util.py

@@ -447,6 +447,9 @@ def load_mechanisms_from_config(config=None):
 
 
 def load_templates_from_config(config=None):
+    """
+    loads the neuron mechanisms and templates provided from BMTK config
+    """
     if config is None:
         config = "simulation_config.json"
     config = load_config(config)

{bmtool-0.7.1.6.dist-info → bmtool-0.7.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.7.1.6
+Version: 0.7.2
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.7.1.6.dist-info → bmtool-0.7.2.dist-info}/RECORD

@@ -6,29 +6,29 @@ bmtool/graphs.py,sha256=gBTzI6c2BBK49dWGcfWh9c56TAooyn-KaiEy0Im1HcI,6717
 bmtool/manage.py,sha256=lsgRejp02P-x6QpA7SXcyXdalPhRmypoviIA2uAitQs,608
 bmtool/plot_commands.py,sha256=Dxm_RaT4CtHnfsltTtUopJ4KVbfhxtktEB_b7bFEXII,12716
 bmtool/singlecell.py,sha256=I2yolbAnNC8qpnRkNdnDCLidNW7CktmBuRrcowMZJ3A,45041
-bmtool/synapses.py,sha256=wlRY7IixefPzafqG6k2sPIK4s6PLG9Kct-oCaVR29wA,64269
+bmtool/synapses.py,sha256=y8UJAqO1jpZY-mY9gVVMN8Dj1r9jD2fI1nAaNQeQfz4,66148
 bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bmtool/analysis/entrainment.py,sha256=PM4Do8Cl248Y2kIXLRFLPmUB_mH38Yhl8CUDDcunGq0,28241
+bmtool/analysis/entrainment.py,sha256=NQloQtVpEWjDzmkZwMWVcm3hSjErHBZfQl1mrBVoIE8,25321
 bmtool/analysis/lfp.py,sha256=S2JvxkjcK3-EH93wCrhqNSFY6cX7fOq74pz64ibHKrc,26556
 bmtool/analysis/netcon_reports.py,sha256=VnPZNKPaQA7oh1q9cIatsqQudm4cOtzNtbGPXoiDCD0,2909
-bmtool/analysis/spikes.py,sha256=iJfoVKl2k1X9s6C3PYz-18zlfahuRM_35wN5H9xDCIg,22715
+bmtool/analysis/spikes.py,sha256=3n-xmyEZ7w6CKEND7-aKOAvdDg0lwDuPI5sMdOuPwa0,24637
 bmtool/bmplot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bmtool/bmplot/connections.py,sha256=P1JBG4xCbLVq4sfQuUE6c3dO949qajrjdQcrazdmDS4,53861
-bmtool/bmplot/entrainment.py,sha256=VSlZvcSeXLr5OxGvmWcGU4s7JS7vOL38lq1XC69O_AE,6926
+bmtool/bmplot/connections.py,sha256=KSORZ43v1B5xfiBN6AnAD7tJySVTkLIY3j_zb2r-YPA,55696
+bmtool/bmplot/entrainment.py,sha256=BrBMerqyiG2YWAO_OEFv7OJf3yeFz3l9jUt4NamluLc,32837
 bmtool/bmplot/lfp.py,sha256=SNpbWGOUnYEgnkeBw5S--aPN5mIGD22Gw2Pwus0_lvY,2034
 bmtool/bmplot/netcon_reports.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bmtool/bmplot/spikes.py,sha256=RJOOtmgWhTvyVi1CghoKTtxvt7MF9cJCrJVm5hV5wA4,11210
+bmtool/bmplot/spikes.py,sha256=odzCSMbFRHp9qthSGQ0WzMWUwNQ7R1Z6gLT6VPF_o5Q,15326
 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/debug/commands.py,sha256=VV00f6q5gzZI503vUPeG40ABLLen0bw_k4-EX-H5WZE,580
 bmtool/debug/debug.py,sha256=9yUFvA4_Bl-x9s29quIEG3pY-S8hNJF3RKBfRBHCl28,208
 bmtool/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/commands.py,sha256=Nn-R-4e9g8ZhSPZvTkr38xeKRPfEMANB9Lugppj82UI,68564
-bmtool/util/util.py,sha256=owce5BEusZO_8T5x05N2_B583G26vWAy7QX29V0Pj0Y,62818
+bmtool/util/util.py,sha256=S8sAXwDiISGAqnSXRIgFqxqCRzL5YcxAqP1UGxGA5Z4,62906
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=lokRLUM1rsdSYBYrNbLBBo39j14mm8TBNVNRnSlhHCk,94868
-bmtool-0.7.1.6.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.7.1.6.dist-info/METADATA,sha256=_jtey-F9b0kjpQ2CELf9SxupFMMv1c-RtgmthDweFJw,3577
-bmtool-0.7.1.6.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-bmtool-0.7.1.6.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.7.1.6.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.7.1.6.dist-info/RECORD,,
+bmtool-0.7.2.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.7.2.dist-info/METADATA,sha256=JacxbP2RvvbSuuveedTUJjl8KeqOCKf4FlW-UrRmfCk,3575
+bmtool-0.7.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bmtool-0.7.2.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.7.2.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.7.2.dist-info/RECORD,,

{bmtool-0.7.1.6.dist-info → bmtool-0.7.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any