bmtool 0.7.1.3__py3-none-any.whl → 0.7.1.5__py3-none-any.whl

bmtool/analysis/entrainment.py

@@ -714,7 +714,17 @@ def calculate_spike_rate_power_correlation(
     return correlation_results, frequencies
 
 
-def get_spikes_in_cycle(spike_df, lfp_data, spike_fs=1000, lfp_fs=400, band=(30, 80)):
+def get_spikes_in_cycle(
+    spike_df,
+    lfp_data,
+    spike_fs=1000,
+    lfp_fs=400,
+    filter_method="butter",
+    lowcut=None,
+    highcut=None,
+    bandwidth=2.0,
+    freq_of_interest=None,
+):
     """
     Analyze spike timing relative to oscillation phases.
 
@@ -733,12 +743,15 @@ def get_spikes_in_cycle(spike_df, lfp_data, spike_fs=1000, lfp_fs=400, band=(30,
     phase_data : dict
         Dictionary containing phase values for each spike and neuron population
     """
-    filtered_lfp = butter_bandpass_filter(lfp_data, band[0], band[1], lfp_fs)
-
-    # Calculate phase using Hilbert transform
-    analytic_signal = signal.hilbert(filtered_lfp)
-    phase = np.angle(analytic_signal)
-    amplitude = np.abs(analytic_signal)
+    phase = get_lfp_phase(
+        lfp_data=lfp_data,
+        fs=lfp_fs,
+        filter_method=filter_method,
+        lowcut=lowcut,
+        highcut=highcut,
+        bandwidth=bandwidth,
+        freq_of_interest=freq_of_interest,
+    )
 
     # Get unique neuron populations
     neuron_pops = spike_df["pop_name"].unique()
@@ -763,4 +776,4 @@ def get_spikes_in_cycle(spike_df, lfp_data, spike_fs=1000, lfp_fs=400, band=(30,
             valid_samples = spike_indices[valid_indices]
             phase_data[pop] = phase[valid_samples]
 
-    return phase_data, filtered_lfp, phase, amplitude
+    return phase_data

bmtool/analysis/spikes.py

@@ -401,7 +401,7 @@ def compare_firing_over_times(
 
 
 def find_bursting_cells(
-    df: pd.DataFrame, burst_threshold: float = 10, rename_bursting_cells: bool = False
+    df: pd.DataFrame, isi_threshold: float = 10, burst_count_threshold: int = 1
 ) -> pd.DataFrame:
     """
     Finds bursting cells in a population based on a time difference threshold.
@@ -410,10 +410,10 @@ def find_bursting_cells(
     ----------
     df : pd.DataFrame
         DataFrame containing spike data with columns for timestamps, node_ids, and pop_name
-    burst_threshold : float, optional
+    isi_threshold : float, optional
         Time difference threshold in milliseconds to identify bursts
-    rename_bursting_cells : bool, optional
-        If True, returns a DataFrame with bursting cells renamed in their pop_name column
+    burst_count_threshold : int, optional
+        Number of bursts required to identify a bursting cell
 
     Returns
     -------
@@ -425,10 +425,11 @@ def find_bursting_cells(
     diff_df["time_diff"] = df.groupby("node_ids")["timestamps"].diff()
 
     # Create a column indicating whether each time difference is a burst
-    diff_df["is_burst_instance"] = diff_df["time_diff"] < burst_threshold
+    diff_df["is_burst_instance"] = diff_df["time_diff"] < isi_threshold
 
     # Group by node_ids and check if any row has a burst instance
-    burst_summary = diff_df.groupby("node_ids")["is_burst_instance"].any()
+    # check if there are enough bursts
+    burst_summary = diff_df.groupby("node_ids")["is_burst_instance"].sum() >= burst_count_threshold
 
     # Convert to a DataFrame with reset index
     burst_cells = burst_summary.reset_index(name="is_burst")
@@ -437,19 +438,16 @@ def find_bursting_cells(
     burst_cells = pd.merge(burst_cells, df, on="node_ids")
 
     # Create a mask for burst cells that don't already have "_bursters" in their name
-    burst_mask = (burst_cells["is_burst"] is True) & (
-        ~burst_cells["pop_name"].str.contains("_bursters")
+    burst_mask = burst_cells["is_burst"] & ~burst_cells["pop_name"].str.contains(
+        "_bursters", na=False
     )
 
     # Add "_bursters" suffix only to those cells
-    if rename_bursting_cells:
-        burst_cells.loc[burst_mask, "pop_name"] = (
-            burst_cells.loc[burst_mask, "pop_name"] + "_bursters"
-        )
+    burst_cells.loc[burst_mask, "pop_name"] = burst_cells.loc[burst_mask, "pop_name"] + "_bursters"
 
-    for pop in burst_cells["pop_name"].unique():
+    for pop in sorted(burst_cells["pop_name"].unique()):
         print(
-            f"Number of bursters in {pop}: {burst_cells[burst_cells['pop_name'] == pop]['node_ids'].nunique()}"
+            f"Number of cells in {pop}: {burst_cells[burst_cells['pop_name'] == pop]['node_ids'].nunique()}"
         )
 
     return burst_cells

{bmtool-0.7.1.3.dist-info → bmtool-0.7.1.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.7.1.3
+Version: 0.7.1.5
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.7.1.3.dist-info → bmtool-0.7.1.5.dist-info}/RECORD

@@ -8,10 +8,10 @@ bmtool/plot_commands.py,sha256=Dxm_RaT4CtHnfsltTtUopJ4KVbfhxtktEB_b7bFEXII,12716
 bmtool/singlecell.py,sha256=I2yolbAnNC8qpnRkNdnDCLidNW7CktmBuRrcowMZJ3A,45041
 bmtool/synapses.py,sha256=wlRY7IixefPzafqG6k2sPIK4s6PLG9Kct-oCaVR29wA,64269
 bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bmtool/analysis/entrainment.py,sha256=uG2TWbeYJEg_VQB6pKEWlrVBzQ6M4h6FSAZR4GMKp-E,28178
+bmtool/analysis/entrainment.py,sha256=PM4Do8Cl248Y2kIXLRFLPmUB_mH38Yhl8CUDDcunGq0,28241
 bmtool/analysis/lfp.py,sha256=S2JvxkjcK3-EH93wCrhqNSFY6cX7fOq74pz64ibHKrc,26556
 bmtool/analysis/netcon_reports.py,sha256=VnPZNKPaQA7oh1q9cIatsqQudm4cOtzNtbGPXoiDCD0,2909
-bmtool/analysis/spikes.py,sha256=Mz0e7XOey_6eWQDZAU0ePjDzDMDTFkMbWSA5YWDooYk,17122
+bmtool/analysis/spikes.py,sha256=IHxV7_X8ojh4NDVBjzHCzfHF8muPPef2UtH3yqYre78,17091
 bmtool/bmplot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/bmplot/connections.py,sha256=P1JBG4xCbLVq4sfQuUE6c3dO949qajrjdQcrazdmDS4,53861
 bmtool/bmplot/entrainment.py,sha256=VSlZvcSeXLr5OxGvmWcGU4s7JS7vOL38lq1XC69O_AE,6926
@@ -26,9 +26,9 @@ bmtool/util/commands.py,sha256=Nn-R-4e9g8ZhSPZvTkr38xeKRPfEMANB9Lugppj82UI,68564
 bmtool/util/util.py,sha256=owce5BEusZO_8T5x05N2_B583G26vWAy7QX29V0Pj0Y,62818
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=lokRLUM1rsdSYBYrNbLBBo39j14mm8TBNVNRnSlhHCk,94868
-bmtool-0.7.1.3.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.7.1.3.dist-info/METADATA,sha256=GpvzWhlfyNgHHCfhakOBeeablgTAOCHeQFvhnExZ-X8,3577
-bmtool-0.7.1.3.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
-bmtool-0.7.1.3.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.7.1.3.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.7.1.3.dist-info/RECORD,,
+bmtool-0.7.1.5.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.7.1.5.dist-info/METADATA,sha256=pvpABD7P2ytzO08EYUC8HrbUTg_fk8pc67mBaEvi7-M,3577
+bmtool-0.7.1.5.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
+bmtool-0.7.1.5.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.7.1.5.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.7.1.5.dist-info/RECORD,,

{bmtool-0.7.1.3.dist-info → bmtool-0.7.1.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.4.0)
+Generator: setuptools (80.7.1)
 Root-Is-Purelib: true
 Tag: py3-none-any