bmtool 0.7.5.1__py3-none-any.whl → 0.7.6__py3-none-any.whl

bmtool/bmplot/connections.py

@@ -661,7 +661,8 @@ def connection_histogram(
                 (edges[source_id_type] == source_id) & (edges[target_id_type] == target_id)
             ]
             if not include_gap:
-                temp = temp[~temp["is_gap_junction"]]
+                gap_col = temp["is_gap_junction"].fillna(False).astype(bool)
+                temp = temp[~gap_col]
             node_pairs = temp.groupby("target_node_id")["source_node_id"].count()
             try:
                 conn_mean = statistics.mean(node_pairs.values)
@@ -1022,8 +1023,8 @@ def plot_synapse_location(config: str, source: str, target: str, sids: str, tids
         )
 
     # Fix the validation logic - it was using 'or' instead of 'and'
-    if syn_feature not in ["afferent_section_id", "afferent_section_pos"]:
-        raise ValueError("Currently only syn features supported are afferent_section_id or afferent_section_pos")
+    #if syn_feature not in ["afferent_section_id", "afferent_section_pos"]:
+    #    raise ValueError("Currently only syn features supported are afferent_section_id or afferent_section_pos")
 
     try:
         # Load mechanisms and template

bmtool/synapses.py

@@ -1175,7 +1175,9 @@ class SynapseTuner:
         amp = np.array(amp)
         amp = amp * 1000  # scale up
         amp = amp.reshape(-1, amp.shape[-1])
-        maxamp = amp.max(axis=1 if normalize_by_trial else None)
+        
+        # Calculate 90th percentile amplitude for normalization
+        percentile_90 = np.percentile(amp, 90)
 
         def format_array(arr):
             """Format an array to 2 significant figures for cleaner output."""
@@ -1187,49 +1189,42 @@ class SynapseTuner:
                 f"Short Term Plasticity Results for {self.train_freq}Hz with {self.train_delay} Delay"
             )
             print("=" * 40)
-            print("PPR: Above 1 is facilitating, below 1 is depressing.")
+            print("PPR: Above 0 is facilitating, below 0 is depressing.")
             print("Induction: Above 0 is facilitating, below 0 is depressing.")
             print("Recovery: A measure of how fast STP decays.\n")
 
-            # PPR Calculation
-            ppr = amp[:, 1:2] / amp[:, 0:1]
+            # PPR Calculation: (Avg 2nd pulse - Avg 1st pulse) / 90th percentile amplitude
+            ppr = (np.mean(amp[:, 1:2]) - np.mean(amp[:, 0:1])) / percentile_90
             print("Paired Pulse Response (PPR)")
-            print("Calculation: 2nd pulse / 1st pulse")
+            print("Calculation: (Avg 2nd pulse - Avg 1st pulse) / 90th percentile amplitude")
             print(
-                f"Values: ({format_array(amp[:, 1:2])}) / ({format_array(amp[:, 0:1])}) = {format_array(ppr)}\n"
+                f"Values: ({np.mean(amp[:, 1:2]):.3f} - {np.mean(amp[:, 0:1]):.3f}) / {percentile_90:.3f} = {ppr:.3f}\n"
             )
 
-            # Induction Calculation
-            induction = np.mean((amp[:, 5:8].mean(axis=1) - amp[:, :1].mean(axis=1)) / maxamp)
+            # Induction Calculation: (Avg (6th, 7th, 8th pulses) - Avg 1st pulse) / 90th percentile amplitude
+            induction = (np.mean(amp[:, 5:8]) - np.mean(amp[:, :1])) / percentile_90
             print("Induction")
-            print("Calculation: (avg(6th, 7th, 8th pulses) - 1st pulse) / max amps")
-            print(
-                f"Values: avg({format_array(amp[:, 5:8])}) - {format_array(amp[:, :1])} / {format_array(maxamp)}"
-            )
+            print("Calculation: (Avg(6th, 7th, 8th pulses) - Avg 1st pulse) / 90th percentile amplitude")
             print(
-                f"({format_array(amp[:, 5:8].mean(axis=1))}) - ({format_array(amp[:, :1].mean(axis=1))}) / {format_array(maxamp)} = {induction:.3f}\n"
+                f"Values: {np.mean(amp[:, 5:8]):.3f} - {np.mean(amp[:, :1]):.3f} / {percentile_90:.3f} = {induction:.3f}\n"
             )
 
-            # Recovery Calculation
-            recovery = np.mean((amp[:, 8:12].mean(axis=1) - amp[:, :4].mean(axis=1)) / maxamp)
+            # Recovery Calculation: (Avg (9th, 10th, 11th, 12th pulses) - Avg (1st, 2nd, 3rd, 4th pulses)) / 90th percentile amplitude
+            recovery = (np.mean(amp[:, 8:12]) - np.mean(amp[:, :4])) / percentile_90
             print("Recovery")
             print(
-                "Calculation: (avg(9th, 10th, 11th, 12th pulses) - avg(1st to 4th pulses)) / max amps"
-            )
-            print(
-                f"Values: avg({format_array(amp[:, 8:12])}) - avg({format_array(amp[:, :4])}) / {format_array(maxamp)}"
+                "Calculation: (Avg(9th, 10th, 11th, 12th pulses) - Avg(1st to 4th pulses)) / 90th percentile amplitude"
             )
             print(
-                f"({format_array(amp[:, 8:12].mean(axis=1))}) - ({format_array(amp[:, :4].mean(axis=1))}) / {format_array(maxamp)} = {recovery:.3f}\n"
+                f"Values: {np.mean(amp[:, 8:12]):.3f} - {np.mean(amp[:, :4]):.3f} / {percentile_90:.3f} = {recovery:.3f}\n"
             )
 
             print("=" * 40 + "\n")
 
-        recovery = np.mean((amp[:, 8:12].mean(axis=1) - amp[:, :4].mean(axis=1)) / maxamp)
-        induction = np.mean((amp[:, 5:8].mean(axis=1) - amp[:, :1].mean(axis=1)) / maxamp)
-        ppr = amp[:, 1:2] / amp[:, 0:1]
-        # maxamp = max(amp, key=lambda x: abs(x[0]))
-        maxamp = maxamp.max()
+        # Calculate final metrics
+        ppr = (np.mean(amp[:, 1:2]) - np.mean(amp[:, 0:1])) / percentile_90
+        induction = (np.mean(amp[:, 5:8]) - np.mean(amp[:, :1])) / percentile_90
+        recovery = (np.mean(amp[:, 8:12]) - np.mean(amp[:, :4])) / percentile_90
 
         return ppr, induction, recovery
 

bmtool/util/util.py

@@ -1,4 +1,5 @@
 import argparse
+from logging import raiseExceptions
 import math
 import os
 import smtplib
@@ -1081,7 +1082,9 @@ def connection_totals(
         total = edges[(edges[source_id_type] == source_id) & (edges[target_id_type] == target_id)]
         if not include_gap:
             try:
-                total = total[~total["is_gap_junction"]]
+                # Handle mixed types and NaN values in is_gap_junction column
+                gap_col = total["is_gap_junction"].fillna(False).astype(bool)
+                total = total[~gap_col]
             except:
                 # If there are no gap junctions, just continue
                 pass
@@ -1129,7 +1132,8 @@ def percent_connections(
         cons = edges[(edges[source_id_type] == source_id) & (edges[target_id_type] == target_id)]
         if not include_gap:
             try:
-                gaps = cons["is_gap_junction"]==True
+                # Handle mixed types and NaN values in is_gap_junction column
+                gaps = cons["is_gap_junction"].fillna(False).astype(bool)
                 cons = cons[~gaps]
             except:
                 raise Exception("no gap junctions found to drop from connections")
@@ -1200,9 +1204,17 @@ def connection_divergence(
         cons = edges[(edges[source_id_type] == source_id) & (edges[target_id_type] == target_id)]
         if not include_gap:
             try:
-                cons = cons[~cons["is_gap_junction"]]
+                # Handle mixed types and NaN values in is_gap_junction column
+                gap_col = cons["is_gap_junction"].fillna(False).astype(bool)
+                cons = cons[~gap_col]
             except:
-                raise Exception("no gap junctions found to drop from connections")
+                raise Exception("error")
+        
+        if cons.empty:
+            if method == "mean+std":
+                return (0, 0)
+            else:
+                return 0
 
         if convergence:
             if method == "min":
@@ -1213,15 +1225,16 @@ def connection_divergence(
                 return round(count, 2)
             elif method == "std":
                 std = cons["target_node_id"].value_counts().std()
-                return round(std, 2)
+                return round(std, 2) if not np.isnan(std) else 0
             elif method == "mean":
                 mean = cons["target_node_id"].value_counts().mean()
-                return round(mean, 2)
+                return round(mean, 2) if not np.isnan(mean) else 0
             elif method == "mean+std":  # default is mean + std
                 mean = cons["target_node_id"].value_counts().mean()
                 std = cons["target_node_id"].value_counts().std()
-                # std = cons.apply(pd.Series.value_counts).target_node_id.dropna().std() no longer a valid way
-                return (round(mean, 2)), (round(std, 2))
+                mean = round(mean, 2) if not np.isnan(mean) else 0
+                std = round(std, 2) if not np.isnan(std) else 0
+                return (mean, std)
         else:  # divergence
             if method == "min":
                 count = cons["source_node_id"].value_counts().min()
@@ -1231,14 +1244,16 @@ def connection_divergence(
                 return round(count, 2)
             elif method == "std":
                 std = cons["source_node_id"].value_counts().std()
-                return round(std, 2)
+                return round(std, 2) if not np.isnan(std) else 0
             elif method == "mean":
                 mean = cons["source_node_id"].value_counts().mean()
-                return round(mean, 2)
+                return round(mean, 2) if not np.isnan(mean) else 0
             elif method == "mean+std":  # default is mean + std
                 mean = cons["source_node_id"].value_counts().mean()
                 std = cons["source_node_id"].value_counts().std()
-                return (round(mean, 2)), (round(std, 2))
+                mean = round(mean, 2) if not np.isnan(mean) else 0
+                std = round(std, 2) if not np.isnan(std) else 0
+                return (mean, std)
 
     return relation_matrix(
         config,
@@ -1442,7 +1457,9 @@ def connection_probabilities(
         ]
         if not include_gap:
             try:
-                relevant_edges = relevant_edges[~relevant_edges["is_gap_junction"]]
+                # Handle mixed types and NaN values in is_gap_junction column
+                gap_col = relevant_edges["is_gap_junction"].fillna(False).astype(bool)
+                relevant_edges = relevant_edges[~gap_col]
             except:
                 raise Exception("no gap junctions found to drop from connections")
         connected_distances = eudist(relevant_edges, dist_X, dist_Y, dist_Z).values.tolist()

{bmtool-0.7.5.1.dist-info → bmtool-0.7.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.7.5.1
+Version: 0.7.6
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.7.5.1.dist-info → bmtool-0.7.6.dist-info}/RECORD

@@ -6,14 +6,14 @@ 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=xqdLM2TjjnL8YyTy-c3WR6mElTv3E4zkZgkfUh4S5X0,47161
-bmtool/synapses.py,sha256=k-xyZjElz2CHM2oGXqBnFOCd0NusoA6JASzPXHPCj5c,106068
+bmtool/synapses.py,sha256=GbnPPdXotl7MTeju_QTBwZfFxYFNCq0fJijntzfttds,106071
 bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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=3n-xmyEZ7w6CKEND7-aKOAvdDg0lwDuPI5sMdOuPwa0,24637
 bmtool/bmplot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bmtool/bmplot/connections.py,sha256=DwnnMp5cUwZC3OqsJqvgTPr4lBzc0sNWYRPmwij0WRk,59337
+bmtool/bmplot/connections.py,sha256=xACgnkLAZrEBpaxa9Ob9MX-B1DO782UAeMvih9DleDk,59400
 bmtool/bmplot/entrainment.py,sha256=BrBMerqyiG2YWAO_OEFv7OJf3yeFz3l9jUt4NamluLc,32837
 bmtool/bmplot/lfp.py,sha256=7JLozQQJ19ty0ZNyfhkuJAr_K8_pVP9C0flVJd_YXaY,2027
 bmtool/bmplot/netcon_reports.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -23,12 +23,12 @@ 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=TAWdGd0tDuouS-JiusMs8WwP7kQpWHPr1nu0XG01TBQ,75056
+bmtool/util/util.py,sha256=HbVgPpvDBSkvXv5gAz7ad1V5GKL26q_LyJGt6ehpGQE,75929
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=lokRLUM1rsdSYBYrNbLBBo39j14mm8TBNVNRnSlhHCk,94868
-bmtool-0.7.5.1.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.7.5.1.dist-info/METADATA,sha256=H1XxiaHJuU-Bq_HTck5_z1fm08rTmSNxZYBA7hVcmNk,3597
-bmtool-0.7.5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bmtool-0.7.5.1.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.7.5.1.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.7.5.1.dist-info/RECORD,,
+bmtool-0.7.6.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.7.6.dist-info/METADATA,sha256=iSIT7erBJsvbZ6vJE1LKOlQPF1ne1BiluVL-81Z8l4U,3595
+bmtool-0.7.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bmtool-0.7.6.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.7.6.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.7.6.dist-info/RECORD,,