bmtool 0.7.5.1__py3-none-any.whl → 0.7.7__py3-none-any.whl

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")
@@ -1159,9 +1163,43 @@ def percent_connections(
         num_sources = s_list[source_id_type].value_counts().sort_index().loc[source_id]
         num_targets = t_list[target_id_type].value_counts().sort_index().loc[target_id]
 
-        total = round(total_cons / (num_sources * num_targets) * 100, 2)
-        uni = round(num_uni / (num_sources * num_targets) * 100, 2)
-        bi = round(num_bi / (num_sources * num_targets) * 100, 2)
+        # Check if this is a recurrent network (same source and target population)
+        # For recurrent networks (e.g., FSI->FSI), we need special handling because:
+        # - Each pair can have at most 2 directed connections (bidirectional)
+        # - We want to count unique pairs, not directed connections
+        # - The denominator should be n*(n-1)/2, not n*n
+        is_recurrent = source_id == target_id
+        
+        if is_recurrent:
+            # For recurrent networks, calculate connectivity based on unique undirected pairs
+            # This avoids double-counting reciprocal connections and uses correct denominator
+            pair_counts = {}
+            for _, row in cons.iterrows():
+                sid = row['source_node_id']
+                tid = row['target_node_id']
+                if sid != tid:  # Exclude self-connections
+                    # Use symmetric pair key to count connections per unique pair
+                    pair_key = (min(sid, tid), max(sid, tid))
+                    if pair_key not in pair_counts:
+                        pair_counts[pair_key] = 0
+                    pair_counts[pair_key] += 1
+            
+            # Count pairs with exactly 1 connection (unidirectional) vs 2 connections (bidirectional)
+            num_uni = sum(1 for count in pair_counts.values() if count == 1)
+            num_bi = sum(1 for count in pair_counts.values() if count == 2)
+            
+            # Total possible unique pairs (excluding self-connections)
+            total_possible = num_sources * (num_sources - 1) / 2
+            total = round((num_uni + num_bi) / total_possible * 100, 2)
+            uni = round(num_uni / total_possible * 100, 2)
+            bi = round(num_bi / total_possible * 100, 2)
+        else:
+            # For non-recurrent networks, use the original calculation
+            # Each connection is unique (no double-counting issues)
+            total = round(total_cons / (num_sources * num_targets) * 100, 2)
+            uni = round(num_uni / (num_sources * num_targets) * 100, 2)
+            bi = round(num_bi / (num_sources * num_targets) * 100, 2)
+        
         if method == "total":
             return total
         if method == "uni":
@@ -1200,9 +1238,17 @@ 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 +1259,16 @@ 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 +1278,16 @@ 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,
@@ -1294,9 +1343,10 @@ def gap_junction_connections(
         s_list = kwargs["source_nodes"]
 
         cons = edges[(edges[source_id_type] == source_id) & (edges[target_id_type] == target_id)]
-        # add functionality that shows only the one's with gap_junctions
+        # print(cons)
+
         try:
-            cons = cons[cons["is_gap_junction"]]
+            cons = cons[cons["is_gap_junction"]==True]
         except:
             raise Exception("no gap junctions found to drop from connections")
 
@@ -1442,7 +1492,9 @@ 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-0.7.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.7.5.1
+Version: 0.7.7
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.7.5.1.dist-info → bmtool-0.7.7.dist-info}/RECORD

@@ -1,19 +1,19 @@
 bmtool/SLURM.py,sha256=UBfITY1MtYo95nyKglgGSqAC9Ds8PBvlHczsiNMFxvc,20573
 bmtool/__init__.py,sha256=r_8fXc-2uj1DndCdhB4jME51r1pn6ESTD5zRc355BrU,134
 bmtool/__main__.py,sha256=uCEqPwRxIuNRUASKhsvh4S8Nkp4dqnvfXTMUv-wWWRU,665
-bmtool/connectors.py,sha256=4SJRqBXM145_-nFycGrnlfjSyaoarOr0QkHl00jWq4I,74384
+bmtool/connectors.py,sha256=tkCh9oVsIgaV5zzBzTFTG2Y6YVAoIHv2Pm-qxZAbca8,93124
 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/singlecell.py,sha256=qcciWdn8RjJCp7z8G2dCdPTLS9Brho3lPFSIsYMw8Ls,65348
+bmtool/synapses.py,sha256=2M0dUBXfdYrJA3FWLbqsZGqAkO0sS2gQ-zq6GHYaVE4,121393
 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=xn9QaNN7fTTVNaalS8QHIp2TVo7nXgiT-nO4nKXOo6w,59612
 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=oXrY-Cc4wxPvgJVg2TqaAPua_gAl1Kj1nqrLgsqsXS8,77815
 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-0.7.7.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.7.7.dist-info/METADATA,sha256=uHViQaXG-O6O_GqENKn1vOkXp6g_yN94M9jSRilSnJU,3595
+bmtool-0.7.7.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bmtool-0.7.7.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.7.7.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.7.7.dist-info/RECORD,,