bmtool 0.6.9.19__py3-none-any.whl → 0.6.9.20__py3-none-any.whl

bmtool/analysis/netcon_reports.py

@@ -0,0 +1,97 @@
+import h5py
+import numpy as np
+import xarray as xr
+import pandas as pd
+from ..util.util import load_nodes_from_config
+
+def load_synapse_report(h5_file_path, config_path):
+    """
+    Load and process a synapse report from a bmtk simulation into an xarray.
+    
+    Parameters:
+    -----------
+    h5_file_path : str
+        Path to the h5 file containing the synapse report
+    config_path : str
+        Path to the simulation configuration file
+        
+    Returns:
+    --------
+    xarray.Dataset
+        An xarray containing the synapse report data with proper population labeling
+    """
+    # Load the h5 file
+    with h5py.File(h5_file_path, 'r') as file:
+        # Get the report data
+        report = file['report']['cortex']
+        mapping = report['mapping']
+        
+        # Get the data - shape is (n_timesteps, n_synapses)
+        data = report['data'][:]
+        
+        # Get time information
+        time_info = mapping['time'][:]  # [start_time, end_time, dt]
+        start_time = time_info[0]
+        end_time = time_info[1]
+        dt = time_info[2]
+        
+        # Create time array
+        n_steps = data.shape[0]
+        time = np.linspace(start_time, start_time + (n_steps-1)*dt, n_steps)
+        
+        # Get mapping information
+        src_ids = mapping['src_ids'][:]
+        trg_ids = mapping['trg_ids'][:]
+        sec_id = mapping['element_ids'][:]
+        sec_x = mapping['element_pos'][:]
+        
+    # Load node information
+    nodes = load_nodes_from_config(config_path)
+    cortex_nodes = nodes['cortex']
+    
+    # Create a mapping from node IDs to population names
+    node_to_pop = dict(zip(cortex_nodes.index, cortex_nodes['pop_name']))
+    
+    # Get the number of synapses
+    n_synapses = data.shape[1]
+    
+    # Create arrays to hold the source and target populations for each synapse
+    source_pops = []
+    target_pops = []
+    connection_labels = []
+    
+    # Process each synapse
+    for i in range(n_synapses):
+        src_id = src_ids[i]
+        trg_id = trg_ids[i]
+        
+        # Get population names (with fallback for unknown IDs)
+        src_pop = node_to_pop.get(src_id, f'unknown_{src_id}')
+        trg_pop = node_to_pop.get(trg_id, f'unknown_{trg_id}')
+        
+        source_pops.append(src_pop)
+        target_pops.append(trg_pop)
+        connection_labels.append(f"{src_pop}->{trg_pop}")
+    
+    # Create xarray dataset
+    ds = xr.Dataset(
+        data_vars={
+            'synapse_value': (['time', 'synapse'], data)
+        },
+        coords={
+            'time': time,
+            'synapse': np.arange(n_synapses),
+            'source_pop': ('synapse', source_pops),
+            'target_pop': ('synapse', target_pops),
+            'source_id': ('synapse', src_ids),
+            'target_id': ('synapse', trg_ids),
+            'sec_id': ('synapse', sec_id),
+            'sec_x': ('synapse', sec_x),
+            'connection_label': ('synapse', connection_labels)
+        },
+        attrs={
+            'description': 'Synapse report data from bmtk simulation'
+        }
+    )
+    
+    return ds

bmtool/util/util.py

@@ -45,7 +45,7 @@ class CellVarsFile(object):
         
         import h5py
         self._h5_handle = h5py.File(filename, 'r')
-        self._h5_root = self._h5_handle[params['h5_root']] if 'h5_root' in params else self._h5_handle['/']
+        self._h5_root = self._h5_handle[params['h5_root']] if 'h5_root' in params else self._h5_handle['/report/cortex']
         self._var_data = {}
         self._var_units = {}
 
@@ -53,6 +53,7 @@ class CellVarsFile(object):
 
         # Look for variabl and mapping groups
         for var_name in self._h5_root.keys():
+            print(self._h5_root.keys())
             hf_grp = self._h5_root[var_name]
 
             if var_name == 'data':
@@ -81,7 +82,7 @@ class CellVarsFile(object):
         if self._mapping is None:
             raise Exception('could not find /mapping group')
         else:
-            gids_ds = self._mapping['gids']
+            gids_ds = self._mapping['node_ids']
             index_pointer_ds = self._mapping['index_pointer']
             for indx, gid in enumerate(gids_ds):
                 self._gid2data_table[gid] = (index_pointer_ds[indx], index_pointer_ds[indx+1])  # slice(index_pointer_ds[indx], index_pointer_ds[indx+1])
@@ -139,6 +140,7 @@ class CellVarsFile(object):
         return self._mapping['element_pos'][bounds[0]:bounds[1]]
 
     def data(self, gid, var_name=VAR_UNKNOWN,time_window=None, compartments='origin'):
+        print(self.variables)
         if var_name not in self.variables:
             raise Exception('Unknown variable {}'.format(var_name))
 

{bmtool-0.6.9.19.dist-info → bmtool-0.6.9.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.6.9.19
+Version: 0.6.9.20
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.6.9.19.dist-info → bmtool-0.6.9.20.dist-info}/RECORD

@@ -10,18 +10,19 @@ bmtool/singlecell.py,sha256=imcdxIzvYVkaOLSGDxYp8WGGssGwXXBCRhzhlqVp7hA,44267
 bmtool/synapses.py,sha256=6h1V64b_KYHN589NFikHrt_Q3lXPvtEgIpwYFlInWb0,64551
 bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/analysis/lfp.py,sha256=KTDMzqhkpTI308sWqoJnbHeCMSFScaJCO4u50Kd4FzA,33570
+bmtool/analysis/netcon_reports.py,sha256=WWh12H9gjEZXhI_q7RErgGQ9iSPoTvCUnUjwNGxRwsY,3071
 bmtool/analysis/spikes.py,sha256=qqJ4zD8xfvSwltlWm_Bhicdngzl6uBqH6Kn5wOMKRc8,11507
 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/debug/commands.py,sha256=AwtcR7BUUheM0NxvU1Nu234zCdpobhJv5noX8x5K2vY,583
 bmtool/debug/debug.py,sha256=xqnkzLiH3s-tS26Y5lZZL62qR2evJdi46Gud-HzxEN4,207
 bmtool/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
-bmtool/util/util.py,sha256=00vOAwTVIifCqouBoFoT0lBashl4fCalrk8fhg_Uq4c,56654
+bmtool/util/util.py,sha256=RItVR56bNvuj8uDjqD3RnIDUfunLtVnQmfU-gcM4NNI,56741
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
-bmtool-0.6.9.19.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.6.9.19.dist-info/METADATA,sha256=xNe4-hvqkNXesi2Y5RgX-6WpAUUNd2n9SXVJ3PERWdg,2769
-bmtool-0.6.9.19.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-bmtool-0.6.9.19.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.6.9.19.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.6.9.19.dist-info/RECORD,,
+bmtool-0.6.9.20.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.9.20.dist-info/METADATA,sha256=5G-e5UTTOhpErogevNUuuvU8IDP6dbPf76zLYbXlAQ4,2769
+bmtool-0.6.9.20.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+bmtool-0.6.9.20.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.9.20.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.9.20.dist-info/RECORD,,