don't load spike times greater than simtime + fixes

Fixes #84

.gitignore

@@ -60,6 +60,14 @@ documentation/
 # Simulation output
 simulation_output_*/
 *.tar
+*.h5
+*.pdf
+*.gdf
+*.eps
+examples/benchmarks
+exmaples/Hagen_et_al_2016_cercor
+jobs
+logs
 
 # compiled NMODL files and folders
 x86_64/

hybridLFPy/gdf.py

@@ -127,7 +127,7 @@ def _blockread(self, fname, skiprows):
                     raise StopIteration
                 yield a
 
-    def create(self, re='brunel-py-ex-*.gdf', index=True, skiprows=0):
+    def create(self, re='brunel-py-ex-*.gdf', index=True, skiprows=0, simtime=None):
         """
         Create db from list of gdf file glob
 
@@ -140,7 +140,9 @@ def create(self, re='brunel-py-ex-*.gdf', index=True, skiprows=0):
             Create index on neurons for speed.
         skiprows : int
             Number of skipped first lines
-
+        simtime : float/int or None
+            if not None, stop reading of gdf files at simtime,
+            assuming that recorded spike times is monotonously increasing
 
         Returns
         -------
@@ -159,10 +161,18 @@ def create(self, re='brunel-py-ex-*.gdf', index=True, skiprows=0):
             print(f)
             while True:
                 try:
-                    for data in self._blockread(f, skiprows):
-                        self.cursor.executemany(
-                            'INSERT INTO spikes VALUES (?, ?)', data)
-                        self.conn.commit()
+                    if simtime is None:
+                        for data in self._blockread(f, skiprows):
+                            self.cursor.executemany(
+                                'INSERT INTO spikes VALUES (?, ?)', data)
+                            self.conn.commit()
+                    else:
+                        for data in self._blockread(f, skiprows):
+                            if data[1] > simtime:
+                                break
+                            self.cursor.executemany(
+                                'INSERT INTO spikes VALUES (?, ?)', data)
+                            self.conn.commit()
                 except RuntimeError:
                     break
 

hybridLFPy/helpers.py

@@ -247,7 +247,7 @@ def setup_file_dest(params, clearDestination=True):
     """
     if RANK == 0:
         if not os.path.isdir(params.savefolder):
-            os.mkdir(params.savefolder)
+            os.makedirs(params.savefolder, exist_ok=True)
             assert(os.path.isdir(params.savefolder))
         else:
             if clearDestination:
@@ -257,35 +257,35 @@ def setup_file_dest(params, clearDestination=True):
                         os.system('find %s -delete' % params.savefolder)
                     except BaseException:
                         shutil.rmtree(params.savefolder)
-                os.mkdir(params.savefolder)
+                os.makedirs(params.savefolder, exist_ok=True)
                 assert(os.path.isdir(params.savefolder))
 
         if not os.path.isdir(params.sim_scripts_path):
             print('creating %s' % params.sim_scripts_path)
-            os.mkdir(params.sim_scripts_path)
+            os.makedirs(params.sim_scripts_path, exist_ok=True)
 
         if not os.path.isdir(params.cells_path):
             print('creating %s' % params.cells_path)
-            os.mkdir(params.cells_path)
+            os.makedirs(params.cells_path, exist_ok=True)
 
         if not os.path.isdir(params.figures_path):
             print('creating %s' % params.figures_path)
-            os.mkdir(params.figures_path)
+            os.makedirs(params.figures_path, exist_ok=True)
 
         if not os.path.isdir(params.populations_path):
             print('creating %s' % params.populations_path)
-            os.mkdir(params.populations_path)
+            os.makedirs(params.populations_path, exist_ok=True)
 
         try:
             if not os.path.isdir(params.raw_nest_output_path):
                 print('creating %s' % params.raw_nest_output_path)
-                os.mkdir(params.raw_nest_output_path)
+                os.makedirs(params.raw_nest_output_path, exist_ok=True)
         except BaseException:
             pass
 
         if not os.path.isdir(params.spike_output_path):
             print('creating %s' % params.spike_output_path)
-            os.mkdir(params.spike_output_path)
+            os.makedirs(params.spike_output_path, exist_ok=True)
 
         for f in ['cellsim16popsParams.py',
                   'cellsim16pops.py',

hybridLFPy/version.py

@@ -1 +1 @@
-version = "0.2"
+version = "0.2.1"