add connectivity plot to notebook, misc. downscale experiments, move …

…where to load spiking in analysis.py

misc/experiments/humam_downscale_examples/experiment_downscale_chi1.0.py

@@ -0,0 +1,31 @@
+# Overwrite values of src/default_net_params.py
+net_params = {
+    'N_scaling': 0.005,
+    'K_scaling': 0.005,
+    'fullscale_rates': './simulated_data/base_theory_rates.pkl',
+    'scaling_type': 'linear',
+    'scaling_factors_recurrent': {
+        # Scale cortico cortical excitatory on excitatory weights
+        'cc_scalingEtoE': 1.0,
+        # Scale cortico cortical excitatory on inhibitory weights
+        'cc_scalingEtoI': 1.0*2.0,
+    }
+}
+
+# Overwrite values of src/default_sim_params.py
+sim_params = {
+    't_sim': 2500.0,
+    'master_seed': 2903
+}
+
+# Parameters for the analysis
+ana_params = {
+    'plotRasterArea': {
+        'fraction': 0.5,
+        'low': 2000,
+        'high': 2500
+    },
+    'functconn_corr': {
+        'exclude_diagonal': False
+    }
+}

misc/experiments/humam_downscale_examples/experiment_downscale_chi2.5.py

@@ -0,0 +1,31 @@
+# Overwrite values of src/default_net_params.py
+net_params = {
+    'N_scaling': 0.005,
+    'K_scaling': 0.005,
+    'fullscale_rates': './simulated_data/base_theory_rates.pkl',
+    'scaling_type': 'linear',
+    'scaling_factors_recurrent': {
+        # Scale cortico cortical excitatory on excitatory weights
+        'cc_scalingEtoE': 2.5,
+        # Scale cortico cortical excitatory on inhibitory weights
+        'cc_scalingEtoI': 2.5*2.0,
+    }
+}
+
+# Overwrite values of src/default_sim_params.py
+sim_params = {
+    't_sim': 2500.0,
+    'master_seed': 2903
+}
+
+# Parameters for the analysis
+ana_params = {
+    'plotRasterArea': {
+        'fraction': 0.5,
+        'low': 2000,
+        'high': 2500
+    },
+    'functconn_corr': {
+        'exclude_diagonal': False
+    }
+}

src/analysis.py

@@ -67,16 +67,16 @@ def __init__(self, ana_params, net_dict, sim_dict, sim_folder,
             os.mkdir(self.plot_folder)
         print('Plots will be written to %s' % self.plot_folder)
 
-    @timeit
-    def fullAnalysis(self):
-        """
-        Execute the full analysis.
-        """
         print('{} Reading popGids'.format(datetime.now().time()))
         self.popGids = self._readPopGids()
         print('{} Reading spikes'.format(datetime.now().time()))
         self.spikes = self._readSpikes()
 
+    @timeit
+    def fullAnalysis(self):
+        """
+        Execute the full analysis.
+        """
         print('{} Calculating rate'.format(datetime.now().time()))
         self.rate = self.meanFiringRate()
         print('{} Calculating population CV ISI'.format(datetime.now().time()))