bug fixes

neuro-team-femto · Apr 22, 2024 · 3548eec · 3548eec
1 parent d09bc58
commit 3548eec
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Showing 8 changed files with 5,400 additions and 5,442 deletions.
diff --git a/python/model.csv b/python/model.csv
diff --git a/python/new_sim.ipynb b/python/new_sim.ipynb
diff --git a/python/palin/internal_noise/double_pass.py b/python/palin/internal_noise/double_pass.py
@@ -18,7 +18,7 @@
 from ..simulation.double_pass_experiment import DoublePassExperiment
 from ..simulation.trial import Int2Trial, Int1Trial 
 from ..simulation.linear_observer import LinearObserver
-from ..simulation.double_pass_statistics import DoublePassStatistics
+from ..simulation import double_pass_statistics as dps
 from ..simulation.simulation import Simulation as Sim
 
 
@@ -149,12 +149,12 @@ def build_model(cls,internal_noise_range=np.arange(0,5,.1),criteria_range=np.ara
 
         sim = Sim(DoublePassExperiment, experiment_params,
               LinearObserver, observer_params, 
-              DoublePassStatistics, analyser_params)
+              dps.DoublePassStatistics, analyser_params)
 
         sim_df = sim.run_all(n_runs=n_runs, verbose=True)
 
         # average measures over all runs
-        sim_df.groupby(['internal_noise_std','criteria'])[DoublePassStatistics.get_metric_names()].mean()
+        sim_df.groupby(['internal_noise_std','criteria'])[dps.DoublePassStatistics.get_metric_names()].mean()
         return sim_df
 
 
diff --git a/python/palin/internal_noise/internal_noise_extractor.py b/python/palin/internal_noise/internal_noise_extractor.py
@@ -18,10 +18,10 @@ def extract_single_internal_noise(cls,data_df, trial_id = 'trial_id', feature_id
         raise NotImplementedError()
 
     @classmethod
-    def extract_internal_noise(cls,data_df, group_ids, trial_id, feature_id, value_id, response_id, normalize = True):
+    def extract_internal_noise(cls,data_df, group_ids, trial_id, feature_id, value_id, response_id, model_file):
 
         # for each level in group, extract internal_noise
         return data_df.groupby(group_ids).apply(lambda group: cls.extract_single_internal_noise(group, 
-            trial_id, feature_id, value_id, response_id)).reset_index()
+            trial_id, feature_id, value_id, response_id, model_file)).reset_index()
 
 
diff --git a/python/palin/simulation/__pycache__/simulation.cpython-38.pyc b/python/palin/simulation/__pycache__/simulation.cpython-38.pyc
diff --git a/python/palin/simulation/kernel_distance.py b/python/palin/simulation/kernel_distance.py
@@ -9,7 +9,7 @@ def __init__(self, kernel_extractor, distance='CORR'):
         self.distance = distance
 
     def get_metric_names(self):
-        return [distance.lower()]
+        return [self.distance.lower()]
 
     def analyse(self, experiment, participant, participant_responses): 
 
@@ -36,7 +36,7 @@ def normalize_kernel(self, kernel):
         return self.kernel_extractor.normalize_kernel(kernel)
 
     def compute_distance(self, kernel_1, kernel_2): 
-        return me.kernel_distance(kernel_1, kernel_2, type=self.distance)
+        return [me.kernel_distance(kernel_1, kernel_2, type=self.distance)]
 
 
 
diff --git a/python/palin/simulation/simulation.py b/python/palin/simulation/simulation.py
@@ -115,7 +115,7 @@ def run(self, config_param):
 
         metrics =  ana.get_metric_names()
         values = ana.analyse(exp, obs, responses)
-
+        
         # return the metrics as a dict of name:value pairs
         results = {}
         for metric,value in zip(metrics,values): 

diff --git a/python/sandbox.ipynb b/python/sandbox.ipynb