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zm711 · Oct 4, 2023 · 1a2b81a · 1a2b81a
1 parent cb11247
commit 1a2b81a
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Showing 2 changed files with 21 additions and 18 deletions.
diff --git a/src/spikeanalysis/curated_spike_analysis.py b/src/spikeanalysis/curated_spike_analysis.py
@@ -7,27 +7,29 @@
 
 from .spike_analysis import SpikeAnalysis
 
+
 def read_responsive_neurons(folder_path) -> dict:
     """
     Function for reading a response profile json file
     and converting into the appropriate dictionary for curation
-    
+
     Parameters
     ----------
     folder_path: str | Path
         The path way to the directory containing the `response_profile.json`
-        
+
     Returns
     -------
     curation: dict
         The curation file that has been previously generated for a dataset
     """
 
     import json
+
     file_path = Path(folder_path)
     assert file_path.is_dir(), "please input the directory containing the response_profile json"
 
-    with open(file_path/'response_profile.json', 'r') as read_file:
+    with open(file_path / "response_profile.json", "r") as read_file:
         response_dict = json.load(read_file)
 
     for stim in response_dict.keys():
@@ -48,7 +50,7 @@ def __init__(self, curation: dict):
         ----------
         curation: dict
             The curation dictionary to be used for curated data
-            
+
         """
 
         self.curation = curation
@@ -69,12 +71,11 @@ def curate(
         by_trial: Literal["all"] | bool = False,
         trial_index: Optional[int] = None,
     ):
-
         """Function for loading the current curation
         Parameters
         ----------
         criteria: str | dict
-            
+
         by_stim: bool, default: False
            Whether to analyze data by a particular stimulus
         by_response: bool, default: False
@@ -83,7 +84,7 @@ def curate(
             *****
         trial_index: Optional[int], default: None
             Must be given if by_trial=True, to indicate which specific trial to be used
-            
+
         """
         curation = self.curation
 
@@ -103,7 +104,7 @@ def curate(
                 ), f"by_trial must be 'all' or boolean you entered {by_trial}"
 
                 if by_trial == "all":
-                    if len(sub_curation.shape)==1:
+                    if len(sub_curation.shape) == 1:
                         sub_curation = np.expand_dims(sub_curation, axis=1)
                     mask = np.all(sub_curation, axis=1)
                     self.cluster_ids = self.cluster_ids[mask]
@@ -114,7 +115,7 @@ def curate(
                     self.cluster_ids = self.cluster_ids[mask]
 
             else:
-                if len(sub_curation.shape)==1:
+                if len(sub_curation.shape) == 1:
                     sub_curation = np.expand_dims(sub_curation, axis=1)
                 mask = np.any(sub_curation, axis=1)
                 self.cluster_ids = self.cluster_ids[mask]
@@ -132,7 +133,7 @@ def curate(
             else:
                 mask_array = np.array(mask_list[0])
 
-            if len(mask_array.shape)==1:
+            if len(mask_array.shape) == 1:
                 mask_array = np.expand_dims(mask_array, axis=1)
 
             if by_trial == "all":
@@ -155,7 +156,7 @@ def curate(
             else:
                 mask_array = np.array(mask_list[0])
 
-            if len(mask_array.shape)==1:
+            if len(mask_array.shape) == 1:
                 mask_array = np.expand_dims(mask_array, axis=1)
 
             if by_trial == "all":

diff --git a/test/test_curated_spike_analysis.py b/test/test_curated_spike_analysis.py
@@ -44,23 +44,25 @@ def test_curation_both(csa):
     csa.curate(criteria={"test": "activated"}, by_stim=True, by_response=True, by_trial=False)
     assert len(csa.cluster_ids) == 1
     csa.revert_curation()
-    assert len(csa.cluster_ids)==2
-    
+    assert len(csa.cluster_ids) == 2
+
 
 def test_curation_stim(csa):
     csa.curate(criteria="test", by_stim=True, by_response=False, by_trial=False)
-    assert len(csa.cluster_ids)==1
+    assert len(csa.cluster_ids) == 1
     csa.revert_curation()
     assert len(csa.cluster_ids) == 2
 
+
 def test_curation_response(csa):
     csa.curate(criteria="activated", by_stim=False, by_response=True, by_trial=False)
-    assert len(csa.cluster_ids)==1
+    assert len(csa.cluster_ids) == 1
     csa.revert_curation()
     assert len(csa.cluster_ids) == 2
 
+
 def test_curation_trial_all(csa):
-    csa.curate(criteria="test", by_stim=True, by_response=False, by_trial='all')
-    assert len(csa.cluster_ids)==1
+    csa.curate(criteria="test", by_stim=True, by_response=False, by_trial="all")
+    assert len(csa.cluster_ids) == 1
     csa.revert_curation()
-    assert len(csa.cluster_ids) == 2
+    assert len(csa.cluster_ids) == 2