From 15bcc09655220669fef5af5a061bbd4041df89d8 Mon Sep 17 00:00:00 2001
From: "a.ott" <a.ott@student.uni-tuebingen.de>
Date: Wed, 20 May 2020 15:23:45 +0200
Subject: [PATCH] add reference and test for detect spikes

---
 unittests/testHelperFunctions.py | 56 +++++++++++++++++++++++++-------
 1 file changed, 45 insertions(+), 11 deletions(-)

diff --git a/unittests/testHelperFunctions.py b/unittests/testHelperFunctions.py
index 76576e2..a64c4c8 100644
--- a/unittests/testHelperFunctions.py
+++ b/unittests/testHelperFunctions.py
@@ -2,9 +2,17 @@ import unittest
 import numpy as np
 import helperFunctions as hF
 import matplotlib.pyplot as plt
+from CellData import icelldata_of_dir
+from Baseline import BaselineCellData
+import os
 
 
 class HelperFunctionsTester(unittest.TestCase):
+    reference_base_spikes = {'2012-12-21-an-invivo-1': 39, '2012-07-12-ag-invivo-1': 21, '2012-12-13-ac-invivo-1': 19,
+                             '2012-12-20-ac-invivo-1': 43, '2013-01-08-ad-invivo-1': 29, '2012-06-27-an-invivo-1': 19,
+                             '2012-12-13-ah-invivo-1': 35, '2012-12-13-ag-invivo-1': 26, '2012-12-13-an-invivo-1': 29,
+                             '2012-12-21-ai-invivo-1': 55, '2012-12-20-aa-invivo-1': 24, '2012-12-21-am-invivo-1': 26,
+                             '2012-06-27-ah-invivo-1': 27, '2012-07-12-ap-invivo-1': 35, '2012-12-21-ak-invivo-1': 30}
 
     noise_levels = [0, 0.05, 0.1, 0.2]
     frequencies = [0, 1, 5, 30, 100, 500, 750, 1000]
@@ -30,18 +38,44 @@ class HelperFunctionsTester(unittest.TestCase):
 
         self.assertEqual(0, round(hF.__vector_strength__(rel_spike_times, eod_durations), 5))
 
-    # def test_eods_around_spikes(self):
-    #
-    #     time = np.arange(0, 3, 0.01)
-    #     eod = np.sin(2*np.pi * 2 * time)
-    #
-    #     spikes = [0.2, 0.5, 0.6]
-    #     indices = np.searchsorted(time, spikes)
-    #
-    #     rel_spike_time, eod_duration = hF.eods_around_spikes(time, eod, indices)
-    #
-    #     print("meep")
+    def test_detect_spiketimes(self):
+        count = 0
+        for cell_data in icelldata_of_dir("./test_data/"):
+            print(cell_data.get_data_path())
+            # if "21-ai" not in cell_data.get_data_path() and "20-ac" not in cell_data.get_data_path():
+            #     continue
 
+            spikes = np.array(cell_data.get_base_spikes()[0])
+
+            time_length = 0.2
+            time = cell_data.get_base_traces(cell_data.TIME)[0]
+            length_data_points = int(time_length / cell_data.get_sampling_interval())
+
+            start_idx = 0
+            end_idx = length_data_points + 1
+            end_idx = end_idx if end_idx <= len(time) else len(time)
+
+            bot_lim_spikes = spikes[spikes > time[start_idx]]
+            top_lim_spikes = bot_lim_spikes[bot_lim_spikes < time[end_idx]]
+
+            expected = self.reference_base_spikes[os.path.basename(cell_data.get_data_path())]
+            if len(top_lim_spikes) == expected:
+                print("yay")
+            else:
+
+                print("detected: {:}, reference: {:}".format(len(top_lim_spikes), expected))
+                print("nay")
+                baseline = BaselineCellData(cell_data)
+                baseline.plot_baseline(position=0, time_length=0.2)
+
+            count += 1
+
+    def test_automatic_splitting(self):
+        for cell_data in icelldata_of_dir("./test_data/"):
+            print(cell_data.get_data_path())
+            v1 = cell_data.get_base_traces(cell_data.V1)[0]
+
+            hF.detect_spike_indices_automatic_split(v1)
 
     # todo
     #  search_eod_start_and_end_times ? (not used anymore ?)