From 4227bfd4471ca3a33e694f5be7ae456ddf70e64a Mon Sep 17 00:00:00 2001
From: efish <efish@localhost.localdomain>
Date: Wed, 21 Nov 2018 15:38:57 +0100
Subject: [PATCH] =?UTF-8?q?eod=20frequenz=20chirps=20=C3=BCber=20zeit?=
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---
 code/eod_frequency_chirp.py  | 39 +++++++++++++++++++++++++
 code/eod_frequency_normal.py | 56 ++++++++++++++++++++++++++++++++++++
 code/read_chirp_data.py      |  2 +-
 3 files changed, 96 insertions(+), 1 deletion(-)
 create mode 100644 code/eod_frequency_chirp.py
 create mode 100644 code/eod_frequency_normal.py

diff --git a/code/eod_frequency_chirp.py b/code/eod_frequency_chirp.py
new file mode 100644
index 0000000..a495601
--- /dev/null
+++ b/code/eod_frequency_chirp.py
@@ -0,0 +1,39 @@
+from read_chirp_data import *
+import os
+from IPython import embed
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+data_dir = "../data"
+dataset = "2018-11-14-ak-invivo-1"
+stim = read_chirp_stimulus(os.path.join(data_dir, dataset))
+
+s = stim[(1, 675.0, 100.0)][0]
+eod = s[1]
+time = s[0]
+
+eod_norm = eod - np.mean(eod)
+# calculate chirp times and indices by zero crossings
+threshold = 0
+shift_eod = np.roll(eod_norm, 1)
+eod_times = time[(eod_norm >= threshold) & (shift_eod < threshold)]
+
+eod_freq_chirp = 1/np.diff(eod_times)
+kernel = np.ones(11)/11
+smooth_eod_freq_chirp = np.convolve(eod_freq_chirp, kernel, mode = 'valid')
+time_axis = np.arange(len(smooth_eod_freq_chirp))
+
+
+fig = plt.plot(time_axis, smooth_eod_freq_chirp)
+plt.xlabel("time [ms]", fontsize = 14)
+plt.xticks(fontsize = 12)
+plt.ylabel("eod frequency [mV]", fontsize = 14)
+plt.yticks(fontsize = 12)
+plt.axis([0, len(time_axis), 0, 2000])
+
+plt.show()
+
+
+
+
diff --git a/code/eod_frequency_normal.py b/code/eod_frequency_normal.py
new file mode 100644
index 0000000..e1a16a9
--- /dev/null
+++ b/code/eod_frequency_normal.py
@@ -0,0 +1,56 @@
+from read_baseline_data import *
+from IPython import embed
+import matplotlib.pyplot as plt
+import numpy as np
+
+data_dir = '../data'
+dataset = '2018-11-09-ad-invivo-1'
+
+# read eod and time of baseline
+time, eod = read_baseline_eod(os.path.join(data_dir, dataset))
+
+eod_norm = eod - np.mean(eod)
+
+# calculate eod times and indices by zero crossings
+threshold = 0
+shift_eod = np.roll(eod_norm, 1)
+eod_times = time[(eod_norm >= threshold) & (shift_eod < threshold)]
+
+
+## normal
+eod_freq_normal = 1/np.diff(eod_times)
+kernel = np.ones(7)/7
+
+smooth_eod_freq_normal = np.convolve(eod_freq_normal, kernel, mode = 'valid')
+time_axis = np.arange(len(smooth_eod_freq_normal))
+#print(eod_freq)
+#print(smooth_eod_freq)
+
+fig = plt.plot(time_axis,smooth_eod_freq_normal, linewidth = 2.0)
+plt.xlabel("time [ms]", fontsize = 14)
+plt.xticks(fontsize = 12)
+plt.ylabel("eod frequency [mV]", fontsize = 14)
+plt.yticks(fontsize = 12)
+plt.axis([0, len(time_axis), 0, 1000])
+
+plt.show()
+
+
+
+
+
+
+
+## beat
+#x = np.arange(0, len(time_axis, 0.000001)  # Start, Stop, Step
+#y = np.sin(x * 2* np.pi * 600)
+#plt.plot(x, y)
+#plt.show()
+
+
+#eod_freq_beat = eod_freq_normal + np.sin(x * 2* np.pi * 600)
+#smooth_eod_freq_beat = np.convolve(eod_freq_beat, kernel, mode = 'valid')
+#fig = plt.plot(time_axis,smooth_eod_freq_beat)
+#plt.xlabel("time [ms]")
+#plt.ylabel("eod frequency [mV]")
+#plt.show()
diff --git a/code/read_chirp_data.py b/code/read_chirp_data.py
index 4491779..fa64675 100644
--- a/code/read_chirp_data.py
+++ b/code/read_chirp_data.py
@@ -116,7 +116,7 @@ def read_chirp_stimulus(dataset):
 
 if __name__ == "__main__":
     data_dir = "../data"
-    dataset = "2018-11-20-ad-invivo-1"
+    dataset = "2018-11-09-ad-invivo-1"
     #spikes = load_chirp_spikes(os.path.join(data_dir, dataset))
     #chirp_times = load_chirp_times(os.path.join(data_dir, dataset))
     #chirp_eod = load_chirp_eod(os.path.join(data_dir, dataset))