created file for all plot functions (calls functions from useful_functions.py)

code/plot_functions.py

@@ -0,0 +1,69 @@
+'''This script contains all functions for various plots that could be relevant 
+for the presentation or protocol of the Grewe GP 2024'''
+
+import os
+import matplotlib.pyplot as plt
+import numpy as np
+import rlxnix as rlx
+from useful_functions import power_spectrum
+
+'''IMPORT DATA'''
+datafolder = '../data' #./ wo ich gerade bin; ../ eine ebene höher; ../../ zwei ebenen höher
+example_file = os.path.join('..', 'data', '2024-10-16-ac-invivo-1.nix')
+
+'''EXTRACT DATA'''
+dataset = rlx.Dataset(example_file)
+
+# get sams
+sams = dataset.repro_runs('SAM')
+sam = sams[2]
+
+# get stims
+stimulus = sam.stimuli[-1]
+stim_count = sam.stimulus_count
+
+'''PLOTS'''
+# create colormap
+colors = plt.cm.prism(np.linspace(0, 1, stim_count))
+
+# plot timeline of whole rec
+dataset.plot_timeline()
+
+# plot voltage over time for whole trace
+def plot_vt_spikes(t, v, spike_t):
+    fig = plt.figure(figsize=(5, 2.5))
+    # alternative to ax = axs[0]
+    ax = fig.add_subplot()
+    # plot vt diagram
+    ax.plot(t[t<0.1], v[t<0.1])
+    # plot spikes into vt diagram, at max V
+    ax.scatter(spike_t[spike_t<0.1], np.ones_like(spike_t[spike_t<0.1]) * np.max(v))
+    plt.show()
+
+# plot scatter plot for one sam with all 3 stims
+def scatter_plot(colormap, stimuli_list, stimulus_count):
+    fig = plt.figure()
+    ax = fig.add_subplot()
+        
+    ax.eventplot(stimuli_list, colors=colormap)
+    ax.set_xlabel('Spike Times [ms]')
+    ax.set_ylabel('Loop #')
+    ax.set_yticks(range(stimulus_count))
+    ax.set_title('Spikes of SAM 3')
+    plt.show()
+    
+# calculate power spectrum
+freq, power = power_spectrum(stimulus)
+
+# plot power spectrum
+def power_spectrum_plot(f, p):
+    # plot power spectrum
+    fig = plt.figure()
+    ax = fig.add_subplot()
+    ax.plot(freq, power)
+    ax.set_xlabel('Frequency [Hz]')
+    ax.set_ylabel('Power [1/Hz]')
+    ax.set_xlim(0, 1000)
+    plt.show()
+    
+####### ADD DIANAS POWER SPECTRUM PLOT

code/useful_functions.py

@@ -120,7 +120,7 @@ def power_spectrum(stimulus):
     Parameters
     ----------
     stimulus : Stimulus object or rlxnix.base.repro module
-        The stimulus from which the data is needed.
+        The stimulus for which the data is needed.
 
     Returns
     -------
@@ -244,13 +244,13 @@ def spike_times(stim):
 
     """
     # reads out the spike times
-    spike_times, _ = stim.trace_data('Spikes-1')
+    spikes, _ = stim.trace_data('Spikes-1')
     # reads out the duration
     stim_dur = stim.duration
     # get the stimulus interval
     ti = stim.trace_info("V-1")
     dt = ti.sampling_interval  
-    return spike_times, stim_dur, dt
+    return spikes, stim_dur, dt # se changed spike_times to spikes so its not the same as name of function
 
 '''TODO: AM-freq plot:
     meaning of am peak in spectrum? why is it there how does it change with stim intensity?