Merge branch 'main' of https://whale.am28.uni-tuebingen.de/git/mbergmann/gpgrewe2024

code/test.py

@@ -60,21 +60,81 @@ def extract_stim_data(stimulus):
         Current EODf.
     stim_freq : float
         The total stimulus frequency (EODF+df).
+    amp_mod : float
+        The current amplitude modulation.
+    ny_freq : float
+        The current nyquist frequency.
 
     '''
     # extract metadata
     # the stim.name adjusts the first key as it changes with every stimulus
     amplitude = stim.metadata[stim.name]['Contrast'][0][0] 
     df = stim.metadata[stim.name]['DeltaF'][0][0]
-    eodf = stim.metadata[stim.name]['EODf'][0][0]
+    eodf = round(stim.metadata[stim.name]['EODf'][0][0])
-    stim_freq = stim.metadata[stim.name]['Frequency'][0][0]
+    stim_freq = round(stim.metadata[stim.name]['Frequency'][0][0])
-    return amplitude, df, eodf, stim_freq
+    # calculates the amplitude modulation
+    amp_mod, ny_freq = AM(eodf, stim_freq)
+    return amplitude, df, eodf, stim_freq, amp_mod, ny_freq
 
+def AM(EODf, stimulus):
+    """
+    Calculates the Amplitude Modulation and Nyquist frequency
+
+    Parameters
+    ----------
+    EODf : float or int
+        The current EODf.
+    stimulus : float or int
+        The absolute frequency of the stimulus.
+
+    Returns
+    -------
+    AM : float 
+        The amplitude modulation resulting from the stimulus.
+    nyquist : float
+        The maximum frequency possible to resolve with the EODf.
+
+    """
+    nyquist = EODf * 0.5
+    AM = np.mod(stimulus, nyquist)
+    return AM, nyquist
+
+def remove_poor(files):
+    """
+    Removes poor datasets from the set of files for analysis
+
+    Parameters
+    ----------
+    files : list 
+        list of files.
+
+    Returns
+    -------
+    good_files : list
+        list of files without the ones with the label poor.
+
+    """
+    # create list for good files
+    good_files = []
+    # loop over files
+    for i in range(len(files)):
+        # print(files[i])
+        # load the file (takes some time)
+        data = rlx.Dataset(files[i])
+        # get the quality
+        quality = str.lower(data.metadata["Recording"]["Recording quality"][0][0])
+        # check the quality
+        if quality != "poor":
+            # if its good or fair add it to the good files
+            good_files.append(files[i])
+    return good_files
 
 #find example data
-datafolder = "../data"
+datafolder = "../../data"
+
+example_file = datafolder + "/" + "2024-10-16-ah-invivo-1.nix"
 
-example_file = datafolder + "/" + "2024-10-16-ad-invivo-1.nix"
+data_files = glob.glob("../../data/*.nix")
 
 #load dataset
 dataset = rlx.Dataset(example_file)
@@ -121,6 +181,10 @@ for stim in stims:
     freq, power = power_spectrum(rate, dt)
     ax2.plot(freq,power)
     ax2.set_xlim(0,1000)
+    plt.close()
+    if stim == stims[-1]:
+        amplitude, df, eodf, stim_freq = extract_stim_data(stim)
+        print(amplitude, df, eodf, stim_freq)
 
 # make an eventplot
 fig = plt.figure(figsize = (5, 3), layout = 'constrained')
@@ -128,4 +192,3 @@ ax = fig.add_subplot()
 ax.eventplot(spikes, linelength = 0.8)
 ax.set_xlabel('time [ms]')
 ax.set_ylabel('loop no.')
-plt.show()

code/useful_functions.py

@@ -0,0 +1,173 @@
+import glob
+import pathlib
+import numpy as np
+import matplotlib.pyplot as plt
+import rlxnix as rlx
+from IPython import embed
+from scipy.signal import welch
+
+def AM(EODf, stimulus):
+    """
+    Calculates the Amplitude Modulation and Nyquist frequency
+
+    Parameters
+    ----------
+    EODf : float or int
+        The current EODf.
+    stimulus : float or int
+        The absolute frequency of the stimulus.
+
+    Returns
+    -------
+    AM : float 
+        The amplitude modulation resulting from the stimulus.
+    nyquist : float
+        The maximum frequency possible to resolve with the EODf.
+
+    """
+    nyquist = EODf * 0.5
+    AM = np.mod(stimulus, nyquist)
+    return AM, nyquist
+
+def binary_spikes(spike_times, duration, dt):
+    """
+    Converts the spike times to a binary representations
+
+    Parameters
+    ----------
+    spike_times : np.array
+        The spike times.
+    duration : float
+        The trial duration:
+    dt : float
+        The temporal resolution.
+
+    Returns
+    -------
+    binary : np.array
+        The binary representation of the spike train.
+
+    """
+    binary = np.zeros(int(np.round(duration / dt))) #create the binary array with the same length as potential
+    
+    spike_indices = np.asarray(np.round(spike_times / dt), dtype = int) # get the indices
+    binary[spike_indices] = 1 # put the indices into binary
+    return binary
+
+def extract_stim_data(stimulus):
+    '''
+    extracts all necessary metadata for each stimulus
+
+    Parameters
+    ----------
+    stimulus : Stimulus object or rlxnix.base.repro module
+        The stimulus from which the data is needed.
+
+    Returns
+    -------
+    amplitude : float
+        The relative signal amplitude in percent.
+    df : float
+        Distance of the stimulus to the current EODf.
+    eodf : float
+        Current EODf.
+    stim_freq : float
+        The total stimulus frequency (EODF+df).
+    amp_mod : float
+        The current amplitude modulation.
+    ny_freq : float
+        The current nyquist frequency.
+
+    '''
+    # extract metadata
+    # the stim.name adjusts the first key as it changes with every stimulus
+    amplitude = stimulus.metadata[stimulus.name]['Contrast'][0][0] 
+    df = stimulus.metadata[stimulus.name]['DeltaF'][0][0]
+    eodf = round(stimulus.metadata[stimulus.name]['EODf'][0][0])
+    stim_freq = round(stimulus.metadata[stimulus.name]['Frequency'][0][0])
+    # calculates the amplitude modulation
+    amp_mod, ny_freq = AM(eodf, stim_freq)
+    return amplitude, df, eodf, stim_freq, amp_mod, ny_freq
+
+def firing_rate(binary_spikes, dt = 0.000025, box_width = 0.01):
+    '''
+    Calculates the firing rate from binary spikes
+
+    Parameters
+    ----------
+    binary_spikes : np.array
+        The binary representation of the spike train.
+    dt : float, optional
+        Time difference between two datapoints. The default is 0.000025.
+    box_width : float, optional
+        Time window on which the rate should be computed on. The default is 0.01.
+
+    Returns
+    -------
+    rate : np.array
+        Array of firing rates.
+
+    '''
+    box = np.ones(int(box_width // dt))
+    box /= np.sum(box) * dt # normalisierung des box kernels to an integral of one
+    rate = np.convolve(binary_spikes, box, mode = 'same') 
+    return rate
+
+def power_spectrum(spike_times, duration, dt):
+    '''
+    Computes a power spectrum based on the spike times
+
+    Parameters
+    ----------
+    spike_times : np.array
+        The spike times.
+    duration : float
+        The trial duration:
+    dt : float
+        The temporal resolution.
+
+    Returns
+    -------
+    freq : np.array
+        All the frequencies of the power spectrum.
+    power : np.array
+        Power of the frequencies calculated.
+
+    '''
+    # binarizes spikes
+    binary = binary_spikes(spike_times, duration, dt)
+    # computes firing rates
+    rate = firing_rate(binary, dt = dt)
+    # creates power spectrum
+    freq, power = welch(rate, fs = 1/dt, nperseg = 2**16, noverlap = 2**15)
+    return freq, power
+
+def remove_poor(files):
+    """
+    Removes poor datasets from the set of files for analysis
+
+    Parameters
+    ----------
+    files : list 
+        list of files.
+
+    Returns
+    -------
+    good_files : list
+        list of files without the ones with the label poor.
+
+    """
+    # create list for good files
+    good_files = []
+    # loop over files
+    for i in range(len(files)):
+        # print(files[i])
+        # load the file (takes some time)
+        data = rlx.Dataset(files[i])
+        # get the quality
+        quality = str.lower(data.metadata["Recording"]["Recording quality"][0][0])
+        # check the quality
+        if quality != "poor":
+            # if its good or fair add it to the good files
+            good_files.append(files[i])
+    return good_files