falscher name

Power spectrum animations for contrast 10% and 20%

code/Animation_ChatGPT.py

@@ -9,12 +9,14 @@ import numpy as np
 import matplotlib.pyplot as plt
 from scipy.signal import welch
 from matplotlib.animation import FuncAnimation, PillowWriter
+import useful_functions as f
 
 # Generate distances and corresponding frequencies
-distances = np.arange(-400, 451, 1)
+distances = np.arange(-400, 2000, 1)
 f1 = 800
 f2 = f1 + distances
 
+
 # Time parameters
 dt = 0.00001
 t = np.arange(0, 2, dt)
@@ -27,37 +29,45 @@ axs[1].set_xlabel('Frequency [Hz]')
 axs[1].set_ylabel('Power [1/Hz]')
 axs[1].set_xlim(0, 1500)
 
-# Function to compute and plot the power spectrum
+
-def plot_powerspectrum(i):
+
+ # Generate the signal as a sum of two sine waves
+def plot_powerspectrum_2(i):
     # Clear the previous plots
     axs[0].cla()
     axs[1].cla()
     
-    # Generate the signal
+    # Generate the signal as a sum of two sine waves
-    x = np.sin(2*np.pi*f1*t) + 0.2 * np.sin(2*np.pi*f2[i]*t)
+    x = np.sin(2 * np.pi * f1 * t) + 0.8 * np.sin(2 * np.pi * f2[i] * t)  # Second wave is 20% as strong
-    x[x < 0] = 0  # Apply half-wave rectification
+    
     
     # Plot the signal (first 20 ms for clarity)
     axs[0].plot(t[t < 0.02], x[t < 0.02])
     axs[0].set_title(f"Signal (f2={f2[i]} Hz)")
     axs[0].set_xlabel('Time [s]')
     axs[0].set_ylabel('Amplitude')
-    axs[0].set_ylim(0, 1.2)
+    axs[0].set_ylim(-2, 2)
 
+    x[x < 0] = 0  # Apply half-wave rectification (optional)
     # Compute power spectrum
     freq, power = welch(x, fs=1/dt, nperseg=2**16)
-
+    pref = np.max(power)
+    decibel_power = 10 * np.log10(power/pref)
+    AM = f.find_AM(f1, 0.5 * f1, f2[i])
     # Plot the power spectrum
     axs[1].plot(freq, power)
-    axs[1].set_xlim(0, 1500)
+    axs[1].set_xlim(0, 3000)
-    axs[1].set_ylim(0, 0.05)
     axs[1].set_title(f'Power Spectrum (f2={f2[i]} Hz)')
     axs[1].set_xlabel('Frequency [Hz]')
     axs[1].set_ylabel('Power [1/Hz]')
+    #axs[1].set_ylim(0, 0.00007)
+    axs[1].plot(f1, power[np.argmin(np.abs(freq-f1))], 'o')
+    axs[1].plot(f2[i], power[np.argmin(np.abs(freq-f2[i]))], 'd')
+    axs[1].plot(AM, power[np.argmin(np.abs(freq-AM))], '*')
+    axs[1].axvline(AM, alpha = 0.5, color = 'r')
 
 # Create the animation
-ani = FuncAnimation(fig, plot_powerspectrum, frames=len(distances), interval=500)
+ani = FuncAnimation(fig, plot_powerspectrum_2, frames=len(distances), interval=500)
 
-# Display the animation
+# Save the animation as a GIF file (optional)
-ani.save("signal_animation.gif", writer=PillowWriter(fps=30))
+ani.save("sum_of_sinewaves.gif", writer=PillowWriter(fps=30))
-plt.show()

code/am_plots_modularized.py

@@ -0,0 +1,162 @@
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+import glob
+import rlxnix as rlx
+from useful_functions import sam_data, sam_spectrum, calculate_integral, contrast_sorting, remove_poor
+from tqdm import tqdm  # Import tqdm for the progress bar
+
+
+def load_files(file_path_pattern):
+    """Load all files matching the pattern and remove poor quality files."""
+    all_files = glob.glob(file_path_pattern)
+    good_files = remove_poor(all_files)
+    return good_files
+
+
+def process_sam_data(sam):
+    """Process data for a single SAM and return necessary frequencies and powers."""
+    _, _, _, _, eodf, nyquist, stim_freq = sam_data(sam)
+    
+    # Skip if stim_freq is NaN
+    if np.isnan(stim_freq):
+        return None
+    
+    # Get power spectrum and frequency index for 1/2 EODf
+    freq, power = sam_spectrum(sam)
+    nyquist_idx = np.searchsorted(freq, nyquist)
+    
+    # Get frequencies and powers before 1/2 EODf
+    freqs_before_half_eodf = freq[:nyquist_idx]
+    powers_before_half_eodf = power[:nyquist_idx]
+    
+    # Get peak frequency and power
+    am_peak_f = freqs_before_half_eodf[np.argmax(powers_before_half_eodf)]
+    _, _, peak_power = calculate_integral(freq, power, am_peak_f)
+    
+    return stim_freq, am_peak_f, peak_power
+
+
+def plot_contrast_data(contrast_dict, file_tag, axs1, axs2):
+    """Loop over all contrasts and plot AM Frequency and AM Power."""
+    for idx, contrast in enumerate(contrast_dict):  # contrasts = keys of dict
+        ax1 = axs1[idx]  # First figure (AM Frequency vs Stimulus Frequency)
+        ax2 = axs2[idx]  # Second figure (AM Power vs Stimulus Frequency)
+        contrast_sams = contrast_dict[contrast]
+
+        # store all stim_freq and peak_power/nyquist_freq for this contrast
+        stim_freqs = []
+        am_freqs = []
+        peak_powers = []
+
+        # loop over all sams of one contrast
+        for sam in contrast_sams:
+            processed_data = process_sam_data(sam)
+            if processed_data is None:
+                continue
+            stim_freq, am_peak_f, peak_power = processed_data
+            stim_freqs.append(stim_freq)
+            am_freqs.append(am_peak_f)
+            peak_powers.append(peak_power)
+
+        # Plot in the first figure (AM Frequency vs Stimulus Frequency)
+        ax1.plot(stim_freqs, am_freqs, '-', label=file_tag)
+        ax1.set_title(f'Contrast {contrast}%')
+        ax1.grid(True)
+        ax1.legend(loc='upper right')
+
+        # Plot in the second figure (AM Power vs Stimulus Frequency)
+        ax2.plot(stim_freqs, peak_powers, '-', label=file_tag)
+        ax2.set_title(f'Contrast {contrast}%')
+        ax2.grid(True)
+        ax2.legend(loc='upper right')
+
+
+def process_file(file, axs1, axs2):
+    """Process a single file: extract SAMs and plot data for each contrast."""
+    dataset = rlx.Dataset(file)
+    sam_list = dataset.repro_runs('SAM')
+    
+    # Extract the file tag (first part of the filename) for the legend
+    file_tag = '-'.join(os.path.basename(file).split('-')[0:4])
+    
+    # Sort SAMs by contrast
+    contrast_dict = contrast_sorting(sam_list)
+    
+    # Plot the data for each contrast
+    plot_contrast_data(contrast_dict, file_tag, axs1, axs2)
+
+
+def loop_over_files(files, axs1, axs2):
+    """Loop over all good files, process each file, and plot the data."""
+    for file in tqdm(files, desc="Processing files"):
+        process_file(file, axs1, axs2)
+
+
+
+def main():
+    # Load files
+    file_path_pattern = '../data/16-10-24/*.nix'
+    good_files = load_files(file_path_pattern)
+
+    # Initialize figures
+    fig1, axs1 = plt.subplots(3, 1, constrained_layout=True, sharex=True)  # For AM Frequency vs Stimulus Frequency
+    fig2, axs2 = plt.subplots(3, 1, constrained_layout=True, sharex=True)  # For AM Power vs Stimulus Frequency
+
+    # Loop over files and process data
+    loop_over_files(good_files, axs1, axs2)
+
+    # Add labels to figures
+    fig1.supxlabel('Stimulus Frequency (df + EODf) [Hz]')
+    fig1.supylabel('AM Frequency [Hz]')
+    fig2.supxlabel('Stimulus Frequency (df + EODf) [Hz]')
+    fig2.supylabel('AM Power')
+    
+    # Show plots
+    plt.show()
+    
+
+
+# Run the main function
+if __name__ == '__main__':
+    main()
+    
+'''
+Function that gets eodf and 1/2 eodf per contrast:
+
+def calculate_mean_eodf(sams):
+    """
+    Calculate mean EODf and mean 1/2 EODf for the given SAM data.
+    
+    Args:
+        sams (list): List of SAM objects.
+    
+    Returns:
+        mean_eodf (float): Mean EODf across all SAMs.
+        mean_half_eodf (float): Mean 1/2 EODf (Nyquist frequency) across all SAMs.
+    """
+    eodfs = []
+    nyquists = []
+    
+    for sam in sams:
+        _, _, _, _, eodf, nyquist, _ = sam_data(sam)
+        
+        # Add to list only if valid
+        if not np.isnan(eodf):
+            eodfs.append(eodf)
+            nyquists.append(nyquist)
+    
+    # Calculate mean EODf and 1/2 EODf
+    mean_eodf = np.mean(eodfs)
+    mean_half_eodf = np.mean(nyquists)
+    
+    return mean_eodf, mean_half_eodf
+'''
+
+# TODO:
+    # display eodf values in plot for one cell, one intensity - integrate function for this
+    # lowpass with gaussian kernel for amplitude plot(0.5 sigma in frequency spectrum (dont filter too narrowly))
+    # fix legends (only for the cells that are being displayed)
+    # save figures
+    # plot remaining 3 plots, make 1 function for every option and put that in main code
+    # push files to git

code/am_plots_oneintensityandcell.py

@@ -0,0 +1,96 @@
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+import rlxnix as rlx
+from useful_functions import sam_data, sam_spectrum, calculate_integral, contrast_sorting
+
+# close all open plots
+plt.close('all')
+
+def plot_am_vs_frequency_single_intensity(file, contrast=20):
+    """
+    Plots AM Power vs Stimulus Frequency and Nyquist Frequency vs Stimulus Frequency for 
+    one intensity and one cell (file).
+    
+    Parameters:
+        file (str): Path to the file (one cell).
+        intensity (int): The intensity level (contrast) to filter by.
+    """
+    # Load the dataset for the given file
+    dataset = rlx.Dataset(file)
+    
+    # Get SAMs for the whole recording
+    sam_list = dataset.repro_runs('SAM')
+    
+    # Extract the file tag (first part of the filename) for the legend
+    file_tag = '-'.join(os.path.basename(file).split('-')[0:4])
+    
+    # Sort SAMs by contrast
+    contrast_dict = contrast_sorting(sam_list)
+    
+    # Get the SAMs for 20% contrast
+    sams = contrast_dict[contrast]
+    
+    # Create a figure with 1 row and 2 columns
+    fig, axs = plt.subplots(2, 1, layout='constrained')
+    
+    # Store all stim_freq, peak_power, and am_freq for the given contrast
+    stim_freqs = []
+    peak_powers = []
+    am_freqs = []
+    
+    # Loop over all SAMs of the specified contrast
+    for sam in sams:
+        
+        # Get stim_freq for each SAM
+        _, _, _, _, eodf, nyquist, stim_freq = sam_data(sam)
+        
+        # Skip over empty SAMs
+        if np.isnan(stim_freq):
+            continue
+        
+        # Get power spectrum from one SAM
+        freq, power = sam_spectrum(sam)
+        
+        # get index of 1/2 eodf frequency
+        nyquist_idx = np.searchsorted(freq, nyquist)
+        
+        # get frequencies until 1/2 eodf and powers for those frequencies
+        freqs_before_half_eodf = freq[:nyquist_idx]
+        powers_before_half_eodf = power[:nyquist_idx]
+    
+        # Get the frequency of the highest peak before 1/2 EODf
+        am_peak_f = freqs_before_half_eodf[np.argmax(powers_before_half_eodf)]
+        
+        # Get the power of the highest peak before 1/2 EODf
+        _, _, peak_power = calculate_integral(freq, power, am_peak_f)
+        
+        # Collect data for plotting
+        stim_freqs.append(stim_freq)
+        peak_powers.append(peak_power)
+        am_freqs.append(am_peak_f)
+    
+    # Plot AM Power vs Stimulus Frequency (first column)
+    ax = axs[0]
+    ax.plot(stim_freqs, am_freqs, '-')
+    ax.set_ylabel('AM Frequency [Hz]')
+    ax.grid(True)
+    
+    # Plot AM Frequency vs Stimulus Frequency (second column)
+    ax = axs[1]
+    ax.plot(stim_freqs, peak_powers, '-')
+    ax.set_ylabel('AM Power')
+    ax.grid(True)
+    
+    # Figure settings
+    fig.suptitle(f"Cell: {file_tag}, Contrast: {contrast}%")
+    fig.supxlabel("Stimulus Frequency (df + EODf) [Hz]")
+    plt.show()
+
+
+# Call function
+file = '../data/16-10-24/2024-10-16-ad-invivo-1.nix'
+
+# Call the function to plot the data for one intensity and one cell
+plot_am_vs_frequency_single_intensity(file)
+

code/plot_functions.py

@@ -72,14 +72,16 @@ functions_path = r"C:\Users\diana\OneDrive - UT Cloud\Master\GPs\GP1_Grewe\Proje
 sys.path.append(functions_path)
 import useful_functions as u
 import matplotlib.ticker as ticker
+import matplotlib.patches as mpatches
+import matplotlib.cm as cm
 
 def float_formatter(x, _):
     """Format the y-axis values as floats with a specified precision."""
     return f'{x:.5f}'
 
-def plot_highlighted_integrals(ax, frequency, power, points, color_mapping, points_categories, delta=2.5):
+def plot_highlighted_integrals(ax, frequency, power, points, nyquist, true_eodf, color_mapping, points_categories, delta=2.5):
     """
-    Highlight integrals on the existing axes of the power spectrum.
+    Highlights integrals on the existing axes of the power spectrum for a given dataset.
 
     Parameters
     ----------
@@ -102,38 +104,51 @@ def plot_highlighted_integrals(ax, frequency, power, points, color_mapping, poin
     -------
     None
     """
-    ax.plot(frequency, power, color = "k")  # Plot power spectrum on the existing axes
+    # Define color mappings for specific categories
+    category_colors = {
+        "AM": "#ff7f0e",
+        "Nyquist": "#2ca02c",
+        "EODf": "#d62728",
+        "Stimulus": "#9467bd",
+        "EODf (awake fish)": "#8c564b"
+    }
 
+    # Plot the power spectrum on the provided axes
     for point in points:
-        # Calculate the integral and local mean
+        # Identify the category for the current point
-        integral, local_mean = u.calculate_integral_2(frequency, power, point)
+        point_category = next((cat for cat, pts in points_categories.items() if point in pts), "Unknown")
         
-        # Check if the point is valid
+        # Assign color based on category, or default to grey if unknown
+        color = color_mapping.get(point_category, 'gray')
+        
+        # Calculate the integral and check validity
+        integral, local_mean = u.calculate_integral_2(frequency, power, point)
         valid = u.valid_integrals(integral, local_mean, point)
         
         if valid:
-            # Define color based on the category of the point
+            # Highlight valid points with a shaded region
-            point_category = next((cat for cat, pts in points_categories.items() if point in pts), "Unknown")
+            ax.axvspan(point - delta, point + delta, color=color, alpha=0.35, label=f'{point_category}')
-            color = next((c for cat, c in color_mapping.items() if point in points_categories[cat]), 'gray')
     
-            # Shade the region around the point where the integral was calculated
+    ax.plot(frequency, power, color="#1f77b4", linewidth=1.5)
-            ax.axvspan(point - delta, point + delta, color=color, alpha=0.2, label=f'{point_category}')
+    # Use the category colors for 'Nyquist' and 'EODf' lines
-
+    ax.axvline(nyquist, color=category_colors.get("Nyquist", "#2ca02c"), linestyle="--")
-            # Text with categories and colors
+    ax.axvline(true_eodf, color=category_colors.get("EODf (awake fish)", "#8c564b"), linestyle="--")
-            ax.text(1000, 5.8e-5, "AM", fontsize=10, color="green", alpha=0.2)
-            ax.text(1000, 5.6e-5, "Nyquist", fontsize=10, color="blue", alpha=0.2)
-            ax.text(1000, 5.4e-5, "EODf", fontsize=10, color="red", alpha=0.2)
-            ax.text(1000, 5.2e-5, "Stimulus frequency", fontsize=10, color="orange", alpha=0.2)
-            ax.text(1000, 5.0e-5, "EODf of awake fish", fontsize=10, color="purple", alpha=0.2)
 
+    # Set plot limits and labels
     ax.set_xlim([0, 1200])
     ax.set_ylim([0, 6e-5])
-    ax.set_xlabel('Frequency (Hz)')
+    ax.set_xlabel('Frequency (Hz)', fontsize=12)
-    ax.set_ylabel('Power')
+    ax.set_ylabel(r'Power [$\frac{\mathrm{Hz^2}}{\mathrm{Hz}}$]', fontsize=12)
-    ax.set_title('Power Spectrum with highlighted Integrals')
+    #ax.set_title('Power Spectrum with highlighted Integrals', fontsize=14)
 
     # Apply float formatting to the y-axis
     ax.yaxis.set_major_formatter(ticker.FuncFormatter(float_formatter))
 
 
     
+
+
+
+
+
+

code/tuning_curve_max.py

@@ -1,26 +1,45 @@
 import glob
 import matplotlib.pyplot as plt
 import numpy as np
+import os
 import rlxnix as rlx
-import scipy as sp
-import time
 import useful_functions as f
+from matplotlib.lines import Line2D
+from tqdm import tqdm
 
-# tatsächliche Power der peaks benutzen
+# plot the tuning curves for all cells y/n
-
+single_plots = True
-
-
 
 # all files we want to use
 files = glob.glob("../data/2024-10-*.nix")
 
+#EODf file for either day
+eodf_file_w = glob.glob('../data/EOD_only/*-16*.nix')[0]
+eodf_file_m = glob.glob('../data/EOD_only/*-21*.nix')[0]
+
 # get only the good and fair filepaths
 new_files = f.remove_poor(files)
 
+#get the filenames as labels for plotting
+labels = [os.path.splitext(os.path.basename(file))[0] for file in new_files]
+
+# dict for all the different contrasts
+contrast_files = {20 : {'power' :[], 'freq' : []},
+                  10 : {'power' :[], 'freq' : []},
+                   5 : {'power' :[], 'freq' : []}}
+norm_contrast_files = {20 : {'power' :[], 'freq' : []},
+                       10 : {'power' :[], 'freq' : []},
+                       5 : {'power' :[], 'freq' : []}}
 
 # loop over all the good files
-for file in new_files:
+for u, file in tqdm(enumerate(new_files), total = len(new_files)):
+    #use correct eodf file
+    if "-16" in file:
+       orig_eodf = f.true_eodf(eodf_file_w)
+    else:
+       orig_eodf = f.true_eodf(eodf_file_m)
        
+    #define lists
     contrast_frequencies = []
     contrast_powers = []
     # load a file
@@ -30,78 +49,145 @@ for file in new_files:
     # get arrays for frequnecies and power
     stim_frequencies = np.zeros(len(sams))
     peak_powers = np.zeros_like(stim_frequencies)
-    # loop over all sams
+    contrast_sams = f.contrast_sorting(sams)
-    # dictionary for the contrasts
+    
-    contrast_sams = {20 : [],
+    eodfs = []
-                     10 : [],
-                     5 : []}
-    # loop over all sams
-    for sam in sams:
-        # get the contrast
-        avg_dur, contrast, _, _, _, _, _ = f.sam_data(sam)
-        # check for valid trails
-        if np.isnan(contrast):
-            continue
-        elif sam.stimulus_count < 3: #aborted trials
-            continue
-        elif avg_dur < 1.7:
-            continue
-        else:
-            contrast = int(contrast) # get integer of contrast
-            # sort them accordingly
-            if contrast == 20:
-                contrast_sams[20].append(sam)
-            if contrast == 10:
-                contrast_sams[10].append(sam)
-            if contrast == 5:
-                contrast_sams[5].append(sam)
-            else:
-                continue
     # loop over the contrasts
     for key in contrast_sams:
         stim_frequencies = np.zeros(len(contrast_sams[key]))
+        norm_stim_frequencies = np.zeros_like(stim_frequencies)
         peak_powers = np.zeros_like(stim_frequencies)
         
         for i, sam in enumerate(contrast_sams[key]):
             # get stimulus frequency and stimuli
-            _, _, _, _, _, _, stim_frequency = f.sam_data(sam)
+            _, _, _, _, eodf, _, stim_frequency = f.sam_data(sam)
-            stimuli = sam.stimuli
+            sam_frequency, sam_power = f.sam_spectrum(sam)
-            # lists for the power spectra
-            frequencies = []
-            powers = []
-            # loop over the stimuli
-            for stimulus in stimuli:
-                # get the powerspectrum for each stimuli
-                frequency, power = f.power_spectrum(stimulus)
-                # append the power spectrum data
-                frequencies.append(frequency)
-                powers.append(power)
-            #average over the stimuli
-            sam_frequency = np.mean(frequencies, axis = 0)
-            sam_power = np.mean(powers, axis = 0)
             # detect peaks
-            integral, surroundings, peak_power = f.calculate_integral(sam_frequency, 
+            _, _, peak_powers[i] = f.calculate_integral(sam_frequency, 
                                                           sam_power, stim_frequency)
             
-            peak_powers[i] = peak_power
             # add the current stimulus frequency
             stim_frequencies[i] = stim_frequency
-        
+            norm_stim_frequencies[i] = stim_frequency - orig_eodf
+            eodfs.append(eodf)
         # replae zeros with NaN
         peak_powers = np.where(peak_powers == 0, np.nan, peak_powers)
-        
         contrast_frequencies.append(stim_frequencies)
         contrast_powers.append(peak_powers)
+        if key == 20:
+            contrast_files[20]['freq'].append(stim_frequencies)
+            contrast_files[20]['power'].append(peak_powers)
+            norm_contrast_files[20]['freq'].append(norm_stim_frequencies)
+            norm_contrast_files[20]['power'].append(peak_powers)
+        elif key == 10:
+            contrast_files[10]['freq'].append(stim_frequencies)
+            contrast_files[10]['power'].append(peak_powers)
+            norm_contrast_files[10]['freq'].append(norm_stim_frequencies)
+            norm_contrast_files[10]['power'].append(peak_powers)
+        else:
+            contrast_files[5]['freq'].append(stim_frequencies)
+            contrast_files[5]['power'].append(peak_powers)
+            norm_contrast_files[5]['freq'].append(norm_stim_frequencies)
+            norm_contrast_files[5]['power'].append(peak_powers)
     
-    fig, ax = plt.subplots(layout = 'constrained')
+    curr_eodf = np.mean(eodfs)
+    if single_plots == True:
+        # one cell with all contrasts in one subplot
+        fig, ax = plt.subplots()
         ax.plot(contrast_frequencies[0], contrast_powers[0])
         ax.plot(contrast_frequencies[1], contrast_powers[1])
+        if contrast_frequencies and contrast_frequencies[-1].size == 0:
+            if contrast_frequencies and contrast_frequencies[-2].size == 0:
+                ax.set_xlim(0,2000)
+            else:
+                ax.set_xlim(0,np.max(contrast_frequencies[-2]))
+        else:
             ax.plot(contrast_frequencies[2], contrast_powers[2])
+            ax.set_xlim(0,np.max(contrast_frequencies[-1]))
+        ax.axvline(orig_eodf, color = 'black',linestyle = 'dashed', alpha = 0.8)
+        ax.axvline(2*curr_eodf, color = 'black', linestyle = 'dotted', alpha = 0.8)
+        ax.set_ylim(0, 0.00014)
         ax.set_xlabel('stimulus frequency [Hz]')
         ax.set_ylabel(r' power [$\frac{\mathrm{mV^2}}{\mathrm{Hz}}$]')
         ax.set_title(f"{file}")
-            
+        fig.legend(labels = ['20 % contrast', '10 % contrast','5 % contrast','EODf of awake fish', '1st harmonic of current EODf' ], loc = 'lower center', ncol = 3)
-    
+        plt.tight_layout(rect=[0, 0.06, 1, 1])
+        plt.savefig(f'../results/tuning_curve{labels[u]}.svg')
+        
+        #one cell with the contrasts in different subplots
+        fig, axs = plt.subplots(1, 3, figsize = [10,6], sharex = True, sharey = True)
+        for p, key in enumerate(contrast_files):
+            ax = axs[p]
+            ax.plot(contrast_files[key]['freq'][-1],contrast_files[key]['power'][-1])
+            ax.set_title(f"{key}")
+            ax.axvline(orig_eodf, color = 'black',linestyle = 'dashed')
+            ax.axvline(2*curr_eodf, color = 'darkblue', linestyle = 'dotted', alpha = 0.8)
+            if p == 0:
+                ax.set_ylabel(r'power [$\frac{\mathrm{mV^2}}{\mathrm{Hz}}$]', fontsize=12)
+        fig.supxlabel('stimulus frequency [Hz]', fontsize=12)
+        fig.suptitle(f'{labels[u]}')
+        fig.legend(labels = ['power of stimulus peak', 'EODf of awake fish','1st harmonic of current EODf'], loc = 'lower center', bbox_to_anchor=(0.5, 0.05), ncol = 3)
+        plt.tight_layout(rect=[0, 0.06, 1, 1])
+        plt.savefig(f'../results/contrast_tuning{labels[u]}.svg')
+        
+cmap = plt.get_cmap('viridis')
+colors = cmap(np.linspace(0, 1, len(new_files)))
+plt.close('all')
+if len(new_files) < 10:
+    lines = []
+    labels_legend = []
+    fig, axs = plt.subplots(1, 3, figsize = [10,6], sharex = True, sharey = True)
+    for p, key in enumerate(contrast_files):
+        ax = axs[p]
+        for i in range(len(contrast_files[key]['power'])):
+            line, = ax.plot(contrast_files[key]['freq'][i],contrast_files[key]['power'][i], label = labels[i], color = colors[i])
+            ax.set_title(f"{key}")
+            ax.axvline(orig_eodf, color = 'black',linestyle = 'dashed')
+            if p == 0:
+                lines.append(line)
+                labels_legend.append(labels[i])
+    fig.supxlabel('stimulus frequency [Hz]', fontsize=12)
+    fig.supylabel(r'power [$\frac{\mathrm{mV^2}}{\mathrm{Hz}}$]', fontsize=12)
+    
+    # Create a single legend beneath the plots with 3 columns
+    lines.append(Line2D([0], [0], color='black', linestyle='--'))  # Custom line for the legend
+    labels_legend.append("Awake fish EODf")  # Custom label
+    fig.legend(lines, labels_legend, loc='upper center', ncol=3, fontsize=10)
+    plt.tight_layout(rect=[0, 0, 1, 0.85])  # Adjust layout to make space for the legend
+    if "-16" in new_files[-1]:
+        plt.savefig('../results/tuning_curves_10_16.svg')
+    elif "-21" in new_files[0]:
+        plt.savefig('../results/tuning_curves_10_21.svg')
+else:
+    for o in range(2):
+        lines = []
+        labels_legend = []
+        fig, axs = plt.subplots(1, 3, figsize = [10,6], sharex = True, sharey = True)
+        for p, key in enumerate(norm_contrast_files):
+            ax = axs[p]
+            for i in range(len(norm_contrast_files[key]['power'])):
+                line, = ax.plot(norm_contrast_files[key]['freq'][i],norm_contrast_files[key]['power'][i], label = labels[i], color = colors[i])
+                ax.set_title(f"{key}")
+                ax.axvline(0, color = 'black',linestyle = 'dashed')
+                if p == 0:
+                    lines.append(line)
+                    labels_legend.append(labels[i])
+        fig.supylabel(r'power [$\frac{\mathrm{mV^2}}{\mathrm{Hz}}$]', fontsize=12)
+        
+        # Create a single legend beneath the plots with 3 columns
+        lines.append(Line2D([0], [0], color='black', linestyle='--'))  # Custom line for the legend
+        labels_legend.append("Awake fish EODf")  # Custom label
+        fig.legend(lines, labels_legend, loc='upper center', ncol=3, fontsize=10)
+        plt.tight_layout(rect=[0, 0, 1, 0.82])  # Adjust layout to make space for the legend
+        if o == 0:
+            ax.set_xlim(-600, 2100)
+            fig.supxlabel('stimulus frequency [Hz]', fontsize=12)
+            plt.savefig('../results/tuning_curves_norm.svg')
+        else:
+            ax.set_xlim(-600, 600)
+            fig.supxlabel(' relative stimulus frequency [Hz]', fontsize=12)
+            plt.savefig('../results/tuning_curves_norm_zoom.svg')
+#plt.close('all')
 
 
     

code/useful_functions.py

@@ -1,42 +1,13 @@
 import numpy as np
 import rlxnix as rlx
 from scipy.signal import welch
+from scipy import signal
+import matplotlib.pyplot as plt
+from scipy.signal import find_peaks
 
 def all_coming_together(freq_array, power_array, points_list, categories, num_harmonics_list, colors, delta=2.5, threshold=0.5):
-    """
+    # Initialize dictionaries and lists
-    Process a list of points, calculating integrals, checking validity, and preparing harmonics for valid points.
+    valid_points = []
-
-    Parameters
-    ----------
-    freq_array : np.array
-        Array of frequencies corresponding to the power values.
-    power_array : np.array
-        Array of power spectral density values.
-    points_list : list
-        List of harmonic frequency points to process.
-    categories : list
-        List of corresponding categories for each point.
-    num_harmonics_list : list
-        List of the number of harmonics for each point.
-    colors : list
-        List of colors corresponding to each point's category.
-    delta : float, optional
-        Radius of the range for integration around each point (default is 2.5).
-    threshold : float, optional
-        Threshold value to compare integrals with local mean (default is 0.5).
-
-    Returns
-    -------
-    valid_points : list
-        A continuous list of harmonics for all valid points.
-    color_mapping : dict
-        A dictionary mapping categories to corresponding colors.
-    category_harmonics : dict
-        A mapping of categories to their harmonic frequencies.
-    messages : list
-        A list of messages for each point, stating whether it was valid or not.
-    """
-    valid_points = []  # A continuous list of harmonics for valid points
     color_mapping = {}
     category_harmonics = {}
     messages = []
@@ -46,21 +17,25 @@ def all_coming_together(freq_array, power_array, points_list, categories, num_ha
         num_harmonics = num_harmonics_list[i]
         color = colors[i]
         
-        # Step 1: Calculate the integral for the point
+        # Calculate the integral for the point
-        integral, local_mean = calculate_integral_2(freq_array, power_array, point, delta)
+        integral, local_mean = calculate_integral_2(freq_array, power_array, point)
         
-        # Step 2: Check if the point is valid
+        # Check if the point is valid
-        valid = valid_integrals(integral, local_mean, point, threshold)
+        valid = valid_integrals(integral, local_mean, point)
         if valid:
-            # Step 3: Prepare harmonics if the point is valid
+            # Prepare harmonics if the point is valid
             harmonics, color_map, category_harm = prepare_harmonic(point, category, num_harmonics, color)
-            valid_points.extend(harmonics)  # Use extend() to append harmonics in a continuous manner
+            valid_points.extend(harmonics)
-            color_mapping.update(color_map)
+            color_mapping[category] = color  # Store color for category
-            category_harmonics.update(category_harm)
+            category_harmonics[category] = harmonics
             messages.append(f"The point {point} is valid.")
         else:
             messages.append(f"The point {point} is not valid.")
 
+    # Debugging print statements
+    print("Color Mapping:", color_mapping)
+    print("Category Harmonics:", category_harmonics)
+
     return valid_points, color_mapping, category_harmonics, messages
 
 
@@ -150,40 +125,42 @@ def calculate_integral(freq, power, point, delta = 2.5):
     local_mean = np.mean([l_integral, r_integral])
     return integral, local_mean, p_power
 
-def calculate_integral_2(freq, power, point, delta = 2.5):   
+
+def calculate_integral_2(freq, power, peak_freq, delta=2.5):
     """
-    Calculate the integral around a single specified point.
+    Calculate the integral around a specified peak frequency and the local mean.
 
     Parameters
     ----------
-    frequency : np.array
+    freq : np.array
         An array of frequencies corresponding to the power values.
     power : np.array
         An array of power spectral density values.
-    point : float
+    peak_freq : float
-        The harmonic frequency at which to calculate the integral.
+        The frequency of the peak around which to calculate the integral.
     delta : float, optional
-        Radius of the range for integration around the point. The default is 2.5.
+        Radius of the range for integration around the peak. The default is 2.5.
 
     Returns
     -------
     integral : float
-        The calculated integral around the point.
+        The calculated integral around the peak frequency.
     local_mean : float
         The local mean value (adjacent integrals).
-    p_power : float
-        The local maxiumum power.
     """
-    indices = (freq >= point - delta) & (freq <= point + delta)
+    # Calculate integral around the peak frequency
+    indices = (freq >= peak_freq - delta) & (freq <= peak_freq + delta)
     integral = np.trapz(power[indices], freq[indices])
     
-    left_indices = (freq >= point - 5 * delta) & (freq < point - delta)
+    # Calculate local mean from adjacent ranges
-    right_indices = (freq > point + delta) & (freq <= point + 5 * delta)
+    left_indices = (freq >= peak_freq - 5 * delta) & (freq < peak_freq - delta)
+    right_indices = (freq > peak_freq + delta) & (freq <= peak_freq + 5 * delta)
     
-    l_integral = np.trapz(power[left_indices], freq[left_indices])
+    l_integral = np.trapz(power[left_indices], freq[left_indices]) if np.any(left_indices) else 0
-    r_integral = np.trapz(power[right_indices], freq[right_indices])
+    r_integral = np.trapz(power[right_indices], freq[right_indices]) if np.any(right_indices) else 0
     
     local_mean = np.mean([l_integral, r_integral])
+    
     return integral, local_mean
 
 def contrast_sorting(sams, con_1 = 20, con_2 = 10, con_3 = 5, stim_count = 3, stim_dur = 2):
@@ -274,44 +251,66 @@ def extract_stim_data(stimulus):
     stim_freq = round(stimulus.metadata[stimulus.name]['Frequency'][0][0])
     stim_dur = stimulus.duration
     # calculates the amplitude modulation
-    amp_mod, ny_freq = AM(eodf, stim_freq)
+    _, ny_freq = AM(eodf, stim_freq)
-    return amplitude, df, eodf, stim_freq,stim_dur, amp_mod, ny_freq
+    amp_mod = find_AM(eodf, ny_freq, stim_freq)
+    return amplitude, df, eodf, stim_freq, stim_dur, amp_mod, ny_freq
 
-def find_exceeding_points(frequency, power, points, delta, threshold):
+def find_AM(eodf, nyquist, stimulus_frequency):
+    t = signal.windows.triang(eodf) * nyquist
+    length_t2 = int(eodf*10)
+    t2 = np.tile(t, length_t2)
+    x_values = np.arange(len(t2))
+    
+    #fig, ax = plt.subplots()
+    #ax.plot(t2)
+    #ax.scatter(stimulus_frequency, t2[np.argmin(np.abs(x_values - stimulus_frequency))])
+    #plt.grid()
+
+    AM = t2[np.argmin(np.abs(x_values - stimulus_frequency))]
+    return AM
+
+
+def find_nearest_peak(freq, power, point, peak_search_range=30, threshold=None):
     """
-    Find the points where the integral exceeds the local mean by a given threshold.
+    Find the nearest peak within a specified range around a given point.
 
     Parameters
     ----------
-    frequency : np.array
+    freq : np.array
         An array of frequencies corresponding to the power values.
     power : np.array
         An array of power spectral density values.
-    points : list
+    point : float
-        A list of harmonic frequencies to evaluate.
+        The harmonic frequency for which to find the nearest peak.
-    delta : float
+    peak_search_range : float, optional
-        Half-width of the range for integration around the point.
+        Range in Hz to search for peaks around the specified point. The default is 30.
-    threshold : float
+    threshold : float, optional
-        Threshold value to compare integrals with local mean.
+        Minimum height of peaks to consider. If None, no threshold is applied.
 
     Returns
     -------
-    exceeding_points : list
+    peak_freq : float
-        A list of points where the integral exceeds the local mean by the threshold.
+        The frequency of the nearest peak within the specified range, or the input point if no peak is found.
     """
-    exceeding_points = []
+    # Define the range for peak searching
+    search_indices = (freq >= point - peak_search_range) & (freq <= point + peak_search_range)
     
-    for point in points:
+    # Find peaks in the specified range
-        # Calculate the integral and local mean for the current point
+    peaks, properties = find_peaks(power[search_indices], height=threshold)
-        integral, local_mean = calculate_integral(frequency, power, point, delta)
  
-        # Check if the integral exceeds the threshold
+    # Adjust peak indices to match the original frequency array
-        valid, message = valid_integrals(integral, local_mean, threshold, point)
+    peaks_freq = freq[search_indices][peaks]
     
-        if valid:
+    if peaks_freq.size == 0:
-            exceeding_points.append(point)
+        # No peaks detected, return the input point
+        return point
+    
+    # Find the nearest peak to the specified point
+    nearest_peak_index = np.argmin(np.abs(peaks_freq - point))
+    peak_freq = peaks_freq[nearest_peak_index]
+    
+    return peak_freq
 
-    return exceeding_points
 
 def firing_rate(binary_spikes, dt = 0.000025, box_width = 0.01):
     '''

results/contrast_tuning2024-10-16-ab-invivo-1.svg

@@ -6,7 +6,7 @@
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