added unfiltered envelope in main plot

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.formatting.provider": "autopep8"
+}

code/chirpdetection.py

@@ -11,6 +11,9 @@ from thunderfish.powerspectrum import spectrogram, decibel
 
 from modules.filters import bandpass_filter, envelope, highpass_filter
 from modules.filehandling import ConfLoader, LoadData
+from modules.plotstyle import PlotStyle
+
+ps = PlotStyle()
 
 
 def instantaneos_frequency(
@@ -275,19 +278,19 @@ def main(datapath: str) -> None:
                 )
 
                 # compute envelopes
-                baseline_envelope = envelope(
+                baseline_envelope_unfiltered = envelope(
                     baseline, data.raw_rate, config.envelope_cutoff)
                 search_envelope = envelope(
                     search, data.raw_rate, config.envelope_cutoff)
 
                 # highpass filter envelopes
                 baseline_envelope = highpass_filter(
-                    baseline_envelope,
+                    baseline_envelope_unfiltered,
                     data.raw_rate,
                     config.envelope_highpass_cutoff
                 )
 
-                baseline_envelope = np.abs(baseline_envelope)
+                # baseline_envelope = np.abs(baseline_envelope)
                 # search_envelope = highpass_filter(
                 #     search_envelope,
                 #     data.raw_rate,
@@ -323,6 +326,7 @@ def main(datapath: str) -> None:
                     int(window_edge), len(baseline_envelope) -
                     int(window_edge)
                 )
+                baseline_envelope_unfiltered = baseline_envelope_unfiltered[valid]
                 baseline_envelope = baseline_envelope[valid]
                 search_envelope = search_envelope[valid]
 
@@ -374,23 +378,22 @@ def main(datapath: str) -> None:
 
                 # plot baseline instantaneos frequency
                 axs[1, i].plot(baseline_freq_time, baseline_freq -
-                               np.median(baseline_freq), marker=".")
+                               np.median(baseline_freq))
 
                 # plot waveform of filtered signal
-                axs[2, i].plot(time_oi, baseline, c="k")
+                axs[2, i].plot(time_oi, baseline, c=ps.green)
 
-                # plot narrow filtered baseline
+                # plot broad filtered baseline
                 axs[2, i].plot(
                     time_oi,
-                    baseline_envelope,
+                    broad_baseline,
-                    c="orange",
                 )
 
-                # plot broad filtered baseline
+                # plot narrow filtered baseline envelope
                 axs[2, i].plot(
                     time_oi,
-                    broad_baseline,
+                    baseline_envelope_unfiltered,
-                    c="green",
+                    c=ps.red
                 )
 
                 # plot waveform of filtered search signal
@@ -400,7 +403,7 @@ def main(datapath: str) -> None:
                 axs[3, i].plot(
                     time_oi,
                     search_envelope,
-                    c="orange",
+                    c=ps.red
                 )
 
                 # plot filtered and rectified envelope
@@ -408,7 +411,7 @@ def main(datapath: str) -> None:
                 axs[4, i].scatter(
                     (time_oi)[baseline_peaks],
                     baseline_envelope[baseline_peaks],
-                    c="red",
+                    c=ps.red,
                 )
 
                 # plot envelope of search signal
@@ -416,7 +419,7 @@ def main(datapath: str) -> None:
                 axs[5, i].scatter(
                     (time_oi)[search_peaks],
                     search_envelope[search_peaks],
-                    c="red",
+                    c=ps.red,
                 )
 
                 # plot filtered instantaneous frequency
@@ -424,7 +427,7 @@ def main(datapath: str) -> None:
                 axs[6, i].scatter(
                     baseline_freq_time[inst_freq_peaks],
                     np.abs(inst_freq_filtered)[inst_freq_peaks],
-                    c="red",
+                    c=ps.red,
                 )
 
                 axs[6, i].set_xlabel("Time [s]")

code/chirpdetector_conf.yml

@@ -13,7 +13,7 @@ search_boundary: 100
 envelope_cutoff: 25
 
 # Cutoff frequency for envelope highpass filter
-envelope_highpass_cutoff: 5
+envelope_highpass_cutoff: 4
 
 # Cutoff frequency for envelope of envelope
 envelope_envelope_cutoff: 5

code/modules/plotstyle.py

@@ -18,17 +18,17 @@ def PlotStyle() -> None:
         black = "#111116"
         white = "#e0e4f7"
         gray = "#6c6e7d"
-        pink = "#f5c2e7"
-        purple = "#cba6f7"
-        red = "#f38ba8"
-        maroon = "#eba0ac"
-        orange = "#fab387"
-        yellow = "#f9e2af"
-        green = "#a6e3a1"
-        teal = "#94e2d5"
-        sky = "#89dceb"
-        sapphire = "#74c7ec"
         blue = "#89b4fa"
+        sapphire = "#74c7ec"
+        sky = "#89dceb"
+        teal = "#94e2d5"
+        green = "#a6e3a1"
+        yellow = "#f9e2af"
+        orange = "#fab387"
+        maroon = "#eba0ac"
+        red = "#f38ba8"
+        purple = "#cba6f7"
+        pink = "#f5c2e7"
         lavender = "#b4befe"
 
         @classmethod
@@ -218,7 +218,7 @@ def PlotStyle() -> None:
     plt.rcParams["image.cmap"] = 'cmo.haline'
     # plt.rcParams["axes.xmargin"] = 0.1
     # plt.rcParams["axes.ymargin"] = 0.15
-    plt.rcParams["axes.titlelocation"] = "center"
+    plt.rcParams["axes.titlelocation"] = "left"
     plt.rcParams["axes.titlesize"] = BIGGER_SIZE
     # plt.rcParams["axes.titlepad"] = -10
     plt.rcParams["legend.frameon"] = False
@@ -244,8 +244,8 @@ def PlotStyle() -> None:
     plt.rcParams["text.color"] = white
     plt.rcParams["axes.facecolor"] = black  # axes background color
     plt.rcParams["axes.edgecolor"] = gray  # axes edge color
-    plt.rcParams["axes.grid"] = True    # display grid or not
+    # plt.rcParams["axes.grid"] = True    # display grid or not
-    plt.rcParams["axes.grid.axis"] = "y"  # which axis the grid is applied to
+    # plt.rcParams["axes.grid.axis"] = "y"  # which axis the grid is applied to
     plt.rcParams["axes.labelcolor"] = white
     plt.rcParams["axes.axisbelow"] = True    # draw axis gridlines and ticks:
     plt.rcParams["axes.spines.left"] = True  # display axis spines
@@ -254,18 +254,18 @@ def PlotStyle() -> None:
     plt.rcParams["axes.spines.right"] = False
     plt.rcParams["axes.prop_cycle"] = cycler(
         'color', [
-            '#f5c2e7',
-            '#cba6f7',
-            '#f38ba8',
-            '#eba0ac',
-            '#fab387',
-            '#f9e2af',
-            '#a6e3a1',
-            '#94e2d5',
-            '#89dceb',
-            '#74c7ec',
-            '#89b4fa',
             '#b4befe',
+            '#89b4fa',
+            '#74c7ec',
+            '#89dceb',
+            '#94e2d5',
+            '#a6e3a1',
+            '#f9e2af',
+            '#fab387',
+            '#eba0ac',
+            '#f38ba8',
+            '#cba6f7',
+            '#f5c2e7',
         ])
     plt.rcParams["xtick.color"] = gray  # color of the ticks
     plt.rcParams["ytick.color"] = gray  # color of the ticks