Merge pull request #15 from tensionhead/14-ensemble-averaged-wavelet-…

…spectrum

14 ensemble averaged wavelet spectrum

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+ignore = E501, E731
+extend_ignore = W503, W504

.gitignore

@@ -1,7 +1,4 @@
 **/__pycache__/
 **/*__pycache__*
-__pycache__
 *.pyc
-**/.DS_store
-.DS_Store
-src/.DS_Store
+dist/

CHANGELOG.md

@@ -1,4 +1,20 @@
-#### pyBOAT 0.9.9
+### pyBOAT 0.9.10
+
+##### New
+
+- Global wavelet spectrum (ensemble average)
+- load and save pyBOAT analysis settings to custom .ini file
+
+##### Changes
+- redesigned "Analyze All" batch processing menu
+- NaN interpolation: now strips of trailing NaNs before interpolation
+
+##### Fixes
+- repaired NaN interpolation, np.nonzero on boolean Series apparently broke
+- minor UI tweaks, further anchor warning boxes
+- fixed period axis for single time averaged wavelet spectra
+
+### pyBOAT 0.9.9
 
 ##### Changes
 - the UI dataviewer is not plotting envelope + trend anymore, but only the envelope (see [here](https://github.com/tensionhead/pyBOAT/discussions/13) for details)
@@ -7,40 +23,40 @@
 ##### Fixes
 - minor UI tweaks, MesageBoxes are anchored to their parent window
 
-#### pyBOAT 0.9.8
+### pyBOAT 0.9.8
 
 - Low-level core.sinc_filter had hardcoded max. size of 2000,
 removed this such that core.sinc_smooth(..., M=..) can freely
 select the filter size again. For the GUI the max. size still
 is 2000, otherwise defaults to signal length if this is smaller.
 
 
-#### pyBOAT 0.9.7
+### pyBOAT 0.9.7
 
 - hotfix: data loading via import menu repaired
 
-#### pyBOAT 0.9.6
+### pyBOAT 0.9.6
 
 - matplotlib >3.5.1 has a new API for the lines drawn on an axis, made the necessary changes
 - improved window closing behavior, 'x' closing the main window should now kill all other open windows
 - fixed time-averaged wavelet (Fourier estimate) save routine to also write out the periods
 - code formatting via black for all source files
 
-#### pyBOAT 0.9.5
+### pyBOAT 0.9.5
 
 - fixed a bunch of additional UI bugs introduced by newer PyQT versions
 - New setting 'Data' for specifying default table output format (csv, txt or xslx)
 
-#### pyBOAT 0.9.4
+### pyBOAT 0.9.4
 
 - just added the link to the gitter chat to the Help menu
 - removed bulky talk pdf
 
-#### pyBOAT 0.9.3
+### pyBOAT 0.9.3
 
 - fixed UI bugs concerning ridge smoothing/thresholding and SSG noise strength
 
-#### pyBOAT 0.9.2
+### pyBOAT 0.9.2
 
 - Scripting interface for significance tests with empirical backgrounds,
 see the new [empirical_backgrounds_demo.py](empirical_backgrounds_demo.py)

pyboat/__init__.py

@@ -4,7 +4,7 @@
 import os
 import argparse
 
-__version__ = "0.9.9"
+__version__ = "0.9.10"
 
 # the object oriented API
 from .api import WAnalyzer

pyboat/plotting.py

@@ -7,10 +7,12 @@
 
 from pyboat.core import get_COI_branches, find_COI_crossing
 
-# --- define colors ---
+# --- Plot Styling ---
+
 rgb_2mpl = lambda R, G, B: np.array((R, G, B)) / 255
 rgba_2mpl = lambda R, G, B, A: np.array((R, G, B, A)) / 255
 
+# data viewer
 SIG_COLOR = "darkslategray"
 TREND_COLOR = rgb_2mpl(165, 105, 189)  # orchidy
 ENVELOPE_COLOR = "orange"
@@ -42,7 +44,7 @@
 # --- define line widths ---
 TREND_LW = 2.0
 SIGNAL_LW = 1.5
-MARKER_SIZE = 4
+MARKER_SIZE = 3
 
 # --- standard sizes ---
 label_size = 18
@@ -52,7 +54,7 @@
 # match dimensions of spectrum and signal plots
 x_size = 6.5
 
-# --- default styles as dictionaries ---
+# default styles as dictionaries
 # can be used with ppl.plot(..., **STYLE)
 
 SIGNAL_STYLE = {
@@ -90,7 +92,7 @@ def get_marker_lw(signal):
     return m, lw
 
 
-# --- Signal and Trend -----------------------------------------------
+# --- Plotting Signal and Trend ---
 
 
 def mk_signal_ax(time_unit="a.u.", fig=None):
@@ -253,7 +255,6 @@ def averaged_Wspec(averaged_Wspec, periods, time_unit="a.u", fig=None):
 
 # --- Wavelet spectrum  ------
 
-
 def mk_signal_modulus_ax(time_unit="a.u.", height_ratios=[1, 2.5], fig=None):
 
     if fig is None:
@@ -274,6 +275,20 @@ def mk_signal_modulus_ax(time_unit="a.u.", height_ratios=[1, 2.5], fig=None):
     return axs
 
 
+def mk_modulus_ax(time_unit="a.u.", fig=None):
+
+    if fig is None:
+        fig = ppl.figure(figsize=(x_size, 6.5))
+        fig.subplots_adjust(bottom=0.07, top=0.97)
+    ax = fig.subplots()
+
+    ax.set_xlabel("Time (" + time_unit + ")", fontsize=label_size)
+    ax.set_ylabel("Period (" + time_unit + ")", fontsize=label_size)
+    ax.tick_params(axis="both", labelsize=tick_label_size)
+
+    return ax
+
+
 def plot_signal_modulus(axs, time_vector, signal, modulus, periods, p_max=None):
 
     """
@@ -322,6 +337,37 @@ def plot_signal_modulus(axs, time_vector, signal, modulus, periods, p_max=None):
     cb.set_label("Wavelet Power", rotation="0", labelpad=-12, fontsize=0.9 * label_size)
 
 
+def plot_modulus(mod_ax, time_vector, modulus, periods, p_max=None):
+
+    """
+    Plot the wavelet power spectrum.
+    """
+
+    # Plot Wavelet Power Spectrum
+
+    extent = (time_vector[0], time_vector[-1], periods[0], periods[-1])
+    im = mod_ax.imshow(
+        modulus[::-1], cmap=CMAP, vmin=0, vmax=p_max, extent=extent, aspect="auto"
+    )
+
+    mod_ax.set_ylim((periods[0], periods[-1]))
+    mod_ax.set_xlim((time_vector[0], time_vector[-1]))
+    mod_ax.grid(axis="y", color="0.6", lw=1.0, alpha=0.5)  # vertical grid lines
+
+    if p_max is None:
+        cb_ticks = [0, int(np.floor(modulus.max()))]
+    else:
+        cb_ticks = [0, p_max]
+
+    cb = ppl.colorbar(
+        im, ax=mod_ax, orientation="horizontal", fraction=0.08, shrink=0.6, pad=0.15
+    )
+    cb.set_ticks(cb_ticks)
+    cb.ax.set_xticklabels(cb_ticks, fontsize=tick_label_size)
+    # cb.set_label('$|\mathcal{W}_{\Psi}(t,T)|^2$',rotation = '0',labelpad = 5,fontsize = 15)
+    cb.set_label("Wavelet Power", rotation="0", labelpad=-12, fontsize=0.9 * label_size)
+
+
 def draw_Wavelet_ridge(ax, ridge_data, marker_size=1.5):
 
     """

pyboat/ui/analysis.py

@@ -240,7 +240,8 @@ def initUI(self, position):
 
         # Start ridge detection
         maxRidgeButton = QPushButton("Detect Maximum Ridge", self)
-        maxRidgeButton.setStatusTip("Finds the time-consecutive power maxima")
+        maxRidgeButton.setStatusTip("Traces the time-consecutive power maxima")
+        maxRidgeButton.setStyleSheet("background-color: lightblue")
 
         maxRidgeButton.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Fixed)
         maxRidgeButton.clicked.connect(self.do_maxRidge_detection)
@@ -566,7 +567,7 @@ def ini_plot_readout(self):
 
     def ini_average_spec(self):
 
-        self.avWspecWindow = AveragedWaveletWindow(self.modulus, parent=self)
+        self.avWspecWindow = AveragedWaveletWindow(parent=self)
 
 
 class mkWaveletCanvas(FigureCanvas):
@@ -730,15 +731,17 @@ def __init__(self):
 
 
 class AveragedWaveletWindow(QMainWindow):
-    def __init__(self, modulus, parent):
+    # `parent` is a `WaveletAnalyzer` instance
+    def __init__(self, parent):
+
         super().__init__(parent=parent)
 
         # --- calculate time averaged power spectrum <-> Fourier estimate ---
-        self.avWspec = np.sum(modulus, axis=1) / modulus.shape[1]
+        self.avWspec = np.sum(parent.modulus, axis=1) / parent.modulus.shape[1]
         # -------------------------------------------------------------------
 
         # the Wavelet analysis window spawning *this* Widget
-        self.parentWA = parent
+        self.parentWA = parent        
         self.DEBUG = parent.DEBUG
         self.initUI()
 
@@ -785,6 +788,7 @@ def initUI(self):
     def save_out(self):
 
         df_out = pd.DataFrame(data=self.avWspec, columns=["power"])
+        df_out.index = self.parentWA.periods
         df_out.index.name = "periods"
 
         dialog = QFileDialog()