Merge branch 'master' into 'develop'

Update from Master

See merge request !35

CHANGELOG.md

+### pyBOAT 0.8.17
 
-#### Version 0.8.16
+- Fixed crashes during batch analysis with thresholded ridges
+- Warning and on-the-fly interpolation of non-contiguous missing values (NaNs)
+
+### pyBOAT 0.8.16
 
 - added the pyBOAT icon
 - changed version numbering scheme
 
-#### Version 0.8.1.5
+### pyBOAT 0.8.1.5
 
 - fixed Fourier spectra crash
 - changed plotting style for short signals
 
-### Version 0.8.1
+### pyBOAT 0.8.1
 
 - fixed COI on thresholded ridge
 - improved summary statistics
 
-### Version 0.8
+### pyBOAT 0.8
 
 - added batch processing menu
 - summary statistics: time-averaged power and ensemble dynamics
 
-### Version 0.7.6.1
+### pyBOAT 0.7.6.1
 
 - reworked the SSG, catching missing parameter crashes
 
-### Version 0.7.6
+### pyBOAT 0.7.6
 
 - Added general data import options with optional missing value interpolation
 - Added NaN interpolation to the core module
 
-### Version 0.7.5
+### pyBOAT 0.7.5
 
 - Synthetic Signal Generator, yeah!
 
-### Version 0.7.4
+### pyBOAT 0.7.4
 
 - Amplitude envelope estimation and removal
 

README.md

@@ -22,14 +22,14 @@ Questions, comments etc. please to <gregor.moenke@embl.de>.
 pyBOAT is written in Python and therefore requires Python to be present
 on the system.
 An easy way to install a cross-platform scientfic Python
-environment is to use the freely availabe [Anaconda](https://www.anaconda.com/products/individual).
+environment is to use the freely availabe [Anaconda Distribution](https://www.anaconda.com/products/individual).
 Installation instructions can be found here: https://docs.anaconda.com/anaconda/install/, 
 a Python 3.x version is needed.
 
 Once the Anaconda installation is complete, starting up the ```Anaconda Navigator```
 will show an interface like this:
 
-<img src="./doc/navigator_install.png" alt="drawing" width="800"/>
+<img src="./doc/navigator_install.png" alt="drawing" width="750"/>
 
 First clicking on ```Channels``` and then on ```Add...``` will open an input field.
 Type ```conda-forge``` into it and
@@ -37,7 +37,7 @@ confirm with the &#9166; enter key. Now after hitting ```Update channels```, the
 community packages hosted on the ```conda-forge``` channel will become available. As pyBOAT
 is also a Navigator App, it will now (along with other apps) show up in the main Navigator window:
 
-<img src="./doc/navigator_install2.png" alt="drawing" width="800"/>
+<img src="./doc/navigator_install2.png" alt="drawing" width="600"/>
 
 Finally hitting ```Install``` will download and install pyBOAT. Thereafter,
 pyBOAT can be started by simply clicking on ```Launch``` inside the Navigator.
@@ -45,9 +45,12 @@ pyBOAT can be started by simply clicking on ```Launch``` inside the Navigator.
 #### Updates
 
 In case you see a little blue arrow next to the version number, this means
-an update is available. Clicking on that cogwheel icon in the upper right corner
+an update is available. Clicking on the cogwheel icon in the upper right corner
 allows to run the update and install the latest version of pyBOAT.
 
+<img src="./doc/navigator_update.png" alt="drawing" width="400"/>
+
+
 #### Installation with Anaconda on the commandline ####
 
 For this, the download and installation of [miniconda](https://docs.conda.io/en/latest/miniconda.html)

pyboat/__init__.py

@@ -3,7 +3,7 @@
 import sys,os
 import argparse
 
-__version__ = '0.8.16'
+__version__ = '0.8.17'
 
 # the object oriented API
 from .api import WAnalyzer

pyboat/api.py

@@ -343,7 +343,14 @@ class WAnalyzer:
         
     def get_averaged_spectrum(self):
 
-        """ Average over time """
+        """ 
+        Average Wavelet spectrum over time.
+
+        Returns
+        -------
+        
+        mfourier : Fourier spectrum estimate
+        """
 
         if not self._has_spec:
             print("Need to compute a wavelet spectrum first!")

pyboat/ensemble_measures.py

@@ -38,6 +38,7 @@ def average_power_distribution(ridge_results, signal_ids = None, exclude_coi = F
     '''
 
     powers = []
+    ids = []
 
     if signal_ids is None:
         signal_ids = np.arange( len(ridge_results) )
@@ -45,17 +46,21 @@ def average_power_distribution(ridge_results, signal_ids = None, exclude_coi = F
     assert len(signal_ids) == len(ridge_results)
 
     # collect the time-averaged powers
-    for rd in ridge_results:
+    for rd,_id in zip(ridge_results, signal_ids):
 
         if exclude_coi:
             # take only ridge power outside of COI
             i_left, i_right = find_COI_crossing(rd)
-            mpower= (rd.power[i_left : i_right]).mean()
+            mpower= (rd.power[i_left : i_right]).mean()            
         else:
             mpower= rd.power.mean()
-        powers.append( mpower )
+
+        # can happen if ridge exclusively inside COI
+        if not np.isnan(mpower):
+            powers.append( mpower )
+            ids.append(_id)
         
-    powers_series = pd.Series(index = signal_ids, data = powers)
+    powers_series = pd.Series(index = ids, data = powers)
         
     # sort by power, descending
     powers_series.sort_values(

pyboat/plotting.py

+''' This module provides all visualizations, both for the ui and the API '''
+
 import matplotlib.pyplot as ppl
 import numpy as np
 from numpy import pi
@@ -102,7 +104,6 @@ def draw_envelope(ax, time_vector, envelope):
     ax.plot(time_vector, envelope, color=ENVELOPE_COLOR,
             alpha=0.8, lw=TREND_LW, label="envelope")
     
-
 def draw_detrended(ax, time_vector, detrended):
 
     m, lw = get_marker_lw(detrended)
@@ -543,7 +544,7 @@ def plot_ensemble_dynamics(
     powers : DataFrame containing the 'median' and the
                  two quartiles 'Q1' and 'Q3' over time
 
-    phases : DataFrame containing 'R'
+    phases : DataFrame containing 1st order parameter 'R'
 
     dt : float, the sampling interval to get a proper time axis
 

pyboat/ui/batch_process.py

@@ -202,6 +202,13 @@ class BatchProcessWindow(QWidget):
         # for each signal and the signal_id as key
         ridge_results = self.do_the_loop()
 
+        # check for empty ridge_results
+        if not ridge_results:
+            self.NoResults = MessageWindow('All ridges below threshold.. no results!','No results')
+            return
+
+        
+        
         # compute the time-averaged powers
         if self.cb_power_dis.isChecked() or self.cb_sorted_powers.isChecked():
             
@@ -209,7 +216,6 @@ class BatchProcessWindow(QWidget):
                                                           ridge_results.keys(),
                                                           exclude_coi = True)
 
-            print(powers_series)
             # sort by power, descending
             powers_series.sort_values(
                 ascending = False,
@@ -357,6 +363,8 @@ class BatchProcessWindow(QWidget):
 
         '''
 
+        EmptyRidge = 0
+
         if self.export_options.isChecked():
             OutPath = self.get_OutPath()
             if OutPath is None:
@@ -415,8 +423,12 @@ class BatchProcessWindow(QWidget):
                 tvec,
                 power_thresh,
                 smoothing_wsize = rsmooth)
-            ridge_results[signal_id] = (ridge_data)
-
+            
+            if ridge_data.empty:
+                EmptyRidge += 1
+            else:
+                ridge_results[signal_id] = ridge_data                            
+            
             # -- Save out individual results --
             
             if self.cb_specs.isChecked():
@@ -435,7 +447,8 @@ class BatchProcessWindow(QWidget):
                 plt.savefig(fname)
                 plt.close()
 
-            if self.cb_readout_plots.isChecked():
+            if self.cb_readout_plots.isChecked() and not ridge_data.empty:
+
                 pl.plot_readout(ridge_data)
                 fname = f'{OutPath}/{signal_id}_readout.png'
                 if self.debug:
@@ -443,14 +456,20 @@ class BatchProcessWindow(QWidget):
                 plt.savefig(fname)
                 plt.close()
                 
-            if self.cb_readout.isChecked():
+            if self.cb_readout.isChecked() and not ridge_data.empty:
+
                 fname = f'{OutPath}/{signal_id}_readout.csv'
                 if self.debug:
                     print(f'Saving ridge reatout to {fname}')
                 ridge_data.to_csv(fname, sep = ',', float_format = '%.3f', index = False)                
 
             self.progress.setValue(i)
-            
+
+        if EmptyRidge > 0:
+            self.NoRidges = MessageWindow(
+                f'{EmptyRidge} ridge readouts entirely below threshold..',
+                'Discarded ridges')
+                
         return ridge_results
 
 

pyboat/ui/data_viewer.py

@@ -717,10 +717,26 @@ class DataViewer(QWidget):
 
         # checks for empty signal_id string
         if signal_id:
-            self.raw_signal = self.df[signal_id]
+            raw_signal = self.df[signal_id]
 
-            # remove NaNs
-            self.raw_signal = self.raw_signal[~np.isnan(self.raw_signal)]
+            NaNswitches = np.sum( np.diff( np.isnan(raw_signal) ) )
+            if NaNswitches > 1:
+                print(f'Warning, non-contiguous NaN region found in {signal_id}!')
+                
+                self.NonContiguous = MessageWindow(
+                '''
+                Non contiguous regions of missing values 
+                encountered, using linear interpolation. 
+
+                Try 'Import..' from the main menu 
+                to interpolate missing values in all signals!
+                '''
+                    , "Missing Values")
+                self.raw_signal = pyboat.core.interpolate_NaNs(raw_signal)
+            else:
+                # remove contiguous (like trailing) NaN region
+                self.raw_signal = raw_signal[~np.isnan(raw_signal)]
+            
             self.tvec = np.arange(0, len(self.raw_signal), step=1) * self.dt
             return True  # success