adjust nperseg for psd calculation for short signals

Author: eneelo

qats/app/funcs.py

@@ -21,7 +21,8 @@ def calculate_psd(container, twin, fargs, nperseg, normalize):
     fargs : tuple
         Filter arguments. Time series are filtered before estimating psd.
     nperseg : int
-        Size of segments used for ustimating PSD using Welch's method.
+        Size of segments used for estimating PSD using Welch's method.
+        NOTE: the minimum of specified `nperseg` and signal length is used.
     normalize : bool
         Normalize power spectral density on maximum density.
 
@@ -33,8 +34,14 @@ def calculate_psd(container, twin, fargs, nperseg, normalize):
     container_out = dict()
 
     for name, ts in container.items():
-        # resampling to average time step for robustness (necessary for series with varying time step)
-        f, s = ts.psd(twin=twin, filterargs=fargs, resample=ts.dt, taperfrac=0.1, nperseg=nperseg, normalize=normalize)
+        # NOTE: nperseg passed on as minimum of specified value and signal input length
+        #       this is done in scipy anyway, which also issues a UserWArnings stating:
+        #       "nperseg = {nperseg} is greater than input length = {input_length:d}, using nperseg = {input_length:d}"
+        t, _ = ts.get(twin=twin, resample=ts.dt)
+        nperseg_ = np.min((nperseg, t.size))
+        # calculate power spectral density 
+        # (resampling to average time step for robustness, necessary for series with varying time step)
+        f, s = ts.psd(twin=twin, filterargs=fargs, resample=ts.dt, taperfrac=0.1, nperseg=nperseg_, normalize=normalize)
         container_out[name] = tuple([f, s])
 
     return container_out

qats/app/gui.py

@@ -1462,12 +1462,12 @@ def __init__(self, psdnorm, nperseg, nbins, twindec, parent=None):
         self.psdnpersegspinbox.setSingleStep(10)
         self.psdnpersegspinbox.setEnabled(True)
         self.psdnpersegspinbox.setValue(nperseg)
-        self.psdnpersegspinbox.setToolTip("When esimtating power spectral density using Welch's method the signal\n"
-                                          "is dived into overlapping segments and psd is estimated for each segment\n"
+        self.psdnpersegspinbox.setToolTip("When estimating power spectral density using Welch's method the signal\n"
+                                          "is divided into overlapping segments and psd is estimated for each segment\n"
                                           "and then averaged. The overlap is half of the segment length. The \n"
                                           "psd-estimate is smoother with shorter segments.")
         psdlayout = QHBoxLayout()
-        psdlayout.addWidget(QLabel("Length of segment used when estimating power spectral density"))
+        psdlayout.addWidget(QLabel("Length of segment used when estimating power spectral density *"))
         psdlayout.addStretch(1)
         psdlayout.addWidget(self.psdnpersegspinbox)
         layout.addLayout(psdlayout)
@@ -1494,14 +1494,15 @@ def __init__(self, psdnorm, nperseg, nbins, twindec, parent=None):
         self.twindecspinbox.setValue(twindec)
         self.twindecspinbox.setToolTip("Number of decimals in the data processing time window from/to boxes.")
         twindeclayout = QHBoxLayout()
-        twindeclayout.addWidget(QLabel("Number of decimals in data processing time window *"))
+        twindeclayout.addWidget(QLabel("Number of decimals in data processing time window **"))
         twindeclayout.addStretch(1)
         twindeclayout.addWidget(self.twindecspinbox)
         layout.addLayout(twindeclayout)
 
         # help text
         helptext = QHBoxLayout()
-        helptext.addWidget(QLabel("* Close and re-open application for this setting to have effect"))
+        helptext.addWidget(QLabel("*  Parameter 'nperseg' in scipy.signal.welch \n    (signal length is used if smaller than specified value)\n"
+                                  "** Close and re-open application for this setting to have effect"))
         helptext.addStretch(1)
         layout.addLayout(helptext)