Updated API. First work on impedance tube code

lasp/filter/__init__.py

@@ -2,4 +2,4 @@ from .soundpressureweighting import *
 from .filterbank_design import *
 from .fir_design import *
 from .colorednoise import *
-
+from .biquad import *

lasp/lasp_imptube.py

@@ -108,10 +108,26 @@ class TwoMicImpedanceTube:
         G_AB = self.K*C[:,1,0]/C[:,0,0]
         return self.getFreq(), self.cut_to_limits(G_AB)
     
+    def k(self, freq):
+        """
+        Wave number, or thermoviscous wave number
+        """
+        if self.thermoviscous:
+            D = self.D_imptube
+            S = pi/4*D**2
+            d = PrsDuct(0, S=S, rh=D/4, cs='circ')
+            d.mat = self.mat
+            omg = 2*pi*freq
+            G, Z = d.GammaZc(omg)
+            return G
+        else:
+            return 2*pi*freq/self.mat.c0
+
+
     def R(self, meas):
         freq, G_AB = self.G_AB(meas)
         s = self.s
-        k = 2*pi*freq/self.mat.c0
+        k = self.k(freq)
         d1 = self.d1
         RpA = (G_AB - exp(-1j*k*s))/(exp(1j*k*s)-G_AB)
 

lasp/lasp_measurement.py

@@ -152,9 +152,11 @@ class IterRawData:
             stop_offset = self.lastblock_stop_offset
         else:
             stop_offset = self.blocksize
+        # print(f'block: {block}, starto: {start_offset}, stopo {stop_offset}')
 
         self.i +=1
-        return self.fa[block,start_offset:stop_offset,self.channels]
+        return self.fa[block,start_offset:stop_offset,:][:,self.channels]
+
 
 class IterData(IterRawData):
     """
@@ -362,25 +364,38 @@ class Measurement:
         """Returns the measurement time in seconds since the epoch."""
         return self._time
 
-    @property
+    def rms(self, channels=None, substract_average=False):
-    def rms(self, channels=None):
         """Returns the root mean square values for each channel
 
+        Args:
+            channels: list of channels
+            substract_average: If set to true, computes the rms of only the
+            oscillating component of the signal, which is in fact the signal
+            variance.
+
         Returns:
             1D array with rms values for each channel
         """
-        #
+        meansquare = 0. # Mean square of the signal, including its average
-        try:
+        sum_ = 0. # Sumf of the values of the signal, used to compute average
-            return self._rms
+        N = 0
-        except AttributeError:
-            pass
-
-        meansquare = 0.
         with self.file() as f:
             for block in self.iterData(channels):
+                Nblock = block.shape[0]
+                sum_ += np.sum(block, axis=0)
+                N += Nblock
                 meansquare += np.sum(block**2, axis=0) / self.N
-        self._rms = np.sqrt(meansquare)
+
-        return self._rms
+        avg = sum_/N
+        # In fact, this is not the complete RMS, as in includes the DC 
+        # If p = p_dc + p_osc, then rms(p_osc) = sqrt(ms(p)-ms(p_dc))
+        if substract_average:
+            meansquare -= avg**2
+        rms = np.sqrt(meansquare)
+        return rms
+
+    def variance(self, channels=None):
+        return self.rms(substract_average=True)
 
     def rawData(self, channels=None, **kwargs):
         """Returns the raw data as stored in the measurement file, 
@@ -406,7 +421,6 @@ class Measurement:
 
         return np.concatenate(rawdata, axis=0)
 
-
     def iterData(self, channels, **kwargs):
         sensitivity = kwargs.pop('sensitivity', self.sensitivity)
         if channels is None:
@@ -484,21 +498,26 @@ class Measurement:
         blocks = [signal[i*N:(i+1)*N] for i in range(Nblocks)]
         
         if noiseCorrection:
-            enp1 = [blocks[i+1] - blocks[i] for i in range(Nblocks-1)]
+            # The difference between the measured signal in the previous block and 
-            noise_est_np1 = [np.average(enp1[i+1]*enp1[i]) for i in range(Nblocks-2)]
+            # the current block
+            en = [None] + [blocks[i] - blocks[i-1] for i in range(1,Nblocks)]
+            
+            noise_est = [None] + [-np.average(en[i]*en[i+1]) for i in range(1,len(en)-1)]
             
             # Create weighting coefficients
-            sum_inverse_noise = sum([1/n for n in noise_est_np1])
+            sum_inverse_noise = sum([1/n for n in noise_est[1:]])
-            c_np1 = [1/(ni*sum_inverse_noise) for ni in noise_est_np1]
+            c_n = [1/(ni*sum_inverse_noise) for ni in noise_est[1:]]
         else:
-            c_np1 = [1/(Nblocks-2)]*(Nblocks-2)
+            c_n = [1/(Nblocks-2)]*(Nblocks-2)
 
-        assert np.isclose(sum(c_np1), 1.0)
+        assert np.isclose(sum(c_n), 1.0)
+        assert Nblocks-2 == len(c_n)
         
         # Average signal over blocks
         avg = np.zeros((blocks[0].shape), dtype=float)
-        for i in range(0, Nblocks-2):
+        for n in range(0, Nblocks-2):
-            avg += c_np1[i]*blocks[i+1]
+            avg += c_n[n]*blocks[n+1]
+
         return avg
 
     def periodicCPS(self, N, channels=None, **kwargs):
@@ -514,7 +533,7 @@ class Measurement:
         window = Window.rectangular
         ps = PowerSpectra(N, window)
 
-        avg = self.periodicAverage(N, channels, **kwargs)
+        avg = np.asfortranarray(self.periodicAverage(N, channels, **kwargs))
         CS = ps.compute(avg)
         freq = getFreq(self.samplerate, N)
 
@@ -554,15 +573,14 @@ class Measurement:
             f.attrs['sensitivity'] = sens
         self._sens = sens
 
-    def checkOverflow(self):
+    def checkOverflow(self, channels):
         """Coarse check for overflow in measurement.
 
         Return:
             True if overflow is possible, else False
         """
 
-        with self.file() as f:
+        for block in self.iterData(channels):
-            for block in self.iterBlocks(f):
             dtype = block.dtype
             if dtype.kind == 'i':
                 # minvalue = np.iinfo(dtype).min