adjusted beer lambert, freq filter, stim to xarray

src/cedalion/accessors.py

@@ -54,7 +54,10 @@ def freq_filter(self, fmin, fmax, butter_order=4):
         array = self._obj
 
         fny = array.cd.sampling_rate / 2
-        b, a = scipy.signal.butter(butter_order, (fmin / fny, fmax / fny), "bandpass")
+        if fmin == 0:
+            b, a = scipy.signal.butter(butter_order, fmax / fny, "lowpass")
+        else:
+            b, a = scipy.signal.butter(butter_order, (fmin / fny, fmax / fny), "bandpass")
 
         if (units := array.pint.units) is not None:
             array = array.pint.dequantify()
@@ -86,3 +89,14 @@ def rename_events(self, rename_dict):
         stim = self._obj
         for old_trial_type, new_trial_type in rename_dict.items():
             stim.loc[stim.trial_type == old_trial_type, "trial_type"] = new_trial_type
+
+    def conditions(self):
+        return self._obj.trial_type.unique()
+
+    def to_xarray(self, time : xr.DataArray):
+        stim = self._obj    
+        conds = self.conditions()
+        stim_arr = xr.DataArray(np.zeros((time.shape[0], len(conds))), dims=["time", "condition"], coords={"time" : time, "condition" : conds})
+        for index, row in stim.iterrows():
+            stim_arr.loc[row.onset, row.trial_type] = 1
+        return stim_arr

src/cedalion/nirs.py

@@ -55,6 +55,7 @@ def beer_lambert(
     geo3d: xr.DataArray,
     dpf: xr.DataArray,
     spectrum: str = "prahl",
+    calc_od: bool = True
 ):
     """Calculate concentration changes from amplitude data."""
     validators.has_channel(amplitudes)
@@ -69,7 +70,10 @@ def beer_lambert(
     dists = channel_distances(amplitudes, geo3d)
     dists = dists.pint.to("mm")
 
-    optical_density = -np.log(amplitudes / amplitudes.mean("time"))
+    if calc_od:
+        optical_density = -np.log(amplitudes / amplitudes.mean("time"))
+    else:
+        optical_density = amplitudes
     # conc = Einv @ (optical_density / ( dists * dpf))
     conc = xr.dot(Einv, optical_density / (dists * dpf), dims=["wavelength"])
     conc = conc.pint.to("micromolar")