Gh2 mnemonics and pulse alignment

Update the GH2 mnemonics and add a function to extract the exposed frames.

src/toolbox_scs/detectors/gotthard2.py

@@ -15,9 +15,13 @@ __all__ = [
 
 log = logging.getLogger(__name__)
 
-def extract_GH2(ds, run, firstFrame=0, bunchPattern='scs_ppl'):
+
+def extract_GH2(ds, run, firstFrame=0, bunchPattern='scs_ppl',
+                gh2_dim='gh2_pId'):
     '''
-    Extract the frames of the Gotthard-II that have been exposed to light.
+    Select and align the frames of the Gotthard-II that have been exposed
+    to light.
+
     Parameters
     ------
     ds: xarray.Dataset
@@ -30,33 +34,42 @@ def extract_GH2(ds, run, firstFrame=0, bunchPattern='scs_ppl'):
         the bunch pattern used to align data. For 'scs_ppl', the gh2_pId
         dimension in renamed 'ol_pId', and for 'sase3' gh2_pId is renamed
         'sa3_pId'.
+    gh2_dim: str
+        The name of the dimension that corresponds to the Gotthard-II frames.
 
     Returns
     -------
     nds: xarray Dataset
-        The aligned and reduced dataset with only-data-containing GH2 variables.
+        The aligned and reduced dataset with only-data-containing GH2
+        variables.
     '''
+    if gh2_dim not in ds.dims:
+        log.warning(f'gh2_dim "{gh2_dim}" not in dataset. Skipping.')
+        return ds
     if bunchPattern == 'scs_ppl':
         pattern = OpticalLaserPulses(run)
-        dim='ol_pId'
+        dim = 'ol_pId'
     else:
         pattern = XrayPulses(run)
-        dim='sa3_pId'
+        dim = 'sa3_pId'
+    others = [var for var in ds if dim in ds[var].coords]
+    nds = ds.drop_dims(dim)
     if pattern.is_constant_pattern():
         pulse_ids = pattern.peek_pulse_ids(labelled=False)
-        nds = ds.isel(gh2_pId=pulse_ids + firstFrame)
-        nds = nds.assign_coords(gh2_pId=pulse_ids)
-        nds = nds.rename(gh2_pId=dim)
+        nds = nds.isel({gh2_dim: pulse_ids + firstFrame})
+        nds = nds.assign_coords({gh2_dim: pulse_ids})
+        nds = nds.rename({gh2_dim: dim})
     else:
         log.warning('The number of pulses has changed during the run.')
         pulse_ids = np.unique(pattern.pulse_ids(labelled=False, copy=False))
-        nds = ds.isel(gh2_pId=pulse_ids + firstFrame)
-        nds = nds.assign_coords(gh2_pId=pulse_ids)
-        nds = nds.rename(gh2_pId=dim)
+        nds = nds.isel({gh2_dim: pulse_ids + firstFrame})
+        nds = nds.assign_coords({gh2_dim: pulse_ids})
+        nds = nds.rename({gh2_dim: dim})
         mask = pattern.pulse_mask(labelled=False)
         mask = xr.DataArray(mask, dims=['trainId', dim],
                             coords={'trainId': run.train_ids,
                                     dim: np.arange(mask.shape[1])})
         mask = mask.sel({dim: pulse_ids})
         nds = nds.where(mask, drop=True)
-    return nds
+    ret = ds[others].merge(nds, join='inner')
+    return ret