updates to container.merge_spectra

	modified:   hera_pspec/container.py
	modified:   pipelines/pspec_pipeline/pspec_pipe.py

hera_pspec/container.py

@@ -317,9 +317,9 @@ def __del__(self):
             pass
 
 
-def merge_spectra(psc, dset_split_str='_x_', ext_split_str='_', verbose=True):
+def merge_spectra(psc, groups=None, dset_split_str='_x_', ext_split_str='_', verbose=True):
     """
-    Iterate through a PSpecContainer and, within each group,
+    Iterate through a PSpecContainer and, within each specified group,
     merge spectra of similar name but different psname extension.
 
     Power spectra to-be-merged are assumed to follow the naming convention
@@ -334,8 +334,11 @@ def merge_spectra(psc, dset_split_str='_x_', ext_split_str='_', verbose=True):
     feed dset_split_str as '' or None. Example, to merge together: uvp_1, uvp_2, uvp_3
     feed dset_split_str=None and ext_split_str='_'.
 
-    Parameters:
-    -----------
+    Parameters
+    ----------
+    groups : list
+        A list of groupnames to operate on. Default is all groups.
+
     dset_split_str : str
         The pattern used to split dset1 from dset2 in the psname.
 
@@ -350,8 +353,12 @@ def merge_spectra(psc, dset_split_str='_x_', ext_split_str='_', verbose=True):
         assert isinstance(psc, PSpecContainer)
 
     # get groups
-    groups = psc.groups()
-    assert len(groups) > 0, "no groups exist in this Container object"
+    _groups = psc.groups()
+    if groups is None:
+        groups = _groups
+    else:
+        groups = [grp for grp in groups if grp in _groups]
+    assert len(groups) > 0, "no specified groups exist in this Container object"
 
     # Iterate over groups
     for grp in groups:

pipelines/pspec_pipeline/pspec_pipe.py

@@ -67,7 +67,6 @@
 # change to working dir
 os.chdir(work_dir)
 
-
 #-------------------------------------------------------------------------------
 # Run Jacknife Data Difference
 #-------------------------------------------------------------------------------
@@ -149,15 +148,16 @@ def pspec(i, outfile=outfname, dt=data_template, st=std_template, jobs=jobs, pol
     hp.utils.log("\nStarting power spectrum file merge: {}\n{}".format(time, '-'*60), f=lf, verbose=verbose)
 
     # Get all groups
+    psc = hp.PSpecContainer(outfname, 'r')
     groups = psc.groups()
+    del psc
 
     # Define merge function
-    def merge(i, filename=filename, groups=groups):
+    def merge(i, groups=groups, filename=outfname):
         try:
             psc = hp.PSpecContainer(filename, mode='rw')
             grp = groups[i]
-            spectra = [os.path.join(grp, sp) for sp in psc.get_spectra(grp)]
-            hp.utils.merge_pspec(psc, spectra=spectra)
+            hp.container.merge_spectra(psc, groups=[grp])
         except:
             hp.utils.log("\nPSPEC MERGE job {} errored with:".format(i), f=ef, tb=sys.exc_info(), verbose=verbose)
             return 1