zproc run group_spectra vs. coadd_spectra

py/desispec/scripts/coadd_spectra.py

@@ -8,6 +8,7 @@
 from __future__ import absolute_import, division, print_function
 
 import os,sys
+import argparse
 import numpy as np
 from astropy.table import Table
 import fitsio
@@ -19,7 +20,6 @@
 from desispec.specscore import compute_coadd_scores
 
 def parse(options=None):
-    import argparse
 
     parser = argparse.ArgumentParser("Coadd all spectra per target, and optionally resample on linear or logarithmic wavelength grid")
     parser.add_argument("-i","--infile", type=str, nargs='+',
@@ -54,11 +54,11 @@ def parse(options=None):
     return args
 
 def main(args=None):
-
     log = get_logger()
 
-    if args is None:
-        args = parse()
+    #- Parse None or list of strings of command line opts
+    if not isinstance(args, argparse.Namespace):
+        args = parse(options=args)
 
     if args.lin_step is not None and args.log10_step is not None :
         log.critical("cannot have both linear and logarthmic bins :-), choose either --lin-step or --log10-step")

py/desispec/scripts/zproc.py

@@ -38,7 +38,7 @@
     camword_to_spectros, columns_to_goodcamword, difference_camwords
 from desispec.io.util import validate_badamps, get_tempfilename, backup_filename
 from desispec.util import runcmd
-from desispec.scripts import group_spectra
+from desispec.scripts import group_spectra, coadd_spectra
 from desispec.parallel import stdouterr_redirected
 from desispec.workflow import batch
 from desispec.workflow.exptable import get_exposure_table_pathname, \
@@ -529,30 +529,43 @@ def main(args=None, comm=None):
             splog = findfile('spectra', logfile=True, **findfileopts)
             coaddfile = findfile('coadd', **findfileopts)
 
-            cmd = f"desi_group_spectra --inframes {' '.join(cframes)} " \
-                  + f"--outfile {spectrafile} " \
-                  + f"--coaddfile {coaddfile} "
+            if os.path.exists(spectrafile):
+                log.info(f'Spectra file {os.path.basename(spectrafile)} already exists; only running coaddition')
+                group_func = coadd_spectra.main
+                inputs = [spectrafile,]
+                outputs = [coaddfile,]
+                cmd = f"desi_coadd_spectra -i {spectrafile} -o {coaddfile}"
+                if groupname != 'healpix':
+                    cmd += ' --onetile'
 
-            if groupname == 'healpix':
-                cmd += f"--healpix {healpix} "
-                cmd += f"--header SURVEY={args.survey} PROGRAM={args.program} "
             else:
-                cmd += "--onetile "
-                cmd += (f"--header SPGRP={groupname} SPGRPVAL={thrunight} "
-                        f"NIGHT={thrunight} TILEID={tileid} SPECTRO={spectro} PETAL={spectro} ")
+                group_func = group_spectra.main
+                inputs = cframes
+                outputs = [spectrafile, coaddfile]
+                cmd = f"desi_group_spectra --inframes {' '.join(cframes)} " \
+                      + f"--outfile {spectrafile} " \
+                      + f"--coaddfile {coaddfile} "
+
+                if groupname == 'healpix':
+                    cmd += f"--healpix {healpix} "
+                    cmd += f"--header SURVEY={args.survey} PROGRAM={args.program} "
+                else:
+                    cmd += "--onetile "
+                    cmd += (f"--header SPGRP={groupname} SPGRPVAL={thrunight} "
+                            f"NIGHT={thrunight} TILEID={tileid} SPECTRO={spectro} PETAL={spectro} ")
 
-                if groupname == 'perexp':
-                    cmd += f'EXPID={expids[0]} '
+                    if groupname == 'perexp':
+                        cmd += f'EXPID={expids[0]} '
 
             cmdargs = cmd.split()[1:]
             if args.dryrun:
                 if rank == 0:
                     log.info(f"dryrun: Would have run {cmd}")
             else:
                 with stdouterr_redirected(splog):
-                    result, success = runcmd(group_spectra.main,
-                                             args=cmdargs, inputs=cframes,
-                                             outputs=[spectrafile, coaddfile])
+                    result, success = runcmd(group_func,
+                                             args=cmdargs, inputs=inputs,
+                                             outputs=outputs)
 
             if not success:
                 log.error(f'desi_group_spectra petal {spectro} failed; see {splog}')