Merge pull request #219 from GeminiDRSoftware/feature/cleanskysub

add rejection of frames that cannot be sky subtracted to avoid contamination of the good ones.

doc/DRAGONS/changes.rst

@@ -6,7 +6,46 @@
 Change Logs
 ***********
 
-[KL: TO REMOVE BEFORE RELEASE.  Last update up to commit  Thu Sep 17 16:57 HST 2020]
+[KL: TO REMOVE BEFORE RELEASE.  Last update up to commit ... need commits
+review since beginning of branch.]
+
+3.0.0
+=====
+
+This release includes new support for GMOS longslit data.  Reduction of
+GMOS longslit data is offered only quicklook mode.  It does not produce
+science quality outputs, yet.
+
+Bug Fixes
+---------
+
+* In imaging mode, the science recipes now include a call to
+``scaleByExposureTime`` before the stacking step.  It is now possible to stack
+frames with different exposure times.
+* In near-IR imaging mode, frames that fail to be sky subtracted are removed
+from the main reduction stream to avoid contamination.  The reduction continues
+with the "good" frames.  If all frames fail the sky subtraction, then all
+frames will be passed to the next step of the reduction.
+
+New Features
+------------
+
+* Quicklook (``ql`` mode) reduction support for GMOS longslit data.
+
+Compatibility
+-------------
+
+* Python 2 support has been dropped.  Starting with v3.0.0, DRAGONS requires
+Python 3.   All tests were run on Python 3.7, and this version of Python
+now serves as the minimal required version.
+
+
+Documentation
+-------------
+
+(KL: When we add them:  New tutorial for the reduction of GMOS longslit data.)
+
+
 
 2.1.2
 =====

geminidr/core/primitives_preprocess.py

@@ -273,6 +273,7 @@ def associateSky(self, adinputs=None, **params):
             ad.update_filename(suffix=sfx, strip=True)
             gt.mark_history(ad, primname=self.myself(), keyword=timestamp_key)
 
+        has_skytable = [False] * len(adinputs)
         if not adinputs or not ad_skies:
             log.warning("Cannot associate sky frames, since at least one "
                         "science AstroData object and one sky AstroData "
@@ -283,7 +284,7 @@ def associateSky(self, adinputs=None, **params):
             sky_times = dict(zip(ad_skies,
                                  [ad.ut_datetime() for ad in ad_skies]))
 
-            for ad in adinputs:
+            for i, ad in enumerate(adinputs):
                 # If use_all is True, use all of the sky AstroData objects for
                 # each science AstroData object
                 if params["use_all"]:
@@ -330,11 +331,32 @@ def associateSky(self, adinputs=None, **params):
                     for sky in sky_list:
                         log.stdinfo("  {}".format(sky.filename))
                     ad.SKYTABLE = sky_table
+                    has_skytable[i] = True
                 else:
                     log.warning("No sky frames available for {}".format(ad.filename))
 
         # Need to update sky stream in case it came from the "sky" parameter
         self.streams['sky'] = ad_skies
+
+        # if none of frames have sky tables, just pass them all through
+        # if only some frames did not have sky corrected, move them out of main and
+        # to the "no_skytable" stream.
+        if not any(has_skytable):  # "all false", none have been sky corrected
+            log.warning('Sky frames could not be associated to any input frames.'
+                        'Sky subtraction will not be possible.')
+        elif not all(has_skytable):  # "some false", some frames were NOT sky corrected
+            log.stdinfo('')  # for readablity
+            false_idx = [idx for idx, trueval in enumerate(has_skytable) if not trueval]
+            for idx in reversed(false_idx):
+                ad = adinputs[idx]
+                log.warning(f'{(ad.filename} does not have any associated sky '
+                            'cannot be sky-subtracted, moving to "no_skies" stream')
+                if "no_skies" in self.streams:
+                    self.streams["no_skies"].append(ad)
+                else:
+                    self.streams["no_skies"] = [ad]
+                del adinputs[idx]
+
         return adinputs
 
     def correctBackgroundToReference(self, adinputs=None, suffix=None,

geminidr/core/primitives_resample.py

@@ -256,7 +256,6 @@ def _resample_to_new_frame(self, adinputs=None, frame=None, order=3,
             output_shape = tuple(int(np.floor(max(corners)) - np.ceil(min(corners)) + 1)
                                  for corners in all_corners)
 
-        print("ORIGIN", origin)
         log.stdinfo("Output image will have shape "+repr(output_shape[::-1]))
         adoutputs = []
         for ad in adinputs: