From 132ffb1e1c1fc0e3d8a180aeaee74add38ad93c2 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Wed, 3 Apr 2024 09:39:03 -0400
Subject: [PATCH] HLA-1209 Bug fix that allows for user inputs in astrodrizzle
 with mdriztab=True (#1774)

---
 CHANGELOG.rst                |  2 ++
 drizzlepac/astrodrizzle.help | 18 ++++++++++++------
 drizzlepac/astrodrizzle.py   | 25 ++++++++++++-------------
 drizzlepac/processInput.py   | 16 +++++++++++-----
 4 files changed, 37 insertions(+), 24 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e4fa82909..1024d371d 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -26,6 +26,8 @@ number of the code change for that issue.  These PRs can be viewed at:
   source catalog before the corresponding bad segments are removed from the
   segmentation image. [#1771]
 
+- Bug fix for mdriztab=True option in Astrodrizzle previously overwriting user inputs. [#1774]
+
 - Reverted PR #1222 allowing pixels to be filled with available data where WHT=0. [#1767]
 
 - Improved calculation of S_REGION using dialation and erosion. [#1762]
diff --git a/drizzlepac/astrodrizzle.help b/drizzlepac/astrodrizzle.help
index a751637bf..0e7fe90dc 100644
--- a/drizzlepac/astrodrizzle.help
+++ b/drizzlepac/astrodrizzle.help
@@ -22,6 +22,12 @@ input : str or list of str (Default = ``'*flt.fits'``)
        will automatically generate the ``IVM`` files itself for each input
        exposure.
 
+mdriztab : bool (Default = False)
+    This button will immediately update the parameter values in the ``TEAL``
+    GUI based on those provided by the ``MDRIZTAB`` reference table referenced
+    in the first input image. This requires that the ``MDRIZTAB`` reference
+    file be available locally.
+
 editpars : bool (Default = False)
     A parameter that allows user to edit input parameters by hand in the GUI.
     ``True`` to use the GUI to edit parameters.
@@ -39,6 +45,12 @@ configobj : ConfigObjPars, ConfigObj, dict (Default = None)
     parameters not provided explicitly will be initialized with their
     default values as described in the "Other Parameters" section.
 
+wcsmap : wcs_functions.WCSMap, None (Default = None)
+    An instance of ``wcs_functions.WCSMap`` which can be used to override the
+    default ``WCS`` mapping for the input images. This parameter is used to
+    specify the mapping between the input images and the output frame. If
+    ``None`` is provided, then the default ``WCS`` mapping will be used.
+
 input_dict : dict, optional
     An optional list of parameters specified by the user, which can also
     be used to override the defaults.
@@ -73,12 +85,6 @@ output : str (Default = '')
     wild-card specification is given as input, then a rootname of ``'final'``
     will be used for the output file name.
 
-mdriztab : bool (Default = False)
-    This button will immediately update the parameter values in the ``TEAL``
-    GUI based on those provided by the ``MDRIZTAB`` reference table referenced
-    in the first input image. This requires that the ``MDRIZTAB`` reference
-    file be available locally.
-
 runfile : str (Default = 'astrodrizzle.log')
    This log file will contain all the output messages generated during
    processing, including full details of any errors/exceptions.
diff --git a/drizzlepac/astrodrizzle.py b/drizzlepac/astrodrizzle.py
index 539121f78..969fe60d4 100644
--- a/drizzlepac/astrodrizzle.py
+++ b/drizzlepac/astrodrizzle.py
@@ -109,20 +109,16 @@ def AstroDrizzle(input=None, mdriztab=False, editpars=False, configobj=None,
         print("Problem with input parameters. Quitting...", file=sys.stderr)
         return
 
-    if not configObj:
-        return
-
+    # add flag to configObj to indicate whether or not to use mdriztab
     configObj['mdriztab'] = mdriztab
-    # If 'editpars' was set to True, util.getDefaultConfigObj() will have
-    # already called 'run()'.
-    if not editpars:
-        run(configObj, wcsmap=wcsmap)
+    
+    run(configObj, wcsmap=wcsmap, input_dict=input_dict)
 
 ##############################
 #   Interfaces used by TEAL  #
 ##############################
 @util.with_logging
-def run(configobj, wcsmap=None):
+def run(configobj, wcsmap=None, input_dict=None):
     """
     Initial example by Nadia ran MD with configobj EPAR using:
     It can be run in one of two ways:
@@ -139,6 +135,8 @@ def run(configobj, wcsmap=None):
         teal.teal('astrodrizzle')
 
         The example config files are in drizzlepac/pars
+        
+    input_dict is a dictionary of user-specified parameters
 
     """
     # turn on logging, redirecting stdout/stderr messages to a log file
@@ -185,8 +183,10 @@ def run(configobj, wcsmap=None):
         # based on input paramters
         imgObjList = None
         procSteps.addStep('Initialization')
-        imgObjList, outwcs = processInput.setCommonInput(configobj)
-        procSteps.endStep('Initialization')
+        imgObjList, outwcs = processInput.setCommonInput(
+            configobj, overwrite_dict=input_dict
+        )
+        procSteps.endStep("Initialization")
 
         if imgObjList is None or not imgObjList:
             errmsg = "No valid images found for processing!\n"
@@ -210,14 +210,14 @@ def run(configobj, wcsmap=None):
         # subtract the sky
         sky.subtractSky(imgObjList, configobj, procSteps=procSteps)
 
-#       _dbg_dump_virtual_outputs(imgObjList)
+        #       _dbg_dump_virtual_outputs(imgObjList)
 
         # drizzle to separate images
         adrizzle.drizSeparate(imgObjList, outwcs, configobj, wcsmap=wcsmap,
                               logfile=logfile,
                               procSteps=procSteps)
 
-#       _dbg_dump_virtual_outputs(imgObjList)
+        #       _dbg_dump_virtual_outputs(imgObjList)
 
         # create the median images from the driz sep images
         createMedian.createMedian(imgObjList, configobj, procSteps=procSteps)
@@ -239,7 +239,6 @@ def run(configobj, wcsmap=None):
               .format(__version__, util._ptime()[0]))
         print("", flush=True)
 
-
     except Exception:
         clean = False
         print(textutil.textbox(
diff --git a/drizzlepac/processInput.py b/drizzlepac/processInput.py
index f54539bed..49e76d13b 100644
--- a/drizzlepac/processInput.py
+++ b/drizzlepac/processInput.py
@@ -59,7 +59,7 @@
     import multiprocessing
 
 
-def setCommonInput(configObj, createOutwcs=True):
+def setCommonInput(configObj, createOutwcs=True, overwrite_dict={}):
     """
     The common interface interpreter for MultiDrizzle tasks which not only runs
     'process_input()' but 'createImageObject()' and 'defineOutput()' as well to
@@ -70,10 +70,11 @@ def setCommonInput(configObj, createOutwcs=True):
     ----------
     configObj : object
         configObj instance or simple dictionary of input parameters
-    imageObjectList : list of imageObject objects
-        list of imageObject instances, 1 for each input exposure
-    outwcs : object
-        imageObject instance defining the final output frame
+    createOutwcs : bool
+        whether of not to update the output WCS infomation
+    overwrite_dict: dict
+        dictionary of user input paramters to overwrite in configObj 
+        (needed in particular for using mdriztab=True option)
 
     Notes
     -----
@@ -129,6 +130,11 @@ def setCommonInput(configObj, createOutwcs=True):
 
         # Update configObj with values from mpars
         cfgpars.mergeConfigObj(configObj, mdriztab_dict)
+    
+    if overwrite_dict:
+        # user inputs are removed in above line, we need to add them back
+        # overwrite values in configObj with those from the input_dict
+        cfgpars.mergeConfigObj(configObj, overwrite_dict)
 
     # Convert interpreted list of input files from process_input into a list
     # of imageObject instances for use by the MultiDrizzle tasks.