From 544d7f603aa93ba150ab824818f729088035957f Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Tue, 22 Oct 2024 15:48:31 -0400
Subject: [PATCH 01/15] initial commit. Changed name of another variable
 (is_zero) to avoid confusion.

---
 drizzlepac/haputils/analyze.py | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 8751f2f9b..7a8ce258c 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -16,7 +16,7 @@
 
 from enum import Enum
 from astropy.io import fits
-from astropy.io.fits import getheader
+from astropy.io.fits import getheader, getdata
 from astropy.table import Table
 from astropy.stats import sigma_clipped_stats
 import numpy as np
@@ -364,6 +364,8 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
     for i, input_file in enumerate(input_file_list):
         header_hdu = 0
         header_data = getheader(input_file, header_hdu)
+        science_hdu = 1
+        science_data = getdata(input_file, science_hdu)
 
         # Keywords to use potentially for downstream analysis
         instrume = (header_data['INSTRUME']).upper()
@@ -424,14 +426,18 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
 
         # Determine if the image has one of these conditions.  The routine
         # will exit processing upon the first satisfied condition.
+        
+        # Science image array is filled with zero values
+        science_array_of_zeros = True if np.all(science_data==0) else False
 
         # Compute if the exposure time is very close to zero as it will be
         # needed when deciding whether or not to use the particular Grism/Prism data
-        is_zero = True if math.isclose(exptime, 0.0, abs_tol=1e-5) else False
+        exposure_time_near_zero = True if math.isclose(exptime, 0.0, abs_tol=1e-5) else False
 
         no_proc_key = None
         no_proc_value = None
         do_process = True
+                
         # Imaging vs spectroscopic or coronagraphic
         if obstype != 'IMAGING':
             no_proc_key = hdr_keys['OBSKEY']
@@ -494,7 +500,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         split_sfilter = sfilter.upper().split('_')
         for item in split_sfilter:
             # This is the only circumstance when Grism/Prism data WILL be processed.
-            if item.startswith(('G', 'PR')) and not is_zero and type.upper() == "SVM":
+            if item.startswith(('G', 'PR')) and not exposure_time_near_zero and type.upper() == "SVM":
                 no_proc_key = None
                 no_proc_value = None
                 log.info("The Grism/Prism data, {}, will be processed.".format(input_file))
@@ -503,7 +509,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
                 if type.upper() == "MVM":
                     no_proc_value += ", Grism/Prism data and MVM processing"
                     log.warning("The Grism/Prism data {} with MVM processing will be ignored.".format(input_file))
-                elif is_zero:
+                elif exposure_time_near_zero:
                     no_proc_value += ", Grism/Prism data and EXPTIME = 0.0"
                     log.warning("The Grism/Prism data {} with zero exposure time will be ignored.".format(input_file))
     
@@ -533,6 +539,10 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
             # GYROS mode so some drift)
             generate_msg(input_file, msg_type, no_proc_key, no_proc_value)
         
+        elif science_array_of_zeros:
+            do_process=False
+            log.warning(f'Science data for {input_file} filled with zeros, not aligning.')
+            
         else:
             analyze_data_good_index.append(i)
 

From 8371898b9c55a18dfea9c62f16027ba75f2a5428 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Wed, 23 Oct 2024 14:49:09 -0400
Subject: [PATCH 02/15] added changelog entry.

---
 CHANGELOG.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 7c7c57f80..21e8012dd 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -21,6 +21,8 @@ number of the code change for that issue.  These PRs can be viewed at:
 3.7.2 (unreleased)
 ==================
 
+- Ensure that exposures with science data of all zeros is not processed. [#998]
+
 - Modifications to support an upgrade to Photutils v1.13.0. Changes were made
   to accommodate new APIs, modified low-level functionality, and address columns
   of a table in get_cutouts() by name rather than position to ensure the correct

From b84b29f1cce943d9d079aa70c63e0166df9226e4 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 12:50:28 -0400
Subject: [PATCH 03/15] ammeded count_sci_extension for analyze.py

---
 drizzlepac/haputils/analyze.py | 21 +++++++++++++++------
 drizzlepac/util.py             | 12 +++++++++---
 2 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 7a8ce258c..6e6d84fa2 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -31,6 +31,7 @@
 from stsci.tools.bitmask import bitfield_to_boolean_mask
 
 from .astrometric_utils import classify_sources
+from ..util import count_sci_extensions
 
 __taskname__ = 'analyze'
 
@@ -364,8 +365,6 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
     for i, input_file in enumerate(input_file_list):
         header_hdu = 0
         header_data = getheader(input_file, header_hdu)
-        science_hdu = 1
-        science_data = getdata(input_file, science_hdu)
 
         # Keywords to use potentially for downstream analysis
         instrume = (header_data['INSTRUME']).upper()
@@ -427,8 +426,18 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         # Determine if the image has one of these conditions.  The routine
         # will exit processing upon the first satisfied condition.
         
-        # Science image array is filled with zero values
-        science_array_of_zeros = True if np.all(science_data==0) else False
+        # Check if all science image arrays are filled with zero values
+        non_zero_data_in_array = False # start assuming data is zeros
+        science_ext_ind_array = count_sci_extensions(input_file_list, return_ind=True)
+        # make sure science extesion exists
+        if len(science_ext_ind_array)>0:
+            for sci_ext_ind in science_ext_ind_array:
+                science_data = getdata(input_file, sci_ext_ind)
+                # change flag if good data in any science array
+                if np.all(science_data==0):
+                    non_zero_data_in_array = True
+        else:
+            raise ValueError(f'No science extension in file: {input_file}')
 
         # Compute if the exposure time is very close to zero as it will be
         # needed when deciding whether or not to use the particular Grism/Prism data
@@ -539,9 +548,9 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
             # GYROS mode so some drift)
             generate_msg(input_file, msg_type, no_proc_key, no_proc_value)
         
-        elif science_array_of_zeros:
+        elif non_zero_data_in_array==False:
             do_process=False
-            log.warning(f'Science data for {input_file} filled with zeros, not aligning.')
+            log.warning(f'Science data for {input_file} filled with zeros. Dataset cannot be aligned.')
             
         else:
             analyze_data_good_index.append(i)
diff --git a/drizzlepac/util.py b/drizzlepac/util.py
index f62b6e182..53db89735 100644
--- a/drizzlepac/util.py
+++ b/drizzlepac/util.py
@@ -436,17 +436,19 @@ def updateNEXTENDKw(fobj):
     if 'nextend' in fobj[0].header:
         fobj[0].header['nextend'] = len(fobj) - 1
 
-def count_sci_extensions(filename):
+def count_sci_extensions(filename, return_ind=False):
     """ Return the number of SCI extensions and the EXTNAME from a input MEF file.
     """
     num_sci = 0
+    index=[]
     extname = 'SCI'
 
     hdu_list = fileutil.openImage(filename, memmap=False)
 
-    for extn in hdu_list:
+    for i, extn in enumerate(hdu_list):
         if 'extname' in extn.header and extn.header['extname'] == extname:
             num_sci += 1
+            index.append(i)
 
     if num_sci == 0:
         extname = 'PRIMARY'
@@ -454,7 +456,11 @@ def count_sci_extensions(filename):
 
     hdu_list.close()
 
-    return num_sci, extname
+    if return_ind:
+        return index
+    
+    else:
+        return num_sci, extname
 
 
 def verifyUniqueWcsname(fname, wcsname, include_primary=True):

From d701a7583330d56ae3f63bbebfad13071f59809c Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 13:51:12 -0400
Subject: [PATCH 04/15] added warning message.

---
 drizzlepac/haputils/analyze.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 6e6d84fa2..9f72d0396 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -436,6 +436,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
                 # change flag if good data in any science array
                 if np.all(science_data==0):
                     non_zero_data_in_array = True
+                    log.warning(f'Warning, (SCI, {sci_ext_ind}) is all zeros, but processing will continue')
         else:
             raise ValueError(f'No science extension in file: {input_file}')
 
@@ -533,6 +534,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
 
         # If no_proc_key is set to a keyword, then this image has been found to not be viable for
         # alignment purposes.
+        import ipdb; ipdb.set_trace()
         if no_proc_key is not None:
             if no_proc_key != hdr_keys['FGSKEY']:
                 do_process = False
@@ -547,7 +549,6 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
             # processing should be allowed, but there may be some issue with the result (e.g.,
             # GYROS mode so some drift)
             generate_msg(input_file, msg_type, no_proc_key, no_proc_value)
-        
         elif non_zero_data_in_array==False:
             do_process=False
             log.warning(f'Science data for {input_file} filled with zeros. Dataset cannot be aligned.')

From a30afff7a7d268a74738cb76b0e0b352f9b774c0 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 14:16:42 -0400
Subject: [PATCH 05/15] fixed bug, better warning message with filename.

---
 drizzlepac/haputils/analyze.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 9f72d0396..9a1a35ef0 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -428,7 +428,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         
         # Check if all science image arrays are filled with zero values
         non_zero_data_in_array = False # start assuming data is zeros
-        science_ext_ind_array = count_sci_extensions(input_file_list, return_ind=True)
+        science_ext_ind_array = count_sci_extensions(input_file, return_ind=True)
         # make sure science extesion exists
         if len(science_ext_ind_array)>0:
             for sci_ext_ind in science_ext_ind_array:
@@ -436,7 +436,8 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
                 # change flag if good data in any science array
                 if np.all(science_data==0):
                     non_zero_data_in_array = True
-                    log.warning(f'Warning, (SCI, {sci_ext_ind}) is all zeros, but processing will continue')
+                    log.warning(f'{input_file} (SCI, {sci_ext_ind}) is all zeros, 
+                                but processing will continue with the other science extensions.')
         else:
             raise ValueError(f'No science extension in file: {input_file}')
 
@@ -534,7 +535,6 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
 
         # If no_proc_key is set to a keyword, then this image has been found to not be viable for
         # alignment purposes.
-        import ipdb; ipdb.set_trace()
         if no_proc_key is not None:
             if no_proc_key != hdr_keys['FGSKEY']:
                 do_process = False

From 481e40eae08d7c916d719473ece04ce9a03b9e22 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 14:22:09 -0400
Subject: [PATCH 06/15] linting issue.

---
 drizzlepac/haputils/analyze.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 9a1a35ef0..85e0f06d0 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -86,7 +86,7 @@
 
 MIN_LINES = 4  # Minimum number of detected lines for consideration of bad guiding
 
-# Return codes 
+# Return codes
 class Ret_code(Enum):
     """
     Define return status codes for Operations 
@@ -305,7 +305,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
     log.setLevel(log_level)
 
     analyze_data_good_index = []
-    
+
     acs_filt_name_list = [DEFAULT_KEYS['FILKEY1'], DEFAULT_KEYS['FILKEY2']]
 
     # Interpret input filenames and adjust size of column accordingly
@@ -425,7 +425,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
 
         # Determine if the image has one of these conditions.  The routine
         # will exit processing upon the first satisfied condition.
-        
+
         # Check if all science image arrays are filled with zero values
         non_zero_data_in_array = False # start assuming data is zeros
         science_ext_ind_array = count_sci_extensions(input_file, return_ind=True)
@@ -436,8 +436,9 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
                 # change flag if good data in any science array
                 if np.all(science_data==0):
                     non_zero_data_in_array = True
-                    log.warning(f'{input_file} (SCI, {sci_ext_ind}) is all zeros, 
-                                but processing will continue with the other science extensions.')
+                    log.warning(
+                        f"{input_file} (SCI, {sci_ext_ind}) is all zeros, but processing will continue with the other science extensions."
+                    )
         else:
             raise ValueError(f'No science extension in file: {input_file}')
 
@@ -448,7 +449,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         no_proc_key = None
         no_proc_value = None
         do_process = True
-                
+
         # Imaging vs spectroscopic or coronagraphic
         if obstype != 'IMAGING':
             no_proc_key = hdr_keys['OBSKEY']
@@ -523,7 +524,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
                 elif exposure_time_near_zero:
                     no_proc_value += ", Grism/Prism data and EXPTIME = 0.0"
                     log.warning("The Grism/Prism data {} with zero exposure time will be ignored.".format(input_file))
-    
+
             if item.startswith(('BLOCK')):
                 no_proc_key = hdr_keys['FILKEY']
                 no_proc_value = sfilter
@@ -552,7 +553,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         elif non_zero_data_in_array==False:
             do_process=False
             log.warning(f'Science data for {input_file} filled with zeros. Dataset cannot be aligned.')
-            
+
         else:
             analyze_data_good_index.append(i)
 

From 93953fbe2d9e3528f108b0c2f260624ecb8659aa Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:01:56 -0400
Subject: [PATCH 07/15] fixed flag. error changed to warning.

---
 drizzlepac/haputils/analyze.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 85e0f06d0..8c7bc762a 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -432,15 +432,16 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         # make sure science extesion exists
         if len(science_ext_ind_array)>0:
             for sci_ext_ind in science_ext_ind_array:
+                import ipdb; ipdb.set_trace()
                 science_data = getdata(input_file, sci_ext_ind)
-                # change flag if good data in any science array
-                if np.all(science_data==0):
+                # change flag if good data in any science extensnion array
+                if np.logical_not(np.all(science_data==0)):
                     non_zero_data_in_array = True
                     log.warning(
                         f"{input_file} (SCI, {sci_ext_ind}) is all zeros, but processing will continue with the other science extensions."
                     )
         else:
-            raise ValueError(f'No science extension in file: {input_file}')
+            log.warning(f'No science extension in file: {input_file}')
 
         # Compute if the exposure time is very close to zero as it will be
         # needed when deciding whether or not to use the particular Grism/Prism data

From 516c3bc4cd3f209f9fb077f2b70f14009f708835 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:03:02 -0400
Subject: [PATCH 08/15] remove set_trace.

---
 drizzlepac/haputils/analyze.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 8c7bc762a..35964c064 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -432,7 +432,6 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         # make sure science extesion exists
         if len(science_ext_ind_array)>0:
             for sci_ext_ind in science_ext_ind_array:
-                import ipdb; ipdb.set_trace()
                 science_data = getdata(input_file, sci_ext_ind)
                 # change flag if good data in any science extensnion array
                 if np.logical_not(np.all(science_data==0)):

From 04878ca399a0dd9d60b1434968e138142679671f Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:50:50 -0400
Subject: [PATCH 09/15] documentation for ammendment to count_sci_extensions
 function.

---
 drizzlepac/util.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/drizzlepac/util.py b/drizzlepac/util.py
index 53db89735..6e93a8eec 100644
--- a/drizzlepac/util.py
+++ b/drizzlepac/util.py
@@ -438,7 +438,21 @@ def updateNEXTENDKw(fobj):
 
 def count_sci_extensions(filename, return_ind=False):
     """ Return the number of SCI extensions and the EXTNAME from a input MEF file.
-    """
+
+    Parameters
+    ----------
+    filename : str
+        Filename of the file you would like to count the extensions of. 
+    return_ind : bool, optional
+        Whether to return a list of the indices of the true "SCI" science extensions, 
+        by default False.
+
+    Returns
+    -------
+    _type_
+        _description_
+    """    
+
     num_sci = 0
     index=[]
     extname = 'SCI'

From fe2bd19422ea063776a47571933a15e7f1fe3af3 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:53:06 -0400
Subject: [PATCH 10/15] comments for returns of count_sci_extensions.

---
 drizzlepac/util.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/drizzlepac/util.py b/drizzlepac/util.py
index 6e93a8eec..abdeaadb1 100644
--- a/drizzlepac/util.py
+++ b/drizzlepac/util.py
@@ -449,8 +449,13 @@ def count_sci_extensions(filename, return_ind=False):
 
     Returns
     -------
-    _type_
-        _description_
+    tuple
+        Science extension and number of extensions. 
+    
+    or (if return_ind=True)
+    
+    list
+        indices of the "SCI" science extensions. 
     """    
 
     num_sci = 0

From d252a329e1e4f1551ee9c15ebcdd1de29319ba3a Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 15:59:20 -0400
Subject: [PATCH 11/15] RAW file comment.

---
 drizzlepac/haputils/analyze.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 35964c064..7d1bda9be 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -426,7 +426,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         # Determine if the image has one of these conditions.  The routine
         # will exit processing upon the first satisfied condition.
 
-        # Check if all science image arrays are filled with zero values
+        # Check if all science image arrays in the RAW file are filled with zero values
         non_zero_data_in_array = False # start assuming data is zeros
         science_ext_ind_array = count_sci_extensions(input_file, return_ind=True)
         # make sure science extesion exists

From a1e466aa3a443c8595f41678d9d680bce0849aa2 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:01:48 -0400
Subject: [PATCH 12/15] np.logical not --> not, spelling mistake.

---
 drizzlepac/haputils/analyze.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 7d1bda9be..29a743ee2 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -429,12 +429,12 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         # Check if all science image arrays in the RAW file are filled with zero values
         non_zero_data_in_array = False # start assuming data is zeros
         science_ext_ind_array = count_sci_extensions(input_file, return_ind=True)
-        # make sure science extesion exists
+        # make sure science extension exists
         if len(science_ext_ind_array)>0:
             for sci_ext_ind in science_ext_ind_array:
                 science_data = getdata(input_file, sci_ext_ind)
                 # change flag if good data in any science extensnion array
-                if np.logical_not(np.all(science_data==0)):
+                if not np.all(science_data==0):
                     non_zero_data_in_array = True
                     log.warning(
                         f"{input_file} (SCI, {sci_ext_ind}) is all zeros, but processing will continue with the other science extensions."

From fba40a116a87bbf9e4bbca8dd5e9554b1a68fe34 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:13:10 -0400
Subject: [PATCH 13/15] warning in correct bool.

---
 drizzlepac/haputils/analyze.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 29a743ee2..fab0047bb 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -436,9 +436,11 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
                 # change flag if good data in any science extensnion array
                 if not np.all(science_data==0):
                     non_zero_data_in_array = True
+                else:
                     log.warning(
                         f"{input_file} (SCI, {sci_ext_ind}) is all zeros, but processing will continue with the other science extensions."
                     )
+    
         else:
             log.warning(f'No science extension in file: {input_file}')
 

From fce11ebbdb0f217a27e4f0ff703d8239c88e987f Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:25:30 -0400
Subject: [PATCH 14/15] spelling mistake.

---
 drizzlepac/haputils/analyze.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index fab0047bb..9bdd81f6b 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -433,7 +433,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
         if len(science_ext_ind_array)>0:
             for sci_ext_ind in science_ext_ind_array:
                 science_data = getdata(input_file, sci_ext_ind)
-                # change flag if good data in any science extensnion array
+                # change flag if good data in any science extension array
                 if not np.all(science_data==0):
                     non_zero_data_in_array = True
                 else:

From 98bbb9d2cd3e687308199ad8ff78aa9caffffe57 Mon Sep 17 00:00:00 2001
From: Steve Goldman <32876747+s-goldman@users.noreply.github.com>
Date: Mon, 28 Oct 2024 16:28:05 -0400
Subject: [PATCH 15/15] added process_msg.

---
 drizzlepac/haputils/analyze.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/drizzlepac/haputils/analyze.py b/drizzlepac/haputils/analyze.py
index 9bdd81f6b..7b206dd36 100644
--- a/drizzlepac/haputils/analyze.py
+++ b/drizzlepac/haputils/analyze.py
@@ -554,6 +554,7 @@ def analyze_data(input_file_list, log_level=logutil.logging.DEBUG, type=""):
             generate_msg(input_file, msg_type, no_proc_key, no_proc_value)
         elif non_zero_data_in_array==False:
             do_process=False
+            process_msg="SCI data all zeros"
             log.warning(f'Science data for {input_file} filled with zeros. Dataset cannot be aligned.')
 
         else: