From a4e36d7109041ed1f04bae3e2ca42cb193468857 Mon Sep 17 00:00:00 2001
From: stscicrawford <scrawford@stsci.edu>
Date: Sun, 28 Jul 2019 16:28:56 -0400
Subject: [PATCH 1/2] added better negative number handling to create_deviation

---
 CHANGES.rst                   |  6 ++++++
 ccdproc/core.py               | 21 ++++++++++++++++++---
 ccdproc/tests/test_ccdproc.py | 26 ++++++++++++++++++++++++++
 3 files changed, 50 insertions(+), 3 deletions(-)

diff --git a/CHANGES.rst b/CHANGES.rst
index 5c691017..af2e393f 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -13,6 +13,9 @@ New Features
 - Add option to use regular expression matching when filtering items in
   ``ImageFileCollection``. [#480, #595, #682]
 
+- Added an option to disregard negative values passed to ``create_deviation``
+  and assume the error is represented by the read noise [#688]
+
 Other Changes and Additions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -34,6 +37,9 @@ Other Changes and Additions
 - When creating a new object in ``wcs_transform``, WCS keywords in the header
   are removed so that they are only stored in the WCS object [#685]
 
+- Improved warning for negative values in the array passed to
+  ``create_deviation`` [#688]
+
 - Removed support for initializing ``ImageFileCollection`` from a table instead
   of files. [#680]
 
diff --git a/ccdproc/core.py b/ccdproc/core.py
index bbcdbf7b..5b711548 100644
--- a/ccdproc/core.py
+++ b/ccdproc/core.py
@@ -273,7 +273,7 @@ def ccd_process(ccd, oscan=None, trim=None, error=False, master_bias=None,
 
 
 @log_to_metadata
-def create_deviation(ccd_data, gain=None, readnoise=None):
+def create_deviation(ccd_data, gain=None, readnoise=None, disregard_nan=False):
     """
     Create a uncertainty frame. The function will update the uncertainty
     plane which gives the standard deviation for the data. Gain is used in
@@ -296,6 +296,10 @@ def create_deviation(ccd_data, gain=None, readnoise=None):
         Read noise per pixel.
         Default is ``None``.
 
+    disregard_nan: boolean
+        If ``True``, any value of nan in the output array will be replaced by
+        the readnoise.
+
     {log}
 
     Raises
@@ -331,9 +335,20 @@ def create_deviation(ccd_data, gain=None, readnoise=None):
     gain_value = float(gain / gain.unit)
     readnoise_value = float(readnoise / readnoise.unit)
 
-    var = (gain_value * ccd_data.data + readnoise_value ** 2) ** 0.5
-    ccd = ccd_data.copy()
+    # remove values that might be negative or treat as nan
+    data = gain_value * ccd_data.data
+    mask = (data < 0)
+    if disregard_nan:
+       data[mask] = 0
+    else:
+       data[mask] = np.nan
+       logging.warning('Negative values in array will be replaced with nan')
+
+    # calculate the deviation
+    var = (data + readnoise_value ** 2) ** 0.5
+
     # ensure uncertainty and image data have same unit
+    ccd = ccd_data.copy()
     var /= gain_value
     ccd.uncertainty = StdDevUncertainty(var)
     return ccd
diff --git a/ccdproc/tests/test_ccdproc.py b/ccdproc/tests/test_ccdproc.py
index 481ce797..26df786a 100644
--- a/ccdproc/tests/test_ccdproc.py
+++ b/ccdproc/tests/test_ccdproc.py
@@ -41,6 +41,7 @@
                          (u.adu, u.photon / u.adu, u.electron, False),
                          ])
 @pytest.mark.data_size(10)
+@pytest.mark.data_mean(100)
 def test_create_deviation(ccd_data, u_image, u_gain, u_readnoise,
                           expect_success):
     ccd_data.unit = u_image
@@ -69,6 +70,31 @@ def test_create_deviation(ccd_data, u_image, u_gain, u_readnoise,
             ccd_var = create_deviation(ccd_data, gain=gain, readnoise=readnoise)
 
 
+@pytest.mark.data_mean(0)
+@pytest.mark.data_scale(10)
+def test_create_deviation_from_negative(ccd_data):
+    ccd_data.unit = u.electron
+    readnoise = 5 * u.electron
+    ccd_var = create_deviation(ccd_data, gain=None, readnoise=readnoise,
+                               disregard_nan=False)
+    np.testing.assert_array_equal(ccd_data.data < 0,
+                                  np.isnan(ccd_var.uncertainty.array))
+
+
+@pytest.mark.data_mean(0)
+@pytest.mark.data_scale(10)
+def test_create_deviation_from_negative(ccd_data):
+    ccd_data.unit = u.electron
+    readnoise = 5 * u.electron
+    ccd_var = create_deviation(ccd_data, gain=None, readnoise=readnoise,
+                               disregard_nan=True)
+    mask = (ccd_data.data < 0)
+    ccd_data.data[mask] = 0
+    expected_var = np.sqrt(ccd_data.data + readnoise.value**2)
+    np.testing.assert_array_equal(ccd_var.uncertainty.array,
+                                  expected_var)
+
+
 def test_create_deviation_keywords_must_have_unit(ccd_data):
     # gain must have units if provided
     with pytest.raises(TypeError):

From 28ba7fe9eeb4a4a04572b7e448086f3f03f41488 Mon Sep 17 00:00:00 2001
From: stscicrawford <scrawford@stsci.edu>
Date: Sun, 28 Jul 2019 20:46:34 -0400
Subject: [PATCH 2/2] fix pep8

---
 ccdproc/core.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/ccdproc/core.py b/ccdproc/core.py
index 5b711548..e12515fa 100644
--- a/ccdproc/core.py
+++ b/ccdproc/core.py
@@ -339,10 +339,10 @@ def create_deviation(ccd_data, gain=None, readnoise=None, disregard_nan=False):
     data = gain_value * ccd_data.data
     mask = (data < 0)
     if disregard_nan:
-       data[mask] = 0
+        data[mask] = 0
     else:
-       data[mask] = np.nan
-       logging.warning('Negative values in array will be replaced with nan')
+        data[mask] = np.nan
+        logging.warning('Negative values in array will be replaced with nan')
 
     # calculate the deviation
     var = (data + readnoise_value ** 2) ** 0.5