Switch to MaskedImage to pass mask to ensure match with previous code.

lsst · May 17, 2022 · bb26e3d · bb26e3d
1 parent c4307e1
commit bb26e3d
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Showing 4 changed files with 26 additions and 15 deletions.
diff --git a/include/lsst/ip/isr/isr.h b/include/lsst/ip/isr/isr.h
@@ -99,7 +99,8 @@ namespace isr {
 
     template<typename ImagePixelT>
     std::vector<double> fitOverscanImage(
-        lsst::afw::image::Image<ImagePixelT> const& overscan,
+        lsst::afw::image::MaskedImage<ImagePixelT> const& overscan,
+        std::vector<std::string> badPixelMask,
         bool isTransposed
         );
 

diff --git a/python/lsst/ip/isr/isr.cc b/python/lsst/ip/isr/isr.cc
@@ -60,7 +60,8 @@ static void declareAll(py::module& mod, std::string const& suffix) {
     declareCountMaskedPixels<PixelT>(mod, suffix);
 
     mod.def("maskNans", &maskNans<PixelT>, "maskedImage"_a, "maskVal"_a, "allow"_a = 0);
-    mod.def("fitOverscanImage", &fitOverscanImage<PixelT>, "maskedImage"_a, "isTransposed"_a);
+    mod.def("fitOverscanImage", &fitOverscanImage<PixelT>,
+            "maskedImage"_a, "badPixelMask"_a, "isTransposed"_a);
 }
 
 }  // namespace lsst::ip::isr::<anonymous>

diff --git a/python/lsst/ip/isr/overscan.py b/python/lsst/ip/isr/overscan.py
@@ -65,7 +65,7 @@ class OverscanCorrectionTaskConfig(pexConfig.Config):
     maskPlanes = pexConfig.ListField(
         dtype=str,
         doc="Mask planes to reject when measuring overscan",
-        default=['SAT'],
+        default=['BAD', 'SAT'],
     )
     overscanIsInt = pexConfig.Field(
         dtype=bool,
@@ -479,11 +479,18 @@ def measureVectorOverscan(self, image):
         masked = self.maskOutliers(calcImage)
 
         startTime = time.perf_counter()
+
         if self.config.fitType == 'MEDIAN_PER_ROW':
-            if isinstance(image, afwImage.MaskedImage):
-                overscanVector = fitOverscanImage(image.getImage(), isTransposed)
-            else:
-                overscanVector = fitOverscanImage(image, isTransposed)
+            mi = afwImage.MaskedImageI(image.getBBox())
+            masked = masked.astype(int)
+            if isTransposed:
+                masked = masked.transpose()
+
+            mi.getImage().getArray()[:, :] = masked.data[:, :]
+            if bool(masked.mask.shape):
+                mi.getMask().getArray()[:, :] = masked.mask[:, :]
+
+            overscanVector = fitOverscanImage(mi, self.config.maskPlanes, isTransposed)
             maskArray = self.maskExtrapolated(overscanVector)
         else:
             collapsed = self.collapseArray(masked)

diff --git a/src/Isr.cc b/src/Isr.cc
@@ -51,10 +51,11 @@ size_t maskNans(afw::image::MaskedImage<PixelT> const& mi, afw::image::MaskPixel
 
 template<typename ImagePixelT>
 std::vector<double> fitOverscanImage(
-    afw::image::Image<ImagePixelT> const& overscan,
+    afw::image::MaskedImage<ImagePixelT> const& overscan,
+    std::vector<std::string> badPixelMask,
     bool isTransposed
 ) {
-    typedef afw::image::Image<ImagePixelT> Image;
+    typedef afw::image::MaskedImage<ImagePixelT> MaskedImage;
 
     /**
     This is transposed here to match the existing numpy-array ordering.
@@ -70,6 +71,8 @@ std::vector<double> fitOverscanImage(
 
     std::vector<double> values(length);
 
+    afw::math::StatisticsControl statControl;
+    statControl.setAndMask(overscan.getMask()->getPlaneBitMask(badPixelMask));
     const int x0 = overscan.getX0();
     const int y0 = overscan.getY0();
     for (int x = 0; x < length; ++x) {
@@ -86,10 +89,9 @@ std::vector<double> fitOverscanImage(
         else {
             bbox = geom::Box2I(geom::Point2I(x0,y0 + x), geom::Extent2I(width,1));
         }
-        Image mi         = Image(overscan, bbox);
-        afw::math::Statistics stats = afw::math::makeStatistics(mi, afw::math::MEDIAN);
+        MaskedImage mi = MaskedImage(overscan, bbox);
 
-        values[x]    = stats.getValue(afw::math::MEDIAN);
+        values[x] = afw::math::makeStatistics(mi, afw::math::MEDIAN, statControl).getValue();
     }
     return values;
 }
@@ -113,13 +115,13 @@ std::string between(std::string &s, char ldelim, char rdelim) {
 
 template
 std::vector<double> fitOverscanImage<int>(
-    afw::image::Image<int> const&, bool isTransposed);
+    afw::image::MaskedImage<int> const&, std::vector<std::string> badPixelMask, bool isTransposed);
 template
 std::vector<double> fitOverscanImage<float>(
-    afw::image::Image<float> const&, bool isTransposed);
+    afw::image::MaskedImage<float> const&, std::vector<std::string> badPixelMask, bool isTransposed);
 template
 std::vector<double> fitOverscanImage<double>(
-    afw::image::Image<double> const&, bool isTransposed);
+    afw::image::MaskedImage<double> const&, std::vector<std::string> badPixelMask, bool isTransposed);
 
 template class CountMaskedPixels<float>;
 template class CountMaskedPixels<double>;