Merge pull request #385 from LCOGT/fix/photometry-edges

Minor fixes for photometry with bad pixels near image edges.

CHANGES.md

@@ -1,3 +1,7 @@
+1.15.1 (2024-02-29)
+-------------------
+- Minor fixes in photometry when there are bad pixels near the image edges
+
 1.15.0 (2024-02-14)
 -------------------
 - Migrated photometry extraction to be done by astropy's photutils instead of SEP.

banzai/photometry.py

@@ -51,10 +51,10 @@ def flag_edge_sources(image, sources, flag_value=8):
     minor_xmax = sources['x'] + sources['b'] * sources['kronrad'] * np.sin(np.deg2rad(sources['theta']))
     minor_ymin = sources['y'] - sources['b'] * sources['kronrad'] * np.cos(np.deg2rad(sources['theta']))
     minor_ymax = sources['y'] + sources['b'] * sources['kronrad'] * np.cos(np.deg2rad(sources['theta']))
-    major_ymin = sources['y'] - sources['a'] * sources['kronrad'] * np.sin(np.deg2rad(sources['theta']))
-    major_ymax = sources['y'] + sources['a'] * sources['kronrad'] * np.sin(np.deg2rad(sources['theta']))
-    major_xmin = sources['x'] - sources['a'] * sources['kronrad'] * np.cos(np.deg2rad(sources['theta']))
-    major_xmax = sources['x'] + sources['a'] * sources['kronrad'] * np.cos(np.deg2rad(sources['theta']))
+    major_ymin = sources['y'] - sources['a'] * sources['kronrad'] * np.cos(np.deg2rad(sources['theta']))
+    major_ymax = sources['y'] + sources['a'] * sources['kronrad'] * np.cos(np.deg2rad(sources['theta']))
+    major_xmin = sources['x'] - sources['a'] * sources['kronrad'] * np.sin(np.deg2rad(sources['theta']))
+    major_xmax = sources['x'] + sources['a'] * sources['kronrad'] * np.sin(np.deg2rad(sources['theta']))
 
     # Note we are already 1 indexed here
     sources_off = np.logical_or(minor_xmin < 1, major_xmin < 1)
@@ -64,7 +64,7 @@ def flag_edge_sources(image, sources, flag_value=8):
     sources_off = np.logical_or(sources_off, major_xmax > nx)
     sources_off = np.logical_or(sources_off, minor_ymax > ny)
     sources_off = np.logical_or(sources_off, major_ymax > ny)
-    sources[sources_off]['flag'] |= flag_value
+    sources['flag'][sources_off] |= flag_value
 
 
 class SourceDetector(Stage):
@@ -145,10 +145,20 @@ def do_stage(self, image):
             # Flag = 16 if source has cosmic ray pixels
             flag_sources(sources, catalog.labels, deblended_seg_map, image.mask, flag=16, mask_value=8)
 
-            sources = array_utils.prune_nans_from_table(sources)
+            rows_with_nans = array_utils.find_nans_in_table(sources)
+            catalog = catalog[~rows_with_nans]
+            sources = sources[~rows_with_nans]
 
             # Cut individual bright pixels. Often cosmic rays
-            sources = sources[sources['fluxrad50'] > 0.5]
+            not_individual_bright_pixels = sources['fluxrad50'] > 0.5
+            catalog = catalog[not_individual_bright_pixels]
+            sources = sources[not_individual_bright_pixels]
+
+            # Cut sources that are less than 2 pixels wide
+            thin_sources = np.logical_or((catalog.bbox_ymax - catalog.bbox_ymin) < 1.5,
+                                         (catalog.bbox_xmax - catalog.bbox_xmin) < 1.5)
+            catalog = catalog[~thin_sources]
+            sources = sources[~thin_sources]
 
             # Calculate the FWHMs of the stars:
             sources['fwhm'] = np.nan

banzai/tests/test_array_utils.py

@@ -6,6 +6,7 @@
 
 pytestmark = pytest.mark.array_utils
 
+
 def test_pruning_nans():
     a = np.arange(100, dtype=float)
     b = np.arange(100, dtype=float) + 100
@@ -16,7 +17,7 @@ def test_pruning_nans():
     c[78] = np.nan
 
     t = Table([a, b, c], names=('a', 'b', 'c'))
-    t = array_utils.prune_nans_from_table(t)
+    t = t[~array_utils.find_nans_in_table(t)]
     assert len(t) == 97
     assert 51 not in t['a']
     assert 32 not in t['a']

banzai/utils/array_utils.py

@@ -6,8 +6,8 @@ def array_indices_to_slices(a):
     return tuple(slice(0, x, 1) for x in a.shape)
 
 
-def prune_nans_from_table(table):
+def find_nans_in_table(table):
     nan_in_row = np.zeros(len(table), dtype=bool)
     for col in table.colnames:
         nan_in_row |= np.isnan(table[col])
-    return table[~nan_in_row]
+    return nan_in_row

helm-chart/banzai/templates/workers-large.yaml

@@ -47,6 +47,7 @@ spec:
             requests:
               cpu: "0.5"
               memory: "10Gi"
+              ephemeral-storage: "128Mi"
             limits:
               cpu: "2"
               memory: "10Gi"

helm-chart/banzai/templates/workers.yaml

@@ -47,9 +47,10 @@ spec:
             requests:
               cpu: "0.5"
               memory: "4Gi"
+              ephemeral-storage: "128Mi"
             limits:
               cpu: "2"
-              memory: "4Gi"
+              memory: "8Gi"
           volumeMounts:
             - name: tmp
               mountPath: /tmp