fix: refactoring of parse_subarray_map_step and test

oirlab · Jul 8, 2024 · 3ca065b · 3ca065b
1 parent 390bafb
commit 3ca065b
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Showing 3 changed files with 16 additions and 272 deletions.
diff --git a/liger_iris_pipeline/parse_subarray_map/parse_subarray_map_step.py b/liger_iris_pipeline/parse_subarray_map/parse_subarray_map_step.py
@@ -8,7 +8,7 @@
 
 SUBARRAY_DQ_BIT = 4
 
-
+# NOTE: xstart/ystart use 1-based indexing
 def parse_subarray_map(subarray_map):
     subarray_metadata = []
     for subarray_id in range(1, 10 + 1):
@@ -46,9 +46,11 @@ def process(self, input):
 
             result = input_model.copy()
 
+            # Create metadata from image ID map
             for each in parse_subarray_map(result["subarr_map"]):
                 result.meta.subarray_map.append(each)
 
+            # Indicate subarrays in dq flags
             result.dq[result["subarr_map"] != 0] = np.bitwise_or(
                 result.dq[result["subarr_map"] != 0],
                 2 ** SUBARRAY_DQ_BIT

diff --git a/liger_iris_pipeline/tests/test_parse_subarray_map.ipynb b/liger_iris_pipeline/tests/test_parse_subarray_map.ipynb
diff --git a/liger_iris_pipeline/tests/test_parse_subarray_map.py b/liger_iris_pipeline/tests/test_parse_subarray_map.py
@@ -5,27 +5,31 @@
 from liger_iris_pipeline import ParseSubarrayMapStep
 import numpy as np
 
+
 def set_subarray_mask(mask_array, subarray_index, xstart, ystart, xsize, ysize):
     xstart = xstart - 1
     ystart = ystart - 1
     mask_array[ystart:ystart + ysize, xstart:xstart + xsize] =  subarray_index
 
+
 def test_parse_subarray_map():
+
+
+    # Define simple subarray metadata and image ID map
+    # ID is just the 1-based index in this list (1, 2, ...)
     subarray_maps_metadata = [
         {"xstart" : 80, "ystart" : 70, "xsize" : 10, "ysize" : 10},
         {"xstart" : 10, "ystart" : 20, "xsize" : 20, "ysize" : 20}
     ]
-
     subarr_map = np.zeros((100,100), dtype=np.int16)
     for i, shape in enumerate(subarray_maps_metadata):
         set_subarray_mask(subarr_map, subarray_index=i+1, **shape)
 
+    # Test parse_subarray_map function
     parse_subarray_map_output = parse_subarray_map(subarr_map)
-
-    # Test parse_subarray_map
     assert subarray_maps_metadata == parse_subarray_map_output
 
-    # Create toy data
+    # Create toy Image object with these subarrays
     image = liger_iris_pipeline.datamodels.LigerIrisImageModel(data=np.zeros((100, 100)))
     image.dq[25, 25] = 16
     image.dq[26, 26] = 1
@@ -35,8 +39,8 @@ def test_parse_subarray_map():
     step = ParseSubarrayMapStep()
     output = step.run(image)
 
-    # Test
-    for each_parsed, each_input in zip(output.subarr_map, subarray_maps_metadata):
+    # Test each parsed subarray map is equal to what we defined above.
+    for each_parsed, each_input in zip(output.meta.subarray_map, subarray_maps_metadata):
         assert each_parsed.instance == each_input
 
     # If a pixel is already flagged as subarray, don't mess it up
@@ -45,11 +49,8 @@ def test_parse_subarray_map():
     # conserve existing flags
     assert output.dq[26, 26] == 17
 
-    # Test
+    # Test DQ flags
     np.testing.assert_array_equal(
         np.bitwise_and(output.dq, int(2**4)) > 0,
-        subarray_map != 0
-    )
-
-
-test_parse_subarray_map()
+        subarr_map != 0
+    )