Merge pull request #76 from oirlab/port_merge_subarrays_step2

Refactored merge_subarrays_step

Makefile

@@ -1,2 +1,2 @@
 test:
-	pytest -v liger_iris_pipeline/tests/test_datamodels.py liger_iris_pipeline/tests/test_dark.py liger_iris_pipeline/tests/test_rop.py liger_iris_pipeline/tests/test_utils.py liger_iris_pipeline/tests/test_normalize.py liger_iris_pipeline/tests/test_assign_wcs.py liger_iris_pipeline/tests/test_asdf_schema.py liger_iris_pipeline/tests/test_preprocess_flatfield.py liger_iris_pipeline/tests/test_image2.py
+	pytest -v liger_iris_pipeline/tests/test_datamodels.py liger_iris_pipeline/tests/test_dark.py liger_iris_pipeline/tests/test_rop.py liger_iris_pipeline/tests/test_utils.py liger_iris_pipeline/tests/test_normalize.py liger_iris_pipeline/tests/test_assign_wcs.py liger_iris_pipeline/tests/test_asdf_schema.py liger_iris_pipeline/tests/test_preprocess_flatfield.py liger_iris_pipeline/tests/test_image2.py liger_iris_pipeline/tests/test_merge_subarrays.py

README.md

@@ -49,4 +49,16 @@ Testing Data
 
 #### test_iris_subtract_bg_flat_cal_20240822.fits
 - Processed Level 2 image data
-- https://figshare.com/articles/dataset/IRIS_Liger_DRS_Test_Data/26492029?file=48737014
+- https://figshare.com/articles/dataset/IRIS_Liger_DRS_Test_Data/26492029?file=48737014
+
+#### reduced_science_frame_sci_subarray_1_20240831.fits
+- Subarray image
+- https://figshare.com/articles/dataset/IRIS_Liger_DRS_Test_Data/26492029?file=48911917
+
+#### reduced_science_frame_sci_subarray_2_20240831.fits
+- Subarray image
+- https://figshare.com/articles/dataset/IRIS_Liger_DRS_Test_Data/26492029?file=48911914
+
+#### reduced_science_frame_sci_with_subarrays_20240831.fits
+- Starting point for merging subarrays 1 & 2 above with nans where subarrays are
+- https://figshare.com/articles/dataset/IRIS_Liger_DRS_Test_Data/26492029?file=48911932

liger_iris_pipeline/merge_subarrays/merge_subarrays.py

@@ -10,14 +10,14 @@ class MergeSubarraysStep(Step):
     """
     ParseSubarrayMapStep: Parse a subarray map
     extension, if available, and create header metadata
-    and data quality flag accordingly
+    and data quality flag accordingly.
     """
 
     def process(self, input):
 
         input = datamodels.open(input)
 
-        # If single input, wrap in a ModelContainer
+        # If single input, just return it
         if not isinstance(input, datamodels.ModelContainer):
             self.log.info("No subarray files provided, return the original model")
             return input
@@ -31,14 +31,13 @@ def process(self, input):
         else:
             raise ValueError("Cannot identify the full frame, it should have SUBARRID=0")
 
-
         # Assume subarrays are in order
         for model in input_models:
 
             i_sub = model.meta.subarray.id
 
+            # Skip the full frame
             if i_sub == 0:
-                # skip the full frame
                 continue
 
             subarray_mask = result.subarr_map == i_sub

liger_iris_pipeline/tests/test_merge_subarrays.py

@@ -0,0 +1,54 @@
+# Imports
+import liger_iris_pipeline
+liger_iris_pipeline.monkeypatch_jwst_datamodels()
+import numpy as np
+
+import json
+
+# See README.md for notes on testing data
+from liger_iris_pipeline.tests.test_utils import get_data_from_url
+
+
+def test_merge_subarrays(tmp_path):
+
+    # Download the test data
+    reduced_science_frame_filename = get_data_from_url("48911932")
+    reduced_subarray1_filename = get_data_from_url("48911917")
+    reduced_subarray2_filename = get_data_from_url("48911914")
+
+    # Create an ASN for this test
+    asn = {
+        "asn_rule": "Asn_Image",
+        "asn_pool": "pool",
+        "asn_type": "image3",
+        "products": [
+            {
+                "name": "test_merge_subarrays_asn",
+                "members": [
+                    {
+                        "expname": reduced_science_frame_filename,
+                        "exptype": "science"
+                    },
+                    {
+                        "expname": reduced_subarray1_filename,
+                        "exptype": "science"
+                    },
+                    {
+                        "expname": reduced_subarray2_filename,
+                        "exptype": "science"
+                    }
+                ]
+            }
+        ]
+    }
+
+    # Save to file
+    asn_temp_filename = tmp_path / "test_asn.json"
+    with open(asn_temp_filename, "w+") as f:
+        json.dump(asn, f)
+
+    # Run the merge subarray pipeline
+    result = liger_iris_pipeline.MergeSubarraysStep().call(asn_temp_filename)
+
+    # Check that the image is valid
+    assert np.all(np.logical_not(np.isnan(result.data)))