Port create subarray dataset

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 liger_iris_pipeline/tests/test_merge_subarrays.py liger_iris_pipeline/tests/test_dark_subarray.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 liger_iris_pipeline/tests/test_dark_subarray.py liger_iris_pipeline/tests/test_create_subarray_dataset.py

liger_iris_pipeline/tests/test_create_subarray_dataset.ipynb

@@ -109,7 +109,7 @@
     "def slice_subarray_mask(mask_array, xstart, ystart, xsize, ysize):\n",
     "    xstart = xstart - 1\n",
     "    ystart = ystart - 1\n",
-    "    return mask_array[ystart:ystart+ysize, xstart:xstart+xsize].copy()              "
+    "    return mask_array[ystart:ystart+ysize, xstart:xstart+xsize].copy()            "
    ]
   },
   {

liger_iris_pipeline/tests/test_create_subarray_dataset.py

@@ -0,0 +1,110 @@
+# Imports
+import liger_iris_pipeline
+liger_iris_pipeline.monkeypatch_jwst_datamodels()
+import numpy as np
+
+# See README.md for notes on testing data
+from liger_iris_pipeline.tests.test_utils import get_data_from_url
+
+
+# Converts 1->0 indexing, sets the subarray index
+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
+
+
+# Converts 1->0 indexing, slices the subarray, and returns a copy
+def slice_subarray_mask(mask_array, xstart, ystart, xsize, ysize):
+    xstart = xstart - 1
+    ystart = ystart - 1
+    return mask_array[ystart:ystart+ysize, xstart:xstart+xsize].copy()
+
+
+def test_create_subarray_dataset(tmp_path):
+
+    # Download the science frame and open
+    raw_science_filename = get_data_from_url("48191524")
+    input_model = liger_iris_pipeline.datamodels.LigerIrisImageModel(raw_science_filename)
+
+    # Setup the subarray params
+    s1 = 300
+    s2 = 100
+    subarray_maps_metadata = []
+
+    # Square subarray
+    # Covers central bright star
+    subarray_maps_metadata.append({
+        "xstart" : 2048 - s1 // 2,
+        "ystart" : 2048 - s1 // 2,
+        "xsize" : s1,
+        "ysize" : s1
+    })
+
+    # Rectangular subarray
+    # Covers bottom left star
+    subarray_maps_metadata.append({
+        "xstart" : 1040 - s2 // 2,
+        "ystart" : 1040 - s2 // 2,
+        "xsize" : s2,
+        "ysize" : s2 // 2
+    })
+
+    # Create the subarray images for each subarray model
+    # based on a copy of the full frame model
+    subarray_models = {}
+    for i, shape in enumerate(subarray_maps_metadata):
+        subarray_models[i+1] = input_model.copy()
+        for ext in ("data", "dq", "err"):
+            subarray_models[i+1][ext] = slice_subarray_mask(input_model[ext], **shape)
+
+    # Set the correct metadata for each subarray model
+    for i, shape in enumerate(subarray_maps_metadata):
+        subarray_models[i+1].meta.subarray.name = "CUSTOM"
+        subarray_models[i+1].meta.subarray.id = i + 1
+        for k, v in shape.items():
+            setattr(subarray_models[i+1].meta.subarray, k, v)
+
+    # Add subarr map to the full frame model
+    input_model.subarr_map = np.zeros_like(input_model.data)
+    for i, shape in enumerate(subarray_maps_metadata):
+        set_subarray_mask(input_model.subarr_map, subarray_index=i+1, **shape)
+
+    # Set all subarray regions to nan in full frame
+    input_model.data[input_model.subarr_map != 0] = np.nan
+
+    # Write the full frame
+    full_frame_filename_temp = tmp_path / "raw_science_frame_sci_with_subarrays.fits"
+    input_model.write(full_frame_filename_temp)
+
+    # Write the subarrays
+    subarray_filenames_temp = {}
+    for k, sub_model in subarray_models.items():
+        subarray_filenames_temp[k] = tmp_path / f"raw_science_frame_sci_subarray_{k}.fits"
+        sub_model.write(subarray_filenames_temp[k])
+
+    # Create and run the pipeline on the full frame
+    pipeline = liger_iris_pipeline.ProcessImagerL2Pipeline()
+    reduced_full_frame = pipeline.call(full_frame_filename_temp, config_file="liger_iris_pipeline/tests/data/image2_iris.cfg")[0]
+
+    # Set the subarray metadata id to 0 (full frame)
+    reduced_full_frame.meta.subarray.id = 0
+
+    # Write the reduced full frame
+    reduced_full_frame.write(str(full_frame_filename_temp).replace("raw", "reduced"))
+
+    # Call the pipeline on the subarrays
+    reduced_subarrays = {}
+    for k in subarray_filenames_temp:
+        reduced_subarrays[k] = pipeline.call(subarray_filenames_temp[k], config_file="liger_iris_pipeline/tests/data/image2_iris.cfg")[0]
+        reduced_subarrays[k].write(str(subarray_filenames_temp[k]).replace("raw", "reduced"))
+
+    # Check the metadata on the reduced full frame model and each reduced subarray model
+    for k, full_frame_meta, each_input in zip(
+            range(1, len(subarray_maps_metadata)+1),
+            reduced_full_frame.meta.subarray_map,
+            subarray_maps_metadata,
+        ):
+        assert full_frame_meta.instance == each_input
+        assert reduced_subarrays[k].meta.subarray.instance == dict(name="CUSTOM", id=k, **each_input)
+