From 5cc07eeb124953cd262540463ad7b6f25f85a6d5 Mon Sep 17 00:00:00 2001
From: D Davis <49163225+ddavis-stsci@users.noreply.github.com>
Date: Fri, 10 Nov 2023 15:51:14 -0500
Subject: [PATCH] RCAL-707 Update elp to replace list as input to tweakreg
 (#985)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 CHANGES.rst                             |  2 +
 romancal/lib/suffix.py                  |  2 +-
 romancal/pipeline/exposure_pipeline.py  |  3 +-
 romancal/pipeline/highlevel_pipeline.py | 80 +++++++++++++++++++++++++
 4 files changed, 84 insertions(+), 3 deletions(-)
 create mode 100644 romancal/pipeline/highlevel_pipeline.py

diff --git a/CHANGES.rst b/CHANGES.rst
index d92674d01..4e3628670 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -14,6 +14,8 @@ dark
 general
 -------
 
+- Update elp pipeline code to capture a list from tweakreg [#985]
+
 - Update pipeline code to correct cal_step and suffixes [#971]
 
 - Update pipeline code to run through tweakreg with single files and associations [#960]
diff --git a/romancal/lib/suffix.py b/romancal/lib/suffix.py
index 9be896fd6..9a17b53b1 100644
--- a/romancal/lib/suffix.py
+++ b/romancal/lib/suffix.py
@@ -63,7 +63,7 @@
 
 # Suffixes that are discovered but should not be considered.
 # Used by `find_suffixes` to remove undesired values it has found.
-SUFFIXES_TO_DISCARD = ["pipeline", "step"]
+SUFFIXES_TO_DISCARD = ["highlevelpipeline", "pipeline", "step"]
 
 
 # Calculated suffixes.
diff --git a/romancal/pipeline/exposure_pipeline.py b/romancal/pipeline/exposure_pipeline.py
index 12566b15b..f6c1402dd 100644
--- a/romancal/pipeline/exposure_pipeline.py
+++ b/romancal/pipeline/exposure_pipeline.py
@@ -191,8 +191,7 @@ def process(self, input):
         if result.meta.exposure.type == "WFI_IMAGE":
             if file_type == "asdf":
                 result.meta.cal_step.tweakreg = "SKIPPED"
-                # mc_result = ModelContainer(result)
-                mc_result = self.tweakreg([result])
+                mc_result = ModelContainer(result)
                 if hasattr(ModelContainer(result), "_models") and mc_result._models:
                     result = mc_result._models.pop()
                 else:
diff --git a/romancal/pipeline/highlevel_pipeline.py b/romancal/pipeline/highlevel_pipeline.py
new file mode 100644
index 000000000..f42bb596d
--- /dev/null
+++ b/romancal/pipeline/highlevel_pipeline.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+import logging
+from os.path import basename
+
+import romancal.datamodels.filetype as filetype
+from romancal.datamodels import ModelContainer
+from romancal.outlier_detection import OutlierDetectionStep
+from romancal.resample import ResampleStep
+
+# step imports
+from romancal.skymatch import SkyMatchStep
+
+from ..stpipe import RomanPipeline
+
+__all__ = ["HighLevelPipeline"]
+
+# Define logging
+log = logging.getLogger()
+log.setLevel(logging.DEBUG)
+
+
+class HighLevelPipeline(RomanPipeline):
+    """
+    HighLevelPipeline: Apply all calibration steps to the roman data
+    to produce level 3 products. Included steps are:
+    skymatch, Outlierdetectionn and resample.
+    """
+
+    class_alias = "roman_hlp"
+
+    spec = """
+        save_results = boolean(default=False)
+    """
+
+    # Define aliases to steps
+    step_defs = {
+        "skymatch": SkyMatchStep,
+        "outlierdet": OutlierDetectionStep,
+        "resample": ResampleStep,
+    }
+
+    # start the actual processing
+    def process(self, input):
+        """Process the Roman WFI data from Level 2 to Level 3"""
+
+        log.info("Starting Roman high level calibration pipeline ...")
+        if isinstance(input, str):
+            input_filename = basename(input)
+        else:
+            input_filename = None
+
+        # open the input file
+        file_type = filetype.check(input)
+        asn = None
+        if file_type == "asdf":
+            log.info("The level three pipeline input needs to be an association")
+            return
+
+        if file_type == "asn":
+            asn = ModelContainer.read_asn(input)
+            self.skymatch.suffix = "skymatch"
+            result = self.skymatch(input)
+            self.skymatch.suffix = "outlierdetection"
+            result = self.outlierdetection(asn)
+            self.skymatch.suffix = "i2d"
+            result = self.resample(result)
+            if input_filename:
+                result.meta.filename = input_filename
+
+        return result
+
+    def setup_output(self, input):
+        """Determine the proper file name suffix to use later"""
+        if input.meta.cal_step.ramp_fit == "COMPLETE":
+            self.suffix = "cal"
+            input.meta.filename = input.meta.filename.replace("uncal", self.suffix)
+            input["output_file"] = input.meta.filename
+            self.output_file = input.meta.filename
+        else:
+            self.suffix = "cal"