From d62a13371870bf5f6e5fd69593d2fc63b275ad4e Mon Sep 17 00:00:00 2001
From: Brett <brettgraham@gmail.com>
Date: Wed, 6 Nov 2024 17:22:13 -0500
Subject: [PATCH] replace pipeline Step.__call__ use with run

---
 romancal/pipeline/exposure_pipeline.py | 22 +++++++++++-----------
 romancal/pipeline/mosaic_pipeline.py   | 14 +++++++-------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/romancal/pipeline/exposure_pipeline.py b/romancal/pipeline/exposure_pipeline.py
index 6fb029620..3dde01e25 100644
--- a/romancal/pipeline/exposure_pipeline.py
+++ b/romancal/pipeline/exposure_pipeline.py
@@ -124,12 +124,12 @@ def process(self, input):
             log.info(f"Processing a WFI exposure {input_filename}")
 
             self.dq_init.suffix = "dq_init"
-            result = self.dq_init(input)
+            result = self.dq_init.run(input)
 
             if input_filename:
                 result.meta.filename = input_filename
 
-            result = self.saturation(result)
+            result = self.saturation.run(result)
 
             # Test for fully saturated data
             if is_fully_saturated(result):
@@ -155,16 +155,16 @@ def process(self, input):
                 results.append(result)
                 return results
 
-            result = self.refpix(result)
-            result = self.linearity(result)
-            result = self.dark_current(result)
-            result = self.rampfit(result)
-            result = self.assign_wcs(result)
+            result = self.refpix.run(result)
+            result = self.linearity.run(result)
+            result = self.dark_current.run(result)
+            result = self.rampfit.run(result)
+            result = self.assign_wcs.run(result)
 
             if result.meta.exposure.type == "WFI_IMAGE":
-                result = self.flatfield(result)
-                result = self.photom(result)
-                result = self.source_catalog(result)
+                result = self.flatfield.run(result)
+                result = self.photom.run(result)
+                result = self.source_catalog.run(result)
                 tweakreg_input.append(result)
                 log.info(
                     f"Number of models to tweakreg:   {len(tweakreg_input), n_members}"
@@ -185,7 +185,7 @@ def process(self, input):
         # Now that all the exposures are collated, run tweakreg
         # Note: this does not cover the case where the asn mixes imaging and spectral
         #          observations. This should not occur on-prem
-        result = self.tweakreg(results)
+        result = self.tweakreg.run(results)
 
         log.info("Roman exposure calibration pipeline ending...")
 
diff --git a/romancal/pipeline/mosaic_pipeline.py b/romancal/pipeline/mosaic_pipeline.py
index f34b8c53c..0276225fe 100644
--- a/romancal/pipeline/mosaic_pipeline.py
+++ b/romancal/pipeline/mosaic_pipeline.py
@@ -72,11 +72,11 @@ def process(self, input):
         if file_type == "asn":
             input = ModelLibrary(input, on_disk=self.on_disk)
             self.flux.suffix = "flux"
-            result = self.flux(input)
+            result = self.flux.run(input)
             self.skymatch.suffix = "skymatch"
-            result = self.skymatch(result)
+            result = self.skymatch.run(result)
             self.outlier_detection.suffix = "outlier_detection"
-            result = self.outlier_detection(result)
+            result = self.outlier_detection.run(result)
             #
             # check to see if the product name contains a skycell name & if true get the skycell record
             product_name = input.asn["products"][0]["name"]
@@ -131,9 +131,9 @@ def process(self, input):
                         wcs_file = asdf.open(self.resample.output_wcs)
                         self.suffix = "i2d"
                         self.output_file = input.asn["products"][0]["name"]
-                        result = self.resample(result)
+                        result = self.resample.run(result)
                         self.sourcecatalog.output_file = self.output_file
-                        result_catalog = self.sourcecatalog(result)
+                        result_catalog = self.sourcecatalog.run(result)
                     else:
                         log.info("resampling a mosaic file is not yet supported")
                         exit(0)
@@ -141,9 +141,9 @@ def process(self, input):
             else:
                 self.resample.suffix = "i2d"
                 self.output_file = input.asn["products"][0]["name"]
-                result = self.resample(result)
+                result = self.resample.run(result)
                 self.sourcecatalog.output_file = self.output_file
-                result_catalog = self.sourcecatalog(result)  # noqa: F841
+                result_catalog = self.sourcecatalog.run(result)  # noqa: F841
                 self.suffix = "i2d"
                 if input_filename:
                     result.meta.filename = self.output_file