Expand on trace

changes/9022.extract_1d.rst

@@ -1 +1,2 @@
-Added on option to calculate a source trace from WCS and expected source positions for NIRSpec BOTS/MOS/FS data and perform a box extraction around that trace.  This option is turned on by default for the BOTS mode.
+Expanded the ``use_source_posn`` option to calculate a source trace from WCS and expected source positions for unresampled NIRSpec and MIRI LRS fixed slit data.
+Added the step parameter ``position_offset`` to allow an additional aperture offset in pixels.

docs/jwst/extract_1d/arguments.rst

@@ -26,21 +26,13 @@ Step Arguments for Slit and Slitless Spectroscopic Data
   file should be shifted to account for the expected position of the source. If None (the default),
   the step will decide whether to use the source position based
   on the observing mode and the source type. By default, source position corrections
-  are attempted only for NIRSpec MOS and NIRSpec and MIRI LRS fixed-slit point sources.
+  are attempted only for point sources in NIRSpec MOS/FS/BOTS and MIRI LRS fixed-slit exposures.
   Set to False to ignore position estimates for all modes; set to True to additionally attempt
-  source position correction for NIRSpec BOTS data or extended sources.
+  source position correction for extended sources.
 
-``--use_trace``
-  Specify whether to calculate a 2D trace and extract the pixels around that trace
-  within the ``extract_width`` defined in the :ref:`EXTRACT1D <extract1d_reffile>`.
-  If None (the default), the step will decide whether to use the source position based
-  on the observing mode.  Currently this option is only available for NIRSpec BOTS, MOS,
-  and fixed-slit modes, where the trace will be calculated from the expected positions 
-  of the sources.  This option is used by default for the NIRSpec BOTS mode.
-
-``--trace_offset``
+``--position_offset``
   Specify a number of pixels (fractional pixels are allowed) to offset the 
-  calculated trace if ``use_trace`` is set to True.  The default is 0.
+  extraction aperture from the nominal position.  The default is 0.
 
 ``--smoothing_length``
   If ``smoothing_length`` is greater than 1 (and is an odd integer), the

jwst/extract_1d/extract_1d_step.py

@@ -162,8 +162,7 @@ class Extract1dStep(Step):
     apply_apcorr = boolean(default=True)  # apply aperture corrections?
 
     use_source_posn = boolean(default=None)  # use source coords to center extractions?
-    use_trace = boolean(default=None)  # use source trace for extraction
-    trace_offset = float(default=0)  # number of pixels to shift source trace in the cross-dispersion direction
+    position_offset = float(default=0)  # number of pixels to shift source trace in the cross-dispersion direction
     smoothing_length = integer(default=None)  # background smoothing size
     bkg_fit = option("poly", "mean", "median", None, default=None)  # background fitting type
     bkg_order = integer(default=None, min=0)  # order of background polynomial fit
@@ -424,8 +423,7 @@ def process(self, input):
                         self.log_increment,
                         self.subtract_background,
                         self.use_source_posn,
-                        self.use_trace,
-                        self.trace_offset,
+                        self.position_offset,
                         self.save_profile,
                         self.save_scene_model,
                     )

jwst/extract_1d/tests/conftest.py

@@ -34,9 +34,24 @@ def simple_wcs_function(x, y):
     # Add a bounding box
     simple_wcs_function.bounding_box = wcs_bbox_from_shape(shape)
 
-    # Add a few expected attributes, so they can be monkeypatched as needed
-    simple_wcs_function.get_transform = None
-    simple_wcs_function.backward_transform = None
+    # Define a simple transform
+    def get_transform(*args, **kwargs):
+        def return_results(*args, **kwargs):
+            if len(args) == 2:
+                zeros = np.zeros(args[0].shape)
+                wave, _ = np.meshgrid(args[0], args[1])
+                return zeros, zeros, wave
+            if len(args) == 3:
+                try:
+                    nx = len(args[0])
+                except TypeError:
+                    nx = 1
+                pix = np.arange(nx)
+                trace = np.ones(nx)
+                return pix, trace
+        return return_results
+
+    simple_wcs_function.get_transform = get_transform
     simple_wcs_function.available_frames = []
 
     return simple_wcs_function
@@ -68,10 +83,17 @@ def simple_wcs_function(x, y):
     # Add a bounding box
     simple_wcs_function.bounding_box = wcs_bbox_from_shape(shape)
 
-    # Add a few expected attributes, so they can be monkeypatched as needed
-    simple_wcs_function.get_transform = None
-    simple_wcs_function.backward_transform = None
-    simple_wcs_function.available_frames = []
+    # Mock a simple backward transform
+    def backward_transform(*args, **kwargs):
+        try:
+            nx = len(args[0])
+        except TypeError:
+            nx = 1
+        pix = np.arange(nx)
+        trace = np.ones(nx)
+        return trace, pix
+
+    simple_wcs_function.backward_transform = backward_transform
 
     return simple_wcs_function