Merge branch 'main' into rcal-930-l3wcs

changes/1593.exposure_pipeline.rst

@@ -0,0 +1 @@
+Fix description of arguments in docs and add description of fully saturated input processing.

changes/1593.resample.rst

@@ -0,0 +1 @@
+Remove unused arguments from step specification.

changes/1593.saturation.rst

@@ -0,0 +1 @@
+Add saturation step docs to package index.

docs/roman/package_index.rst

@@ -14,6 +14,7 @@
    references_general/index.rst
    refpix/index.rst
    resample/index.rst
+   saturation/index.rst
    skymatch/index.rst
    source_catalog/index.rst
    stpipe/index.rst

docs/roman/pipeline/exposure_pipeline.rst

@@ -39,18 +39,7 @@ table below.
 
 Arguments
 ---------
-The ``exposure`` pipeline has an optional argument::
-
-  --use_ramp_jump_detection  boolean  default=True
-
-When set to ``True``, the pipeline will perform jump detection as a part of the ramp
-fitting  step. The data at this stage of the pipeline are still in the form of the original
-3D ramps ( ngroups x ncols x nrows ) and have had all of the detector-level
-correction steps applied to it, up to but not including the detection and flagging of
-Cosmic-Ray (CR) hits within each ramp (integration). For this case the  jump detection
-module in :ref:`ramp_fitting <ramp_fitting_step>` will update the dq array with the CR hits (jumps) that
-are identified in the step.
-
+The ``exposure`` pipeline has no arguments
 
 Inputs
 ------
@@ -78,6 +67,16 @@ extensions. When such a file is loaded into the pipeline, it is immediately
 converted into a `~romancal.datamodels.RampModel`, and has all additional data arrays
 for errors and Data Quality flags created and initialized.
 
+When the ``ExposurePipeline`` processes a fully saturated input (all pixels flagged as saturated).
+The corresponding output image will:
+
+- contain all 0 data arrays
+- contain all 0 variance arrays
+- not be processed by steps beyond saturation
+
+A single fully saturated input will also cause :ref:`tweakreg <tweakreg_step>` to be skipped
+for all input images.
+
 Outputs
 -------
 

docs/roman/references_general/references_general.rst

@@ -51,8 +51,6 @@ documentation on each reference file.
 +---------------------------------------------+--------------------------------------------------+
 | :ref:`flatfield <flatfield_step>`           | :ref:`FLAT <flat_reffile>`                       |
 +---------------------------------------------+--------------------------------------------------+
-| :ref:`GAIN <gain_reffile>`                       | :ref:`ramp_fitting <ramp_fitting_step>`     |
-+---------------------------------------------+--------------------------------------------------+
 | :ref:`linearity <linearity_step>`           | :ref:`LINEARITY <linearity_reffile>`             |
 +---------------------------------------------+--------------------------------------------------+
 | :ref:`photom <photom_step>`                 | :ref:`PHOTOM <photom_reffile>`                   |
@@ -74,6 +72,8 @@ documentation on each reference file.
 +--------------------------------------------------+---------------------------------------------+
 | :ref:`FLAT <flat_reffile>`                       | :ref:`flatfield <flatfield_step>`           |
 +--------------------------------------------------+---------------------------------------------+
+| :ref:`GAIN <gain_reffile>`                       | :ref:`ramp_fitting <ramp_fitting_step>`     |
++--------------------------------------------------+---------------------------------------------+
 | :ref:`LINEARITY <linearity_reffile>`             | :ref:`linearity <linearity_step>`           |
 +--------------------------------------------------+---------------------------------------------+
 | :ref:`MASK <mask_reffile>`                       | :ref:`dq_init <dq_init_step>`               |

docs/roman/resample/arguments.rst

@@ -82,24 +82,6 @@ image.
     If `weight_type=exptime`, the scaling value will be set equal to the
     exposure time found in the image header.
 
-``--single`` (bool, default=False)
-    If set to `True`, resample each input image into a separate output.  If
-    `False` (the default), each input is resampled additively (with weights) to
-    a common output
-
-``--blendheaders`` (bool, default=True)
-    Blend metadata from all input images into the resampled output image.
-
-``--allowed_memory`` (float, default=None)
-    Specifies the fractional amount of free memory to allow when creating the
-    resampled image. If ``None``, the environment variable
-    ``DMODEL_ALLOWED_MEMORY`` is used. If not defined, no check is made. If the
-    resampled image would be larger than specified, an ``OutputTooLargeError``
-    exception will be generated.
-
-    For example, if set to ``0.5``, only resampled images that use less than
-    half the available memory can be created.
-
 ``--in_memory`` (bool, default=True)
     If set to `False`, write output datamodel to disk.
 

docs/roman/stpipe/config_asdf.rst

@@ -70,7 +70,6 @@ entries for clarity:
       output_use_model: false
       post_hooks: []
       pre_hooks: []
-      save_calibrated_ramp: false
       save_results: true
       search_output_file: true
       skip: false

docs/roman/stpipe/user_pipeline.rst

@@ -63,7 +63,6 @@ class:
     output_use_model: false
     post_hooks: []
     pre_hooks: []
-    save_calibrated_ramp: false
     save_results: true
     search_output_file: true
     skip: false

romancal/pipeline/exposure_pipeline.py

@@ -46,7 +46,6 @@ class ExposurePipeline(RomanPipeline):
     class_alias = "roman_elp"
 
     spec = """
-        save_calibrated_ramp = boolean(default=False)
         save_results = boolean(default=False)
         suffix = string(default="cal")
     """

romancal/resample/resample.py

@@ -48,7 +48,6 @@ def __init__(
         input_models,
         output=None,
         single=False,
-        blendheaders=True,
         pixfrac=1.0,
         kernel="square",
         fillval="INDEF",
@@ -90,7 +89,6 @@ def __init__(
         self.output_filename = output
         self.pscale_ratio = pscale_ratio
         self.single = single
-        self.blendheaders = blendheaders
         self.pixfrac = pixfrac
         self.kernel = kernel
         self.fillval = fillval
@@ -143,23 +141,6 @@ def __init__(
 
         log.debug(f"Output mosaic size: {self.output_wcs.array_shape}")
 
-        # NOTE: should we enable memory allocation?
-
-        # can_allocate, required_memory = datamodels.util.check_memory_allocation(
-        #     self.output_wcs.array_shape,
-        #     kwargs['allowed_memory'],
-        #     datamodels.ImageModel
-        # )
-        # if not can_allocate:
-        #     raise OutputTooLargeError(
-        #         f'Combined ImageModel size {self.output_wcs.array_shape} '
-        #         f'requires {bytes2human(required_memory)}. '
-        #         f'Model cannot be instantiated.'
-        #     )
-
-        # NOTE: wait for William to fix bug in datamodels' init and then
-        # use datamodels.ImageModel(shape=(nx, ny)) instead of mk_datamodel()
-
         # n_images sets the number of context image planes.
         # This should be 1 to start (not the default of 2).
         self.blank_output = maker_utils.mk_datamodel(
@@ -341,9 +322,6 @@ def resample_many_to_one(self):
         ) is not None:
             output_model.meta.asn.table_name = asn_table_name
 
-        if self.blendheaders:
-            log.info("Skipping blendheaders for now.")
-
         # Initialize the output with the wcs
         driz = gwcs_drizzle.GWCSDrizzle(
             output_model,

romancal/resample/resample_step.py

@@ -66,9 +66,6 @@ class ResampleStep(RomanStep):
         pixel_scale_ratio = float(default=1.0) # Ratio of input to output pixel scale
         pixel_scale = float(default=None) # Absolute pixel scale in arcsec
         output_wcs = string(default='')  # Custom output WCS.
-        single = boolean(default=False)
-        blendheaders = boolean(default=True)
-        allowed_memory = float(default=None)  # Fraction of memory to use for the combined image.
         in_memory = boolean(default=True)
         good_bits = string(default='~DO_NOT_USE+NON_SCIENCE')  # The good bits to use for building the resampling mask.
     """
@@ -80,7 +77,6 @@ def process(self, input):
             input_models = ModelLibrary([input])
             # set output filename from meta.filename found in the first datamodel
             output = input.meta.filename
-            self.blendheaders = False
         elif isinstance(input, str):
             # either a single asdf filename or an association filename
             try:
@@ -118,7 +114,6 @@ def process(self, input):
         self.wht_type = self.weight_type
         self.log.info("Setting drizzle's default parameters...")
         kwargs = self.set_drizzle_defaults()
-        kwargs["allowed_memory"] = self.allowed_memory
 
         # Issue a warning about the use of exptime weighting
         if self.wht_type == "exptime":

romancal/resample/tests/test_resample.py

@@ -290,8 +290,6 @@ def test_resampledata_init(exposure_1):
     """Test that ResampleData can set initial values."""
     input_models = ModelLibrary(exposure_1)
     output = "output.asdf"
-    single = False
-    blendheaders = False
     pixfrac = 0.8
     kernel = "turbo"
     fillval = 0.0
@@ -304,8 +302,6 @@ def test_resampledata_init(exposure_1):
     resample_data = ResampleData(
         input_models,
         output=output,
-        single=single,
-        blendheaders=blendheaders,
         pixfrac=pixfrac,
         kernel=kernel,
         fillval=fillval,
@@ -320,8 +316,6 @@ def test_resampledata_init(exposure_1):
     assert resample_data.input_models == input_models
     assert resample_data.output_filename == output
     assert resample_data.pscale_ratio == pscale_ratio
-    assert resample_data.single == single
-    assert resample_data.blendheaders == blendheaders
     assert resample_data.pixfrac == pixfrac
     assert resample_data.kernel == kernel
     assert resample_data.fillval == fillval
@@ -341,8 +335,6 @@ def test_resampledata_init_default(exposure_1):
     assert resample_data.input_models == input_models
     assert resample_data.output_filename is None
     assert resample_data.pscale_ratio == 1.0
-    assert not resample_data.single
-    assert resample_data.blendheaders
     assert resample_data.pixfrac == 1.0
     assert resample_data.kernel == "square"
     assert resample_data.fillval == "INDEF"