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rcal-890 Update Docs for B15 #1396

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rcal-890 Update Docs for B15
ddavis-stsci Sep 4, 2024
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rcal-890 Updates from review comments
ddavis-stsci Sep 6, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 6, 2024
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62 changes: 33 additions & 29 deletions docs/roman/data_products/product_types.rst
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Expand Up @@ -24,35 +24,39 @@ The following table contains lists of all data product types for the Exposure pi
are the only files that are produced in the standard processing. All the other are optional (opt) files that can be produced when
the user is running the pipeline. The input for each optional step is the output of the preceding step.

+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| Pipeline Step | Input | Output suffix | Data Model | Units | Description |
+================================================+=================+==========================+==================+=====================+=======================================+
| | | uncal | ScienceRawModel | DN | 3-D uncalibrated exposure data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`dq_init <dq_init_step>` | uncal | dqinit (opt) | RampModel | DN | 3-D data quality flags applied |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`saturation <saturation_step>` | | saturation (opt) | RampModel | DN | 3-D data saturated values flagged |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`refpix <refpix>` | | refpix (opt) | RampModel | DN | 3-D ref pix corrected data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`linearity <linearity_step>` | | linearity (opt) | RampModel | DN | 3-D linearity corrected data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`dark_current <dark_current_step>` | | darkcurrent (opt) | RampModel | DN | 3-D dark current subtracted data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`ramp_fitting <ramp_fitting_step>` | | rampfit (opt) | ImageModel | DN/s | 2-D slope corrected data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`assign_wcs <assign_wcs_step>` | | assignwcs (opt) | ImageModel | DN/s | 2-D data with gwcs |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`flatfield <flatfield_step>` | | flat (opt) | ImageModel | DN/s | 2-D QE corrected data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`photom <photom_step>` | | photom (opt) | ImageModel | DN/s | Add phometric data to header |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`source_detection <source_detection_step>`| | sourcedetectionstep (opt)| ImageModel | DN/s | Sources identified in the data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| :ref:`tweakreg <tweakreg_step>` | | tweakregstep (opt) | ImageModel | DN/s | WCS aligned with GAIA |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
| | | cal | ImageModel | DN/s | 2-D calibrated exposure data |
+------------------------------------------------+-----------------+--------------------------+------------------+---------------------+---------------------------------------+
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| Pipeline Step | Input | Output suffix | Data Model | Units | Description |
+================================================+=================+==========================+=====================+==================+=======================================+
| | | uncal | ScienceRawModel | DN | 3-D uncalibrated exposure data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`dq_init <dq_init_step>` | uncal | dqinit (opt) | RampModel | DN | 3-D data quality flags applied |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`saturation <saturation_step>` | | saturation (opt) | RampModel | DN | 3-D data saturated values flagged |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`refpix <refpix>` | | refpix (opt) | RampModel | DN | 3-D ref pix corrected data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`linearity <linearity_step>` | | linearity (opt) | RampModel | DN | 3-D linearity corrected data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`dark_current <dark_current_step>` | | darkcurrent (opt) | RampModel | DN | 3-D dark current subtracted data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`ramp_fitting <ramp_fitting_step>` | | rampfit (opt) | ImageModel | DN/s | 2-D slope corrected data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`assign_wcs <assign_wcs_step>` | | assignwcs (opt) | ImageModel | DN/s | 2-D data with gwcs |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`flatfield <flatfield_step>` | | flat (opt) | ImageModel | DN/s | 2-D QE corrected data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`photom <photom_step>` | | photom (opt) | ImageModel | DN/s | Add phometric data to header |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`source_catalog <source_catalog_step>` | | sourcecatalogstep (opt) | ImageModel | DN/s | 2-D data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| | cat | astropy.table | Sources identified in the data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| | segm |SegmentationMapModel | | segmentation map |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| :ref:`tweakreg <tweakreg_step>` | | tweakregstep (opt) | ImageModel | DN/s | WCS aligned with GAIA |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+
| | | cal | ImageModel | DN/s | 2-D calibrated exposure data |
+------------------------------------------------+-----------------+--------------------------+---------------------+------------------+---------------------------------------+



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21 changes: 19 additions & 2 deletions docs/roman/pipeline/exposure_pipeline.rst
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Expand Up @@ -32,7 +32,7 @@ table below.
:ref:`assign_wcs <assign_wcs_step>` |check| |check| |check|
:ref:`flatfield <flatfield_step>` |check|
:ref:`photom <photom_step>` |check|
:ref:`source_detection <source_detection_step>` |check|
:ref:`source_catalog <source_catalog_step>` |check|
:ref:`tweakreg <tweakreg_step>` |check|
================================================== ========= ========= =========

Expand Down Expand Up @@ -87,9 +87,26 @@ Outputs
:Data model: `~romancal.datamodels.ImageModel`
:File suffix: _cal

Catalog file (SourceCatalog)
+++++++++++++++++++++++++++++++++++

The catalog data is in

:Data model: `astropy.table.Table`
:File suffix: _cat

Segmentation Map (SegmentationMapModel)
++++++++++++++++++++++++++++++++++++++++

The segmentation map is

:Data model: `~romancal.datamodels.MosaicSegmentationMapModel`
:File suffix: _segm

Result of applying all pipeline steps up through the
:ref:`tweakreg <tweakreg_step>` step is to produce calibrated data with the image WCS
aligned to Gaia, and is 2D image data, which will have one less data dimensions as the input
raw 3D data. In addition to being a 2-dimensional
image the output from the pipeline has the :ref:`reference pixels <refpix>`
removed from the edges of the science array and saved as additional 3D arrays.
removed from the edges of the science array and saved as additional 3D arrays. The
source catalog and segmentation map from the individual exposues is also saved.
11 changes: 7 additions & 4 deletions docs/roman/pipeline/mosaic_pipeline.rst
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Expand Up @@ -9,9 +9,11 @@ Mosaic Level Image Processing

The ``MosaicPipeline`` applies corrections to an overlapping group of images
and is setup to process only imaging observations.
This pipeline is used to determine a common background, :ref:`skymatch <skymatch_step>`, detect pixels the are
not consistent with the other datasets, :ref:`outlier_detection <outlier_detection_step>`, and resample the image to a
single undistorted image, :ref:`resample <resample_step>`.
This pipeline is used to apply the flux scale factor, :ref:`flux <flux_step>`,
determine a common background, :ref:`skymatch <skymatch_step>`, detect pixels the are
not consistent with the other datasets, :ref:`outlier_detection <outlier_detection_step>`, resample the image to a
single undistorted image, :ref:`resample <resample_step>`, and to run :ref:`source_catalog <source_catalog_step>`
on the resulting corrected image.

The list of steps applied by the ``MosaicPipeline`` pipeline is shown in the
table below.
Expand All @@ -22,6 +24,7 @@ table below.
======================================================= ========= ========= =========
Step WFI-Image WFI-Prism WFI-Grism
======================================================= ========= ========= =========
:ref:`flux <flux_step>` |check| |xmark| |xmark|
:ref:`skymatch <skymatch_step>` |check| |xmark| |xmark|
:ref:`outlier_detection <outlier_detection_step>` |check| |xmark| |xmark|
:ref:`resample <resample_step>` |check| |xmark| |xmark|
Expand All @@ -38,7 +41,7 @@ You can see the options for strun using:

strun --help roman_mos

and this will list all the strun options all well as the step options for the roman_mos.
and this will list all the strun options as well as the step options for the roman_mos.


Inputs
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2 changes: 1 addition & 1 deletion romancal/pipeline/mosaic_pipeline.py
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Expand Up @@ -34,7 +34,7 @@ class MosaicPipeline(RomanPipeline):
"""
MosaicPipeline: Apply all calibration steps to the roman data
to produce level 3 products. Included steps are:
``skymatch``, ``outlier_detection`` and ``resample``.
``flux``, ``skymatch``, ``outlier_detection``, ``resample`` and ``source catalog``.
"""

class_alias = "roman_mos"
Expand Down